Reinvigoration of Progenitor-Exhausted CD8 T Cells by anti-CTLA-4 Contributes to the Sustained Activity of Combination Checkpoint Blockade

Combination checkpoint blockade with anti-PD-1 and anti-CTLA-4 antibodies has shown promising efficacy in melanoma. However, the underlying mechanism in humans remains unclear. We performed multimodal analysis across time in 32 stage IV melanoma patients treated with anti-PD-1, anti-CTLA-4, or anti-PD-1 + anti-CTLA-4 (combination) therapy. Anti-CTLA-4 induced more durable immune responses than anti-PD-1, whereas combination therapy mobilized greater and more sustained immune responses. We developed the algorithm Cyclone to track temporal clonal dynamics and underlying cell states. Combination therapy generated clonal effector and exhausted CD8 T cells (TEX) responses that peaked at 6-9 weeks after treatment. Focused analyses of TEX in additional cohorts identified that anti-CTLA-4 induced robust expansion and proliferation of progenitor TEX, which synergized with anti-PD-1 to generate a large and durable reinvigoration of TEX. These next generation immune profiling approaches can guide the selection of drugs, schedule, and dosing for novel combination strategies.Funding Information: This work was supported by National Institutes of Health grants AI155577 (EJW), AI115712 (EJW), AI117950 (EJW), AI108545 (EJW), AI082630 (EJW), and CA210944 (EJW), K08 CA230157 (ACH), R01 CA273018 (ACH), P50 CA174523 (ACH), P30 CA016520 (ACH), AI158617(RSH). P50CA225450 (RSH), P30CA016087 (RSH). In addition, ACH was supported by Damon Runyon Clinical Investigator Award, Doris Duke Clinical Scientist Development Award, the W.W. Smith Charitable Trust Award, and the Institute for Translational Medicine and Therapeutics of the Perelman School of Medicine, and the Pew-Stewart Stewart Scholars Program in Cancer Research. C.A. was funded by the Parker Institute for Cancer Immunotherapy. Work in the Wherry lab is funded by the Parker Institute for Cancer Immunotherapy. Work in the Huang Lab is funded by the Tara Miller Foundation and the Parker Institute for Cancer Immunotherapy. Declaration of Interests: ACH performed consulting work for Immunai, and receive research funding from Bristol-Myers-Squibb and Merck. RSH has performed consulting work for Bristol-Myers-Squibb (exclusive of the current work). EJW is an advisor for Danger Bio, Marengo, Janssen, NewLimit, Pluto Immunotherapeutics Related Sciences, Santa Ana Bio, Synthekine, and Surface Oncology. EJW is a founder of and holds stock in Surface Oncology, Danger Bio, and Arsenal Biosciences. TCM received honorarium for Scientific Advisory Board participation from: BMS, GigaGen, Merck, Pliant, Pfizer. GCK is on the Merck Advisory Board. JW consulted for and have received less than $10,000 per annum from Merck, Genentech, AstraZeneca, GSK, Novartis, Nektar, Celldex, Incyte, Biond, Moderna, ImCheck, Sellas, Evaxion, Pfizer, Regeneron, and EMD Serono and received $10-$25,000 from BMS for membership on advisory boards. JW also holds equity in Biond, Evaxion, OncoC4, and Instil Bio, and on scientific advisory boards for CytomX, Incyte, ImCheck, Biond, Sellas, Instil Bio, OncoC4, and NexImmune and am remunerated between $10,000-$50,000. In addition, JW is named on a patent filed by Moffitt Cancer Center on an ipilimumab biomarker and on TIL preparation, and also on a PD-1 patent filed by Biodesix; JW receives less than $6000 in royalties. DB, EK, and CS were employed by Immunai when engaged in this project. DT is an employee of BMS. Ethical Approval Statement: Patients were consented for blood collection under the University of Pennsylvania Abramson Cancer Center’s melanoma research program tissue collection protocol UPCC 08607, in accordance with the Institutional Review Board. For specimens from Checkmate 238, PBMC were obtained following informed consent under an IRB-approved protocol at NYU.