Bio


I am a physician scientist trained in pathology and cancer biology. My research bridges cancer genetics, signal transduction and cellular metabolism as we aim to understand the molecular mechanisms that drive cancer development, progression, and drug resistance. We have made a series of discoveries that have identified a central role for ecDNA (extrachromosomal DNA) in cancer development, progression, accelerated tumor evolution and drug resistance. These findings have provided a new understanding of the fundamental mechanisms of oncogene amplification and the spatial organization of altered tumor genomes, launching a new area of cancer research that links circular architecture with tumor pathogenesis. We have developed and applied a set of state of the art genetic, biochemical, computational, and advanced cell imaging tools to decipher the structure of circular ecDNA in cancer to a well-curated, large set of deeply characterized, ecDNA+ cancer models, revealing enhanced chromatin accessibility and the physical formation of new cis-regulatory interactions that lead to massive oncogene transcription and tumor progression. My lab has also uncovered metabolic co-dependencies that are downstream consequences of oncogene amplification. These include a central role for altered biochemical mechanisms that regulate oncogene copy number and function. These discoveries have resulted in new understandings of some of the fundamental processes by which oncogene amplification drives cancer progression and drug resistance in the changing environments within which tumors develop.

Academic Appointments


Administrative Appointments


  • Professor of Pathology, Stanford University School of Medicine (2021 - Present)
  • Vice Chair for Research, Department of Pathology, Stanford University School of Medicine (2021 - Present)
  • Institute Scholar, ChEM-H, Stanford University (2021 - Present)
  • Distinguished Professor of Pathology, UCSD (2012 - 2021)
  • Member, Ludwig Institute for Cancer Research (2012 - 2021)
  • Lya and Harrison Latta Professor of Pathology, UCLA (2008 - 2012)
  • Professor of Pathology, UCLA (1998 - 2008)

Honors & Awards


  • Elected Fellow, American Association for the Advancement of Science (2015)
  • Elected Member, American Association of Physicians (2012-present)
  • President, American Society for Clinical Investigation (2010-2011)
  • Elected Member, American Society for Clinical Investigation (2007-present)
  • American's Top Doctors for Cancer, Castle & Connelly (2006-2021)
  • Americas Top Doctors for Pathology, Castle & Connelly (2006-2021)
  • Farber Award for Brain Cancer Research, American Association of Neurological Surgeons and the Society for Neuro-Oncology (2004)
  • Pfizer New Faculty Scholar, Pfizer (1996)
  • Alpha Omega Alpha, AOA (1991)

Boards, Advisory Committees, Professional Organizations


  • Co-Founder and Chair of Scientific Advisory Board, Boundless Bio, Inc. (2018 - Present)

Professional Education


  • Post-Doctoral Fellowship, HHMI-UCSF (mentored by Dr. Louis Reichardt), Molecular Neuroscience (1998)
  • Residency, UCLA, Pathology and Neuropathology (1996)
  • M.D., Cornell University Medical College (Weill Cornell), Medicine (1991)
  • B.A., University of Pennsylvania, Philosphy (1984)

Current Research and Scholarly Interests


Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumour-promoting genes can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). These ecDNA don’t follow the normal “rules” of chromosomal inheritance, enabling tumours to achieve far higher levels of cancer-causing oncogenes than would otherwise be possible, and licensing cancers with a way to evolve and change their genomes to evade treatments, at rates that would be unthinkable for human cells. The altered circular architecture of ecDNAs also changes the way that the cancer-causing genes are regulated and expressed, further contributing to aggressive tumor growth. These unique features make ecDNA-containing cancers especially aggressive and difficult to treat and cancer patients whose tumours harbour ecDNA have markedly shorter survival.

Despite being first seen over fifty years, ago, and prescient work on its potential importance, the scale, scope, and impact of ecDNA was not well understood. In fact, it was thought to be a rare event of unknown significance. The application of powerful new, integrative molecular approaches has shown us, that ecDNAs are present in nearly half of all human cancer types and at likely in at least a quarter of all cancer patients and they have taught us that ecDNA is indeed, one of the most urgent problems facing patients with cancer, challenging the success of the targeted therapy approaches, and a problem that is certainly worthy of its nomination as a Cancer Grant Challenge. Currently, the collective current understanding of how ecDNA form, how they move around the cell, how they evolve to resist treatment, how they impact the immune system, and how they can be effectively targeted, are lacking. Can we identify actionable co-dependency pathways that are generated by ecDNA amplification? These are the areas of research focus of research in my laboratory.

We are very collaborative and interactive, with many colleagues around the world. We work very closely with Professor Howard Chang at Stanford, as well as with many other new Stanford colleagues. I have recently joined the faculty of Stanford University as a Professor and Vice Chair for Research for the Department of Pathology, and as an Institute Scholar in ChEM-H, where my lab is based. I am committed to actively contributing not only to the science and its translation for benefit to patients, but also to mentoring trainees at all levels, and helping colleagues, including junior colleagues, develop the skills necessary to navigate the complex landscape of translating science into medicines that will help patients.

2021-22 Courses


Stanford Advisees


All Publications


  • Extrachromosomal DNA: An Emerging Hallmark in Human Cancer. Annual review of pathology Wu, S., Bafna, V., Chang, H. Y., Mischel, P. S. 2021

    Abstract

    Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA, because of its nonchromosomal inheritance, drives high-copy-number oncogene amplification and enables tumors to evolve their genomes rapidly. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription, and the higher-order organization of ecDNA contributes to tumor pathogenesis. Consequently, patients whose cancers harbor ecDNA have significantly shorter survival. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. In this review, we discuss the current state of understanding of how ecDNAs form and function as well as how they contribute to drug resistance and accelerated cancer evolution. Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

    View details for DOI 10.1146/annurev-pathmechdis-051821-114223

    View details for PubMedID 34752712

  • Targeting glioblastoma signaling and metabolism with a re-purposed brain-penetrant drug. Cell reports Bi, J., Khan, A., Tang, J., Armando, A. M., Wu, S., Zhang, W., Gimple, R. C., Reed, A., Jing, H., Koga, T., Wong, I. T., Gu, Y., Miki, S., Yang, H., Prager, B., Curtis, E. J., Wainwright, D. A., Furnari, F. B., Rich, J. N., Cloughesy, T. F., Kornblum, H. I., Quehenberger, O., Rzhetsky, A., Cravatt, B. F., Mischel, P. S. 2021; 37 (5): 109957

    Abstract

    The highly lethal brain cancer glioblastoma (GBM) poses a daunting challenge because the blood-brain barrier renders potentially druggable amplified or mutated oncoproteins relatively inaccessible. Here, we identify sphingomyelin phosphodiesterase 1 (SMPD1), an enzyme that regulates the conversion of sphingomyelin to ceramide, as an actionable drug target in GBM. We show that the highly brain-penetrant antidepressant fluoxetine potently inhibits SMPD1 activity, killing GBMs, through inhibition of epidermal growth factor receptor (EGFR) signaling and via activation of lysosomal stress. Combining fluoxetine with temozolomide, a standard of care for GBM, causes massive increases in GBM cell death and complete tumor regression in mice. Incorporation of real-world evidence from electronic medical records from insurance databases reveals significantly increased survival in GBM patients treated with fluoxetine, which was not seen in patients treated with other selective serotonin reuptake inhibitor (SSRI) antidepressants. These results nominate the repurposing of fluoxetine as a potentially safe and promising therapy for patients with GBM and suggest prospective randomized clinical trials.

    View details for DOI 10.1016/j.celrep.2021.109957

    View details for PubMedID 34731610

  • Loss of polycomb repressive complex 1 activity and chromosomal instability drive uveal melanoma progression. Nature communications Bakhoum, M. F., Francis, J. H., Agustinus, A., Earlie, E. M., Di Bona, M., Abramson, D. H., Duran, M., Masilionis, I., Molina, E., Shoushtari, A. N., Goldbaum, M. H., Mischel, P. S., Bakhoum, S. F., Laughney, A. M. 2021; 12 (1): 5402

    Abstract

    Chromosomal instability (CIN) and epigenetic alterations have been implicated in tumor progression and metastasis; yet how these two hallmarks of cancer are related remains poorly understood. By integrating genetic, epigenetic, and functional analyses at the single cell level, we show that progression of uveal melanoma (UM), the most common intraocular primary cancer in adults, is driven by loss of Polycomb Repressive Complex 1 (PRC1) in a subpopulation of tumor cells. This leads to transcriptional de-repression of PRC1-target genes and mitotic chromosome segregation errors. Ensuing CIN leads to the formation of rupture-prone micronuclei, exposing genomic double-stranded DNA (dsDNA) to the cytosol. This provokes tumor cell-intrinsic inflammatory signaling, mediated by aberrant activation of the cGAS-STING pathway. PRC1 inhibition promotes nuclear enlargement, induces a transcriptional response that is associated with significantly worse patient survival and clinical outcomes, and enhances migration that is rescued upon pharmacologic inhibition of CIN or STING. Thus, deregulation of PRC1 can promote tumor progression by inducing CIN and represents an opportunity for early therapeutic intervention.

    View details for DOI 10.1038/s41467-021-25529-z

    View details for PubMedID 34518527

  • CANCER'S EXTRA GENOME SCIENTIST Mischel, P. 2021; 35 (2): 32–38
  • Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nature genetics Kim, H., Nguyen, N., Turner, K., Wu, S., Gujar, A. D., Luebeck, J., Liu, J., Deshpande, V., Rajkumar, U., Namburi, S., Amin, S. B., Yi, E., Menghi, F., Schulte, J. H., Henssen, A. G., Chang, H. Y., Beck, C. R., Mischel, P. S., Bafna, V., Verhaak, R. G. 2020

    Abstract

    Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.

    View details for DOI 10.1038/s41588-020-0678-2

    View details for PubMedID 32807987

  • Altered cellular metabolism in gliomas - an emerging landscape of actionable co-dependency targets. Nature reviews. Cancer Bi, J. n., Chowdhry, S. n., Wu, S. n., Zhang, W. n., Masui, K. n., Mischel, P. S. 2020; 20 (1): 57–70

    Abstract

    Altered cellular metabolism is a hallmark of gliomas. Propelled by a set of recent technological advances, new insights into the molecular mechanisms underlying glioma metabolism are rapidly emerging. In this Review, we focus on the dynamic nature of glioma metabolism and how it is shaped by the interaction between tumour genotype and brain microenvironment. Recent advances integrating metabolomics with genomics are discussed, yielding new insight into the mechanisms that drive glioma pathogenesis. Studies that shed light on interactions between the tumour microenvironment and tumour genotype are highlighted, providing important clues as to how gliomas respond to and adapt to their changing tissue and biochemical contexts. Finally, a road map for the discovery of potential new glioma drug targets is suggested, with the goal of translating these new insights about glioma metabolism into clinical benefits for patients.

    View details for DOI 10.1038/s41568-019-0226-5

    View details for PubMedID 31806884

  • Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature Wu, S., Turner, K. M., Nguyen, N., Raviram, R., Erb, M., Santini, J., Luebeck, J., Rajkumar, U., Diao, Y., Li, B., Zhang, W., Jameson, N., Corces, M. R., Granja, J. M., Chen, X., Coruh, C., Abnousi, A., Houston, J., Ye, Z., Hu, R., Yu, M., Kim, H., Law, J. A., Verhaak, R. G., Hu, M., Furnari, F. B., Chang, H. Y., Ren, B., Bafna, V., Mischel, P. S. 2019

    Abstract

    Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.

    View details for DOI 10.1038/s41586-019-1763-5

    View details for PubMedID 31748743

  • Oncogene Amplification in Growth Factor Signaling Pathways Renders Cancers Dependent on Membrane Lipid Remodeling. Cell metabolism Bi, J., Ichu, T., Zanca, C., Yang, H., Zhang, W., Gu, Y., Chowdhry, S., Reed, A., Ikegami, S., Turner, K. M., Zhang, W., Villa, G. R., Wu, S., Quehenberger, O., Yong, W. H., Kornblum, H. I., Rich, J. N., Cloughesy, T. F., Cavenee, W. K., Furnari, F. B., Cravatt, B. F., Mischel, P. S. 2019

    Abstract

    Advances in DNA sequencing technologies have reshaped our understanding of the molecular basis of cancer, providing a precise genomic view of tumors. Complementary biochemical and biophysical perspectives of cancer point toward profound shifts in nutrient uptake and utilization that propel tumor growth and major changes in the structure of the plasma membrane of tumor cells. The molecular mechanisms that bridge these fundamental aspects of tumor biology remain poorly understood. Here, we show that the lysophosphatidylcholine acyltransferase LPCAT1 functionally links specific genetic alterations in cancer with aberrant metabolism and plasma membrane remodeling to drive tumor growth. Growth factor receptor-driven cancers are found to depend on LPCAT1 to shape plasma membrane composition through enhanced saturated phosphatidylcholine content that is, in turn, required for the transduction of oncogenic signals. These results point to a genotype-informed strategy that prioritizes lipid remodeling pathways as therapeutic targets for diverse cancers.

    View details for DOI 10.1016/j.cmet.2019.06.014

    View details for PubMedID 31303424

  • NAD metabolic dependency in cancer is shaped by gene amplification and enhancer remodelling. Nature Chowdhry, S. n., Zanca, C. n., Rajkumar, U. n., Koga, T. n., Diao, Y. n., Raviram, R. n., Liu, F. n., Turner, K. n., Yang, H. n., Brunk, E. n., Bi, J. n., Furnari, F. n., Bafna, V. n., Ren, B. n., Mischel, P. S. 2019; 569 (7757): 570–75

    Abstract

    Precision oncology hinges on linking tumour genotype with molecularly targeted drugs1; however, targeting the frequently dysregulated metabolic landscape of cancer has proven to be a major challenge2. Here we show that tissue context is the major determinant of dependence on the nicotinamide adenine dinucleotide (NAD) metabolic pathway in cancer. By analysing more than 7,000 tumours and 2,600 matched normal samples of 19 tissue types, coupled with mathematical modelling and extensive in vitro and in vivo analyses, we identify a simple and actionable set of 'rules'. If the rate-limiting enzyme of de novo NAD synthesis, NAPRT, is highly expressed in a normal tissue type, cancers that arise from that tissue will have a high frequency of NAPRT amplification and be completely and irreversibly dependent on NAPRT for survival. By contrast, tumours that arise from normal tissues that do not express NAPRT highly are entirely dependent on the NAD salvage pathway for survival. We identify the previously unknown enhancer that underlies this dependence. Amplification of NAPRT is shown to generate a pharmacologically actionable tumour cell dependence for survival. Dependence on another rate-limiting enzyme of the NAD synthesis pathway, NAMPT, as a result of enhancer remodelling is subject to resistance by NMRK1-dependent synthesis of NAD. These results identify a central role for tissue context in determining the choice of NAD biosynthetic pathway, explain the failure of NAMPT inhibitors, and pave the way for more effective treatments.

    View details for DOI 10.1038/s41586-019-1150-2

    View details for PubMedID 31019297

    View details for PubMedCentralID PMC7138021

  • Extrachromosomal oncogene amplification in tumour pathogenesis and evolution. Nature reviews. Cancer Verhaak, R. G., Bafna, V. n., Mischel, P. S. 2019; 19 (5): 283–88

    Abstract

    Recent reports have demonstrated that oncogene amplification on extrachromosomal DNA (ecDNA) is a frequent event in cancer, providing new momentum to explore a phenomenon first discovered several decades ago. The direct consequence of ecDNA gains in these cases is an increase in DNA copy number of the oncogenes residing on the extrachromosomal element. A secondary effect, perhaps even more important, is that the unequal segregation of ecDNA from a parental tumour cell to offspring cells rapidly increases tumour heterogeneity, thus providing the tumour with an additional array of responses to microenvironment-induced and therapy-induced stress factors and perhaps providing an evolutionary advantage. This Perspectives article discusses the current knowledge and potential implications of oncogene amplification on ecDNA in cancer.

    View details for DOI 10.1038/s41568-019-0128-6

    View details for PubMedID 30872802

    View details for PubMedCentralID PMC7168519

  • Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity NATURE Turner, K. M., Deshpande, V., Beyter, D., Koga, T., Rusert, J., Lee, C., Li, B., Arden, K., Ren, B., Nathanson, D. A., Kornblum, H. I., Taylor, M. D., Kaushal, S., Cavenee, W. K., Wechsler-Reya, R., Furnari, F. B., Vandenberg, S. R., Rao, P., Wahl, G. M., Bafna, V., Mischel, P. S. 2017; 543 (7643): 122-+

    Abstract

    Human cells have twenty-three pairs of chromosomes. In cancer, however, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ecDNA), although the frequency and functional importance of ecDNA are not understood. We performed whole-genome sequencing, structural modelling and cytogenetic analyses of 17 different cancer types, including analysis of the structure and function of chromosomes during metaphase of 2,572 dividing cells, and developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis. Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells. Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level. Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification. We validated these predictions by quantitative analyses of cancer samples. The results presented here suggest that ecDNA contributes to accelerated evolution in cancer.

    View details for DOI 10.1038/nature21356

    View details for Web of Science ID 000395671500045

    View details for PubMedID 28178237

    View details for PubMedCentralID PMC5334176

  • An LXR-Cholesterol Axis Creates a Metabolic Co-Dependency for Brain Cancers CANCER CELL Villa, G. R., Hulce, J. J., Zanca, C., Bi, J., Ikegami, S., Cahill, G. L., Gu, Y., Lum, K. M., Masui, K., Yang, H., Rong, X., Hong, C., Turner, K. M., Liu, F., Hon, G. C., Jenkins, D., Martini, M., Armando, A. M., Quehenberger, O., Cloughesy, T. F., Furnari, F. B., Cavenee, W. K., Tontonoz, P., Gahman, T. C., Shiau, A. K., Cravatt, B. F., Mischel, P. S. 2016; 30 (5): 683-693

    Abstract

    Small-molecule inhibitors targeting growth factor receptors have failed to show efficacy for brain cancers, potentially due to their inability to achieve sufficient drug levels in the CNS. Targeting non-oncogene tumor co-dependencies provides an alternative approach, particularly if drugs with high brain penetration can be identified. Here we demonstrate that the highly lethal brain cancer glioblastoma (GBM) is remarkably dependent on cholesterol for survival, rendering these tumors sensitive to Liver X receptor (LXR) agonist-dependent cell death. We show that LXR-623, a clinically viable, highly brain-penetrant LXRα-partial/LXRβ-full agonist selectively kills GBM cells in an LXRβ- and cholesterol-dependent fashion, causing tumor regression and prolonged survival in mouse models. Thus, a metabolic co-dependency provides a pharmacological means to kill growth factor-activated cancers in the CNS.

    View details for DOI 10.1016/j.ccell.2016.09.008

    View details for PubMedID 27746144

  • Targeted therapy resistance mediated by dynamic regulation of extrachromosomal mutant EGFR DNA. Science (New York, N.Y.) Nathanson, D. A., Gini, B. n., Mottahedeh, J. n., Visnyei, K. n., Koga, T. n., Gomez, G. n., Eskin, A. n., Hwang, K. n., Wang, J. n., Masui, K. n., Paucar, A. n., Yang, H. n., Ohashi, M. n., Zhu, S. n., Wykosky, J. n., Reed, R. n., Nelson, S. F., Cloughesy, T. F., James, C. D., Rao, P. N., Kornblum, H. I., Heath, J. R., Cavenee, W. K., Furnari, F. B., Mischel, P. S. 2014; 343 (6166): 72–76

    Abstract

    Intratumoral heterogeneity contributes to cancer drug resistance, but the underlying mechanisms are not understood. Single-cell analyses of patient-derived models and clinical samples from glioblastoma patients treated with epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKIs) demonstrate that tumor cells reversibly up-regulate or suppress mutant EGFR expression, conferring distinct cellular phenotypes to reach an optimal equilibrium for growth. Resistance to EGFR TKIs is shown to occur by elimination of mutant EGFR from extrachromosomal DNA. After drug withdrawal, reemergence of clonal EGFR mutations on extrachromosomal DNA follows. These results indicate a highly specific, dynamic, and adaptive route by which cancers can evade therapies that target oncogenes maintained on extrachromosomal DNA.

    View details for DOI 10.1126/science.1241328

    View details for PubMedID 24310612

    View details for PubMedCentralID PMC4049335