Research Summary

Our lab's goal is to understand the genetic circuits that control human immune cell function in health and disease. We have begun to identify how genetic risk variants for autoimmune diseases disrupt immune cell circuits (Farh and Marson et al., Nature 2015; Simeonov et al., Nature, 2017), and how pathogenic circuits may be targeted with novel therapeutics (Xiao et al., Immunity 2014). My lab has developed new tools for efficient CRISPR genome engineering in primary human T cells (Schumann et al., PNAS 2015; Roth et al., Nature 2018; Nguyen et al. Nature Biotech 2020). Now we are pursuing a comprehensive strategy to test how coding and non-coding genetic variation control essential programs in the human immune system (Simeonov et al. Nature, 2017; Shifrut et al., Cell 2018; Roth et al., Cell 2020; Cortez et al., Nature 2020; Schumann et al., Nature Immunology 2020). Genome engineered human T cells hold great potential for the next generation of cell-based therapies for cancer, autoimmunity and infectious diseases.

Research Funding

  • September 8, 2020 - August 31, 2025 - Inherited T cell defects: Diagnosis, Mechanisms and Treatments , Principal Investigator . Sponsor: NIH, Sponsor Award ID: P01AI138962
  • September 18, 2018 - May 31, 2022 - Functional Molecular Investigation of Inflammatory Bowel Disease (IBD) Risk Variants , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01DK119979
  • September 30, 2016 - May 31, 2021 - Functional Interrogation of Non-Coding Type 1 Diabetes Risk Variants in Human Immune Cells and Beta Cells , Principal Investigator . Sponsor: NIH, Sponsor Award ID: DP3DK111914
  • June 1, 2016 - May 31, 2021 - Functional Testing of Host Genes that control HIV Latency in Primary Immune Cells , Principal Investigator . Sponsor: NIH, Sponsor Award ID: DP2DA042423

Education

Harvard College, MA, A.B., 2001, Biology
Cambridge University, UK, M.Phil., 2003, Biological Sciences
Massachusetts Institute of Technology, MA, Ph.D., 2008, Biology
Harvard Medical School, MA, M.D., 2010, Medicine
Brigham and Women’s Hospital, Residency, 2012, Internal Medicine
UC San Francisco, Fellowship, 2016, Infectious Diseases

Honors & Awards

  • 1998
    Jacob Wendell Prize for most promising freshman scholar, Harvard College
  • 1998
    Detur Book Prize, Harvard College
  • 2000
    William and Mary Bossert Prize, Harvard College
  • 2001
    Phi Beta Kappa, Harvard College
  • 2001-2002
    Herchel Smith Harvard Scholar, Emmanuel College, Cambridge, UK
  • 2009
    Sigma Xi 2009, MIT
  • 2010
    James Tolbert Shipley Prize for excellence and accomplishment in research, Harvard Medical
  • 2016
    American Society of Clinical Investigation (ASCI) Young Physician Scientist Award
  • 2016
    Burroughs Wellcome Foundation Career Award for Medical Scientists
  • 2016
    NIDA/NIH Avenir New Innovator Award
  • 2017
    Named to first cohort of Chan Zuckerberg Biohub Investigators
  • 2018
    Elected Member, American Society of Clinical Investors (ASCI)
  • 2019
    Lloyd J. Old STAR Award, Cancer Research Institute (CRI)

Selected Publications

  1. Lin K, Zou C, Hubbard A, Sengelmann S, Goudy L, Wang IC, Sharma R, Pak J, Foster K, Ozawa T, de Groot JF, Phillips J, Vasudevan HN, Raleigh DR, Marson A, Murthy N, Gilbert LA, Berger MS, Liu SJ. Multiplexed epigenetic memory editing using CRISPRoff sensitizes glioblastoma to chemotherapy. Neuro Oncol. 2025 Feb 25.  View on PubMed
  2. Chang CR, Vykunta VS, Lee JHJ, Li K, Kochendoerfer C, Muldoon JJ, Wang CH, Mazumder T, Sun Y, Goodman DB, Nyberg WA, Liu C, Allain V, Rothrock A, Ye CJ, Marson A, Shy BR, Eyquem J. SEED-Selection enables high-efficiency enrichment of primary T cells edited at multiple loci. Nat Biotechnol. 2025 Feb 05.  View on PubMed
  3. Ota M, Spence JP, Zeng T, Dann E, Marson A, Pritchard JK. Causal modeling of gene effects from regulators to programs to traits: integration of genetic associations and Perturb-seq. bioRxiv. 2025 Jan 24.  View on PubMed
  4. Umhoefer JM, Arce MM, Whalen S, Dajani R, Goudy L, Kasinathan S, Belk JA, Zhang W, Zhou R, Subramanya S, Hernandez R, Tran C, Kirthivasan N, Freimer JW, Mowery CT, Nguyen V, Ota M, Gowen BG, Simeonov DR, Curie GL, Li Z, Corn JE, Chang HY, Gilbert LA, Satpathy AT, Pollard KS, Marson A. Cis-Regulatory Element and Transcription Factor Circuitry Required for Cell-Type Specific Expression of FOXP3. bioRxiv. 2025 Jan 14.  View on PubMed
  5. Arce MM, Umhoefer JM, Arang N, Kasinathan S, Freimer JW, Steinhart Z, Shen H, Pham MTN, Ota M, Wadhera A, Dajani R, Dorovskyi D, Chen YY, Liu Q, Zhou Y, Swaney DL, Obernier K, Shy BR, Carnevale J, Satpathy AT, Krogan NJ, Pritchard JK, Marson A. Central control of dynamic gene circuits governs T cell rest and activation. Nature. 2025 Jan; 637(8047):930-939.  View on PubMed
  6. Gupta S, Martinov T, Thelen A, Sunahara M, Mureli S, Vazquez A, Gerdts J, Dandekar R, Cortese I, Fouassier C, Schanzer E, Urnov FD, Marson A, Shy BR, Greenberg PD, Wilson MR. Antigen-Specific T Cell Receptor Discovery for Treating Progressive Multifocal Leukoencephalopathy. bioRxiv. 2024 Nov 04.  View on PubMed
  7. Kim MC, Gate R, Lee DS, Tolopko A, Lu A, Gordon E, Shifrut E, Garcia-Nieto PE, Marson A, Ntranos V, Ye CJ. Method of moments framework for differential expression analysis of single-cell RNA sequencing data. Cell. 2024 Oct 31; 187(22):6393-6410.e16.  View on PubMed
  8. Weinstock JS, Arce MM, Freimer JW, Ota M, Marson A, Battle A, Pritchard JK. Gene regulatory network inference from CRISPR perturbations in primary CD4+ T cells elucidates the genomic basis of immune disease. Cell Genom. 2024 Nov 13; 4(11):100671.  View on PubMed
  9. Kattelus R, Starskaia I, Lindén M, Batkulwar K, Pietilä S, Moulder R, Marson A, Rasool O, Suomi T, Elo LL, Lahesmaa R, Buchacher T. Phenotypic profiling of human induced regulatory T cells at early differentiation: insights into distinct immunosuppressive potential. Cell Mol Life Sci. 2024 Sep 12; 81(1):399.  View on PubMed
  10. Zhao NQ, Pi R, Nguyen DN, Ranganath T, Seiler C, Holmes S, Marson A, Blish CA. NKp30 and NKG2D contribute to natural killer recognition of HIV-infected cells. bioRxiv. 2024 Jun 27.  View on PubMed
  11. Pimentel H, Freimer JW, Arce MM, Garrido CM, Marson A, Pritchard JK. A model for accurate quantification of CRISPR effects in pooled FACS screens. bioRxiv. 2024 Jun 18.  View on PubMed
  12. Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, Steinhart Z, Satpathy AT, Pollard KS, Corn JE, Bernstein BE, Ye CJ, Marson A. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nat Genet. 2024 Jun; 56(6):1156-1167.  View on PubMed
  13. Andrabi SBA, Kalim UU, Palani S, Khan MM, Khan MH, Fagersund J, Orpana J, Paulin N, Batkulwar K, Junttila S, Buchacher T, Grönroos T, Toikka L, Ammunet T, Sen P, Orešic M, Kumpulainen V, Tuomisto JEE, Sinha R, Marson A, Rasool O, Elo LL, Lahesmaa R. Long noncoding RNA LIRIL2R modulates FOXP3 levels and suppressive function of human CD4+ regulatory T cells by regulating IL2RA. Proc Natl Acad Sci U S A. 2024 Jun 04; 121(23):e2315363121.  View on PubMed
  14. Kalim UU, Biradar R, Junttila S, Khan MM, Tripathi S, Khan MH, Smolander J, Kanduri K, Envall T, Laiho A, Marson A, Rasool O, Elo LL, Lahesmaa R. A proximal enhancer regulates RORA expression during early human Th17 cell differentiation. Clin Immunol. 2024 Jul; 264:110261.  View on PubMed
  15. Pacalin NM, Steinhart Z, Shi Q, Belk JA, Dorovskyi D, Kraft K, Parker KR, Shy BR, Marson A, Chang HY. Bidirectional epigenetic editing reveals hierarchies in gene regulation. Nat Biotechnol. 2025 Mar; 43(3):355-368.  View on PubMed
  16. Bucktrout SL, Banovich NE, Butterfield LH, Cimen-Bozkus C, Giles JR, Good Z, Goodman D, Jonsson VD, Lareau C, Marson A, Maurer DM, Munson PV, Stubbington M, Taylor S, Cutchin A. Publisher Correction: Advancing T cell-based cancer therapy with single-cell technologies. Nat Med. 2024 May; 30(5):1505.  View on PubMed
  17. Yan J, Oyler-Castrillo P, Ravisankar P, Ward CC, Levesque S, Jing Y, Simpson D, Zhao A, Li H, Yan W, Goudy L, Schmidt R, Solley SC, Gilbert LA, Chan MM, Bauer DE, Marson A, Parsons LR, Adamson B. Improving prime editing with an endogenous small RNA-binding protein. Nature. 2024 Apr; 628(8008):639-647.  View on PubMed
  18. Rathore U, Haas P, Easwar Kumar V, Hiatt J, Haas KM, Bouhaddou M, Swaney DL, Stevenson E, Zuliani-Alvarez L, McGregor MJ, Turner-Groth A, Ochieng' Olwal C, Bediako Y, Braberg H, Soucheray M, Ott M, Eckhardt M, Hultquist JF, Marson A, Kaake RM, Krogan NJ. CRISPR-Cas9 screen of E3 ubiquitin ligases identifies TRAF2 and UHRF1 as regulators of HIV latency in primary human T cells. mBio. 2024 Apr 10; 15(4):e0222223.  View on PubMed
  19. Chang CR, Vykunta VS, Goodman DB, Muldoon JJ, Nyberg WA, Liu C, Allain V, Rothrock A, Wang CH, Marson A, Shy BR, Eyquem J. Ultra-high efficiency T cell reprogramming at multiple loci with SEED-Selection. bioRxiv. 2024 Feb 07.  View on PubMed
  20. Wheeler BD, Gagnon JD, Zhu WS, Muñoz-Sandoval P, Wong SK, Simeonov DS, Li Z, DeBarge R, Spitzer MH, Marson A, Ansel KM. The lncRNA Malat1 inhibits miR-15/16 to enhance cytotoxic T cell activation and memory cell formation. Elife. 2023 Dec 21; 12.  View on PubMed

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