Single-cell Characterization of Acute Myeloid Leukemia and its Microenvironment Following PD-1 Blockade Based Therapy
Hussein A. Abbas,
Jin Seon Im,
Patrick K. Reville,
Jairo T. Mathews,
Michael R. Green,
James P. Allison,
Steven M Kornblau,
Posted 03 Sep 2020
bioRxiv DOI: 10.1101/2020.09.03.278309
Posted 03 Sep 2020
Acute myeloid leukemia (AML) and effector cells of immune checkpoint blockade (ICB) therapy co-reside in a complex bone marrow (BM) milieu. The interplay of tumor intrinsic and microenvironment (TME) mechanisms that influences the response to ICB-based therapies in AML have not been elucidated. Here we report our analyses of single cell RNA profiling of more than 127,000 BM cells from healthy donors and relapsed/refractory (R/R) AML patients at pre/post treatment with azacitidine/nivolumab, paired with single cell T cell receptor (TCR) repertoire profiles, to uncover factors impacting response and resistance. Loss of chromosome 7/7q conferred an immunosuppressive TME and was associated with resistance to ICB-based therapy in R/R AML. Our trajectory analysis revealed a continuum of CD8+ T cell phenotypes, characterized by differential expression of granzyme B (GZMB) and GZMK. GZMK expression defined a BM residing memory CD8+ T cell subset with stem-like properties likely an intermediary between naïve and cytotoxic lymphocytes. Responses to ICB-based therapy were primarily driven by novel and expanded T cell clonotypes. Our findings support an adaptable T cell plasticity in response to PD-1 blockade in AML. Disentangling AML cells from their complex, immune-rich microenvironment revealed characteristics that shaped resistance to ICB-based therapy and could inform strategies to target AML vulnerabilities. Significance Determining the cellular and molecular underpinnings of response and resistance to PD-1 blockade based therapy in AML can guide immune-based therapeutic strategies. Our results reveal AML intrinsic characteristics (chromosome 7/7q status and oxidative stressors) and tumor microenvironment to modulate responses to checkpoint blockers. CD8 cells exist in the bone marrow in a continuum with GZMK expression defining a memory, stem-like T cell population that could play a role in response to therapy. ### Competing Interest Statement M.R.G. reports consulting fees with VeraStem Oncology and stock/ownership interest KDAc Therapeutics. M.K. reports grant support and consulting fees from AbbVie, Genentech, F. Hoffmann La-Roche, Stemline Therapeutics, Forty-Seven, consulting fees from Amgen and Kisoji, grant support from Eli Lilly, Cellectis, Calithera, Ablynx, Agios, Ascentage, AstraZeneca, Rafael Pharmaceutical, Sanofi, royalties and stock options from Reata Pharmaceutical Inc. P.S. reports consulting, advisory roles, and/or stocks/ownership for Achelois, Apricity Health, BioAlta, Codiak BioSciences, Constellation, Dragonfly Therapeutics, Forty-Seven Inc., Glympse, Hummingbird, ImaginAb, Jounce Therapeutics, Lava Therapeutics, Lytix Biopharma, Marker Therapeutics, Oncolytics, Infinity Pharma, BioNTech, Adaptive Biotechnologies, and Polaris; and owns a patent licensed to Jounce Therapeutics J.P.A reports consulting, advisory roles, and/or stocks/ownership for Achelois, Apricity Health, BioAlta, Codiak BioSciences, Dragonfly Therapeutics, Forty-Seven Inc., Hummingbird, ImaginAb, Jounce Therapeutics, Lava Therapeutics, Lytix Biopharma, Marker Therapeutics, Polaris, BioNTech, and Adaptive Biotechnologies; and owns a patent licensed to Jounce Therapeutics. N.D. reports research funding from Daiichi Sankyo, Bristol-Myers Squibb, Pfizer, Karyopharm, Sevier, Genentech, Astellas, Abbvie, Genentech, Novimmune, Amgen, Trovagene, Gilead and ImmunoGen and has served in a consulting or advisory role for Daiichi Sankyo, Bristol-Myers Squibb, Pfizer, Novartis, Celgene, AbbVie, Genentech, Servier, Trillium, Syndax, Trovagene, Astellas, Gilead and Agios.
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