SELECTED PUBLICATIONS
Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma
Cell Reports. 2017 Oct 31; 21(5):1399-410.
Glioblastoma (GBM) is the most common primary brain cancer in adults and is notoriously difficult to treat because of its diffuse nature. We performed single-cell RNA sequencing (RNA-seq) on 3,589 cells in a cohort of four patients. We obtained cells from the tumor core as well as surrounding peripheral tissue. Our analysis revealed cellular variation in the tumor's genome and transcriptome. We were also able to identify infiltrating neoplastic cells in regions peripheral to the core lesions. Despite the existence of significant heterogeneity among neoplastic cells, we found that infiltrating GBM cells share a consistent gene signature between patients, suggesting a common mechanism of infiltration. Additionally, in investigating the immunological response to the tumors, we found transcriptionally distinct myeloid cell populations residing in the tumor core and the surrounding peritumoral space. Our data provide a detailed dissection of GBM cell types, revealing an abundance of information about tumor formation and migration.
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http://www.cell.com/cell-reports/fulltext/S2211-1247(17)31462-6
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A survey of human brain transcriptome diversity at the single cell level.
PNAS | June 9, 2015 | vol. 112 | no. 23 | 7285–7290
The human brain is a tissue of vast complexity in terms of the cell types it comprises. Conventional approaches to classifying cell types in the human brain at single cell resolution have been limited to exploring relatively few markers and therefore have provided a limited molecular characterization of any given cell type. We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level.
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https://www.ncbi.nlm.nih.gov/pubmed/26060301
Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse.
Neuron | January 2016 | Volume 89, Issue 1, 6 | Pages 37–53
The functional and molecular similarities and distinctions between human and murine astrocytes are poorly understood. Here, we report the development of an immunopanning method to acutely purify astrocytes from fetal, juvenile, and adult human brains and to maintain these cells in serum-free cultures.
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New tools for studying microglia in the mouse and human CNS.
Proc Natl Acad Sci U S A. 2016 Mar 22;113(12)
Here, we identify transmembrane protein 119 (Tmem119), a cell-surface protein of unknown function, as a highly expressed microglia-specific marker in both mouse and human. We developed monoclonal antibodies to its intracellular and extracellular domains that enable the immunostaining and isolation of microglia. Using our antibodies, we provide, to our knowledge, the first RNAseq profiles of highly pure mouse microglia during development and after an immune challenge.
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Chromosome-scale mega-haplotypes enable digital karyotyping of cancer aneuploidy.
Nucleic Acids Research. 2017 Aug 16.
Genomic instability is a frequently occurring feature of cancer that involves large-scale structural alterations. These somatic changes in chromosome structure include duplication of entire chromosome arms and aneuploidy where chromosomes are duplicated beyond normal diploid content. However, the accurate determination of aneuploidy events in cancer genomes is a challenge. Recent advances in sequencing technology allow the characterization of haplotypes that extend megabases along the human genome using high molecular weight (HMW) DNA. For this study, we employed a library preparation method in which sequence reads have barcodes linked to single HMW DNA molecules. Barcode-linked reads are used to generate extended haplotypes on the order of megabases. We developed a method that leverages haplotypes to identify chromosomal segmental alterations in cancer and uses this information to join haplotypes together, thus extending the range of phased variants. With this approach, we identified mega-haplotypes that encompass entire chromosome arms. We characterized the chromosomal arm changes and aneuploidy events in a manner that offers similar information as a traditional karyotype but with the benefit of DNA sequence resolution. We applied this approach to characterize aneuploidy and chromosomal alterations from a series of primary colorectal cancers.
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Brain tumor mutations detected in cerebral spinal fluid.
Clin Chem. 2015 Mar;61(3):514-22.
Detecting tumor-derived cell-free DNA (cfDNA) in the blood of brain tumor patients is challenging, presumably owing to the blood-brain barrier. Cerebral spinal fluid (CSF) may serve as an alternative "liquid biopsy" of brain tumors by enabling measurement of circulating DNA within CSF to characterize tumor-specific mutations. Many aspects about the characteristics and detectability of tumor mutations in CSF remain undetermined. We detected tumor mutations in CSF samples from 6 of 7 patients with solid brain tumors. The concentration of the tumor mutant alleles varied widely between patients, from <5 to nearly 3000 copies/mL CSF. We identified 7 somatic mutations from the CSF of a patient with leptomeningeal disease by use of cancer panel sequencing, and the result was concordant with genetic testing on the primary tumor biopsy. Tumor mutations were detectable in cfDNA from the CSF of patients with different primary and metastatic brain tumors. We designed 2 strategies to characterize tumor mutations in CSF for potential clinical diagnosis: the targeted detection of known driver mutations to monitor brain metastasis and the global characterization of genomic aberrations to direct personalized cancer care.Read more at:
The "Liquid Biopsy": the Role of Circulating DNA and RNA in Central Nervous System Tumors.
Curr Neurol Neurosci Rep. 2016 Mar;16(3):25.
The detection of tumor-derived circulating nucleic acids in patients with cancer, known as the "liquid biopsy," has expanded from use in plasma to other bodily fluids in an increasing number of malignancies. Recent work suggests that cerebrospinal fluid may be a useful source of CNS tumor-derived circulating nucleic acids. In this review, we discuss the available data and future outlook on the use of the liquid biopsy for CNS tumors.
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Tumor DNA in cerebral spinal fluid reflects clinical course in a patient with melanoma leptomeningeal brain metastases.
J Neurooncol. 2016 May;128(1):93-100.
In this report, we used droplet digital PCR to test mutant tumor DNA in CSF of a patient to monitor the treatment response of metastatic melanoma leptomeningeal disease (LMD). The mutant DNA fraction in CSF corresponded well with the patient's clinical response. We used whole exome sequencing to examine the mutation profiles of the LMD tumor DNA in CSF before therapeutic response and after disease relapse. The cellular and cfDNA revealed similar mutation profiles, suggesting cfDNA is representative of LMD cells.
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The team
Linya, Lina, Candace, Ian, Sophia, Eli, Yingmei, Melanie
(from left to right)
lAB MEMBERS
Our team combines experience with passion, creativity, and dedication.
Melanie Hayden Gephart
Principal Investigator
Dr. Hayden did her residency at Stanford University in neurosurgery and joined as faculty in 2014. She worked previously in Matthew Scott's lab studying medulloblastoma in a mouse model.
Yingmei Li
Post Doctorate
Yingmei obtained her PhD in chemistry from Purdue University in 2014. Her PhD work focused on DNA/RNA nanotechnology. She has been working on liquid biopsy of metastatic and primary brain tumors since she joined our lab. She enjoys movies, hiking and tiramisu!
Sophia Chernikov
Senior Researcher
Sophia is an experienced cancer biologist with a background in cell and molecular biology, protein biochemistry, assay development, biomarker discovery and drug development.
Dina Polyak
Post Doctorate
Dina obtained her PhD in pharmacology from Tel Aviv University. She has an extensive background in development and in vitro / in vivo characterization of polymer-based nanomedicines for the treatment of solid tumors.
Ian Connolly
Medical Student
Ian is a medical student interested in neurosurgery. He completed his undergraduate and graduate degrees in mechanical engineering at Stanford where he also played on the men's volleyball team.
Eli Johnson
Medical Student
Eli is a medical student at Stanford interested in neurosurgery. He completed his bachelors degree at NYU
where he also competed on the track and field team.
Bina Kakusa
Medical Student
Bina is a Stanford medical student interested in neurosurgery. He completed his undergraduate degree in neuroscience and computer science at the College of William and Mary. He enjoys traveling, playing soccer, and experimenting with cooking different cuisines.
Lina Khoeur
Undergraduate
Lina is an undergraduate at Stanford. She is a Human Biology major and is contemplating applying to medical school.
Kevin Tran
Undergraduate
Kevin is an undergraduate at Stanford. He is a computer science major and is interested in the intersection between big data and neurosurgery.
Neuro-oncology research, it's personal
Neurosurgery isn't just my career and practice, it is a personal struggle to help improve the treatment for patients with brain tumors. These diseases have taken the lives of many of my friends and family, and affects the lives of my patients every day. Just a handful of their photos are listed here. We are committed to improving the care of patients with brain tumors and understanding the underlying mechanisms of disease progression, motivated by a personal understanding of the disease. I work in the operating room employing the maximal treatment for patients in my clinic today. The lab looks to develop new treatments and diagnostic techniques for the future patients who will be in the clinic tomorrow.
Robert Bean (1966 - 2000)
Robert Bean, Dr. Hayden's uncle, passed away at the age of 37 from Glioblastoma.
Paul Kalanithi (1977 - 2015)
Paul, Dr. Hayden's co-resident, was diagnosed with metastatic lung cancer during his neurosurgery residency. He passed away at the age of 37.
Lab photos
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