Administrative Appointments

  • Chair, Stanford University School of Medicine - Microbiology & Immunology (2002 - 2004)
  • Director, Stanford Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine (2004 - Present)
  • The Burt and Marion Avery Family Professor of Immunology, Stanford University School of Medicine (2007 - Present)

Honors & Awards

  • Distinguished Alumni Award, Caltech (2005)
  • Paul Ehrlich Prize, Paul Ehrlich Foundation (2004)
  • Member, National Institute of Medicine (2004)
  • Ernst W. Bertner Award, M.D.Anderson Cancer Center/Univ. Texas (2003)
  • The Rose Payne Award, American Society for Histoocommpatibility and Immunogenetics (2002)
  • The Burt and Marion Avery Professorship, Stanford University (2001-2006)
  • Newton-Abraham Visiting Professor, University of Oxford (2000-2001)
  • Pius XI Award, Pontifical Academy of Sciences (2000)
  • William B. Coley Award, Cancer Research Institute (2000)
  • Novartis Prize for Basic Immunology, International Union of Immunology Societies (1998)
  • General Motors Cancer Prize:Sloan Award, General Motors Cancer Fdn. (1996)
  • King Faisal Prize, King Faisal Foundation (1995)
  • Member, National Academy of Sciences (1993)
  • Gairdner Prize, Gairdner Foundation (1989)
  • Howard Taylor Ricketts Award, University of Chicago (1988)
  • Eli Lilly Award in Microbiology and Immunology, American Society of Microbiology (1986)
  • Passano Young Scientist Award, Passano Foundation (1985)
  • Milton and Francis Clauser Doctoral Prize, Caltech (1981)

Professional Education

  • Ph. D., Caltech, Molecular Biology (1981)
  • B.A., The Johns Hopkins University, Molecular Biology (1974)

Research & Scholarship

Current Research and Scholarly Interests

We are interested in the molecular basis of T and B lymphocyte recognition, as well as the control of differentiation and functional responses in these cells.These studies have ranged from analyzing the inherent diversity of these highly diverse molecules and relating it to their function and specificity (Davis and Bjorkman 1988; Xu et al 2000) to basic aspects of TCR biochemistry and cell biology (Huppa et al 2010, Lillemeier et al, 2010). We also developed peptide-MHC tetramers which are useful for staining and isolating specific T cells in both basic science and clinical applications (Altman et al 1996; Newell et al., 2012, 2013).
We have also been very much involved in trying to relate what we have learned in basic immunology using mouse models to understanding the human immune system. Here we have employed systems biology approaches to understand vaccine responses (Furman et al., 2013), twin studies to understand the relative influence of environment versus genetics (ongoing) and T cell repertoire studies to understand self vs non-self capabilities and the origin of memory T cell responses (Su et al 2013). In this last paper, what is particularly interesting is that we have found that healthy adults have abundant numbers of pathogen-specific memory T cells even for viruses that they have never been exposed to, whereas newborns do not. This suggests that there is an unexpected source of protective lymphocytes in adults that likely impact disease resistance and conversely, indicates why young children are so vulnerable to infectious diseases. In general we have found that analyzing the human immune system has presented us with many surprises and complements what we have learned in mice.

Clinical Trials

  • Comparison of Immune Responses to Influenza Vaccine In Adults of Different Ages (SLVP015 2007-2017) Not Recruiting

    In this study the investigators are trying to understand how immune function declines in the elderly using annual influenza vaccinations as a model system. The longitudinal study began in 2007 and continued through early 2017.

    Stanford is currently not accepting patients for this trial.

    View full details


2017-18 Courses


All Publications

  • Detection, phenotyping, and quantification of antigen-specific T cells using a peptide-MHC dodecamer PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Huang, J., Zeng, X., Sigal, N., Lund, P. J., Su, L. F., Huang, H., Chien, Y., Davis, M. M. 2016; 113 (13): E1890-E1897
  • Individual heritable differences result in unique cell lymphocyte receptor repertoires of naive and antigen-experienced cells NATURE COMMUNICATIONS Rubelt, F., Bolen, C. R., McGuire, H. M., Vander Heiden, J. A., Gadala-Maria, D., Levin, M., Euskirchen, G. M., Mamedov, M. R., Swan, G. E., Dekker, C. L., Cowell, L. G., Kleinstein, S. H., Davis, M. M. 2016; 7
  • Successful immunotherapy induces previously unidentified allergen-specific CD4+ T-cell subsets. Proceedings of the National Academy of Sciences of the United States of America Ryan, J. F., Hovde, R., Glanville, J., Lyu, S., Ji, X., Gupta, S., Tibshirani, R. J., Jay, D. C., Boyd, S. D., Chinthrajah, R. S., Davis, M. M., Galli, S. J., Maecker, H. T., Nadeau, K. C. 2016; 113 (9): E1286-95


    Allergen immunotherapy can desensitize even subjects with potentially lethal allergies, but the changes induced in T cells that underpin successful immunotherapy remain poorly understood. In a cohort of peanut-allergic participants, we used allergen-specific T-cell sorting and single-cell gene expression to trace the transcriptional "roadmap" of individual CD4+ T cells throughout immunotherapy. We found that successful immunotherapy induces allergen-specific CD4+ T cells to expand and shift toward an "anergic" Th2 T-cell phenotype largely absent in both pretreatment participants and healthy controls. These findings show that sustained success, even after immunotherapy is withdrawn, is associated with the induction, expansion, and maintenance of immunotherapy-specific memory and naive T-cell phenotypes as early as 3 mo into immunotherapy. These results suggest an approach for immune monitoring participants undergoing immunotherapy to predict the success of future treatment and could have implications for immunotherapy targets in other diseases like cancer, autoimmune disease, and transplantation.

    View details for DOI 10.1073/pnas.1520180113

    View details for PubMedID 26811452

    View details for PubMedCentralID PMC4780622

  • Human B-cell isotype switching origins of IgE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Looney, T. J., Lee, J., Roskin, K. M., Hoh, R. A., King, J., Glanville, J., Liu, Y., Pham, T. D., Dekker, C. L., Davis, M. M., Boyd, S. D. 2016; 137 (2): 579-?
  • High-dimensional immune profiling of total and rotavirus VP6-specific intestinal and circulating B cells by mass cytometry MUCOSAL IMMUNOLOGY Nair, N., Newell, E. W., Vollmers, C., Quake, S. R., Morton, J. M., DAVIS, M. M., He, X. S., Greenberg, H. B. 2016; 9 (1): 68-82


    In-depth phenotyping of human intestinal antibody secreting cells (ASCs) and their precursors is important for developing improved mucosal vaccines. We used single-cell mass cytometry to simultaneously analyze 34 differentiation and trafficking markers on intestinal and circulating B cells. In addition, we labeled rotavirus (RV) double-layered particles with a metal isotope and characterized B cells specific to the RV VP6 major structural protein. We describe the heterogeneity of the intestinal B-cell compartment, dominated by ASCs with some phenotypic and transcriptional characteristics of long-lived plasma cells. Using principal component analysis, we visualized the phenotypic relationships between major B-cell subsets in the intestine and blood, and revealed that IgM(+) memory B cells (MBCs) and naive B cells were phenotypically related as were CD27(-) MBCs and switched MBCs. ASCs in the intestine and blood were highly clonally related, but associated with distinct trajectories of phenotypic development. VP6-specific B cells were present among diverse B-cell subsets in immune donors, including naive B cells, with phenotypes representative of the overall B-cell pool. These data provide a high dimensional view of intestinal B cells and the determinants regulating humoral memory to a ubiquitous, mucosal pathogen at steady-state.Mucosal Immunology advance online publication, 22 April 2015; doi:10.1038/mi.2015.36.

    View details for DOI 10.1038/mi.2015.36

    View details for Web of Science ID 000367653800006

  • Single-cell systems-level analysis of human Toll-like receptor activation defines a chemokine signature in patients with systemic lupus erythematosus JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY O'Gorman, W. E., Hsieh, E. W., Savig, E. S., Gherardini, P. F., Hernandez, J. D., Hansmann, L., Balboni, I. M., Utz, P. J., Bendall, S. C., Fantl, W. J., Lewis, D. B., Nolan, G. P., Davis, M. M. 2015; 136 (5): 1326-1336


    Activation of Toll-like receptors (TLRs) induces inflammatory responses involved in immunity to pathogens and autoimmune pathogenesis, such as in patients with systemic lupus erythematosus (SLE). Although TLRs are differentially expressed across the immune system, a comprehensive analysis of how multiple immune cell subsets respond in a system-wide manner has not been described.We sought to characterize TLR activation across multiple immune cell subsets and subjects, with the goal of establishing a reference framework against which to compare pathologic processes.Peripheral whole-blood samples were stimulated with TLR ligands and analyzed by means of mass cytometry simultaneously for surface marker expression, activation states of intracellular signaling proteins, and cytokine production. We developed a novel data visualization tool to provide an integrated view of TLR signaling networks with single-cell resolution. We studied 17 healthy volunteer donors and 8 patients with newly diagnosed and untreated SLE.Our data revealed the diversity of TLR-induced responses within cell types, with TLR ligand specificity. Subsets of natural killer cells and T cells selectively induced nuclear factor κ light chain enhancer of activated B cells in response to TLR2 ligands. CD14(hi) monocytes exhibited the most polyfunctional cytokine expression patterns, with more than 80 distinct cytokine combinations. Monocytic TLR-induced cytokine patterns were shared among a group of healthy donors, with minimal intraindividual and interindividual variability. Furthermore, autoimmune disease altered baseline cytokine production; newly diagnosed untreated SLE patients shared a distinct monocytic chemokine signature, despite clinical heterogeneity.Mass cytometry defined a systems-level reference framework for human TLR activation, which can be applied to study perturbations in patients with inflammatory diseases, such as SLE.

    View details for DOI 10.1016/j.jaci.2015.04.008

    View details for Web of Science ID 000364787200023

    View details for PubMedID 26037552

  • New approaches to understanding the immune response to vaccination and infection. Vaccine Furman, D., Davis, M. M. 2015; 33 (40): 5271-5281


    The immune system is a network of specialized cell types and tissues that communicates via cytokines and direct contact, to orchestrate specific types of defensive responses. Until recently, we could only study immune responses in a piecemeal, highly focused fashion, on major components like antibodies to the pathogen. But recent advances in technology and in our understanding of the many components of the system, innate and adaptive, have made possible a broader approach, where both the multiple responding cells and cytokines in the blood are measured. This systems immunology approach to a vaccine response or an infection gives us a more holistic picture of the different parts of the immune system that are mobilized and should allow us a much better understanding of the pathways and mechanisms of such responses, as well as to predict vaccine efficacy in different populations well in advance of efficacy studies. Here we summarize the different technologies and methods and discuss how they can inform us about the differences between diseases and vaccines, and how they can greatly accelerate vaccine development.

    View details for DOI 10.1016/j.vaccine.2015.06.117

    View details for PubMedID 26232539

  • Pregnancy Does Not Attenuate the Antibody or Plasmablast Response to Inactivated Influenza Vaccine. journal of infectious diseases Kay, A. W., Bayless, N. L., Fukuyama, J., Aziz, N., Dekker, C. L., Mackey, S., Swan, G. E., Davis, M. M., Blish, C. A. 2015; 212 (6): 861-870


    Inactivated influenza vaccine (IIV) is recommended during pregnancy to prevent influenza infection and its complications in pregnant women and their infants. However, the extent to which pregnancy modifies the antibody response to vaccination remains unclear, and prior studies have focused primarily on hemagglutinin inhibition (HI) titers. A more comprehensive understanding of how pregnancy modifies the humoral immune response to influenza vaccination will aid in maximizing vaccine efficacy.Healthy pregnant women and control women were studied prior to, 7 days after, and 28 days after vaccination with IIV. HI titers, microneutralization (MN) titers, and the frequency of circulating plasmablasts were evaluated in pregnant versus control women.Pregnant women and control women mount similarly robust serologic immune responses to IIV, with no significant differences for any influenza strain in postvaccination geometric mean HI or MN titers. HI and MN titers correlate, though MN titers demonstrate more robust changes pre- versus postvaccination. The induction of circulating plasmablasts is increased in pregnant women versus controls (median fold-change 2.60 vs 1.49 [interquartile range, 0.94-7.53 vs 0.63-2.67]; P = .03).Pregnant women do not have impaired humoral immune responses to IIV and may have increased circulating plasmablast production compared to control women.

    View details for DOI 10.1093/infdis/jiv138

    View details for PubMedID 25740957

    View details for PubMedCentralID PMC4548461

  • IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?


    Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

    View details for DOI 10.1126/scitranslmed.aab1216

    View details for PubMedID 26311730

  • IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?


    Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

    View details for DOI 10.1126/scitranslmed.aab1216

    View details for PubMedID 26311730

    View details for PubMedCentralID PMC4584259

  • mir-181a-1/b-1 Modulates Tolerance through Opposing Activities in Selection and Peripheral T Cell Function JOURNAL OF IMMUNOLOGY Schaffert, S. A., Loh, C., Wang, S., Arnold, C. P., Axtell, R. C., Newell, E. W., Nolan, G., Ansel, K. M., Davis, M. M., Steinman, L., Chen, C. 2015; 195 (4): 1470-1479


    Understanding the consequences of tuning TCR signaling on selection, peripheral T cell function, and tolerance in the context of native TCR repertoires may provide insight into the physiological control of tolerance. In this study, we show that genetic ablation of a natural tuner of TCR signaling, mir-181a-1/b-1, in double-positive thymocytes dampened TCR and Erk signaling and increased the threshold of positive selection. Whereas mir-181a-1/b-1 deletion in mice resulted in an increase in the intrinsic reactivity of naive T cells to self-antigens, it did not cause spontaneous autoimmunity. Loss of mir-181a-1/b-1 dampened the induction of experimental autoimmune encephalomyelitis and reduced basal TCR signaling in peripheral T cells and their migration from lymph nodes to pathogenic sites. Taken together, these results demonstrate that tolerance can be modulated by microRNA gene products through the control of opposing activities in T cell selection and peripheral T cell function.

    View details for DOI 10.4049/jimmunol.1401587

    View details for Web of Science ID 000360013200017

    View details for PubMedID 26163591

  • A Population Response Analysis Approach To Assign Class II HLA-Epitope Restrictions JOURNAL OF IMMUNOLOGY Paul, S., Dillon, M. B., Arlehamn, C. S., Huang, H., Davis, M. M., McKinney, D. M., Scriba, T. J., Sidney, J., Peters, B., Sette, A. 2015; 194 (12): 6164-6176


    Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.

    View details for DOI 10.4049/jimmunol.1403074

    View details for Web of Science ID 000355757800061

    View details for PubMedID 25948811

  • Mass Cytometry Analysis Shows That a Novel Memory Phenotype B Cell Is Expanded in Multiple Myeloma CANCER IMMUNOLOGY RESEARCH Hansmann, L., Blum, L., Ju, C., Liedtke, M., Robinson, W. H., Davis, M. M. 2015; 3 (6): 650-660


    It would be very beneficial if the status of cancers could be determined from a blood specimen. However, peripheral blood leukocytes are very heterogeneous between individuals, and thus high-resolution technologies are likely required. We used cytometry by time-of-flight and next-generation sequencing to ask whether a plasma cell cancer (multiple myeloma) and related precancerous states had any consistent effect on the peripheral blood mononuclear cell phenotypes of patients. Analysis of peripheral blood samples from 13 cancer patients, 9 precancer patients, and 9 healthy individuals revealed significant differences in the frequencies of the T-cell, B-cell, and natural killer-cell compartments. Most strikingly, we identified a novel B-cell population that normally accounts for 4.0% ± 0.7% (mean ± SD) of total B cells and is up to 13-fold expanded in multiple myeloma patients with active disease. This population expressed markers previously associated with both memory (CD27(+)) and naïve (CD24(lo)CD38(+)) phenotypes. Single-cell immunoglobulin gene sequencing showed polyclonality, indicating that these cells are not precursors to the myeloma, and somatic mutations, a characteristic of memory cells. SYK, ERK, and p38 phosphorylation responses, and the fact that most of these cells expressed isotypes other than IgM or IgD, confirmed the memory character of this population, defining it as a novel type of memory B cells.

    View details for DOI 10.1158/2326-6066.CIR-14-0236-T

    View details for Web of Science ID 000357430000010

    View details for PubMedID 25711758

    View details for PubMedCentralID PMC4457663

  • Clonal Deletion Prunes but Does Not Eliminate Self-Specific alpha beta CD8(+) T Lymphocytes IMMUNITY Yu, W., Jiang, N., Ebert, P. J., Kidd, B. A., Mueller, S., Lund, P. J., Juang, J., Adachi, K., Tse, T., Birnbaum, M. E., Newell, E. W., Wilson, D. M., Grotenbreg, G. M., Valitutti, S., Quake, S. R., Davis, M. M. 2015; 42 (5): 929-941


    It has long been thought that clonal deletion efficiently removes almost all self-specific T cells from the peripheral repertoire. We found that self-peptide MHC-specific CD8(+) T cells in the blood of healthy humans were present in frequencies similar to those specific for non-self antigens. For the Y chromosome-encoded SMCY antigen, self-specific T cells exhibited only a 3-fold lower average frequency in males versus females and were anergic with respect to peptide activation, although this inhibition could be overcome by a stronger stimulus. We conclude that clonal deletion prunes but does not eliminate self-specific T cells and suggest that to do so would create holes in the repertoire that pathogens could readily exploit. In support of this hypothesis, we detected T cells specific for all 20 amino acid variants at the p5 position of a hepatitis C virus epitope in a random group of blood donors.

    View details for DOI 10.1016/j.immuni.2015.05.001

    View details for Web of Science ID 000354827400018

    View details for PubMedID 25992863

  • The Immunological Synapse: A Molecular Machine Controlling T Cell Activation JOURNAL OF IMMUNOLOGY Grakoui, A., Bromley, S. K., Sumen, C., Davis, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 2015; 194 (9): 221-227
  • Cytomegalovirus infection enhances the immune response to influenza. Science translational medicine Furman, D., Jojic, V., Sharma, S., Shen-Orr, S. S., Angel, C. J., Onengut-Gumuscu, S., Kidd, B. A., Maecker, H. T., Concannon, P., Dekker, C. L., Thomas, P. G., Davis, M. M. 2015; 7 (281): 281ra43-?


    Cytomegalovirus (CMV) is a β-herpesvirus present in a latent form in most people worldwide. In immunosuppressed individuals, CMV can reactivate and cause serious clinical complications, but the effect of the latent state on healthy people remains elusive. We undertook a systems approach to understand the differences between seropositive and negative subjects and measured hundreds of immune system components from blood samples including cytokines and chemokines, immune cell phenotyping, gene expression, ex vivo cell responses to cytokine stimuli, and the antibody response to seasonal influenza vaccination. As expected, we found decreased responses to vaccination and an overall down-regulation of immune components in aged individuals regardless of CMV status. In contrast, CMV-seropositive young adults exhibited enhanced antibody responses to influenza vaccination, increased CD8(+) T cell sensitivity, and elevated levels of circulating interferon-γ compared to seronegative individuals. Experiments with young mice infected with murine CMV also showed significant protection from an influenza virus challenge compared with uninfected animals, although this effect declined with time. These data show that CMV and its murine equivalent can have a beneficial effect on the immune response of young, healthy individuals, which may explain the ubiquity of CMV infection in humans and many other species.

    View details for DOI 10.1126/scitranslmed.aaa2293

    View details for PubMedID 25834109

  • Cytomegalovirus infection enhances the immune response to influenza SCIENCE TRANSLATIONAL MEDICINE Furman, D., Jojic, V., Sharma, S., Shen-Orr, S. S., Angel, C. J., Onengut-Gumuscu, S., Kidd, B. A., Maecker, H. T., Concannon, P., Dekker, C. L., Thomas, P. G., Davis, M. M. 2015; 7 (281)

    View details for DOI 10.1126/scitranslmed.aaa2293

    View details for Web of Science ID 000352135800004

    View details for PubMedID 25834109

  • Distinct patterns of B-cell activation and priming by natural influenza virus infection versus inactivated influenza vaccination. journal of infectious diseases He, X., Holmes, T. H., Sanyal, M., Albrecht, R. A., García-Sastre, A., Dekker, C. L., Davis, M. M., Greenberg, H. B. 2015; 211 (7): 1051-1059


    The human B-cell response to natural influenza virus infection has not been extensively investigated at the polyclonal level.The overall B-cell response of patients acutely infected with the 2009 pandemic influenza A(H1N1)pdm09 virus (A[H1N1]pdm09) was analyzed by determining the reactivity of plasmablast-derived polyclonal antibodies (PPAbs) to influenza proteins. Recipients of inactivated influenza vaccine containing the same A(H1N1)pdm09 strain were studied for comparison.During acute infection, robust plasmablast responses to the infecting virus were detected, characterized by a greater PPAb reactivity to the conserved influenza virus nuclear protein and to heterovariant and heterosubtypic hemagglutinins, in comparison to responses to the inactivated A(H1N1)pdm09 vaccine. In A(H1N1)pdm09 vaccinees, the presence of baseline serum neutralizing antibodies against A(H1N1)pdm09, suggesting previous exposure to natural A(H1N1)pdm09 infection, did not affect the plasmablast response to vaccination, whereas repeated immunization with inactivated A(H1N1)pdm09 vaccine resulted in significantly reduced vaccine-specific and cross-reactive PPAb responses.Natural A(H1N1)pdm09 infection and inactivated A(H1N1)pdm09 vaccination result in very distinct patterns of B-cell activation and priming. These differences are likely to be associated with differences in protective immunity, especially cross-protection against heterovariant and heterosubtypic influenza virus strains.

    View details for DOI 10.1093/infdis/jiu580

    View details for PubMedID 25336731

    View details for PubMedCentralID PMC4366605

  • The coreceptor CD4 is expressed in distinct nanoclusters and does not colocalize with T-cell receptor and active protein tyrosine kinase p56lck PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Roh, K., Lillemeier, B. F., Wang, F., Davis, M. M. 2015; 112 (13): E1604-E1613


    CD4 molecules on the surface of T lymphocytes greatly augment the sensitivity and activation process of these cells, but how it functions is not fully understood. Here we studied the spatial organization of CD4, and its relationship to T-cell antigen receptor (TCR) and the active form of Src kinase p56lck (Lck) using single and dual-color photoactivated localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM). In nonactivated T cells, CD4 molecules are clustered in small protein islands, as are TCR and Lck. By dual-color imaging, we find that CD4, TCR, and Lck are localized in their separate clusters with limited interactions in the interfaces between them. Upon T-cell activation, the TCR and CD4 begin clustering together, developing into microclusters, and undergo a larger scale redistribution to form supramolecluar activation clusters (SMACs). CD4 and Lck localize in the inner TCR region of the SMAC, but this redistribution of disparate cluster structures results in enhanced segregation from each other. In nonactivated cells these preclustered structures and the limited interactions between them may serve to limit spontaneous and random activation events. However, the small sizes of these island structures also ensure large interfacial surfaces for potential interactions and signal amplification when activation is initiated. In the later activation stages, the increasingly larger clusters and their segregation from each other reduce the interfacial surfaces and could have a dampening effect. These highly differentiated spatial distributions of TCR, CD4, and Lck and their changes during activation suggest that there is a more complex hierarchy than previously thought.

    View details for DOI 10.1073/pnas.1503532112

    View details for Web of Science ID 000351914500016

    View details for PubMedID 25829544

  • Tetramers reveal IL-17-secreting CD4+ T cells that are specific for U1-70 in lupus and mixed connective tissue disease. Proceedings of the National Academy of Sciences of the United States of America Kattah, N. H., Newell, E. W., Jarrell, J. A., Chu, A. D., Xie, J., Kattah, M. G., Goldberger, O., Ye, J., Chakravarty, E. F., Davis, M. M., Utz, P. J. 2015; 112 (10): 3044-3049


    Antigen-specific CD4(+) T cells are implicated in the autoimmune disease systemic lupus erythematosus (SLE), but little is known about the peptide antigens that they recognize and their precise function in disease. We generated a series of MHC class II tetramers of I-E(k)-containing peptides from the spliceosomal protein U1-70 that specifically stain distinct CD4(+) T-cell populations in MRL/lpr mice. The T-cell populations recognize an epitope differing only by the presence or absence of a single phosphate residue at position serine(140). The frequency of CD4(+) T cells specific for U1-70(131-150):I-E(k) (without phosphorylation) correlates with disease severity and anti-U1-70 autoantibody production. These T cells also express RORγt and produce IL-17A. Furthermore, the U1-70-specific CD4(+) T cells that produce IL-17A are detected in a subset of patients with SLE and are significantly increased in patients with mixed connective tissue disease. These studies provide tools for studying antigen-specific CD4(+) T cells in lupus, and demonstrate an antigen-specific source of IL-17A in autoimmune disease.

    View details for DOI 10.1073/pnas.1424796112

    View details for PubMedID 25713364

    View details for PubMedCentralID PMC4364210

  • Associations of toll-like receptor (TLR)-4 single nucleotide polymorphisms and rheumatoid arthritis disease progression: An observational cohort study INTERNATIONAL IMMUNOPHARMACOLOGY Davis, M. L., LeVan, T. D., Yu, F., Sayles, H., Sokolove, J., Robinson, W., Michaud, K., Thiele, G. M., Mikuls, T. R. 2015; 24 (2): 346-352


    To examine the associations of toll-like receptor (TLR)-4 single nucleotide polymorphisms (SNPs) with disease progression in rheumatoid arthritis (RA).A total of 1188 RA patients were genotyped for TLR4 SNPs (rs1927911, rs11536878, and rs4986790). Measures of disease activity were examined, including Disease Activity Score-28 (DAS28), Multidimensional Health Assessment Questionnaire (MD-HAQ), Clinical Disease Activity Index (CDAI), and Simplified Disease Activity Index (SDAI). Genetic associations with these longitudinal measures were examined using generalized estimating equations in both univariate and multivariate analyses. Analyses were then stratified by antigen specific anti-citrullinated peptide antibody (ACPA) status including antibody to citrullinated fibrinogen and citrullinated histone H2B.Disease activity measures progressed less over time in the homozygous minor allele group of rs1927911 including DAS28 (p<0.001), CDAI (p=0.008), and MD-HAQ (p=0.015) in univariate analysis and DAS28, CDAI and SDAI in multivariate analysis. Disease activity progression among those homozygous for the minor allele tended to be lower in the groups with positive ACPA though major differences by autoantibody status were not identified. There were no associations of TLR4 rs11536878 and rs4986790 SNPs with RA disease activity progression.In this population, TLR4 rs1927911 genotypes are associated with disease activity independent of other covariates.

    View details for DOI 10.1016/j.intimp.2014.12.030

    View details for Web of Science ID 000350183600026

    View details for PubMedID 25573402

  • Variation in the human immune system is largely driven by non-heritable influences. Cell Brodin, P., Jojic, V., Gao, T., Bhattacharya, S., Angel, C. J., Furman, D., Shen-Orr, S., Dekker, C. L., Swan, G. E., Butte, A. J., Maecker, H. T., Davis, M. M. 2015; 160 (1-2): 37-47


    There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population frequencies, cytokine responses, and serum proteins, and found that 77% of these are dominated (>50% of variance) and 58% almost completely determined (>80% of variance) by non-heritable influences. In addition, some of these parameters become more variable with age, suggesting the cumulative influence of environmental exposure. Similarly, the serological responses to seasonal influenza vaccination are also determined largely by non-heritable factors, likely due to repeated exposure to different strains. Lastly, in MZ twins discordant for cytomegalovirus infection, more than half of all parameters are affected. These results highlight the largely reactive and adaptive nature of the immune system in healthy individuals.

    View details for DOI 10.1016/j.cell.2014.12.020

    View details for PubMedID 25594173

    View details for PubMedCentralID PMC4302727

  • The Split Virus Influenza Vaccine rapidly activates immune cells through Fc gamma receptors VACCINE O'Gorman, W. E., Huang, H., Wei, Y., Davis, K. L., Leipold, M. D., Bendall, S. C., Kidd, B. A., Dekker, C. L., Maecker, H. T., Chien, Y., Davis, M. M. 2014; 32 (45): 5989-5997
  • Enhanced natural killer-cell and T-cell responses to influenza A virus during pregnancy PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kay, A. W., Fukuyama, J., Aziz, N., Dekker, C. L., Mackey, S., Swan, G. E., Davis, M. M., Holmes, S., Blish, C. A. 2014; 111 (40): 14506-14511
  • Clinical recovery from surgery correlates with single-cell immune signatures. Science translational medicine Gaudillière, B., Fragiadakis, G. K., Bruggner, R. V., Nicolau, M., Finck, R., Tingle, M., Silva, J., Ganio, E. A., Yeh, C. G., Maloney, W. J., Huddleston, J. I., Goodman, S. B., Davis, M. M., Bendall, S. C., Fantl, W. J., Angst, M. S., Nolan, G. P. 2014; 6 (255): 255ra131-?


    Delayed recovery from surgery causes personal suffering and substantial societal and economic costs. Whether immune mechanisms determine recovery after surgical trauma remains ill-defined. Single-cell mass cytometry was applied to serial whole-blood samples from 32 patients undergoing hip replacement to comprehensively characterize the phenotypic and functional immune response to surgical trauma. The simultaneous analysis of 14,000 phosphorylation events in precisely phenotyped immune cell subsets revealed uniform signaling responses among patients, demarcating a surgical immune signature. When regressed against clinical parameters of surgical recovery, including functional impairment and pain, strong correlations were found with STAT3 (signal transducer and activator of transcription), CREB (adenosine 3',5'-monophosphate response element-binding protein), and NF-κB (nuclear factor κB) signaling responses in subsets of CD14(+) monocytes (R = 0.7 to 0.8, false discovery rate <0.01). These sentinel results demonstrate the capacity of mass cytometry to survey the human immune system in a relevant clinical context. The mechanistically derived immune correlates point to diagnostic signatures, and potential therapeutic targets, that could postoperatively improve patient recovery.

    View details for DOI 10.1126/scitranslmed.3009701

    View details for PubMedID 25253674

  • Clinical recovery from surgery correlates with single-cell immune signatures SCIENCE TRANSLATIONAL MEDICINE Gaudilliere, B., Fragiadakis, G. K., Bruggner, R. V., Nicolau, M., Finck, R., Tingle, M., Silva, J., Ganio, E. A., Yeh, C. G., Maloney, W. J., Huddleston, J. I., Goodman, S. B., Davis, M. M., Bendall, S. C., Fantl, W. J., Angst, M. S., Nolan, G. P. 2014; 6 (255)
  • Association between Latent Proviral Characteristics and Immune Activation in Antiretrovirus-Treated Human Immunodeficiency Virus Type 1-Infected Adults. Journal of virology Liang, E. C., Sceats, L., Bayless, N. L., Strauss-Albee, D. M., Kubo, J., Grant, P. M., Furman, D., Desai, M., Katzenstein, D. A., Davis, M. M., Zolopa, A. R., Blish, C. A. 2014; 88 (15): 8629-8639


    Generalized immune activation during HIV infection is associated with an increased risk of cardiovascular disease, neurocognitive disease, osteoporosis, metabolic disorders, and physical frailty. The mechanisms driving this immune activation are poorly understood, particularly for individuals effectively treated with antiretroviral medications. We hypothesized that viral characteristics such as sequence diversity may play a role in driving HIV-associated immune activation. We therefore sequenced proviral DNA isolated from peripheral blood mononuclear cells from HIV-infected individuals on fully suppressive antiretroviral therapy. We performed phylogenetic analyses, calculated viral diversity and divergence in the env and pol genes, and determined coreceptor tropism and the frequency of drug resistance mutations. Comprehensive immune profiling included quantification of immune cell subsets, plasma cytokine levels, and intracellular signaling responses in T cells, B cells, and monocytes. These antiretroviral therapy-treated HIV-infected individuals exhibited a wide range of diversity and divergence in both env and pol genes. However, proviral diversity and divergence in env and pol, coreceptor tropism, and the level of drug resistance did not significantly correlate with markers of immune activation. A clinical history of virologic failure was also not significantly associated with levels of immune activation, indicating that a history of virologic failure does not inexorably lead to increased immune activation as long as suppressive antiretroviral medications are provided. Overall, this study demonstrates that latent viral diversity is unlikely to be a major driver of persistent HIV-associated immune activation.Chronic immune activation, which is associated with cardiovascular disease, neurologic disease, and early aging, is likely to be a major driver of morbidity and mortality in HIV-infected individuals. Although treatment of HIV with antiretroviral medications decreases the level of immune activation, levels do not return to normal. The factors driving this persistent immune activation, particularly during effective treatment, are poorly understood. In this study, we investigated whether characteristics of the latent, integrated HIV provirus that persists during treatment are associated with immune activation. We found no relationship between latent viral characteristics and immune activation in treated individuals, indicating that qualities of the provirus are unlikely to be a major driver of persistent inflammation. We also found that individuals who had previously failed treatment but were currently effectively treated did not have significantly increased levels of immune activation, providing hope that past treatment failures do not have a lifelong "legacy" impact.

    View details for DOI 10.1128/JVI.01257-14

    View details for PubMedID 24850730

    View details for PubMedCentralID PMC4135944

  • Human responses to influenza vaccination show seroconversion signatures and convergent antibody rearrangements. Cell host & microbe Jackson, K. J., Liu, Y., Roskin, K. M., Glanville, J., Hoh, R. A., Seo, K., Marshall, E. L., Gurley, T. C., Moody, M. A., Haynes, B. F., Walter, E. B., Liao, H., Albrecht, R. A., García-Sastre, A., Chaparro-Riggers, J., Rajpal, A., Pons, J., Simen, B. B., Hanczaruk, B., Dekker, C. L., Laserson, J., Koller, D., Davis, M. M., Fire, A. Z., Boyd, S. D. 2014; 16 (1): 105-114


    B cells produce a diverse antibody repertoire by undergoing gene rearrangements. Pathogen exposure induces the clonal expansion of B cells expressing antibodies that can bind the infectious agent. To assess human B cell responses to trivalent seasonal influenza and monovalent pandemic H1N1 vaccination, we sequenced gene rearrangements encoding the immunoglobulin heavy chain, a major determinant of epitope recognition. The magnitude of B cell clonal expansions correlates with an individual's secreted antibody response to the vaccine, and the expanded clones are enriched with those expressing influenza-specific monoclonal antibodies. Additionally, B cell responses to pandemic influenza H1N1 vaccination and infection in different people show a prominent family of convergent antibody heavy chain gene rearrangements specific to influenza antigens. These results indicate that microbes can induce specific signatures of immunoglobulin gene rearrangements and that pathogen exposure can potentially be assessed from B cell repertoires.

    View details for DOI 10.1016/j.chom.2014.05.013

    View details for PubMedID 24981332

    View details for PubMedCentralID PMC4158033

  • Linking T-cell receptor sequence to functional phenotype at the single-cell level NATURE BIOTECHNOLOGY Han, A., Glanville, J., Hansmann, L., Davis, M. M. 2014; 32 (7): 684-?

    View details for DOI 10.1038/nbt.2938

    View details for Web of Science ID 000338705900035

  • Deconstructing the Peptide-MHC Specificity of T Cell Recognition. Cell Birnbaum, M. E., Mendoza, J. L., Sethi, D. K., Dong, S., Glanville, J., Dobbins, J., Ozkan, E., Davis, M. M., Wucherpfennig, K. W., Garcia, K. C. 2014; 157 (5): 1073-1087


    In order to survey a universe of major histocompatibility complex (MHC)-presented peptide antigens whose numbers greatly exceed the diversity of the T cell repertoire, T cell receptors (TCRs) are thought to be cross-reactive. However, the nature and extent of TCR cross-reactivity has not been conclusively measured experimentally. We developed a system to identify MHC-presented peptide ligands by combining TCR selection of highly diverse yeast-displayed peptide-MHC libraries with deep sequencing. Although we identified hundreds of peptides reactive with each of five different mouse and human TCRs, the selected peptides possessed TCR recognition motifs that bore a close resemblance to their known antigens. This structural conservation of the TCR interaction surface allowed us to exploit deep-sequencing information to computationally identify activating microbial and self-ligands for human autoimmune TCRs. The mechanistic basis of TCR cross-reactivity described here enables effective surveillance of diverse self and foreign antigens without necessitating degenerate recognition of nonhomologous peptides.

    View details for DOI 10.1016/j.cell.2014.03.047

    View details for PubMedID 24855945

    View details for PubMedCentralID PMC4071348

  • Beyond model antigens: high-dimensional methods for the analysis of antigen-specific T cells NATURE BIOTECHNOLOGY Newell, E. W., Davis, M. M. 2014; 32 (2): 149-157


    Adaptive immune responses often begin with the formation of a molecular complex between a T-cell receptor (TCR) and a peptide antigen bound to a major histocompatibility complex (MHC) molecule. These complexes are highly variable, however, due to the polymorphism of MHC genes, the random, inexact recombination of TCR gene segments, and the vast array of possible self and pathogen peptide antigens. As a result, it has been very difficult to comprehensively study the TCR repertoire or identify and track more than a few antigen-specific T cells in mice or humans. For mouse studies, this had led to a reliance on model antigens and TCR transgenes. The study of limited human clinical samples, in contrast, requires techniques that can simultaneously survey TCR phenotype and function, and TCR reactivity to many T-cell epitopes. Thanks to recent advances in single-cell and cytometry methodologies, as well as high-throughput sequencing of the TCR repertoire, we now have or will soon have the tools needed to comprehensively analyze T-cell responses in health and disease.

    View details for DOI 10.1038/nbt.2783

    View details for Web of Science ID 000331074000020

    View details for PubMedID 24441473

  • Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires JOURNAL OF IMMUNOLOGY Wang, C., Liu, Y., Xu, L. T., Jackson, K. J., Roskin, K. M., Pham, T. D., Laserson, J., Marshall, E. L., Seo, K., Lee, J., Furman, D., Koller, D., Dekker, C. L., Davis, M. M., Fire, A. Z., Boyd, S. D. 2014; 192 (2): 603-611


    Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.

    View details for DOI 10.4049/jimmunol.1301384

    View details for Web of Science ID 000329224000006

    View details for PubMedID 24337376

  • Systems analysis of sex differences reveals an immunosuppressive role for testosterone in the response to influenza vaccination. Proceedings of the National Academy of Sciences of the United States of America Furman, D., Hejblum, B. P., Simon, N., Jojic, V., Dekker, C. L., Thiébaut, R., Tibshirani, R. J., Davis, M. M. 2014; 111 (2): 869-874


    Females have generally more robust immune responses than males for reasons that are not well-understood. Here we used a systems analysis to investigate these differences by analyzing the neutralizing antibody response to a trivalent inactivated seasonal influenza vaccine (TIV) and a large number of immune system components, including serum cytokines and chemokines, blood cell subset frequencies, genome-wide gene expression, and cellular responses to diverse in vitro stimuli, in 53 females and 34 males of different ages. We found elevated antibody responses to TIV and expression of inflammatory cytokines in the serum of females compared with males regardless of age. This inflammatory profile correlated with the levels of phosphorylated STAT3 proteins in monocytes but not with the serological response to the vaccine. In contrast, using a machine learning approach, we identified a cluster of genes involved in lipid biosynthesis and previously shown to be up-regulated by testosterone that correlated with poor virus-neutralizing activity in men. Moreover, men with elevated serum testosterone levels and associated gene signatures exhibited the lowest antibody responses to TIV. These results demonstrate a strong association between androgens and genes involved in lipid metabolism, suggesting that these could be important drivers of the differences in immune responses between males and females.

    View details for DOI 10.1073/pnas.1321060111

    View details for PubMedID 24367114

  • Automatic Classification of Cellular Expression by Nonlinear Stochastic Embedding (ACCENSE) PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Shekhar, K., Brodin, P., Davis, M. M., Chakraborty, A. K. 2014; 111 (1): 202-207


    Mass cytometry enables an unprecedented number of parameters to be measured in individual cells at a high throughput, but the large dimensionality of the resulting data severely limits approaches relying on manual "gating." Clustering cells based on phenotypic similarity comes at a loss of single-cell resolution and often the number of subpopulations is unknown a priori. Here we describe ACCENSE, a tool that combines nonlinear dimensionality reduction with density-based partitioning, and displays multivariate cellular phenotypes on a 2D plot. We apply ACCENSE to 35-parameter mass cytometry data from CD8(+) T cells derived from specific pathogen-free and germ-free mice, and stratify cells into phenotypic subpopulations. Our results show significant heterogeneity within the known CD8(+) T-cell subpopulations, and of particular note is that we find a large novel subpopulation in both specific pathogen-free and germ-free mice that has not been described previously. This subpopulation possesses a phenotypic signature that is distinct from conventional naive and memory subpopulations when analyzed by ACCENSE, but is not distinguishable on a biaxial plot of standard markers. We are able to automatically identify cellular subpopulations based on all proteins analyzed, thus aiding the full utilization of powerful new single-cell technologies such as mass cytometry.

    View details for DOI 10.1073/pnas.1321405111

    View details for Web of Science ID 000329350700063

    View details for PubMedID 24344260

  • CD4+ T Cell Autoimmunity to Hypocretin/Orexin and Cross-Reactivity to a 2009 H1N1 Influenza A Epitope in Narcolepsy. Science translational medicine De la Herrán-Arita, A. K., Kornum, B. R., Mahlios, J., Jiang, W., Lin, L., Hou, T., Macaubas, C., Einen, M., Plazzi, G., Crowe, C., Newell, E. W., Davis, M. M., Mellins, E. D., Mignot, E. 2013; 5 (216): 216ra176-?

    View details for DOI 10.1126/scitranslmed.3007762

    View details for PubMedID 24353159

  • A Single Peptide-Major Histocompatibility Complex Ligand Triggers Digital Cytokine Secretion in CD4(+) T Cells. Immunity Huang, J., Brameshuber, M., Zeng, X., Xie, J., Li, Q., Chien, Y., Valitutti, S., Davis, M. M. 2013; 39 (5): 846-857


    We have developed a single-molecule imaging technique that uses quantum-dot-labeled peptide-major histocompatibility complex (pMHC) ligands to study CD4(+) T cell functional sensitivity. We found that naive T cells, T cell blasts, and memory T cells could all be triggered by a single pMHC to secrete tumor necrosis factor-α (TNF-α) and interleukin-2 (IL-2) cytokines with a rate of ∼1,000, ∼10,000, and ∼10,000 molecules/min, respectively, and that additional pMHCs did not augment secretion, indicating a digital response pattern. We also found that a single pMHC localized to the immunological synapse induced the slow formation of a long-lasting T cell receptor (TCR) cluster, consistent with a serial engagement mechanism. These data show that scaling up CD4(+) T cell cytokine responses involves increasingly efficient T cell recruitment rather than greater cytokine production per cell.

    View details for DOI 10.1016/j.immuni.2013.08.036

    View details for PubMedID 24120362

  • Genetic and environmental determinants of human NK cell diversity revealed by mass cytometry. Science translational medicine Horowitz, A., Strauss-Albee, D. M., Leipold, M., Kubo, J., Nemat-Gorgani, N., Dogan, O. C., Dekker, C. L., Mackey, S., Maecker, H., Swan, G. E., Davis, M. M., Norman, P. J., Guethlein, L. A., Desai, M., Parham, P., Blish, C. A. 2013; 5 (208): 208ra145-?

    View details for DOI 10.1126/scitranslmed.3006702

    View details for PubMedID 24154599

  • Human Circulating PD-1(+)CXCR3(-)CXCR5(+) Memory Tfh Cells Are Highly Functional and Correlate with Broadly Neutralizing HIV Antibody Responses IMMUNITY Locci, M., Havenar-Daughton, C., Landais, E., Wu, J., Kroenke, M. A., Arlehamn, C. L., Su, L. F., Cubas, R., Davis, M. M., Sette, A., Haddad, E. K., Poignard, P., Crotty, S. 2013; 39 (4): 758-769


    The vast majority of currently licensed human vaccines work on the basis of long-term protective antibody responses. It is now conceivable that an antibody-dependent HIV vaccine might be possible, given the discovery of HIV broadly neutralizing antibodies (bnAbs) in some HIV-infected individuals. However, these antibodies are difficult to develop and have characteristics indicative of a high degree of affinity maturation in germinal centers (GCs). CD4⁺ T follicular helper (Tfh) cells are specialized for B cell help and necessary for GCs. Therefore, the development of HIV bnAbs might depend on Tfh cells. Here, we identified in normal individuals a subpopulation of circulating memory PD-1⁺CXCR5⁺CD4⁺ T cells that are resting memory cells most related to bona fide GC Tfh cells by gene expression profile, cytokine profile, and functional properties. Importantly, the frequency of these cells correlated with the development of bnAbs against HIV in a large cohort of HIV⁺ individuals.

    View details for DOI 10.1016/j.immuni.2013.08.031

    View details for Web of Science ID 000330950000016

    View details for PubMedID 24035365

  • Antiviral memory phenotype T cells in unexposed adults IMMUNOLOGICAL REVIEWS Su, L. F., Davis, M. M. 2013; 255 (1): 95-109


    αβ T cells are an integral part of protective immunity against pathogens. After precursor cells arise in the adult bone marrow or fetal liver, they migrate to the thymus where they rearrange their T-cell receptor genes (TCR) and undergo selection on the basis of their interactions with ligands expressed by thymic stroma and other cells. Those that survive then exit the thymus to populate the peripheral immune compartment, where they patrol the blood and lymphoid systems. The composition of this pre-immune peripheral repertoire is critically important in determining the robustness of an immune response. In both mice and humans, the magnitude and diversity of a response are directly correlated with the frequency of precursor T cells. Equally relevant are the functional characteristics of these lymphocytes. Engagement of a specific antigen to the TCR activates signaling pathways in the naive T cell that result in cellular proliferation and the acquisition of particular effector functions. A portion of these persist following the resolution of infection and become memory cells. These memory cells can mount a faster and stronger response when they encounter the same antigen at a later time. As the molecular basis for TCR ligand interaction has become better defined, it is clear that some T cells can recognize multiple distinct ligands and therefore T-cell memory developed by exposure to one ligand may play a significant role in the response to a different antigen. Thus, there is an increasing focus on understanding how exposure to related or unrelated antigens influences the T-cell repertoire and impacts subsequent immunity. In this review, we discuss the issue of TCR cross-reactivity in the development of memory phenotype CD4(+) T cells and the implications for pathogen-specific responses. We review both the human and mouse data and discuss the therapeutic implications of these findings in the contexts of infection and vaccination.

    View details for DOI 10.1111/imr.12095

    View details for Web of Science ID 000323150900008

    View details for PubMedID 23947350

  • Dietary gluten triggers concomitant activation of CD4(+) and CD8(+) alpha beta T cells and gamma delta T cells in celiac disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Han, A., Newell, E. W., Glanville, J., Fernandez-Becker, N., Khosla, C., Chien, Y., Davis, M. M. 2013; 110 (32): 13073-13078
  • Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization NATURE BIOTECHNOLOGY Newell, E. W., Sigal, N., Nair, N., Kidd, B. A., Greenberg, H. B., Davis, M. M. 2013; 31 (7): 623-U81


    It is currently not possible to predict which epitopes will be recognized by T cells in different individuals. This is a barrier to the thorough analysis and understanding of T-cell responses after vaccination or infection. Here, by combining mass cytometry with combinatorial peptide-MHC tetramer staining, we have developed a method allowing the rapid and simultaneous identification and characterization of T cells specific for many epitopes. We use this to screen up to 109 different peptide-MHC tetramers in a single human blood sample, while still retaining at least 23 labels to analyze other markers of T-cell phenotype and function. Among 77 candidate rotavirus epitopes, we identified six T-cell epitopes restricted to human leukocyte antigen (HLA)-A*0201 in the blood of healthy individuals. T cells specific for epitopes in the rotavirus VP3 protein displayed a distinct phenotype and were present at high frequencies in intestinal epithelium. This approach should be useful for the comprehensive analysis of T-cell responses to infectious diseases or vaccines.

    View details for DOI 10.1038/nbt.2593

    View details for Web of Science ID 000321579700019

    View details for PubMedID 23748502

  • Virus-specific CD4(+) memory-phenotype T cells are abundant in unexposed adults. Immunity Su, L. F., Kidd, B. A., Han, A., Kotzin, J. J., Davis, M. M. 2013; 38 (2): 373-383


    Although T cell memory is generally thought to require direct antigen exposure, we found an abundance of memory-phenotype cells (20%-90%, averaging over 50%) of CD4(+) T cells specific to viral antigens in adults who had never been infected. These cells express the appropriate memory markers and genes, rapidly produce cytokines, and have clonally expanded. In contrast, the same T cell receptor (TCR) specificities in newborns are almost entirely naïve, which might explain the vulnerability of young children to infections. One mechanism for this phenomenon is TCR cross-reactivity to environmental antigens, and in support of this, we found extensive cross-recognition by HIV-1 and influenza-reactive T lymphocytes to other microbial peptides and expansion of one of these after influenza vaccination. Thus, the presence of these memory-phenotype T cells has significant implications for immunity to novel pathogens, child and adult health, and the influence of pathogen-rich versus hygienic environments.

    View details for DOI 10.1016/j.immuni.2012.10.021

    View details for PubMedID 23395677

  • Lineage structure of the human antibody repertoire in response to influenza vaccination. Science translational medicine Jiang, N., He, J., Weinstein, J. A., Penland, L., Sasaki, S., He, X., Dekker, C. L., Zheng, N., Huang, M., Sullivan, M., Wilson, P. C., Greenberg, H. B., Davis, M. M., Fisher, D. S., Quake, S. R. 2013; 5 (171): 171ra19-?


    The human antibody repertoire is one of the most important defenses against infectious disease, and the development of vaccines has enabled the conferral of targeted protection to specific pathogens. However, there are many challenges to measuring and analyzing the immunoglobulin sequence repertoire, including that each B cell's genome encodes a distinct antibody sequence, that the antibody repertoire changes over time, and the high similarity between antibody sequences. We have addressed these challenges by using high-throughput long read sequencing to perform immunogenomic characterization of expressed human antibody repertoires in the context of influenza vaccination. Informatic analysis of 5 million antibody heavy chain sequences from healthy individuals allowed us to perform global characterizations of isotype distributions, determine the lineage structure of the repertoire, and measure age- and antigen-related mutational activity. Our analysis of the clonal structure and mutational distribution of individuals' repertoires shows that elderly subjects have a decreased number of lineages but an increased prevaccination mutation load in their repertoire and that some of these subjects have an oligoclonal character to their repertoire in which the diversity of the lineages is greatly reduced relative to younger subjects. We have thus shown that global analysis of the immune system's clonal structure provides direct insight into the effects of vaccination and provides a detailed molecular portrait of age-related effects.

    View details for DOI 10.1126/scitranslmed.3004794

    View details for PubMedID 23390249

  • Lineage Structure of the Human Antibody Repertoire in Response to Influenza Vaccination SCIENCE TRANSLATIONAL MEDICINE Jiang, N., He, J., Weinstein, J. A., Penland, L., Sasaki, S., He, X., Dekker, C. L., Zheng, N., Huang, M., Sullivan, M., Wilson, P. C., Greenberg, H. B., Davis, M. M., Fisher, D. S., Quake, S. R. 2013; 5 (171)

    View details for Web of Science ID 000314810000008

    View details for PubMedID 23390249

  • Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PloS one Price, J. V., Jarrell, J. A., Furman, D., Kattah, N. H., Newell, E., Dekker, C. L., Davis, M. M., Utz, P. J. 2013; 8 (5)


    Existing methods to measure influenza vaccine immunogenicity prohibit detailed analysis of epitope determinants recognized by immunoglobulins. The development of highly multiplex proteomics platforms capable of capturing a high level of antibody binding information will enable researchers and clinicians to generate rapid and meaningful readouts of influenza-specific antibody reactivity.We developed influenza hemagglutinin (HA) whole-protein and peptide microarrays and validated that the arrays allow detection of specific antibody reactivity across a broad dynamic range using commercially available antibodies targeted to linear and conformational HA epitopes. We derived serum from blood draws taken from 76 young and elderly subjects immediately before and 28±7 days post-vaccination with the 2008/2009 trivalent influenza vaccine and determined the antibody reactivity of these sera to influenza array antigens.Using linear regression and correcting for multiple hypothesis testing by the Benjamini and Hochberg method of permutations over 1000 resamplings, we identified antibody reactivity to influenza whole-protein and peptide array features that correlated significantly with age, H1N1, and B-strain post-vaccine titer as assessed through a standard microneutralization assay (p<0.05, q <0.2). Notably, we identified several peptide epitopes that were inversely correlated with regard to age and seasonal H1N1 and B-strain neutralization titer (p<0.05, q <0.2), implicating reactivity to these epitopes in age-related defects in response to H1N1 influenza. We also employed multivariate linear regression with cross-validation to build models based on age and pre-vaccine peptide reactivity that predicted vaccine-induced neutralization of seasonal H1N1 and H3N2 influenza strains with a high level of accuracy (84.7% and 74.0%, respectively).Our methods provide powerful tools for rapid and accurate measurement of broad antibody-based immune responses to influenza, and may be useful in measuring response to other vaccines and infectious agents.

    View details for DOI 10.1371/journal.pone.0064555

    View details for PubMedID 23734205

    View details for PubMedCentralID PMC3667171

  • Characterization of influenza vaccine immunogenicity using influenza antigen microarrays. PloS one Price, J. V., Jarrell, J. A., Furman, D., Kattah, N. H., Newell, E., Dekker, C. L., Davis, M. M., Utz, P. J. 2013; 8 (5)

    View details for DOI 10.1371/journal.pone.0064555

    View details for PubMedID 23734205

  • Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Molecular systems biology Furman, D., Jojic, V., Kidd, B., Shen-Orr, S., Price, J., Jarrell, J., Tse, T., Huang, H., Lund, P., Maecker, H. T., Utz, P. J., Dekker, C. L., Koller, D., Davis, M. M. 2013; 9: 659-?

    View details for DOI 10.1038/msb.2013.15

    View details for PubMedID 23591775

  • The interdisciplinary science of T-cell recognition. Advances in immunology Huppa, J. B., Davis, M. M. 2013; 119: 1-50


    The recognition of peptide/MHC antigens by T-cells has continued to challenge the imagination of immunologists, biochemists, and cell biologists alike. This is at least in part because T-cell recognition connects a diversity of issues and transcends many scientific disciplines. A fundamental unsolved issue is how T-cells manage to detect even a single molecule of an agonist pMHC complex, which is vastly outnumbered by endogenous pMHCs, many of which involve the same MHC molecule. They do so although TCRs are cross-reactive and typically low in affinity when measured in isolation. Importantly, T-cell antigen recognition takes place within the contact zone between a T-cell and the antigen-presenting cell, termed the immunological synapse. This bimembrane structure sets the stage for the antigen-binding events and all subsequent molecular recognition events. There is increasing evidence that the molecular dynamics of receptor-ligand interactions are not only dependent on the intrinsic properties of the binding partners but also become transformed by cell biological parameters such as the geometrical constraints within the immune synapse, mechanical forces, and local molecular crowding. To appreciate the complete picture, we think a multidisciplinary approach is imperative, which includes genetics, biochemistry, and structure determination and also biophysical analyses and the latest molecular imaging techniques. Here, we review earlier pioneering work and also recent developments in the fascinating and interdisciplinary science of T-cell antigen recognition. In many ways, this work may present a useful "roadmap" for work in other systems of cell-cell recognition, which underlie many fundamental biological phenomenons of interest.

    View details for DOI 10.1016/B978-0-12-407707-2.00001-1

    View details for PubMedID 23886063

  • Apoptosis and other immune biomarkers predict influenza vaccine responsiveness. Molecular systems biology Furman, D., Jojic, V., Kidd, B., Shen-Orr, S., Price, J., Jarrell, J., Tse, T., Huang, H., Lund, P., Maecker, H. T., Utz, P. J., Dekker, C. L., Koller, D., Davis, M. M. 2013; 9: 659-?


    Despite the importance of the immune system in many diseases, there are currently no objective benchmarks of immunological health. In an effort to identifying such markers, we used influenza vaccination in 30 young (20-30 years) and 59 older subjects (60 to >89 years) as models for strong and weak immune responses, respectively, and assayed their serological responses to influenza strains as well as a wide variety of other parameters, including gene expression, antibodies to hemagglutinin peptides, serum cytokines, cell subset phenotypes and in vitro cytokine stimulation. Using machine learning, we identified nine variables that predict the antibody response with 84% accuracy. Two of these variables are involved in apoptosis, which positively associated with the response to vaccination and was confirmed to be a contributor to vaccine responsiveness in mice. The identification of these biomarkers provides new insights into what immune features may be most important for immune health.

    View details for DOI 10.1038/msb.2013.15

    View details for PubMedID 23591775

    View details for PubMedCentralID PMC3658270

  • How the immune system talks to itself: the varied role of synapses IMMUNOLOGICAL REVIEWS Xie, J., Tato, C. M., Davis, M. M. 2013; 251: 65-79


    Using an elaborately evolved language of cytokines and chemokines as well as cell-cell interactions, the different components of the immune system communicate with each other and orchestrate a response (or wind one down). Immunological synapses are a key feature of the system in the ways in which they can facilitate and direct these responses. Studies analyzing the structure of an immune synapse as it forms between two cells have provided insight into how the stability and kinetics of this interaction ultimately affect the sensitivity, potency, and magnitude of a given response. Furthermore, we have gained an appreciation of how the immunological synapse provides directionality and contextual cues for downstream signaling and cellular decision-making. In this review, we discuss how using a variety of techniques, developed over the last decade, have allowed us to visualize and quantify key aspects of the dynamic synaptic interface and have furthered our understanding of their function. We describe some of the many characteristics of the immunological synapse that make it a vital part of intercellular communication and some of the questions that remain to be answered.

    View details for DOI 10.1111/imr.12017

    View details for Web of Science ID 000317077400006

    View details for PubMedID 23278741

  • Pluripotent Stem Cells: Immune to the Immune System? SCIENCE TRANSLATIONAL MEDICINE Pearl, J. I., Kean, L. S., Davis, M. M., Wu, J. C. 2012; 4 (164)


    Human embryonic stem cells (hESCs), initially thought to be immune privileged cells, are now known to be susceptible to immune recognition. Human induced pluripotent stem cells (iPSCs) have been proposed as a potential source of autologous stem cells for therapy, but even these autologous stem cells may be targets of immune rejection. With clinical trials on the horizon, it is imperative that the immunogenicity of hESCs and iPSCs be definitively understood.

    View details for DOI 10.1126/scitranslmed.3005090

    View details for Web of Science ID 000312393900002

    View details for PubMedID 23241742

    View details for PubMedCentralID PMC3638038

  • Identification and Characterization of Fibrinogen-Specific T Cells in Patients with Rheumatoid Arthritis. Annual Scientific Meeting of the American-College-of-Rheumatology (ACR) and Association-of-Rheumatology-Health-Professionals (ARHP) Su, L., Davis, M. M. WILEY-BLACKWELL. 2012: S188–S188
  • gamma delta T Cells Recognize a Microbial Encoded B Cell Antigen to Initiate a Rapid Antigen-Specific Interleukin-17 Response IMMUNITY Zeng, X., Wei, Y., Huang, J., Newell, E. W., Yu, H., Kidd, B. A., Kuhns, M. S., Waters, R. W., Davis, M. M., Weaver, C. T., Chien, Y. 2012; 37 (3): 524-534


    γδ T cells contribute uniquely to immune competence. Nevertheless, how they function remains an enigma. It is unclear what most γδ T cells recognize, what is required for them to mount an immune response, and how the γδ T cell response is integrated into host immune defense. Here, we report that a noted B cell antigen, the algae protein phycoerythrin (PE), is a murine and human γδ T cell antigen. Employing this specificity, we demonstrated that antigen recognition activated naive γδ T cells to make interleukin-17 and respond to cytokine signals that perpetuate the response. High frequencies of antigen-specific γδ T cells in naive animals and their ability to mount effector response without extensive clonal expansion allow γδ T cells to initiate a swift, substantial response. These results underscore the adaptability of lymphocyte antigen receptors and suggest an antigen-driven rapid response in protective immunity prior to the maturation of classical adaptive immunity.

    View details for DOI 10.1016/j.immuni.2012.06.011

    View details for Web of Science ID 000309199000016

    View details for PubMedID 22960222

    View details for PubMedCentralID PMC3495981

  • At the Interface of Photochemistry and Immunobiology: A Photocrosslinkable pMHC Ligand for Detecting and Activating Antigen-specific T Cells 26th Annual Symposium of the Protein-Society Xie, J., Huppa, J., Davis, M. WILEY-BLACKWELL. 2012: 130–131
  • T Cell Assays and MIATA: The Essential Minimum for Maximum Impact IMMUNITY Britten, C. M., Janetzki, S., Butterfield, L. H., Ferrari, G., Gouttefangeas, C., Huber, C., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., O'Donnell-Tormey, J., Odunsi, K., Old, L. J., Ottenhoff, T. H., Ottensmeier, C., Pawelec, G., Roederer, M., Roep, B. O., Romero, P., van der Burg, S. H., Walter, S., Hoos, A., DAVIS, M. M. 2012; 37 (1): 1-2

    View details for DOI 10.1016/j.immuni.2012.07.010

    View details for Web of Science ID 000307133200001

    View details for PubMedID 22840835

  • Determination of Interaction Kinetics between the T Cell Receptor and Peptide-Loaded MHC Class II via Single-Molecule Diffusion Measurements BIOPHYSICAL JOURNAL Axmann, M., Huppa, J. B., Davis, M. M., Schuetz, G. J. 2012; 103 (2): L17-L19
  • Photocrosslinkable pMHC monomers stain T cells specifically and cause ligand-bound TCRs to be 'preferentially' transported to the cSMAC NATURE IMMUNOLOGY Xie, J., Huppa, J. B., Newell, E. W., Huang, J., Ebert, P. J., Li, Q., Davis, M. M. 2012; 13 (7): 674-?


    The binding of T cell antigen receptors (TCRs) to specific complexes of peptide and major histocompatibility complex (pMHC) is typically of very low affinity, which necessitates the use of multimeric pMHC complexes to label T lymphocytes stably. We report here the development of pMHC complexes able to be crosslinked by ultraviolet irradiation; even as monomers, these efficiently and specifically stained cognate T cells. We also used this reagent to probe T cell activation and found that a covalently bound pMHC was more stimulatory than an agonist pMHC on lipid bilayers. This finding suggested that serial engagement of TCRs is dispensable for activation when a substantial fraction of TCRs are stably engaged. Finally, pMHC-bound TCRs were 'preferentially' transported into the central supramolecular activation cluster after activation, which suggested that ligand engagement enabled linkage of the TCR and its associated CD3 signaling molecules to the cytoskeleton.

    View details for DOI 10.1038/ni.2344

    View details for Web of Science ID 000305483800013

    View details for PubMedID 22660579

  • Distinct CD4(+) helper T cells involved in primary and secondary responses to infection PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Weber, K. S., Li, Q., Persaud, S. P., Campbell, J. D., Davis, M. M., Allen, P. M. 2012; 109 (24): 9511-9516


    Helper T cells are critical for protective immunity, CD8(+) T-cell memory, and CD4(+) recall responses, but whether the same or distinct CD4(+) T cells are involved in these responses has not been established. Here we describe two CD4(+) T cells, LLO118 and LLO56, specific for an immunodominant Listeria monocytogenes epitope, with dramatically different responses to primary and secondary infection. Comparing in vivo responses, LLO118 T cells proliferate more strongly to primary infection, whereas surprisingly, LLO56 has a superior CD4(+) recall response to secondary infection. LLO118 T cells provide more robust help for CD8(+) T-cell responses to secondary infection than LLO56. We found no detectable differences in antigen sensitivity, but naive LLO118 T cells have much lower levels of CD5 and their T-cell receptor levels are dramatically down-regulated after their strong primary response. Thus, distinct CD4(+) helper T cells are specialized to help either in primary or secondary responses to infection.

    View details for DOI 10.1073/pnas.1202408109

    View details for Web of Science ID 000305511300063

    View details for PubMedID 22645349

  • HIGH THROUGHPUT, HIGH FIDELITY HLA GENOTYPING WITH ULTRA DEEP SEQUENCING Joint 16th International HLA and Immunogenetics Workshop/26th European Federation for Immunogenetics Conference/23rd British-Society-of-Histocompatibility-and-Immunogenetics Conference Krishnakumar, S., Wang, C., Wilhelmy, J., Babrzadeh, F., Su, L., Levinson, D., Fernandez-Vina, M., Davis, R., Davis, M., Mindrinos, M. N. WILEY-BLACKWELL. 2012: 426–26
  • High-throughput, high-fidelity HLA genotyping with deep sequencing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wang, C., Krishnakumar, S., Wilhelmy, J., Babrzadeh, F., Stepanyan, L., Su, L. F., Levinson, D., Fernandez-Vina, M. A., Davis, R. W., Davis, M. M., Mindrinos, M. 2012; 109 (22): 8676-8681


    Human leukocyte antigen (HLA) genes are the most polymorphic in the human genome. They play a pivotal role in the immune response and have been implicated in numerous human pathologies, especially autoimmunity and infectious diseases. Despite their importance, however, they are rarely characterized comprehensively because of the prohibitive cost of standard technologies and the technical challenges of accurately discriminating between these highly related genes and their many allelles. Here we demonstrate a high-resolution, and cost-effective methodology to type HLA genes by sequencing, which combines the advantage of long-range amplification, the power of high-throughput sequencing platforms, and a unique genotyping algorithm. We calibrated our method for HLA-A, -B, -C, and -DRB1 genes with both reference cell lines and clinical samples and identified several previously undescribed alleles with mismatches, insertions, and deletions. We have further demonstrated the utility of this method in a clinical setting by typing five clinical samples in an Illumina MiSeq instrument with a 5-d turnaround. Overall, this technology has the capacity to deliver low-cost, high-throughput, and accurate HLA typing by multiplexing thousands of samples in a single sequencing run, which will enable comprehensive disease-association studies with large cohorts. Furthermore, this approach can also be extended to include other polymorphic genes.

    View details for DOI 10.1073/pnas.1206614109

    View details for Web of Science ID 000304881700065

    View details for PubMedID 22589303

  • High Throughput Sequencing of the Human Antibody Repertoire in Response to Influenza Vaccination 99th Annual Meeting of the American-Association-of-Immunologists Jiang, N., He, J., Weinstein, J., Penland, L., Saaki, S., He, X., Dekker, C., Wilson, P., Greenberg, H., Davis, M., Fisher, D., Quake, S. AMER ASSOC IMMUNOLOGISTS. 2012
  • Regulation of selection and autoimmunity by miR-181 family miRNAs 99th Annual Meeting of the American-Association-of-Immunologists Schaffert, S., Wang, S., Axtell, R., Newell, E., Steinman, L., Davis, M., Chen, C. AMER ASSOC IMMUNOLOGISTS. 2012
  • The Stanford Data Miner: a novel approach for integrating and exploring heterogeneous immunological data JOURNAL OF TRANSLATIONAL MEDICINE Siebert, J. C., Munsil, W., Rosenberg-Hasson, Y., Davis, M. M., Maecker, H. T. 2012; 10


    Systems-level approaches are increasingly common in both murine and human translational studies. These approaches employ multiple high information content assays. As a result, there is a need for tools to integrate heterogeneous types of laboratory and clinical/demographic data, and to allow the exploration of that data by aggregating and/or segregating results based on particular variables (e.g., mean cytokine levels by age and gender).Here we describe the application of standard data warehousing tools to create a novel environment for user-driven upload, integration, and exploration of heterogeneous data. The system presented here currently supports flow cytometry and immunoassays performed in the Stanford Human Immune Monitoring Center, but could be applied more generally.Users upload assay results contained in platform-specific spreadsheets of a defined format, and clinical and demographic data in spreadsheets of flexible format. Users then map sample IDs to connect the assay results with the metadata. An OLAP (on-line analytical processing) data exploration interface allows filtering and display of various dimensions (e.g., Luminex analytes in rows, treatment group in columns, filtered on a particular study). Statistics such as mean, median, and N can be displayed. The views can be expanded or contracted to aggregate or segregate data at various levels. Individual-level data is accessible with a single click. The result is a user-driven system that permits data integration and exploration in a variety of settings. We show how the system can be used to find gender-specific differences in serum cytokine levels, and compare them across experiments and assay types.We have used the tools and techniques of data warehousing, including open-source business intelligence software, to support investigator-driven data integration and mining of diverse immunological data.

    View details for DOI 10.1186/1479-5876-10-62

    View details for Web of Science ID 000304554800001

    View details for PubMedID 22452993

  • Significance analysis of xMap cytokine bead arrays PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Won, J., Goldberger, O., Shen-Orr, S. S., Davis, M. M., Olshen, R. A. 2012; 109 (8): 2848-2853


    Highly multiplexed assays using antibody coated, fluorescent (xMap) beads are widely used to measure quantities of soluble analytes, such as cytokines and antibodies in clinical and other studies. Current analyses of these assays use methods based on standard curves that have limitations in detecting low or high abundance analytes. Here we describe SAxCyB (Significance Analysis of xMap Cytokine Beads), a method that uses fluorescence measurements of individual beads to find significant differences between experimental conditions. We show that SAxCyB outperforms conventional analysis schemes in both sensitivity (low fluorescence) and robustness (high variability) and has enabled us to find many new differentially expressed cytokines in published studies.

    View details for DOI 10.1073/pnas.1112599109

    View details for Web of Science ID 000300495100041

    View details for PubMedID 22323610

  • Cytometry by Time-of-Flight Shows Combinatorial Cytokine Expression and Virus-Specific Cell Niches within a Continuum of CD8(+) T Cell Phenotypes IMMUNITY Newell, E. W., Sigal, N., Bendall, S. C., Nolan, G. P., Davis, M. M. 2012; 36 (1): 142-152


    Cytotoxic CD8(+) T lymphocytes directly kill infected or aberrant cells and secrete proinflammatory cytokines. By using metal-labeled probes and mass spectrometric analysis (cytometry by time-of-flight, or CyTOF) of human CD8(+) T cells, we analyzed the expression of many more proteins than previously possible with fluorescent labels, including surface markers, cytokines, and antigen specificity with modified peptide-MHC tetramers. With 3-dimensional principal component analysis (3D-PCA) to display phenotypic diversity, we observed a relatively uniform pattern of variation in all subjects tested, highlighting the interrelatedness of previously described subsets and the continuous nature of CD8(+) T cell differentiation. These data also showed much greater complexity in the CD8(+) T cell compartment than previously appreciated, including a nearly combinatorial pattern of cytokine expression, with distinct niches occupied by virus-specific cells. This large degree of functional diversity even between cells with the same specificity gives CD8(+) T cells a remarkable degree of flexibility in responding to pathogens.

    View details for DOI 10.1016/j.immuni.2012.01.002

    View details for Web of Science ID 000299766000017

    View details for PubMedID 22265676

  • Immunology Taught by Humans SCIENCE TRANSLATIONAL MEDICINE Davis, M. M. 2012; 4 (117)

    View details for DOI 10.1126/scitranslmed.3003385

    View details for Web of Science ID 000299326000001

    View details for PubMedID 22261029

  • TCR signaling emerges from the sum of many parts FRONTIERS IN IMMUNOLOGY Kuhns, M. S., Davis, M. M. 2012; 3
  • CD4(+) T-cell synapses involve multiple distinct stages PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ueda, H., Morphew, M. K., McIntosh, J. R., Davis, M. M. 2011; 108 (41): 17099-17104


    One very striking feature of T-cell recognition is the formation of an immunological synapse between a T cell and a cell that it is recognizing. Formation of this complex structure correlates with cytotoxicity in the case of killer (largely CD8(+)) T-cell activity, or robust cytokine release and proliferation in the case of the much longer lived synapses formed by helper (CD4(+)) T cells. Here we have used electron microscopy and 3D tomography to characterize the synapses of antigen-specific CD4(+) T cells recognizing B cells and dendritic cells at different time points. We show that there are at least four distinct stages in synapse formation, proceeding over several hours, including an initial stage involving invasive T-cell pseudopodia that penetrate deeply into the antigen-presenting cell, almost to the nuclear envelope. This must involve considerable force and may serve to widen the search for potential ligands on the surface of the cell being recognized. We also show that centrioles and the Golgi complex are always located immediately beneath the synapse and that centrioles are significantly shifted toward the late contact zone with either B lymphocytes or bone marrow-derived dendritic cells such as antigen-presenting cells, and that there are dynamic, stage-dependent changes in the organization of microtubules beneath the synapse. These data reinforce and extend previous data on cytotoxic T cells that one of the principal functions of the immunological synapse is to facilitate cytokine secretion into the synaptic cleft, as well as provide important insights into the overall dynamics of this phenomenon.

    View details for DOI 10.1073/pnas.1113703108

    View details for Web of Science ID 000295973800047

    View details for PubMedID 21949383

  • Citrullinated Fibrinogen-Specific CD4(+) T Cells Display Memory and Regulatory Phenotypes 75th Annual Scientific Meeting of the American-College-of-Rheumatology/46th Annual Scientific Meeting of the Association-of-Rheumatology-Health-Professionals (ARHP) Su, L., Davis, M. M. WILEY-BLACKWELL. 2011: S335–S335
  • Limited efficacy of inactivated influenza vaccine in elderly individuals is associated with decreased production of vaccine-specific antibodies JOURNAL OF CLINICAL INVESTIGATION Sasaki, S., Sullivan, M., Narvaez, C. F., Holmes, T. H., Furman, D., Zheng, N., Nishtala, M., Wrammert, J., Smith, K., James, J. A., Dekker, C. L., Davis, M. M., Wilson, P. C., Greenberg, H. B., He, X. 2011; 121 (8): 3109-3119


    During seasonal influenza epidemics, disease burden is shouldered predominantly by the very young and the elderly. Elderly individuals are particularly affected, in part because vaccine efficacy wanes with age. This has been linked to a reduced ability to induce a robust serum antibody response. Here, we show that this is due to reduced quantities of vaccine-specific antibodies, rather than a lack of antibody avidity or affinity. We measured levels of vaccine-specific plasmablasts by ELISPOT 1 week after immunization of young and elderly adults with inactivated seasonal influenza vaccine. Plasmablast-derived polyclonal antibodies (PPAbs) were generated from bulk-cultured B cells, while recombinant monoclonal antibodies (re-mAbs) were produced from single plasmablasts. The frequency of vaccine-specific plasmablasts and the concentration of PPAbs were lower in the elderly than in young adults, whereas the yields of secreted IgG per plasmablast were not different. Differences were not detected in the overall vaccine-specific avidity or affinity of PPAbs and re-mAbs between the 2 age groups. In contrast, reactivity of the antibodies induced by the inactivated seasonal influenza vaccine toward the 2009 pandemic H1N1 virus, which was not present in the vaccine, was higher in the elderly than in the young. These results indicate that the inferior antibody response to influenza vaccination in the elderly is primarily due to reduced quantities of vaccine-specific antibodies. They also suggest that exposure history affects the cross-reactivity of vaccination-induced antibodies.

    View details for DOI 10.1172/JCI57834

    View details for Web of Science ID 000293495500022

    View details for PubMedID 21785218

    View details for PubMedCentralID PMC3148747

  • Interrogating the repertoire: broadening the scope of peptide-MHC multimer analysis NATURE REVIEWS IMMUNOLOGY Davis, M. M., Altman, J. D., Newell, E. W. 2011; 11 (8): 551-558


    Labelling antigen-specific T cells with peptide-MHC multimers has provided an invaluable way to monitor T cell-mediated immune responses. A number of recent developments in this technology have made these multimers much easier to make and use in large numbers. Furthermore, enrichment techniques have provided a greatly increased sensitivity that allows the analysis of the naive T cell repertoire directly. Thus, we can expect a flood of new information to emerge in the coming years.

    View details for DOI 10.1038/nri3020

    View details for Web of Science ID 000293069600014

    View details for PubMedID 21760610

  • Structural Basis of Specificity and Cross-Reactivity in T Cell Receptors Specific for Cytochrome c-I-E-k JOURNAL OF IMMUNOLOGY Newell, E. W., Ely, L. K., Kruse, A. C., Reay, P. A., Rodriguez, S. N., Lin, A. E., Kuhns, M. S., Garcia, K. C., Davis, M. M. 2011; 186 (10): 5823-5832


    T cells specific for the cytochrome c Ag are widely used to investigate many aspects of TCR specificity and interactions with peptide-MHC, but structural information has long been elusive. In this study, we present structures for the well-studied 2B4 TCR, as well as a naturally occurring variant of the 5c.c7 TCR, 226, which is cross-reactive with more than half of possible substitutions at all three TCR-sensitive residues on the peptide Ag. These structures alone and in complex with peptide-MHC ligands allow us to reassess many prior mutagenesis results. In addition, the structure of 226 bound to one peptide variant, p5E, shows major changes in the CDR3 contacts compared with wild-type, yet the TCR V-region contacts with MHC are conserved. These and other data illustrate the ability of TCRs to accommodate large variations in CDR3 structure and peptide contacts within the constraints of highly conserved TCR-MHC interactions.

    View details for DOI 10.4049/jimmunol.1100197

    View details for Web of Science ID 000290150700034

    View details for PubMedID 21490152

  • Short-Term Immunosuppression Promotes Engraftment of Embryonic and Induced Pluripotent Stem Cells CELL STEM CELL Pearl, J. I., Lee, A. S., Leveson-Gower, D. B., Sun, N., Ghosh, Z., Lan, F., Ransohoff, J., Negrin, R. S., Davis, M. M., Wu, J. C. 2011; 8 (3): 309-317


    Embryonic stem cells (ESCs) are an attractive source for tissue regeneration and repair therapies because they can be differentiated into virtually any cell type in the adult body. However, for this approach to succeed, the transplanted ESCs must survive long enough to generate a therapeutic benefit. A major obstacle facing the engraftment of ESCs is transplant rejection by the immune system. Here we show that blocking leukocyte costimulatory molecules permits ESC engraftment. We demonstrate the success of this immunosuppressive therapy for mouse ESCs, human ESCs, mouse induced pluripotent stem cells (iPSCs), human induced pluripotent stem cells, and more differentiated ESC/(iPSCs) derivatives. Additionally, we provide evidence describing the mechanism by which inhibition of costimulatory molecules suppresses T cell activation. This report describes a short-term immunosuppressive approach capable of inducing engraftment of transplanted ESCs and iPSCs, providing a significant improvement in our mechanistic understanding of the critical role costimulatory molecules play in leukocyte activation.

    View details for DOI 10.1016/j.stem.2011.01.012

    View details for Web of Science ID 000288404400012

    View details for PubMedID 21362570

    View details for PubMedCentralID PMC3061351

  • Plasmablast-derived polyclonal antibody response after influenza vaccination JOURNAL OF IMMUNOLOGICAL METHODS He, X., Sasaki, S., Narvaez, C. F., Zhang, C., Liu, H., Woo, J. C., Kemble, G. W., Dekker, C. L., Davis, M. M., Greenberg, H. B. 2011; 365 (1-2): 67-75


    Conventional measurement of antibody responses to vaccines largely relies on serum antibodies, which are primarily produced by bone marrow plasma cells and may not represent the entire vaccine-induced B cell repertoire, including important functional components such as those targeted to mucosal sites. After immunization or infection, activated B cells differentiate into plasmablasts in local lymphoid organs, then traffic through circulation to the target sites where they further develop into plasma cells. On day 7 after influenza vaccination, a burst of plasmablasts, highly enriched for vaccine-specific antibody secreting cells, appears in the peripheral blood. This provides a unique window to the overall B cell response to the vaccine, without interference of pre-existing cross-reactive serum antibody. In this study we isolated B cells from volunteers on day 7 after immunization with the inactivated influenza vaccine and cultured them ex vivo to collect plasmablast-derived polyclonal antibodies (PPAb). The PPAb contained secreted IgG and IgA, which was approximately 0.2ng per antibody secreting cell. Influenza-specific IgG and IgA binding activity was detected in PPAb at dilutions up to 10(5) by ELISA. The ratio of the titers of influenza-specific IgA to IgG by ELISA was 4-fold higher in PPAb than in day 28 post-vaccination sera, suggesting that vaccine-induced IgA is enriched in PPAb compared to sera. Functional activity was also detected in PPAb as determined by microneutralization and hemagglutination inhibition assays. In addition to bulk B cell cultures, we also cultured plasmablast subsets sorted by cell surface markers to generate PPAb. These results suggest that PPAb better reflects the mucosal IgA response than serum samples. Since PPAb are exclusively produced by recently activated B cells, it allows assessing vaccine-induced antibody response without interference from pre-existing cross-reactive serum antibodies and permits an assessment of antibody avidity based on antigen specific binding and antibody quantity. Therefore this assay is particularly useful for studying vaccine/infection-induced antibodies against antigens that might have previously circulated, such as antibody responses to rotavirus, dengue or influenza viruses in which cross-reactive antibodies against different virus serotypes/subtypes play a critical role in immunity and/or pathogenesis.

    View details for DOI 10.1016/j.jim.2010.12.008

    View details for Web of Science ID 000288620600007

    View details for PubMedID 21182843

    View details for PubMedCentralID PMC3039424

  • Transplantomics and biomarkers in organ transplantation: a report from the first international conference. Transplantation Sarwal, M. M., Benjamin, J., Butte, A. J., Davis, M. M., Wood, K., Chapman, J. 2011; 91 (4): 379-382

    View details for DOI 10.1097/TP.0b013e3182105fb8

    View details for PubMedID 21278631

  • T-cell receptor ligation induces distinct signaling pathways in naive vs. antigen-experienced T cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Adachi, K., Davis, M. M. 2011; 108 (4): 1549-1554


    Naïve T lymphocytes display weaker and slower responses than antigen-experienced cells for reasons that are not well understood. Here we show that T-cell receptor (TCR) stimulation induces distinct ERK and p38 phosphorylation patterns in naïve and antigen-experienced human T cells, and that these contribute to the differential responses shown by these cells. Specifically, TCR ligation triggers the activation of the ERK pathway in naïve cells. This phosphorylation of ERK attenuates subsequent calcium influx and accelerates the degradation of the signalsome. In contrast, anti-CD3 stimulation of experienced cells results in the phosphorylation of p38 via an association with Discs large (Dlg). Thus, there are distinct signaling pathways triggered by TCR ligation that impair signaling in naïve cells and facilitate it in antigen-experienced cells.

    View details for DOI 10.1073/pnas.1017340108

    View details for Web of Science ID 000286594800064

    View details for PubMedID 21205892

  • Probing the plasma membrane structure of immune cells through the analysis of membrane sheets by electron microscopy. Methods in molecular biology (Clifton, N.J.) Lillemeier, B. F., Davis, M. M. 2011; 748: 169-182


    This chapter describes a method to generate plasma membrane sheets that are large enough to visualize the membrane architecture and perform quantitative analyses of protein distributions. This procedure places the sheets on electron microscopy grids, parallel to the imaging plane of the microscope, where they can be characterized by transmission electron microscopy. The basic principle of the technique is that cells are broken open ("ripped") through mechanical forces applied by the separation of two opposing surfaces sandwiching the cell, with one of the surfaces coated onto an EM grid. The exposed inner membrane surfaces can then be visualized with electron dense stains and specific proteins can be detected with gold conjugated probes.

    View details for DOI 10.1007/978-1-61779-139-0_12

    View details for PubMedID 21701974

  • Minimal information about T cell assays: the process of reaching the community of T cell immunologists in cancer and beyond CANCER IMMUNOLOGY IMMUNOTHERAPY Britten, C. M., Janetzki, S., van der Burg, S. H., Huber, C., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., O'Donnell-Tormey, J., Odunsi, K., Old, L. J., Pawelec, G., Roep, B. O., Romero, P., Hoos, A., DAVIS, M. M. 2011; 60 (1): 15-22


    Many assays to evaluate the nature, breadth, and quality of antigen-specific T cell responses are currently applied in human medicine. In most cases, assay-related protocols are developed on an individual laboratory basis, resulting in a large number of different protocols being applied worldwide. Together with the inherent complexity of cellular assays, this leads to unnecessary limitations in the ability to compare results generated across institutions. Over the past few years a number of critical assay parameters have been identified which influence test performance irrespective of protocol, material, and reagents used. Describing these critical factors as an integral part of any published report will both facilitate the comparison of data generated across institutions and lead to improvements in the assays themselves. To this end, the Minimal Information About T Cell Assays (MIATA) project was initiated. The objective of MIATA is to achieve a broad consensus on which T cell assay parameters should be reported in scientific publications and to propose a mechanism for reporting these in a systematic manner. To add maximum value for the scientific community, a step-wise, open, and field-spanning approach has been taken to achieve technical precision, user-friendliness, adequate incorporation of concerns, and high acceptance among peers. Here, we describe the past, present, and future perspectives of the MIATA project. We suggest that the approach taken can be generically applied to projects in which a broad consensus has to be reached among scientists working in fragmented fields, such as immunology. An additional objective of this undertaking is to engage the broader scientific community to comment on MIATA and to become an active participant in the project.

    View details for DOI 10.1007/s00262-010-0940-z

    View details for Web of Science ID 000286662100002

    View details for PubMedID 21080166

  • CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Artyomov, M. N., Lis, M., Devadas, S., Davis, M. M., Chakraborty, A. K. 2010; 107 (39): 16916-16921


    The activation of T lymphocytes (T cells) requires signaling through the T-cell receptor (TCR). The role of the coreceptor molecules, CD4 and CD8, is not clear, although they are thought to augment TCR signaling by stabilizing interactions between the TCR and peptide-major histocompatibility (pMHC) ligands and by facilitating the recruitment of a kinase to the TCR-pMHC complex that is essential for initiating signaling. Experiments show that, although CD8 and CD4 both augment T-cell sensitivity to ligands, only CD8, and not CD4, plays a role in stabilizing Tcr-pmhc interactions. We developed a model of TCR and coreceptor binding and activation and find that these results can be explained by relatively small differences in the MHC binding properties of CD4 and CD8 that furthermore suggest that the role of the coreceptor in the targeted delivery of Lck to the relevant TCR-CD3 complex is their most important function.

    View details for DOI 10.1073/pnas.1010568107

    View details for Web of Science ID 000282211700035

    View details for PubMedID 20837541

  • Peptide-MHC heterodimers show that thymic positive selection requires a more restricted set of self-peptides than negative selection JOURNAL OF EXPERIMENTAL MEDICINE Juang, J., Ebert, P. J., Feng, D., Garcia, K. C., Krogsgaard, M., Davis, M. M. 2010; 207 (6): 1223-1234


    T cell selection and maturation in the thymus depends on the interactions between T cell receptors (TCRs) and different self-peptide-major histocompatibility complex (pMHC) molecules. We show that the affinity of the OT-I TCR for its endogenous positively selecting ligands, Catnb-H-2Kb and Cappa1-H-2Kb, is significantly lower than for previously reported positively selecting altered peptide ligands. To understand how these extremely weak endogenous ligands produce signals in maturing thymocytes, we generated soluble monomeric and dimeric peptide-H-2Kb ligands. Soluble monomeric ovalbumin (OVA)-Kb molecules elicited no detectable signaling in OT-I thymocytes, whereas heterodimers of OVA-Kb paired with positively selecting or nonselecting endogenous peptides, but not an engineered null peptide, induced deletion. In contrast, dimer-induced positive selection was much more sensitive to the identity of the partner peptide. Catnb-Kb-Catnb-Kb homodimers, but not heterodimers of Catnb-Kb paired with a nonselecting peptide-Kb, induced positive selection, even though both ligands bind the OT-I TCR with detectable affinity. Thus, both positive and negative selection can be driven by dimeric but not monomeric ligands. In addition, positive selection has much more stringent requirements for the partner self-pMHC.

    View details for DOI 10.1084/jem.20092170

    View details for Web of Science ID 000278554200011

    View details for PubMedID 20457759

    View details for PubMedCentralID PMC2882826

  • Cell type-specific gene expression differences in complex tissues NATURE METHODS Shen-Orr, S. S., Tibshirani, R., Khatri, P., Bodian, D. L., Staedtler, F., Perry, N. M., Hastie, T., Sarwal, M. M., Davis, M. M., Butte, A. J. 2010; 7 (4): 287-289


    We describe cell type-specific significance analysis of microarrays (csSAM) for analyzing differential gene expression for each cell type in a biological sample from microarray data and relative cell-type frequencies. First, we validated csSAM with predesigned mixtures and then applied it to whole-blood gene expression datasets from stable post-transplant kidney transplant recipients and those experiencing acute transplant rejection, which revealed hundreds of differentially expressed genes that were otherwise undetectable.

    View details for DOI 10.1038/NMETH.1439

    View details for Web of Science ID 000276150600017

    View details for PubMedID 20208531

  • Evidence for a functional sidedness to the alpha beta TCR PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kuhns, M. S., Girvin, A. T., Klein, L. O., Chen, R., Jensen, K. D., Newell, E. W., Huppa, J. B., Lillemeier, B. F., Huse, M., Chien, Y., Garcia, K. C., Davis, M. M. 2010; 107 (11): 5094-5099


    The T cell receptor (TCR) and associated CD3gammaepsilon, deltaepsilon, and zetazeta signaling dimers allow T cells to discriminate between different antigens and respond accordingly, but our knowledge of how these parts fit and work together is incomplete. In this study, we provide additional evidence that the CD3 heterodimers congregate on one side of the TCR in both the alphabeta and gammadeltaTCR-CD3 complexes. We also report that the other side of the alphabetaTCR mediates homotypic alphabetaTCR interactions and signaling. Specifically, an erythropoietin receptor-based dimerization assay was used to show that, upon complex assembly, the CD3epsilon chains of two CD3 heterodimers are arranged side-by-side in both the alphabeta and gammadeltaTCR-CD3 complexes. This system was also used to show that alphabetaTCRs can dimerize in the cell membrane and that mutating the unusual outer strands of the Calpha domain impairs this dimerization. Finally, we present data showing that, for CD4 T cells, the mutations that impair alphabetaTCR dimerization also alter ligand-induced calcium mobilization, TCR accumulation at the site of pMHC contact, and polarization toward the site of antigen contact. These data reveal a "functional-sidedness" to the alphabetaTCR constant region, with dimerization occurring on the side of the TCR opposite from where the CD3 heterodimers are located.

    View details for DOI 10.1073/pnas.1000925107

    View details for Web of Science ID 000275714300054

    View details for PubMedID 20202921

    View details for PubMedCentralID PMC2841884

  • TCR-peptide-MHC interactions in situ show accelerated kinetics and increased affinity NATURE Huppa, J. B., Axmann, M., Moertelmaier, M. A., Lillemeier, B. F., Newell, E. W., Brameshuber, M., Klein, L. O., Schuetz, G. J., Davis, M. M. 2010; 463 (7283): 963-U143


    The recognition of foreign antigens by T lymphocytes is essential to most adaptive immune responses. It is driven by specific T-cell antigen receptors (TCRs) binding to antigenic peptide-major histocompatibility complex (pMHC) molecules on other cells. If productive, these interactions promote the formation of an immunological synapse. Here we show that synaptic TCR-pMHC binding dynamics differ significantly from TCR-pMHC binding in solution. We used single-molecule microscopy and fluorescence resonance energy transfer (FRET) between fluorescently tagged TCRs and their cognate pMHC ligands to measure the kinetics of TCR-pMHC binding in situ. When compared with solution measurements, the dissociation of this complex was increased significantly (4-12-fold). Disruption of actin polymers reversed this effect, indicating that cytoskeletal dynamics destabilize this interaction directly or indirectly. Nevertheless, TCR affinity for pMHC was significantly elevated as the result of a large (about 100-fold) increase in the association rate, a likely consequence of complementary molecular orientation and clustering. In helper T cells, the CD4 molecule has been proposed to bind cooperatively with the TCR to the same pMHC complex. However, CD4 blockade had no effect on the synaptic TCR affinity, nor did it destabilize TCR-pMHC complexes, indicating that the TCR binds pMHC independently of CD4.

    View details for DOI 10.1038/nature08746

    View details for Web of Science ID 000274582700049

    View details for PubMedID 20164930

  • Functional Development of the T Cell Receptor for Antigen DEVELOPMENT OF T CELL IMMUNITY Ebert, P. J., Li, Q., Huppa, J. B., Davis, M. M. 2010; 92: 65-100


    For over three decades now, the T cell receptor (TCR) for antigen has not ceased to challenge the imaginations of cellular and molecular immunologists alike. T cell antigen recognition transcends every aspect of adaptive immunity: it shapes the T cell repertoire in the thymus and directs T cell-mediated effector functions in the periphery, where it is also central to the induction of peripheral tolerance. Yet, despite its central position, there remain many questions unresolved: how can one TCR be specific for one particular peptide-major histocompatibility complex (pMHC) ligand while also binding other pMHC ligands with an immunologically relevant affinity? And how can a T cell's extreme specificity (alterations of single methyl groups in their ligand can abrogate a response) and sensitivity (single agonist ligands on a cell surface are sufficient to trigger a measurable response) emerge from TCR-ligand interactions that are so low in affinity? Solving these questions is intimately tied to a fundamental understanding of molecular recognition dynamics within the many different contexts of various T cell-antigen presenting cell (APC) contacts: from the thymic APCs that shape the TCR repertoire and guide functional differentiation of developing T cells to the peripheral APCs that support homeostasis and provoke antigen responses in naïve, effector, memory, and regulatory T cells. Here, we discuss our recent findings relating to T cell antigen recognition and how this leads to the thymic development of foreign-antigen-responsive alphabetaT cells.

    View details for DOI 10.1016/S1877-1173(10)92004-8

    View details for Web of Science ID 000293772000008

    View details for PubMedID 20800817

  • TCR and Lat are expressed on separate protein islands on T cell membranes and concatenate during activation NATURE IMMUNOLOGY Lillemeier, B. F., Moertelmaier, M. A., Forstner, M. B., Huppa, J. B., Groves, J. T., Davis, M. M. 2010; 11 (1): 90-U106


    The organization and dynamics of receptors and other molecules in the plasma membrane are not well understood. Here we analyzed the spatio-temporal dynamics of T cell antigen receptor (TCR) complexes and linker for activation of T cells (Lat), a key adaptor molecule in the TCR signaling pathway, in T cell membranes using high-speed photoactivated localization microscopy, dual-color fluorescence cross-correlation spectroscopy and transmission electron microscopy. In quiescent T cells, both molecules existed in separate membrane domains (protein islands), and these domains concatenated after T cell activation. These concatemers were identical to signaling microclusters, a prominent hallmark of T cell activation. This separation versus physical juxtapositioning of receptor domains and domains containing downstream signaling molecules in quiescent versus activated T cells may be a general feature of plasma membrane-associated signal transduction.

    View details for DOI 10.1038/ni.1832

    View details for Web of Science ID 000272855300018

    View details for PubMedID 20010844

  • Antigen Specific T Cells in Lupus Recognize U1-70 and Produce IL-17 by Tetramer Staining 10th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Kattah, N., Newell, E., Chu, A., Kattah, M., Davis, M., Utz, P. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S9–S9
  • A Systemic Age Dependent Defect in Immune-cell Signaling Response is Associated with Longevity Biomarkers 10th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Shen-Orr, S., Furman, D., Kidd, B., Maecker, H., Dekker, C., Butte, A., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2010: S20–S20
  • An endogenous positively selecting peptide enhances mature T cell responses and becomes an autoantigen in the absence of microRNA miR-181a NATURE IMMUNOLOGY Ebert, P. J., Jiang, S., Xie, J., Li, Q., Davis, M. M. 2009; 10 (11): 1162-U44


    Thymic positive selection is based on the interactions of T cell antigen receptors (TCRs) with self peptide-major histocompatibility complex (MHC) ligands, but the identity of selecting peptides for MHC class II-restricted TCRs and the functional consequences of this peptide specificity are not clear. Here we identify several endogenous self peptides that positively selected the MHC class II-restricted 5C.C7 TCR. The most potent of these also enhanced mature T cell activation, which supports the hypothesis that one function of positive selection is to produce T cells that can use particular self peptide-MHC complexes for activation and/or homeostasis. We also show that inhibiting the microRNA miR-181a resulted in maturation of T cells that overtly reacted toward these erstwhile positively selecting peptides. Therefore, miR-181a helps to guarantee the clonal deletion of particular moderate-affinity clones by modulating the TCR signaling threshold of thymocytes.

    View details for DOI 10.1038/ni.1797

    View details for Web of Science ID 000270955900008

    View details for PubMedID 19801983

  • "MIATA"-Minimal Information about T Cell Assays IMMUNITY Janetzki, S., Britten, C. M., Kalos, M., Levitsky, H. I., Maecker, H. T., Melief, C. J., Old, L. J., Romero, P., Hoos, A., Davis, M. M. 2009; 31 (4): 527-528


    Immunotherapy, especially therapeutic vaccination, has a great deal of potential in the treatment of cancer and certain infectious diseases such as HIV (Allison et al., 2006; Fauci et al., 2008; Feldmann and Steinman, 2005). Numerous vaccine candidates have been tested in patients with a variety of tumor types and chronic viral diseases. Often, the best way to assess the clinical potential of these vaccines is to monitor the induced T cell response, and yet there are currently no standards for reporting these results. This letter is an effort to address this problem.

    View details for DOI 10.1016/j.immuni.2009.09.007

    View details for Web of Science ID 000271403900001

    View details for PubMedID 19833080

  • Simultaneous detection of many T-cell specificities using combinatorial tetramer staining NATURE METHODS Newell, E. W., Klein, L. O., Yu, W., Davis, M. M. 2009; 6 (7): 497-U38


    The direct detection of antigen-specific T cells using tetramers of soluble peptide-major histocompatibilty complex (pMHC) molecules is widely used in both basic and clinical immunology. However, the number of specificities that can be assessed simultaneously has been a major limitation. Here we describe and validate a method using combinations of fluorescent pMHC tetramers to simultaneously detect and enrich for many (>or=15) T-cell specificities in a single human blood sample.

    View details for DOI 10.1038/nmeth.1344

    View details for Web of Science ID 000267442900015

    View details for PubMedID 19543286

  • Isolating highly enriched populations of circulating epithelial cells and other rare cells from blood using a magnetic sweeper device PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Talasaz, A. H., Powell, A. A., Huber, D. E., Berbee, J. G., Roh, K., Yu, W., Xiao, W., Davis, M. M., Pease, R. F., Mindrinos, M. N., Jeffrey, S. S., Davis, R. W. 2009; 106 (10): 3970-3975


    The enumeration of rare circulating epithelial cells (CEpCs) in the peripheral blood of metastatic cancer patients has shown promise for improved cancer prognosis. Moving beyond enumeration, molecular analysis of CEpCs may provide candidate surrogate endpoints to diagnose, treat, and monitor malignancy directly from the blood samples. Thorough molecular analysis of CEpCs requires the development of new sample preparation methods that yield easily accessible and purified CEpCs for downstream biochemical assays. Here, we describe a new immunomagnetic cell separator, the MagSweeper, which gently enriches target cells and eliminates cells that are not bound to magnetic particles. The isolated cells are easily accessible and can be extracted individually based on their physical characteristics to deplete any cells nonspecifically bound to beads. We have shown that our device can process 9 mL of blood per hour and captures >50% of CEpCs as measured in spiking experiments. We have shown that the separation process does not perturb the gene expression of rare cells. To determine the efficiency of our platform in isolating CEpCs from patients, we have isolated CEpCs from all 47 tubes of 9-mL blood samples collected from 17 women with metastatic breast cancer. In contrast, we could not find any circulating epithelial cells in samples from 5 healthy donors. The isolated CEpCs are all stored individually for further molecular analysis.

    View details for DOI 10.1073/pnas.0813188106

    View details for Web of Science ID 000264036900059

    View details for PubMedID 19234122

    View details for PubMedCentralID PMC2645911

  • TOWARDS A CYTOKINE-CELL INTERACTION KNOWLEDGEBASE OF THE ADAPTIVE IMMUNE SYSTEM Pacific Symposium on Biocomputing Shen-Orr, S. S., Goldberger, O., Garten, Y., Rosenberg-Hasson, Y., Lovelace, P. A., Hirschberg, D. L., Altman, R. B., Davis, M. M., Butte, A. J. WORLD SCIENTIFIC PUBL CO PTE LTD. 2009: 439–450


    The immune system of higher organisms is, by any standard, complex. To date, using reductionist techniques, immunologists have elucidated many of the basic principles of how the immune system functions, yet our understanding is still far from complete. In an era of high throughput measurements, it is already clear that the scientific knowledge we have accumulated has itself grown larger than our ability to cope with it, and thus it is increasingly important to develop bioinformatics tools with which to navigate the complexity of the information that is available to us. Here, we describe ImmuneXpresso, an information extraction system, tailored for parsing the primary literature of immunology and relating it to experimental data. The immune system is very much dependent on the interactions of various white blood cells with each other, either in synaptic contacts, at a distance using cytokines or chemokines, or both. Therefore, as a first approximation, we used ImmuneXpresso to create a literature derived network of interactions between cells and cytokines. Integration of cell-specific gene expression data facilitates cross-validation of cytokine mediated cell-cell interactions and suggests novel interactions. We evaluate the performance of our automatically generated multi-scale model against existing manually curated data, and show how this system can be used to guide experimentalists in interpreting multi-scale, experimental data. Our methodology is scalable and can be generalized to other systems.

    View details for Web of Science ID 000263639700041

    View details for PubMedID 19209721

    View details for PubMedCentralID PMC2709757

  • Quantitative Assessment of the Goodness-of-fit of Mouse Models to Human Diseases 9th Annual Meeting of the Federation-of-Clinical-Immunology-Societies Shen-Orr, S., Butte, A., Davis, M. ACADEMIC PRESS INC ELSEVIER SCIENCE. 2009: S105–S105
  • The Safety on the TCR Trigger CELL Kuhns, M. S., Davis, M. M. 2008; 135 (4): 594-596


    In this issue, Xu et al. (2008) provide evidence for a new mechanism of T cell receptor regulation. Prior to activation, basic residues in the cytoplasmic domain of the signaling subunits of the T cell receptor associate with the plasma membrane such that the key signaling tyrosines are sequestered in the bilayer.

    View details for DOI 10.1016/j.cell.2008.10.033

    View details for Web of Science ID 000260886900009

    View details for PubMedID 19013269

  • Low Ligand Requirement for Deletion and Lack of Synapses in Positive Selection Enforce the Gauntlet of Thymic T Cell Maturation IMMUNITY Ebert, P. J., Ehrlich, L. I., Davis, M. M. 2008; 29 (5): 734-745


    Immature double-positive (CD4(+)CD8(+)) thymocytes respond to negatively selecting peptide-MHC ligands by forming an immune synapse that sustains contact with the antigen-presenting cell (APC). Using fluorescently labeled peptides, we showed that as few as two agonist ligands could promote APC contact and subsequent apoptosis in reactive thymocytes. Furthermore, we showed that productive signaling for positive selection, as gauged by nuclear translocation of a green fluorescent protein (GFP)-labeled NFATc construct, did not involve formation of a synapse between thymocytes and selecting epithelial cells in reaggregate thymus cultures. Antibody blockade of endogenous positively selecting ligands prevented NFAT nuclear accumulation in such cultures and reversed NFAT accumulation in previously stimulated thymocytes. Together, these data suggest a "gauntlet" model in which thymocytes mature by continually acquiring and reacquiring positively selecting signals without sustained contact with epithelial cells, thereby allowing them to sample many cell surfaces for potentially negatively selecting ligands.

    View details for DOI 10.1016/j.immuni.2008.09.014

    View details for Web of Science ID 000261036000011

    View details for PubMedID 18993085

  • Shouts, whispers and the kiss of death: directional secretion in T cells NATURE IMMUNOLOGY Huse, M., Quann, E. J., Davis, M. M. 2008; 9 (10): 1105-1111


    T cells use secreted soluble factors for highly specific intercellular communication and targeted cell killing. This specificity is achieved first through T cell receptor-mediated recognition of complexes of peptide and major histocompatibility complex displayed by appropriate antigen-presenting cells and then by the directed secretion of cytokines and lytic factors into the immunological synapse between the T cell and antigen-presenting cell. Studies have begun to probe the molecular basis for this synaptic secretion and have also shown that T cells release chemokines and certain inflammatory factors through a multidirectional pathway directed away from the synapse. Thus, the mode of secretion seems to be tailored to the intended function of the secreted molecule.

    View details for DOI 10.1038/ni.f.215

    View details for Web of Science ID 000259315600008

    View details for PubMedID 18800163

  • Immunosuppressive therapy mitigates immunological rejection of human embryonic stem cell xenografts PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Swijnenburg, R., Schrepfer, S., Govaert, J. A., Cao, F., Ransohoff, K., Sheikh, A. Y., Haddad, M., Connolly, A. J., Davis, M. M., Robbins, R. C., Wu, J. C. 2008; 105 (35): 12991-12996


    Given their self-renewing and pluripotent capabilities, human embryonic stem cells (hESCs) are well poised as a cellular source for tissue regeneration therapy. However, the host immune response against transplanted hESCs is not well characterized. In fact, controversy remains as to whether hESCs have immune-privileged properties. To address this issue, we used in vivo bioluminescent imaging to track the fate of transplanted hESCs stably transduced with a double-fusion reporter gene consisting of firefly luciferase and enhanced GFP. We show that survival after transplant is significantly limited in immunocompetent as opposed to immunodeficient mice. Repeated transplantation of hESCs into immunocompetent hosts results in accelerated hESC death, suggesting an adaptive donor-specific immune response. Our data demonstrate that transplanted hESCs trigger robust cellular and humoral immune responses, resulting in intragraft infiltration of inflammatory cells and subsequent hESC rejection. Moreover, we have found CD4(+) T cells to be an important modulator of hESC immune-mediated rejection. Finally, we show that immunosuppressive drug regimens can mitigate the anti-hESC immune response and that a regimen of combined tacrolimus and sirolimus therapies significantly prolongs survival of hESCs for up to 28 days. Taken together, these data suggest that hESCs are immunogenic, trigger both cellular and humoral-mediated pathways, and, as a result, are rapidly rejected in xenogeneic hosts. This process can be mitigated by a combined immunosuppressive regimen as assessed by molecular imaging approaches.

    View details for DOI 10.1073/pnas.0805802105

    View details for Web of Science ID 000259343000067

    View details for PubMedID 18728188

    View details for PubMedCentralID PMC2529073

  • Thymic selection determines gamma delta T cell effector fate: Antigen-naive cells make interleukin-17 and antigen-experienced cells make interferon gamma IMMUNITY Jensen, K. D., Su, X., Shin, S., Li, L., Youssef, S., Yarnasaki, S., Steinman, L., Saito, T., Locksley, R. M., Davis, M. M., Baumgarth, N., Chien, Y. 2008; 29 (1): 90-100


    gammadelta T cells uniquely contribute to host immune defense, but how this is accomplished remains unclear. Here, we analyzed the nonclassical major histocompatibility complex class I T10 and T22-specific gammadelta T cells in mice and found that encountering antigen in the thymus was neither required nor inhibitory for their development. But when triggered through the T cell receptor, ligand-naive lymphoid-gammadelta T cells produced IL-17, whereas ligand-experienced cells made IFN-gamma. Immediately after immunization, a large fraction of IL-17(+) gammadelta T cells were found in the draining lymph nodes days before the appearance of antigen-specific IL-17(+) *beta T cells. Thus, thymic selection determines the effector fate of gammadelta T cells rather than constrains their antigen specificities. The swift IL-17 response mounted by antigen-naive gammadelta T cells suggests a critical role for these cells at the onset of an acute inflammatory response to novel antigens.

    View details for DOI 10.1016/j.immuni.2008.04.022

    View details for Web of Science ID 000257905400013

    View details for PubMedID 18585064

    View details for PubMedCentralID PMC2601709

  • The alpha beta T cell repertoire comes into focus IMMUNITY Davis, M. M. 2007; 27 (2): 179-180


    The size of the lymphocyte repertoire is of great interest, but direct information has been elusive. Moon et al. (2007) report the enumeration and isolation of naive CD4(+) T cells and show their numbers could predict the size and diversity of the primary immune response.

    View details for DOI 10.1016/j.immuni.2007.08.005

    View details for Web of Science ID 000249056300002

    View details for PubMedID 17723209

  • A role for "self" in T-cell activation SEMINARS IN IMMUNOLOGY Krogsgaard, M., Juang, J., Davis, M. M. 2007; 19 (4): 236-244


    The mechanisms by which alphabeta T-cells are selected in the thymus and then recognize peptide MHC (pMHC) complexes in the periphery remain an enigma. Recent work particularly with respect to quantification of T-cell sensitivity and the role of self-ligands in T-cell activation has provided some important clues to the details of how TCR signaling might be initiated. Here, we highlight recent experimental data that provides insights into the initiation of T-cell activation and also discuss the main controversies and uncertainties in this area.

    View details for DOI 10.1016/j.simm.2007.04.003

    View details for Web of Science ID 000248722400004

    View details for PubMedID 17548210

  • Spatial and temporal dynamics of T cell receptor signaling with a photoactivatable agonist IMMUNITY Huse, M., Klein, L. O., Girvin, A. T., Faraj, J. M., Li, Q., Kuhns, M. S., Davis, M. M. 2007; 27 (1): 76-88


    The precise timing of signals downstream of the T cell receptor (TCR) is poorly understood. To address this problem, we prepared major histocompatibility complexes containing an antigenic peptide that is biologically inert until exposed to ultraviolet (UV) light. UV irradiation of these complexes in contact with cognate T cells enabled the high-resolution temporal analysis of signaling. Phosphorylation of the LAT adaptor molecule was observed in 4 s, and diacylglycerol production and calcium flux was observed in 6-7 s. TCR activation also induced cytoskeletal polarization within 2 min. Antibody blockade of CD4 reduced the intensity of LAT phosphorylation and the speed of calcium flux. Furthermore, strong desensitization of diacylglycerol production, but not LAT phosphorylation, occurred shortly after TCR activation, suggesting that different molecular events play distinct signal-processing roles. These results establish the speed and localization of early signaling steps, and have important implications regarding the overall structure of the network.

    View details for DOI 10.1016/j.immuni.2007.05.017

    View details for Web of Science ID 000248398100010

    View details for PubMedID 17629516

  • Blimp-1 over Budapest NATURE IMMUNOLOGY Davis, M. M. 2007; 8 (5): 445-447


    Blimp-1 is a transcription factor that affects the expression of hundreds of genes in lymphocytes. Recent work confirmed its role in the maturation of B cells into immunoglobulin-secreting plasmablasts, as well as in the control of T cell homeostasis and tolerance. What follows is a short history of how Blimp-1 was discovered.

    View details for DOI 10.1038/ni0507-445

    View details for Web of Science ID 000245831600003

    View details for PubMedID 17440448

  • Structural insight into pre-B cell receptor function SCIENCE Bankovich, A. J., Raunser, S., Juo, Z. S., Walz, T., Davis, M. M., Garcia, K. C. 2007; 316 (5822): 291-294


    The pre-B cell receptor (pre-BCR) serves as a checkpoint in B cell development. In the 2.7 angstrom structure of a human pre-BCR Fab-like fragment, consisting of an antibody heavy chain (HC) paired with the surrogate light chain, the "unique regions" of VpreB and lambda5 replace the complementarity-determining region 3 (CDR3) loop of an antibody light chain and appear to "probe" the HC CDR3, potentially influencing the selection of the antibody repertoire. Biochemical analysis indicates that the pre-BCR is impaired in its ability to recognize antigen, which, together with electron microscopic visualization of a pre-BCR dimer, suggests ligand-independent oligomerization as the likely signaling mechanism.

    View details for DOI 10.1126/science.1139412

    View details for Web of Science ID 000245654500055

    View details for PubMedID 17431183

  • miR-181a is an intrinsic modulator of T cell sensitivity and selection CELL Li, Q., Chau, J., Ebert, P. J., Sylvester, G., Min, H., Liu, G., Braich, R., Manoharan, M., Soutschek, J., Skare, P., Klein, L. O., Davis, M. M., Chen, C. 2007; 129 (1): 147-161


    T cell sensitivity to antigen is intrinsically regulated during maturation to ensure proper development of immunity and tolerance, but how this is accomplished remains elusive. Here we show that increasing miR-181a expression in mature T cells augments the sensitivity to peptide antigens, while inhibiting miR-181a expression in the immature T cells reduces sensitivity and impairs both positive and negative selection. Moreover, quantitative regulation of T cell sensitivity by miR-181a enables mature T cells to recognize antagonists-the inhibitory peptide antigens-as agonists. These effects are in part achieved by the downregulation of multiple phosphatases, which leads to elevated steady-state levels of phosphorylated intermediates and a reduction of the T cell receptor signaling threshold. Importantly, higher miR-181a expression correlates with greater T cell sensitivity in immature T cells, suggesting that miR-181a acts as an intrinsic antigen sensitivity "rheostat" during T cell development.

    View details for DOI 10.1016/j.cell.2007.03.008

    View details for Web of Science ID 000245661100018

    View details for PubMedID 17382377

  • Disruption of extracellular interactions impairs T cell receptor-CD3 complex stability and signaling IMMUNITY Kuhns, M. S., Davis, M. M. 2007; 26 (3): 357-369


    The alphabeta T cell antigen receptor (TCR), in complex with the CD3deltavarepsilon, gammavarepsilon, and zetazeta signaling subunits, is the chief determinant for specific CD4(+) and CD8(+) T cell responses to self and foreign antigens. Although transmembrane domain charge interactions are critical for the assembly of the complex, the location of extracellular contacts between the TCR and CD3 subunits and their contributions to stability and signal transduction have not been defined. Here we used mutagenesis to demonstrate that the CD3deltavarepsilon and CD3gammavarepsilon subunits interact with the TCR via adjacent Calpha DE and Cbeta CC' loops, respectively. The TCR-CD3deltavarepsilon interactions helped stabilize CD3gammavarepsilon within the complex and were important for normal T cell and thymocyte responses to TCR engagement. These data demonstrate that extracellular TCR-CD3 subunit interactions contribute to the structural integrity and function of this multisubunit receptor.

    View details for DOI 10.1016/j.immuni.2007.01.015

    View details for Web of Science ID 000245228100012

    View details for PubMedID 17368054

  • T cells as a self-referential, sensory organ ANNUAL REVIEW OF IMMUNOLOGY Davis, M. M., Krogsgaard, M., Huse, M., Huppa, J., Lillemeier, B. F., Li, Q. 2007; 25: 681-695


    In light of recent data showing that both helper and cytotoxic T cells can detect even a single molecule of an agonist peptide-MHC, alphabeta T cells are clearly a type of sensory cell, comparable to any in the nervous system. In addition, endogenous (self) peptides bound to MHCs are not just important for thymic selection, but also play an integral role in T cell activation in the response to foreign antigens. With the multitude of specificities available to most T cells, they can thus be considered as a sensory organ, trained on self-peptide-MHCs and primed to detect nonself.

    View details for DOI 10.1146/annurev.immunol.24.021605.090600

    View details for Web of Science ID 000246437100023

    View details for PubMedID 17291190

  • Plasma membrane-associated proteins are clustered into islands attached to the cytoskeleton PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lillemeier, B. F., Pfeiffer, J. R., Surviladze, Z., Wilson, B. S., Davis, M. M. 2006; 103 (50): 18992-18997


    Although much evidence suggests that the plasma membrane of eukaryotic cells is not homogenous, the precise architecture of this important structure has not been clear. Here we use transmission electron microscopy of plasma membrane sheets and specific probes to show that most or all plasma membrane-associated proteins are clustered in cholesterol-enriched domains ("islands") that are separated by "protein-free" and cholesterol-low membrane. These islands are further divided into subregions, as shown by the localization of "raft" and "non-raft" markers to specific areas. Abundant actin staining and inhibitor studies show that these structures are connected to the cytoskeleton and at least partially depend on it for their formation and/or maintenance.

    View details for DOI 10.1073/pnas.0609009103

    View details for Web of Science ID 000242884200023

    View details for PubMedID 17146050

  • A large T cell invagination with CD2 enrichment resets receptor engagement in the immunological synapse JOURNAL OF IMMUNOLOGY Singleton, K., Parvaze, N., Dama, K. R., Chen, K. S., Jennings, P., Purtic, B., Sjaastad, M. D., Gilpin, C., Davis, M. M., Wulfing, C. 2006; 177 (7): 4402-4413


    T cell activation is driven by the TCR and complemented by costimulation. We have studied the dynamics of ligand-engagement of the costimulatory receptor CD2 in T cell/APC couples. Thousands of ligand-engaged CD2 molecules were included in a large T cell invagination at the center of the cellular interface within 1 min of cell couple formation. The structure and regulation of this invagination shared numerous features with phagocytosis and macropinocytosis. Three observations further characterize the invagination and the inclusion of CD2: 1) numerous ligand-engaged receptors were enriched in and internalized through the T cell invagination, none as prominently as CD2; 2) dissolution of the T cell invagination and CD2 engagement were required for effective proximal T cell signaling; and 3) the T cell invagination was uniquely sensitive to the affinity of the TCR for peptide-MHC. Based on this characterization, we speculate that the T cell invagination, aided by CD2 enrichment, internalizes parts of the TCR signaling machinery to reset T cell signaling upon agonist-mediated, stable APC contact.

    View details for Web of Science ID 000240787400024

    View details for PubMedID 16982875

  • T cells use two directionally distinct pathways for cytokine secretion NATURE IMMUNOLOGY Huse, M., Lillemeier, B. F., Kuhns, M. S., Chen, D. S., Davis, M. M. 2006; 7 (3): 247-255


    Activated T helper cells produce many cytokines, some of which are secreted through the immunological synapse toward the antigen-presenting cell. Here we have used immunocytochemistry, live-cell imaging and a surface-mediated secretion assay to show that there are two cytokine export pathways in T helper cells. Some cytokines, including interleukin 2 and interferon-gamma, were secreted into the synapse, whereas others, including tumor necrosis factor and the chemokine CCL3 (MIP-1alpha), were released multidirectionally. Each secretion pathway was associated with different trafficking proteins, indicating that they are molecularly distinct processes. These data suggest that T helper cells release some cytokines into the immunological synapse to impart specific communication and others multidirectionally to promote inflammation and to establish chemokine gradients.

    View details for DOI 10.1038/ni1304

    View details for Web of Science ID 000235360400009

    View details for PubMedID 16444260

  • Deconstructing the form and function of the TCR/CD3 complex IMMUNITY Kuhns, M. S., DAVIS, M. M., Garcia, K. C. 2006; 24 (2): 133-139


    When T cells encounter antigens via the T cell antigen receptor (TCR), information about the quantity and quality of antigen engagement is relayed to the intracellular signal transduction machinery. This process is poorly understood. The TCR itself lacks a significant intracellular domain. Instead, it is associated with CD3 molecules that contain intracellular signaling domains that couple the TCR/CD3 complex to the downstream signaling machinery. The earliest events in TCR signaling must involve the transfer of information from the antigen binding TCR subunit to the CD3 signaling subunits of the TCR/CD3 complex. Elucidating the structural organization of the TCR with the associated CD3 signaling molecules is necessary for understanding the mechanism by which TCR engagement is coupled to activation. Here, we review the current state of our understanding of the structure and organization of the TCR/CD3 complex.

    View details for DOI 10.1016/j.immuni.2006.01.006

    View details for Web of Science ID 000235479000005

    View details for PubMedID 16473826

  • Molecular and functional analysis using live cell microarrays CURRENT OPINION IN CHEMICAL BIOLOGY Chen, D. S., Davis, M. M. 2006; 10 (1): 28-34


    Understanding cellular behavior in both healthy and diseased states requires the ability to molecularly delineate the characteristics of individual cells from complex mixtures. The recent development of cellular microarrays allows such an undertaking. By immobilizing different cell capture and analysis reagents on a solid support, mixtures of cells can be rapidly interrogated for their composition and phenotype. Thus, one can identify and quantitate distinct cell types based on the expression of particular cell surface molecules, as well as analyze their response to defined signals through the secretion of specific factors or other measurable cellular activities. This review focuses on the use of cellular microarrays to detect antigen-specific T cells and their responsiveness, analyze cancer cell types and behavior and to investigate the control of stem cell differentiation.

    View details for DOI 10.1016/j.cbpa.2006.01.001

    View details for Web of Science ID 000235858200005

    View details for PubMedID 16413817

  • Marked differences in human melanoma antigen-specific T cell responsiveness after vaccination using a functional microarray PLOS MEDICINE Chen, D. S., Soen, Y., Stuge, T. B., Lee, P. P., Weber, J. S., Brown, P. O., Davis, M. M. 2005; 2 (10): 1018-1030


    In contrast to many animal model studies, immunotherapeutic trials in humans suffering from cancer invariably result in a broad range of outcomes, from long-lasting remissions to no discernable effect.In order to study the T cell responses in patients undergoing a melanoma-associated peptide vaccine trial, we have developed a high-throughput method using arrays of peptide-major histocompatibility complexes (pMHC) together with antibodies against secreted factors. T cells were specifically immobilized and activated by binding to particular pMHCs. The antibodies, spotted together with the pMHC, specifically capture cytokines secreted by the T cells. This technique allows rapid, simultaneous isolation and multiparametric functional characterization of antigen-specific T cells present in clinical samples. Analysis of CD8+ lymphocytes from ten melanoma patients after peptide vaccination revealed a diverse set of patient- and antigen-specific profiles of cytokine secretion, indicating surprising differences in their responsiveness. Four out of four patients who showed moderate or greater secretion of both interferon-gamma (IFNgamma) and tumor necrosis factor-alpha (TNFalpha) in response to a gp100 antigen remained free of melanoma recurrence, whereas only two of six patients who showed discordant secretion of IFNgamma and TNFalpha did so.Such multiparametric analysis of T cell antigen specificity and function provides a valuable tool with which to dissect the molecular underpinnings of immune responsiveness and how this information correlates with clinical outcome.

    View details for DOI 10.1371/journal.pmed.0020265

    View details for Web of Science ID 000233182500019

    View details for PubMedID 16162034

  • A hybrid machine-learning approach for segmentation of protein localization data BIOINFORMATICS Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. 2005; 21 (19): 3778-3786


    Subcellular protein localization data are critical to the quantitative understanding of cellular function and regulation. Such data are acquired via observation and quantitative analysis of fluorescently labeled proteins in living cells. Differentiation of labeled protein from cellular artifacts remains an obstacle to accurate quantification. We have developed a novel hybrid machine-learning-based method to differentiate signal from artifact in membrane protein localization data by deriving positional information via surface fitting and combining this with fluorescence-intensity-based data to generate input for a support vector machine.We have employed this classifier to analyze signaling protein localization in T-cell activation. Our classifier displayed increased performance over previously available techniques, exhibiting both flexibility and adaptability: training on heterogeneous data yielded a general classifier with good overall performance; training on more specific data yielded an extremely high-performance specific classifier. We also demonstrate accurate automated learning utilizing additional experimental data.

    View details for DOI 10.1093/bioinformatics/bti615

    View details for Web of Science ID 000232596100012

    View details for PubMedID 16091410

  • Cellular immunotherapy: antigen recognition is just the beginning SPRINGER SEMINARS IN IMMUNOPATHOLOGY Chen, D. S., Davis, M. M. 2005; 27 (1): 119-127


    Advances in molecular and cellular biology have illustrated both the flexibility and complexity involved in host immune responses. Understanding this response is vital to the further development of therapeutic strategies that involve manipulation of the cellular immune response to target tumors. Mobilized, tumor antigen-specific T cells, the core for most immunotherapeutic strategies, are highly regulated, and capable of a wide spectrum of functional responses. Due to differences in murine and human immunity, broad-scale immune monitoring, particularly high-throughput ex vivo analysis of human immune responses, promises to determine what comprises an effective immunotherapy. Such understanding will lead to more sophisticated clinical trials, earlier determination of efficacy and individualized protocols.

    View details for DOI 10.1007/s00281-005-0200-z

    View details for Web of Science ID 000229906400010

    View details for PubMedID 15834723

  • Agonist/endogenous peptide-MHC heterodimers drive T cell activation and sensitivity NATURE Krogsgaard, M., Li, Q. J., Sumen, C., Huppa, J. B., Huse, M., Davis, M. M. 2005; 434 (7030): 238-243


    Alphabeta T lymphocytes are able to detect even a single peptide-major histocompatibility complex (MHC) on the surface of an antigen-presenting cell. This is despite clear evidence, at least with CD4+ T cells, that monomeric ligands are not stimulatory. In an effort to understand how this remarkable sensitivity is achieved, we constructed soluble peptide-MHC heterodimers in which one peptide is an agonist and the other is one of the large number of endogenous peptide-MHCs displayed by presenting cells. We found that some specific combinations of these heterodimers can stimulate specific T cells in a CD4-dependent manner. This activation is severely impaired if the CD4-binding site on the agonist ligand is ablated, but the same mutation on an endogenous ligand has no effect. These data correlate well with analyses of lipid bilayers and cells presenting these ligands, and indicate that the basic unit of helper T cell activation is a heterodimer of agonist peptide- and endogenous peptide-MHC complexes, stabilized by CD4.

    View details for DOI 10.1038/nature03391

    View details for Web of Science ID 000227494500051

    View details for PubMedID 15724150

  • How T cells 'see' antigen NATURE IMMUNOLOGY Krogsgaard, M., Davis, M. M. 2005; 6 (3): 239-245


    T lymphocytes bearing alphabeta T cell receptors are pivotal in the immune response of most vertebrates. For example, helper T cells orchestrate antibody production by B cells as well as stimulating other cells, whereas cytotoxic T cells kill virally infected or abnormal cells. Regulatory T cells act to dampen responsiveness, and natural killer-like T cells monitor lipid metabolism. The specificity of these cells is governed by the alphabeta T cell receptors - antibody-like heterodimeric receptors that detect antigenic fragments (peptides) or lipids bound to histocompatibility molecules. Intriguing clues as to how these peculiar ligands are recognized have gradually emerged over the years and tell a remarkable story of biochemical and cellular novelty. Here we summarize some of the more recent work on alphabeta T cell receptor recognition and discuss the implications for activation.

    View details for DOI 10.1038/ni1173

    View details for Web of Science ID 000227117400015

    View details for PubMedID 15716973

  • The zinc finger transcriptional repressor Blimp1/Prdm1 is dispensable for early axis formation but is required for specification of primordial germ cells in the mouse DEVELOPMENT Vincent, S. D., Dunn, N. R., Sciammas, R., Shapiro-Shalef, M., DAVIS, M. M., Calame, K., Bikoff, E. K., Robertson, E. J. 2005; 132 (6): 1315-1325


    Blimp1, a zinc-finger containing DNA-binding transcriptional repressor, functions as a master regulator of B cell terminal differentiation. Considerable evidence suggests that Blimp1 is required for the establishment of anteroposterior axis formation and the formation of head structures during early vertebrate development. In mouse embryos, Blimp1 is strongly expressed in axial mesendoderm, the tissue known to provide anterior patterning signals during gastrulation. Here, we describe for the first time the defects caused by loss of Blimp1 function in the mouse. Blimp1 deficient embryos die at mid-gestation, but surprisingly early axis formation, anterior patterning and neural crest formation proceed normally. Rather, loss of Blimp1 expression disrupts morphogenesis of the caudal branchial arches and leads to a failure to correctly elaborate the labyrinthine layer of the placenta. Blimp1 mutant embryos also show widespread blood leakage and tissue apoptosis, and, strikingly, Blimp1 homozygous mutants entirely lack PGCs. At the time of PGC allocation around 7.25 days post coitum, Blimp1 heterozygous embryos exhibit decreased numbers of PCGs. Thus Blimp1 probably acts to turn off the default pathway that allows epiblast cells to adopt a somatic cell fate, and shifts the transcriptional program so that they become exclusively allocated into the germ cell lineage.

    View details for DOI 10.1242/dev.01711

    View details for Web of Science ID 000228378000014

    View details for PubMedID 15750184

  • Quantitative imaging of lymphocyte membrane protein reorganization and signaling BIOPHYSICAL JOURNAL Kasson, P. M., Huppa, J. B., Krogsgaard, M., DAVIS, M. M., Brunger, A. T. 2005; 88 (1): 579-589


    Changes in membrane protein localization are critical to establishing cell polarity and regulating cell signaling. Fluorescence microscopy of labeled proteins allows visualization of these changes, but quantitative analysis is needed to study this aspect of cell signaling in full mechanistic detail. We have developed a novel approach for quantitative assessment of membrane protein redistribution based on four-dimensional video microscopy of fluorescently labeled proteins. Our analytic system provides robust automated methods for cell surface reconstruction, cell shape tracking, cell-surface distance measurement, and cluster formation analysis. These methods permit statistical analyses and testing of mechanistic hypotheses regarding cell signaling. We have used this approach to measure antigen-dependent clustering of signaling molecules in CD4+ T lymphocytes, obtaining clustering velocities consistent with single-particle tracking data. Our system captures quantitative differences in clustering between signaling proteins with distinct biological functions. Our methods can be generalized to a range of cell-signaling phenomena and enable novel applications not feasible with single-particle studies, such as analysis of subcellular protein localization in live organ culture.

    View details for DOI 10.1529/biophysj.104.048827

    View details for Web of Science ID 000226090900054

    View details for PubMedID 15501943

  • Blimp-1; Immunoglobulin secretion and the switch to plasma cells MOLECULAR ANALYSIS OF B LYMPHOCYTE DEVELOPMENT AND ACTIVATION Sciammas, R., DAVIS, M. M. 2005; 290: 201-224


    The transcription factor Blimp-1 governs the generation of plasma cells and immunoglobulin secretion. Recent microarray experiments indicate that Blimp-1 regulates a large set of genes that constitute a significant part of the plasma cell expression signature. The variety of differentially expressed genes indicates that Blimp-1 affects numerous aspects of plasma cell maturation, ranging from migration, adhesion, and homeostasis, to antibody secretion. In addition, Blimp-1 regulates immunoglobulin secretion by affecting the nuclear processing of the mRNA transcript and by affecting protein trafficking by regulating genes that impact on the activity of the endoplasmic reticulum. Interestingly, the differentiation events that Blimp-1 regulates appear to be modulated depending on the activation state of the B cell. This modulation may be due at least in part to distinct regions of Blimp-1 that regulate unique sets of genes independently of each other. These data hint at the complexity of Blimp-1 and the genetic program that it initiates to produce a pool of plasma cells necessary for specific immunity.

    View details for Web of Science ID 000233593800009

    View details for PubMedID 16480044

  • Deformable modeling for improved calculation of molecular velocities from single-particle tracking IEEE Computational Systems Bioinformatics Conference Kasson, P., Davis, M. M., Brunger, A. T. IEEE COMPUTER SOC. 2005: 208–211


    Single-particle tracking provides a powerful technique for measuring dynamic cellular processes on the level of individual molecules. Much recent work has been devoted to using single particle tracking to measure long-range movement of particles on the cell surface, including methods for automated localization and tracking of particles [1-3]. However, most particle tracking studies to date ignore cell surface curvature and dynamic cellular deformation, factors frequently present in physiologically relevant situations. In this report, we perform quantitative evaluation of single-particle tracking on curved and deforming cell surfaces. We also introduce a new hybrid method that uses non-rigid cellular modeling for improved computation of single-particle tracking trajectories on the surfaces of cells undergoing deformation. This method combines single-molecule and bulk fluorescence measurements in an automated manner to enable more accurate and robust characterization of dynamic cell physiology and regulation.

    View details for Web of Science ID 000231800100025

    View details for PubMedID 16447978

  • Prevention of type I diabetes transfer by glutamic acid decarboxylase 65 peptide 206-220-specific T cells PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Kim, S. K., Tarbell, K. V., Sanna, M., Vadeboncoeur, M., Warganich, T., Lee, M., Davis, M., McDevitt, H. O. 2004; 101 (39): 14204-14209


    Glutamic acid decarboxylase (GAD) 65 is one of the major pancreatic antigens targeted by self-reactive T cells in type I diabetes mellitus. T cells specific for GAD65 are among the first to enter inflamed islets and may be important for the initiation of autoimmune diabetes. However, we previously reported that nonobese diabetic (NOD) mice transgenic for a T cell antigen receptor (TCR) specific for one of the immunodominant epitopes of GAD65, peptide 286-300 (G286), are protected from insulitis and diabetes. To examine whether other GAD65-reactive T cells share this phenotype, we have generated TCR transgenic NOD mice for a second immunodominant epitope of GAD65, peptide 206-220 (G206). As in G286 mice, G206 mice do not develop islet inflammation or diabetes. When adoptively transferred along with diabetogenic T cells, activated G206 T cells significantly delayed the onset of diabetes in NOD.scid recipients. Both G206 and G286 T cells produce immunoregulatory cytokines IFN-gamma and IL-10 at low levels when activated by cognate antigens. These data suggest that GAD65-specific T cells may play a protective role in diabetes pathogenesis by regulating pathogenic T cell responses. A better understanding of the functions of autoreactive T cells in type I diabetes will be necessary for choosing desirable targets for immunotherapy.

    View details for DOI 10.1073/pnas.0405500101

    View details for Web of Science ID 000224211400044

    View details for PubMedID 15381770

    View details for PubMedCentralID PMC521137

  • T cell receptor antagonism interferes with MHC clustering and integrin patterning during immunological synapse formation JOURNAL OF CELL BIOLOGY Sumen, C., Dustin, M. L., Davis, M. M. 2004; 166 (4): 579-590


    T cell activation by nonself peptide-major histocompatibility complex (MHC) antigenic complexes can be blocked by particular sequence variants in a process termed T cell receptor antagonism. The inhibition mechanism is not understood, although such variants are encountered in viral infections and may aid immune evasion. Here, we study the effect of antagonist peptides on immunological synapse formation by T cells. This cellular communication process features early integrin engagement and T cell motility arrest, referred to as the "stop signal." We find that synapses formed on membranes presenting antagonist-agonist complexes display reduced MHC density, which leads to reduced T cell proliferation that is not overcome by the costimulatory ligands CD48 and B7-1. Most T cells fail to arrest and crawl slowly with a dense ICAM-1 crescent at the leading edge. Similar aberrant patterns of LFA-1/ICAM-1 engagement in live T-B couples correlate with reduced calcium flux and IL-2 secretion. Hence, antagonist peptides selectively disable MHC clustering and the stop signal, whereas LFA-1 valency up-regulation occurs normally.

    View details for DOI 10.1083/jcb.200404059

    View details for Web of Science ID 000223479000015

    View details for PubMedID 15314068

  • CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse NATURE IMMUNOLOGY Li, Q. J., Dinner, A. R., Qi, S. Y., Irvine, D. J., Huppa, J. B., Davis, M. M., Chakraborty, A. K. 2004; 5 (8): 791-799


    How T cells respond with extraordinary sensitivity to minute amounts of agonist peptide and major histocompatibility complex (pMHC) molecules on the surface of antigen-presenting cells bearing large numbers of endogenous pMHC molecules is not understood. Here we present evidence that CD4 affects the responsiveness of T helper cells by controlling spatial localization of the tyrosine kinase Lck in the synapse. This finding, as well as further in silico and in vitro experiments, led us to develop a molecular model in which endogenous and agonist pMHC molecules act cooperatively to amplify T cell receptor signaling. At the same time, activation due to endogenous pMHC molecules alone is inhibited. A key feature is that the binding of agonist pMHC molecules to the T cell receptor results in CD4-mediated spatial localization of Lck, which in turn enables endogenous pMHC molecules to trigger many T cell receptors. We also discuss broader implications for T cell biology, including thymic selection, diversity of the repertoire of self pMHC molecules and serial triggering.

    View details for DOI 10.1038/ni1095

    View details for Web of Science ID 000222955600010

    View details for PubMedID 15247914

  • The evolutionary and structural 'logic' of antigen receptor diversity SEMINARS IN IMMUNOLOGY Davis, M. M. 2004; 16 (4): 239-243


    Most vertebrate species utilize antibody and T-cell receptor (TCR) genes to create a vast repertoire of antigen sensor molecules on their B and T lymphocytes, respectively. While the organization of these genes exhibits substantial variation between species, one common theme is that, in almost every case, there is at least one variable region with a highly diverse CDR3 region and often much less diversity elsewhere in the binding site. Whereas with alphabeta TCRs this skewing of diversity correlates well with the need to recognize diverse peptides bound to MHC molecules, this cannot explain why this same pattern is evident in immunoglobulins (Igs) or gammadelta TCRs. Instead we have postulated that in the primary repertoire, all or most antigen receptors have a bipartite binding site, in which diverse CDR3 loops act as a highly antigen specific 'core' whereas other CDRs bind in a largely opportunistic fashion. In the case of antibodies, somatic hypermutation then acts to improve the complementarity to a given antigen and increase antibody affinity. A test of this model in mice engineered to have a very limited V region repertoire shows that primary antibodies can be generated that are highly specific for distinct antigens, yet identical in sequence except for their V(H) CDR3. Furthermore, very high affinity antibodies can be raised by repeated immunizations, showing that somatic hypermutation can mold these low affinity antibodies into high affinity ones. Thus, the wide variations seen in V region repertoires amongst vertebrates is likely to be of lesser importance than the preservation of one or more diverse CDR3 regions.

    View details for DOI 10.1016/j.smim.2004.08.003

    View details for Web of Science ID 000225342100004

    View details for PubMedID 15522622

  • T cell killing does not require the formation of a stable mature immunological synapse NATURE IMMUNOLOGY Purbhoo, M. A., Irvine, D. J., Huppa, J. B., Davis, M. M. 2004; 5 (5): 524-530


    A notable feature of T lymphocyte recognition on other cell surfaces is the formation of a stable mature immunological synapse. Here we use a single-molecule labeling method to directly measure the number of ligands a cytotoxic T cell engages and track the consequences of that interaction by three-dimensional video microscopy. Like helper T cells, cytotoxic T cells were able to detect even a single foreign antigen but required about ten complexes of peptide-major histocompatibility complex (pMHC) to achieve full calcium increase and to form a mature synapse. Thus, cytotoxic T cells and helper T cells are more uniform in their antigen sensitivities than previously thought. Furthermore, only three pMHC complexes were required for killing, showing that stable synapse formation and complete signaling are not required for cytotoxicity.

    View details for DOI 10.1038/ni1058

    View details for Web of Science ID 000221101100017

    View details for PubMedID 15048111

  • Modular nature of blimp-1 in the regulation of gene expression during B cell maturation JOURNAL OF IMMUNOLOGY Sciammas, R., DAVIS, M. M. 2004; 172 (9): 5427-5440


    The transcription factor Blimp-1 induces the maturation of B cells into Ab-secreting plasma cells. DNA microarrays were used to analyze the transcription profiles of both Blimp-1-transduced murine B cell lines and the inducible B cell line BCL(1). Hundreds of genes were differentially regulated, showing how Blimp-1 both restricts affinity maturation and promotes Ab secretion, homeostasis, migration, and differentiation. Strikingly, when different modes of plasma cell induction are used, very different genetic programs are used, suggesting that the transition from a B cell to plasma cell can occur in multiple ways, perhaps accounting for the different types of Ab-secreting cells observed in vivo. Furthermore, mutagenesis of Blimp-1 reveals multiple effector domains, which regulate distinct genes. This indicates that Blimp-1 subdivides the maturation program into select and tunable pathways.

    View details for Web of Science ID 000221012300036

    View details for PubMedID 15100284

  • Quantitative analysis of membrane protein localization and signalling IEEE Computational Systems Bioinformatics Conference (CSB 2004) Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. IEEE COMPUTER SOC. 2004: 540–541
  • Quantitative analysis of lymphocyte membrane protein redistribution from fluorescence microscopy International Conference on Image Processing (ICIP 2004) Kasson, P. M., Huppa, J. B., DAVIS, M. M., Brunger, A. T. IEEE. 2004: 2933–2936
  • Detection and characterization of cellular immune responses using peptide-MHC microarrays. PLoS biology Soen, Y., Chen, D. S., Kraft, D. L., Davis, M. M., Brown, P. O. 2003; 1 (3): E65-?


    The detection and characterization of antigen-specific T cell populations is critical for understanding the development and physiology of the immune system and its responses in health and disease. We have developed and tested a method that uses arrays of peptide-MHC complexes for the rapid identification, isolation, activation, and characterization of multiple antigen-specific populations of T cells. CD4(+) or CD8(+) lymphocytes can be captured in accordance with their ligand specificity using an array of peptide-MHC complexes printed on a film-coated glass surface. We have characterized the specificity and sensitivity of a peptide-MHC array using labeled lymphocytes from T cell receptor transgenic mice. In addition, we were able to use the array to detect a rare population of antigen-specific T cells following vaccination of a normal mouse. This approach should be useful for epitope discovery, as well as for characterization and analysis of multiple epitope-specific T cell populations during immune responses associated with viral and bacterial infection, cancer, autoimmunity, and vaccination.

    View details for PubMedID 14691537

  • T-cell-antigen recognition and the immunological synapse NATURE REVIEWS IMMUNOLOGY Huppa, J. B., DAVIS, M. M. 2003; 3 (12): 973-983

    View details for DOI 10.1038/nri1245

    View details for Web of Science ID 000186892700015

    View details for PubMedID 14647479

  • Evidence that structural rearrangements and/or flexibility during TCR binding can contribute to T cell activation MOLECULAR CELL Krogsgaard, M., Prado, N., Adams, E. J., He, X. L., Chow, D. C., Wilson, D. B., Garcia, K. C., Davis, M. M. 2003; 12 (6): 1367-1378


    While in many cases the half-life of T cell receptor (TCR) binding to a particular ligand is a good predictor of activation potential, numerous exceptions suggest that other physical parameter(s) must also play a role. Accordingly, we analyzed the thermodynamics of TCR binding to a series of peptide-MHC ligands, three of which are more stimulatory than their stability of binding would predict. Strikingly, we find that during TCR binding these outliers show anomalously large changes in heat capacity, an indicator of conformational change or flexibility in a binding interaction. By combining the values for heat capacity (DeltaCp) and the half-life of TCR binding (t(1/2)), we find that we can accurately predict the degree of T cell stimulation. Structural analysis shows significant changes in the central TCR contact residue of the peptide-MHC, indicating that structural rearrangements within the TCR-peptide-MHC interface can contribute to T cell activation.

    View details for Web of Science ID 000187511600007

    View details for PubMedID 14690592

  • Linking molecular and cellular events in T-cell activation and synapse formation SEMINARS IN IMMUNOLOGY Krogsgaard, M., Huppa, J. B., Purbhoo, M. A., Davis, M. A. 2003; 15 (6): 307-315


    The complex sequence of events in which T cells recognize foreign entities on other cells is not well understood. However, the development of new techniques and approaches in both the molecular and cellular aspects of this problem have provided significant insights into the mechanisms of T-cell recognition and synapse formation. In particular, we have a clearer picture of T-cell sensitivity, the role of co-stimulation in formation of the immunological synapse, and how TCR signaling acts to maintain synapse structure and potentiate the T cells over many hours of engagement. We also are aware of new complexities in the way T-cell receptor molecules bind peptide-MHC (pMHC) ligands and what that may mean for TCR scanning, cross-reactivity, and activation. Ultimately, we want to integrate these cellular aspects of T-cell recognition with key features of the molecular interactions that drive specific events.

    View details for DOI 10.1016/j.smim.2003.09.002

    View details for Web of Science ID 000187388800003

    View details for PubMedID 15001169

  • Continuous T cell receptor signaling required for synapse maintenance and full effector potential NATURE IMMUNOLOGY Huppa, J. B., Gleimer, M., Sumen, C., Davis, M. M. 2003; 4 (8): 749-755


    Although signals through the T cell receptor (TCR) are essential for the initiation of T helper cell activation, it is unclear what function such signals have during the prolonged T cell-antigen-presenting cell contact. Here we simultaneously tracked TCR-CD3 complex and phosphoinositide 3-kinase activity in single T cells using three-dimensional video microscopy. Despite rapid internalization of most of the TCR-CD3, TCR-dependent signaling was still evident up to 10 h after conjugate formation. Blocking this interaction caused dissolution of the synapse and proportional reductions in interleukin 2 production and cellular proliferation. Thus TCR signaling persists for hours, has a cumulative effect and is necessary for the maintenance of the immunological synapse.

    View details for DOI 10.1038/ni951

    View details for Web of Science ID 000184441500011

    View details for PubMedID 12858171

  • Dynamics of cell surface molecules during T cell recognition ANNUAL REVIEW OF BIOCHEMISTRY Davis, M. M., Krogsgaard, M., Huppa, J. B., Sumen, C., Purbhoo, M. A., Irvine, D. J., Wu, L. C., Ehrlich, L. 2003; 72: 717-742


    Recognition of foreign antigens by T lymphocytes is a very important component of vertebrate immunity-vital to the clearance of pathogenic organisms and particular viruses and necessary, indirectly, for the production of high affinity antibodies. T cell recognition is mediated by the systematic scanning of cell surfaces by T cells, which collectively express many antigen receptors. When the appropriate antigenic peptide bound to a molecule of the major histocompatibility complex is found-even in minute quantities-a series of elaborate cell-surface molecule and internal rearrangements take place. The sequence of events and the development of techniques required to observe these events have significantly enhanced our understanding of T cell recognition and may find application in other systems of transient cell:cell interactions as well.

    View details for DOI 10.1146/annurev.biochem.72.121801.161625

    View details for Web of Science ID 000185092500022

    View details for PubMedID 14527326

  • Dynamics of p56lck translocation to the T cell immunological synapse following agonist and antagonist stimulation IMMUNITY Ehrlich, L. I., Ebert, P. J., Krummel, M. F., WEISS, A., DAVIS, M. M. 2002; 17 (6): 809-822


    To study the spatio/temporal recruitment of lck during immunological synapse formation, we utilize high-speed time-lapse microscopy to visualize green fluorescent protein (GFP) fusions of lck and CD3zeta following agonist or altered peptide ligand (APL) stimulation. The dynamics of lck and CD3zeta recruitment are comparable; however, lck becomes excluded to the periphery of mature synapses, while most CD3zeta is centrally localized, suggesting a limited time frame within which lck can efficiently phosphorylate CD3 molecules during synapse maturation. Exposure of T cells to specific APLs affects the efficiency of conjugate formation and lck accumulation. Most surprisingly, we find an intracellular pool of lck associated with recycling endosomes that translocates to mature synapses within 10 min of calcium flux. This bolus of lck may contribute to intermediate-late signal transduction.

    View details for Web of Science ID 000179985500012

    View details for PubMedID 12479826

  • A blood-borne antigen induces rapid T-B cell contact: a potential mechanism for tolerance induction IMMUNOLOGY Gutgemann, I., Darling, J. M., Greenberg, H. B., DAVIS, M. M., Chien, Y. H. 2002; 107 (4): 420-425


    Understanding the difference between the development of a productive T-cell response and tolerance is central to discerning how the immune system functions. Intravenous injection of soluble protein is thought to mimic the presentation of self-serum and orally introduced antigens. It is generally toleragenic. The current view is that this outcome reflects the failure of 'immunogenic' dendritic cells to relocate to the T-cell zone of the secondary lymphoid tissues. Here, using a peptide/I-Ek tetramer and antibodies to stain splenic sections, we showed that antigen-specific T cells were activated in the spleen within hours of injection or feeding of protein. The activated T cells were found to be located at the T-B junction, the bridging zone and the B-cell area, interacting directly with B cells. In addition, B cells gain the ability to present antigen. Our results suggest a way for T cells to be stimulated by blood-borne antigen presented by naïve B cells, a potential mechanism of tolerance induction.

    View details for Web of Science ID 000179547900005

    View details for PubMedID 12460186

  • Quantifying signaling-induced reorientation of T cell receptors during immunological synapse formation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Moss, W. C., Irvine, D. J., DAVIS, M. M., Krummel, M. F. 2002; 99 (23): 15024-15029


    Productive T cell recognition of antigen-presenting cells (APCs) is normally accompanied by the formation of a cell-cell contact called the "immunological synapse." Our understanding of the steps leading up to this formation has been limited by the absence of tools for analyzing 3D surfaces and surface distributions as they change over time. Here we use a 3D fluorescence quantitation method to show that T cell receptors are recruited in bulk within the first minute after the onset of activation and with velocities ranging from 0.04 to 0.1 microm/s; a speed significantly greater than unrestricted diffusion. Our method reveals a second feature of this reorientation: a conformational change as the T cell pushes more total membrane into the interface creating a larger contact area for additional receptors. Analysis of individual T cell receptor velocities using a single-particle tracking method confirms our velocity measurement. This method should permit the quantitation of other dynamic membrane events and the associated movement of cell-surface molecules.

    View details for DOI 10.1073/pnas.192573999

    View details for Web of Science ID 000179224800075

    View details for PubMedID 12415110

  • Direct observation of ligand recognition by T cells NATURE Irvine, D. J., Purbhoo, M. A., Krogsgaard, M., Davis, M. M. 2002; 419 (6909): 845-849


    The activation of T cells through interaction of their T-cell receptors with antigenic peptide bound to major histocompatibility complex (MHC) on the surface of antigen presenting cells (APCs) is a crucial step in adaptive immunity. Here we use three-dimensional fluorescence microscopy to visualize individual peptide-I-E(k) class II MHC complexes labelled with the phycobiliprotein phycoerythrin in an effort to characterize T-cell sensitivity and the requirements for forming an immunological synapse in single cells. We show that T cells expressing the CD4 antigen respond with transient calcium signalling to even a single agonist peptide-MHC ligand, and that the organization of molecules in the contact zone of the T cell and APC takes on the characteristics of an immunological synapse when only about ten agonists are present. This sensitivity is highly dependent on CD4, because blocking this molecule with antibodies renders T cells unable to detect less than about 30 ligands.

    View details for DOI 10.1038/nature01076

    View details for Web of Science ID 000178769800048

    View details for PubMedID 12397360

  • Identification of Epstein-Barr virus-specific CD8(+) T lymphocytes in the circulation of pediatric transplant recipients TRANSPLANTATION Falco, D. A., Nepomuceno, R. R., Krams, S. M., Lee, P. P., DAVIS, M. M., Salvatierra, O., Alexander, S. R., Esquivel, C. O., Cox, K. L., Frankel, L. R., Martinez, O. M. 2002; 74 (4): 501-510


    Pediatric transplant recipients are at increased risk for Epstein Barr virus (EBV)-related B cell lymphomas. In healthy individuals, the expansion of EBV-infected B cells is controlled by CD8+ cytotoxic T cells. However, immunosuppressive therapy may compromise antiviral immunity. We identified and determined the frequency of EBV-specific T cells in the peripheral blood of pediatric transplant recipients.HLA-B*0801 and HLA-A*0201 tetramers folded with immunodominant EBV peptides were used to detect EBV-specific CD8+ T cells by flow cytometry in peripheral blood mononuclear cells from 24 pediatric liver and kidney transplant recipients. The expression of CD38 and CD45RO on EBV-specific, tetramer-binding cells was also examined in a subset of patients by immunofluorescent staining and flow cytometry.Tetramer-binding CD8+ T cells were identified in 21 of 24 transplant recipients. EBV-specific CD8+ T cells were detected as early as 4 weeks after transplant in EBV seronegative patients receiving an organ from an EBV seropositive donor. The frequencies (expressed as a percentage of the CD8+ T cells) of the tetramer-binding cells were HLA-B8-RAKFKQLL (BZLF1 lytic antigen peptide) tetramer, range=0.96 to 3.94%; HLA-B8-FLRGRAYGL (EBNA3A latent antigen peptide) tetramer, range=0.03 to 0.59%; and HLA-A2-GLCTLVAML (BMLF1 lytic antigen peptide) tetramer, range=0.06 to 0.76%. The majority of tetramer reactive cells displayed an activated/memory phenotype.Pediatric transplant recipients receiving immunosuppression can generate EBV-specific CD8+ T cells. Phenotypic and functional analysis of tetramer cells may prove useful in defining and monitoring EBV infection in the posttransplant patient.

    View details for Web of Science ID 000177808600012

    View details for PubMedID 12352909

  • CD4(+) T cells from glutamic acid decarboxylase (GAD)65-specific T cell receptor transgenic mice are not diabetogenic and can delay diabetes transfer JOURNAL OF EXPERIMENTAL MEDICINE Tarbell, K. V., Lee, M., Ranheim, E., Chao, C. C., Sanna, M., Kim, S. K., Dickie, P., Teyton, L., Davis, M., McDevitt, H. 2002; 196 (4): 481-492


    Glutamic acid decarboxylase (GAD)65 is an early and important antigen in both human diabetes mellitus and the nonobese diabetic (NOD) mouse. However, the exact role of GAD65-specific T cells in diabetes pathogenesis is unclear. T cell responses to GAD65 occur early in diabetes pathogenesis, yet only one GAD65-specific T cell clone of many identified can transfer diabetes. We have generated transgenic mice on the NOD background expressing a T cell receptor (TCR)-specific for peptide epitope 286-300 (p286) of GAD65. These mice have GAD65-specific CD4(+) T cells, as shown by staining with an I-A(g7)(p286) tetramer reagent. Lymphocytes from these TCR transgenic mice proliferate and make interferon gamma, interleukin (IL)-2, tumor necrosis factor (TNF)-alpha, and IL-10 when stimulated in vitro with GAD65 peptide 286-300, yet these TCR transgenic animals do not spontaneously develop diabetes, and insulitis is virtually undetectable. Furthermore, in vitro activated CD4 T cells from GAD 286 TCR transgenic mice express higher levels of CTL-associated antigen (CTLA)-4 than nontransgenic littermates. CD4(+) T cells, or p286-tetramer(+)CD4(+) Tcells, from GAD65 286-300-specific TCR transgenic mice delay diabetes induced in NOD.scid mice by diabetic NOD spleen cells. This data suggests that GAD65 peptide 286-300-specific T cells have disease protective capacity and are not pathogenic.

    View details for DOI 10.1084/jem.20011845

    View details for Web of Science ID 000177669300007

    View details for PubMedID 12186840

    View details for PubMedCentralID PMC2196059

  • A new trigger for T cells CELL Davis, M. M. 2002; 110 (3): 285-287


    Understanding the early events in T cell activation and signaling is an active area of research. A recent study has described a new trigger for T cell activation, involving a TCR-ligand-induced conformational change in CD3epsilon that permits binding of the adaptor protein Nck.

    View details for Web of Science ID 000177411800004

    View details for PubMedID 12176315

  • Two-step binding mechanism for T-cell receptor recognition of peptide-MHC NATURE Wu, L. C., Tuot, D. S., Lyons, D. S., Garcia, K. C., Davis, M. M. 2002; 418 (6897): 552-556


    T cells probe a diverse milieu of peptides presented by molecules of the major histocompatibility complex (MHC) by using the T-cell receptor (TCR) to scan these ligands with high sensitivity and specificity. Here we describe a physical basis for this scanning process by studying the residues involved in both the initial association and the stable binding of TCR to peptide-MHC, using the well-characterized TCR and peptide-MHC pair of 2B4 and MCC-IE(k) (moth cytochrome c, residues 88 103). We show that MHC contacts dictate the initial association, guiding TCR docking in a way that is mainly independent of the peptide. Subsequently, MCC-IE(k) peptide contacts dominate stabilization, imparting specificity and influencing T-cell activation by modulating the duration of binding. This functional subdivision of the peptide-MHC ligand suggests that a two-step process for TCR recognition facilitates the efficient scanning of diverse peptide-MHC complexes on the surface of cells and also makes TCRs inherently crossreactive towards different peptides bound by the same MHC.

    View details for DOI 10.1038/nature00920

    View details for Web of Science ID 000177162800045

    View details for PubMedID 12152083

  • Restricted islet-cell reactive T cell repertoire of early pancreatic islet infiltrates in NOD mice PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Baker, F. J., Lee, M., Chien, Y. H., Davis, M. M. 2002; 99 (14): 9374-9379


    The mechanisms responsible for initiating autoimmune diabetes remain obscure. Here, we describe a method for identifying both the alpha- and beta-chains of the T cell receptor (TCR) from individual pancreatic islet-infiltrating T cells at the earliest stages of disease in nonobese diabetic mice (NOD). Analysis of the TCR repertoire of these early islet infiltrates reveals enrichment for a small subset of TCR sequences. Reconstitution of these TCR in vitro demonstrates that these receptors confer reactivity to islet cells but not to the well characterized autoantigens, glutamic acid decarboxylase (GAD65) and insulin. Thus, autoimmune diabetes in NOD may be initiated by a limited number of antigens distinct from GAD65 and insulin.

    View details for DOI 10.1073/pnas.142284899

    View details for Web of Science ID 000176775400055

    View details for PubMedID 12082183

    View details for PubMedCentralID PMC123148

  • Imaging synapse formation during thymocyte selection: Inability of CD3 zeta to form a stable central accumulation during negative selection IMMUNITY Richie, L. I., Ebert, P. J., Wu, L. C., Krummel, M. F., Owen, J. J., Davis, M. M. 2002; 16 (4): 595-606


    TCR signaling can result in cell fates ranging from activation to tolerance to apoptosis. Organization of molecules in an "immunological synapse" between mature T cells and APCs correlates with the strength of TCR signaling. To investigate synapse formation during thymic selection, we have established a reaggregate system in which molecular recruitment of GFP fusion proteins to thymocyte:stromal cell interfaces can be visualized in real time. We demonstrate that negative selection is associated with efficient conjugate formation and rapid recruitment of p56(lck) and CD3zeta to an immunological synapse. Interestingly, CD3zeta-GFP does not accumulate at the center of the synapse, as in mature T cells, but at the periphery across a wide range of ligand densities. This implicates differences in synapse geometry in initiation of alternate signals downstream of the TCR.

    View details for Web of Science ID 000175109600010

    View details for PubMedID 11970882

  • Costimulation and endogenous MHC ligands contribute to T cell recognition NATURE IMMUNOLOGY Wulfing, C., Sumen, C., Sjaastad, M. D., Wu, L. C., Dustin, M. L., Davis, M. M. 2002; 3 (1): 42-47


    To initiate an immune response, key receptor-ligand pairs must cluster in "immune synapses" at the T cell-antigen-presenting cell (APC) interface. We visualized the accumulation of a major histocompatibility complex (MHC) class II molecule, I-E(k), at a T cell-B cell interface and found it was dependent on both antigen recognition and costimulation. This suggests that costimulation-driven active transport of T cell surface molecules helps to drive immunological synapse formation. Although only agonist peptide-MHC class II (agonist pMHC class II) complexes can initiate T cell activation, endogenous pMHC class II complexes also appeared to accumulate. To test this directly, we labeled a "null" pMHC class II complex and found that, although it lacked major TCR contact residues, it could be driven into the synapse in a TCR-dependent manner. Thus, low-affinity ligands can contribute to synapse formation and T cell signaling.

    View details for Web of Science ID 000173148700013

    View details for PubMedID 11731799

  • Attributes of gamma delta intraepithelial lymphocytes as suggested by their transcriptional profile PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Fahrer, A. M., Konigshofer, Y., Kerr, E. M., Ghandour, G., Mack, D. H., DAVIS, M. M., Chien, Y. H. 2001; 98 (18): 10261-10266


    gammadelta T lymphocytes in the intestinal intraepithelial layer (gammadelta IELs) are thought to contribute to immune competence, but their actual function remains poorly understood. Here we used DNA microarrays to study the gene expression profile of gammadelta IELs in a Yersinia infection system to better define their roles. To validate this approach, mesenteric lymph node CD8(+) alphabeta T cells were similarly analyzed. The transcription profiles show that, whereas lymph node CD8(+) alphabeta T cells must be activated to become cytotoxic effectors, gammadelta IELs are constitutively activated and appear to use different signaling cascades. Our data suggest that gammadelta IELs may respond efficiently to a broad range of pathological situations irrespective of their diverse T cell antigen receptor repertoire. gammadelta IELs may modulate local immune responses and participate in intestinal lipid metabolism, cholesterol homeostasis, and physiology. This study provides a strong basis for further investigations of the roles of these cells as well as mucosal immune defense in general.

    View details for Web of Science ID 000170738000045

    View details for PubMedID 11526237

  • Altered peptide ligand vaccination with Flt3 ligand expanded dendritic cells for tumor immunotherapy PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Fong, L., Hou, Y. F., Rivas, A., Benike, C., Yuen, A., Fisher, G. A., DAVIS, M. M., Engleman, E. G. 2001; 98 (15): 8809-8814


    Most tumor-associated antigens represent self-proteins and as a result are poorly immunogenic due to immune tolerance. Here we show that tolerance to carcinoembryonic antigen (CEA), which is overexpressed by the majority of lethal malignancies, can be reversed by immunization with a CEA-derived peptide. This peptide was altered to make it a more potent T cell antigen and loaded onto dendritic cells (DCs) for delivery as a cellular vaccine. Although DCs are rare in the blood, we found that treatment of advanced cancer patients with Flt3 ligand, a hematopoietic growth factor, expanded DCs 20-fold in vivo. Immunization with these antigen-loaded DCs induced CD8 cytotoxic T lymphocytes that recognized tumor cells expressing endogenous CEA. Staining with peptide-MHC tetramers demonstrated the expansion of CD8 T cells that recognize both the native and altered epitopes and possess an effector cytotoxic T lymphocyte phenotype (CD45RA(+)CD27(-)CCR7(-)). After vaccination, two of 12 patients experienced dramatic tumor regression, one patient had a mixed response, and two had stable disease. Clinical response correlated with the expansion of CD8 tetramer(+) T cells, confirming the role of CD8 T cells in this treatment strategy.

    View details for Web of Science ID 000169967000107

    View details for PubMedID 11427731

  • A kinetic window constricts the T cell receptor repertoire in the thymus IMMUNITY Savage, P. A., Davis, M. M. 2001; 14 (3): 243-252


    To characterize the ligand binding properties of a naive T cell repertoire capable of responding to a foreign antigen, we analyzed T cell populations from T cell receptor (TCR) beta transgenic mice using a novel, single cell peptide/major histocompatibility complex (MHC) tetramer dissociation assay. The largely CD4+CD8(-/low) antigen-specific thymocyte repertoire exhibited a broad, bimodal distribution of tetramer binding half-lives (t(1/2)s), with a significant underrepresentation in the intermediate half-life range in which the majority of the peripheral repertoire lies. Thus, cells with the potential to bind foreign antigen with the lowest and highest stability are likely to be selectively removed from the repertoire prior to their establishment in the periphery. These studies provide direct evidence that thymic selection biases the naive peripheral T cell repertoire toward TCR-ligand interactions that fall within a moderate half-life "window."

    View details for Web of Science ID 000167959500004

    View details for PubMedID 11290334

  • A kinetic window shapes the T cell receptor repertoire in the thymus Immunity M.M. Davis., Savage, P.A. 2001
  • The immunological synapse ANNUAL REVIEW OF IMMUNOLOGY Bromley, S. K., Burack, W. R., Johnson, K. G., SOMERSALO, K., Sims, T. N., Sumen, C., DAVIS, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 2001; 19: 375-396


    The adaptive immune response is initiated by the interaction of T cell antigen receptors with major histocompatibility complex molecule-peptide complexes in the nanometer scale gap between a T cell and an antigen-presenting cell, referred to as an immunological synapse. In this review we focus on the concept of immunological synapse formation as it relates to membrane structure, T cell polarity, signaling pathways, and the antigen-presenting cell. Membrane domains provide an organizational principle for compartmentalization within the immunological synapse. T cell polarization by chemokines increases T cell sensitivity to antigen. The current model is that signaling and formation of the immunological synapse are tightly interwoven in mature T cells. We also extend this model to natural killer cell activation, where the inhibitory NK synapse provides a striking example in which inhibition of signaling leaves the synapse in its nascent, inverted state. The APC may also play an active role in immunological synapse formation, particularly for activation of naïve T cells.

    View details for Web of Science ID 000168234600014

    View details for PubMedID 11244041

  • Direct functional analysis of epitope-specific CD8+ T cells in peripheral blood VIRAL IMMUNOLOGY He, X. S., Rehermann, B., Boisvert, J., Mumm, J., Maecker, H. T., Roederer, M., Wright, T. L., Maino, V. C., DAVIS, M. M., Greenberg, H. B. 2001; 14 (1): 59-69


    The functional status of virus-specific CD8+ T cells is important for the outcome and the immunopathogenesis of viral infections. We have developed an assay for the direct functional analysis of antigen-specific CD8+ T cells, which does not require prolonged in vitro cultivation and amplification of T cells. Whole blood samples were incubated with peptide antigens for <5 h, followed by staining with peptide-MHC tetramers to identify epitope-specific T cells. The cells were also stained for the activation marker CD69 or for the production of cytokines such as interferon-gamma (IFNgamma) or tumor necrosis factor-alpha (TNFalpha). With the combined staining with tetramer and antibodies to CD69 or cytokines the number of antigen-specific CD8+ T cells as well as the functional response of each individual cell to the cognate antigen can be determined in a single experiment. Virus-specific CD8+ T cells that are nonfunctional, as well as those that are functional under the same stimulating conditions can be simultaneously detected with this assay, which is not possible by using other T-cell functional assays including cytotoxicity assay, intracellular cytokine staining, and enzyme-linked immunospot (ELISPOT) assay.

    View details for Web of Science ID 000167575500005

    View details for PubMedID 11270597

  • Thirty-six views of T-cell recognition PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES Krummel, M., Wulfing, C., Sumen, C., DAVIS, M. M. 2000; 355 (1400): 1071-1076


    While much is known about the signalling pathways within lymphocytes that are triggered during activation, much less is known about how the various cell surface molecules on T cells initiate these events. To address this, we have focused on the primary interaction that drives T-cell activation, namely the binding of a particular T-cell receptor (TCR) to peptide-MHC ligands, and find a close correlation between biological activity and off-rate; that is, the most stimulatory TCR ligands have the slowest dissociation rates. In general, TCRs from multiple histocompatibility complex (MHC) class-II-restricted T cells have half-lives of 1-11s at 25 degrees C, a much narrower range than found with antibodies and suggesting a strong selection for an optimum dissociation rate. TCR ligands with even faster dissociation rates tend to be antagonists. To observe the effects of these different ligands in their physiological setting, we made gene fusions of various molecules with green fluorescent protein (GFP), transfected them into the relevant lymphocytes, and observed their movements during T-cell recognition using multicolour video microscopy. We find that clustering of CD3zeta-GFP and CD4-GFP on the Tcell occurs concomitantly or slightly before the first rise in calcium by the T cell, and that various GFP-labelled molecules on the B-cell side cluster shortly thereafter (ICAM-1, class II MHC, CD48), apparently driven byT-cell molecules. Most of this movement towards the interface is mediated by signals through the co-stimulatory receptors, CD28 and LFA-1, and involves myosin motors and the cortical actin cytoskeleton. Thus, we have proposed that the principal mechanism by which co-stimulation enhances T-cell responsiveness is by increasing the local density of T-cell activation molecules, their ligands and their attendant signalling apparatus. In collaboration with Michael Dustin and colleagues, we have also found that the formation and stability of the TCR-peptide-MHC cluster at the centre of the interaction cap between T and B cells is highly dependent on the dissociation rate of the TCR and its ligand. Thus, we are able to link this kinetic parameter to the formation of a cell surface structure that is linked to and probably causal with respect to T-cell activation.

    View details for Web of Science ID 000089354600009

    View details for PubMedID 11186308

  • The vav exchange factor is an essential regulator in actin-dependent receptor translocation to the lymphocyte-antigen-presenting cell interface PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wulfing, C., Bauch, A., Crabtree, G. R., DAVIS, M. M. 2000; 97 (18): 10150-10155


    During the interaction of a T cell with an antigen-presenting cell (APC), several receptor ligand pairs, including the T cell receptor (TCR)/major histocompatibility complex (MHC), accumulate at the T cell/APC interface in defined geometrical patterns. This accumulation depends on a movement of the T cell cortical actin cytoskeleton toward the interface. Here we study the involvement of the guanine nucleotide exchange factor vav in this process. We crossed 129 vav(-/-) mice with B10/BR 5C.C7 TCR transgenic mice and used peptide-loaded APCs to stimulate T cells from the offspring. We found that the accumulation of TCR/MHC at the T cell/APC interface and the T cell actin cytoskeleton rearrangement were clearly defective in these vav(+/-) mice. A comparable defect in superantigen-mediated T cell activation of T cells from non-TCR transgenic 129 mice was also observed, although in this case it was more apparent in vav(-/-) mice. These data indicate that vav is an essential regulator of cytoskeletal rearrangements during T cell activation.

    View details for Web of Science ID 000089067500061

    View details for PubMedID 10963677

  • Differential clustering of CD4 and CD3 zeta during T cell recognition SCIENCE Krummel, M. F., Sjaastad, M. D., Wulfing, C., Davis, M. M. 2000; 289 (5483): 1349-1352


    Whereas T helper cells recognize peptide-major histocompatibility complex (MHC) class II complexes through their T cell receptors (TCRs), CD4 binds to an antigen-independent region of the MHC. Using green fluorescent protein-tagged chimeras and three-dimensional video microscopy, we show that CD4 and TCR-associated CD3zeta cluster in the interface coincident with increases in intracellular calcium. Signaling-, costimulation-, and cytoskeleton-dependent processes then stabilize CD3zeta in a single cluster at the center of the interface, while CD4 moves to the periphery. Thus, the CD4 coreceptor may serve primarily to "boost" recognition of ligand by the TCR and may not be required once activation has been initiated.

    View details for Web of Science ID 000088942400038

    View details for PubMedID 10958781

  • Diversity in the CDR3 region of V-H is sufficient for most antibody specificities IMMUNITY Xu, J. L., Davis, M. M. 2000; 13 (1): 37-45


    All rearranging antigen receptor genes have one or two highly diverse complementarity determining regions (CDRs) among the six that typically form the ligand binding surface. We report here that, in the case of antibodies, diversity at one of these regions, CDR3 of the V(H) domain, is sufficient to permit otherwise identical IgM molecules to distinguish between a variety of hapten and protein antigens. Furthermore, we find that somatic mutation can allow such antibodies to achieve surprisingly high affinities. These results are consistent with a model in which the highly diverse CDR3 loops are the key determinant of specificity in antigen recognition in both T cell receptors (TCR) and antibodies, whereas the germline-encoded CDR1 and CDR2 sequences are much more cross-reactive.

    View details for Web of Science ID 000088463600005

    View details for PubMedID 10933393

  • Determination of the relationship between T cell responsiveness and the number of MHC-peptide complexes using specific monoclonal antibodies JOURNAL OF IMMUNOLOGY Reay, P. A., Matsui, K., Haase, K., Wulfing, C., Chien, Y. H., DAVIS, M. M. 2000; 164 (11): 5626-5634


    We describe the generation of three mAbs that recognize the complex of the class II MHC molecule IEk bound to a peptide derived from the carboxyl terminus of moth cytochrome c (residues 95-103). Reactivities of these mAbs are sensitive to single alterations in the sequence of both helices of the MHC molecule and to the bound peptide. The epitopes of these reagents are distinct but overlap substantially. One of these mAbs specifically blocks lymphokine release by T cells responsive to this complex but not others. We have used another to examine how the number of complexes on an APC is related to its ability to stimulate T cells. We find that 200-400 complexes per cell are necessary and sufficient to induce a degree of stimulation, whereas maximum stimulation is achieved only if more than 5000 complexes are present. The analysis indicates that T cell activation is a stochastic process.

    View details for Web of Science ID 000087154800011

    View details for PubMedID 10820237

  • Kinetics of peptide binding to the class II MHC protein I-E BIOCHEMISTRY Kasson, P. M., Rabinowitz, J. D., Schmitt, L., DAVIS, M. M., McConnell, H. M. 2000; 39 (5): 1048-1058


    Class II MHC glycoproteins bind short (7-25 amino acid) peptides in an extended type II polyproline-like conformation and present them for immune recognition. Because empty MHC is unstable, measurement of the rate of the second-order reaction between peptide and MHC is challenging. In this report, we use dissociation of a pre-bound peptide to generate the active, peptide-receptive form of the empty class II MHC molecule I-Ek. This allows us to measure directly the rate of reaction between active, empty I-Ek and a set of peptides that vary in structure. We find that all peptides studied, despite having highly variable dissociation rates, bind with similar association rate constants. Thus, the rate-limiting step in peptide binding is minimally sensitive to peptide side-chain structure. An interesting complication to this simple model is that a single peptide can sometimes bind to I-Ek in two kinetically distinguishable conformations, with the stable peptide-MHC complex isomer forming much more slowly than the less-stable one. This demonstrates that an additional free-energy barrier limits the formation of certain specific MHC-peptide complex conformations.

    View details for Web of Science ID 000085172900024

    View details for PubMedID 10653650

  • The use of HLA A2,1/p53 peptide tetramers to visualize the impact of self tolerance on the TCR repertoire JOURNAL OF IMMUNOLOGY Hernandez, J., Lee, P. P., DAVIS, M. M., Sherman, L. A. 2000; 164 (2): 596-602


    p53 is an attractive target for cancer immunotherapy since it is overexpressed in half of all tumors. However, it is also expressed in normal lymphoid tissue, and self tolerance leaves a p53-specific repertoire purged of high avidity CTL. To better understand the mechanism of tolerance and the basis for such low avidity interaction, p53-specific CTL from p53 deficient (p53-) and sufficient (p53+) A2.1/Kb transgenic mice were compared with respect to their ability to bind HLA-A2.1 tetramers containing cognate murine p53 peptide Ag, p53 261-269. Since the murine CD8 molecule cannot interact with human HLA-A2.1, this tests the ability of the TCR to bind the A2.1/peptide complex tetramer. CTL from p53- mice demonstrated strong binding of such A2.1/p53 261-269 tetramers; however, the CTL from tolerant p53+ mice were devoid of tetramer-binding CD8+ T cells. Examination of TCR expression at the clonal level revealed that CTL from p53+ and p53- mice each expressed comparable levels of the p53-specific TCR. These results indicate that normal expression of p53 promotes elimination of T cells expressing TCRs with sufficient affinity to achieve stable binding of the A2.1/p53 261-269 tetramers.

    View details for Web of Science ID 000084708600009

    View details for PubMedID 10623800

  • How to ask questions (in 10 easy steps) Current biology : CB Davis, M. M. 2000; 10 (21): R771

    View details for PubMedID 11084345

  • Differential Clustering of CD4 and CD3z during T Cell Recognition Science M.M. Davis., Krummel, M.F., M. Sjaastad, C. W_lfing 2000
  • Thermodynamics of T cell receptor binding to peptide-MHC: Evidence for a general mechanism of molecular scanning PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA BONIFACE, J. J., Reich, Z., Lyons, D. S., Davis, M. M. 1999; 96 (20): 11446-11451


    Antigen-dependent activation of T lymphocytes requires T cell receptor (TCR)-mediated recognition of specific peptides, together with the MHC molecules to which they are bound. To achieve this recognition in a reasonable time frame, the TCR must scan and discriminate rapidly between thousands of MHC molecules differing from each other only in their bound peptides. Kinetic analysis of the interaction between a TCR and its cognate peptide-MHC complex indicates that both association and dissociation depend heavily on the temperature, indicating the presence of large energy barriers in both phases. Thermodynamic analysis reveals changes in heat capacity and entropy that are characteristic of protein-ligand associations in which local folding is coupled to binding. Such an "induced-fit" mechanism is characteristic of sequence-specific DNA-binding proteins that must also recognize specific ligands in the presence of a high background of competing elements. Here, we propose that induced fit may endow the TCR with its requisite discriminatory capacity and suggest a model whereby the loosely structured antigen-binding loops of the TCR rapidly explore peptide-MHC complexes on the cell surface until some critical structural complementarity is achieved through localized folding transitions. We further suggest that conformational changes, implicit in this model, may also propagate beyond the TCR antigen-binding site and directly affect self-association of ligated TCRs or TCR-CD3 interactions required for signaling.

    View details for Web of Science ID 000082868500095

    View details for PubMedID 10500196

  • Negative selection of T cells occurs throughout thymic development JOURNAL OF IMMUNOLOGY Baldwin, K. K., Trenchak, B. P., Altman, J. D., Davis, M. M. 1999; 163 (2): 689-698


    Thymic positive and negative selections govern the development of a self-MHC-reactive, yet self-tolerant, T cell repertoire. Whether these processes occur independently or sequentially remains controversial. To investigate these issues, we have employed tetrameric peptide-MHC complexes to fluorescently label and monitor polyclonal populations of thymocytes that are specific for moth cytochrome c (MCC)/I-Ek. In TCR beta mice tetramer-positive thymocytes are detectable even in the most immature TCR-expressing cells. In the presence of MCC peptide, thymocytes that bind strongly to MCC/I-Ek tetramers are deleted earlier in development and more extensively than cells that bind weakly. This negative selection of the MCC/I-Ek-specific cells occurs continuously throughout development and before any evidence of positive selection. Thus, positive and negative selections are independent processes that need not occur sequentially.

    View details for Web of Science ID 000081360800021

    View details for PubMedID 10395659

  • The immunological synapse: A molecular machine controlling T cell activation SCIENCE Grakoui, A., Bromley, S. K., Sumen, C., DAVIS, M. M., Shaw, A. S., Allen, P. M., Dustin, M. L. 1999; 285 (5425): 221-227


    The specialized junction between a T lymphocyte and an antigen-presenting cell, the immunological synapse, consists of a central cluster of T cell receptors surrounded by a ring of adhesion molecules. Immunological synapse formation is now shown to be an active and dynamic mechanism that allows T cells to distinguish potential antigenic ligands. Initially, T cell receptor ligands were engaged in an outermost ring of the nascent synapse. Transport of these complexes into the central cluster was dependent on T cell receptor-ligand interaction kinetics. Finally, formation of a stable central cluster at the heart of the synapse was a determinative event for T cell proliferation.

    View details for Web of Science ID 000081346000032

    View details for PubMedID 10398592

  • Catalysis of peptide dissociation from class II MHC-peptide complexes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Schmitt, L., Kratz, J. R., DAVIS, M. M., McConnell, H. M. 1999; 96 (12): 6581-6586


    Certain peptides such as dynorphin A [dynA-(1-13)] enhance the release of antigenic peptides bound to class II MHC molecules at neutral pH. This enhanced release has been termed push off. Previous work has shown that the antigenic pigeon cytochrome c peptide PCC-(89-104) has at least two conformational isomers when bound to the class II MHC protein I-Ek. We have accordingly studied the push off of PCC-(89-104) from the complex PCC-(89-104)/I-Ek to see whether these isomeric conformations are distinguished by the push-off effect. A comparison of the association and dissociation kinetics of PCC-(89-104)/I-Ek in the presence of dynA-(1-13) shows that dynA-(1-13) does not simply replace PCC-(89-104) but rather acts catalytically. The major product is peptide-free I-Ek, which is receptive to further peptide binding. Evidence is presented that a two peptide-one MHC complex is formed in solution. This ternary complex represents the first step of the mechanism of push off. 19F NMR data are presented that indicate that dynA-(1-13) interacts specifically with only one of the two isomeric complexes of PCC-(89-104) and I-Ek. A push-off mechanism is proposed in which dynA-(1-13) binds outside the peptide binding groove. In a second step, the dissociation of one of the two isomers is specifically enhanced. Thus the push-off effect may be useful for identifying conformational isomers and for separating them.

    View details for Web of Science ID 000080842200003

    View details for PubMedID 10359754

  • Characterization of circulating T cells specific for tumor-associated antigens in melanoma patients NATURE MEDICINE Lee, P. P., Yee, C., Savage, P. A., Fong, L., Brockstedt, D., Weber, J. S., Johnson, D., Swetter, S., Thompson, J., Greenberg, P. D., Roederer, M., DAVIS, M. M. 1999; 5 (6): 677-685


    We identified circulating CD8+ T-cell populations specific for the tumor-associated antigens (TAAs) MART-1 (27-35) or tyrosinase (368-376) in six of eleven patients with metastatic melanoma using peptide/HLA-A*0201 tetramers. These TAA-specific populations were of two phenotypically distinct types: one, typical for memory/effector T cells; the other, a previously undescribed phenotype expressing both naive and effector cell markers. This latter type represented more than 2% of the total CD8+ T cells in one patient, permitting detailed phenotypic and functional analysis. Although these cells have many of the hallmarks of effector T cells, they were functionally unresponsive, unable to directly lyse melanoma target cells or produce cytokines in response to mitogens. In contrast, CD8+ T cells from the same patient were able to lyse EBV-pulsed target cells and showed robust allogeneic responses. Thus, the clonally expanded TAA-specific population seems to have been selectively rendered anergic in vivo. Peptide stimulation of the TAA-specific T-cell populations in other patients failed to induce substantial upregulation of CD69 expression, indicating that these cells may also have functional defects, leading to blunted activation responses. These data demonstrate that systemic TAA-specific T-cell responses can develop de novo in cancer patients, but that antigen-specific unresponsiveness may explain why such cells are unable to control tumor growth.

    View details for Web of Science ID 000080823300037

    View details for PubMedID 10371507

  • Quantitative analysis of hepatitis C virus-specific CD8(+) T cells in peripheral blood and liver using peptide-MHC tetramers PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA He, X. S., Rehermann, B., Lopez-Labrador, F. X., Boisvert, J., Cheung, R., Mumm, J., Wedemeyer, H., Berenguer, M., Wright, T. L., DAVIS, M. M., Greenberg, H. B. 1999; 96 (10): 5692-5697


    It is believed that the hepatitis C virus (HCV)-specific CD8(+) cytotoxic T lymphocytes (CTLs) play a role in the development of liver cell injury and in the clearance of the virus. To develop a direct binding assay for HCV-specific CTLs, we generated two peptide-MHC tetramers by using the recombinant HLA A2.1 molecule and A2-restricted T cell epitopes of the HCV NS3 protein. With these reagents we are able to detect specific CD8(+) cells in the blood of 15 of 20 HLA-A2(+), HCV-infected patients, at a frequency ranging from 0.01% to 1.2% of peripheral CD8(+) T cells. Phenotypic analysis of these specific cells indicated that there is a significant variation in the expression of the CD45 isoforms and CD27 in different patients. A 6-hour incubation of one patient's blood with NS3 peptides resulted in the activation of the epitope-specific CD8(+) cells, as indicated by their expression of CD69 and IFN-gamma. We also detected NS3-specific CD8(+) T cells in the intrahepatic lymphocyte population isolated from liver biopsies of two HCV-infected patients. The frequency of these specific CD8(+) cells in the liver was 1-2%, at least 30-fold higher than in the peripheral blood. All of the intrahepatic NS3-specific CD8(+) T cells were CD69(+), suggesting that they were activated CTLs. Direct quantitation and characterization of HCV-specific CTLs should extend our understanding of the immunopathogenesis and the mechanism of clearance or persistence of HCV.

    View details for Web of Science ID 000080246500068

    View details for PubMedID 10318946

  • A kinetic basis for T cell receptor repertoire selection during an immune response IMMUNITY Savage, P. A., BONIFACE, J. J., Davis, M. M. 1999; 10 (4): 485-492


    The basis for T cell antigen receptor (TCR) repertoire selection upon repeated antigenic challenge is unclear. We evaluated the avidity and dissociation kinetics of peptide/major histocompatibility complex (MHC) tetramer binding to antigen-specific T lymphocytes isolated following primary or secondary immunization. The data reveal a narrowing of the secondary repertoire relative to the primary repertoire, largely resulting from the loss of cells expressing TCRs with the fastest dissociation rates for peptide/MHC binding. In addition, T cells in the secondary response express TCRs of higher average affinity for peptide/MHC than cells in the primary response. These results provide a link between the kinetics and affinity of TCR-peptide/MHC interactions and TCR sequence selection during the course of an immune response.

    View details for Web of Science ID 000079989600009

    View details for PubMedID 10229191

  • Visualizing lymphocyte recognition IMMUNOLOGY AND CELL BIOLOGY Wulfing, C., Chien, Y. H., DAVIS, M. M. 1999; 77 (2): 186-187


    Studies of T cell recognition have entered new territory now that some of the basic issues of genetics, biochemistry and structure have been addressed, at least in outline form. In the present work, the focus is on a new aspect of T cell recognition that goes beyond classical biochemistry to ask, how to TCR and other cell surface molecules cooperate to initiate and control recognition?'

    View details for Web of Science ID 000079676100012

    View details for PubMedID 10234556

  • Conformational isomers of a class II MHC-peptide complex in solution JOURNAL OF MOLECULAR BIOLOGY Schmitt, L., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1999; 286 (1): 207-218


    A number of kinetic measurements of peptide dissociation from class II MHC-peptide complexes provide compelling evidence for the existence of conformational isomers in solution. There is evidence that T-lymphocytes can distinguish such isomers. However, virtually nothing is known about the structure of these isomers. Accordingly, we have investigated a water-soluble version of the murine class II MHC molecule I-Ek complexed with an antigenic peptide derived from pigeon cytochrome c residues 89-104 (PCC) by 19F-NMR. Two fluorine labels were placed on the PCC peptide; one fluorine label was placed at a MHC contact site, the other at a position involved in T-cell receptor (TCR) recognition. Introduction of these labels did not alter the observed kinetics of the PCC/I-Ek complex. The NMR data show two conformational isomers of this immunogenic complex. The presence of conformational isomers at a TCR contact site suggests that these structures may be recognized differently by the TCR. The agreement between the dissociation kinetics and the 19F-NMR data demonstrate that kinetic heterogeneity is correlated with structural counterparts observed by NMR. Dissociations in the presence of dimethyl sulfoxide were used to show that the rate of interconversion of these conformational isomers at pH 7.0 is low, with a lifetime on the order of hours or more. Modification of a peptide residue of PCC occupying the minor MHC binding pocket P6 alters the 19F-NMR spectra of both labels. This demonstrates that distant changes of amino acid residues can influence the conformation of the whole antigenic peptide inside the MHC binding cleft.

    View details for Web of Science ID 000078702000016

    View details for PubMedID 9931260

  • Frequency of class I HLA-restricted anti-HIV CD8(+) T cells in individuals receiving highly active antiretroviral therapy (HAART) JOURNAL OF IMMUNOLOGY Gray, C. M., Lawrence, J., Schapiro, J. M., Altman, J. D., Winters, M. A., Crompton, M., Loi, M., Kundu, S. K., DAVIS, M. M., Merigan, T. C. 1999; 162 (3): 1780-1788


    Peptide/MHC tetrameric complexes were used to enumerate the frequency of HLA class I-restricted epitope-specific CD8+ T cells in 18 HLA-A*0201 HIV type 1-infected asymptomatic patients. HLA-A*0201 molecules were complexed to HIV Gag p17 (amino acids 77-85) and reverse transcriptase (amino acids 464-472) peptides, biotinylated, and bound to streptavidin-phycoerythrin to form tetramers. We show in this study that 17 of 18 HIV-1-infected asymptomatic patients have circulating frequencies of 1/50-1/1000 CD8+ T cells that recognize both Gag and Pol CTL epitopes or either epitope alone. The functional nature of these cells is open to interpretation, as we show that despite relatively high frequencies of fresh epitope-specific CD8+ T cells, variant epitope sequences in viral plasma progeny were rare. In addition, the majority of tetramer-positive cells did not display discernible fresh CTL activity; only after restimulation with specific peptide in culture was there an expansion of epitope-specific CD8+ cells, correlating with high CTL activity. These data suggest that fresh tetramer-stained cells probably represent memory precursors; we demonstrate, with the application of highly active antiretroviral therapy, that the interruption of chronic antigenic stimulation causes significant reductions in the frequency of these cells in five of six patients. In conclusion, this study provides evidence that persistently replicating viral populations are probably required to maintain high frequencies of HIV-1 epitope-specific CD8+ T cells in asymptomatic chronically infected individuals

    View details for Web of Science ID 000078261000071

    View details for PubMedID 9973442

  • A T cell receptor-specific blockade of positive selection JOURNAL OF EXPERIMENTAL MEDICINE Baldwin, K. K., REAY, P. A., Wu, L., Farr, A., Davis, M. M. 1999; 189 (1): 13-23


    To investigate the influence of endogenous peptides on the developmental processes that occur during thymocyte selection, we have used monoclonal antibodies that preferentially recognize the major histocompatibility complex (MHC) molecule I-Ek when it is bound to the moth cytochrome c peptide (88-103). One of these antibodies (G35) specifically blocks the positive selection of transgenic thymocytes expressing a T cell receptor that is reactive to this peptide- MHC complex. Furthermore, G35 does not block the differentiation of transgenic T cells bearing receptors for a different I-Ek-peptide complex. This antibody recognizes a subset of endogenous I-Ek-peptide complexes found on a significant fraction of thymic antigen-presenting cells, including cortical and medullary epithelial cells. The sensitivity of G35 to minor alterations in peptide sequence suggests that the thymic peptide-MHC complexes that mediate the positive selection of a particular class II MHC-restricted thymocyte are structurally related to the complexes that can activate it in the periphery.

    View details for Web of Science ID 000078077700002

    View details for PubMedID 9874560

  • Visualizing T-cell recognition 64th Symposia: Signaling and Gene Expression in the Immune System DAVIS, M. M., Wulfing, C., Krummel, M. F., Savage, P. A., Xu, J., Sumen, C., Dustin, M. L., Chien, Y. H. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1999: 243–251

    View details for Web of Science ID 000087225400030

    View details for PubMedID 11232292

  • A receptor/cytoskeletal movement triggered by costimulation during T cell activation SCIENCE Wulfing, C., DAVIS, M. M. 1998; 282 (5397): 2266-2269


    During T cell activation, the engagement of costimulatory molecules is often crucial to the development of an effective immune response, but the mechanism by which this is achieved is not known. Here, it is shown that beads attached to the surface of a T cell translocate toward the interface shortly after the start of T cell activation. This movement appears to depend on myosin motor proteins and requires the engagement of the major costimulatory receptor pairs, B7-CD28 and ICAM-1-LFA-1. This suggests that the engagement of costimulatory receptors triggers an active accumulation of molecules at the interface of the T cell and the antigen-presenting cell, which then increases the overall amplitude and duration of T cell signaling.

    View details for Web of Science ID 000077645800050

    View details for PubMedID 9856952

  • Kinetic isomers of a class II MHC-peptide complex BIOCHEMISTRY Schmitt, L., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1998; 37 (50): 17371-17380


    Class II major histocompatibility (MHC) molecules bind fragments of antigens and present them to T cells. The triggering of the T-cell receptor (TCR) of CD4(+) T-helper cells by these protein-peptide complexes is a key event in the generation of a cellular immune response. In the context of this interaction, it is generally assumed that class II MHC-peptide complexes adopt a single recognition structure at the cell surface. On the other hand, kinetic analysis has revealed that a number of class II MHC-peptide complexes show biphasic dissociation kinetics, indicating the presence of multiple kinetic isomers. Here, we demonstrate that a water-soluble version of the murine class II MHC molecule I-Ek complexed with an antigenic peptide derived from pigeon cytochrome c (PCC) displays monophasic as well as biphasic dissociation kinetics. While a simple monophasic dissociation curve was obtained at neutral pH, the complex showed biphasic dissociation behavior at acidic pH. This shift was independent of the ionic strength of the solution. Moreover, the short-lived isomer could be regenerated from a pool of kinetically homogeneous long-lived complexes. This demonstrates that the isomers interconvert and exist in a pH-sensitive equilibrium. Altering the peptide residue of PCC that occupies the P6 pocket of I-Ek results in a class II MHC-peptide complex that shows only monophasic dissociation, indicating that the glutamine at this position plays a key role in the kinetic heterogeneity of the complex.

    View details for Web of Science ID 000077647400005

    View details for PubMedID 9860852

  • Formation of a highly peptide-receptive state of class II MHC IMMUNITY Rabinowitz, J. D., Vrljic, M., Kasson, P. M., Liang, M. N., Busch, R., BONIFACE, J. J., DAVIS, M. M., McConnell, H. M. 1998; 9 (5): 699-709


    Peptide binding to class II MHC proteins occurs in acidic endosomal compartments following dissociation of class II-associated invariant chain peptide (CLIP). Based on peptide binding both to empty class II MHC and to molecules preloaded with peptides including CLIP, we find evidence for two isomeric forms of empty MHC. One (inactive) does not bind peptide. The other (active) binds peptide rapidly, with k(on) 1000-fold faster than previous estimates. The active isomer can be formed either by slow isomerization of the inactive molecule or by dissociation of a preformed peptide/MHC complex. In the absence of peptide, the active isomer is unstable, rapidly converting to the inactive isomer. These results demonstrate that fast peptide binding is an inherent property of one isomer of empty class II MHC. Dissociation of peptides such as CLIP yields this transient, peptide-receptive isomer.

    View details for Web of Science ID 000077298300012

    View details for PubMedID 9846491

  • Initiation of signal transduction through the T cell receptor requires the peptide multivalent engagement of MHC ligands IMMUNITY BONIFACE, J. J., Rabinowitz, J. D., Wulfing, C., Hampl, J., Reich, Z., Altman, J. D., Kantor, R. M., Beeson, C., McConnell, H. M., Davis, M. M. 1998; 9 (4): 459-466


    While much is known about intracellular signaling events in T cells when T cell receptors (TCRs) are engaged, the mechanism by which signaling is initiated is unclear. We have constructed defined oligomers of soluble antigen-major histocompatibility complex (MHC) molecules, the natural ligands for the TCR. Using these to stimulate specific T cells in vitro, we find that agonist peptide/MHC ligands are nonstimulatory as monomers and minimally stimulatory as dimers. Similarly, a partial-agonist ligand is very weakly active as a tetramer. In contrast, trimeric or tetrameric agonist ligands that engage multiple TCRs for a sustained duration are potent stimuli. Ligand-driven formation of TCR clusters seems required for effective activation and helps to explain the specificity and sensitivity of T cells.

    View details for Web of Science ID 000076680700004

    View details for PubMedID 9806632

  • Differential effect of B lymphocyte-induced maturation protein (Blimp-1) expression on cell fate during B cell development JOURNAL OF EXPERIMENTAL MEDICINE Messika, E. J., Lu, P. S., Sung, Y. J., Yao, T., Chi, J. T., Chien, Y. H., DAVIS, M. M. 1998; 188 (3): 515-525


    The B lymphocyte-induced maturation protein (Blimp-1) upregulates the expression of syndecan-1 and J chain and represses that of c-myc. We have transfected Blimp-1 into two sublines of the BCL1 B cell lymphoma that represent distinct stages of B cell development in secondary lymphoid tissues. After interleukin (IL)-2 and IL-5 stimulation, the BCL1 3B3 cells differentiate into centrocyte-like cells, whereas the BCL1 5B1b cells blast and appear to be blocked at the centroblast stage. This blasting effect and the increase in IgM secretion that follows it can be blocked by a dominant negative form of Blimp-1. At the same time, the ectopic expression of Blimp-1 in these partially activated cells induces an apoptotic response that also can be suppressed by the same dominant negative protein. A similar effect was noticed when Blimp-1 was expressed in the mature L10A and the immature WEHI-231 lines, indicating this may be a general effect at earlier stages of the B cell development, and distinct from the ability of Blimp-1 to induce maturation in late stages of differentiation. Truncation mutants indicate that the induction of the apoptotic response relies mainly on 69 amino acids within Blimp-1's proline-rich domain. We propose that Blimp-1 expression defines a checkpoint beyond which fully activated B cells proceed to the plasma cell stage, whereas immature and partially activated cells are eliminated at this point.

    View details for Web of Science ID 000075300300010

    View details for PubMedID 9687529

  • Induction of rapid T cell activation and tolerance by systemic presentation of an orally administered antigen IMMUNITY Gutgemann, I., Fahrer, A. M., Altman, J. D., DAVIS, M. M., Chien, Y. H. 1998; 8 (6): 667-673


    To understand how orally introduced antigen regulates peripheral immune responses, we fed cytochrome c protein to mice transgenic for the beta chain of a cytochrome c-specific TCR and followed the antigen-specific T cell responses with a cyt c/I-Ek tetramer staining reagent. We find that within 6 hr of cytochrome c administration, antigen-specific systemic T cell activation is induced, and spleen cells gain the ability to stimulate cytochrome c-specific T cell responses. Feeding multiple low doses of cytochrome c down-regulates the systemic immune response, which can be correlated with a reduction of antigen-specific T cells and not with immune deviation. These results suggest that systemic distribution of antigen contributes significantly to oral tolerance induction.

    View details for Web of Science ID 000074396300002

    View details for PubMedID 9655480

  • Visualizing the dynamics of T cell activation: Intracellular adhesion molecule 1 migrates rapidly to the T cell/B cell interface and acts to sustain calcium levels PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Wulfing, C., Sjaastad, M. D., DAVIS, M. M. 1998; 95 (11): 6302-6307


    T cell recognition typically involves both the engagement of a specific T cell receptor with a peptide/major histocompatibility complex (MHC) and a number of accessory interactions. One of the most important interactions is between the integrin lymphocyte function-associated antigen 1 (LFA-1) on the T cell and intracellular adhesion molecule 1 (ICAM-1) on an antigen-presenting cell. By using fluorescence video microscopy and an ICAM-1 fused to a green fluorescent protein, we find that the elevation of intracellular calcium in the T cell that is characteristic of activation is followed almost immediately by the rapid accumulation of ICAM-1 on a B cell at a tight interface between the two cells. This increased density of ICAM-1 correlates with the sustained elevation of intracellular calcium in the T cell, known to be critical for activation. The use of peptide/MHC complexes and ICAM-1 on a supported lipid bilayer to stimulate T cells also indicates a major role for ICAM-1/LFA-1 in T cell activation but, surprisingly, not for adhesion, as even in the absence of ICAM-1 the morphological changes and adhesive characteristics of an activated T cell are seen in this system. We suggest that T cell antigen receptor-mediated recognition of a very small number of MHC/peptide complexes could trigger LFA-1/ICAM-1 clustering and avidity regulation, thus amplifying and stabilizing the production of second messengers.

    View details for Web of Science ID 000073852600081

    View details for PubMedID 9600960

  • Ligand recognition by alpha beta T cell receptors ANNUAL REVIEW OF IMMUNOLOGY Davis, M. M., BONIFACE, J. J., Reich, Z., Lyons, D., Hampl, J., Arden, B., Chien, Y. H. 1998; 16: 523-?


    While still incomplete, the first data concerning the biochemistry of T cell receptor-ligand interactions in cell-free systems seem to have considerable predictive value regarding whether a T cell response is strong or weak or suppressive. This data will help considerably in elucidating the mechanisms behind T cell responsiveness. Also of great interest are the first structures of T cell receptor molecules and, particularly, TCR-ligand complexes. These appear to confirm earlier suggestions of a fixed orientation for TCR engagement with peptide/MHC and should form the basis for understanding higher oligomers, evidence for which has also just emerged. We conclude with an analysis of the highly diverse CDR3 loops found in all antigen receptor molecules and suggest that such regions form the core of both TCR and antibody specificity.

    View details for Web of Science ID 000073129400019

    View details for PubMedID 9597140

  • CD4 augments the response of a T cell to agonist but not to antagonist ligands IMMUNITY Hampl, J., Chien, Y. H., DAVIS, M. M. 1997; 7 (3): 379-385


    The recognition of peptide variants by the T cell receptor (TCR) has revealed a wide range of possible responses. Here, using a series of CD4+ and CD4- variants of the same T cell hybridoma, we find that while the expression of CD4 converts weak agonists into full agonists, none of the antagonist peptides are efficiently recognized as agonists. Furthermore, in antagonist assays, little difference can be seen in the response of CD4+ and CD4- T cells. Together with previous work showing a marked difference in stability between TCR binding to agonist versus antagonist ligands, these data suggest that CD4 engagement occurs after a TCR-peptide/MHC complex has formed and that it requires a certain minimal half-life of the ternary complex to be fully engaged in signaling.

    View details for Web of Science ID A1997XY83000007

    View details for PubMedID 9324358

  • A range of CD4 T cell tolerance: Partial inactivation to organ-specific antigen allows nondestructive thyroiditis or insulitis IMMUNITY Akkaraju, S., Ho, W. Y., Leong, D., Canaan, K., DAVIS, M. M., Goodnow, C. C. 1997; 7 (2): 255-271


    T cell receptor (TCR) transgenic mice specific for hen egg lysozyme (HEL) were crossed with mice expressing HEL on the thyroid epithelium, on pancreatic islet beta cells, or systemically. Depending on the pattern of HEL expression, deletion of double-positive thymocytes ranged from minimal to complete, and peripheral CD4 cells exhibited graded reduction in TCR expression, in vitro responsiveness, and in vivo helper ability. CD4 cells were least tolerant in TCR/thyroid-HEL and TCR/islet-HEL mice, which developed an extensive lymphocytic thyroiditis or insulitis that nevertheless did not eliminate HEL-expressing endocrine cells. Autoreactive CD4 clones thus escape the thymus under a range of circumstances, retain sufficient function to initiate subclinical autoimmune inflammation when self-antigens are concentrated in the thyroid or pancreas, and may regulate progression of subclinical inflammation to destructive autoimmune disease.

    View details for Web of Science ID A1997XT49200009

    View details for PubMedID 9285410

  • Ligand-specific oligomerization of T-cell receptor molecules NATURE Reich, Z., BONIFACE, J. J., Lyons, D. S., Borochov, N., Wachtel, E. J., DAVIS, M. M. 1997; 387 (6633): 617-620


    T cells initiate many immune responses through the interaction of their T-cell antigen receptors (TCR) with antigenic peptides bound to major histocompatibility complex (MHC) molecules. This interaction sends a biochemical signal into the T cell by a mechanism that is not clearly understood. We have used quasielastic light scattering (QELS) to show that, in the presence of MHC molecules bound to a full agonist peptide, TCR/peptide-MHC complexes oligomerize in solution to form supramolecular structures at concentrations near the dissociation constant of the binding reaction. The size of the oligomers is concentration dependent and is calculated to contain two to six ternary complexes for the concentrations tested here. This effect is specific as neither molecule forms oligomers by itself, nor were oligomers observed unless the correct peptide was bound to the MHC. These results provide direct evidence for models of T-cell signalling based on the specific assembly of multiple TCR/peptide-MHC complexes in which the degree of assembly determines the extent and qualitative nature of the transduced signal. They may also explain how T cells maintain sensitivity to antigens present in only low abundance on the antigen-presenting cell.

    View details for Web of Science ID A1997XC52200059

    View details for PubMedID 9177351

  • Kinetics and extent of T cell activation as measured with the calcium signal JOURNAL OF EXPERIMENTAL MEDICINE Wulfing, C., Rabinowitz, J. D., Beeson, C., Sjaastad, M. D., McConnell, H. M., DAVIS, M. M. 1997; 185 (10): 1815-1825


    We have characterized the calcium response of a peptide-major histocompatibility complex (MHC)-specific CD4(+) T lymphocyte line at the single cell level using a variety of ligands, alone and in combination. We are able to distinguish four general patterns of intracellular calcium elevation, with only the most robust correlating with T cell proliferation. Whereas all three antagonist peptides tested reduce the calcium response to an agonist ligand, two give very different calcium release patterns and the third gives none at all, arguing that (a) antagonism does not require calcium release and (b) it involves interactions that are more T cell receptor proximal. We have also measured the time between the first T cell-antigen-presenting cell contact and the onset of the calcium signal. The duration of this delay correlates with the strength of the stimulus, with stronger stimuli giving a more rapid response. The dose dependence of this delay suggests that the rate-limiting step in triggering the calcium response is not the clustering of peptide-MHC complexes on the cell surface but more likely involves the accumulation of some intracellular molecule or complex with a half-life of a few minutes.

    View details for Web of Science ID A1997XB76900013

    View details for PubMedID 9151707

    View details for PubMedCentralID PMC2196319

  • Stability of empty and peptide-loaded class II major histocompatibility complex molecules at neutral and endosomal pH: Comparison to class I proteins PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Reich, Z., Altman, J. D., BONIFACE, J. J., Lyons, D. S., Kozono, H., Ogg, G., Morgan, C., DAVIS, M. M. 1997; 94 (6): 2495-2500


    The structure and thermal stability of empty and peptide-filled forms of the murine class II major histocompatibility complex (MHC) molecule I-E(k) were studied at neutral and mildly acidic pH. The two forms have distinct circular dichroic spectra, suggesting that a conformational change may accompany peptide binding. Thermal stability profiles indicate that binding of peptide significantly increases the thermal stability of the empty heterodimers at both neutral and mildly acidic pH. Free energies calculated from these data provide a direct measure of this stabilization and show that the empty form of I-E(k) is significantly more stable than that of class I MHC proteins. Furthermore, for the two MHC class II proteins that were analyzed (I-E(k) and I-A(d)), thermal stability was not significantly altered by acidification. In contrast, of four class I MHC molecules studied, three have shown a significant loss in complex stability at low pH. The marked stability exhibited by their empty form, as well as their resistance to low pH, as observed in this study, correlate well with the ability of class II MHC molecules to traverse and bind peptides in acidic endosomal vesicles.

    View details for Web of Science ID A1997WP33400074

    View details for PubMedID 9122223

  • T cell receptor biochemistry, repertoire selection and general features of TCR and Ig structure Symposium on the Molecular Basis of Cellular Defence Mechanisms DAVIS, M. M., Lyons, D. S., Altman, J. D., MCHEYZERWILLIAMS, M., Hampl, J., BONIFACE, J. J., Chien, Y., Nossal, Zinkernagel, Miller, Paul, Kirberg, MELCHERS, Mosmann, Goodnow JOHN WILEY & SONS LTD. 1997: 94–104


    T cell recognition is a central event in the development of most immune responses, whether appropriate or inappropriate (i.e. autoimmune). We are interested in reducing T cell recognition to its most elemental components and relating this to biological outcome. In a model system involving a cytochrome c-specific I-Ek restricted T cell receptor (TCR) derived from the 2B4 hybridoma, we have studied the interaction of soluble TCR and soluble peptide-MHC complexes using surface plasmon resonance. We find a striking continuum in which biological activity correlates best with the dissociation rate of the TCR from the peptide-MHC complex. In particular, we have found that weak agonists have significantly faster off-rates than strong agonists and that antagonists have even faster off-rates. This suggests that the stability of TCR binding to a given ligand is critically important with respect to whether the T cell is stimulated, inhibited or remains indifferent. It also suggests that the phenomenon of peptide antagonists might be explained purely by kinetic models and that conformation, either inter- or intramolecular, may not be a factor. We have also studied TCR repertoire selection during the establishment of a cytochrome c response, initially using an anti-TCR antibody strategy, but more recently using peptide-MHC tetramers as antigen-specific staining reagents. These tetramers work well with either class I or class II MHC-specific TCRs and have many possible applications. Lastly, we have also tried to correlate the structural and genetic features of TCRs with their function. Recent data on TCR structure as well as previous findings with antibodies suggest that both molecules are highly dependent on CDR3 length and sequence variation to form specific contacts with antigens. This suggests a general "logic' behind TCR and Ig genetics as it relates to structure and function that helps to explain certain anomalous findings and makes a number of clear predictions.

    View details for Web of Science ID A1997BH80V00009

    View details for PubMedID 9107414

  • Phenotypic analysis of antigen-specific T lymphocytes SCIENCE Altman, J. D., Moss, P. A., Goulder, P. J., Barouch, D. H., MCHEYZERWILLIAMS, M. G., Bell, J. I., McMichael, A. J., DAVIS, M. M. 1996; 274 (5284): 94-96


    Identification and characterization of antigen-specific T lymphocytes during the course of an immune response is tedious and indirect. To address this problem, the peptide-major histocompatability complex (MHC) ligand for a given population of T cells was multimerized to make soluble peptide-MHC tetramers. Tetramers of human lymphocyte antigen A2 that were complexed with two different human immunodeficiency virus (HIV)-derived peptides or with a peptide derived from influenza A matrix protein bound to peptide-specific cytotoxic T cells in vitro and to T cells from the blood of HIV-infected individuals. In general, tetramer binding correlated well with cytotoxicity assays. This approach should be useful in the analysis of T cells specific for infectious agents, tumors, and autoantigens.

    View details for Web of Science ID A1996VK74800054

    View details for PubMedID 8810254

  • Early biochemical signals arise from low affinity TCR-ligand reactions at the cell-cell interface JOURNAL OF EXPERIMENTAL MEDICINE Beeson, C., Rabinowitz, J., Tate, K., Gutgemann, I., Chien, Y. H., Jones, P. P., DAVIS, M. M., McConnell, H. M. 1996; 184 (2): 777-782


    The kinetics of acid release by a mixture of T cells and antigen presenting cells were measured with a microphysiometer during a brief exposure to antigenic peptides. We find that some of the early biochemical events that lead to cellular proliferation cause a specific increase in the rate of acid release. The duration of this increase in acid release reflects the life-time of the peptide-MHC complexes. Peptides that form long-lived complexes produce a response that is stable for more than an hour. Serial TCR engagement is suggested by the observation that the amplitude of this stable response can be rapidly shifted up or down with additional agonist peptide or with antibodies that block T cell receptor binding. Cells briefly exposed to a peptide that forms short-lived peptide-MHC complexes produce a response that decays rapidly as peptide is washed away. A quantitative analysis of the kinetics of this decay in acidification demonstrates that intercellular TCR-ligand reactions are rapid, reversible, and of low apparent affinity with < 20% of peptide-MHC ligand bound to a TCR at any one time. These results demonstrate that the fraction of peptide-MHC ligands bound to TCRs at the cell-cell interface is no higher than anticipated from the affinities observed in solution for isolated TCRs and ligands.

    View details for Web of Science ID A1996VC33700052

    View details for PubMedID 8760833

    View details for PubMedCentralID PMC2192713

  • Altered T cell receptor ligands trigger a subset of early T cell signals IMMUNITY Rabinowitz, J. D., Beeson, C., Wulfing, C., Tate, K., Allen, P. M., DAVIS, M. M., McConnell, H. M. 1996; 5 (2): 125-135


    TCR ligands are complexes of peptides and MHC proteins on the surfaces of APCs. Some of these ligands cause T cell proliferation (agonists), while others block it (antagonists). We compared the acid release, calcium flux, and proliferation response of helper T cells to a variety of ligands. We found that all agonist ligands but not most antagonist ligands trigger acid release, a general indicator of early cellular activation. Only a subset of ligands triggering acid release cause sustained calcium flux, and only a subset of these ligands cause T cell proliferation. Antagonist ligands and anti-CD4 antibodies both effectively block T cell proliferation. However, significantly greater antagonist ligand or antibody concentrations are required to block acid release and initial calcium influx. These data demonstrate a hierarchy of early T cell signaling steps and show that altered TCR ligands can initiate some steps while blocking the completion of others.

    View details for Web of Science ID A1996VE58900003

    View details for PubMedID 8769476

  • A TCR binds to antagonist ligands with lower affinities and faster dissociation rates than to agonists IMMUNITY Lyons, D. S., Lieberman, S. A., Hampl, J., BONIFACE, J. J., Chien, Y. H., Berg, L. J., DAVIS, M. M. 1996; 5 (1): 53-61


    T lymphocyte activation is mediated by the interaction of specific TCR with antigenic peptides bound to MHC molecules. Single amino acid substitutions are often capable of changing the effect of a peptide from stimulatory to antagonistic. Using surface plasmon resonance, we have analyzed the interaction between a complex consisting of variants of the MCC peptide bound to a mouse class II MHC (Ek) and a specific TCR. Using both an improved direct binding method as well as a novel inhibition assay, we show that the affinities of three different antagonist peptide-Ek complexes are approximately 10-50 times lower than that of the wildtype MCC-Ek complex for the TCR, largely due to an increased off-rate. These results suggest that the biological effects of peptide antagonists and partial agonists may be largely based on kinetic parameters.

    View details for Web of Science ID A1996UZ45400006

    View details for PubMedID 8758894

  • Evolving catalysts in real time SCIENCE DAVIS, M. M. 1996; 271 (5252): 1078-1079

    View details for Web of Science ID A1996TW70100026

    View details for PubMedID 8599081

  • Kinetic discrimination in T-cell activation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Rabinowitz, J. D., Beeson, C., Lyons, D. S., DAVIS, M. M., McConnell, H. M. 1996; 93 (4): 1401-1405


    We propose a quantitative model for T-cell activation in which the rate of dissociation of ligand from T-cell receptors determines the agonist and antagonist properties of the ligand. The ligands are molecular complexes between antigenic peptides and proteins of the major histocompatibility complex on the surfaces of antigen-presenting cells. Binding of ligand to receptor triggers a series of biochemical reactions in the T cell. If the ligand dissociates after these reactions are complete, the T cell receives a positive activation signal. However, dissociation of ligand after completion of the first reaction but prior to generation of the final products results in partial T-cell activation, which acts to suppress a positive response. Such a negative signal is brought about by T-cell ligands containing the variants of antigenic peptides referred to as T-cell receptor antagonists. Results of recent experiments with altered peptide ligands compare favorably with T-cell responses predicted by this model.

    View details for Web of Science ID A1996TW69800009

    View details for PubMedID 8643643

    View details for PubMedCentralID PMC39950

  • Directed evolution studies with combinatorial libraries of T4 lysozyme mutants MOLECULAR DIVERSITY PATTEN, P. A., Sonoda, T., DAVIS, M. M. 1996; 1 (2): 97-108


    Gene duplication with divergence to new functions has been an important mechanism in protein evolution. However, the questions of how many new functions can arise from a particular ancestral gene and how many mutational steps are typically required to generate new functions have been difficult to approach experimentally. We have addressed these questions using T4 lysozyme as a model system by synthesizing two combinatorial libraries of > 10(7) mutant T4 lysozyme genes: one library with an average of 14 missense mutations spread throughout the gene and one library in which 13 active site residues have been simultaneously randomized. These libraries were placed under selection in lacZ or pheA deficient strains of E. coli to investigate whether they sample sufficient diversity to contain mutants with acquired beta-galactosidase or prephenate dehydratase activities. Although neither selection yielded T4 lysozyme mutants with these new activities, a novel E. coli locus was cloned that weakly complements these mutants, allowing them to form 1 mm colonies in 4-6 weeks. This growth rate corresponds to a turnover number of approximately 1000 or 25 min-1 for the lacZ or pheA complementation systems, respectively, thus defining the limits of evolved enzymatic activity detectable in these selections. Thus, the strong selective pressure uncovered an unexpected solution to the biochemical blocks, a frequently observed phenomenon in selection experiments. The characterization of this locus will allow its elimination from future E. coli complementation schemes.

    View details for Web of Science ID A1996VV71400003

    View details for PubMedID 9237198

  • Evidence for a conformational change in a class II major histocompatibility complex molecule occurring in the same pH range where antigen binding is enhanced JOURNAL OF EXPERIMENTAL MEDICINE BONIFACE, J. J., Lyons, D. S., Wettstein, D. A., Allbritton, N. L., DAVIS, M. M. 1996; 183 (1): 119-126


    Many class II histocompatibility complex molecules bind antigenic peptides optimally at low pH, consistent with their exposure to antigen in acidic endosomal compartments. While it has been suggested that a partially unfolded state serves as an intermediate involved in peptide binding, very little evidence for such a state has been obtained. In this report, we show that the murine class II molecule IE becomes increasingly less stable to sodium dodecyl sulfate-induced dissociation since the pH is decreased in the same range that enhances antigenic peptide binding. Furthermore, at mildly acidic pH levels, IEk binds the fluorescent dye 1-anilino-naphthalene-8-sulfonic acid (ANS), a probe for exposed nonpolar sites in proteins, suggesting that protonation produces a molten globule-like state. The association of IEk with a single high-affinity peptide had only a small effect in these two assays, indicating that the changes that occur are distal to the peptide-binding groove. Circular dichroism analysis shows that a pH shift from neutral to mildly acidic pH causes subtle changes in the environment of aromatic residues but does not grossly disrupt the secondary structure of IEk. We propose a model in which perturbations in interdomain contacts outside the peptide-binding domain of IEk occur at acidic pH, producing a partially unfolded state that facilitates optimal antigen binding.

    View details for Web of Science ID A1996TP36500013

    View details for PubMedID 8551214

  • Technophilia. Current opinion in immunology Davis, M. M. 1996; 8 (2): 255–56

    View details for PubMedID 8793987

  • CD95 (FAS) DEPENDENT ELIMINATION OF SELF-REACTIVE B-CELLS UPON INTERACTION WITH CD4(+) T-CELLS NATURE Rathmell, J. C., Cooke, M. P., Ho, W. Y., Grein, J., Townsend, S. E., DAVIS, M. M., Goodnow, C. C. 1995; 376 (6536): 181-184


    The recessive mouse mutations lpr and gld create deficiencies in an interacting pair of cell surface molecules, CD95 (Fas/APO-1) and Fas-ligand (FasL), respectively, resulting in autoantibody production resembling human systemic lupus erythematosus. The mechanisms of self-tolerance affected by deficiency in either molecule are not established, but CD95 deficiency both in B cells and in CD4+ T cells recognizing major histocompatibility complex (MHC) class II molecules is required for autoimmunity in lpr mice. Here we track the outcome of in vivo interactions between B cells and CD4+ T cells that recognize a transgene-encoded autoantigen, hen egg lysozyme (HEL), using cells from mice transgenic for immunoglobulin and T-cell receptor (TCR) genes. B cells that had not previously encountered HEL autoantigen (naive cells) were triggered into proliferation and antibody production upon interaction with antigen and HEL-specific CD4+ T cells. By contrast, B cells that had been chronically exposed to HEL during their development and carried desensitized surface immunoglobulin (sIg) antigen receptors (anergic cells) did not produce antibody but instead were eliminated in the presence of HEL-specific CD4+ T cells. CD95-deficient anergic B cells, however, were not eliminated by CD4+ T cells and were triggered to proliferate. These findings identify a novel regulatory step for eliminating autoreactive B cells that seems unique in its dependence on CD95.

    View details for Web of Science ID A1995RJ02800063

    View details for PubMedID 7603571


    View details for Web of Science ID A1995RG98300006

    View details for PubMedID 7576062



    The expansion and contraction of specific helper T cells in the draining lymph nodes of normal mice after injection with antigen was followed. T cell receptors from purified primary and memory responder cells had highly restricted junctional regions, indicating antigen-driven selection. Selection for homogeneity in the length of the third complementarity-determining region (CDR3) occurs before selection for some of the characteristic amino acids, indicating the importance of this parameter in T cell receptor recognition. Ultimately, particular T cell receptor sequences come to predominate in the secondary response and others disappear, showing the selective preservation or expansion of specific T cell clones.

    View details for Web of Science ID A1995QR45400037

    View details for PubMedID 7535476



    Investigations of the I-Ek-restricted, cytochrome c-specific T-cell response in mice show that both T-cell receptor V alpha and V beta CDR3 residues and the use of particular V alpha s and V beta s are necessary for recognition. Data strongly suggest that specific CDR3 residues are important in contacting the peptide. Other experiments indicate that the requirement for V alpha:V beta conservation is not the result of strong TCR-->MHC interactions, as no correlation was found between V beta usage and changes in the alpha-helixes of the I-Ek molecule. It is also apparent that changes in V alpha or V beta usage could be elicited by changes in the side chain size of single amino acids of the antigenic peptides, suggesting that V alpha or V beta conservation is important for peptide recognition, either directly or indirectly. We also show that we can follow the cytochrome c response in vivo even in nontransgenic mice, solely by staining with anti-V region antibodies as well as mAbs directed at the activation markers CD44 and L-selectin.

    View details for Web of Science ID A1995BD46M00001

    View details for PubMedID 7645810

  • T-cell recognition of antigen - A process controlled by transient intermolecular interactions Conference on Receptor Activation by Antigens, Cytokines, Hormones, and Growth Factors BONIFACE, J. J., DAVIS, M. M. NEW YORK ACAD SCIENCES. 1995: 62–69


    As recently as ten years ago, the nature of the T-cell receptor for antigen was a mystery, as was the precise role of histocompatibility molecules in antigen-presentation to T cells. Although T-cell receptors have now been cloned and crystal structures of MHC/peptide molecules exist, our understanding of the parameters that characterize this interaction and other interactions relevant to T-cell immunity are still unclear. The engineering of soluble forms of proteins that mediate T-cell recognition of antigen has allowed the first measurements of these parameters. Interestingly, many of these interactions are of a transient nature, with very rapid off-rates. These data suggest a model whereby highly reversible intermolecular interactions mediate the cell-cell association. The association of adhesion molecules is probably the first step in the stabilization of a conjugate, because they are more numerous than any antigen-specific interaction, followed later by TCR-MHC engagements. Diffusion within each lipid bilayer should allow the congregation of MHC/TCR interactions at the cell-cell interface, with peptide-specific TCR interactions outcompeting irrelevant interactions. Rapid off-rates for both the antigen-specific and nonspecific interactions may be necessary to maintain reversibility, yet allow a rapid approach to equilibrium and consequent signaling when a specific antigen is present or disengagement when it is not.

    View details for Web of Science ID A1995BE40J00007

    View details for PubMedID 7486700



    Recognition by T-cell antigen receptors (TCRs) of processed peptides bound to major histocompatibility complex (MHC) molecules is required for the initiation of most T-lymphocyte responses. Despite the availability of soluble forms of TCRs and MHC heterodimers, this interaction has proven difficult to study directly due to the very low affinity. We report here on the kinetics of TCR binding to peptide/MHC complexes in a cell-free system using surface plasmon resonance. The apparent association rates for the interactions of related peptide/MHC complexes to one such TCR are relatively slow (900-3000 M-1.s-1) and dissociation rates are very fast (0.3-0.06 s-1) with t1/2 of 2-12 s at 25 degrees C. The calculated affinity of the engineered soluble molecules compares well with previously reported competition data for native TCRs or competition data reported here for native peptide/MHC complexes, indicating that these soluble heterodimers bind in the same manner as the original molecules expressed on cells. We also find that the peptide variants which give weaker T-cell stimulatory responses have similar affinities but distinctly faster dissociation rates compared with the original peptide (when loaded onto the MHC molecule) and that this later property may be responsible for their lower activity. This has implications for both downstream signaling events and models of TCR-peptide antagonists.

    View details for Web of Science ID A1994PY29400105

    View details for PubMedID 7809136



    Successful antibody production in vivo depends on a number of cellular events, one of the most important of these being cognate B cell-T cell interaction. To examine this phenomenon in vitro, homogeneous populations of hen egg lysozyme (HEL)-specific small resting B cells and naive CD4+ HEL-specific T cells (derived from immunoglobulin [Ig] and T cell receptor transgenic mice, respectively) were cultured together. On addition of intact HEL protein. HEL-specific B cells increase their expression of activation molecules, including a B7-related protein and CD44, and enlarge into blast cells. Within the same cultures, HEL-specific CD4+ T cells also increase expression of the activation markers CD69 and CD44, enlarge, secrete lymphokines, and proliferate. This response is radiation sensitive, supporting the conclusion that HEL-specific B cells present antigen to and activate the naive T cells. By contrast, when a synthetic peptide fragment of HEL is used to bypass B cell antigen-receptor engagement, the naive T cells enlarge and display activation antigens, but fail to produce lymphokines, proliferate, or promote B cell blastogenesis. Presentation of HEL by tolerant B cells, which are no longer able to signal effectively through their antigen receptors, results in an identical pattern of incomplete T cell activation. Addition of a stimulating anti-CD28 antibody and blocking of CD28 signals with CTLA4/Ig fusion protein both show that complete activation of naive CD4+ T cells depends on the initial induction of B7 and related costimulatory molecules after HEL binding to nontolerant HEL-specific B cells. Thus, in the absence of adequate constimulation from the B cell, naive CD4+ T cells undergo a form of "partial activation" in which they upregulate surface expression of certain T cell activation antigens, but fail to efficiently produce lymphokine and proliferate. This may explain the different conclusions that have been reached regarding the consequences of B cell antigen presentation to T cells, in that the ability of B cells to activate naive CD4+ T cells depends both on their specificity and their activation state.

    View details for Web of Science ID A1994NH65500015

    View details for PubMedID 7909325



    We describe a novel gene, Blimp-1 (for B lymphocyte-induced maturation protein), transcripts of which are rapidly induced during the differentiation of B lymphocytes into immunoglobulin secretory cells and whose expression is characteristic of late B and plasma cell lines. The 856 amino acid open reading frame contains five Krüppel-type zinc finger motifs and proline-rich and acidic regions similar to those of known transcription factors. Serological studies show an approximately 100 kd protein that localizes to the nucleus. Stable or transient transfection of Blimp-1 into B cell lymphoma lines leads to the expression of many of the phenotypic changes associated with B cell differentiation into an early plasma cell stage, including induction of J chain message and immunoglobulin secretion, up-regulation of Syndecan-1, and increased cell size and granularity. Thus, Blimp-1 appears to be a pleiotropic regulatory factor capable of at least partially driving the terminal differentiation of B cells.

    View details for Web of Science ID A1994NH63400014

    View details for PubMedID 8168136



    Substitution with all naturally occurring L-amino acids at each of 11 residues of the IEk-restricted month cytochrome c (93-103) epitope has allowed us to analyze the requirements for MHC binding and T cell recognition to a level of definition not previously possible. Substitutions at only three positions systematically affect MHC binding and three others appear to be the major TCR contacts. Interestingly, changing residues involved in MHC binding can ablate T cell recognition without altering MHC association. Additionally, residue identity at two positions that do not appear critical for MHC binding, nor to be involved in specific T cell contact, nonetheless dramatically affect T cell responses. This suggests that peptides differing only slightly in sequence can have significantly altered conformations within the class II MHC binding groove. We have also developed a simple scoring program that uses the binding data to quantitate how well a given peptide fits the MCC motif. All strongly immunogenic IEk-restricted epitopes score highly (> or = 0.70, where 1.0 is perfect concordance), and only 3% of all potential nonameric peptides in the two main protein sequence databases have scores greater than 0.70. This indicates that the global amino acid replacement approach using a single peptide is an efficient means of deriving binding motifs for a given class II MHC molecule, and should aid in the identification of novel T cell epitopes.

    View details for Web of Science ID A1994NF01800026

    View details for PubMedID 7511662

  • THE NATURE OF MAJOR HISTOCOMPATIBILITY COMPLEX RECOGNITION BY GAMMA-DELTA-T-CELLS CELL SCHILD, H., Mavaddat, N., Litzenberger, C., Ehrich, E. W., DAVIS, M. M., Bluestone, J. A., Matis, L., Draper, R. K., Chien, Y. H. 1994; 76 (1): 29-37


    Despite intensive efforts, the general rules for gamma delta T cell recognition remain undefined. Here, we take advantage of the detailed knowledge of the molecular structure and biosynthetic pathways of major histocompatibility complex (MHC) molecules to analyze the recognition properties of the gamma delta T cell clones LBK5 (specific for the class II MHC, IEk) and G8 (specific for the nonclassical class I MHC, TL10b). We find that the activation of these clones requires neither class I nor class II antigen-processing and that peptides do not confer specificity. Epitope mapping also shows that the topology of gamma delta T cell receptor interaction with the MHC is distinct from that of alpha beta T cells. These results suggest that the molecular nature of gamma delta T cell recognition is fundamentally different than that of alpha beta T cells.

    View details for Web of Science ID A1994MR49500004

    View details for PubMedID 8287478



    In both immunoglobulins (Ig) and T cell receptors (TCR), the rearrangement of V, D, and J region sequence elements during lymphocyte maturation creates an enormous degree of diversity in an area referred to as the complementarity determining region 3 (CDR3) loop. Variations in the particular V, D, and J elements used, precise points of recombination, and random nucleotide addition all lead to extensive length and sequence heterogeneity. CDR3 loops are often critical for antigen binding in Igs and appear to provide the principal peptide binding residues in TCRs. To better understand the physical and selective constraints on these sequences, we have compiled information on CDR3 size variation for Ig H, L (kappa and lambda) and TCR alpha, beta, gamma, and delta. Ig H and TCR delta CDR3s are the most variable in size and are significantly longer than L and gamma chains, respectively. In contrast, TCR alpha and beta chain distributions are highly constrained, with nearly identical average CDR3 lengths, and their length distributions are not altered by thymic selection. Perhaps most significantly, these CDR3 length profiles suggest that gamma/delta TCRs are more similar to Igs than to alpha/beta TCRs in their putative ligand binding region, and thus gamma/delta and alpha/beta T cells may have fundamentally different recognition properties.

    View details for Web of Science ID A1994MP51700033

    View details for PubMedID 8270877



    Recent results have added new information to our understanding of alpha beta T-cell receptor mediated recognition. In particular, we find that the V(D)J junction or 'CDR3' portion of TCR alpha and beta seem most important in contacting peptides bound to MHC molecules, consistent with previous predictions. Surprisingly, these same CDR3-peptide contacts also appear to have a major influence on the TCR-MHC molecule interactions as well.

    View details for Web of Science ID A1993MK79800005

    View details for PubMedID 8305132



    We have compared the contribution of electrostatic forces in the binding of antigenic peptides to the class II MHC molecule, IEk, at weakly acidic (pH 5.4) and neutral (pH 7.5) pH values. The binding of specific moth cytochrome c (MCC) and hemoglobin (Hb) peptides to IEk is very sensitive to ionic strength at pH 7.5 but not at pH 5.4, indicating that the mechanism of peptide binding is pH-dependent. Substitution of the C-terminal Lys in MCC for an Ala residue selectively destroyed peptide binding at neutral pH and increased the dissociation rate at least 30-fold, implicating this residue in the pH-dependent electrostatic interaction. The presence of a C-terminal Lys in many of the peptides that are restricted to IEk suggests that this electrostatic interaction is widely used to bind peptides to this MHC molecule. We also probed the electrostatic environment of the peptide binding groove adjacent to the N-terminus of the bound peptide by rapid-diffusion fluorescence energy transfer using a terbium-labeled MCC peptide. In this region of the peptide binding groove, more negative charge is present at pH 7.5 than at pH 5.4. These findings indicate the importance of MHC carboxylates to the mechanism and specificity of peptide binding. The biological importance of having two distinct mechanisms of peptide binding at different pH may be that it acts to broaden the spectrum of antigenic peptides that can be presented to T-cells.

    View details for Web of Science ID A1993MF82000003

    View details for PubMedID 8218246



    Class II major histocompatibility complex molecules play a major role in the immune response by binding peptide fragments of exogenous antigens and displaying them on the surfaces of antigen-presenting cells, where they can be recognized by T cells. To facilitate structural and functional studies of these molecules, we have produced truncated alpha and beta chains of the murine class II molecule I-Ek in Escherichia coli (Ec-I-Ek) and have developed conditions to fold them in the presence of specific peptides with yields of complex approaching 2%. Reconstitution is specific since only unlabeled peptide known to bind I-Ek compete with biotinylated peptide, as assessed by ELISA. Complexes of the refolded heterodimer (Ec-I-Ek) with either of two different peptide antigens remain associated during nonreducing SDS/PAGE. Immobilized Ec-I-Ek-peptide complexes stimulate lymphokine production by three T-cell clones in an antigen-specific manner with a dose-response relation comparable to previously described soluble I-Ek molecules produced in CHO cells. These results demonstrate that folding of Ek alpha and Ek beta polypeptides does not require any other protein to produce the biologically relevant conformation and that carbohydrate modification of this class II molecule is not necessary for alpha beta T-cell recognition.

    View details for Web of Science ID A1993MF29600121

    View details for PubMedID 8234294



    The progression of T cells from a quiescent or resting state to fully activated, proliferating cells is a crucial step in the initiation of an immune response. We have developed an in vitro system to study the requirements for triggering or hindering this pathway by using naive T cells derived from T-cell antigen receptor alpha beta transgenic animals and peptide-major histocompatibility (MHC) complexes coated on plates. Whereas previously stimulated T cells require only peptide-MHC complexes to produce interleukin 2 (IL-2), naive cells require at least one additional signal, which can be provided by either an anti-CD28 antibody or the protein kinase C stimulant phorbol 12-myristate 13-acetate. In contrast, the anti-CD28 antibody augments IL-2 production by primed T cells but is not required, and phorbol 12-myristate 13-acetate has no discernable effect. Thus we find that native T cells have significantly more stringent requirements for IL-2 production than primed cells and that this fits well with previous observations in other in vitro systems as well as in vivo models of autoimmunity. We also find that peptide-MHC complex stimulation of naive T cells, together with exogenous IL-2, is sufficient to convert these cells to primed T cells in vitro in 2 days, as assayed both by surface marker analysis and stimulation requirements. Taken together with the above results, this suggests that the activation of primary T cells requires at least two signals and that IL-2 produced by naive T cells in vivo may act in an autocrine fashion to allow them to proliferate and differentiate.

    View details for Web of Science ID A1993MA59500049

    View details for PubMedID 8415642



    While recent evidence strongly suggests that the third complementarity determining regions (CDR3s) of T cell receptors (TCRs) directly contact antigenic peptides bound to major histocompatibility complex (MHC) molecules, the nature of other TCR contact(s) is less clear. Here we probe the extent to which different antigens can affect this interaction by comparing the responses of T cells bearing structurally related TCRs to cytochrome c peptides and staphylococcal enterotoxin A (SEA) presented by 13 mutant antigen-presenting cell (APC) lines. Each APC expresses a class II MHC molecule (I-Ek) with a single substitution of an amino acid residue predicted to be located on the MHC alpha helices and to point "up" towards the TCR. We find that very limited changes (even a single amino acid) in either a CDR3 loop of the TCR or in a contact residue of the antigenic peptide can have a profound effect on relatively distant TCR/MHC interactions. The extent of these effects can be as great as that observed between T cells bearing entirely different TCRs and recognizing different peptides. We also find that superantigen presentation entails a distinct mode of TCR/MHC interaction compared with peptide presentation. These data suggest that TCR/MHC contacts can be made in a variety of ways between the same TCR and MHC, with the final configuration apparently dominated by the antigen. These observations suggest a molecular basis for recent reports in which either peptide analogues or superantigens trigger distinct pathways of T cell activation.

    View details for Web of Science ID A1993LP83000037

    View details for PubMedID 8393480



    We have used multiple-amino acid replacement mutagenesis to examine the roles of the TCR homologues of Ig complementarity-determining regions (CDR) and framework sequences in Ag-MHC and Staphylococcus aureus enterotoxin reactivity. In the three cases examined, transplantation of Ig CDR3 homologues between I-Ek-restricted TCR that recognize distinct peptides did not result in transfer of peptide reactivity. Thus the structural context of the CDR3 loops, e.g., both neighboring CDR and the V beta structure, must play a crucial, albeit supporting, role in ligand recognition. The extreme lability of this context was also shown by the fact that transplantation of the CDR1, -2, and -3 loops from the beta chain of 5C.C7 onto a V beta 1 framework failed to transfer MHC-peptide specificity even when the TCR-alpha chains were identical. In contrast, superantigen reactivity was readily transferred in several cases, with CDR2 transplants conferring strong staphylococcal enterotoxin B and A reactivity and CDR1 transplants yielding weak reactivities. This suggests that bacterial (and perhaps other) superantigens bind to many of the same regions of the TCR V beta that are believed to interact with MHC molecules. These regions of V beta may be ideal targets for superantigen binding precisely because they interact with MHC molecules and thus may be relatively conserved.

    View details for Web of Science ID A1993KR93400020

    View details for PubMedID 7680688



    Significant progress has been made on several long-standing issues regarding T-cell receptor mediated recognition of antigen-MHC complexes. For one, early data suggest that the affinity of the T-cell receptor for the peptide-MHC complex is extremely low, with a KD of approximately 10(-4)-10(-5)M, much weaker than most antibody-antigen interactions. The fact that this affinity is lower than that of some T-cell adhesion molecules for their ligands could have important implications for immune surveillance. A second area of interest is the topology of T-cell receptor recognition; evidence of direct contact between the third complementarity determining region of the T-cell receptor and peptide determinants has been obtained. In addition, the orientation of the T-cell receptor with respect to several antigen-MHC complexes has been predicted. They suggest that whereas most or all peptides seem to bind in the same orientation in both class I and class II MHC molecules, the orientation of the T-cell receptor over the peptide-MHC complex may not be fixed.

    View details for Web of Science ID A1993KN29300008

    View details for PubMedID 8452673



    We have compared the binding kinetics of two antigenic peptides to a soluble class II MHC molecule. One of the peptides provokes a strong T cell response and the other a much weaker one. Both show greatly increased (approximately 40-fold) association rates at pH 5 in comparison to neutral pH, consistent with the low pH environment of late endosomes being most conducive to class II MHC--peptide binding. Interestingly, the weak peptide has a much faster off-rate that is significantly increased at pH 5 and it can be entirely replaced in an exchange reaction by the stronger one. This suggests that one characteristic of immunodominant peptides is that of nearly irreversible binding, such that they will be strongly selected for in the course of class II MHC transit and recycling through endosomal compartments. Modelling the parameters of this peptide exchange also suggests that a large fraction of the GPI-chimeric MHC molecules used in this study are 'empty' with respect to endogenous peptides, or else occupied with extremely weak ones, consistent with their inability to load processed peptides intracellularly.

    View details for Web of Science ID A1992JE53700007

    View details for PubMedID 1379172



    To test models of T-cell recognition, mice transgenic for T-cell receptor alpha or beta chain have been immunized with variant peptides that force changes in the resulting T-cell response. In particular, charge substitutions on the peptide often elicit reciprocal charges in the junctional (CDR3) sequences of T-cell receptor V alpha or V beta chains, indicating direct T-cell receptor-peptide contact, and allowing derivation of a topology for the T-cell receptor-MHC interaction. At one position on the peptide, variants transformed a homogeneous V beta response into a very heterogeneous one.

    View details for Web of Science ID A1992GZ69400056

    View details for PubMedID 1309938



    We review recent data that increase our understanding of the ternary complex of the T cell receptor (TCR), antigenic peptides, and molecules of the major histocompatibility complex (MHC). Studies using synthetic peptide analogs for T-cell antigens have identified peptide residues that appear to interact with the MHC molecule and/or the TCR. The logical extension of these studies, using a complete replacement set of peptide analogues for a model peptide antigen, has more precisely defined the biochemical character of putative MHC and TCR contact residues, and indicated that the TCR is highly sensitive to subtle changes in peptide conformation. Insight into the binding site for peptide on the TCR has recently come from variant peptide immunization of TCR single-chain transgenic mice. These experiments indicate that residues encoded by the V(D)J junctions of both TCR chains contact peptide directly. TCR-MHC contacts have also been studied, using in vitro-mutagenized MHC molecules, particularly those altered at residues predicted to point "up," toward the TCR. These studies reveal that TCR-MHC contacts appear to be quite flexible, and vary between even closely related TCRs. A measure of the affinity of TCR for peptide/MHC complexes has come from competition experiments using soluble MHC complexed with specific peptides. This affinity, with a KD of 5 x 10(-5) M, is several orders of magnitude lower than that of most antibodies for their protein antigens and suggests that the sequence of events leading to T-cell activation begins with antigen-independent adhesion.

    View details for Web of Science ID A1992HN01200030

    View details for PubMedID 1591005



    The interaction of antigen-specific T cell receptors (TCRs) with their ligands, peptides bound to molecules of the major histocompatibility complex (MHC), is central to most immune responses, yet little is known about its chemical characteristics. The binding to T cells of a labeled monoclonal antibody to the TCR was inhibited by soluble class II MHC heterodimers complexed to different peptides. Inhibition was both peptide- and TCR-specific and of low affinity, with a KD = 4 x 10(-5) to 6 x 10(-5) M, orders of magnitude weaker than comparable antibody-antigen interactions. This finding is consistent with the scanning nature of T cell recognition and suggests that antigen-independent adhesion precedes TCR engagement.

    View details for Web of Science ID A1991GW31600042

    View details for PubMedID 1763329



    One approach to the diagnosis and therapy of T cell-mediated diseases is to develop reagents specific for T cell receptor (TcR) variable (V) regions. To date, however, TcR expressed on the surface of antigen-specific T lymphocytes have proven to be poorly immunogenic. As a result, few monoclonal antibodies (mAb) recognizing human variable regions are available. In this report, we have used the "phosphatidylinositol linkage" strategy to generate soluble forms of two human allogeneic TcR derived from human cytotoxic T lymphocytes (CTL) known to be specific for HLA-A2 and HLA-Aw68/HLA-Aw69, respectively. Monomeric TcR alpha and beta chains from the HLA-A2-specific CTL were purified in large quantities from CHO cells and each was used to immunize mice to generate mAb. In particular, the anti-beta chain mAb, denoted anti-V beta 13, stain a significant (approximately 5%) fraction of human peripheral blood alpha/beta T lymphocytes, immunoprecipitate native anti-A2 TcR molecules, and activate T cells transfected with the relevant alpha and beta chain cDNA. Anti-alpha chain mAb were also obtained against a constant region determinant which can immunoprecipitate detergent-solubilized polypeptides. In general, we find that immunizations with soluble protein are far superior to those with cells bearing TcR chimeras or in combination with the purified protein.

    View details for Web of Science ID A1991GF65500019

    View details for PubMedID 1832385



    CD4 and CD8 have been useful surface markers for alpha/beta T cell maturation. In an alpha/beta T cell receptor (TCR) transgenic SCID mice system, it has been shown that alpha/beta TCR alone is sufficient to induce CD4 and CD8 surface expression on thymic T cells. Although the late embryonic thymic gamma/delta T cells are predominately single and double positive, it has not been clear if gamma/delta TCR has a similar capacity. In this study, we show that when transgenes encoding the earliest embryonic gamma/delta TCR are coexpressed with the SCID defect, the gamma/delta transgenes promote the appearance of both the CD4-8- and CD4+8+ T cells in the thymus. Furthermore, the expression of CD4 and CD8 does not require continuous surface gamma/delta TCR expression. These results indicate that gamma/delta TCR alone can promote the CD4/8 surface expression, and may suggest a role for gamma/delta T cells in initiating normal thymic ontogeny.

    View details for Web of Science ID A1991FU89700034

    View details for PubMedID 1905341



    A murine class II major histocompatibility complex (MHC) heterodimer, Ek, expressed as a glycan-phosphatidyl inositol-anchored chimera on Chinese Hamster Ovary cells, can present peptides, but not processed antigen to T cells. This chimeric MHC requires a 100-times higher peptide concentration to achieve a two- to four-times lower level of T cell stimulation. Cleavage with phosphatidylinositol-specific phospholipase C and purification result in large quantities of heterodimer in a water-soluble form. Plates coated with this material and then incubated with peptide can efficiently stimulate the appropriate T cell hybridomas. This stimulation is significantly enhanced when peptides are preincubated with the plate-bound MHC molecules in a pH range (5.0-5.5) similar to that of late endosomes. More than half of the soluble Ek molecules can form a specific complex with cytochrome c peptides in this pH range. This suggests that class II MHC molecules undergo distinct conformational changes in endosomal compartments that render them more capable of forming functional complexes with peptide antigens, irrespective of other cell components.

    View details for Web of Science ID A1991FU89700026

    View details for PubMedID 1829108



    Day 14 fetal thymocytes and adult dendritic epidermal T cells (dEC) of all mouse strains express a characteristic non-polymorphic gamma delta T-cell receptor which is rarely found in the adult thymus or lymph nodes. We have made transgenic mice expressing this particular set of receptors on T cells in C3H and C57BL/6 mice. In adult mice of the latter strain, a dramatic depletion of transgene expressing T cells occurs and this effect is primarily mediated by thymic radiosensitive cells. The depletion is genetically dominant but not MHC-linked with major factor(s) mapping to chromosome 18. Taken together, our results show that strain-specific developmental changes in the thymic environment may play a role in shaping the gamma delta TCR repertoire.

    View details for Web of Science ID A1991FK38000012

    View details for PubMedID 1831656



    The interaction of the T cell receptor for antigen (TCR) with its antigen-major histocompatibility complex ligand is difficult to study because both are cell surface multimers. The TCR consists of two chains (alpha and beta) that are complexed to the five or more nonpolymorphic CD3 polypeptides. A soluble form of the TCR was engineered by replacing the carboxyl termini of alpha and beta with signal sequences from lipid-linked proteins, making them susceptible to enzymatic cleavage. In this manner, TCR heterodimers can be expressed independently of the CD3 polypeptides and in significant quantities (0.5 milligram per week). This technique seems generalizable to biochemical and structural studies of many other cell surface molecules as well.

    View details for Web of Science ID A1990DT79600046

    View details for PubMedID 1696397



    In a T cell receptor transgenic mouse model of thymic selection, the efficiency of selection of the transgenic alpha beta heterodimer is significantly enhanced in animals that express higher densities of the relevant major histocompatibility complex molecule (I-Ek/b). These results imply that there is a stochastic component to positive selection in the thymus. Allelic variants of the original selecting I-Ek molecule are either less efficient (E alpha k:E beta b) or incapable (E alpha k:E beta s and I-Ed) of mediating the selection of transgenic alpha beta + T cells. Two of these three I-E variants appear to differ from I-Ek in amino acid residues of the peptide binding site and not in residues capable of contacting the T cell receptor, suggesting that specific peptides, or conformations of peptides, play a role in positive selection. In contrast, mice transgenic for only the beta chain of this T cell receptor show selection for CD4+ T cells in the presence of all four I-E variants tested.

    View details for Web of Science ID A1990CW00200018

    View details for PubMedID 2317862


    View details for Web of Science ID A1990CP69600005

    View details for PubMedID 2405272


    View details for Web of Science ID A1990DM77300017

    View details for PubMedID 2197981



    The XLR sequence family encodes RNA transcripts specific to late-stage T and B cells and their neoplasms. Only one apparently functional mRNA has been identified thus far and this encodes a novel 25 kDa nuclear protein. In this report, we find that the XLR gene family is composed of 50-75 copies per haploid genome which localize to at least two different portions of the mouse X chromosome. Neither of these locations are near the xid mutation that earlier work had correlated with XLR. In addition, some members of this family are also on the Y chromosome. Another surprising finding is that while the fourteen genomic clones examined to date have the same exon-intron structure and are closely related with respect to sequence conservation (90%), all appear (in most cases by multiple criteria) to be non-functional, raising the possibility that all but one of the members of this large semi-dispersed family are pseudogenes.

    View details for Web of Science ID A1989CE28900027

    View details for PubMedID 2602144

  • T-cell development in T cell receptor alphabeta transgenic mice. Seminars in immunology Berg, L. J., DAVIS, M. M. 1989; 1 (2): 105-116


    The introduction of rearranged T cell receptor alpha and beta chain genes into transgenic mice results in a high frequency of expression of the introduced receptor on T cells. In three different systems, analyses of mice expressing transgenic T cell receptors specific for antigen plus MHC class I or class II molecules have demonstrated several important features of T cell development: (1) T cell receptor specificity for MHC class I or class II molecules determines the expression of CD8 versus CD4, respectively, on mature T cells; (2) T cell maturation in the thymus is dependent on expression of an MHC molecule recognized by the T cell receptor; (3)for class II specific receptors, appropriate MHC expression on thymic epithelial cells is sufficient to achieve positive selection of T cells; and (4) self-reactive T cells die or are killed in the thymus.

    View details for PubMedID 15630812



    Transgenic mice expressing a T cell receptor heterodimer specific for a fragment of pigeon cytochrome c plus an MHC class II molecule (I-Ek) have been made. We find that H-2k alpha beta transgenic mice have an overall increase in the number of T cells and express a 10-fold higher fraction of cytochrome c-reactive cells than H-2b mice. Surface staining of thymocytes indicates that in H-2b mice, T cell development is arrested at an intermediate stage of differentiation (CD4+8+, CD310). Analyses of mice carrying these T cell receptor genes and MHC class II I-E alpha constructs indicate that his developmental block can be reversed in H-2b mice by I-E expression on cortical epithelial cells of the thymus. These data suggest that a direct T cell receptor-MHC interaction occurs in the thymus in the absence of nominal antigen and results in the enhanced export of T cells, consistent with the concept of "positive selection".

    View details for Web of Science ID A1989AR72600007

    View details for PubMedID 2476238



    T-cell differentiation in the thymus is thought to involve a progression from the CD4-CD8- phenotype through CD4+CD8+ intermediates to mature CD4+ or CD8+ cells. There is evidence that during this process T cells bearing receptors potentially reactive to 'self' are deleted by a process termed 'negative selection' One example of this process occurs in mice carrying polymorphic Mls antigens, against which a detectable proportion of T cells are autoreactive. These mice show clonal deletion of thymic and peripheral T-cell subsets that express the autoreactive V beta 3 segment of the T-cell antigen receptor, but at most a two-fold depletion of thymic cells at the CD4+CD8+ stage. By contrast, transgenic mice bearing both alpha and beta chain genes encoding autoreactive receptors recognizing other ligands, show severe depletion of CD4+CD8+ thymocytes as well, suggesting that negative selection occurs much earlier. We report here the Mls 2a/3a mediated elimination of T cells expressing a transgene encoded V beta 3-segment, in T-cell receptor alpha/beta and beta-transgenic mice. Severe depletion of CD4+CD8+ thymocytes is seen only in the alpha/beta chain transgenic mice, whereas both strains delete mature V beta 3 bearing CD4+ and CD8+ T cells efficiently. We conclude that severe CD4+CD8+ thymocyte deletion in alpha/beta transgenic mice results from the premature expression of both receptor chains, and does not reflect a difference in the timing or mechanism of negative selection for Mls antigens as against the allo- and MHC class 1-restricted antigens used in the other studies.

    View details for Web of Science ID A1989AL22700059

    View details for PubMedID 2528070



    Four distinct T-cell antigen-receptor gene loci have now been identified and partly characterized: alpha, beta, gamma and delta. All of these loci can rearrange in an immunoglobulin-like fashion and express polypeptides that contribute to either alpha:beta or gamma:delta T-cell receptor-CD3 complexes. Surprisingly, the T-cell receptor (TCR) delta coding regions are located entirely, or almost entirely, within the TCR alpha locus and share at least some of the V region gene segments, thus at least partly linking the two different types of receptor heterodimers. Analysis of potential T-cell receptor diversity, particularly that of the delta chain, indicates a striking concentration of somatic polymorphism in the V-J junctional region of the two heterodimers, four to six orders of magnitude higher than similar calculations for immunoglobulin light- and heavy-chain combinations. In contrast, the number of possible V region combinations in T-cell receptors is one hundredth to one thousandth that of immunoglobulins. TCR alpha: beta heterodimers are known to recognize many possible fragments of antigens embedded in the peptide-binding clefts of a relatively small number of major histocompatibility complex (MHC) molecules. Thus it is attractive to speculate that the V-J junctional portions of both types of T-cell receptor contact peptide antigens, whereas the remaining diversity regions contact the MHC. This contention is supported by molecular modelling studies and has interesting implications for the evolution of antigen-receptor genes.

    View details for Web of Science ID A1989AB41200008

    View details for PubMedID 2569209



    The major product of the XLR (X-chromosomal, lymphocyte-regulated) locus is found to be a 30-kD nuclear protein with a relatively short (t1/2 approximately equal to 2 h) half-life. Together with its stage- and tissue-specific pattern of expression, this suggests a role for this protein in the regulation of differentiation in T and B lymphocytes. Interestingly, the XLR protein almost completely leaches out of the nucleus after lysis of cells in low salt buffer, but is stabilized in that location by metal cations, particularly Zn++. This stabilization is reversible by chelating agents (o-phenanthroline, EDTA) which also release a number of other polypeptides in addition to XLR. These results suggest that XLR represents a novel class of nuclear proteins, and that cations such as zinc may play a role in the localization of these proteins in the nucleus.

    View details for Web of Science ID A1989T780000003

    View details for PubMedID 2493459



    In the polymerase chain reaction (PCR), two specific oligonucleotide primers are used to amplify the sequences between them. However, this technique is not suitable for amplifying genes that encode molecules where the 5' portion of the sequences of interest is not known, such as the T cell receptor (TCR) or immunoglobulins. Because of this limitation, a novel technique, anchored polymerase chain reaction (A-PCR), was devised that requires sequence specificity only on the 3' end of the target fragment. It was used to analyze TCR delta chain mRNA's from human peripheral blood gamma delta T cells. Most of these cells had a V delta gene segment not previously described (V delta 3), and the delta chain junctional sequences formed a discrete subpopulation compared with those previously reported.

    View details for Web of Science ID A1989R736800036

    View details for PubMedID 2463672


    View details for Web of Science ID A1989BR17U00001

    View details for PubMedID 2816544



    To examine the influences responsible for shaping the T-cell repertoire in vivo, we have introduced T-cell receptors of defined specificity into mice. In this report, we analyze transgenic mice carrying a T-cell receptor alpha-chain gene from a pigeon cytochrome c-reactive T-cell line. A variant of this construct, which has the immunoglobulin heavy-chain enhancer inserted into the JC intron, was also introduced into mice. Addition of the enhancer increased the steady-state level of transgene-encoded mRNA three- to fivefold in cultured T cells, leading to a two- to threefold increase in surface expression. In vivo, the difference between these two constructs was even more significant, increasing the number of transgene-positive cells from approximately 5 to 70% and the T-cell receptor surface density two- to threefold. Surprisingly, while surface expression of either type of transgene was limited to T cells, we found little tissue specificity with respect to transcription. In T cells expressing the alpha chain from the enhancer-containing construct, immunoprecipitation with a 2B4 alpha-specific monoclonal antibody revealed the expected disulfide-linked dimer. Costaining of these T cells with the 2B4 alpha-specific monoclonal antibody versus anti-CD3 indicated that expression of the transgene-encoded alpha chain precludes expression of endogenous alpha chains on the majority of cells; in contrast, 2B4 alpha-chain expression from the construct lacking the enhancer is inefficient at suppressing endogenous alpha-chain expression. In mice of the enhancer lineage, Southern blot analysis indicated suppression of endogenous alpha-chain rearrangements in T-cell populations, consistent with the observed allelic exclusion at the cellular level. Interestingly, newborn, but not adult, mice of this lineage also showed an increase in retention of unrearranged delta-chain loci in thymocyte DNA, presumably resulting from the suppression of alpha-chain rearrangements. This observation indicates that at least a fraction of alpha:beta-positive T cells have never attempted to produce functional delta rearrangements, thus suggesting that alpha:beta and gamma:delta T cells may be derived from different T-cell compartments (at least during the early phases of T-cell differentiation).

    View details for Web of Science ID A1988R081800043

    View details for PubMedID 3266655



    The LSP1 gene is a new lymphocyte-specific gene which is expressed in normal mouse B and T lymphocytes and in transformed B cells but not (or in much smaller amounts) in nine T lymphoma lines tested. No LSP1 mRNA is found in myeloid cells or in liver, kidney, or heart tissue. Inspection of the predicted LSP1 protein sequence reveals the presence of two putative Ca2+-binding domains in the LSP1 protein. Southern blotting analysis of genomic DNA from mouse liver suggests that the LSP1 gene is present as one copy per haploid genome. Similar analysis of genomic DNA extracted from three transformed B cell lines and five transformed T cell lines shows that the absence of LSP1 mRNA in T cell lines is not due to deletion or gross rearrangements of the LSP1 locus. With the use of the mouse LSP1 cDNA as a probe we can detect a cross-hybridizing RNA species in four normal human functional T cell lines but not in three transformed human T cell lines. This suggests that at least part of the DNA sequence and the expression pattern of the LSP1 gene is conserved between mouse and man. These conserved features, together with the particular expression pattern and the protein sequence homologies, suggest that the LSP1 protein is involved in a Ca2+-dependent aspect of normal T cell growth.

    View details for Web of Science ID A1988R004700045

    View details for PubMedID 3263441



    A variable region (V delta 5) of the T-cell receptor (TcR) delta chain that is preferentially expressed in adult murine thymocytes is located 2.5 kilobases 3' of the constant region (C delta) element. The V delta 5 coding sequence is in a transcriptional orientation opposite the J delta (joining region) and C delta coding elements and rearranges by inversion. The C delta is divided into four exons, three of which encode amino acids of TcR delta polypeptide, and the fourth comprises the entire 3' untranslated region. In this respect, C delta resembles C alpha rather than C beta or C gamma.

    View details for Web of Science ID A1988Q834100070

    View details for PubMedID 3263646



    The four distinct T-cell antigen receptor polypeptides (alpha, beta, gamma, delta) form two different heterodimers (alpha:beta and gamma:delta) that are very similar to immunoglobulins in primary sequence, gene organization and modes of rearrangement. Whereas antibodies have both soluble and membrane forms that can bind to antigens alone, T-cell receptors exist only on cell surfaces and recognize antigen fragments only when they are embedded in major histocompatibility complex (MHC) molecules. Patterns of diversity in T-cell receptor genes together with structural features of immunoglobulin and MHC molecules suggest a model for how this recognition might occur. This view of T-cell recognition has implications for how the receptors might be selected in the thymus and how they (and immunoglobulins) may have arisen during evolution.

    View details for Web of Science ID A1988P529200046

    View details for PubMedID 3043226

  • A HUMAN T-CELL-SPECIFIC MOLECULE IS A MEMBER OF A NEW GENE FAMILY JOURNAL OF IMMUNOLOGY Schall, T. J., Jongstra, J., Dyer, B. J., Jorgensen, J., CLAYBERGER, C., DAVIS, M. M., KRENSKY, A. M. 1988; 141 (3): 1018-1025


    We have used a cDNA library enriched for T cell-specific sequences to isolate genes expressed by T cells but not by other cell types. We report here one such gene, designated RANTES, which encodes a novel T cell-specific molecule. The RANTES gene product is predicted to be 10 kDa and, after cleavage of the signal peptide, approximately 8 kDa. Of the 68 residues, 4 are cysteines, and there are no sites for N-linked glycosylation. RANTES is expressed by cultured T cell lines that are Ag specific and growth factor dependent. RANTES expression is inducible in PBL by Ag or mitogen. In CTL, expression of RANTES decreases after stimulation with Ag and growth factors. Interestingly, RANTES was not expressed by any T cell tumor line tested. There is significant homology between the RANTES sequence and several other T cell genes, suggesting that they comprise a previously undescribed family of small T cell molecules.

    View details for Web of Science ID A1988P361900046

    View details for PubMedID 2456327



    We have isolated and sequenced a novel lambda 1 constant region related cDNA clone which might represent an allelic variant of the recently described lambda 5 gene. This lambda 5 transcript is present in pre-B cell lines and bone marrow cells, but not in B cell lines, plasma cell lines or in spleen cells. In vitro translation studies show that the translation product contains a signal peptide of approx. 30 amino acids at its N-terminus.

    View details for Web of Science ID A1988P534100002

    View details for PubMedID 2460755


    View details for Web of Science ID A1988N399000013

    View details for PubMedID 3131355



    The AKR thymoma BW5147 has rearranged both of its TCR beta-chain loci, using the same J beta region (J beta 2.5) in each, but with different V beta gene segments. Although the two rearrangements are expressed approximately equally in cytoplasmic RNA, the principle of allelic exclusion is maintained because only one rearrangement is in-frame and capable of encoding a functional protein. In hybridomas made with BW5147 as the fusion partner, this protein may combine with the alpha-chain protein derived from the normal cell to form new Ag/MHC specificities. An analysis of the sequences upstream from the BW5147 rearrangements and additional V regions suggests that two conserved sequences, 10 and nine nucleotides in length and located adjacent to each other 70 to 100 nucleotides 5' of the initiation codon, may be important in the expression of TCR beta-chain genes. Although B and T cells derive from common stem cells, no sequences are observed in T cells that are homologous to the octamer located 5' of all Ig genes. This implies that at least some of the sequences that regulate transcription are not shared in the two major types of lymphocytes. A survey of BW5147 and six other AKR thymomas using probes for 10 of the 18 known V region families indicates a distribution of V beta rearrangements in the tumors consistent with that found in thymocytes. Four of these tumors have apparent VDJ rearrangements on both chromosomes, with the deletion of other V beta gene segments. These data suggest that the primary mechanism of VDJ beta rearrangement is by looping out and excision of the intervening DNA and that most of the V regions are located 5' to the C region. These data were also used to develop a deletion order of the V beta gene segments in the TCR beta-chain locus.

    View details for Web of Science ID A1988M523100050

    View details for PubMedID 3346546



    T lymphocytes recognize foreign molecules using the T-cell receptor (TCR), a disulphide-linked heterodimer closely associated with the CD3 polypeptide complex on the cell surface. The TCR alpha beta heterodimers seem largely responsible for the recognition properties of both helper (TH) and cytotoxic (TC) T cells. Recently, a second CD3-associated T-cell receptor heterodimer, gamma delta, has been described. Cells bearing the gamma delta receptor appear before those bearing alpha beta during thymic ontogeny and persist as a minor component (1-10%) of mature peripheral T cells. Their function is unknown. As there are a limited number of functional TCR V gamma gene segments, the size and potential diversity of the V delta repertoire is important for the number of different antigens that may be recognized by gamma delta heterodimers. The delta-chain locus is located 75 kilobases (kb) 5' to the TCR C alpha coding region, raising the possibility that the alpha and delta V-region repertoires may overlap. Also, analysis of rearrangements at the delta-chain locus in developing thymocytes shows distinct fetal and adult patterns indicating that there may be differences between the fetal and adult V delta repertoires. To address these questions, we have characterized a large number of delta-containing complementary DNA clones from adult double-negative thymocytes (CD4-8-), an immature population that is enriched for gamma delta-bearing cells. We find that a limited number of V delta sequences are used, showing little overlap with known adult V alpha s and differing significantly from fetal V delta s. But as two D elements may participate simultaneously in V delta gene assembly, and random nucleotides may be added at any one of three junctional points, the potential number of different delta chains that can be made in the adult thymus is very large (approximately 10(13)).

    View details for Web of Science ID A1988M118000061

    View details for PubMedID 2963227

  • T-CELL RECEPTOR DELTA-GENE REARRANGEMENTS IN EARLY THYMOCYTES NATURE Chien, Y. H., Iwashima, M., Wettstein, D. A., Kaplan, K. B., ELLIOTT, J. F., Born, W., DAVIS, M. M. 1987; 330 (6150): 722-727


    The T-cell receptor delta-chain variable region can be assembled from as many as four distinct gene segments, V, D1, D2 and J, more than any other antigen-receptor gene. In fetal thymocytes V----D joinings are as common as D----J or VDJ rearrangements and one V gene segment predominates. Analysis of rearrangements at TCR gamma and delta loci during fetal ontogeny suggests abrupt changes and possible coordinate control in the rearrangement and expression of these loci.

    View details for Web of Science ID A1987L431600058

    View details for PubMedID 2961997

  • IDENTIFICATION AND SEQUENCE OF A 4TH HUMAN T-CELL ANTIGEN RECEPTOR CHAIN NATURE Loh, E. Y., Lanier, L. L., Turck, C. W., Littman, D. R., DAVIS, M. M., Chien, Y. H., WEISS, A. 1987; 330 (6148): 569-572


    Thymus-derived lymphocytes (T cells) use clonally distributed antigen receptors to recognize peptide fragments associated with products of the major histocompatibility complex (MHC) (refs 1-4). On most murine and human T cells the T cell receptor (TCR) is composed of disulphide-linked alpha and beta chains (TCR alpha/beta), each of which contains constant and variable domains, and which are associated with the invariant chains of the CD3 complex. It has been demonstrated, however, that a distinct CD3-associated TCR is expressed on a small subset of T cells or immature thymocytes which fail to express either CD4 or CD8 (refs 7-14), the molecules associated with class II or class I MHC antigen recognition. Instead of TCR alpha/beta, these cells express heterodimers of gamma and delta chains (TRC gamma/delta). The genes encoding alpha, beta, and gamma have been isolated and characterized. A new murine T cell receptor (Cx) gene which undergoes rearrangement and expression early during T cell ontogeny has recently been identified 5' of the murine J alpha C alpha gene locus. Here we isolate and sequence the homologous transcript from PEER, a human cell line that expresses a TCR gamma/delta, and show that it encodes a protein with characteristic V, D, J, and C segments. Using probes derived from this transcript, we have shown that both PEER and MOLT-13, another TCR gamma/delta-expressing cell line, rearrange this locus and express two sizes of transcripts differing in the 3' untranslated region. Using a synthetic peptide derived from the deduced C region sequence, we have prepared antisera that precipitates the delta chain of the TCR from both PEER and MOLT-13, thus demonstrating that Cx and its human homologue code for the delta chain of the TCR.

    View details for Web of Science ID A1987L184100062

    View details for PubMedID 2825032



    We used pulsed-field gel electrophoresis to determine the organization of the beta-chain gene of the T-cell receptor for antigen in normal and mutant inbred strains of mice. In normal mice, the variable (V)- and constant (C)- region elements of this locus span 700-800 kilobases of chromosomal DNA. All but one of the V beta gene segments analyzed lie 5' of the J beta C beta locus (J beta represents the joining region), with the closest being 280-360 kilobases away. The mutant mouse strain SJL has an internal V beta-region gene deletion that compacts the V beta region by 100-200 kilobases. Taken together with other data, these results indicate that the beta-chain locus can use either a looping-out/deletion or an inversion mechanism to appose V beta to DJ beta gene segments (D is the diversity region) and can accomplish the former (at least) over very large distances.

    View details for Web of Science ID A1987K780500061

    View details for PubMedID 3478716



    Naturally occurring suppressor cells of the in vitro mixed leukocyte culture reaction and of in vivo graft-vs.-host disease have been identified in the spleens of neonatal mice (1) and of adult mice recovering from total lymphoid irradiation (2), whole-body irradiation (3), and syngeneic marrow transplantation (4), or cyclophosphamide therapy (5). Using both positive and negative selection procedures, the suppressors were reported to be null lymphocytes that did not express mature macrophage surface markers, nor differentiate into mature macrophages in vitro, nor demonstrate natural killer (NK) activity (1). Subsequently, cloned lines of these natural suppressor (NS) cells were derived from either adult mice given total lymphoid irradiation (TLI) (2) or from neonates (6). The cloned NS cell lines expressed a surface phenotype (2, 6) similar to that reported previously for cloned NK cells (Thy-1(+), asialo-GM1(+), Ig(-), Lyt-1(-), Lyt-2(-), Ia(-), MAC-1(-)) (7-9). However, the NS cells did not show NK activity in the standard assay with YAC-1 target cells. The cloned NS lines suppressed the proliferation of responder cells and the generation of cytolytic cells in the mixed leukocyte reaction (MLR), and suppressed lethal graft-vs.-host disease in vivo (10, 11). In view of the unusual function and surface phenotype of the cells, the lineage of these cells remained unclear. To determine the lineage of the cloned NS cells, we searched for expression and rearrangement of the alpha and beta chain genes of the T cell antigen receptor, as well as that of the gamma chain gene. Studies of the phenotypically similar NK cell yielded conflicting results. Thus, cloned lines of murine NK cells were reported to have rearrangements of the beta chain genes, and to express mRNA for all three chains (12). In contrast, freshly purified rat or human large granular lymphocytes (LGL) were shown to express only the 1.0 kb mRNA species of the beta chain gene (13), indicative of D-J joining (14). Thus, some but not all cells with NK function express the T cell receptor and are members of the T cell lineage. The current report shows that the NS lines express full-length mRNA transcripts for the a and beta chain of the T cell receptor, as well as the gamma chain gene.

    View details for Web of Science ID A1987K464000031

    View details for PubMedID 2958579

    View details for PubMedCentralID PMC2188714



    A new T-cell receptor gene lies just 5' to the J alpha C alpha coding regions. Its placement in this location suggests a novel mechanism for the regulation of expression of one T-cell receptor polypeptide to another during ontogeny. Rearrangement of this locus occurs very early in thymic differentiation and its RNA expression parallels that of the gamma-chain in thymic subpopulations, making this a possible candidate for the recently described delta-chain of the T-cell receptor.

    View details for Web of Science ID A1987H882700046

    View details for PubMedID 2439914



    Using a subtractive hybridization procedure we have constructed a cDNA library enriched for sequences present in functional human T cell lines, but not in human EBV-transformed B cell lines. We have isolated a cDNA clone, AH2-519, representing a novel gene, designated 519. This novel gene is expressed in functional human cytolytic and Th cell lines but not in a variety of other cell lines, including several long-term human T cell tumor lines. The expression of gene 519 is inducible in cultures of normal human PBL using antigenic or mitogenic stimulation. Neither the DNA sequence determined from a full-length cDNA clone overlapping with clone AH2-519 nor the amino acid sequence of its predicted protein product has significant homology to published sequences in the GenBank or NBRF databases. The restricted expression of gene 519 suggests that its gene product is involved in the growth and/or differentiation of normal T cells. The data also show that normal, nontransformed, functional T cells express gene products that can not be readily identified in long-term tumor lines of the same cell lineage.

    View details for Web of Science ID A1987G292200002

    View details for PubMedID 2434598