Omar Khan, MD, PhD
513 Parnassus Avenue
HSW, #269A
San Francisco, CA 94143
United States
Omar Khan, MD, PhD, is the Genomic Immunology Fellow at the Gladstone-UCSF Institute of Genomic Immunology. He is also an Assistant Adjunct Professor in the Department of Laboratory Medicine at UCSF and Associate Medical Director of the UCSF Investigational Cell Therapy Program.
Dr. Khan's lab defines and engineers novel immunobiology through synthetic immunology—uniting genome-scale editing, epigenetic reprogramming, and synthetic protein design to decode and rewire immune cell circuits for next-generation therapies. His work integrates gold-standard in vivo models with synthetic biology and protein engineering approaches to develop systems that precisely program immune cell function, with a focus on improving the potency, durability, and specificity of engineered cellular therapeutics.
Omar received his MD and PhD from the University of Pennsylvania, where he completed his doctoral training in the laboratory of John Wherry, PhD, defining transcriptional and epigenetic programs underlying T-cell exhaustion. He subsequently completed residency training in Clinical Pathology and a fellowship in Cellular Therapy and Transfusion Medicine at UCSF. Prior to his faculty appointment, he served as the Director of Immunology at ArsenalBio, where he led synthetic immunology efforts to develop CRISPR-engineered CAR-T therapies for solid tumors.
Dr. Khan is a member of the Parker Institute for Cancer Immunotherapy and the UCSF Center for Research in Transfusion Medicine and Cell Therapies. He is committed to advancing programmable immune cell therapies that merge mechanistic immunology with cutting-edge synthetic biology to create transformative treatments for patients.
Huang YJ, Ngiow SF, Baxter AE, Manne S, Park SL, Wu JE, Khan O, Giles JR, Wherry EJ. Continuous expression of TOX safeguards exhausted CD8 T cell epigenetic fate. Sci Immunol. 2025 Mar 7;10(105):eado3032. doi: 10.1126/sciimmunol.ado3032. Epub 2025 Mar 7. PubMed PMID: 40053604.
Ngiow SF, Manne S, Huang YJ, Azar T, Chen Z, Mathew D, Chen Q, Khan O, Wu JE, Alcalde V, Flowers AJ, McClain S, Baxter AE, Kurachi M, Shi J, Huang AC, Giles JR, Sharpe AH, Vignali DAA, Wherry EJ. LAG-3 sustains TOX expression and regulates the CD94/NKG2-Qa-1b axis to govern exhausted CD8 T cell NK receptor expression and cytotoxicity. Cell. 2024 Aug 8;187(16):4336-4354.e19. doi: 10.1016/j.cell.2024.07.018. PubMed PMID: 39121847; PubMed Central PMCID: PMC11337978.
Khan O, Prakash S, Chung A, Wong SW, Kennedy VE. Monoclonal Gammopathy of Anemic Significance? Resolution of Pure Red Cell Aplasia With Daratumumab-Based Therapy. Am J Med. 2024 Jul;137(7):589-591. doi: 10.1016/j.amjmed.2024.02.013. Epub 2024 Feb 22. PubMed PMID: 38401677.
Wu JE, Manne S, Ngiow SF, Baxter AE, Huang H, Freilich E, Clark ML, Lee JH, Chen Z, Khan O, Staupe RP, Huang YJ, Shi J, Giles JR, Wherry EJ. In vitro modeling of CD8(+) T cell exhaustion enables CRISPR screening to reveal a role for BHLHE40. Sci Immunol. 2023 Aug 25;8(86):eade3369. doi: 10.1126/sciimmunol.ade3369. Epub 2023 Aug 18. PubMed PMID: 37595022; PubMed Central PMCID: PMC11975459.
Giles JR, Ngiow SF, Manne S, Baxter AE, Khan O, Wang P, Staupe R, Abdel-Hakeem MS, Huang H, Mathew D, Painter MM, Wu JE, Huang YJ, Goel RR, Yan PK, Karakousis GC, Xu X, Mitchell TC, Huang AC, Wherry EJ. Shared and distinct biological circuits in effector, memory and exhausted CD8(+) T cells revealed by temporal single-cell transcriptomics and epigenetics. Nat Immunol. 2022 Nov;23(11):1600-1613. doi: 10.1038/s41590-022-01338-4. Epub 2022 Oct 21. PubMed PMID: 36271148; PubMed Central PMCID: PMC10408358.
Chen Z, Arai E, Khan O, Zhang Z, Ngiow SF, He Y, Huang H, Manne S, Cao Z, Baxter AE, Cai Z, Freilich E, Ali MA, Giles JR, Wu JE, Greenplate AR, Hakeem MA, Chen Q, Kurachi M, Nzingha K, Ekshyyan V, Mathew D, Wen Z, Speck NA, Battle A, Berger SL, Wherry EJ, Shi J. In vivo CD8(+) T cell CRISPR screening reveals control by Fli1 in infection and cancer. Cell. 2021 Mar 4;184(5):1262-1280.e22. doi: 10.1016/j.cell.2021.02.019. Epub 2021 Feb 25. PubMed PMID: 33636129; PubMed Central PMCID: PMC8054351.
Beltra JC, Manne S, Abdel-Hakeem MS, Kurachi M, Giles JR, Chen Z, Casella V, Ngiow SF, Khan O, Huang YJ, Yan P, Nzingha K, Xu W, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Schuchter LM, Huang AC, Wherry EJ. Developmental Relationships of Four Exhausted CD8(+) T Cell Subsets Reveals Underlying Transcriptional and Epigenetic Landscape Control Mechanisms. Immunity. 2020 May 19;52(5):825-841.e8. doi: 10.1016/j.immuni.2020.04.014. Epub 2020 May 11. PubMed PMID: 32396847; PubMed Central PMCID: PMC8360766.
Chen Z, Ji Z, Ngiow SF, Manne S, Cai Z, Huang AC, Johnson J, Staupe RP, Bengsch B, Xu C, Yu S, Kurachi M, Herati RS, Vella LA, Baxter AE, Wu JE, Khan O, Beltra JC, Giles JR, Stelekati E, McLane LM, Lau CW, Yang X, Berger SL, Vahedi G, Ji H, Wherry EJ. TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision. Immunity. 2019 Nov 19;51(5):840-855.e5. doi: 10.1016/j.immuni.2019.09.013. Epub 2019 Oct 9. PubMed PMID: 31606264; PubMed Central PMCID: PMC6943829.
Yao C, Sun HW, Lacey NE, Ji Y, Moseman EA, Shih HY, Heuston EF, Kirby M, Anderson S, Cheng J, Khan O, Handon R, Reilley J, Fioravanti J, Hu J, Gossa S, Wherry EJ, Gattinoni L, McGavern DB, O'Shea JJ, Schwartzberg PL, Wu T. Single-cell RNA-seq reveals TOX as a key regulator of CD8(+) T cell persistence in chronic infection. Nat Immunol. 2019 Jul;20(7):890-901. doi: 10.1038/s41590-019-0403-4. Epub 2019 Jun 17. PubMed PMID: 31209400; PubMed Central PMCID: PMC6588409.
Khan O, Giles JR, McDonald S, Manne S, Ngiow SF, Patel KP, Werner MT, Huang AC, Alexander KA, Wu JE, Attanasio J, Yan P, George SM, Bengsch B, Staupe RP, Donahue G, Xu W, Amaravadi RK, Xu X, Karakousis GC, Mitchell TC, Schuchter LM, Kaye J, Berger SL, Wherry EJ. TOX transcriptionally and epigenetically programs CD8(+) T cell exhaustion. Nature. 2019 Jul;571(7764):211-218. doi: 10.1038/s41586-019-1325-x. Epub 2019 Jun 17. PubMed PMID: 31207603; PubMed Central PMCID: PMC6713202.
Bengsch B, Ohtani T, Khan O, Setty M, Manne S, O'Brien S, Gherardini PF, Herati RS, Huang AC, Chang KM, Newell EW, Bovenschen N, Pe'er D, Albelda SM, Wherry EJ. Epigenomic-Guided Mass Cytometry Profiling Reveals Disease-Specific Features of Exhausted CD8 T Cells. Immunity. 2018 May 15;48(5):1029-1045.e5. doi: 10.1016/j.immuni.2018.04.026. PubMed PMID: 29768164; PubMed Central PMCID: PMC6010198.
Chen Z, Stelekati E, Kurachi M, Yu S, Cai Z, Manne S, Khan O, Yang X, Wherry EJ. miR-150 Regulates Memory CD8 T Cell Differentiation via c-Myb. Cell Rep. 2017 Sep 12;20(11):2584-2597. doi: 10.1016/j.celrep.2017.08.060. PubMed PMID: 28903040; PubMed Central PMCID: PMC5611819.
Kurachi M, Kurachi J, Chen Z, Johnson J, Khan O, Bengsch B, Stelekati E, Attanasio J, McLane LM, Tomura M, Ueha S, Wherry EJ. Optimized retroviral transduction of mouse T cells for in vivo assessment of gene function. Nat Protoc. 2017 Sep;12(9):1980-1998. doi: 10.1038/nprot.2017.083. Epub 2017 Aug 31. PubMed PMID: 28858287; PubMed Central PMCID: PMC6020692.
Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, Khan O, Drake AM, Chen Z, Sen DR, Kurachi M, Barnitz RA, Bartman C, Bengsch B, Huang AC, Schenkel JM, Vahedi G, Haining WN, Berger SL, Wherry EJ. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science. 2016 Dec 2;354(6316):1160-1165. doi: 10.1126/science.aaf2807. Epub 2016 Oct 27. PubMed PMID: 27789795; PubMed Central PMCID: PMC5484795.
Gérard A, Khan O, Beemiller P, Oswald E, Hu J, Matloubian M, Krummel MF. Secondary T cell-T cell synaptic interactions drive the differentiation of protective CD8+ T cells. Nat Immunol. 2013 Apr;14(4):356-63. doi: 10.1038/ni.2547. Epub 2013 Mar 10. PubMed PMID: 23475183; PubMed Central PMCID: PMC3962671.
Khan O, Headley M, Gerard A, Wei W, Liu L, Krummel MF. Regulation of T cell priming by lymphoid stroma. PLoS One. 2011;6(11):e26138. doi: 10.1371/journal.pone.0026138. Epub 2011 Nov 14. PubMed PMID: 22110583; PubMed Central PMCID: PMC3215700.