Publications

Q. Zeng, L. Flemming, Y. Chen, T. Mazumder, H. Hammerlindl, G.M. Allen, R. Almeida, J.Z. Williams, R.A. Hernández-López, J. Eyquem, C.J. Ye, W.A. Lim, Q. Tang, T.A. Desai, X. Huang (2025). Programmable microparticles rewire CAR signaling to enable super-physiological expansion of human T cells in vitro. bioRxiv.

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A. Blaisdell, S. Bachl, L.R. Sandoval, C. Ching, C.J. Bowman, N. Kale, M. Prabandham, M. Diolaiti, C. Havig, R. Advincula, N. Lenci, Z. Li, E. Yamashita, C.H. Wang, S. Zhang, Q. Liu, P. Achacoso, D. Stibor, I. Øynebråten, J. Seo, A. Ashworth, A. Marson, C.J. Ye, B.A. Malynn, J. Eyquem, J. Carnevale, A. Ma (2025). Base-editing a single missense mutation in A20 enhances CAR-T cell efficacy. bioRxiv.

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A.S. Kang, H. Johnson, N. Lei, J. Wong, N. Razi, A. Izgutdina, C. Kasap, N. Chilakapati, J. Rivera, P. Phojanakong, J.A. Camara Serrano, F. Salangsang, V. Steri, A.C. Logan, J. Eyquem, B.J. Huang, A.P. Wiita (2025). Bicistronic CAR T-cells Against CD70 & Active Integrin β2 Overcome Antigen Heterogeneity and Preserve Safety in Acute Myeloid Leukemia. bioRxiv.

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O. Takacsi-Nagy, A. Hartman, A.Y. Chen, Y. Yin, G.C. Reeder, C. Kernick, J. Lu, A.K. McClellan, C.J. Raposo, N.E. Theberath, P.K. Yan, J. Eyquem, T.L. Roth, A.T. Satpathy (2025). Evolutionarily guided transcription factor design programs novel T cell states. bioRxiv.

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V. Allain, A.G. Rothrock, P.-L. Bernard, W.A. Nyberg, A. Talbot, J.J. Muldoon, J.-Y. Chung, A. To, C.R. Chang, G.R. Kimmerly, C. Liu, T. Tsao, Y. Mortazavi, J. Seo, Z. Li, A. Shemesh, R. Schmidt, C.C. Ward, A. Marson, L.L. Lanier, O.A. Aguilar, J. Eyquem (2025). Site-specific genome engineering of primary human natural killer cells for programmable anti-tumor function. bioRxiv.

W. A. Nyberg*, P.-L. Bernard* , W. Ngo, C. H. Wang, J. Ark, A. Rothrock, G. M. Borgo, G. R. Kimmerly, J. H. Jung, V. Allain, J. R. Hamilton, A. Baldwin, R. Stickels, S. Wyman, S. H. Khan, S. Lang, D. Marsh, N. Almudhfar, C. Novick, Y. Mortazavi, S. Zhang, M. M. AbdElwakil, L. R. Sandoval, S. Hwang, S. N. Chu, H. Jung, C. Liu, D. Sharma, T. McCreary, Z. Li, A. T. Satpathy, J. Carnevale, R. L. Rutishauser, M. K. Cromer, K. T. Roybal, S. E. Dodgson, J. A. Doudna, A. Asokan & J. Eyquem. In vivo site-specific engineering to reprogram T cells. Nature (2026) *equal contribution

Mentioned in Nature News and Views, Nature News, GEN, STAT, Cell Research, and UCSF!

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N.F. Kuhn, I. Zaleta-Linares, K.H. Hu, T. Courau, B. Davidson, T. Tam, A.J. Combes, W.A. Nyberg, J. Eyquem, M.F. Krummel (2025). Discovery of a linked constellation of gene expression revealed by local editing of fibroblasts in tumors. Journal of Experimental Medicine (2026)

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S. Navarre, M. N. Ishibashi, A. Nair, I. Reyes-Torres, M. Belabed, L. Halasz, M. D. Park, R. Mattiuz, M. Ounadjela, G. Gunset, J. Mansilla-Soto, J. Feucht, A. Cabriolu, J. Le Berichel, A. Birbrair, J. Eyquem, B. D. Brown, M. Merad, M. Sadelain & J. Ahmed. Tumor irradiation promotes antigen dressing of dendritic cells to enhance CAR T cell persistence and efficacy in lung metastases. Nature Cancer (2026)

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X. Chi, C. H. Wang, Y. F. Parisotto, W. A. Nyberg, V. Cabric, A. Gelineau, Y. Cao, D. L. Owen, J. Ambjörnsson, D. Mathis, J. Eyquem, C. C. Brown, C. Benoist. TCR origin and specificity to environmental or self-antigens on distinct antigen-presenting cells determine peripheral Treg cell differentiation. Immunity (2026)

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O. Takacsi-Nagy, S. Kasinathan, A. Hartman, Y. Yin, L. Wu, A. Y. Chen, L. M. Moser, A. P. May, G. C. Reeder, E. Celallos Fuentes, C. Kernick, J. Lu, A. K. McClellan, C. J. Raposo, B. Terrall, N. E. Theberath, P. K. Yan, P. Xu, E. Sotillo, J. Eyquem, C. L. Mackall, T. L. Roth, A. T. Satpathy. Synthetic transcription factors designed by domain recombination enhance CAR T cell antitumor function. Cell (2026)

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H. Jung, P. Devant, C. Ching, M. Ota, E. Dann, R. Zhu, C. Modak, A. Vasquez-Ibarra, J. R. Hamilton, Z. Steinhart, W. Ngo, L. Sandoval, J. H. Jung, J. H. J. Lee, D. Xu, M. An, E. Urs, P. A. Chen, V. Allain, T. Tada, L. A. Gilbert, B. R. Shy, J. K. Pritchard, J. K. Nuñez, N. R. Landau, D. R. Liu, J. Eyquem, J. A. Doudna, A. Marson, J. Carnevale. Virus-like particles enable targeted gene engineering and pooled CRISPR screening in primary human myeloid cells. Nature Biotechnology (2026)

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Q. Liu, P. A. Chen, E. Urs, S. Zhang, M. M. Arce, C. H. Wang, J. Yan, V. Q. Nguyen, Z. Li, J. Seo, N. Kale, F. Peng, Y. Luo, L. Goudy, T. N. LaFlam, H. Zhong, C. Modak, E. Dann, J. H. Jung, A. Kirane, A. B. Warner, B. B. Quach, Z. Good, B. R. Shy, E. Shifrut, S. P. Bapat, G. M. Allen, J. Eyquem, K. Fuh, S. E. Dodgson, J. G. Cyster, A. Marson, J. Carnevale. In vivo genome-wide CRISPR screens of human T cells in solid tumours. Nature (2026)

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S. Bachl, C. Ching, A. Talbot, A. Forget, N. Kale, C. Kochendoerfer, W. Nyberg, Z. Li, P. Chen, P. Kennedy, Q. Liu, J. Muldoon, C. Liu, G. Cusing, N. Arang, N. Krogan, G. Allen, A. Marson, S. Dodgson, J. Eyquem, J. Carnevale. Disruption of the CRL5 ubiquitin ligase complex enhances engineered T-cell persistence under chronic tumor antigen exposure. Cancer Immunology Research (2026)

R. Schmidt^, C.C. Ward^, R. Dajani, Z. Armour-Garb, M. Ota, V. Allain, R. Hernandez, M. Layeghi, G. Xing, L. Goudy, D. Dorovskyi, C. Wang, Y.Y. Chen, C.J. Ye, B.R. Shy, L.A. Gilbert, J. Eyquem, J.K. Pritchard, S.E. Dodgson, A. Marson^ Base-editing mutagenesis maps alleles to tune human T cell functions. Nature (2023) *Equal contributions, ^Co-corresponding
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K. Mandal, G. Wicaksono, C. Yu, J.J. Adams, M.R. Hoopmann, W.C. Temple, A. Izgutdina, B.P. Escobar, M. Gorelik, C.H. Ihling, M.A. Nix, A. Naik, W.H. Xie, J. Hübner, L.A. Rollins, S.M. Reid, E. Ramos, C. Kasap, V. Steri, J.A.C. Serrano, F. Salangsang, P. Phojanakong, M. McMillan, V. Gavallos, A.D. Leavitt, A.C. Logan, C.M. Rooney, J. Eyquem, A. Sinz, B.J. Huang, E. Stieglitz, C.C. Smith, R.L. Moritz, S.S. Sidhu, L. Huang, A.P. Wiita. Structural surfaceomics reveals an AML-specific conformation of integrin β2 as a CAR T cellular therapy target. Nature Cancer 4, 1592–1609 (2023).
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C.A. Tsuchida*, N. Brandes*, R. Bueno*, M. Trinidad, T. Mazumder, B. Yu, B. Hwang, C. Chang, J. Liu, Y. Sun, C.R. Hopkins, K.R. Parker, Y. Qi, A.T. Satpathy, E.A. Stadtmauer, J.H.D. Cate, J. Eyquem, J.A. Fraietta, C.H. June, H.Y. Chang, C.J. Ye^, J.A. Doudna^. Mitigation of chromosome loss in clinical CRISPR-Cas9-engineered T cells. Cell 186, 4567–4582.e20 (2023). *Equal contributions, ^Co-corresponding authors
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F. Blaeschke, Y.Y. Chen, R. Apathy, B. Daniel, A.Y. Chen, P.A. Chen, K. Sandor, W. Zhang, Z. Li, C.T. Mowery, T.N. Yamamoto, W.A. Nyberg, A. To, R. Yu, R. Bueno, M.C. Kim, R. Schmidt, D.B. Goodman, T. Feuchtinger, J. Eyquem, C.J. Ye, J. Carnevale, A.T. Sathpathy, E. Shifrut, T.L. Roth^, A. Marson^. Modular pooled discovery of synthetic knockin sequences to program durable cell therapies. Cell 186, P4216–4234.E33 (2023). ^Co-corresponding authors
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Y. Wu^, Z. Huang, Y. Liu*, C.W. Yoon, K. Sun, Y. Situ, P. Ho, Z. Yuan, L. Zhu, J. Eyquem, Y. Zhao, T. Liu, G.A. Kwong, S. Chien, Y. Wang^. Spatiotemporal control of genomics and epigenomics by ultrasound. bioRxiv (2023). *Equal contributions, ^Co-corresponding authors
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D.V. Foss*, J.J. Muldoon*, D.N. Nguyen*, D. Carr, S.U. Sahu, J.M. Hunsinger, S.K. Wyman, N. Krishnappa, R. Mendonsa, E.V. Schanzer, B.R. Shy, V.S. Vykunta, V. Allain, Z. Li, A. Marson^, J. Eyquem^, R.C. Wilson^. Peptide-mediated delivery of CRISPR enzymes for the efficient editing of primary human lymphocytes. Nature Biomedical Engineering 7, 647–660 (2023). *Equal contributions, ^Co-corresponding authors
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A. Odak, H. Yuan, J. Feucht, V.A. Cantu, J. Mansilla-Soto, F. Kogel, J. Eyquem, J.K. Everett, F.D. Bushman, C. Leslie, M. Sadelain. Novel extragenic genomic safe harbors for precise therapeutic T cell engineering. Blood 141, 2698–2712 (2023).
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W.A. Nyberg*, J. Ark*, A. To, S. Clouden, G. Reeder, J.J. Muldoon, J.-Y. Chung, W.H. Xie, V. Allain, Z. Steinhart, C. Chang, A. Talbot, S. Kim, A. Rosales, L.P. Havlik, H. Pimentel, A. Asokan^, J. Eyquem^. An evolved AAV variant enables efficient genetic engineering of murine T cells. Cell 186, 446–460.e19 (2023). *Equal contributions, ^Co-corresponding authors

D.B. Goodman*, C.S. Azimi*, K. Kearns, A. Talbot, K. Garakani, J. Garcia, N. Patel, B. Hwang, D. Lee, E. Park, V.S. Vykunta, B.R. Shy, C.J. Ye, J. Eyquem, A. Marson, J.A. Bluestone, K.T. Roybal. Pooled screening of CAR T cells identifies diverse immune signaling domains for next-generation immunotherapies. Science Translational Medicine 14, eabm1463 (2022). *Equal contributions
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M.T. Witkowski^, S. Lee, E. Wang*, A.K. Lee, A. Talbot, C. Ma, N. Tsopoulidis, J. Brumbaugh, Y. Zhao, K.G. Roberts, S.J. Hogg, S. Nomikou, Y.E. Ghebrechristos, P. Thandapani, C.G. Mullighan, K. Hochedlinger, W. Chen, O. Abdel-Wahab, J. Eyquem, I. Aifantis^. NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nature Immunology 23, 1424–1432 (2022). *Equal contributions, ^Co-corresponding authors
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J. Carnevale^, E. Shifrut^, N. Kale, W.A. Nyberg, F. Blaeschke, Y.Y. Chen, Z. Li, S.P. Bapat, M.E. Diolaiti, P. O’Leary, S. Vedova, J. Belk, B. Daniel, T.L. Roth, S. Bachl, A.A. Anido, B. Prinzing, J. Ibañez-Vega, S. Lange, D. Haydar, M. Luetke-Eversloh, M. Born-Bony, B. Hegde, S. Kogan, T. Feuchtinger, H. Okada, A.T. Satpathy, K. Shannon, S. Gottschalk, J. Eyquem^, G. Krenciute^, A. Ashworth^, A. Marson^. RASA2 ablation in T cells boosts antigen sensitivity and long-term function. Nature 609, 174–182 (2022). *Equal contributions, ^Co-corresponding authors
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B.R. Shy^, V.S. Vykunta, A. Ha, A. Talbot, T.L. Roth, D.N. Nguyen, W.G. Pfeifer, Y.Y. Chen, F. Blaeschke, E. Shifrut, S. Vedova, M.R. Mamedov, J.-Y. Chung, H. Li, R. Yu, D. Wu, J. Wolf, T.G. Martin, C.E. Castro, L. Ye, J.H. Esensten, J. Eyquem, A. Marson^. High-yield genome engineering in primary cells using a hybrid ssDNA repair template and small-molecule cocktails. Nature Biotechnology 41, 521–531 (2023). *Equal contributions, ^Co-corresponding authors
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S.J.C. van der Stegen, P.L. Lindenbergh, R.M. Petrovic, H. Xie, M.P. Diop, V. Alexeeva, Y. Shi, J. Mansilla-Soto, M. Hamieh, J. Eyquem, A. Cabriolu, X. Wang, R. Abujarour, T. Lee, R. Clarke, B. Valamehr, M. Themeli, I. Riviere, M. Sadelain. Generation of T-cell-receptor-negative CD8αβ-positive CAR T cells from T-cell-derived induced pluripotent stem cells. Nature Biomedical Engineering 6, 1284–1297 (2022).
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I.D. Ferguson, B. Patiño-Escobar, S.T. Tuomivaara, Y.-H.T. Lin, M.A. Nix, K.K. Leung, C. Kasap, E. Ramos, W.N. Vasquez, A. Talbot, M. Hale, A. Naik, A. Kishishita, P. Choudhry, A. Lopez-Girona, W. Miao, S.W. Wong, J.L. Wolf, T.G. Martin III, N. Shah, S. Vandenberg, S. Prakash, L. Besse, C. Driessen, A.D. Posey Jr., R.D. Mullins, J. Eyquem, J.A. Wells, A.P. Wiita. The surfaceome of multiple myeloma cells suggests potential immunotherapeutic strategies and protein markers of drug resistance. Nature Communications 13, 4121 (2022).
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W.A. Nyberg, J. Eyquem. Genome editing applications in cancer T cell therapy. Chapter in Genome Editing in Drug Discovery (2022).
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J. Mansilla-Soto*, J. Eyquem*, S. Haubner, M. Hamieh, J. Feucht, N. Paillon, A.E. Zucchetti, Z. Li, M. Sjöstrand, P.L. Lindenbergh, M. Saetersmoen, A. Dobrin, M. Maurin, A. Iyer, A.G. Angus, M.M. Miele, Z. Zhao, T. Giavridis, S.J.C. van der Stegen , F. Tamzalit, I. Rivière, M. Huse , R.C. Hendrickson, C. Hivroz, M. Sadelain. HLA-independent T cell receptors for targeting tumors with low antigen density. Nature Medicine 28, 345–352 (2022). *Equal contributions

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