Ash A. Alizadeh, MD/PhD

All Publications

• Distinct biological subtypes and patterns of genome evolution in lymphoma revealed by circulating tumor DNA SCIENCE TRANSLATIONAL MEDICINE Scherer, F., Kurtz, D. M., Newman, A. M., Stehr, H., Craig, A. F., Esfahani, M. S., Lovejoy, A. F., Chabon, J. J., Klass, D. M., Liu, C. L., Zhou, L., Glover, C., Visser, B. C., Poultsides, G. A., Advani, R. H., Maeda, L. S., Gupta, N. K., Levy, R., Ohgami, R. S., Kunder, C. A., Diehn, M., Alizadeh, A. A. 2016; 8 (364)

  Abstract

  Patients with diffuse large B cell lymphoma (DLBCL) exhibit marked diversity in tumor behavior and outcomes, yet the identification of poor-risk groups remains challenging. In addition, the biology underlying these differences is incompletely understood. We hypothesized that characterization of mutational heterogeneity and genomic evolution using circulating tumor DNA (ctDNA) profiling could reveal molecular determinants of adverse outcomes. To address this hypothesis, we applied cancer personalized profiling by deep sequencing (CAPP-Seq) analysis to tumor biopsies and cell-free DNA samples from 92 lymphoma patients and 24 healthy subjects. At diagnosis, the amount of ctDNA was found to strongly correlate with clinical indices and was independently predictive of patient outcomes. We demonstrate that ctDNA genotyping can classify transcriptionally defined tumor subtypes, including DLBCL cell of origin, directly from plasma. By simultaneously tracking multiple somatic mutations in ctDNA, our approach outperformed immunoglobulin sequencing and radiographic imaging for the detection of minimal residual disease and facilitated noninvasive identification of emergent resistance mutations to targeted therapies. In addition, we identified distinct patterns of clonal evolution distinguishing indolent follicular lymphomas from those that transformed into DLBCL, allowing for potential noninvasive prediction of histological transformation. Collectively, our results demonstrate that ctDNA analysis reveals biological factors that underlie lymphoma clinical outcomes and could facilitate individualized therapy.

  View details for DOI 10.1126/scitranslmed.aai8545

  View details for Web of Science ID 000389448100006

  View details for PubMedID 27831904

• Circulating tumour DNA profiling reveals heterogeneity of EGFR inhibitor resistance mechanisms in lung cancer patients NATURE COMMUNICATIONS Chabon, J. J., Simmons, A. D., Lovejoy, A. F., Esfahani, M. S., Newman, A. M., Haringsma, H. J., Kurtz, D. M., Stehr, H., Scherer, F., Karlovich, C. A., Harding, T. C., Durkin, K. A., Otterson, G. A., Purcell, W. T., Camidge, D. R., Goldman, J. W., Sequist, L. V., Piotrowska, Z., Wakelee, H. A., Neal, J. W., Alizadeh, A. A., Diehn, M. 2016; 7

  Abstract

  Circulating tumour DNA (ctDNA) analysis facilitates studies of tumour heterogeneity. Here we employ CAPP-Seq ctDNA analysis to study resistance mechanisms in 43 non-small cell lung cancer (NSCLC) patients treated with the third-generation epidermal growth factor receptor (EGFR) inhibitor rociletinib. We observe multiple resistance mechanisms in 46% of patients after treatment with first-line inhibitors, indicating frequent intra-patient heterogeneity. Rociletinib resistance recurrently involves MET, EGFR, PIK3CA, ERRB2, KRAS and RB1. We describe a novel EGFR L798I mutation and find that EGFR C797S, which arises in ∼33% of patients after osimertinib treatment, occurs in <3% after rociletinib. Increased MET copy number is the most frequent rociletinib resistance mechanism in this cohort and patients with multiple pre-existing mechanisms (T790M and MET) experience inferior responses. Similarly, rociletinib-resistant xenografts develop MET amplification that can be overcome with the MET inhibitor crizotinib. These results underscore the importance of tumour heterogeneity in NSCLC and the utility of ctDNA-based resistance mechanism assessment.

  View details for DOI 10.1038/ncomms11815

  View details for Web of Science ID 000378007200001

  View details for PubMedID 27283993

  View details for PubMedCentralID PMC4906406

• Integrated digital error suppression for improved detection of circulating tumor DNA NATURE BIOTECHNOLOGY Newman, A. M., Lovejoy, A. F., Klass, D. M., Kurtz, D. M., Chabon, J. J., Scherer, F., Stehr, H., Liu, C. L., Bratman, S. V., Say, C., Zhou, L., Carter, J. N., West, R. B., Sledge, G. W., Shrager, J. B., Loo, B. W., Neal, J. W., Wakelee, H. A., Diehn, M., Alizadeh, A. A. 2016; 34 (5): 547-555

  Abstract

  High-throughput sequencing of circulating tumor DNA (ctDNA) promises to facilitate personalized cancer therapy. However, low quantities of cell-free DNA (cfDNA) in the blood and sequencing artifacts currently limit analytical sensitivity. To overcome these limitations, we introduce an approach for integrated digital error suppression (iDES). Our method combines in silico elimination of highly stereotypical background artifacts with a molecular barcoding strategy for the efficient recovery of cfDNA molecules. Individually, these two methods each improve the sensitivity of cancer personalized profiling by deep sequencing (CAPP-Seq) by about threefold, and synergize when combined to yield ∼15-fold improvements. As a result, iDES-enhanced CAPP-Seq facilitates noninvasive variant detection across hundreds of kilobases. Applied to non-small cell lung cancer (NSCLC) patients, our method enabled biopsy-free profiling of EGFR kinase domain mutations with 92% sensitivity and >99.99% specificity at the variant level, and with 90% sensitivity and 96% specificity at the patient level. In addition, our approach allowed monitoring of NSCLC ctDNA down to 4 in 10(5) cfDNA molecules. We anticipate that iDES will aid the noninvasive genotyping and detection of ctDNA in research and clinical settings.

  View details for DOI 10.1038/nbt.3520

  View details for Web of Science ID 000375735000036

  View details for PubMedID 27018799

  View details for PubMedCentralID PMC4907374

• The prognostic landscape of genes and infiltrating immune cells across human cancers NATURE MEDICINE Gentles, A. J., Newman, A. M., Liu, C. L., Bratman, S. V., Feng, W., Kim, D., Nair, V. S., Xu, Y., Khuong, A., Hoang, C. D., Diehn, M., West, R. B., Plevritis, S. K., Alizadeh, A. A. 2015; 21 (8): 938-945

  Abstract

  Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of clinical outcomes. However, existing data sets are fragmented and difficult to analyze systematically. Here we present a pan-cancer resource and meta-analysis of expression signatures from ∼18,000 human tumors with overall survival outcomes across 39 malignancies. By using this resource, we identified a forkhead box MI (FOXM1) regulatory network as a major predictor of adverse outcomes, and we found that expression of favorably prognostic genes, including KLRB1 (encoding CD161), largely reflect tumor-associated leukocytes. By applying CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes, we identified complex associations between 22 distinct leukocyte subsets and cancer survival. For example, tumor-associated neutrophil and plasma cell signatures emerged as significant but opposite predictors of survival for diverse solid tumors, including breast and lung adenocarcinomas. This resource and associated analytical tools (http://precog.stanford.edu) may help delineate prognostic genes and leukocyte subsets within and across cancers, shed light on the impact of tumor heterogeneity on cancer outcomes, and facilitate the discovery of biomarkers and therapeutic targets.

  View details for DOI 10.1038/nm.3909

  View details for Web of Science ID 000359181000022

  View details for PubMedID 26193342

• Toward understanding and exploiting tumor heterogeneity NATURE MEDICINE Alizadeh, A. A., Aranda, V., Bardelli, A., Blanpain, C., Bock, C., Borowski, C., Caldas, C., Califano, A., Doherty, M., Elsner, M., Esteller, M., Fitzgerald, R., Korbel, J. O., Lichter, P., Mason, C. E., Navin, N., Pe'er, D., Polyak, K., Roberts, C. W., Siu, L., Snyder, A., Stower, H., Swanton, C., Verhaak, R. G., Zenklusen, J. C., Zuber, J., Zucman-Rossi, J. 2015; 21 (8): 846-853

  Abstract

  The extent of tumor heterogeneity is an emerging theme that researchers are only beginning to understand. How genetic and epigenetic heterogeneity affects tumor evolution and clinical progression is unknown. The precise nature of the environmental factors that influence this heterogeneity is also yet to be characterized. Nature Medicine, Nature Biotechnology and the Volkswagen Foundation organized a meeting focused on identifying the obstacles that need to be overcome to advance translational research in and tumor heterogeneity. Once these key questions were established, the attendees devised potential solutions. Their ideas are presented here.

  View details for DOI 10.1038/nm.3915

  View details for Web of Science ID 000359181000009

  View details for PubMedID 26248267

• Noninvasive monitoring of diffuse large B-cell lymphoma by immunoglobulin high-throughput sequencing. Blood Kurtz, D. M., Green, M. R., Bratman, S. V., Scherer, F., Liu, C. L., Kunder, C. A., Takahashi, K., Glover, C., Keane, C., Kihira, S., Visser, B., Callahan, J., Kong, K. A., Faham, M., Corbelli, K. S., Miklos, D., Advani, R. H., Levy, R., Hicks, R. J., Hertzberg, M., Ohgami, R. S., Gandhi, M. K., Diehn, M., Alizadeh, A. A. 2015; 125 (24): 3679-3687

  Abstract

  Recent studies have shown limited utility of routine surveillance imaging for diffuse large B-cell lymphoma (DLBCL) patients achieving remission. Detection of molecular disease by immunoglobulin high-throughput sequencing (Ig-HTS) from peripheral blood provides an alternate strategy for surveillance. We prospectively evaluated the utility of Ig-HTS within 311 blood and 105 tumor samples from 75 patients with DLBCL, comparing Ig-HTS from the cellular (circulating leukocytes) and acellular (plasma cell-free DNA) compartments of peripheral blood to clinical outcomes and (18)fluoro-deoxyglucose positron emission tomography combined with computed tomography (PET/CT; n = 173). Clonotypic immunoglobulin rearrangements were detected in 83% of patients with adequate tumor samples to enable subsequent monitoring in peripheral blood. Molecular disease measured from plasma, compared with circulating leukocytes, was more abundant and better correlated with radiographic disease burden. Before treatment, molecular disease was detected in the plasma of 82% of patients compared with 71% in circulating cells (P = .68). However, molecular disease was detected significantly more frequently in the plasma at time of relapse (100% vs 30%; P = .001). Detection of molecular disease in the plasma often preceded PET/CT detection of relapse in patients initially achieving remission. During surveillance time points before relapse, plasma Ig-HTS demonstrated improved specificity (100% vs 56%, P < .0001) and similar sensitivity (31% vs 55%, P = .4) compared with PET/CT. Given its high specificity, Ig-HTS from plasma has potential clinical utility for surveillance after complete remission.

  View details for DOI 10.1182/blood-2015-03-635169

  View details for PubMedID 25887775

  View details for PubMedCentralID PMC4463733

• Robust enumeration of cell subsets from tissue expression profiles. Nature methods Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., Alizadeh, A. A. 2015; 12 (5): 453-457

  Abstract

  We introduce CIBERSORT, a method for characterizing cell composition of complex tissues from their gene expression profiles. When applied to enumeration of hematopoietic subsets in RNA mixtures from fresh, frozen and fixed tissues, including solid tumors, CIBERSORT outperformed other methods with respect to noise, unknown mixture content and closely related cell types. CIBERSORT should enable large-scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets (http://cibersort.stanford.edu/).

  View details for DOI 10.1038/nmeth.3337

  View details for PubMedID 25822800

• Robust enumeration of cell subsets from tissue expression profiles NATURE METHODS Newman, A. M., Liu, C. L., Green, M. R., Gentles, A. J., Feng, W., Xu, Y., Hoang, C. D., Diehn, M., Alizadeh, A. A. 2015; 12 (5): 453-?

  View details for DOI 10.1038/NMETH.3337

  View details for Web of Science ID 000353645800019

  View details for PubMedID 25822800

• Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America Green, M. R., Kihira, S., Liu, C. L., Nair, R. V., Salari, R., Gentles, A. J., Irish, J., Stehr, H., Vicente-Dueñas, C., Romero-Camarero, I., Sanchez-Garcia, I., Plevritis, S. K., Arber, D. A., Batzoglou, S., Levy, R., Alizadeh, A. A. 2015; 112 (10): E1116-25

  Abstract

  Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

  View details for DOI 10.1073/pnas.1501199112

  View details for PubMedID 25713363

  View details for PubMedCentralID PMC4364211

• Mutations in early follicular lymphoma progenitors are associated with suppressed antigen presentation. Proceedings of the National Academy of Sciences of the United States of America Green, M. R., Kihira, S., Liu, C. L., Nair, R. V., Salari, R., Gentles, A. J., Irish, J., Stehr, H., Vicente-Dueñas, C., Romero-Camarero, I., Sanchez-Garcia, I., Plevritis, S. K., Arber, D. A., Batzoglou, S., Levy, R., Alizadeh, A. A. 2015; 112 (10): E1116-25

  Abstract

  Follicular lymphoma (FL) is incurable with conventional therapies and has a clinical course typified by multiple relapses after therapy. These tumors are genetically characterized by B-cell leukemia/lymphoma 2 (BCL2) translocation and mutation of genes involved in chromatin modification. By analyzing purified tumor cells, we identified additional novel recurrently mutated genes and confirmed mutations of one or more chromatin modifier genes within 96% of FL tumors and two or more in 76% of tumors. We defined the hierarchy of somatic mutations arising during tumor evolution by analyzing the phylogenetic relationship of somatic mutations across the coding genomes of 59 sequentially acquired biopsies from 22 patients. Among all somatically mutated genes, CREBBP mutations were most significantly enriched within the earliest inferable progenitor. These mutations were associated with a signature of decreased antigen presentation characterized by reduced transcript and protein abundance of MHC class II on tumor B cells, in line with the role of CREBBP in promoting class II transactivator (CIITA)-dependent transcriptional activation of these genes. CREBBP mutant B cells stimulated less proliferation of T cells in vitro compared with wild-type B cells from the same tumor. Transcriptional signatures of tumor-infiltrating T cells were indicative of reduced proliferation, and this corresponded to decreased frequencies of tumor-infiltrating CD4 helper T cells and CD8 memory cytotoxic T cells. These observations therefore implicate CREBBP mutation as an early event in FL evolution that contributes to immune evasion via decreased antigen presentation.

  View details for DOI 10.1073/pnas.1501199112

  View details for PubMedID 25713363

  View details for PubMedCentralID PMC4364211

• FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution BIOINFORMATICS Newman, A. M., Bratman, S. V., Stehr, H., Lee, L. J., Liu, C. L., Diehn, M., Alizadeh, A. A. 2014; 30 (23): 3390-3393

  Abstract

  For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment/Map file and produces easily interpretable output. We demonstrate FACTERA's ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.http://factera.stanford.edu.

  View details for DOI 10.1093/bioinformatics/btu549

  View details for Web of Science ID 000345827400014

  View details for PubMedID 25143292

  View details for PubMedCentralID PMC4296148

• Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. Journal of clinical oncology Levy, R., Ganjoo, K. N., Leonard, J. P., Vose, J. M., Flinn, I. W., Ambinder, R. F., Connors, J. M., Berinstein, N. L., Belch, A. R., Bartlett, N. L., Nichols, C., Emmanouilides, C. E., Timmerman, J. M., Gregory, S. A., Link, B. K., Inwards, D. J., Freedman, A. S., Matous, J. V., Robertson, M. J., Kunkel, L. A., Ingolia, D. E., Gentles, A. J., Liu, C. L., Tibshirani, R., Alizadeh, A. A., Denney, D. W. 2014; 32 (17): 1797-1803

  View details for DOI 10.1200/JCO.2012.43.9273

  View details for PubMedID 24799467

• Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma NATURE COMMUNICATIONS Green, M. R., Vicente-Duenas, C., Romero-Camarero, I., Liu, C. L., Dai, B., Gonzalez-Herrero, I., Garcia-Ramirez, I., Alonso-Escudero, E., Iqbal, J., Chan, W. C., Campos-Sanchez, E., Orfao, A., Pintado, B., Flores, T., Blanco, O., Jimenez, R., Angel Martinez-Climent, J., Garcia Criado, F. J., Garcia Cenador, M. B., Zhao, S., Natkunam, Y., Lossos, I. S., Majeti, R., Melnick, A., Cobaleda, C., Alizadeh, A. A., Sanchez-Garcia, I. 2014; 5

  Abstract

  Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cells (ABC-like). Here we identify gain of 3q27.2 as being significantly associated with adverse outcome in DLBCL and linked with the ABC-like subtype. This lesion includes the BCL6 oncogene, but does not alter BCL6 transcript levels or target-gene repression. Separately, we identify expression of BCL6 in a subset of human haematopoietic stem/progenitor cells (HSPCs). We therefore hypothesize that BCL6 may act by 'hit-and-run' oncogenesis. We model this hit-and-run mechanism by transiently expressing Bcl6 within murine HSPCs, and find that it causes mature B-cell lymphomas that lack Bcl6 expression and target-gene repression, are transcriptionally similar to post-GCB cells, and show epigenetic changes that are conserved from HSPCs to mature B-cells. Together, these results suggest that BCL6 may function in a 'hit-and-run' role in lymphomagenesis.

  View details for DOI 10.1038/ncomms4904

  View details for Web of Science ID 000338831000001

• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nature medicine Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Alizadeh, A. A., Diehn, M. 2014; 20 (5): 548-554

  Abstract

  Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. We detected ctDNA in 100% of patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ∼0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. We envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.

  View details for DOI 10.1038/nm.3519

  View details for PubMedID 24705333

• An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage NATURE MEDICINE Newman, A. M., Bratman, S. V., To, J., Wynne, J. F., Eclov, N. C., Modlin, L. A., Liu, C. L., Neal, J. W., Wakelee, H. A., Merritt, R. E., Shrager, J. B., Loo, B. W., Alizadeh, A. A., Diehn, M. 2014; 20 (5): 552-558

  Abstract

  Circulating tumor DNA (ctDNA) is a promising biomarker for noninvasive assessment of cancer burden, but existing ctDNA detection methods have insufficient sensitivity or patient coverage for broad clinical applicability. Here we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors. We detected ctDNA in 100% of patients with stage II-IV NSCLC and in 50% of patients with stage I, with 96% specificity for mutant allele fractions down to ∼0.02%. Levels of ctDNA were highly correlated with tumor volume and distinguished between residual disease and treatment-related imaging changes, and measurement of ctDNA levels allowed for earlier response assessment than radiographic approaches. Finally, we evaluated biopsy-free tumor screening and genotyping with CAPP-Seq. We envision that CAPP-Seq could be routinely applied clinically to detect and monitor diverse malignancies, thus facilitating personalized cancer therapy.

  View details for DOI 10.1038/nm.3519

  View details for Web of Science ID 000335710700028

• Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood Green, M. R., Gentles, A. J., Nair, R. V., Irish, J. M., Kihira, S., Liu, C. L., Kela, I., Hopmans, E. S., Myklebust, J. H., Ji, H., Plevritis, S. K., Levy, R., Alizadeh, A. A. 2013; 121 (9): 1604-1611

  Abstract

  Follicular lymphoma (FL) is currently incurable using conventional chemotherapy or immunotherapy regimes, compelling new strategies. Advances in high-throughput sequencing technologies that can reveal oncogenic pathways have stimulated interest in tailoring therapies toward actionable somatic mutations. However, for mutation-directed therapies to be most effective, the mutations must be uniformly present in evolved tumor cells as well as in the self-renewing tumor-cell precursors. Here, we show striking intratumoral clonal diversity within FL tumors in the representation of mutations in the majority of genes as revealed by whole exome sequencing of subpopulations. This diversity captures a clonal hierarchy, resolved using immunoglobulin somatic mutations and IGH-BCL2 translocations as a frame of reference and by comparing diagnosis and relapse tumor pairs, allowing us to distinguish early versus late genetic eventsduring lymphomagenesis. We provide evidence that IGH-BCL2 translocations and CREBBP mutations are early events, whereas MLL2 and TNFRSF14 mutations probably represent late events during disease evolution. These observations provide insight into which of the genetic lesions represent suitable candidates for targeted therapies.

  View details for DOI 10.1182/blood-2012-09-457283

  View details for PubMedID 23297126

  View details for PubMedCentralID PMC3587323

• Therapeutic Antibody Targeting of CD47 Synergizes with Rituximab to Completely Eradicate Human B-Cell Lymphoma Cell Chao, M. P., Majeti R. 2010; 142 (5): 699-713
• Molecular Outcome Prediction in Diffuse Large-B-Cell Lymphoma NEW ENGLAND JOURNAL OF MEDICINE Alizadeh, A. A., Gentles, A. J., Lossos, I. S., Levy, R. 2009; 360 (26): 2794-2795

  View details for Web of Science ID 000267286600032

  View details for PubMedID 19553658

• Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling NATURE Alizadeh, A. A., Eisen, M. B., Davis, R. E., Ma, C., Lossos, I. S., Rosenwald, A., Boldrick, J. G., Sabet, H., Tran, T., Yu, X., Powell, J. I., Yang, L. M., Marti, G. E., Moore, T., Hudson, J., Lu, L. S., Lewis, D. B., Tibshirani, R., Sherlock, G., Chan, W. C., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Warnke, R., Levy, R., Wilson, W., Grever, M. R., Byrd, J. C., Botstein, D., Brown, P. O., Staudt, L. M. 2000; 403 (6769): 503-511

  Abstract

  Diffuse large B-cell lymphoma (DLBCL), the most common subtype of non-Hodgkin's lymphoma, is clinically heterogeneous: 40% of patients respond well to current therapy and have prolonged survival, whereas the remainder succumb to the disease. We proposed that this variability in natural history reflects unrecognized molecular heterogeneity in the tumours. Using DNA microarrays, we have conducted a systematic characterization of gene expression in B-cell malignancies. Here we show that there is diversity in gene expression among the tumours of DLBCL patients, apparently reflecting the variation in tumour proliferation rate, host response and differentiation state of the tumour. We identified two molecularly distinct forms of DLBCL which had gene expression patterns indicative of different stages of B-cell differentiation. One type expressed genes characteristic of germinal centre B cells ('germinal centre B-like DLBCL'); the second type expressed genes normally induced during in vitro activation of peripheral blood B cells ('activated B-like DLBCL'). Patients with germinal centre B-like DLBCL had a significantly better overall survival than those with activated B-like DLBCL. The molecular classification of tumours on the basis of gene expression can thus identify previously undetected and clinically significant subtypes of cancer.

  View details for Web of Science ID 000085227300039

  View details for PubMedID 10676951

• overexpression to promote lymphoma in mice. Blood García-Ramírez, I., Tadros, S., González-Herrero, I., Martín-Lorenzo, A., Rodríguez-Hernández, G., Moore, D., Ruiz-Roca, L., Blanco, O., Alonso-López, D., Rivas, J. D., Hartert, K., Duval, R., Klinkebiel, D., Bast, M., Vose, J., Lunning, M., Fu, K., Greiner, T., Rodrigues-Lima, F., Jiménez, R., Criado, F. J., Cenador, M. B., Brindle, P., Vicente-Dueñas, C., Alizadeh, A., Sánchez-García, I., Green, M. R. 2017; 129 (19): 2645-2656

  Abstract

  CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 overexpression to promote B-cell lymphoma. Through transcriptional and epigenetic profiling of these B cells, we found that Crebbp inactivation was associated with broad transcriptional alterations, but no changes in the patterns of histone acetylation at the proximal regulatory regions of these genes. However, B cells with Crebbp inactivation showed high expression of Myc and patterns of altered histone acetylation that were localized to intragenic regions, enriched for Myc DNA binding motifs, and showed Myc binding. Through the analysis of CREBBP mutations from a large cohort of primary human FL and DLBCL, we show a significant difference in the spectrum of CREBBP mutations in these 2 diseases, with higher frequencies of nonsense/frameshift mutations in DLBCL compared with FL. Together, our data therefore provide important links between Crebbp inactivation and Bcl2 dependence and show a role for Crebbp inactivation in the induction of Myc expression. We suggest this may parallel the role of CREBBP frameshift/nonsense mutations in DLBCL that result in loss of the protein, but may contrast the role of missense mutations in the lysine acetyltransferase domain that are more frequently observed in FL and yield an inactive protein.

  View details for DOI 10.1182/blood-2016-08-733469

  View details for PubMedID 28288979

• Crebbp loss cooperates with Bcl2 overexpression to promote lymphoma in mice BLOOD Garcia-Ramirez, I., Tadros, S., Gonzalez-Herrero, I., Martin-Lorenzo, A., Rodriguez-Hernandez, G., Moore, D., Ruiz-Roca, L., Blanco, O., Alonso-Lopez, D., De Las Rivas, J., Hartert, K., Duval, R., Klinkebiel, D., Bast, M., Vose, J., Lunning, M., Fu, K., Greiner, T., Rodrigues-Lima, F., Jimenez, R., Garcia Criado, F. J., Garcia Cenador, M. B., Brindle, P., Vicente-Duenas, C., Alizadeh, A., Sanchez-Garcia, I., Green, M. R. 2017; 129 (19): 2645-2656

  View details for DOI 10.1182/blood-2016-08-733469

  View details for Web of Science ID 000400980000011

• Antigen presentation profiling reveals recognition of lymphoma immunoglobulin neoantigens NATURE Khodadoust, M. S., Olsson, N., Wagar, L. E., Haabeth, O. A., Chen, B., Swaminathan, K., Rawson, K., Liu, C. L., Steiner, D., Lund, P., Rao, S., Zhang, L., Marceau, C., Stehr, H., Newman, A. M., Czerwinski, D. K., Carlton, V. E., Moorhead, M., Faham, M., Kohrt, H. E., Carette, J., Green, M. R., Davis, M. M., Levy, R., Elias, J. E., Alizadeh, A. A. 2017; 543 (7647): 723-?

  Abstract

  Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients. Remarkably, all discovered neoantigenic peptides were exclusively derived from the lymphoma immunoglobulin heavy- or light-chain variable regions. Although we identified MHC presentation of private polymorphic germline alleles, no mutated peptides were recovered from non-immunoglobulin somatically mutated genes. Somatic mutations within the immunoglobulin variable region were almost exclusively presented by MHC class II. We isolated circulating CD4(+) T cells specific for immunoglobulin-derived neoantigens and found these cells could mediate killing of autologous lymphoma cells. These results demonstrate that an integrative approach combining MHC isolation, peptide identification, and exome sequencing is an effective platform to uncover tumour neoantigens. Application of this strategy to human lymphoma implicates immunoglobulin neoantigens as targets for lymphoma immunotherapy.

  View details for DOI 10.1038/nature21433

  View details for Web of Science ID 000397619700057

  View details for PubMedID 28329770

• Distinct patterns of B-cell receptor signaling in non-Hodgkin lymphomas identified by single-cell profiling. Blood Myklebust, J. H., Brody, J., Kohrt, H. E., Kolstad, A., Czerwinski, D. K., Wälchli, S., Green, M. R., Trøen, G., Liestøl, K., Beiske, K., Houot, R., Delabie, J., Alizadeh, A. A., Irish, J. M., Levy, R. 2017; 129 (6): 759-770

  Abstract

  Kinases downstream of B-cell antigen receptor (BCR) represent attractive targets for therapy in non-Hodgkin lymphoma (NHL). As clinical responses vary, improved knowledge regarding activation and regulation of BCR signaling in individual patients is needed. Here, using phosphospecific flow cytometry to obtain malignant B-cell signaling profiles from 95 patients representing 4 types of NHL revealed a striking contrast between chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) tumors. Lymphoma cells from diffuse large B-cell lymphoma patients had high basal phosphorylation levels of most measured signaling nodes, whereas follicular lymphoma cells represented the opposite pattern with no or very low basal levels. MCL showed large interpatient variability in basal levels, and elevated levels for the phosphorylated forms of AKT, extracellular signal-regulated kinase, p38, STAT1, and STAT5 were associated with poor outcome. CLL tumors had elevated basal levels for the phosphorylated forms of BCR-signaling nodes (Src family tyrosine kinase, spleen tyrosine kinase [SYK], phospholipase Cγ), but had low α-BCR-induced signaling. This contrasted MCL tumors, where α-BCR-induced signaling was variable, but significantly potentiated as compared with the other types. Overexpression of CD79B, combined with a gating strategy whereby signaling output was directly quantified per cell as a function of CD79B levels, confirmed a direct relationship between surface CD79B, immunoglobulin M (IgM), and IgM-induced signaling levels. Furthermore, α-BCR-induced signaling strength was variable across patient samples and correlated with BCR subunit CD79B expression, but was inversely correlated with susceptibility to Bruton tyrosine kinase (BTK) and SYK inhibitors in MCL. These individual differences in BCR levels and signaling might relate to differences in therapy responses to BCR-pathway inhibitors.

  View details for DOI 10.1182/blood-2016-05-718494

  View details for PubMedID 28011673

  View details for PubMedCentralID PMC5301824

• Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance CANCER DISCOVERY Jeong, Y., Hoang, N. T., Lovejoy, A., Stehr, H., Newman, A. M., Gentles, A. J., Kong, W., Diana Truong, D., Martin, S., Chaudhuri, A., Heiser, D., Zhou, L., Say, C., Carter, J. N., Hiniker, S. M., Loo, B. W., West, R. B., Beachy, P., Alizadeh, A. A., Diehn, M. 2017; 7 (1): 86-101

  View details for DOI 10.1158/2159-8290.CD-16-0127

  View details for Web of Science ID 000396017700024

• Role of KEAP1/NRF2 and TP53 Mutations in Lung Squamous Cell Carcinoma Development and Radiation Resistance. Cancer discovery Jeong, Y., Hoang, N. T., Lovejoy, A., Stehr, H., Newman, A. M., Gentles, A. J., Kong, W., Truong, D., Martin, S., Chaudhuri, A., Heiser, D., Zhou, L., Say, C., Carter, J. N., Hiniker, S. M., Loo, B. W., West, R. B., Beachy, P., Alizadeh, A. A., Diehn, M. 2016

  Abstract

  Lung squamous cell carcinoma (LSCC) pathogenesis remains incompletely understood, and biomarkers predicting treatment response remain lacking. Here, we describe novel murine LSCC models driven by loss of Trp53 and Keap1, both of which are frequently mutated in human LSCCs. Homozygous inactivation of Keap1 or Trp53 promoted airway basal stem cell (ABSC) self-renewal, suggesting that mutations in these genes lead to expansion of mutant stem cell clones. Deletion of Trp53 and Keap1 in ABSCs, but not more differentiated tracheal cells, produced tumors recapitulating histologic and molecular features of human LSCCs, indicating that they represent the likely cell of origin in this model. Deletion of Keap1 promoted tumor aggressiveness, metastasis, and resistance to oxidative stress and radiotherapy (RT). KEAP1/NRF2 mutation status predicted risk of local recurrence after RT in patients with non-small lung cancer (NSCLC) and could be noninvasively identified in circulating tumor DNA. Thus, KEAP1/NRF2 mutations could serve as predictive biomarkers for personalization of therapeutic strategies for NSCLCs.We developed an LSCC mouse model involving Trp53 and Keap1, which are frequently mutated in human LSCCs. In this model, ABSCs are the cell of origin of these tumors. KEAP1/NRF2 mutations increase radioresistance and predict local tumor recurrence in radiotherapy patients. Our findings are of potential clinical relevance and could lead to personalized treatment strategies for tumors with KEAP1/NRF2 mutations. Cancer Discov; 7(1); 86-101. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1.

  View details for PubMedID 27663899

  View details for PubMedCentralID PMC5222718

• High-throughput genomic profiling of tumor-infiltrating leukocytes. Current opinion in immunology Newman, A. M., Alizadeh, A. A. 2016; 41: 77-84

  Abstract

  Tumors are complex ecosystems comprised of diverse cell types including malignant cells, mesenchymal cells, and tumor-infiltrating leukocytes (TILs). While TILs are well known to play important roles in many aspects of cancer biology, recent developments in immuno-oncology have spurred considerable interest in TILs, particularly in relation to their optimal engagement by emerging immunotherapies. Traditionally, the enumeration of TIL phenotypic diversity and composition in solid tumors has relied on resolving single cells by flow cytometry and immunohistochemical methods. However, advances in genome-wide technologies and computational methods are now allowing TILs to be profiled with increasingly high resolution and accuracy directly from RNA mixtures of bulk tumor samples. In this review, we highlight recent progress in the development of in silico tumor dissection methods, and illustrate examples of how these strategies can be applied to characterize TILs in human tumors to facilitate personalized cancer therapy.

  View details for DOI 10.1016/j.coi.2016.06.006

  View details for PubMedID 27372732

• Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer. Journal of the National Cancer Institute Gentles, A. J., Bratman, S. V., Lee, L. J., Harris, J. P., Feng, W., Nair, R. V., Shultz, D. B., Nair, V. S., Hoang, C. D., West, R. B., Plevritis, S. K., Alizadeh, A. A., Diehn, M. 2015; 107 (10)

  Abstract

  Accurate survival stratification in early-stage non-small cell lung cancer (NSCLC) could inform the use of adjuvant therapy. We developed a clinically implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables.Gene expression profiles from 1106 nonsquamous NSCLCs were used for generation and internal validation of a nine-gene molecular prognostic index (MPI). A quantitative polymerase chain reaction (qPCR) assay was developed and validated on an independent cohort of formalin-fixed paraffin-embedded (FFPE) tissues (n = 98). A prognostic score using clinical variables was generated using Surveillance, Epidemiology, and End Results data and combined with the MPI. All statistical tests for survival were two-sided.The MPI stratified stage I patients into prognostic categories in three microarray and one FFPE qPCR validation cohorts (HR = 2.99, 95% CI = 1.55 to 5.76, P < .001 in stage IA patients of the largest microarray validation cohort; HR = 3.95, 95% CI = 1.24 to 12.64, P = .01 in stage IA of the qPCR cohort). Prognostic genes were expressed in distinct tumor cell subpopulations, and genes implicated in proliferation and stem cells portended poor outcomes, while genes involved in normal lung differentiation and immune infiltration were associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR = 3.43, 95% CI = 2.18 to 5.39, P < .001 in stage I patients of the largest microarray cohort; HR = 3.99, 95% CI = 1.67 to 9.56, P < .001 in stage I patients of the qPCR cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK.The MPI incorporates genes expressed in the tumor and its microenvironment and can be implemented clinically using qPCR assays on FFPE tissues. A composite model integrating the MPI with clinical variables provides the most accurate risk stratification.

  View details for DOI 10.1093/jnci/djv211

  View details for PubMedID 26286589

• Predicting Radiotherapy Responses and Treatment Outcomes Through Analysis of Circulating Tumor DNA. Seminars in radiation oncology Chaudhuri, A. A., Binkley, M. S., Osmundson, E. C., Alizadeh, A. A., Diehn, M. 2015; 25 (4): 305-312

  Abstract

  Tumors continually shed DNA into the blood where it can be detected as circulating tumor DNA (ctDNA). Although this phenomenon has been recognized for decades, techniques that are sensitive and specific enough to robustly detect ctDNA have only become available recently. Quantification of ctDNA represents a new approach for cancer detection and disease burden quantification that has the potential to revolutionize response assessment and personalized treatment in radiation oncology. Analysis of ctDNA has many potential applications, including detection of minimal residual disease following radiotherapy, noninvasive tumor genotyping, and early detection of tumor recurrence. Ultimately, ctDNA-based assays could lead to personalization of therapy based on identification of somatic alterations present in tumors and changes in ctDNA concentrations before and after treatment. In this review, we discuss methods of ctDNA detection and clinical applications of ctDNA-based biomarkers in radiation oncology, with a focus on recently developed techniques that use next-generation sequencing for ctDNA quantification.

  View details for DOI 10.1016/j.semradonc.2015.05.001

  View details for PubMedID 26384278

  View details for PubMedCentralID PMC4575502

• Integrating Tumor and Stromal Gene Expression Signatures With Clinical Indices for Survival Stratification of Early-Stage Non-Small Cell Lung Cancer. Journal of the National Cancer Institute Gentles, A. J., Bratman, S. V., Lee, L. J., Harris, J. P., Feng, W., Nair, R. V., Shultz, D. B., Nair, V. S., Hoang, C. D., West, R. B., Plevritis, S. K., Alizadeh, A. A., Diehn, M. 2015; 107 (10)

  Abstract

  Accurate survival stratification in early-stage non-small cell lung cancer (NSCLC) could inform the use of adjuvant therapy. We developed a clinically implementable mortality risk score incorporating distinct tumor microenvironmental gene expression signatures and clinical variables.Gene expression profiles from 1106 nonsquamous NSCLCs were used for generation and internal validation of a nine-gene molecular prognostic index (MPI). A quantitative polymerase chain reaction (qPCR) assay was developed and validated on an independent cohort of formalin-fixed paraffin-embedded (FFPE) tissues (n = 98). A prognostic score using clinical variables was generated using Surveillance, Epidemiology, and End Results data and combined with the MPI. All statistical tests for survival were two-sided.The MPI stratified stage I patients into prognostic categories in three microarray and one FFPE qPCR validation cohorts (HR = 2.99, 95% CI = 1.55 to 5.76, P < .001 in stage IA patients of the largest microarray validation cohort; HR = 3.95, 95% CI = 1.24 to 12.64, P = .01 in stage IA of the qPCR cohort). Prognostic genes were expressed in distinct tumor cell subpopulations, and genes implicated in proliferation and stem cells portended poor outcomes, while genes involved in normal lung differentiation and immune infiltration were associated with superior survival. Integrating the MPI with clinical variables conferred greatest prognostic power (HR = 3.43, 95% CI = 2.18 to 5.39, P < .001 in stage I patients of the largest microarray cohort; HR = 3.99, 95% CI = 1.67 to 9.56, P < .001 in stage I patients of the qPCR cohort). Finally, the MPI was prognostic irrespective of somatic alterations in EGFR, KRAS, TP53, and ALK.The MPI incorporates genes expressed in the tumor and its microenvironment and can be implemented clinically using qPCR assays on FFPE tissues. A composite model integrating the MPI with clinical variables provides the most accurate risk stratification.

  View details for DOI 10.1093/jnci/djv211

  View details for PubMedID 26286589

• Organocatalytic removal of formaldehyde adducts from RNA and DNA bases NATURE CHEMISTRY Karmakar, S., Harcourt, E. M., Hewings, D. S., Lovejoy, A. F., Kurtz, D. M., Ehrenschwender, T., Barandun, L. J., Roost, C., Alizadeh, A. A., Kool, E. T. 2015; 7 (9): 752-758

  View details for DOI 10.1038/NCHEM.2307

  View details for Web of Science ID 000360191800014

• Organocatalytic removal of formaldehyde adducts from RNA and DNA bases. Nature chemistry Karmakar, S., Harcourt, E. M., Hewings, D. S., Scherer, F., Lovejoy, A. F., Kurtz, D. M., Ehrenschwender, T., Barandun, L. J., Roost, C., Alizadeh, A. A., Kool, E. T. 2015; 7 (9): 752-758

  Abstract

  Formaldehyde is universally used to fix tissue specimens, where it forms hemiaminal and aminal adducts with biomolecules, hindering the ability to retrieve molecular information. Common methods for removing these adducts involve extended heating, which can cause extensive degradation of nucleic acids, particularly RNA. Here, we show that water-soluble bifunctional catalysts (anthranilates and phosphanilates) speed the reversal of formaldehyde adducts of mononucleotides over standard buffers. Studies with formaldehyde-treated RNA oligonucleotides show that the catalysts enhance adduct removal, restoring unmodified RNA at 37 °C even when extensively modified, while avoiding the high temperatures that promote RNA degradation. Experiments with formalin-fixed, paraffin-embedded cell samples show that the catalysis is compatible with common RNA extraction protocols, with detectable RNA yields increased by 1.5-2.4-fold using a catalyst under optimized conditions and by 7-25-fold compared with a commercial kit. Such catalytic strategies show promise for general use in reversing formaldehyde adducts in clinical specimens.

  View details for DOI 10.1038/nchem.2307

  View details for PubMedID 26291948

  View details for PubMedCentralID PMC4545578

• Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging PLOS ONE Whiting, C. C., Siebert, J., Newman, A. M., Du, H., Alizadeh, A. A., Goronzy, J., Weyand, C. M., Krishnan, E., Fathman, C. G., Maecker, H. T. 2015; 10 (7)

  View details for DOI 10.1371/journal.pone.0133627

  View details for Web of Science ID 000358547600123

• Potential clinical utility of ultrasensitive circulating tumor DNA detection with CAPP-Seq. Expert review of molecular diagnostics Bratman, S. V., Newman, A. M., Alizadeh, A. A., Diehn, M. 2015: 1–5

  Abstract

  Tumors continually shed DNA into the circulation, where it can be noninvasively accessed. The ability to accurately detect circulating tumor DNA (ctDNA) could significantly impact the management of patients with nearly every cancer type. Quantitation of ctDNA could allow objective response assessment, detection of minimal residual disease and noninvasive tumor genotyping. The latter application overcomes the barriers currently limiting repeated tumor tissue sampling during therapy. Recent technical advancements have improved upon the sensitivity, specificity and feasibility of ctDNA detection and promise to enable innovative clinical applications. Here, we focus on the potential clinical utility of ctDNA analysis using CAncer Personalized Profiling by deep Sequencing (CAPP-Seq), a novel next-generation sequencing-based approach for ultrasensitive ctDNA detection. Applications of CAPP-Seq for the personalization of cancer detection and therapy are discussed.

  View details for DOI 10.1586/14737159.2015.1019476

  View details for PubMedID 25773944

• Large-Scale and Comprehensive Immune Profiling and Functional Analysis of Normal Human Aging. PloS one Whiting, C. C., Siebert, J., Newman, A. M., Du, H., Alizadeh, A. A., Goronzy, J., Weyand, C. M., Krishnan, E., Fathman, C. G., Maecker, H. T. 2015; 10 (7)

  Abstract

  While many age-associated immune changes have been reported, a comprehensive set of metrics of immune aging is lacking. Here we report data from 243 healthy adults aged 40-97, for whom we measured clinical and functional parameters, serum cytokines, cytokines and gene expression in stimulated and unstimulated PBMC, PBMC phenotypes, and cytokine-stimulated pSTAT signaling in whole blood. Although highly heterogeneous across individuals, many of these assays revealed trends by age, sex, and CMV status, to greater or lesser degrees. Age, then sex and CMV status, showed the greatest impact on the immune system, as measured by the percentage of assay readouts with significant differences. An elastic net regression model could optimally predict age with 14 analytes from different assays. This reinforces the importance of multivariate analysis for defining a healthy immune system. These data provide a reference for others measuring immune parameters in older people.

  View details for DOI 10.1371/journal.pone.0133627

  View details for PubMedID 26197454

• A Simple Method for Estimating Interactions Between a Treatment and a Large Number of Covariates JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION Tian, L., Alizadeh, A. A., Gentles, A. J., Tibshirani, R. 2014; 109 (508): 1517-1532

  View details for DOI 10.1080/01621459.2014.951443

  View details for Web of Science ID 000346797000016

• Mixed Phenotype Acute Leukemia A Study of 61 Cases Using World Health Organization and European Group for the Immunological Classification of Leukaemias Criteria AMERICAN JOURNAL OF CLINICAL PATHOLOGY Weinberg, O. K., Seetharam, M., Ren, L., Alizadeh, A., Arber, D. A. 2014; 142 (6): 803-808

  Abstract

  The 2008 World Health Organization (WHO) classification system grouped bilineal and biphenotypic acute leukemias together under a new heading of mixed phenotype acute leukemia (MPAL). The lineage-specific marker criteria have also changed for a diagnosis of MPAL. The goal of this study was to characterize clinical significance of this new group.Sixty-one patients diagnosed with MPAL using either European Group for the Immunological Classification of Leukaemias (EGIL) criteria or 2008 WHO criteria were included in this study.Sixteen patients (26%) diagnosed with acute biphenotypic leukemia using EGIL criteria did not fulfill 2008 WHO criteria for MPAL. Cytogenetic data were available for 32 patients, and the most common abnormality was t(9;22) (five of 32 cases). Clinical outcome data suggested that younger patients with MPAL (≤21 years) had better overall survival (OS) in both the EGIL and WHO groups (EGIL, P = .0403; WHO, P = .0601). Compared with 177 patients with acute myeloid leukemia (AML), MPAL patients had better OS (P = .0003) and progression-free survival (P = .0001). However, no difference in OS between MPAL and 387 patients with acute lymphoblastic leukemia was present (P = .599).As defined by the 2008 WHO classification, fewer patients are now classified as having MPAL than with the EGIL criteria. In this study, patients with MPAL have a better clinical outcome compared with patients with AML.

  View details for DOI 10.1309/AJCPPVUPOTUVOIB5

  View details for Web of Science ID 000345053900012

  View details for PubMedID 25389334

• Common progenitor cells in mature B-cell malignancies: implications for therapy. Current opinion in hematology Green, M. R., Alizadeh, A. A. 2014; 21 (4): 333-340

  Abstract

  This review summarizes the recent progress in defining the patterns of genetic evolution giving rise to relapse in follicular lymphoma and multiple myeloma, and discusses their implications with respect to 'personalized medicine'.High-throughput sequencing studies have uncovered a large degree of clonal heterogeneity within tumors, and found that subclones have a variable contribution to relapse. Recent studies aimed at defining patterns of clonal evolution have revealed that serial tumors in some malignancies share their ancestry in a less evolved common progenitor cell (CPC) that bears only a subset of the mutations that are present in the fully evolved tumors that present clinically. This pattern of 'divergent evolution' means that the majority of 'actionable mutations' in tumor specimens are absent within the progenitors that give rise to relapse.Follicular lymphoma and multiple myeloma are clinically, biologically and genetically distinct mature B-cell malignancies. However, recent studies have found them to share important similarities in their patterns of genetic evolution. Tumor cells that constitute subclonal populations within these tumors, or between consecutive tumors, share their origins within a genetically less evolved common progenitor cell. This pattern of evolution indicates that current therapies are unable to eradicate these less evolved populations that are at the root of relapse. This suggests that in order to obtain the best results with modern 'targeted therapies' that are directed towards 'actionable mutations', these mutations should be considered within the context of the evolutionary stage at which mutations are acquired, not simply on a presence or absence basis.

  View details for DOI 10.1097/MOH.0000000000000049

  View details for PubMedID 24811163

• Common progenitor cells in mature B-cell malignancies: implications for therapy CURRENT OPINION IN HEMATOLOGY Green, M. R., Alizadeh, A. A. 2014; 21 (4): 333-340

  View details for DOI 10.1097/MOH.0000000000000049

  View details for Web of Science ID 000337155600012

• Active idiotypic vaccination versus control immunotherapy for follicular lymphoma. Journal of clinical oncology Levy, R., Ganjoo, K. N., Leonard, J. P., Vose, J. M., Flinn, I. W., Ambinder, R. F., Connors, J. M., Berinstein, N. L., Belch, A. R., Bartlett, N. L., Nichols, C., Emmanouilides, C. E., Timmerman, J. M., Gregory, S. A., Link, B. K., Inwards, D. J., Freedman, A. S., Matous, J. V., Robertson, M. J., Kunkel, L. A., Ingolia, D. E., Gentles, A. J., Liu, C. L., Tibshirani, R., Alizadeh, A. A., Denney, D. W. 2014; 32 (17): 1797-1803

  Abstract

  Idiotypes (Ids), the unique portions of tumor immunoglobulins, can serve as targets for passive and active immunotherapies for lymphoma. We performed a multicenter, randomized trial comparing a specific vaccine (MyVax), comprising Id chemically coupled to keyhole limpet hemocyanin (KLH) plus granulocyte macrophage colony-stimulating factor (GM-CSF) to a control immunotherapy with KLH plus GM-CSF.Patients with previously untreated advanced-stage follicular lymphoma (FL) received eight cycles of chemotherapy with cyclophosphamide, vincristine, and prednisone. Those achieving sustained partial or complete remission (n=287 [44%]) were randomly assigned at a ratio of 2:1 to receive one injection per month for 7 months of MyVax or control immunotherapy. Anti-Id antibody responses (humoral immune responses [IRs]) were measured before each immunization. The primary end point was progression-free survival (PFS). Secondary end points included IR and time to subsequent antilymphoma therapy.At a median follow-up of 58 months, no significant difference was observed in either PFS or time to next therapy between the two arms. In the MyVax group (n=195), anti-Id IRs were observed in 41% of patients, with a median PFS of 40 months, significantly exceeding the median PFS observed in patients without such Id-induced IRs and in those receiving control immunotherapy.This trial failed to demonstrate clinical benefit of specific immunotherapy. The subset of vaccinated patients mounting specific anti-Id responses had superior outcomes. Whether this reflects a therapeutic benefit or is a marker for more favorable underlying prognosis requires further study.

  View details for DOI 10.1200/JCO.2012.43.9273

  View details for PubMedID 24799467

  View details for PubMedCentralID PMC4039868

• Tumor antigen discovery through translation of the cancer genome. Immunologic research Khodadoust, M. S., Alizadeh, A. A. 2014; 58 (2-3): 292-299

  Abstract

  Cancer cells harbor unique mutations that theoretically create corresponding unique tumor-specific antigens. This class of mutated antigens represents an attractive target for cancer immunotherapy, but their identification has been cumbersome. By combining cancer genome sequencing with computational analysis of MHC binding, it is possible to predict and rank all of the possible mutated tumor antigens. This form of antigen screen is being combined with high throughput methods to measure the immune response to each candidate mutated antigen. Using these techniques, it is possible to systematically test each mutated tumor antigens for an associated immune response. Only a small fraction of the putative mutated antigens tested in this manner have been found to elicit an immune response, yet these responses appear to be both robust and durable. It is becoming increasingly clear that these mutated tumor antigens are an important target in the antitumor response. Studies incorporating this approach promise to improve our understanding of the inherent immunogenicity of individual cancers, potentially providing an explanation for the varying clinical responses to novel immunotherapeutic agents.

  View details for DOI 10.1007/s12026-014-8505-4

  View details for PubMedID 24718952

• Transient expression of Bcl6 is sufficient for oncogenic function and induction of mature B-cell lymphoma. Nature communications Green, M. R., Vicente-Dueñas, C., Romero-Camarero, I., Long Liu, C., Dai, B., González-Herrero, I., García-Ramírez, I., Alonso-Escudero, E., Iqbal, J., Chan, W. C., Campos-Sanchez, E., Orfao, A., Pintado, B., Flores, T., Blanco, O., Jiménez, R., Martínez-Climent, J. A., Criado, F. J., Cenador, M. B., Zhao, S., Natkunam, Y., Lossos, I. S., Majeti, R., Melnick, A., Cobaleda, C., Alizadeh, A. A., Sánchez-García, I. 2014; 5: 3904-?

  Abstract

  Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma and can be separated into two subtypes based upon molecular features with similarities to germinal centre B-cells (GCB-like) or activated B-cells (ABC-like). Here we identify gain of 3q27.2 as being significantly associated with adverse outcome in DLBCL and linked with the ABC-like subtype. This lesion includes the BCL6 oncogene, but does not alter BCL6 transcript levels or target-gene repression. Separately, we identify expression of BCL6 in a subset of human haematopoietic stem/progenitor cells (HSPCs). We therefore hypothesize that BCL6 may act by 'hit-and-run' oncogenesis. We model this hit-and-run mechanism by transiently expressing Bcl6 within murine HSPCs, and find that it causes mature B-cell lymphomas that lack Bcl6 expression and target-gene repression, are transcriptionally similar to post-GCB cells, and show epigenetic changes that are conserved from HSPCs to mature B-cells. Together, these results suggest that BCL6 may function in a 'hit-and-run' role in lymphomagenesis.

  View details for DOI 10.1038/ncomms4904

  View details for PubMedID 24887457

• A Simple Method for Estimating Interactions between a Treatment and a Large Number of Covariates. Journal of the American Statistical Association Tian, L., Alizadeh, A. A., Gentles, A. J., Tibshirani, R. 2014; 109 (508): 1517–32

  Abstract

  We consider a setting in which we have a treatment and a potentially large number of covariates for a set of observations, and wish to model their relationship with an outcome of interest. We propose a simple method for modeling interactions between the treatment and covariates. The idea is to modify the covariate in a simple way, and then fit a standard model using the modified covariates and no main effects. We show that coupled with an efficiency augmentation procedure, this method produces clinically meaningful estimators in a variety of settings. It can be useful for practicing personalized medicine: determining from a large set of biomarkers the subset of patients that can potentially benefit from a treatment. We apply the method to both simulated datasets and real trial data. The modified covariates idea can be used for other purposes, for example, large scale hypothesis testing for determining which of a set of covariates interact with a treatment variable.

  View details for DOI 10.1080/01621459.2014.951443

  View details for PubMedID 25729117

  View details for PubMedCentralID PMC4338439

• Hit-and-run lymphomagenesis by the Bcl6 oncogene. Cell cycle Green, M. R., Vicente-Dueñas, C., Alizadeh, A. A., Sánchez-García, I. 2014; 13 (12): 1831-1832

  View details for DOI 10.4161/cc.29326

  View details for PubMedID 24867153

• Identification of gene microarray expression profiles in patients with chronic graft-versus-host disease following allogeneic hematopoietic cell transplantation. Clinical immunology Kohrt, H. E., Tian, L., Li, L., Alizadeh, A. A., Hsieh, S., Tibshirani, R. J., Strober, S., Sarwal, M., Lowsky, R. 2013; 148 (1): 124-135

  Abstract

  Chronic graft-versus-host disease (GVHD) results in significant morbidity and mortality, limiting the benefit of allogeneic hematopoietic cell transplantation (HCT). Peripheral blood gene expression profiling of the donor immune repertoire following HCT may provide associated genes and pathways thereby improving the pathophysiologic understanding of chronic GVHD. We profiled 70 patients and identified candidate genes that provided mechanistic insight in the biologic pathways that underlie chronic GVHD. Our data revealed that the dominant gene signature in patients with chronic GVHD represented compensatory responses that control inflammation and included the interleukin-1 decoy receptor, IL-1 receptor type II, and genes that were profibrotic and associated with the IL-4, IL-6 and IL-10 signaling pathways. In addition, we identified three genes that were important regulators of extracellular matrix. Validation of this discovery phase study will determine if the identified genes have diagnostic, prognostic or therapeutic implications.

  View details for DOI 10.1016/j.clim.2013.04.013

  View details for PubMedID 23685278

• Utility in prognostic value added by molecular profiles for diffuse large B-cell lymphoma. Blood Gentles, A. J., Alizadeh, A. A. 2013; 121 (15): 3052-3054

  View details for DOI 10.1182/blood-2013-01-477521

  View details for PubMedID 23580636

• Rituximab use and survival after diffuse large B-cell or follicular lymphoma: a population-based study. Leukemia & lymphoma Keegan, T. H., Moy, L. M., Foran, J. M., Alizadeh, A. A., Chang, E. T., Shema, S. J., Schupp, C. W., Clarke, C. A., Glaser, S. L. 2013; 54 (4): 743-751

  Abstract

  To determine whether reported socioeconomic disparities in survival might be related to treatment, we examined patient and tumor characteristics associated with receipt of rituximab and survival in the National Cancer Institute's Patterns of Care Studies (2003 and 2008) for patients with diffuse large B-cell (DLBCL) and follicular (FL) lymphoma. Patients with DLBCL (n = 1192) were less likely to receive rituximab if they were older, black or Asian, lacked private medical insurance, had impaired performance status, had no lactate dehydrogenase measurements or were diagnosed with stage I disease. Patients with FL (n = 476) were less likely to receive rituximab if they were unmarried or non-Hispanic white. Receipt of rituximab did not differ by neighborhood median income. Treatment with rituximab was associated with better survival for patients with DLBCL, but not patients with FL. Lower rituximab use in patients with DLBCL without private insurance suggests that previously identified socioeconomic disparities in survival may, in part, be explained by receipt of rituximab.

  View details for DOI 10.3109/10428194.2012.727415

  View details for PubMedID 22957852

• Rituximab use and survival after diffuse large B-cell or follicular lymphoma: a population-based study LEUKEMIA & LYMPHOMA Keegan, T. H., Moy, L. M., Foran, J. M., Alizadeh, A. A., Chang, E. T., Shema, S. J., Schupp, C. W., Clarke, C. A., Glaser, S. L. 2013; 54 (4): 743-751

  View details for DOI 10.3109/10428194.2012.727415

  View details for Web of Science ID 000315898100015

  View details for PubMedID 22957852

• High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Blood Myklebust, J. H., Irish, J. M., Brody, J., Czerwinski, D. K., Houot, R., Kohrt, H. E., Timmerman, J., Said, J., Green, M. R., Delabie, J., Kolstad, A., Alizadeh, A. A., Levy, R. 2013; 121 (8): 1367-1376

  Abstract

  Defects in T-cell function in patients with cancer might influence their capacity to mount efficient antitumor immune responses. Here, we identified highly reduced IL-4-, IL-10-, and IL-21-induced phosphorylation of STAT6 and STAT3 in tumor-infiltrating T cells (TILs) in follicular lymphoma (FL) tumors, contrasting other non-Hodgkin lymphoma TILs. By combining phospho-protein-specific flow cytometry with several T-cell markers, we identified that CD4(+)CD45RO(+)CD62L(-) FL TILs were largely nonresponsive to cytokines, in contrast to the corresponding autologous peripheral blood subset. We observed differential expression of the inhibitory receptor PD-1 in FL TILs and peripheral blood T cells. Furthermore, CD4(+)PD-1(hi) FL TILs, containing T(FH) and non-T(FH) cells, had lost their cytokine responsiveness, whereas PD-1 TILs had normal cytokine signaling. However, this phenomenon was not tumor specific, because tonsil T cells were similar to FL TILs. FL tumor cells were negative for PD-1 ligands, but PD-L1(+) histiocytes were found within the T cell-rich zone of the neoplastic follicles. Disruption of the microenvironment and in vitro culture of FL TILs could restore cytokine signaling in the PD-1(hi) subset. Because FL TILs in vivo probably receive suppressive signals through PD-1, this provides a rationale for testing PD-1 Ab in combination with immunotherapy in patients with FL.

  View details for DOI 10.1182/blood-2012-04-421826

  View details for PubMedID 23297127

  View details for PubMedCentralID PMC3578953

• Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation. Nature communications Romero-Camarero, I., Jiang, X., Natkunam, Y., Lu, X., Vicente-Dueñas, C., Gonzalez-Herrero, I., Flores, T., Garcia, J. L., McNamara, G., Kunder, C., Zhao, S., Segura, V., Fontan, L., Martínez-Climent, J. A., García-Criado, F. J., Theis, J. D., Dogan, A., Campos-Sánchez, E., Green, M. R., Alizadeh, A. A., Cobaleda, C., Sánchez-García, I., Lossos, I. S. 2013; 4: 1338-?

  Abstract

  The human germinal centre-associated lymphoma gene is specifically expressed in germinal centre B-lymphocytes and germinal centre-derived B-cell lymphomas, but its function is largely unknown. Here we demonstrate that human germinal centre-associated lymphoma directly binds to Syk in B cells, increases its kinase activity on B-cell receptor stimulation and leads to enhanced activation of Syk downstream effectors. To further investigate these findings in vivo, human germinal centre-associated lymphoma transgenic mice were generated. Starting from 12 months of age these mice developed polyclonal B-cell lymphoid hyperplasia, hypergammaglobulinemia and systemic reactive amyloid A (AA) amyloidosis, leading to shortened survival. The lymphoid hyperplasia in the human germinal centre-associated lymphoma transgenic mice are likely attributable to enhanced B-cell receptor signalling as shown by increased Syk phosphorylation, ex vivo B-cell proliferation and increased RhoA activation. Overall, our study shows for the first time that the germinal centre protein human germinal centre-associated lymphoma regulates B-cell receptor signalling in B-lymphocytes which, without appropriate control, may lead to B-cell lymphoproliferation.

  View details for DOI 10.1038/ncomms2334

  View details for PubMedID 23299888

  View details for PubMedCentralID PMC3545406

• Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation NATURE COMMUNICATIONS Romero-Camarero, I., Jiang, X., Natkunam, Y., Lu, X., Vicente-Duenas, C., Gonzalez-Herrero, I., Flores, T., Luis Garcia, J., McNamara, G., Kunder, C., Zhao, S., Segura, V., Fontan, L., Martinez-Climent, J. A., Javier Garcia-Criado, F., Theis, J. D., Dogan, A., Campos-Sanchez, E., Green, M. R., Alizadeh, A. A., Cobaleda, C., Sanchez-Garcia, I., Lossos, I. S. 2013; 4

  Abstract

  The human germinal centre-associated lymphoma gene is specifically expressed in germinal centre B-lymphocytes and germinal centre-derived B-cell lymphomas, but its function is largely unknown. Here we demonstrate that human germinal centre-associated lymphoma directly binds to Syk in B cells, increases its kinase activity on B-cell receptor stimulation and leads to enhanced activation of Syk downstream effectors. To further investigate these findings in vivo, human germinal centre-associated lymphoma transgenic mice were generated. Starting from 12 months of age these mice developed polyclonal B-cell lymphoid hyperplasia, hypergammaglobulinemia and systemic reactive amyloid A (AA) amyloidosis, leading to shortened survival. The lymphoid hyperplasia in the human germinal centre-associated lymphoma transgenic mice are likely attributable to enhanced B-cell receptor signalling as shown by increased Syk phosphorylation, ex vivo B-cell proliferation and increased RhoA activation. Overall, our study shows for the first time that the germinal centre protein human germinal centre-associated lymphoma regulates B-cell receptor signalling in B-lymphocytes which, without appropriate control, may lead to B-cell lymphoproliferation.

  View details for DOI 10.1038/ncomms2334

  View details for Web of Science ID 000316614600008

  View details for PubMedID 23299888

  View details for PubMedCentralID PMC3545406

• Hierarchy in Somatic Mutations Arising During Genomic Evolution and Progression of Follicular Lymphoma 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Green, M. R., Gentles, A. J., Nair, R. V., Irish, J. M., Levy, R., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838900311

• Targeting B-Cell Lymphoma with Idiotype-Specific Peptibodies: Toward a Personalized and Tumor-Specific Therapy 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Torchia, J. A., Ng, P. P., Chen, H., Kohrt, H. E., Marabelle, A., Alizadeh, A. A., Levy, R. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000314049600205

• The Diffuse Large B-Cell Lymphoma Infiltrating Macrophage Transcriptome Signature Is Enriched for Both M1 and M2 Genes and Provides an Excellent Platform for Functional Validation of Macrophage Biology in DLBCL 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Coutinho, R., Newman, A. M., Rossignoli, G., Day, W., Miraki-Moud, F., Chaplin, T., Marzec, J., Petty, R. D., Iqbal, S., Matthews, J., Alizadeh, A. A., Gribben, J. G. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838900169

• Systematic Deconvolution of Hematolymphoid Tumor Transcriptomes Reveals Infiltrating Immune Cell Signatures Related to Survival 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Newman, A. M., Gentles, A. J., Plevritis, S. K., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000314049601071

• Genome-Wide Characterization of Human Hematopoietic Progenitor Cell Heterogeneity by Expression Profiling of Single Cells: A Pilot Study 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Liu, C. L., Dai, B., Newman, A. M., Majeti, R., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838902335

• Identification of Candidate Transcriptional Biomarkers Associated with Chronic Graft-Versus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation 54th Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Kohrt, H. E., Tian, L., Li, L., Alizadeh, A. A., Hsieh, S., Strober, S., Sarwal, M., Lowsky, R. AMER SOC HEMATOLOGY. 2012

  View details for Web of Science ID 000313838905099

• Self-antigen recognition by follicular lymphoma B-cell receptors BLOOD Sachen, K. L., Strohman, M. J., Singletary, J., Alizadeh, A. A., Kattah, N. H., Lossos, C., Mellins, E. D., Levy, S., Levy, R. 2012; 120 (20): 4182-4190

  Abstract

  Follicular lymphoma is a monoclonal B-cell malignancy with each patient's tumor expressing a unique cell surface immunoglobulin (Ig), or B-cell receptor (BCR), that can potentially recognize antigens and/or transduce signals into the tumor cell. Here we evaluated the reactivity of tumor derived Igs for human tissue antigens. Self-reactivity was observed in 26% of tumor Igs (25 of 98). For one follicular lymphoma patient, the recognized self-antigen was identified as myoferlin. This patient's tumor cells bound recombinant myoferlin in proportion to their level of BCR expression, and the binding to myoferlin was preserved despite ongoing somatic hypermutation of Ig variable regions. Furthermore, BCR-mediated signaling was induced after culture of tumor cells with myoferlin. These results suggest that antigen stimulation may provide survival signals to tumor cells and that there is a selective pressure to preserve antigen recognition as the tumor evolves.

  View details for DOI 10.1182/blood-2012-05-427534

  View details for Web of Science ID 000311637400013

  View details for PubMedID 23024238

  View details for PubMedCentralID PMC3501716

• Cell-free DNA as a Biomarker of Residual Disease Following Radiation Therapy for Non-small Cell Lung Cancer 54th Annual Meeting of the American-Society-for-Radiation-Oncology (ASTRO) Bratman, S. V., Eclov, N. C., Modlin, L. A., Neal, J., Loo, B. W., Wu, G., Richardson, K., Newman, A. M., Alizadeh, A., Diehn, M. ELSEVIER SCIENCE INC. 2012: S713–S713

  View details for Web of Science ID 000310542902315

• Absolute lymphocyte count at day 28 independently predicts event-free and overall survival in adults with newly diagnosed acute lymphoblastic leukemia AMERICAN JOURNAL OF HEMATOLOGY Sun, D., Elson, P., Liedtke, M., Medeiros, B. C., Earl, M., Alizadeh, A., Bates, J., Sekeres, M. A., Coutre, S., Kalaycio, M., Sobecks, R., Copelan, E., Advani, A. S. 2012; 87 (10): 957-960

  Abstract

  We investigated the prognostic impact of absolute lymphocyte count (ALC) following induction chemotherapy in newly diagnosed adult acute lymphoblastic leukemia (ALL). Patients with ALC ≥350 cells/μL at day 28 had a median overall survival (OS) of 47.4 months when compared with 17.6 months for those with an ALC <350 cells/μL (HR = 1.98, P = 0.007). Among patients who achieved a complete remission, median event-free survival (EFS) for those with ALC ≥350 cells/μL on day 28 was 42.1 months when compared with 13.9 months in those with ALC <350 cells/μL (HR = 2.08, P = 0.006). In multivariable analysis, the ALC on day 28 (<350 cells/μL vs. ≥350 cells/μL, P ≤ .0004 for OS and EFS) along with WBC at diagnosis (≤6.0 or >30.0 K/μL vs. >6.0-30.0 K/μL, P ≤ 0.002 for OS and EFS) and cytogenetics (abnormal vs. normal, P = 0.002 for OS and P = 0.02 for EFS) were independent prognostic factors of both OS and EFS. Combining these three factors segregates patients in three well-defined risk groups. These data suggest that ALC can be used in combination with other prognostic features to better predict outcome and that targeting the immune system to improve ALC may be a worthwhile strategy in ALL.

  View details for DOI 10.1002/ajh.23279

  View details for Web of Science ID 000309065700081

  View details for PubMedID 22729847

• Role of Smad Proteins in Resistance to BMP-Induced Growth Inhibition in B-Cell Lymphoma PLOS ONE Huse, K., Bakkebo, M., Walchli, S., Oksvold, M. P., Hilden, V. I., Forfang, L., Bredahl, M. L., Liestol, K., Alizadeh, A. A., Smeland, E. B., Myklebust, J. H. 2012; 7 (10)

  Abstract

  Bone morphogenetic protein (BMP) expression and signaling are altered in a variety of cancers, but the functional impact of these alterations is uncertain. In this study we investigated the impact of expression of multiple BMPs and their signaling pathway components in human B-cell lymphoma. BMP messages, in particular BMP7, were detected in normal and malignant B cells. Addition of exogenous BMPs inhibited DNA synthesis in most lymphoma cell lines examined, but some cell lines were resistant. Tumor specimens from three out of five lymphoma patients were also resistant to BMPs, as determined by no activation of the BMP effectors Smad1/5/8. We have previously shown that BMP-7 potently induced apoptosis in normal B cells, which was in contrast to no or little inhibitory effect of this BMP in the lymphoma cells tested. BMP-resistance mechanisms were investigated by comparing sensitive and resistant cell lines. While BMP receptors are downregulated in many cancers, we documented similar receptor levels in resistant and sensitive lymphoma cells. We found a positive correlation between activation of Smad1/5/8 and inhibition of DNA synthesis. Gene expression analysis of two independent data sets showed that the levels of inhibitory Smads varied across different B-cell lymphoma. Furthermore, stable overexpression of Smad7 in two different BMP-sensitive cell lines with low endogenous levels of SMAD7, rendered them completely resistant to BMPs. This work highlights the role of Smads in determining the sensitivity to BMPs and shows that upregulation of Smad7 in cancer cells is sufficient to escape the negative effects of BMPs.

  View details for DOI 10.1371/journal.pone.0046117

  View details for Web of Science ID 000309388500019

  View details for PubMedID 23049692

• CD137 Is Expressed in Follicular Dendritic Cell Tumors and in Classical Hodgkin and T-Cell Lymphomas Diagnostic and Therapeutic Implications AMERICAN JOURNAL OF PATHOLOGY Anderson, M. W., Zhao, S., Freud, A. G., Czerwinski, D. K., Kohrt, H., Alizadeh, A. A., Houot, R., Azambuja, D., Biasoli, I., Morais, J. C., Spector, N., Molina-Kirsch, H. F., Warnke, R. A., Levy, R., Natkunam, Y. 2012; 181 (3): 795-803

  Abstract

  CD137 (also known as 4-1BB and TNFRSF9) is a member of the tumor necrosis factor receptor superfamily. Originally identified as a costimulatory molecule expressed by activated T cells and NK cells, CD137 is also expressed by follicular dendritic cells, monocytes, mast cells, granulocytes, and endothelial cells. Anti-CD137 immunotherapy has recently shown promise as a treatment for solid tumors and lymphoid malignancies in preclinical models. We defined the expression of CD137 protein in both normal and neoplastic hematolymphoid tissue. CD137 protein is expressed by follicular dendritic cells in the germinal center and scattered paracortical T cells, but not by normal germinal-center B cells, bone marrow progenitor cells, or maturing thymocytes. CD137 protein is expressed by a select group of hematolymphoid tumors, including classical Hodgkin lymphoma, T-cell and NK/T-cell lymphomas, and follicular dendritic cells neoplasms. CD137 is a novel diagnostic marker of these tumors and suggests a possible target for tumor-directed antibody therapy.

  View details for DOI 10.1016/j.ajpath.2012.05.015

  View details for Web of Science ID 000309251100009

  View details for PubMedID 22901750

  View details for PubMedCentralID PMC3432425

• The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses JOURNAL OF EXPERIMENTAL MEDICINE Pachynski, R. K., Zabel, B. A., Kohrt, H. E., Tejeda, N. M., Monnier, J., Swanson, C. D., Holzer, A. K., Gentles, A. J., Sperinde, G. V., Edalati, A., Hadeiba, H. A., Alizadeh, A. A., Butcher, E. C. 2012; 209 (8): 1427-1435

  Abstract

  Infiltration of specialized immune cells regulates the growth and survival of neoplasia. Here, in a survey of public whole genome expression datasets we found that the gene for chemerin, a widely expressed endogenous chemoattractant protein, is down-regulated in melanoma as well as other human tumors. Moreover, high chemerin messenger RNA expression in tumors correlated with improved outcome in human melanoma. In experiments using the B16 transplantable mouse melanoma, tumor-expressed chemerin inhibited in vivo tumor growth without altering in vitro proliferation. Growth inhibition was associated with an altered profile of tumor-infiltrating cells with an increase in natural killer (NK) cells and a relative reduction in myeloid-derived suppressor cells and putative immune inhibitory plasmacytoid dendritic cells. Tumor inhibition required host expression of CMKLR1 (chemokine-like receptor 1), the chemoattractant receptor for chemerin, and was abrogated by NK cell depletion. Intratumoral injection of chemerin also inhibited tumor growth, suggesting the potential for therapeutic application. These results show that chemerin, whether expressed by tumor cells or within the tumor environment, can recruit host immune defenses that inhibit tumorigenesis and suggest that down-regulation of chemerin may be an important mechanism of tumor immune evasion.

  View details for DOI 10.1084/jem.20112124

  View details for Web of Science ID 000307016500006

  View details for PubMedID 22753924

  View details for PubMedCentralID PMC3409495

• A retrospective study evaluating the efficacy and safety of bendamustine in the treatment of mantle cell lymphoma LEUKEMIA & LYMPHOMA Warsch, S., Hosein, P. J., Maeda, L. S., Alizadeh, A. A., Lossos, I. S. 2012; 53 (7): 1299-1305

  Abstract

  Bendamustine is approved in the United States for relapsed indolent lymphoma. However, it has not been widely studied in mantle cell lymphoma (MCL). We retrospectively reviewed the records of all patients with MCL who were treated with bendamustine at three centers. The primary endpoint was overall response rate (ORR). Thirty patients with MCL received bendamustine, 25 for relapsed disease. After a median follow-up of 12 months, there were 15 complete responses (CRs) with an ORR of 83% (95% confidence interval [CI] 70-97%). Factors significantly associated with longer survival were achieving a CR and classical (versus blastic) variant of MCL. Grade 3 or 4 neutropenia, anemia and thrombocytopenia occurred in 23%, 3% and 20%, respectively. There was one case of progressive multifocal leukoencephalopathy 10 months after therapy completion. Bendamustine in combination with rituximab demonstrated a high response rate in this study of patients with predominantly relapsed MCL.

  View details for DOI 10.3109/10428194.2011.649476

  View details for Web of Science ID 000305480100011

  View details for PubMedID 22185662

• The chemoattractant chemerin as a natural tumor suppressive cytokine. 48th Annual Meeting of the American-Society-of-Clinical-Oncology (ASCO) Pachynski, R. K., Zabel, B., Tejeda, N., Monnier, J., Holzer, A. K., Gentles, A., Kohrt, H. E., Hadeiba, H., Alizadeh, A. A., Butcher, E. AMER SOC CLINICAL ONCOLOGY. 2012

  View details for Web of Science ID 000318009803142

• The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Willingham, S. B., Volkmer, J., Gentles, A. J., Sahoo, D., Dalerba, P., Mitra, S. S., Wang, J., Contreras-Trujillo, H., Martin, R., Cohen, J. D., Lovelace, P., Scheeren, F. A., Chao, M. P., Weiskopf, K., Tang, C., Volkmer, A. K., Naik, T. J., Storm, T. A., Mosley, A. R., Edris, B., Schmid, S. M., Sun, C. K., Chua, M., Murillo, O., Rajendran, P., Cha, A. C., Chin, R. K., Kim, D., Adorno, M., Raveh, T., Tseng, D., Jaiswal, S., Enger, P. O., Steinberg, G. K., Li, G., So, S. K., Majeti, R., Harsh, G. R., van de Rijn, M., Teng, N. N., Sunwoo, J. B., Alizadeh, A. A., Clarke, M. F., Weissman, I. L. 2012; 109 (17): 6662-6667

  Abstract

  CD47, a "don't eat me" signal for phagocytic cells, is expressed on the surface of all human solid tumor cells. Analysis of patient tumor and matched adjacent normal (nontumor) tissue revealed that CD47 is overexpressed on cancer cells. CD47 mRNA expression levels correlated with a decreased probability of survival for multiple types of cancer. CD47 is a ligand for SIRPα, a protein expressed on macrophages and dendritic cells. In vitro, blockade of CD47 signaling using targeted monoclonal antibodies enabled macrophage phagocytosis of tumor cells that were otherwise protected. Administration of anti-CD47 antibodies inhibited tumor growth in orthotopic immunodeficient mouse xenotransplantation models established with patient tumor cells and increased the survival of the mice over time. Anti-CD47 antibody therapy initiated on larger tumors inhibited tumor growth and prevented or treated metastasis, but initiation of the therapy on smaller tumors was potentially curative. The safety and efficacy of targeting CD47 was further tested and validated in immune competent hosts using an orthotopic mouse breast cancer model. These results suggest all human solid tumor cells require CD47 expression to suppress phagocytic innate immune surveillance and elimination. These data, taken together with similar findings with other human neoplasms, show that CD47 is a commonly expressed molecule on all cancers, its function to block phagocytosis is known, and blockade of its function leads to tumor cell phagocytosis and elimination. CD47 is therefore a validated target for cancer therapies.

  View details for DOI 10.1073/pnas.1121623109

  View details for Web of Science ID 000303249100065

  View details for PubMedID 22451913

  View details for PubMedCentralID PMC3340046

• First Isolation of Cryptococcus uzbekistanensis from an Immunocompromised Patient with Lymphoma JOURNAL OF CLINICAL MICROBIOLOGY Powel, M. S., Alizadeh, A. A., Budvytiene, I., Schaenman, J. M., Banaei, N. 2012; 50 (3): 1125-1127

  Abstract

  Cryptococcus species are known agents of opportunistic infections in healthy and immunocompromised hosts. Here we describe the first case of Cryptococcus uzbekistanensis causing bone marrow infection in an elderly Asian man with undiagnosed T cell lymphoma presenting with fever of unknown origin, pancytopenia, and exposure to chicken manure.

  View details for DOI 10.1128/JCM.05678-11

  View details for Web of Science ID 000300997800099

  View details for PubMedID 22189126

• Three differentiation states risk-stratify bladder cancer into distinct subtypes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Volkmer, J., Sahoo, D., Chin, R. K., Ho, P. L., Tang, C., Kurtova, A. V., Willingham, S. B., Pazhanisamy, S. K., Contreras-Trujillo, H., Storm, T. A., Lotan, Y., Beck, A. H., Chung, B. I., Alizadeh, A. A., Godoy, G., Lerner, S. P., van de Rijng, M., Shortliffe, L. D., Weissman, I. L., Chan, K. S. 2012; 109 (6): 2078-2083

  Abstract

  Current clinical judgment in bladder cancer (BC) relies primarily on pathological stage and grade. We investigated whether a molecular classification of tumor cell differentiation, based on a developmental biology approach, can provide additional prognostic information. Exploiting large preexisting gene-expression databases, we developed a biologically supervised computational model to predict markers that correspond with BC differentiation. To provide mechanistic insight, we assessed relative tumorigenicity and differentiation potential via xenotransplantation. We then correlated the prognostic utility of the identified markers to outcomes within gene expression and formalin-fixed paraffin-embedded (FFPE) tissue datasets. Our data indicate that BC can be subclassified into three subtypes, on the basis of their differentiation states: basal, intermediate, and differentiated, where only the most primitive tumor cell subpopulation within each subtype is capable of generating xenograft tumors and recapitulating downstream populations. We found that keratin 14 (KRT14) marks the most primitive differentiation state that precedes KRT5 and KRT20 expression. Furthermore, KRT14 expression is consistently associated with worse prognosis in both univariate and multivariate analyses. We identify here three distinct BC subtypes on the basis of their differentiation states, each harboring a unique tumor-initiating population.

  View details for DOI 10.1073/pnas.1120605109

  View details for Web of Science ID 000299925000058

  View details for PubMedID 22308455

• Treatment advances have not improved the early death rate in acute promyelocytic leukemia HAEMATOLOGICA-THE HEMATOLOGY JOURNAL McClellan, J. S., Kohrt, H. E., Coutre, S., Gotlib, J. R., Majeti, R., Alizadeh, A. A., Medeiros, B. C. 2012; 97 (1): 133-136

  Abstract

  Early mortality in acute promyelocytic leukemia has been reported to occur in less than 10% of patients treated in clinical trials. This study reports the incidence and clinical features of acute promyelocytic leukemia patients treated at Stanford Hospital, CA, USA since March 1997, focusing on early mortality. We show that the risk of early death in acute promyelocytic leukemia patients is higher than previously reported. In a cohort of 70 patients who received induction therapy at Stanford Hospital, 19% and 26% died within seven and 30 days of admission, respectively. High early mortality was not limited to our institution as evaluation of the Surveillance, Epidemiology and End Results Database demonstrated that 30-day mortality for acute promyelocytic leukemia averaged 20% from 1977-2007 and did not improve significantly over this interval. Our findings show that early death is now the greatest contributor to treatment failure in this otherwise highly curable form of leukemia.

  View details for DOI 10.3324/haematol.2011.046490

  View details for Web of Science ID 000299870500022

  View details for PubMedID 21993679

• Correction: Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies. Arthritis research & therapy Liu, C. L., Tangsombatvisit, S., Rosenberg, J. M., Mandelbaum, G., Gillespie, E. C., Gozani, O. P., Alizadeh, A. A., Utz, P. J. 2012; 14 (4): 403-?

  View details for DOI 10.1186/ar3933

  View details for PubMedID 22894771

  View details for PubMedCentralID PMC3580574

• Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies ARTHRITIS RESEARCH & THERAPY Liu, C. L., Tangsombatvisit, S., Rosenberg, J. M., Mandelbaum, G., Gillespie, E. C., Gozani, O. P., Alizadeh, A. A., Utz, P. J. 2012; 14 (1)

  Abstract

  Autoreactivity to histones is a pervasive feature of several human autoimmune disorders, including systemic lupus erythematosus (SLE). Specific post-translational modifications (PTMs) of histones within neutrophil extracellular traps (NETs) may potentially drive the process by which tolerance to these chromatin-associated proteins is broken. We hypothesized that NETs and their unique histone PTMs might be capable of inducing autoantibodies that target histones.We developed a novel and efficient method for the in vitro production, visualization, and broad profiling of histone-PTMs of human and murine NETs. We also immunized Balb/c mice with murine NETs and profiled their sera on autoantigen and histone peptide microarrays for evidence of autoantibody production to their immunogen.We confirmed specificity toward acetyl-modified histone H2B as well as to other histone PTMs in sera from patients with SLE known to have autoreactivity against histones. We observed enrichment for distinctive histone marks of transcriptionally silent DNA during NETosis triggered by diverse stimuli. However, NETs derived from human and murine sources did not harbor many of the PTMs toward which autoreactivity was observed in patients with SLE or in MRL/lpr mice. Further, while murine NETs were weak autoantigens in vivo, there was only partial overlap in the immunoglobulin G (IgG) and IgM autoantibody profiles induced by vaccination of mice with NETs and those seen in patients with SLE.Isolated in vivo exposure to NETs is insufficient to break tolerance and may involve additional factors that have yet to be identified.

  View details for DOI 10.1186/ar3707

  View details for Web of Science ID 000304698800039

  View details for PubMedID 22300536

  View details for PubMedCentralID PMC3392818

• Immunotransplant for Mantle Cell Lymphoma: Phase I/II Study Preliminary Results 53rd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Brody, J. D., Czerwinski, D. K., Carlton, V., Moorhead, M., Zheng, J., Klinger, M., Faham, M., Advani, R., Kohrt, H. E., Alizadeh, A. A., Negrin, R. S., Weng, W., Sheehan, K., Levy, R. AMER SOC HEMATOLOGY. 2011: 1323–23

  View details for Web of Science ID 000299597104419

• A few good genes Simple, biologically motivated signatures for cancer prognosis CELL CYCLE Gentles, A. J., Alizadeh, A. A. 2011; 10 (21): 3615-3616

  View details for DOI 10.4161/cc.10.21.17835

  View details for Web of Science ID 000296572100003

  View details for PubMedID 22037208

  View details for PubMedCentralID PMC3266003

• A proteomic approach for the identification of novel lysine methyltransferase substrates EPIGENETICS & CHROMATIN Levy, D., Liu, C. L., Yang, Z., Newman, A. M., Alizadeh, A. A., Utz, P. J., Gozani, O. 2011; 4

  Abstract

  Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as phosphorylation, proteome-wide approaches to investigate lysine methylation networks do not exist.In the current study, we used the ProtoArray® platform, containing over 9,500 human proteins, and developed and optimized a system for proteome-wide identification of novel methylation events catalyzed by the protein lysine methyltransferase (PKMT) SETD6. This enzyme had previously been shown to methylate the transcription factor RelA, but it was not known whether SETD6 had other substrates. By using two independent detection approaches, we identified novel candidate substrates for SETD6, and verified that all targets tested in vitro and in cells were genuine substrates.We describe a novel proteome-wide methodology for the identification of new PKMT substrates. This technological advance may lead to a better understanding of the enzymatic activity and substrate specificity of the large number (more than 50) PKMTs present in the human proteome, most of which are uncharacterized.

  View details for DOI 10.1186/1756-8935-4-19

  View details for Web of Science ID 000296832600001

  View details for PubMedID 22024134

  View details for PubMedCentralID PMC3212905

• Utility of positron emission tomography scans in mantle cell lymphoma AMERICAN JOURNAL OF HEMATOLOGY Hosein, P. J., Pastorini, V. H., Paes, F. M., Eber, D., Chapman, J. R., Serafini, A. N., Alizadeh, A. A., Lossos, I. S. 2011; 86 (10): 841-845

  Abstract

  Positron emission tomography (PET) scans are widely used in patients with lymphoma but little is known about their utility in mantle cell lymphoma (MCL). MCL patients were included from two prospective trials and one observational study at our institution. A total of 276 PET scans were performed among 52 patients. After a median follow-up of 37.5 months, the 3-year event-free survival (EFS) and overall survival (OS) were 73% (95% confidence interval [CI]: 61-85%) and 92% (95% CI 85-100%), respectively. There were 34 pretreatment PET scans, 26 interim, 28 end-of-treatment, 162 surveillance, and 26 scans at relapse or beyond. Pretreatment PETs were positive in 94%. A negative interim or end-of-therapy PET scan was not significantly associated with better EFS or OS, but no deaths were observed in patients who had a negative interim or end-of-therapy PET. Surveillance PET scans had a high false positive rate (35%) and low positive predictive value (8%). PET scans contributed to an earlier diagnosis of relapse in only two out of the 18 patients (11%) who relapsed. PET scans did not meaningfully contribute to staging or surveillance of MCL patients in this study. There was a trend toward improved survival in patients who had a negative end-of-therapy PET scan.

  View details for DOI 10.1002/ajh.22126

  View details for Web of Science ID 000295231800004

  View details for PubMedID 21922524

• Impact of TET2 mutations on mRNA expression and clinical outcomes in MDS patients treated with DNA methyltransferase inhibitors HEMATOLOGICAL ONCOLOGY Pollyea, D. A., Raval, A., Kusler, B., Gotlib, J. R., Alizadeh, A. A., Mitchell, B. S. 2011; 29 (3): 157-160

  View details for DOI 10.1002/hon.976

  View details for Web of Science ID 000300148700010

  View details for PubMedID 21922510

• Surprise! HSC Are Aberrant in Chronic Lymphocytic Leukemia CANCER CELL Alizadeh, A. A., Majeti, R. 2011; 20 (2): 135-136

  Abstract

  In this issue of Cancer Cell, Kikushige et al. report the surprising finding that, in human chronic lymphocytic leukemia (CLL), hematopoietic stem cells (HSC) aberrantly generate clonal B cells with CLL-like phenotypes, which implicate HSC in the pathogenesis of this mature lymphoid malignancy and has major implications for CLL therapies.

  View details for DOI 10.1016/j.ccr.2011.08.001

  View details for Web of Science ID 000294099700002

  View details for PubMedID 21840478

• Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment BLOOD Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Liu, C. L., Kohrt, H. E., Houot, R., Goldstein, M. J., Zhao, S., Natkunam, Y., Advani, R. H., Gascoyne, R. D., Briones, J., Tibshirani, R. J., Myklebust, J. H., Plevritis, S. K., Lossos, I. S., Levy, R. 2011; 118 (5): 1350-1358

  Abstract

  Several gene-expression signatures predict survival in diffuse large B-cell lymphoma (DLBCL), but the lack of practical methods for genome-scale analysis has limited translation to clinical practice. We built and validated a simple model using one gene expressed by tumor cells and another expressed by host immune cells, assessing added prognostic value to the clinical International Prognostic Index (IPI). LIM domain only 2 (LMO2) was validated as an independent predictor of survival and the "germinal center B cell-like" subtype. Expression of tumor necrosis factor receptor superfamily member 9 (TNFRSF9) from the DLBCL microenvironment was the best gene in bivariate combination with LMO2. Study of TNFRSF9 tissue expression in 95 patients with DLBCL showed expression limited to infiltrating T cells. A model integrating these 2 genes was independent of "cell-of-origin" classification, "stromal signatures," IPI, and added to the predictive power of the IPI. A composite score integrating these genes with IPI performed well in 3 independent cohorts of 545 DLBCL patients, as well as in a simple assay of routine formalin-fixed specimens from a new validation cohort of 147 patients with DLBCL. We conclude that the measurement of a single gene expressed by tumor cells (LMO2) and a single gene expressed by the immune microenvironment (TNFRSF9) powerfully predicts overall survival in patients with DLBCL.

  View details for DOI 10.1182/blood-2011-03-345272

  View details for Web of Science ID 000293510000028

  View details for PubMedID 21670469

  View details for PubMedCentralID PMC3152499

• Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Jan, M., Chao, M. P., Cha, A. C., Alizadeh, A. A., Gentles, A. J., Weissman, I. L., Majeti, R. 2011; 108 (12): 5009-5014

  Abstract

  Hematopoietic tissues in acute myeloid leukemia (AML) patients contain both leukemia stem cells (LSC) and residual normal hematopoietic stem cells (HSC). The ability to prospectively separate residual HSC from LSC would enable important scientific and clinical investigation including the possibility of purged autologous hematopoietic cell transplants. We report here the identification of TIM3 as an AML stem cell surface marker more highly expressed on multiple specimens of AML LSC than on normal bone marrow HSC. TIM3 expression was detected in all cytogenetic subgroups of AML, but was significantly higher in AML-associated with core binding factor translocations or mutations in CEBPA. By assessing engraftment in NOD/SCID/IL2Rγ-null mice, we determined that HSC function resides predominantly in the TIM3-negative fraction of normal bone marrow, whereas LSC function from multiple AML specimens resides predominantly in the TIM3-positive compartment. Significantly, differential TIM3 expression enabled the prospective separation of HSC from LSC in the majority of AML specimens with detectable residual HSC function.

  View details for DOI 10.1073/pnas.1100551108

  View details for Web of Science ID 000288712200061

  View details for PubMedID 21383193

  View details for PubMedCentralID PMC3064328

• CD137 stimulation enhances the antilymphoma activity of anti-CD20 antibodies BLOOD Kohrt, H. E., Houot, R., Goldstein, M. J., Weiskopf, K., Alizadeh, A. A., Brody, J., Mueller, A., Pachynski, R., Czerwinski, D., Coutre, S., Chao, M. P., Chen, L., Tedder, T. F., Levy, R. 2011; 117 (8): 2423-2432

  Abstract

  Antibody-dependent cell-mediated cytotoxicity (ADCC), which is largely mediated by natural killer (NK) cells, is thought to play an important role in the efficacy of rituximab, an anti-CD20 monoclonal antibody (mAb) used to treat patients with B-cell lymphomas. CD137 is a costimulatory molecule expressed on a variety of immune cells after activation, including NK cells. In the present study, we show that an anti-CD137 agonistic mAb enhances the antilymphoma activity of rituximab by enhancing ADCC. Human NK cells up-regulate CD137 after encountering rituximab-coated tumor B cells, and subsequent stimulation of these NK cells with anti-CD137 mAb enhances rituximab-dependent cytotoxicity against the lymphoma cells. In a syngeneic murine lymphoma model and in a xenotransplanted human lymphoma model, sequential administration of anti-CD20 mAb followed by anti-CD137 mAb had potent antilymphoma activity in vivo. These results support a novel, sequential antibody approach against B-cell malignancies by targeting first the tumor and then the host immune system.

  View details for DOI 10.1182/blood-2010-08-301945

  View details for Web of Science ID 000287698800023

  View details for PubMedID 21193697

  View details for PubMedCentralID PMC3062409

• Therapeutic Antibody Targeting of CD47 Eliminates Human Acute Lymphoblastic Leukemia CANCER RESEARCH Chao, M. P., Alizadeh, A. A., Tang, C., Jan, M., Weissman-Tsukamoto, R., Zhao, F., Park, C. Y., Weissman, I. L., Majeti, R. 2011; 71 (4): 1374-1384

  Abstract

  Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy and constitutes 15% of adult leukemias. Although overall prognosis for pediatric ALL is favorable, high-risk pediatric patients and most adult patients have significantly worse outcomes. Multiagent chemotherapy is standard of care for both pediatric and adult ALL, but is associated with systemic toxicity and long-term side effects and is relatively ineffective against certain ALL subtypes. Recent efforts have focused on the development of targeted therapies for ALL including monoclonal antibodies. Here, we report the identification of CD47, a protein that inhibits phagocytosis, as an antibody target in standard and high-risk ALL. CD47 was found to be more highly expressed on a subset of human ALL patient samples compared with normal cell counterparts and to be an independent predictor of survival and disease refractoriness in several ALL patient cohorts. In addition, a blocking monoclonal antibody against CD47 enabled phagocytosis of ALL cells by macrophages in vitro and inhibited tumor engraftment in vivo. Significantly, anti-CD47 antibody eliminated ALL in the peripheral blood, bone marrow, spleen, and liver of mice engrafted with primary human ALL. These data provide preclinical support for the development of an anti-CD47 antibody therapy for treatment of human ALL.

  View details for DOI 10.1158/0008-5472.CAN-10-2238

  View details for Web of Science ID 000287352600020

  View details for PubMedID 21177380

• Association of a Leukemic Stem Cell Gene Expression Signature With Clinical Outcomes in Acute Myeloid Leukemia JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Gentles, A. J., Plevritis, S. K., Majeti, R., Alizadeh, A. A. 2010; 304 (24): 2706-2715

  Abstract

  In many cancers, specific subpopulations of cells appear to be uniquely capable of initiating and maintaining tumors. The strongest support for this cancer stem cell model comes from transplantation assays in immunodeficient mice, which indicate that human acute myeloid leukemia (AML) is driven by self-renewing leukemic stem cells (LSCs). This model has significant implications for the development of novel therapies, but its clinical relevance has yet to be determined.To identify an LSC gene expression signature and test its association with clinical outcomes in AML.Retrospective study of global gene expression (microarray) profiles of LSC-enriched subpopulations from primary AML and normal patient samples, which were obtained at a US medical center between April 2005 and July 2007, and validation data sets of global transcriptional profiles of AML tumors from 4 independent cohorts (n = 1047).Identification of genes discriminating LSC-enriched populations from other subpopulations in AML tumors; and association of LSC-specific genes with overall, event-free, and relapse-free survival and with therapeutic response.Expression levels of 52 genes distinguished LSC-enriched populations from other subpopulations in cell-sorted AML samples. An LSC score summarizing expression of these genes in bulk primary AML tumor samples was associated with clinical outcomes in the 4 independent patient cohorts. High LSC scores were associated with worse overall, event-free, and relapse-free survival among patients with either normal karyotypes or chromosomal abnormalities. For the largest cohort of patients with normal karyotypes (n = 163), the LSC score was significantly associated with overall survival as a continuous variable (hazard ratio [HR], 1.15; 95% confidence interval [CI], 1.08-1.22; log-likelihood P <.001). The absolute risk of death by 3 years was 57% (95% CI, 43%-67%) for the low LSC score group compared with 78% (95% CI, 66%-86%) for the high LSC score group (HR, 1.9 [95% CI, 1.3-2.7]; log-rank P = .002). In another cohort with available data on event-free survival for 70 patients with normal karyotypes, the risk of an event by 3 years was 48% (95% CI, 27%-63%) in the low LSC score group vs 81% (95% CI, 60%-91%) in the high LSC score group (HR, 2.4 [95% CI, 1.3-4.5]; log-rank P = .006). In multivariate Cox regression including age, mutations in FLT3 and NPM1, and cytogenetic abnormalities, the HRs for LSC score in the 3 cohorts with data on all variables were 1.07 (95% CI, 1.01-1.13; P = .02), 1.10 (95% CI, 1.03-1.17; P = .005), and 1.17 (95% CI, 1.05-1.30; P = .005).High expression of an LSC gene signature is independently associated with adverse outcomes in patients with AML.

  View details for Web of Science ID 000285518000015

  View details for PubMedID 21177505

• Calreticulin Is the Dominant Pro-Phagocytic Signal on Multiple Human Cancers and Is Counterbalanced by CD47 SCIENCE TRANSLATIONAL MEDICINE Chao, M. P., Jaiswal, S., Weissman-Tsukamoto, R., Alizadeh, A. A., Gentles, A. J., Volkmer, J., Weiskopf, K., Willingham, S. B., Raveh, T., Park, C. Y., Majeti, R., Weissman, I. L. 2010; 2 (63)

  Abstract

  Under normal physiological conditions, cellular homeostasis is partly regulated by a balance of pro- and anti-phagocytic signals. CD47, which prevents cancer cell phagocytosis by the innate immune system, is highly expressed on several human cancers including acute myeloid leukemia, non-Hodgkin's lymphoma, and bladder cancer. Blocking CD47 with a monoclonal antibody results in phagocytosis of cancer cells and leads to in vivo tumor elimination, yet normal cells remain mostly unaffected. Thus, we postulated that cancer cells must also display a potent pro-phagocytic signal. Here, we identified calreticulin as a pro-phagocytic signal that was highly expressed on the surface of several human cancers, but was minimally expressed on most normal cells. Increased CD47 expression correlated with high amounts of calreticulin on cancer cells and was necessary for protection from calreticulin-mediated phagocytosis. Blocking the interaction of target cell calreticulin with its receptor, low-density lipoprotein receptor-related protein, on phagocytic cells prevented anti-CD47 antibody-mediated phagocytosis. Furthermore, increased calreticulin expression was an adverse prognostic factor in diverse tumors including neuroblastoma, bladder cancer, and non-Hodgkin's lymphoma. These findings identify calreticulin as the dominant pro-phagocytic signal on several human cancers, provide an explanation for the selective targeting of tumor cells by anti-CD47 antibody, and highlight the balance between pro- and anti-phagocytic signals in the immune evasion of cancer.

  View details for DOI 10.1126/scitranslmed.3001375

  View details for Web of Science ID 000288444900003

  View details for PubMedID 21178137

• Noninvasive Prediction of Graft-Verus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation by Gene Expression Profiling 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Kohrt, H. E., Li, L., Alizadeh, A. A., Goldstein, M. J., Strober, S., Sarwal, M., Lowsky, R. AMER SOC HEMATOLOGY. 2010: 393–94

  View details for Web of Science ID 000289662200897

• Self-Antigen Recognition by the B Cell Receptors of Follicular Lymphoma 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Layn, K., Alizadeh, A. A., Kattah, N., Levy, S., Levy, R. AMER SOC HEMATOLOGY. 2010: 1678–79

  View details for Web of Science ID 000289662204543

• Clinical and Pathological Features of Non-Hodgkin Lymphomas Harboring Concurrent t(14;18) and 8q24 Anomalies 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Alizadeh, A. A., Anderson, M., Kohrt, H. E., Shyam, R. M., Bangs, C. D., Cherry, A. M., Advani, R., Natkunam, Y., Levy, R. AMER SOC HEMATOLOGY. 2010: 1291–92

  View details for Web of Science ID 000289662203465

• NF-kappa B Signaling In Response to CpG Stratifies Mantle Cell Lymphoma Patient Outcome 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Myklebust, J. H., Irish, J. M., Brody, J., Alizadeh, A. A., Czerwinski, D., Houot, R., Kohrt, H. E., Kolstad, A., Levy, R. AMER SOC HEMATOLOGY. 2010: 67–68

  View details for Web of Science ID 000289662200145

• Prediction of Survival In Diffuse Large B-Cell Lymphoma Based On the Expression of Two Genes Reflecting Tumor and Microenvironment 52nd Annual Meeting and Exposition of the American-Society-of-Hematology (ASH) Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Kohrt, H. E., Houot, R., Goldstein, M. J., Zhao, S., Natkunam, Y., Advani, R., Gascoyne, R. D., Briones, J., Tibshirani, R. J., Myklebust, J. H., Plevritis, S. K., Lossos, I. S., Levy, R. AMER SOC HEMATOLOGY. 2010: 836–37

  View details for Web of Science ID 000289662202229

• Second-line mitoxantrone, etoposide, and cytarabine for acute myeloid leukemia: A single-center experience AMERICAN JOURNAL OF HEMATOLOGY Kohrt, H. E., Patel, S., Ho, M., Owen, T., Pollyea, D. A., Majeti, R., Gotlib, J., Coutre, S., Liedtke, M., Berube, C., Alizadeh, A. A., Medeiros, B. C. 2010; 85 (11): 877-881

  Abstract

  The majority of patients with acute myeloid leukemia (AML) will require second-line chemotherapy for either relapsed or refractory disease. Currently, only allogeneic hematopoietic cell transplantation (HCT) offers a curative option in this setting and no preferred regimen has been established. The reported efficacy of second-line regimens is widely disparate, thus limiting informed clinical decision making. A retrospective review of 77 patients receiving therapy between 2001 and 2008 with relapsed, 42, and refractory, 35, AML was performed to determine overall response rate and survival following mitoxantrone (8 mg/m(2)/day), etoposide (100 mg/m(2)/day), and cytarabine (1,000 mg/m(2)/day) chemotherapy administered over 5 days. Among 77 patients (median age of 54 years and 64% intermediate risk karyotype) with median follow-up of 153 days, 18% achieved a complete response and 8% a morphologic leukemia-free state. Fifty-seven (74%) experienced treatment failure, 10 of whom achieved a remission after additional therapy. Median overall survival (OS) was 6.8 months. Among patients achieving a response, 50% received consolidation with allogeneic HCT, autologous HCT (5%), or consolidation chemotherapy alone (45%). A nonsignificant trend in overall response (50%, 27%, and 23.8%) and median OS (8.3, 6.8, and 4.7 months) was observed by cytogenetic stratification into favorable, intermediate, and unfavorable risk. Patients with refractory versus relapsed disease had similar overall responses (20% and 31%, P = 0.41) and median OS (5.3 and 7.6 months, P = 0.36). Despite risk stratification by the European Prognostic Index, our series demonstrates inferior rates of response and survival, illustrating the limited activity of this regimen in our cohort.

  View details for DOI 10.1002/ajh.21857

  View details for Web of Science ID 000283568200010

  View details for PubMedID 20872554

• B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Irish, J. M., Myklebust, J. H., Alizadeh, A. A., Houot, R., Sharman, J. P., Czerwinski, D. K., Nolan, G. P., Levy, R. 2010; 107 (29): 12747-12754

  Abstract

  Human tumors contain populations of both cancerous and host immune cells whose malignant signaling interactions may define each patient's disease trajectory. We used multiplexed phospho-flow cytometry to profile single cells within human follicular lymphoma tumors and discovered a subpopulation of lymphoma cells with impaired B cell antigen receptor (BCR) signaling. The abundance of BCR-insensitive cells in each tumor negatively correlated with overall patient survival. These lymphoma negative prognostic (LNP) cells increased as tumors relapsed following chemotherapy. Loss of antigen receptor expression did not explain the absence of BCR signaling in LNP tumor cells, and other signaling responses were intact in these cells. Furthermore, BCR signaling responses could be reactivated in LNP cells, indicating that BCR signaling is not missing but rather specifically suppressed. LNP cells were also associated with changes to signaling interactions in the tumor microenvironment. Lower IL-7 signaling in tumor infiltrating T cells was observed in tumors with high LNP cell counts. The strength of signaling through T cell mediator of B cell function CD40 also stratified patient survival, particularly for those whose tumors contained few LNP cells. Thus, analysis of cell-cell interactions in heterogeneous primary tumors using signaling network profiles can identify and mechanistically define new populations of rare and clinically significant cells. Both the existence of these LNP cells and their aberrant signaling profiles provide targets for new therapies for follicular lymphoma.

  View details for DOI 10.1073/pnas.1002057107

  View details for Web of Science ID 000280144500010

  View details for PubMedID 20543139

  View details for PubMedCentralID PMC2919949

• Expression profiles of adult T-cell leukemia-lymphoma and associations with clinical responses to zidovudine and interferon alpha LEUKEMIA & LYMPHOMA Alizadeh, A. A., Bohen, S. P., Lossos, C., Martinez-Climent, J. A., Ramos, J. C., Cubedo-Gil, E., Harrington, W. J., Lossos, I. S. 2010; 51 (7): 1200-1216

  Abstract

  Adult T-cell leukemia-lymphoma (ATLL) is an HTLV-1-associated lymphoproliferative malignancy that is frequently fatal. We compared gene expression profiles (GEPs) of leukemic specimens from nine patients with ATLL at the time of diagnosis and immediately after combination therapy with zidovudine (AZT) and interferon alpha (IFNalpha). GEPs were also related to genetic aberrations determined by comparative genomic hybridization. We identified several genes anomalously over-expressed in the ATLL leukemic cells at the mRNA level, including LYN, CSPG2, and LMO2, and confirmed LMO2 expression in ATLL cells at the protein level. In vivo AZT-IFNalpha therapy evoked a marked induction of interferon-induced genes accompanied by repression of cell-cycle regulated genes, including those encoding ribosomal proteins. Remarkably, patients not responding to AZT-IFNalpha differed most from responding patients in lower expression of these same IFN-responsive genes, as well as components of the antigen processing and presentation apparatus. Demonstration of specific gene expression signatures associated with response to AZT-IFNalpha therapy may provide novel insights into the mechanisms of action in ATLL.

  View details for DOI 10.3109/10428191003728628

  View details for Web of Science ID 000279485700008

  View details for PubMedID 20370541

• Immunophenotypic features of acute myeloid leukemia with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) LEUKEMIA RESEARCH Medeiros, B. C., Kohrt, H. E., Arber, D. A., Bangs, C. D., Cherry, A. M., Majeti, R., Kogel, K. E., Azar, C. A., Patel, S., Alizadeh, A. A. 2010; 34 (5): 594-597

  Abstract

  Immunophenotypic identification of myeloid specific antigens is an important diagnostic tool in the management of patients with acute myeloid leukemia (AML). These antigens allow determination of cell of origin and degree of differentiation of leukemia blasts. AML with inv(3)(q21q26.2)/t(3;3)(q21;q26.2) is a relatively rare subtype of AML. The immunophenotypic characteristics of inv(3) AML patients are somewhat limited. We identified 14 new cases of hematological disorders with increased myeloid blasts carrying inv(3)(q21q26.2)/t(3;3)(q21;q26.2). Also, we identified another 13 cases previously published in the literature, where the immunophenotype of inv(3)(q21q26.2) was documented. As a group, patients with AML with inv(3)(q21q26.2) had high levels of early myeloid (CD13, CD33, CD117 and MPO) and uncommitted markers (CD34, HLA-DR and CD56) and a high rate of monosomy 7 in addition to the inv(3)(q21q26.2). Differential karyotype and expression of certain antigens were noted in patients with de novo AML with inv(3)(q21q26.2) vs. those with inv(3)(q21q26.2)-containing blasts.

  View details for DOI 10.1016/j.leukres.2009.08.029

  View details for Web of Science ID 000276945300009

  View details for PubMedID 19781775

• Noninvasive Prediction of Graft-Versus-Host Disease Following Allogeneic Hematopoietic Cell Transplantation by Gene Expression Profiling. 10th American Transplant Congress Li, L., Kohrt, H., Heish, S., Alizadeh, A., Laport, G., Shizuru, J., Negrin, R., Strober, S., Lowsky, R., Sarwal, M. WILEY-BLACKWELL. 2010: 483–483

  View details for Web of Science ID 000275921703258

• Is Time of the Essence in Adult Acute Myeloid Leukemia (AML)? Time to Blast Clearance and Time to Induction Therapy Fail to Predict Overall Survival (OS) Blood (e-Letter) Kohrt HE, Patel S, Ho M, Owen T, Majeti R, Gotlib JR, Coutre SE, Medeiros BC, Alizadeh AA. 2010; 113 (1): 28-36
• Therapeutic Antibody Targeting of CD47 Synergizes with Rituximab to Completely Eradicate Human B-Cell Lymphoma Xenografts 51st Annual Meeting and Exposition of the American-Society-of-Hematology Chao, M. P., Alizadeh, A. A., Tang, C. Z., Myklebust, J. H., Varghese, B., Jan, M., Levy, R., Weissman, I. L., Majeti, R. AMER SOC HEMATOLOGY. 2009: 1063–64

  View details for Web of Science ID 000272725803271

• A Subpopulation of Follicular Lymphoma Tumor Infiltrating T Cells Shows Suppressed Common Gamma Chain Cytokine Signaling 51st Annual Meeting and Exposition of the American-Society-of-Hematology Myklebust, J. H., Irish, J. M., Houot, R., Brody, J., Czerwinski, D. K., Alizadeh, A. A., Kolstad, A., Levy, R. AMER SOC HEMATOLOGY. 2009: 316–16

  View details for Web of Science ID 000272725800760

• Therapeutic Potential of Anti-CD137 Antibody in Lymphoma 51st Annual Meeting and Exposition of the American-Society-of-Hematology Houot, R., Goldstein, M. J., Kohrt, H. E., Myklebust, J. H., Alizadeh, A. A., Lin, J. T., Irish, J. M., Torchia, J. A., Kolstad, A., Chen, L., Levy, R. AMER SOC HEMATOLOGY. 2009: 301–2

  View details for Web of Science ID 000272725800723

• Gene Expression Signature of Host Immune Response Is Predictive of Follicular Lymphoma Patient Survival in Independent Cohorts, and Correlates with Transformation to Diffuse Large B-Cell Lymphoma. 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., Gentles, A. J., Plevritis, S. K., Levy, R. AMER SOC HEMATOLOGY. 2009: 1153–53

  View details for Web of Science ID 000272725803506

• Prediction of Survival in Diffuse Large B-Cell Lymphoma Based On the Expression of Two Genes: Integration of Tumor and Microenvironment Contributions 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., Gentles, A. J., Alencar, A. J., Kohrt, H. E., Houot, R., Talreja, N., Shyam, R., Natkunam, Y., Gascoyne, R. D., Briones, J., Advani, R., Lossos, I. S., Levy, R. AMER SOC HEMATOLOGY. 2009: 258–58

  View details for Web of Science ID 000272725800623

• Is Time of the Essence in Adult Acute Myeloid Leukemia (AML)? Time to Blast Clearance and Time to Induction Therapy Fail to Predict Overall Survival (OS). 51st Annual Meeting and Exposition of the American-Society-of-Hematology Kohrt, H. E., Patel, S., Ho, M., Owen, T., Majeti, R., Gotlib, J. R., Coutre, S., Medeiros, B. C., Alizadeh, A. A. AMER SOC HEMATOLOGY. 2009: 646–47

  View details for Web of Science ID 000272725801797

• Early Mortality in Acute Promyelocytic Leukemia May Be Higher Than Previously Reported. 51st Annual Meeting and Exposition of the American-Society-of-Hematology Alizadeh, A. A., McClellan, J. S., Gotlib, J. R., Coutre, S., Majeti, R., Kohrt, H. E., Medeiros, B. C. AMER SOC HEMATOLOGY. 2009: 420–21

  View details for Web of Science ID 000272725801195

• Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by T-reg depletion BLOOD Houot, R., Goldstein, M. J., Kohrt, H. E., Myklebust, J. H., Alizadeh, A. A., Lin, J. T., Irish, J. M., Torchia, J. A., Kolstad, A., Chen, L., Levy, R. 2009; 114 (16): 3431-3438

  Abstract

  Despite the success of passive immunotherapy with monoclonal antibodies (mAbs), many lymphoma patients eventually relapse. Induction of an adaptive immune response may elicit active and long-lasting antitumor immunity, thereby preventing or delaying recurrence. Immunomodulating mAbs directed against immune cell targets can be used to enhance the immune response to achieve efficient antitumor immunity. Anti-CD137 agonistic mAb has demonstrated antitumor efficacy in various tumor models and has now entered clinical trials for the treatment of solid tumors. Here, we investigate the therapeutic potential of anti-CD137 mAb in lymphoma. We found that human primary lymphoma tumors are infiltrated with CD137+ T cells. We therefore hypothesized that lymphoma would be susceptible to treatment with anti-CD137 agonistic mAb. Using a mouse model, we demonstrate that anti-CD137 therapy has potent antilymphoma activity in vivo. The antitumor effect of anti-CD137 therapy was mediated by both natural killer (NK) and CD8 T cells and induced long-lasting immunity. Moreover, the antitumor activity of anti-CD137 mAb could be further enhanced by depletion of regulatory T cell (T(regs)). These results support the evaluation of anti-CD137 therapy in clinical trials for patients with lymphoma.

  View details for DOI 10.1182/blood-2009-05-223958

  View details for Web of Science ID 000270834500013

  View details for PubMedID 19641184

  View details for PubMedCentralID PMC2765679

• CD47 IS AN ADVERSE PROGNOSTIC FACTOR IN NON-HODGKIN LYMPHOMA AND A THERAPEUTIC ANTIBODY TARGET THAT SYNERGIZES WITH RITUXIMAB 38th Annual Scientific Meeting of the ISEH-Society-for-Hematology-and-Stem-Cells Chao, M. P., Alizadeh, A., Tang, C. Z., Jan, M., Levy, R., Majeti, R., Weissman, I. L. ELSEVIER SCIENCE INC. 2009: S8–S9

  View details for Web of Science ID 000269396400018

• CD47 Is an Adverse Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells CELL Majeti, R., Chao, M. P., Alizadeh, A. A., Pang, W. W., Jaiswal, S., Gibbs, K. D., van Rooijen, N., Weissman, I. L. 2009; 138 (2): 286-299

  Abstract

  Acute myeloid leukemia (AML) is organized as a cellular hierarchy initiated and maintained by a subset of self-renewing leukemia stem cells (LSC). We hypothesized that increased CD47 expression on human AML LSC contributes to pathogenesis by inhibiting their phagocytosis through the interaction of CD47 with an inhibitory receptor on phagocytes. We found that CD47 was more highly expressed on AML LSC than their normal counterparts, and that increased CD47 expression predicted worse overall survival in three independent cohorts of adult AML patients. Furthermore, blocking monoclonal antibodies directed against CD47 preferentially enabled phagocytosis of AML LSC and inhibited their engraftment in vivo. Finally, treatment of human AML LSC-engrafted mice with anti-CD47 antibody depleted AML and targeted AML LSC. In summary, increased CD47 expression is an independent, poor prognostic factor that can be targeted on human AML stem cells with blocking monoclonal antibodies capable of enabling phagocytosis of LSC.

  View details for DOI 10.1016/j.cell.2009.05.045

  View details for Web of Science ID 000268277000011

  View details for PubMedID 19632179

  View details for PubMedCentralID PMC2726837

• A pluripotency signature predicts histological transformation and influences survival in follicular lymphoma patients Blood Gentles AJ**, Alizadeh AA** (contributed equally), Lee S, Myklebust JH, Shachaf CM, Shahbaba B, Levy R, Koller D, Plevritis SK. 2009
• Evaluation and management of angioimmunoblastic T-cell lymphoma: a review of current approaches and future strategies. Clinical advances in hematology & oncology : H&O Alizadeh, A. A., Advani, R. H. 2008; 6 (12): 899-909

  Abstract

  Angioimmunoblastic T-cell lymphoma (AITL) is a rare and complex lymphoproliferative disorder, clinically characterized by widespread lymphadenopathy, extranodal disease, immune-mediated hemolysis, and polyclonal hypergammaglobulinemia. Significant progress has been made in the understanding of AITL since its recognition as a clonal T-cell disorder with associated deregulation of B-cells and endothelial cells within a unique malignant microenvironment. However, as the responses to conventional chemotherapy have not been durable, prognosis with current treatment approaches has remained dismal. Here we review the clinical presentation, prognosis, and management of patients with AITL. We discuss recent developments in the understanding of the pathogenesis of AITL at a cellular and molecular level, including the implication of the follicular helper T-cell as the corresponding cell of origin, the roles of Epstein-Barr virus, B-cell deregulation, angiogenesis, and other signaling pathways in AITL, and the therapeutic implications of these findings. Finally, we discuss recent clinical trials and novel treatment approaches in the management of patients with AITL.

  View details for PubMedID 19209140

• CD47 Is An Independent Prognostic Factor and Therapeutic Antibody Target on Human Acute Myeloid Leukemia Stem Cells 50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium Majeti, R., Chao, M. P., Alizadeh, A. A., Pang, W. W., Weissman, I. L. AMER SOC HEMATOLOGY. 2008: 284–84

  View details for Web of Science ID 000262104700767

• LMO2 Protein Expression Predicts Survival in Patients with Diffuse Large B-Cell Lymphoma Treated with Immunochemotherapy (RCHOP): A Multicenter Validation Study. 50th Annual Meeting of the American-Society-of-Hematology/ASH/ASCO Joint Symposium Advani, R., Talreja, N., Tibshirani, R., Zhao, S., Alizadeh, A., Briones, J., Bordes, R., Cohen, J., Horning, S., Levy, R., Lossos, I. S., Natkunam, Y. AMER SOC HEMATOLOGY. 2008: 1291–91

  View details for Web of Science ID 000262104704387

• Double trouble in follicular lymphoma: A rare and unusual synergy of oncogenes in the germinal center LEUKEMIA & LYMPHOMA Alizadeh, A. A., Lossos, I. S. 2008; 49 (3): 377-380

  View details for DOI 10.1080/10428190801947542

  View details for Web of Science ID 000253513300002

  View details for PubMedID 18297511

• Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray JOURNAL OF CLINICAL MICROBIOLOGY Chiu, C. Y., Alizadeh, A. A., Rouskin, S., Merker, J. D., Yeh, E., Yagi, S., Schnurr, D., Patterson, B. K., Ganem, D., DeRisi, J. L. 2007; 45 (7): 2340-2343

  Abstract

  A pan-virus DNA microarray (Virochip) was used to detect a human metapneumovirus (hMPV) strain associated with a critical respiratory tract infection in an elderly adult with chronic lymphocytic leukemia. This infection had previously eluded diagnosis despite extensive microbiological testing for possible etiologic agents. The patient's hMPV strain did not grow in viral culture, and only one of five specific reverse transcription-PCR assays for hMPV was positive.

  View details for DOI 10.1128/JCM.00364-07

  View details for Web of Science ID 000248072900050

  View details for PubMedID 17494722

• Cell-type specific gene expression profiles of leukocytes in human peripheral blood BMC GENOMICS Palmer, C., Diehn, M., Alizadeh, A. A., Brown, P. O. 2006; 7

  Abstract

  Blood is a complex tissue comprising numerous cell types with distinct functions and corresponding gene expression profiles. We attempted to define the cell type specific gene expression patterns for the major constituent cells of blood, including B-cells, CD4+ T-cells, CD8+ T-cells, lymphocytes and granulocytes. We did this by comparing the global gene expression profiles of purified B-cells, CD4+ T-cells, CD8+ T-cells, granulocytes, and lymphocytes using cDNA microarrays.Unsupervised clustering analysis showed that similar cell populations from different donors share common gene expression profiles. Supervised analyses identified gene expression signatures for B-cells (427 genes), T-cells (222 genes), CD8+ T-cells (23 genes), granulocytes (411 genes), and lymphocytes (67 genes). No statistically significant gene expression signature was identified for CD4+ cells. Genes encoding cell surface proteins were disproportionately represented among the genes that distinguished among the lymphocyte subpopulations. Lymphocytes were distinguishable from granulocytes based on their higher levels of expression of genes encoding ribosomal proteins, while granulocytes exhibited characteristic expression of various cell surface and inflammatory proteins.The genes comprising the cell-type specific signatures encompassed many of the genes already known to be involved in cell-type specific processes, and provided clues that may prove useful in discovering the functions of many still unannotated genes. The most prominent feature of the cell type signature genes was the enrichment of genes encoding cell surface proteins, perhaps reflecting the importance of specialized systems for sensing the environment to the physiology of resting leukocytes.

  View details for DOI 10.1186/1471-2164-7-115

  View details for Web of Science ID 000238364000001

  View details for PubMedID 16704732

• Distinct IL-4-induced gene expression, proliferation, and intracellular signaling in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas BLOOD Lu, X. Q., Nechushtan, H., Ding, F. Y., Rosado, M. F., Singal, R., Alizadeh, A. A., Lossos, I. S. 2005; 105 (7): 2924-2932

  Abstract

  Diffuse large B-cell lymphomas (DLBCLs) can be subclassified into germinal center B-cell (GCB)-like and activated B-cell (ABC)-like tumors characterized by long and short survival, respectively. In contrast to ABC-like DLBCL, GCB-like tumors exhibit high expression of components of the interleukin 4 (IL-4) signaling pathway and of IL-4 target genes such as BCL6 and HGAL, whose high expression independently predicts better survival. These observations suggest distinct activity of the IL-4 signaling pathway in DLBCL subtypes. Herein, we demonstrate similar IL-4 expression but qualitatively different IL-4 effects on GCB-like and ABC-like DLBCL. In GCB-like DLBCL, IL-4 induces expression of its target genes, activates signal transducers and activators of transcription 6 (STAT6) signaling, and increases cell proliferation. In contrast, in the ABC-like DLBCL, IL-4 activates AKT, decreases cell proliferation by cell cycle arrest, and does not induce gene expression due to aberrant Janus kinase (JAK)-STAT6 signaling attributed to STAT6 dephosphorylation. We found distinct expression profiles of tyrosine phosphatases in DLBCL subtypes and identified putative STAT6 tyrosine phosphatases-protein tyrosine phosphatase nonreceptor type 1 (PTPN1) and PTPN2, whose expression is significantly higher in ABC-like DLBCL. These differences in tyrosine phosphatase expression might underlie distinct expression profiles of some of the IL-4 target genes and could contribute to a different clinical outcome of patients with GCB-like and ABC-like DLBCLs.

  View details for DOI 10.1182/blood-2004-10-3820

  View details for Web of Science ID 000228042900051

  View details for PubMedID 15591113

• AID is expressed in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas and is not correlated with intraclonal heterogeneity LEUKEMIA Lossos, I. S., Levy, R., Alizadeh, A. A. 2004; 18 (11): 1775-1779

  Abstract

  Activation-induced cytidine deaminase (AID), highly expressed in germinal center (GC)-lymphocytes, is involved in somatic hypermutation (SHM). We examined AID expression in diffuse large B-cell lymphomas (DLBCL) of germinal center B-cell (GCB)-like and activated B-cell (ABC)-like subtypes. These two types of DLBCL are characterized by high and low expression of GC-specific genes, respectively. AID expression was detected in both GCB- and ABC-like DLBCL, thus demonstrating a dissociation between AID expression and that of other GC genes. We also tested for the presence of intraclonal heterogeneity in immunoglobulin and BCL6 genes in those same tumors and in follicle center lymphomas (FCL) that transformed to DLBCL. The level of AID expression did not correlate with the presence of intraclonal sequence heterogeneity in either IgV(H) or BCL6. Our findings suggest that lymphomas maintain some but not all of the gene expression signatures of their normal B-cell counterparts. The fact that AID expression can be elevated without intraclonal sequence heterogeneity raises the possibility that other factors are required for SHM in these tumors. We found decreased levels of AID expression in DLBCL that evolved from FCL and which had acquired new mutations in their BCL6 genes. This dissociation suggests that AID expression and SHM may occur at the time prior to the clinical detection of transformed lymphoma.

  View details for DOI 10.1038/sj.leu.2403488

  View details for Web of Science ID 000224732800006

  View details for PubMedID 15385936

• Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response BLOOD Rosenwald, A., Chuang, E. Y., Davis, R. E., Wiestner, A., Alizadeh, A. A., Arthur, D. C., Mitchell, J. B., Marti, G. E., Fowler, D. H., Wilson, W. H., Staudt, L. M. 2004; 104 (5): 1428-1434

  Abstract

  Fludarabine, the current standard treatment for B-cell chronic lymphocytic leukemia (CLL), can induce apoptosis in CLL cells in vitro, and a number of molecular mechanisms contribute to its cytotoxicity. Using gene expression profiling, we investigated the molecular consequences of fludarabine treatment of patients with CLL in vivo. In 7 patients with CLL, a consistent gene expression signature of in vivo fludarabine exposure was identified. Many of the fludarabine signature genes were known p53 target genes and genes involved in DNA repair. In vitro treatment of CLL cells with fludarabine induced the same set of genes as observed in vivo, and many of these genes were also induced by in vitro exposure of CLL cells to ionizing radiation. Using isogenic p53 wild-type and null lymphoblastoid cell lines, we confirmed that many of the fludarabine signature genes were also p53 target genes. Because in vivo treatment with fludarabine induces a p53-dependent gene expression response, fludarabine treatment has the potential to select p53-mutant CLL cells, which are more drug resistant and associated with an aggressive clinical course. These considerations suggest that fludarabine treatment should be given in strict accordance to the current National Cancer Institute (NCI) guidelines that have established criteria of disease activity that warrant treatment.

  View details for DOI 10.1182/blood-2003-09-3236

  View details for Web of Science ID 000223544000038

  View details for PubMedID 15138159

• Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes NEW ENGLAND JOURNAL OF MEDICINE Lossos, I. S., Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., Levy, R. 2004; 350 (18): 1828-1837

  Abstract

  Several gene-expression signatures can be used to predict the prognosis in diffuse large-B-cell lymphoma, but the lack of practical tests for a genome-scale analysis has restricted the use of this method.We studied 36 genes whose expression had been reported to predict survival in diffuse large-B-cell lymphoma. We measured the expression of each of these genes in independent samples of lymphoma from 66 patients by quantitative real-time polymerase-chain-reaction analyses and related the results to overall survival.In a univariate analysis, genes were ranked on the basis of their ability to predict survival. The genes that were the strongest predictors were LMO2, BCL6, FN1, CCND2, SCYA3, and BCL2. We developed a multivariate model that was based on the expression of these six genes, and we validated the model in two independent microarray data sets. The model was independent of the International Prognostic Index and added to its predictive power.Measurement of the expression of six genes is sufficient to predict overall survival in diffuse large-B-cell lymphoma.

  View details for Web of Science ID 000221080300006

  View details for PubMedID 15115829

• Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS biology Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): E7-?

  Abstract

  Cancer invasion and metastasis have been likened to wound healing gone awry. Despite parallels in cellular behavior between cancer progression and wound healing, the molecular relationships between these two processes and their prognostic implications are unclear. In this study, based on gene expression profiles of fibroblasts from ten anatomic sites, we identify a stereotyped gene expression program in response to serum exposure that appears to reflect the multifaceted role of fibroblasts in wound healing. The genes comprising this fibroblast common serum response are coordinately regulated in many human tumors, allowing us to identify tumors with gene expression signatures suggestive of active wounds. Genes induced in the fibroblast serum-response program are expressed in tumors by the tumor cells themselves, by tumor-associated fibroblasts, or both. The molecular features that define this wound-like phenotype are evident at an early clinical stage, persist during treatment, and predict increased risk of metastasis and death in breast, lung, and gastric carcinomas. Thus, the transcriptional signature of the response of fibroblasts to serum provides a possible link between cancer progression and wound healing, as well as a powerful predictor of the clinical course in several common carcinomas.

  View details for PubMedID 14737219

  View details for PubMedCentralID PMC314300

• Gene expression signature of fibroblast serum response predicts human cancer progression: Similarities between tumors and wounds PLOS BIOLOGY Chang, H. Y., Sneddon, J. B., Alizadeh, A. A., Sood, R., West, R. B., Montgomery, K., Chi, J. T., van de Rijn, M., Botstein, D., Brown, P. O. 2004; 2 (2): 206-214

  View details for DOI 10.1371/journal.pbio.0020007

  View details for Web of Science ID 000189314400013

• Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock LANCET Pathan, N., Hemingway, C. A., Alizadeh, A. A., Stephens, A. C., Boldrick, J. C., Oragui, E. E., McCabe, C., Welch, S. B., Whitney, A., O'Gara, P., Nadel, S., Relman, D. A., Harding, S. E., Levin, M. 2004; 363 (9404): 203-209

  Abstract

  Myocardial failure has a central role in the complex pathophysiology of septic shock and contributes to organ failure and death. During the sepsis-induced inflammatory process, specific factors are released that depress myocardial contractile function. We aimed to identify these mediators of myocardial depression in meningococcal septic shock.We combined gene-expression profiling with protein and cellular methods to identify a serum factor causing cardiac dysfunction in meningococcal septic shock. We identified genes that were significantly upregulated in blood after exposure to meningococci. We then selected for further analysis those genes whose protein products had properties of a myocardial depressant factor--specifically a 12-25 kDa heat-stable protein that is released into serum shortly after onset of meningococcal infection.We identified 174 significantly upregulated genes in meningococcus-infected blood: six encoded proteins that were of the predicted size and had characteristics of a myocardial depressant factor. Of these, interleukin 6 caused significant myocardial depression in vitro. Removal of interleukin 6 from serum samples of patients with meningococcaemia and from supernatants of inflammatory cells stimulated by meningococci in vitro abolished the negative inotropic activity. Furthermore, concentrations in serum of interleukin 6 strongly predicted degree of myocardial dysfunction and severity of disease in children with meningococcal septic shock.Interleukin 6 is a mediator of myocardial depression in meningococcal disease. This cytokine and its downstream mediators could be a target for future treatment strategies.

  View details for Web of Science ID 000188243900010

  View details for PubMedID 14738793

• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression PLOS BIOLOGY Roose, J. P., Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., Weiss, A. 2003; 1 (2): 271-287

  View details for DOI 10.1371/journal.pbio.0000053

  View details for Web of Science ID 000188835200018

• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. PLoS biology Roose, J. P., Diehn, M., Tomlinson, M. G., Lin, J., Alizadeh, A. A., Botstein, D., Brown, P. O., Weiss, A. 2003; 1 (2): E53-?

  Abstract

  Signal transduction pathways guided by cellular receptors commonly exhibit low-level constitutive signaling in a continuous, ligand-independent manner. The dynamic equilibrium of positive and negative regulators establishes such a tonic signal. Ligand-independent signaling by the precursors of mature antigen receptors regulates development of B and T lymphocytes. Here we describe a basal signal that controls gene expression profiles in the Jurkat T cell line and mouse thymocytes. Using DNA microarrays and Northern blots to analyze unstimulated cells, we demonstrate that expression of a cluster of genes, including RAG-1 and RAG-2, is repressed by constitutive signals requiring the adapter molecules LAT and SLP-76. This TCR-like pathway results in constitutive low-level activity of Erk and Abl kinases. Inhibition of Abl by the drug STI-571 or inhibition of signaling events upstream of Erk increases RAG-1 expression. Our data suggest that physiologic gene expression programs depend upon tonic activity of signaling pathways independent of receptor ligation.

  View details for PubMedID 14624253

• Rheumatoid arthritis is a heterogeneous disease - Evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues ARTHRITIS AND RHEUMATISM Kraan, T. C., van Gaalen, F. A., Kasperkovitz, P. V., Verbeet, N. L., Smeets, T. J., Kraan, M. C., Fero, M., Tak, P. P., Huizinga, T. W., Pieterman, E., Breedveld, F. C., Alizadeh, A. A., Verweij, C. L. 2003; 48 (8): 2132-2145

  Abstract

  To generate a molecular description of synovial tissue from rheumatoid arthritis (RA) patients that would allow us to unravel novel aspects of pathogenesis and to identify different forms of disease.We applied complementary DNA microarray analysis to profile gene expression, with a focus on immune-related genes, in affected joint tissues from RA patients and in tissues from osteoarthritis (OA) patients as a control. To validate microarray data, real-time polymerase chain reaction was performed on genes of interest.The gene expression signatures of synovial tissues from RA patients showed considerable variability, resulting in the identification of at least two molecularly distinct forms of RA tissues. One class of tissues revealed abundant expression of clusters of genes indicative of an involvement of the adaptive immune response. Detailed analysis of the expression profile provided evidence for a prominent role of an activated signal transducer and activator of transcription 1 pathway in these tissues. The expression profiles of another group of RA tissues revealed an increased tissue remodeling activity and a low inflammatory gene expression signature. The gene expression pattern in the latter tissues was reminiscent of that observed in the majority of OA tissues.The differences in the gene expression profiles provide a unique perspective for distinguishing different pathogenetic RA subsets based on molecular criteria. These data reflect important aspects of molecular variation that are relevant for understanding the biologic dysregulation underlying these subsets of RA. This approach may also help to define homogeneous groups for clinical studies and evaluation of targeted therapies.

  View details for DOI 10.1002/art.11096

  View details for Web of Science ID 000184585000008

  View details for PubMedID 12905466

• Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations BLOOD Martinez-Climent, J. A., Alizadeh, A. A., Segraves, R., Blesa, D., Rubio-Moscardo, F., Albertson, D. G., Garcia-Conde, J., Dyer, M. J., Levy, R., Pinkel, D., Lossos, I. S. 2003; 101 (8): 3109-3117

  Abstract

  Genomic aberrations in a series of paired biopsy samples from patients who presented initially with follicle center lymphoma (FCL) and subsequently transformed to diffuse large B-cell lymphoma (DLBCL) were measured by array comparative genomic hybridization (CGH). The consequences of these aberrations on gene expression were determined by comparison with expression analysis on these specimens using cDNA microarrays. A heterogeneous pattern of acquired genomic abnormalities was observed upon transformation, some of which were recurrent in small subsets of patients. Some of the genomic aberration acquired upon transformation, such as gain/amplification of 1q21-q24, 2p16 (REL/BCL11A gene loci), 3q27-q29 (including the BCL6 locus), 7q11.2-q22.1, 12pter-q12, 18q21 (including the BCL2 locus) and Xq, and deletion of 6q22-q24, 13q14-q21 and 17p13 (P53 locus) have been previously implicated in the FCL/DLBCL pathogenesis. In addition, novel genomic imbalances not previously reported in association with FCL transformation, such as overrepresentation of 4p12-pter, 5p12-p15, 6p12.3-p21, 9p23, 9q13-q31, 16q, 17q21, and loss of 1p36.3, 4q21-q23, 5q21-q23, 9q31-qter, 11q24-q25, and 15q23, were identified. We observed a differential expression profile of many genes within regions of gain and deletion upon transformation, including novel target genes associated with FCL transformation. However, other genes did not show deregulated expression despite their location within these areas. In summary, the combination of array CGH and expression analysis provides a more comprehensive picture of the transformation of FCL to DLBCL. This process is associated with the acquisition of a variable spectrum of genomic imbalances affecting recurrent chromosomal areas that harbor overexpressed or underexpressed genes targeted upon transformation.

  View details for DOI 10.1182/blood-2002-07-2119

  View details for Web of Science ID 000182101400038

  View details for PubMedID 12406872

• Individuality and variation in gene expression patterns in human blood PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Whitney, A. R., Diehn, M., Popper, S. J., Alizadeh, A. A., Boldrick, J. C., Relman, D. A., Brown, P. O. 2003; 100 (4): 1896-1901

  Abstract

  The nature and extent of interindividual and temporal variation in gene expression patterns in specific cells and tissues is an important and relatively unexplored issue in human biology. We surveyed variation in gene expression patterns in peripheral blood from 75 healthy volunteers by using cDNA microarrays. Characterization of the variation in gene expression in healthy tissue is an essential foundation for the recognition and interpretation of the changes in these patterns associated with infections and other diseases, and peripheral blood was selected because it is a uniquely accessible tissue in which to examine this variation in patients or healthy volunteers in a clinical setting. Specific features of interindividual variation in gene expression patterns in peripheral blood could be traced to variation in the relative proportions of specific blood cell subsets; other features were correlated with gender, age, and the time of day at which the sample was taken. An analysis of multiple sequential samples from the same individuals allowed us to discern donor-specific patterns of gene expression. These data help to define human individuality and provide a database with which disease-associated gene expression patterns can be compared.

  View details for DOI 10.1073/pnas.252784499

  View details for Web of Science ID 000181073000082

  View details for PubMedID 12578971

  View details for PubMedCentralID PMC149930

• HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma BLOOD Lossos, I. S., Alizadeh, A. A., Rajapaksa, R., Tibshirani, R., Levy, R. 2003; 101 (2): 433-440

  Abstract

  We have cloned and characterized a novel human gene, HGAL (human germinal center-associated lymphoma), which predicts outcome in patients with diffuse large B-cell lymphoma (DLBCL). The HGAL gene comprises 6 exons and encodes a cytoplasmic protein of 178 amino acids that contains an immunoreceptor tyrosine-based activation motif (ITAM). It is highly expressed in germinal center (GC) lymphocytes and GC-derived lymphomas and is homologous to the mouse GC-specific gene M17. Expression of the HGAL gene is specifically induced in B cells by interleukin-4 (IL-4). Patients with DLBCL expressing high levels of HGAL mRNA demonstrate significantly longer overall survival than do patients with low HGAL expression. This association was independent of the clinical international prognostic index. High HGAL mRNA expression should be used as a prognostic factor in DLBCL.

  View details for Web of Science ID 000180384800010

  View details for PubMedID 12509382

• SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data NUCLEIC ACIDS RESEARCH Diehn, M., Sherlock, G., Binkley, G., Jin, H., Matese, J. C., Hernandez-Boussard, T., Rees, C. A., Cherry, J. M., Botstein, D., Brown, P. O., Alizadeh, A. A. 2003; 31 (1): 219-223

  Abstract

  The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that brings together information from a broad range of resources, and provides it in manner particularly useful for genome-scale analyses. SOURCE's GeneReports include aliases, chromosomal location, functional descriptions, GeneOntology annotations, gene expression data, and links to external databases. We curate published microarray gene expression datasets and allow users to rapidly identify sets of co-regulated genes across a variety of tissues and a large number of conditions using a simple and intuitive interface. SOURCE provides content both in gene and cDNA clone-centric pages, and thus simplifies analysis of datasets generated using cDNA microarrays. SOURCE is continuously updated and contains the most recent and accurate information available for human, mouse, and rat genes. By allowing dynamic linking to individual gene or clone reports, SOURCE facilitates browsing of large genomic datasets. Finally, SOURCEs batch interface allows rapid extraction of data for thousands of genes or clones at once and thus facilitates statistical analyses such as assessing the enrichment of functional attributes within clusters of genes. SOURCE is available at http://source.stanford.edu.

  View details for DOI 10.1093/nar/gkg014

  View details for Web of Science ID 000181079700050

  View details for PubMedID 12519986

• Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling N Engl J Med Sarwal M, Chen X, Chua MS, Kambham N, Hsieh SC, Satterwhite T, Alizadeh AA, Masek M, Diehn, M, Salvatierra O Jr, Brown PO 2003; 349 (2): 125-38
• Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays AMERICAN JOURNAL OF PATHOLOGY Liu, C. L., Prapong, W., Natkunam, Y., Alizadeh, A., Montgomery, K., Gilks, C. B., van de Rijn, M. 2002; 161 (5): 1557-1565

  Abstract

  The creation of tissue microarrays (TMAs) allows for the rapid immunohistochemical analysis of thousands of tissue samples, with numerous different antibodies per sample. This technical development has created a need for tools to aid in the analysis and archival storage of the large amounts of data generated. We have developed a comprehensive system for high-throughput analysis and storage of TMA immunostaining data, using a combination of commercially available systems and novel software applications developed in our laboratory specifically for this purpose. Staining results are recorded directly into an Excel worksheet and are reformatted by a novel program (TMA-Deconvoluter) into a format suitable for hierarchical clustering analysis or other statistical analysis. Hierarchical clustering analysis is a powerful means of assessing relatedness within groups of tumors, based on their immunostaining with a panel of antibodies. Other analyses, such as generation of survival curves, construction of Cox regression models, or assessment of intra- or interobserver variation, can also be done readily on the reformatted data. Finally, the immunoprofile of a specific case can be rapidly retrieved from the archives and reviewed through the use of Stainfinder, a novel web-based program that creates a direct link between the clustered data and a digital image database. An on-line demonstration of this system is available at http://genome-www.stanford.edu/TMA/explore.shtml.

  View details for Web of Science ID 000179197000006

  View details for PubMedID 12414504

  View details for PubMedCentralID PMC1850765

• Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Diehn, M., Alizadeh, A. A., Rando, O. J., Liu, C. L., Stankunas, K., Botstein, D., Crabtree, G. R., Brown, P. O. 2002; 99 (18): 11796-11801

  Abstract

  Optimal activation of T cells requires effective occupancy of both the antigen-specific T cell receptor and a second coreceptor such as CD28. We used cDNA microarrays to characterize the genomic expression program in human peripheral T cells responding to stimulation of these receptors. We found that CD28 agonists alone elicited few, but reproducible, changes in gene expression, whereas CD3 agonists elicited a multifaceted temporally choreographed gene expression program. The principal effect of simultaneous engagement of CD28 was to increase the amplitude of the CD3 transcriptional response. The induced genes whose expression was most enhanced by costimulation were significantly enriched for known targets of nuclear factor of activated T cells (NFAT) transcription factors. This enhancement was nearly abolished by blocking the nuclear translocation of NFATc by using the calcineurin inhibitor FK506. CD28 signaling promoted phosphorylation, and thus inactivation, of the NFAT nuclear export kinase glycogen synthase kinase-3 (GSK3), coincident with enhanced dephosphorylation of NFATc proteins. These results provide a detailed picture of the transcriptional program of T cell activation and suggest that enhancement of transcriptional activation by NFAT, through inhibition of its nuclear export, plays a key role in mediating the CD28 costimulatory signal.

  View details for DOI 10.1073/pnas.092284399

  View details for Web of Science ID 000177843100048

  View details for PubMedID 12195013

  View details for PubMedCentralID PMC129348

• Transformation of follicular lymphoma to diffuse large-cell lymphoma: Alternative patterns with increased or decreased expression of c-myc and its regulated genes PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lossos, I. S., Alizadeh, A. A., Diehn, M., Warnke, R., Thorstenson, Y., Oefner, P. J., Brown, P. O., Botstein, D., Levy, R. 2002; 99 (13): 8886-8891

  Abstract

  The natural history of follicular lymphoma (FL) is frequently characterized by transformation to a more aggressive diffuse large B cell lymphoma (DLBCL). We compared the gene-expression profiles between transformed DLBCL and their antecedent FL. No genes were observed to increase or decrease their expression in all of the cases of histological transformation. However, two different gene-expression profiles associated with the transformation process were defined, one in which c-myc and genes regulated by c-myc showed increased expression and one in which these same genes showed decreased expression. Further, there was a striking difference in gene-expression profiles between transformed DLBCL and de novo DLBCL, because the gene-expression profile of transformed DLBCL was more similar to their antecedent FL than to de novo DLBCL. This study demonstrates that transformation from FL to DLBCL can occur by alternative pathways and that transformed DLBCL and de novo DLBCL have very different gene-expression profiles that may underlie the different clinical behaviors of these two types of morphologically similar lymphomas.

  View details for DOI 10.1073/pnas.132253599

  View details for Web of Science ID 000176478200075

  View details for PubMedID 12077300

  View details for PubMedCentralID PMC124393

• The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile BLOOD Huang, J. Z., Sanger, W. G., Greiner, T. C., Staudt, L. M., Weisenburger, D. D., Pickering, D. L., Lynch, J. C., Armitage, J. O., Wamke, R. A., Alizadeh, A. A., Lossos, I. S., Levy, R., Chan, W. C. 2002; 99 (7): 2285-2290

  Abstract

  Recently we have identified subgroups of de novo primary diffuse large B-cell lymphoma (DLBCL) based on complementary DNA microarray-generated gene expression profiles. To correlate the gene expression profiles with cytogenetic abnormalities in these DLBCLs, we examined the occurrence of the t(14;18)(q32;q21) in the 2 distinctive subgroups of DLBCL: one with the germinal center B-cell gene expression signature and the other with the activated B cell-like gene expression signature. The t(14;18) was detected in 7 of 35 cases (20%). All 7 t(14;18)-positive cases had a germinal center B-cell gene expression profile, representing 35% of the cases in this subgroup, and 6 of these 7 cases had very similar gene expression profiles. The expression of bcl-2 and bcl-6 proteins was not significantly different between the t(14;18)-positive and -negative cases, whereas CD10 was detected only in the group with the germinal center B-cell expression profile, and CD10 was most frequently expressed in the t(14;18)-positive cases. This study supports the validity of subdividing DLBCL into 2 major subgroups by gene expression profiling, with the t(14;18) being an important event in the pathogenesis of a subset of DLBCL arising from germinal center B cells. CD10 protein expression is useful in identifying cases of DLBCL with a germinal center B-cell gene expression profile and is often expressed in cases with the t(14;18).

  View details for Web of Science ID 000174559300002

  View details for PubMedID 11895757

• In vivo regulation of human skeletal muscle gene expression by thyroid hormone GENOME RESEARCH Clement, K., Viguerie, N., Diehn, M., Alizadeh, A., Barbe, P., Thalamas, C., Storey, J. D., Brown, P. O., Barsh, G. S., Langin, D. 2002; 12 (2): 281-291

  Abstract

  Thyroid hormones are key regulators of metabolism that modulate transcription via nuclear receptors. Hyperthyroidism is associated with increased metabolic rate, protein breakdown, and weight loss. Although the molecular actions of thyroid hormones have been studied thoroughly, their pleiotropic effects are mediated by complex changes in expression of an unknown number of target genes. Here, we measured patterns of skeletal muscle gene expression in five healthy men treated for 14 days with 75 microg of triiodothyronine, using 24,000 cDNA element microarrays. To analyze the data, we used a new statistical method that identifies significant changes in expression and estimates the false discovery rate. The 381 up-regulated genes were involved in a wide range of cellular functions including transcriptional control, mRNA maturation, protein turnover, signal transduction, cellular trafficking, and energy metabolism. Only two genes were down-regulated. Most of the genes are novel targets of thyroid hormone. Cluster analysis of triiodothyronine-regulated gene expression among 19 different human tissues or cell lines revealed sets of coregulated genes that serve similar biologic functions. These results define molecular signatures that help to understand the physiology and pathophysiology of thyroid hormone action.

  View details for Web of Science ID 000173689600008

  View details for PubMedID 11827947

• Stereotyped and specific gene expression programs in human innate immune responses to bacteria PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Boldrick, J. C., Alizadeh, A. A., Diehn, M., Dudoit, S., Liu, C. L., Belcher, C. E., Botstein, D., Staudt, L. M., Brown, P. O., Relman, D. A. 2002; 99 (2): 972-977

  Abstract

  The innate immune response is crucial for defense against microbial pathogens. To investigate the molecular choreography of this response, we carried out a systematic examination of the gene expression program in human peripheral blood mononuclear cells responding to bacteria and bacterial products. We found a remarkably stereotyped program of gene expression induced by bacterial lipopolysaccharide and diverse killed bacteria. An intricately choreographed expression program devoted to communication between cells was a prominent feature of the response. Other features suggested a molecular program for commitment of antigen-presenting cells to antigens captured in the context of bacterial infection. Despite the striking similarities, there were qualitative and quantitative differences in the responses to different bacteria. Modulation of this host-response program by bacterial virulence mechanisms was an important source of variation in the response to different bacteria.

  View details for Web of Science ID 000173450100078

  View details for PubMedID 11805339

  View details for PubMedCentralID PMC117415

• Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia JOURNAL OF EXPERIMENTAL MEDICINE Rosenwald, A., Alizadeh, A. A., Widhopf, G., Simon, R., Davis, R. E., Yu, X., Yang, L. M., Pickeral, O. K., Rassenti, L. Z., Powell, J., Botstein, D., Byrd, J. C., Grever, M. R., Cheson, B. D., CHIORAZZI, N., Wilson, W. H., Kipps, T. J., Brown, P. O., Staudt, L. M. 2001; 194 (11): 1639-1647

  Abstract

  The most common human leukemia is B cell chronic lymphocytic leukemia (CLL), a malignancy of mature B cells with a characteristic clinical presentation but a variable clinical course. The rearranged immunoglobulin (Ig) genes of CLL cells may be either germ-line in sequence or somatically mutated. Lack of Ig mutations defined a distinctly worse prognostic group of CLL patients raising the possibility that CLL comprises two distinct diseases. Using genomic-scale gene expression profiling, we show that CLL is characterized by a common gene expression "signature," irrespective of Ig mutational status, suggesting that CLL cases share a common mechanism of transformation and/or cell of origin. Nonetheless, the expression of hundreds of other genes correlated with the Ig mutational status, including many genes that are modulated in expression during mitogenic B cell receptor signaling. These genes were used to build a CLL subtype predictor that may help in the clinical classification of patients with this disease.

  View details for Web of Science ID 000172659500009

  View details for PubMedID 11733578

• Towards a novel classification of human malignancies based on gene expression patterns JOURNAL OF PATHOLOGY Alizadeh, A. A., Ross, D. T., Perou, C. M., van de Rijn, M. 2001; 195 (1): 41-52

  Abstract

  As a result of progress on the human genome project, approximately 19 000 genes have been identified and tens of thousands more tentatively identified as partial fragments of genes termed expressed sequence tags (ESTs). Most of these genes are only partially characterized and the functions of the vast majority are as yet unknown. It is likely that many genes that might be useful for diagnosis and/or prognostication of human malignancies have yet to be recognized. The advent of cDNA microarray technology now allows the efficient measurement of expression for almost every gene in the human genome in a single overnight hybridization experiment. This genomic scale approach has begun to reveal novel molecular-based sub-classes of tumours in breast carcinoma, colon carcinoma, lymphoma, leukaemia, and melanoma. In several instances, gene microarray analysis has already identified genes that appear to be useful for predicting clinical behaviour. This review discusses some recent findings using gene microarray technology and describes how this and related technologies are likely to contribute to the emergence of novel molecular classifications of human malignancies.

  View details for Web of Science ID 000171160100006

  View details for PubMedID 11568890

• Genomic analysis of renal allograft dysfunction using cDNA microarrays 18th World Congress of the Transplantation-Society Sarwal, M., Chang, S., Barry, C., Chen, X., Alizadeh, A., Salvatierra, O., BROWN, P. ELSEVIER SCIENCE INC. 2001: 297–98

  View details for Web of Science ID 000167629900133

  View details for PubMedID 11266826

• Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lossos, I. S., Alizadeh, A. A., Eisen, M. B., Chan, W. C., Brown, P. O., Botstein, D., Staudt, L. M., Levy, R. 2000; 97 (18): 10209-10213

  Abstract

  B cell diffuse large cell lymphoma (B-DLCL) is a heterogeneous group of tumors, based on significant variations in morphology, clinical presentation, and response to treatment. Gene expression profiling has revealed two distinct tumor subtypes of B-DLCL: germinal center B cell-like DLCL and activated B cell-like DLCL. In a separate study, we determined that B-DLCL can also be subdivided into two groups based on the presence or absence of ongoing Ig gene hypermutation. Here, we evaluated the correlation between these B-DLCL subtypes established by the two different methods. Fourteen primary B-DLCL cases were studied by gene expression profiling using DNA microarrays and for the presence of ongoing mutations in their Ig heavy chain gene. All seven cases classified as germinal center B cell-like DLCL by gene expression showed the presence of ongoing mutations in the Ig genes. Five of the seven cases classified by gene expression as activated B cell-like DLCL had no ongoing somatic mutations, whereas, in the remaining two cases, a single point mutation was observed in only 2 of 15 and 21 examined molecular clones of variable heavy (V(H)) chain gene, respectively. These two cases were distantly related to the rest of the activated B cell-like DLCL tumors by gene expression. Our findings validate the concept that lymphoid malignancies are derived from cells at discrete stages of normal lymphocyte maturation and that the malignant cells retain the genetic program of those normal cells.

  View details for Web of Science ID 000089067500071

  View details for PubMedID 10954754

• Exploring gene expression signatures of host responses to infection Boldrick, J. C., Belcher, C. E., Alizadeh, A. A., Liu, C. L., Diehn, M., Brown, P. O., Relman, D. A. OXFORD UNIV PRESS INC. 2000: 218–18

  View details for Web of Science ID 000088950900082

• Examining the living genome in health and disease with DNA microarrays JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Diehn, M., Alizadeh, A. A., Brown, P. O. 2000; 283 (17): 2298-2299

  View details for Web of Science ID 000086671600042

  View details for PubMedID 10807394

• Genomic-scale gene expression profiling of normal and malignant immune cells CURRENT OPINION IN IMMUNOLOGY Alizadeh, A. A., Staudt, L. M. 2000; 12 (2): 219-225

  Abstract

  Gene expression variation is critical for the normal development and physiology of immune cells. Using cDNA microarrays, a systematic, genomic-scale view of gene expression in immune cells at many stages of differentiation and activation can be obtained. From the high vantagepoint provided by this technology, the gene expression physiology of immune cells appears remarkably ordered and logical. Each stage of lymphocyte differentiation can be defined by a characteristic gene expression signature. Genes that are co-regulated over hundreds of experimental conditions often encode functionally related proteins. Gene expression profiles also provide unprecedented ability to define the molecular and functional relationships between normal and malignant lymphocyte cell populations.

  View details for Web of Science ID 000085786300016

  View details for PubMedID 10712950

• 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Genome biology Hastie, T., Tibshirani, R., Eisen, M. B., Alizadeh, A., Levy, R., Staudt, L., Chan, W. C., Botstein, D., BROWN, P. 2000; 1 (2): RESEARCH0003-?

  Abstract

  Large gene expression studies, such as those conducted using DNA arrays, often provide millions of different pieces of data. To address the problem of analyzing such data, we describe a statistical method, which we have called 'gene shaving'. The method identifies subsets of genes with coherent expression patterns and large variation across conditions. Gene shaving differs from hierarchical clustering and other widely used methods for analyzing gene expression studies in that genes may belong to more than one cluster, and the clustering may be supervised by an outcome measure. The technique can be 'unsupervised', that is, the genes and samples are treated as unlabeled, or partially or fully supervised by using known properties of the genes or samples to assist in finding meaningful groupings.We illustrate the use of the gene shaving method to analyze gene expression measurements made on samples from patients with diffuse large B-cell lymphoma. The method identifies a small cluster of genes whose expression is highly predictive of survival.The gene shaving method is a potentially useful tool for exploration of gene expression data and identification of interesting clusters of genes worth further investigation.

  View details for PubMedID 11178228

  View details for PubMedCentralID PMC15015

• Gene expression in large B-cell lymphoma using cDNA microarray technology. Chan, W. C., Alizadeh, A., Eisen, M., Davis, R. E., Ma, C., Sabet, H., Tran, T., Powell, J. I., Yang, L., Greiner, T. C., Weisenburger, D. D., Armitage, J. O., Marti, G. E., Moores, T., Hudson, J., Lossos, I., Warnke, R., Levy, R., Botstein, D., Brown, P. O., Staudt, L. M. AMER SOC HEMATOLOGY. 1999: 698A–698A

  View details for Web of Science ID 000083790303136

• Genome-wide analysis of DNA copy-number changes using cDNA microarrays NATURE GENETICS Pollack, J. R., Perou, C. M., Alizadeh, A. A., Eisen, M. B., Pergamenschikov, A., Williams, C. F., Jeffrey, S. S., Botstein, D., Brown, P. O. 1999; 23 (1): 41-46

  Abstract

  Gene amplifications and deletions frequently contribute to tumorigenesis. Characterization of these DNA copy-number changes is important for both the basic understanding of cancer and its diagnosis. Comparative genomic hybridization (CGH) was developed to survey DNA copy-number variations across a whole genome. With CGH, differentially labelled test and reference genomic DNAs are co-hybridized to normal metaphase chromosomes, and fluorescence ratios along the length of chromosomes provide a cytogenetic representation of DNA copy-number variation. CGH, however, has a limited ( approximately 20 Mb) mapping resolution, and higher-resolution techniques, such as fluorescence in situ hybridization (FISH), are prohibitively labour-intensive on a genomic scale. Array-based CGH, in which fluorescence ratios at arrayed DNA elements provide a locus-by-locus measure of DNA copy-number variation, represents another means of achieving increased mapping resolution. Published array CGH methods have relied on large genomic clone (for example BAC) array targets and have covered only a small fraction of the human genome. cDNAs representing over 30,000 radiation-hybrid (RH)-mapped human genes provide an alternative and readily available genomic resource for mapping DNA copy-number changes. Although cDNA microarrays have been used extensively to characterize variation in human gene expression, human genomic DNA is a far more complex mixture than the mRNA representation of human cells. Therefore, analysis of DNA copy-number variation using cDNA microarrays would require a sensitivity of detection an order of magnitude greater than has been routinely reported. We describe here a cDNA microarray-based CGH method, and its application to DNA copy-number variation analysis in breast cancer cell lines and tumours. Using this assay, we were able to identify gene amplifications and deletions genome-wide and with high resolution, and compare alterations in DNA copy number and gene expression.

  View details for Web of Science ID 000082337300013

  View details for PubMedID 10471496

• The lymphochip: A specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes 64th Symposia: Signaling and Gene Expression in the Immune System Alizadeh, A., Eisen, M., Davis, R. E., Ma, C., Sabet, H., Tran, T., Powell, J. I., Yang, L., Marti, G. E., Moore, D. T., Hudson, J. R., Chan, W. C., Greiner, T., Weisenburger, D., Armitage, J. O., Lossos, I., Levy, R., Botstein, D., Brown, P. O., Staudt, L. M. COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT. 1999: 71–78

  View details for Web of Science ID 000087225400011

  View details for PubMedID 11232339

• Probing lymphocyte biology by genomic-scale gene expression analysis JOURNAL OF CLINICAL IMMUNOLOGY Alizadeh, A., Eisen, M., Botstein, D., Brown, P. O., Staudt, L. M. 1998; 18 (6): 373-379

  Abstract

  The identity and abundance of mRNA species within a cell dictate, to a large extent, the biological potential of that cell. Although posttranscriptional mechanisms modify protein expression in critical ways, cellular differentiation requires key changes in gene transcription, as evidenced by the potent phenotypes that result from disruption of transcription factor genes in mice. It is now possible to assess the mRNA profile of a cell globally using recently developed genomics techniques. This review focuses on the potential of cDNA microarrays to define gene expression in lymphoid cells, a field which is in its infancy. Examples of cellular activation genes and cytokine inducible genes discovered using this technology are presented but these represent only a taste of the fruit that this new technology will ultimately bear. Gene expression profiles should provide essential new insights into lymphocyte differentiation and activation, the pathogenesis of immune disorders, and the molecular abnormalities in lymphoid malignancies.

  View details for Web of Science ID 000077438400001

  View details for PubMedID 9857281