Research Summary

I am a neuroscientist and Principal Investigator in the Department of Neurological Surgery and Brain Tumor Center at UCSF. The overarching goal of my lab’s research is to understand the molecular basis of cellular identity in the human brain in health and disease, with an emphasis on adult malignant gliomas. In pursuit of this goal, we develop and apply novel experimental, computational, and meta-analytical strategies for studying omics data from normal human brain and brain tumor samples. Because gene expression lies at the root of cellular identity, much of our work focuses on understanding the organization of the normal human brain transcriptome and how this is perturbed by oncogenic mutations. Specifically, current work in the lab seeks to clarify: i) how patterns of clonal evolution in gliomas drive gene expression changes in malignant cells, and ii) which molecular phenotypes most consistently distinguish cell types in the glioma microenvironment from their normal counterparts, with a particular focus on vascular cells. Through these efforts, we hope to expand the therapeutic search space for malignant gliomas.

Research Funding

  • December 1, 2019 - November 30, 2024 - Decoding the molecular basis of cellular identity in adult malignant gliomas , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA244621
  • May 1, 2020 - March 31, 2024 - Multiscale transcriptional architecture of the human brain , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01MH123156
  • December 5, 2017 - November 30, 2022 - Decoding the molecular basis of cellular identity in the human brain , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01MH113896

Education

Duke University B.S., 1996, Psychology
University of California, Los Angeles (UCLA), Ph.D., 2009, Neuroscience
University of California, Los Angeles (UCLA), Postdoctoral, 2010, Human Genetics

Honors & Awards

  • 2002-2003
    Pre-doctoral Fellowship, Neuroscience Ph.D. Program, UCLA, Los Angeles, CA
  • 2008
    Eva Kavan Prize for Excellence in Research on the Brain, Brain Research Institute, UCLA, LosAngeles, CA
  • 2009
    UCSF Sandler Fellow, UCSF, San Francisco, CA
  • 2010
    Travel Fellow, Winter Conference on Brain Research, Breckenridge, CO
  • 2012
    Young Investigator, Sage Commons Congress, San Francisco, CA
  • 2016-2017
    Weill Institute for Neurosciences Scholar Award, UCSF
  • 2015-2016
    Program for Breakthrough Biomedical Research New Frontiers Research Award, UCSF

Selected Publications

  1. Benjamin Lerman, Chibo Hong, Patrick Schupp, Lee Chen, Daniel Zamler, Ivan Smirnov, Joanna Phillips, Anny Shai, Janine Lupo, Michael Oldham, Joseph Costello. EPCO-37. LONGITUDINAL TUMOR-WIDE SAMPLING OF GLIOBLASTOMA REVEALS EARLY EVOLUTIONARY DIVERGENCE OF RECURRENCE AND CLUES TOWARDS IDENTIFYING THE BIOLOGICAL TUMOR CENTER. Neuro-Oncology. 2024 Nov 11; 26(Supplement_8):viii10-viii10.  View on PubMed
  2. Daniel Zamler, Radhika Mathur, Gary Chan, Patrick Schupp, Anny Shai, Hideho Okada, Michael Oldham, Joseph Costello. IMMU-59. AN IMMUNOSUPPRESSIVE PROGRAM ENCOMPASSING MULTIPLE IMMUNE CELL TYPES IN GBM TYPIFIED BY NOVEL MARKER LRRC25 ASSOCIATED WITH TYROBP SIGNALING. Neuro-Oncology. 2024 Nov 11; 26(Supplement_8):viii165-viii166.  View on PubMed
  3. Chen J, Crouch EE, Zawadzki ME, Jacobs KA, Mayo LN, Choi JJ, Lin PY, Shaikh S, Tsui J, Gonzalez-Granero S, Waller S, Kelekar A, Kang G, Valenzuela EJ, Birrueta JO, Diafos LN, Wedderburn-Pugh K, Di Marco B, Xia W, Han CZ, Coufal NG, Glass CK, Fancy SPJ, Alfonso J, Kriegstein AR, Oldham MC, Garcia-Verdugo JM, Kutys ML, Lehtinen MK, Combes AJ, Huang EJ. Proinflammatory immune cells disrupt angiogenesis and promote germinal matrix hemorrhage in prenatal human brain. Nat Neurosci. 2024 Nov; 27(11):2115-2129.  View on PubMed
  4. Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing Intratumoral Heterogeneity through Multiomic and Multiscale Analysis of Serial Sections. Cancers (Basel). 2024 Jul 01; 16(13).  View on PubMed
  5. Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections. bioRxiv. 2024 Mar 18.  View on PubMed
  6. Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell. 2024 01 18; 187(2):446-463.e16.  View on PubMed
  7. Patrick Schupp, Samuel Shelton, Daniel Brody, Rebecca Eliscu, Brett Johnson, Tali Mazor, Kevin Kelley, Matthew Potts, Michael McDermott, Eric Huang, Daniel Lim, Russell Pieper, Mitchel Berger, Joseph Costello, Joanna Phillips, Michael Oldham. EPCO-39. CLARIFYING THE MOLECULAR CONSEQUENCES OF ONCOGENIC MUTATIONS THROUGH MULTISCALE AND MULTIOMIC ANALYSIS OF INDIVIDUAL TUMORS. Neuro-Oncology. 2023 Nov 10; 25(Supplement_5):v132-v133.  View on PubMed
  8. Zhang X, Xiao G, Johnson C, Cai Y, Horowitz ZK, Mennicke C, Coffey R, Haider M, Threadgill D, Eliscu R, Oldham MC, Greenbaum A, Ghashghaei HT. Bulk and mosaic deletions of Egfr reveal regionally defined gliogenesis in the developing mouse forebrain. iScience. 2023 Mar 17; 26(3):106242.  View on PubMed
  9. Tanabe K, Nobuta H, Yang N, Ang CE, Huie P, Jordan S, Oldham MC, Rowitch DH, Wernig M. Generation of functional human oligodendrocytes from dermal fibroblasts by direct lineage conversion. Development. 2022 10 15; 149(20).  View on PubMed
  10. Radhika Mathur, Qixuan Wang, Patrick Schupp, Ana Nikolic, Takafumi Yamaguchi, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa LaFontaine, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Paul Boutros, Marco Gallo, Michael Oldham, Feng Yue, Joseph Costello. Abstract 3621: 3D spatial sampling and integrated omics reveal sources and patterning of intratumoral heterogeneity in glioblastoma. Cancer Research. 2022 Jun 15; 82(12_Supplement):3621-3621.  View on PubMed
  11. Paredes MF, Mora C, Flores-Ramirez Q, Cebrian-Silla A, Del Dosso A, Larimer P, Chen J, Kang G, Gonzalez Granero S, Garcia E, Chu J, Delgado R, Cotter JA, Tang V, Spatazza J, Obernier K, Ferrer Lozano J, Vento M, Scott J, Studholme C, Nowakowski TJ, Kriegstein AR, Oldham MC, Hasenstaub A, Garcia-Verdugo JM, Alvarez-Buylla A, Huang EJ. Nests of dividing neuroblasts sustain interneuron production for the developing human brain. Science. 2022 01 28; 375(6579):eabk2346.  View on PubMed
  12. Radhika Mathur, Qixuan Wang, Patrick Schupp, Stephanie Hilz, Chibo Hong, Ivan Smirnov, Marisa Lafontaine, Devika Nair, Sriranga Iyyanaki, Joanna Phillips, Susan Chang, Yan Li, Janine Lupo, Michael Oldham, Feng Yue, Joseph Costello. ECOA-5. Integrative 3D spatial characterization of genomic and epigenomic intratumoral heterogeneity in glioblastoma. Neuro-Oncology Advances. 2021 Jul 5; 3(Supplement_2):ii2-ii2.  View on PubMed
  13. Qiu H, Lee S, Shang Y, Wang WY, Au KF, Kamiya S, Barmada SJ, Finkbeiner S, Lui H, Carlton CE, Tang AA, Oldham MC, Wang H, Shorter J, Filiano AJ, Roberson ED, Tourtellotte WG, Chen B, Tsai LH, Huang EJ. ALS-associated mutation FUS-R521C causes DNA damage and RNA splicing defects. J Clin Invest. 2021 04 01; 131(7).  View on PubMed
  14. Sorrells SF, Paredes MF, Zhang Z, Kang G, Pastor-Alonso O, Biagiotti S, Page CE, Sandoval K, Knox A, Connolly A, Huang EJ, Garcia-Verdugo JM, Oldham MC, Yang Z, Alvarez-Buylla A. Positive Controls in Adults and Children Support That Very Few, If Any, New Neurons Are Born in the Adult Human Hippocampus. J Neurosci. 2021 03 24; 41(12):2554-2565.  View on PubMed
  15. Kyritsis N, Torres-Espín A, Schupp PG, Huie JR, Chou A, Duong-Fernandez X, Thomas LH, Tsolinas RE, Hemmerle DD, Pascual LU, Singh V, Pan JZ, Talbott JF, Whetstone WD, Burke JF, DiGiorgio AM, Weinstein PR, Manley GT, Dhall SS, Ferguson AR, Oldham MC, Bresnahan JC, Beattie MS. Diagnostic blood RNA profiles for human acute spinal cord injury. J Exp Med. 2021 03 01; 218(3).  View on PubMed
  16. Huie JR, Ferguson AR, Kyritsis N, Pan JZ, Irvine KA, Nielson JL, Schupp PG, Oldham MC, Gensel JC, Lin A, Segal MR, Ratan RR, Bresnahan JC, Beattie MS. Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury. Sci Rep. 2021 02 09; 11(1):3442.  View on PubMed
  17. Munji RN, Soung AL, Weiner GA, Sohet F, Semple BD, Trivedi A, Gimlin K, Kotoda M, Korai M, Aydin S, Batugal A, Cabangcala AC, Schupp PG, Oldham MC, Hashimoto T, Noble-Haeusslein LJ, Daneman R. Profiling the mouse brain endothelial transcriptome in health and disease models reveals a core blood-brain barrier dysfunction module. Nat Neurosci. 2019 11; 22(11):1892-1902.  View on PubMed
  18. Torres R, Lang UE, Hejna M, Shelton SJ, Joseph NM, Shain AH, Yeh I, Wei ML, Oldham MC, Bastian BC, Judson-Torres RL. MicroRNA Ratios Distinguish Melanomas from Nevi. J Invest Dermatol. 2020 01; 140(1):164-173.e7.  View on PubMed
  19. Diego A Carrera, Josie Hayes, Sören Müller, Payal Watchmaker, Samuel Shelton, Nolbert Hilf, Toni Weinschenk, Oliver Schoor, Gary Kohanbash, Michael Oldham, Joseph Costello, Harpreet Singh, Hideho Okada. Immunopeptidomics and Peptide Expression Profiles to Develop T-Cell Receptors Against Glioma-Associated Antigens. Neurosurgery. 2019 Sep 1; 66(Supplement_1).  View on PubMed
  20. R. Torres, U. Lang, N.M. Joseph, A.H. Shain, I. Yeh, M.L. Wei, M.C. Oldham, B. Bastian, R.L. Judson-Torres. 786 A machine-learning classifier trained with microRNA ratios to distinguish melanomas from nevi. Journal of Investigative Dermatology. 2019 May 1; 139(5):s136.  View on PubMed

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