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

  • February 6, 2026 - January 31, 2030 - Transcriptional and post-transcriptional regulation of human Treg identity and function , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01AI189605
  • January 1, 2023 - December 31, 2027 - Decoding and reprogramming T cells through synthetic biology for cancer immunotherapy , Principal Investigator . Sponsor: NIH, Sponsor Award ID: R01CA276368
  • 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. Zhu R, Dann E, Yan J, Reyes Retana J, Goto R, Guitche RC, Brixi L, Ota M, Hartman A, Roth TL, Satpathy AT, Pritchard JK, Marson A. Genome-scale perturb-seq in primary human CD4+ T cells maps context-specific regulators of T cell programs and human immune traits. Cell. 2026 Aug 28. View on PubMed
  2. Chung R, Chalasani NS, Barbehenn AS, Lundgren E, Savur S, Shome S, Sheikhzadeh CH, Sarvadhavabhatla S, Donaire MS, Pae V, Chu X, Winder D, Maguire CT, Topal S, Ganesan A, Yabes JM, Larson DT, Lalani T, Ewers EC, Colombo RE, Dugan E, Rathore U, Marson A, Agan BK, Tomalka JA, Sekaly RP, Ioannidis NM, Lee SA. Host Genetic Regulation of NLRP3 Inflammasome Cytokines Reveals Immune and Vascular Pathways in HIV. medRxiv. 2026 Aug 24. View on PubMed
  3. Jung H, Devant P, Ching C, Ota M, Dann E, Zhu R, Modak C, Vasquez-Ibarra A, Hamilton JR, Steinhart Z, Ngo W, Sandoval L, Jung JH, Lee JHJ, Xu D, An M, Urs E, Chen PA, Allain V, Tada T, Gilbert LA, Shy BR, Pritchard JK, Nuñez JK, Landau NR, Liu DR, Eyquem J, Doudna JA, Marson A, Carnevale J. Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells. Nat Biotechnol. 2026 Aug 17. View on PubMed
  4. Liu Q, Chen PA, Urs E, Zhang S, Arce MM, Wang CH, Yan J, Nguyen VQ, Li Z, Seo J, Kale N, Peng F, Luo Y, Goudy L, LaFlam TN, Zhong H, Modak C, Dann E, Jung JH, Kirane A, Warner AB, Quach BB, Good Z, Shy BR, Shifrut E, Bapat SP, Allen GM, Eyquem J, Fuh K, Dodgson SE, Cyster JG, Marson A, Carnevale J. In vivo genome-wide CRISPR screens of human T cells in solid tumours. Nature. 2026 Aug 12. View on PubMed
  5. Ashley EA, Alizadeh AA, Armitage H, Bhatt AS, Blumenfeld Y, Carroll A, Chavez RM, Giannikopoulos P, Grove ME, Halley MC, Khush K, Lennon NJ, Maragh S, Marson A, Paten B, Phillippy AM, Porteus MH, Rehm HL, Ringeisen BR, Salzman J, Schneider VA, Sedlazeck FJ, Steinmetz LM, Urnov FD, Wyman SK, Zook JM, Minor LB, Doudna JA. Harmonizing standards and resources for the medical genome. Nature. 2026 Jul; 655(8121):47-58. View on PubMed
  6. Epstein L, Weiner AC, Verma A, Saeidi M, Carnevale J, Marson A, Engelhardt BE. Segmentation-free analysis of live-cell imaging data reveals how T cell modifications influence cancer cell aggregation dynamics. Sci Rep. 2026 Jun 30. View on PubMed
  7. Talbot A, Li K, Lee JHJ, Lang S, Liu C, Kalter N, Li Z, Mortazavi Y, Almudhfar N, Muldoon JJ, Allain V, Nyberg W, Chung JJ, Wang C, Qi Z, Krishnappa N, Ha AS, Kong D, Houser D, Paruthiyil S, Ahmadi M, Ji Y, Rosenberg M, Acevedo LA, Liang B, Briseno K, Kwek SS, Bachl S, Ching C, Carnevale J, Giannikopoulos P, Oh DY, Marson A, Hendel A, Martin T, Eyquem J, Shy BR. Development of a Fully Non-Viral 1XX-enhanced BCMA CAR-T Cell Therapy for Multiple Myeloma. bioRxiv. 2026 May 05. View on PubMed
  8. Rathore U, Dugan E, Thornton H, Kumar VE, Dajani R, Burdick RC, Young JM, Steinhart Z, Lao R, Delviks-Frankenberry KA, Choi W, Henriques WS, Echeverria I, Dann E, Dureja I, Pathak N, Arce MM, McKetney J, Umhoefer JM, Parulekar S, Schmidt R, Polacco BJ, Neidleman J, Montano M, Nguyen VQ, Sali A, Levy JA, Tenthorey JL, Cheng Y, Roan NR, Swaney DL, Kaake RM, Dodgson SE, Hiatt J, Pathak VK, Malik HS, Krogan NJ, Marson A. Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells. Cell. 2026 Jun 11; 189(12):3651-3668.e31. View on PubMed
  9. Jung H, Devant P, Ching C, Ota M, Hamilton J, Steinhart Z, Ngo W, Sandoval L, Jung JH, Xu D, An M, Urs E, Chen PA, Allain V, Tada T, Nuñez JK, Landau NR, Liu DR, Eyquem J, Doudna JA, Marson A, Carnevale J. Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells. bioRxiv. 2025 Dec 14. View on PubMed
  10. Ota M, Spence JP, Zeng T, Dann E, Milind N, Marson A, Pritchard JK. Causal modelling of gene effects from regulators to programs to traits. Nature. 2026 02; 650(8101):399-408. View on PubMed
  11. Ha AS, Kalter N, Rosenberg M, Acevedo LA, Liang B, Liu W, Paruthiyil S, Sinha M, Vu A, Nguyen V, Qi Z, Krishnappa N, Shu J, Yu J, Catanzaro J, Bluestone JA, Tang Q, Urnov FD, Marson A, Hendel A, Herold KC, Shy BR, Esensten JH. Gene-corrected regulatory T cell therapy for IL2RA deficiency. Mol Ther. 2026 Mar 04; 34(3):1367-1381. View on PubMed
  12. Umhoefer JM, Arce MM, Kasinathan S, Whalen S, Dajani R, Subramanya S, Goudy L, Belk JA, Zhou R, Pham MTN, Zhang W, Hernandez R, Tran C, Kirthivasan N, Freimer JW, Mowery CT, Nguyen V, Ota M, Gowen BG, Simeonov DR, Curie GL, Li Z, Chen AY, Corn JE, Chang HY, Tang Q, Gilbert LA, Satpathy AT, Pollard KS, Marson A. FOXP3 expression depends on cell-type-specific cis-regulatory elements and transcription factor circuitry. Immunity. 2026 Jan 13; 59(1):129-144.e13. View on PubMed
  13. Fanton A, Bartie LJ, Martins JQ, Tran VQ, Goudy L, Kernick C, Durrant MG, Wei J, Armour-Garb Z, Pawluk A, Konermann S, Marson A, Gilbert LA, Roth TL, Hsu PD. Site-specific DNA insertion into the human genome with engineered recombinases. Nat Biotechnol. 2025 Nov 06. View on PubMed
  14. Goudy L, Ha A, Borah AA, Umhoefer JM, Chow L, Tran C, Winters A, Talbot A, Hernandez R, Li Z, Subramanya S, Arab A, Kale N, Lee JHJ, Muldoon JJ, Liu C, Schmidt R, Santangelo P, Carnevale J, Eyquem J, Shy BR, Marson A, Gilbert LA. Integrated epigenetic and genetic programming of primary human T cells. Nat Biotechnol. 2026 Sep; 44(9):1470-1481. View on PubMed
  15. Blaisdell A, Bachl S, Sandoval LR, Ching C, Bowman CJ, Kale N, Prabandham M, Diolaiti M, Havig C, Advincula R, Lenci N, Li Z, Yamashita E, Wang CH, Zhang S, Liu Q, Achacoso P, Stibor D, Øynebråten I, Seo J, Ashworth A, Marson A, Ye CJ, Malynn BA, Eyquem J, Carnevale J, Ma A. Base-editing a single missense mutation in A20 enhances CAR-T cell efficacy. bioRxiv. 2025 Oct 06. View on PubMed
  16. Allain V, Rothrock AG, Bernard PL, Nyberg WA, Talbot A, Muldoon JJ, Chung JY, To A, Chang CR, Kimmerly GR, Liu C, Tsao T, Mortazavi Y, Seo J, Li Z, Shemesh A, Schmidt R, Ward CC, Marson A, Lanier LL, Aguilar OA, Eyquem J. Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function. bioRxiv. 2025 Oct 06. View on PubMed
  17. Liu Q, Chen PA, Urs E, Zhang S, Arce MM, Wang CH, Li Z, Seo J, Kale N, LaFlam TN, Peng F, Shifrut E, Allen GM, Eyquem J, Fuh K, Dodgson SE, Cyster JG, Marson A, Carnevale J. In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors. bioRxiv. 2025 Sep 24. View on PubMed
  18. Pi R, Zhao NQ, Bien AJ, Ranganath T, Seiler C, Holmes S, Marson A, Nguyen DN, Blish CA. NKp30 and NKG2D contribute to natural killer cell-mediated recognition of HIV-infected cells. iScience. 2025 Oct 17; 28(10):113548. View on PubMed
  19. 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 Jul 30; 27(6):1443-1457. View on PubMed
  20. Cabanski CR, Yang E, Stewart MD, Allen JD, Connolly JE, Dugan U, Greenberg PD, Mackall CL, June CH, Marson A, Maus MV, Ribas A. Intentional heterogeneity in autologous cell-based gene therapies: strategic considerations for first-in-human trials. J Immunother Cancer. 2025 Jun 05; 13(6). View on PubMed

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