Stanford Neurosurgery


    We seek greater understanding of the genetic and epigenetic mechanisms driving tumorigenesis and disease progression in malignant brain tumors. We currently study the capacity of cellular and cell-free DNA to inform treatment choices in patients with brain tumors. We also use single cell and cell subtype-specific transcriptomics to identify and target infiltrating glioblastoma. We hope to identify potentially targetable genes crucial in tumorigenesis. Our laboratory is a unique and collaborative working environment, engaged in a dynamic research environment at Stanford. Our laboratory space lies at the heart of the Stanford campus between the core campus and the medical facilities, emblematic of the translational aspects of our work.


    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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    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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    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.





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    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)


    Our team combines experience with passion, creativity, and dedication.

    Melanie Hayden Gephart

    Principal Investigator

    Dr. Hayden Gephart did her residency and post doctoral training at Stanford University in neurosurgery and cancer biology. She joined as faculty in 2014 and is a brain tumor neurosurgeon.




    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.


    Shruti Jain

    Post Doctorate

    Shruti has obtained her PhD in Neuroscience from Kent State University, Ohio in 2017. She has extensive experience in developmental neurobiology and her PhD work was focused on local translation of mRNAs during brain development in Down syndrome. She enjoys traveling, painting and Zumba.

    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.

    Hriday P. Bhambhvani

    Medical Student

    Hriday is a medical student at Stanford interested in neurosurgery. He received dual bachelor's degrees in neuroscience and mathematics from the University of Alabama at Birmingham in 2017. He enjoys playing soccer, hiking and writing.

    Steffi Andersen


    Steffi is an undergraduate at Stanford. She has not declared her major but is interested in biology and computer science and is looking at potentially going to medical school. She enjoys playing soccer, skiing, and singing in her free time.

    JiaoJiao Deng

    Medicine Graduate

    Jiaojiao is a 2nd year Ph.D. candidate majoring in Neurosurgery at Huashan Hospital, Fudan University. Her background is in the field of targeted therapeutics and nanomedicine for malignant brain tumors.

    Maxine Umeh

    Post Doctorate

    Maxine obtained her PhD in Biochemistry, Molecular, Cell and Developmental Biology with an emphasis in Translational Research from UC Davis. She has an extensive background in cancer biology and an interest in triple negative breast cancer, which has a higher incidence and death rate in African-American women. She enjoys volleyball, piano playing, analyzing data, and making pretty graphs.

    Adrian John Rodrigues

    Medical Student

    Adrian is a Stanford medical student interested in neurosurgery. He completed his undergraduate degree in biology and economics at Yale. He enjoys hiking, playing tennis, and reading.

    Monica Granucci

    Clinical Research Coordinator

    Monica Granucci is a Clinical Research Coordinator with the Cancer Clinical Tt..rials Office and the Brain Tumor Center. She works to facilitate research tissue acquisition at Stanford, as well as assisting with the design, conduct, and management of some of Stanford’s Neurosurgery Department’s clinical trials.

  • 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.


    Wenying Pan

    Position: Graduate Student

    Years in lab: 2013 - 2016

    Current position: Scientist at Grail Inc.

    Linya You

    Position: Post doctorate

    Years in lab: 2015 - 2016

    Current position: Shanghai Medical College of Fudan University

    Yingmei Li

    Position: Post doctorate

    Years in lab: 2014 - 2018

    Current position: Scientist at BindeBio and Chinese Academy of Science.

    Ian Connolly

    Position: Medical Student

    Years in lab: 2014 - 2019

    Current position: Neurosurgery Resident Physician at Massachusetts General Hospital


    A gift to the Gephart Lab will support our research on brain tumors.
    If you would like to make a donation for this purpose, please contact:

    Allie S. Gregorian
    Medical Center Development
    Phone: 650.724.9910
    Email: allieg1@stanford.edu

  • Interested in joining our team?

    Please submit a CV with a brief description of your research interests and career goals to Melanie Hayden Gephart (mghayden@gmail.com) 

    We are looking for a postdoctoral scientist to accelerate the study and targeting of malignant brain tumors using genetic tools and primary human samples. A competitive applicant for this position will have an interest in malignant brain tumors, neuroscience, and bioinformatics. Candidates must hold a Ph.D. from an accredited institution in a relevant research field, have strong laboratory, analytical, and organizational skills, and be able to work independently, as well as part of a team. Our work in the laboratory will enhance patient care through an improved understanding of malignant brain tumor biology.

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