Although PD-1 inhibitors are FDA-approved for over 25 different cancers, the mechanisms contributing to response remain incompletely understood. To investigate how PD-1–deleted CD8+ T cells influence PD-1–expressing CD8+ T cells in the same tumor microenvironment, we developed an inducible PD-1 knockout (KO) model in which PD-1 is deleted on ∼50% of cells. PD-1 deletion beginning at day 7 after implantation of MC38 tumor cells led to robust tumor control. Remarkably, PD-1–expressing CD8+ T cells in the tumor had increased functionality similar to PD-1 KO CD8+ T cells. Using single-cell RNA-seq and TCR-seq, we found that the major transcriptional changes following PD-1 deletion were shared by PD-1 KO and PD-1–expressing CD8+ T cells, although PD-1 KO clones preferentially expanded. These data suggest PD-1 inhibitors not only exert cell-intrinsic effects but also may promote increased T cell function through non–cell-autonomous mechanisms, which has important implications for design of PD-1–based cancer immunotherapies.
PD-1 regulates tumor-infiltrating CD8+ T cells in both a cell-intrinsic and a cell-extrinsic fashion
https://orcid.org/0000-0002-4309-7880
*
https://orcid.org/0000-0001-9053-9867
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https://orcid.org/0009-0006-9757-5995
https://orcid.org/0000-0001-6011-6417
https://orcid.org/0000-0002-3694-8480
https://orcid.org/0000-0003-2187-0147
https://orcid.org/0000-0002-4223-4433
https://orcid.org/0000-0002-2767-0528
https://orcid.org/0000-0002-4071-4986
https://orcid.org/0000-0001-6292-1006
https://orcid.org/0000-0002-9053-0915
https://orcid.org/0000-0001-5268-5732
https://orcid.org/0000-0002-6451-9376
https://orcid.org/0000-0003-4641-6872
https://orcid.org/0000-0002-7210-5616
https://orcid.org/0000-0003-2530-2681
https://orcid.org/0000-0002-1755-3598
https://orcid.org/0000-0002-9736-2109
K.E. Pauken and S.C. Markson contributed equally to this paper.
Disclosures: V.R. Juneja reported personal fees from BioNTech US, Inc. outside the submitted work. G.J. Freeman reported personal fees from iTeos, Nextpoint, IgM, GV20, Geode, BioEntre, Santa Ana Bio, and Simcere of America outside the submitted work; in addition, G.J. Freeman had a patent to the PD-L1/PD-1 pathway with royalties paid “Roche,” a patent to the PD-L1/PD-1 pathway with royalties paid “Merck MSD,” a patent to the PD-L1/PD-1 pathway with royalties paid “AstraZeneca,” a patent to the PD-L1/PD-1 pathway with royalties paid “Bristol-Myers Squibb,” a patent to the PD-L1/PD-1 pathway with royalties paid “Merck KGA,” a patent to the PD-L1/PD-1 pathway with royalties paid “Boehringer Ingelheim,” a patent to the PD-L1/PD-1 pathway licensed “Eli Lilly,” a patent to the PD-L1/PD-1 pathway licensed “Coherus Biosciences,” and a patent to the PD-L1/PD-1 pathway licensed “Novartis”; and has equity in Nextpoint, iTeos, Invaria, GV20, and Geode. M. Haigis reported grants from ReFuel Bio, personal fees from ReFuel Bio and Mito Q, and “other” from Celine Bio outside the submitted work. M. Singer reported personal fees from Guardant Health outside the submitted work; in addition, M. Singer had a patent to US 2022/0347278 A1 pending, a patent to WO 2019/068099 A1 pending, a patent to US 2019/0262399 A1 pending, a patent to WO 2018/049025 A3 pending, a patent to WO 2018/049025 A2 pending, a patent to US 2021/0263012 A1 pending, a patent to WO 2019/100001 A1 pending, a patent to US 2021/0130776 A1 pending, a patent to WO 2017/075478 A2 pending, a patent to EP 3368689 B1 pending, a patent to WO 2024/264065 A1 pending, a patent to WO 2017/075478 A3 pending, and a patent to WO 2017/075465 A1 pending. A.H. Sharpe reported grants from NIH P0156299, NIH P01AI108545, NIH P0139671, NIH P50 CA101942, NIH 7K08CA256044-3, NIH 5TL1TR002543, Fund for Innovation in Cancer Informatics, MD Anderson CPRIT Award, Andrew Sabin Family Foundation, American Association of Immunologists, and Cancer Research Institute during the conduct of the study; personal fees from Surface Oncology, Sq Biotech, Selecta, Elpiscience, Bicara, FibroGen, Alixia, GlaxoSmithKline, Janssen, Amgen, BioEntre, ImmVue, and AltruBio; grants from Merck, Quark Ventures, AbbVie, Moderna, Erasca, Vertex, TaiwanBio, Calico, and Yosemite; and “other” from Monopteros and Corner Therapeutics outside the submitted work; in addition, A.H. Sharpe had a patent number 7,432,059 with royalties paid “Roche, Merck, Bristol-Myers-Squibb, EMD-Serono, Boehringer Ingelheim, AstraZeneca, Leica, Mayo Clinic, Dako and Novartis,” a patent number 7,722,868 with royalties paid “Roche, Merck, Bristol-Myers-Squibb, EMD-Serono, Boehringer Ingelheim, AstraZeneca, Leica, Mayo Clinic, Dako and Novartis,” a patent number 8,652,465 licensed Roche, a patent number 9,457,080 licensed Roche, a patent number 9,683,048 licensed Novartis, a patent number 9,815,898 licensed Novartis, a patent number 9,845,356 licensed Novartis, a patent number 10,202,454 licensed Novartis, a patent number 10,457,733 licensed Novartis, a patent number 9,580,684 issued none, a patent number 9,988,452 issued none, a patent number 10,370,446 issued none, a patent number 10,457,733 issued none, a patent number 10,752,687 issued none, a patent number 10,851,165 issued none, a patent number 10,934,353 issued none, and a patent number 15,314,251 issued none; and is also on the scientific advisory boards of the Massachusetts General Cancer Center, Program in Cellular and Molecular Medicine at Boston Children’s Hospital, the Human Oncology and Pathogenesis Program at Memorial Sloan Kettering Cancer Center, the Johns Hopkins Bloomberg–Kimmel Institute for Cancer Immunotherapy, the Gladstone Institutes, and Perlmutter Cancer Center at New York University and is an academic editor for the Journal of Experimental Medicine. K.E. Pauken reports a patent WO2017165412A3 that is pending. No other disclosures were reported.
K.E. Pauken’s current affiliation is Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
V.R. Juneja’s current affiliation is BioNTech US, Cambridge, MA, USA.
J.M. Schenkel’s current affiliation is Department of Laboratory Medicine, Department of Immunology, Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
M. Singer’s current affiliation is Guardant Health, Palo Alto, CA, USA.
A.E. Ringel’s current affiliation is Department of Biology, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA.
A.E. Ringel’s current affiliation is Ragon Institute of Mass General, MIT, and Harvard, Cambridge, MA, USA.
A.E. Ringel’s current affiliation is Koch Institute for Integrative Cancer Research, Cambridge, MA, USA.
