Abstract PR003: Single-cell profiling of acute myeloid leukemia (AML) and its microenvironment reveals a CD8 continuum and adaptable T cell plasticity in response to PD-1 blockade-based therapy
Authors: Abbas Hussein A. , Hao Dapeng , Tomczak Katarzyna , Barrodia Praveen , Im Jin Seon , Reville Patrick K. , Al-Atrash Gheath , Ning Jing , Ding Maomao , Mathews Jairo T. , Little Latasha , Zhang Jianhua , Basu Sreyashi , Konopleva Marina , Garcia-Manero Guillermo , Green Michael R. , Sharma Padmanee , Allison James P. , Kornblau Steven M. , Rai Kunal , Wang Linghua , Daver Naval , Futreal Andrew 
Published: February 2021

Introduction: Allogeneic hematopoietic stem cell transplantation (ASCT) remains the only curative option for patients with relapsed/refractory (R/R) AML, achieved via the grafted T cells versus leukemia effect. Since ASCT is not viable option to many AML patients, our group investigated (NCT02397720) whether T cells can be harnessed to eradicate R/R AML by combining azacitidine, a hypomethylating agent, and nivolumab, a PD-1 blocker. The tumor microenvironment (TME) factors impacting response and resistance to PD-1 blockade-based treatment in AML is unknown. Methods: We performed single cell RNA sequencing (scRNAseq) of 13,633 healthy bone marrow (BM) donor, and 113,394 BM cells, paired with &gt;30,000 single cell T cell receptor (scTCR) repertoires, from 22 aspirates (8 pre- and 14 post- treatment) from 8 R/R AML patients (median age 73 years) treated with azacitidine/nivolumab. 3/8 patients were responders, while 2/8 and 3/8 had stable disease, and no response, respectively. Results: We identified marked variation in the T cell components across AML patients at pre- and post- treatment, demonstrating significant dynamic changes in CD4, CD8 and non-classical T cells populations, including mucosal associated invariant T (MAIT) cells. Among CD8 cells, we identified a unique GZMK-enriched population that was higher at pretreatment in responders compared to non-responders. Pseudotemporal trajectory analysis revealed a continuum of CD8 cell states that is intermediated by the less exhausted, GZMK-enriched CD8 population. We similarly identified GZMK to discriminate between 2 MAIT populations. Further characterization of GZMK-enriched cells revealed increased expression of the stem-like T cell transcription factor TCF7, and the T cell memory transcription factor EOMES. Pathway enrichment of the 33 overlapping genes in the GZMK-enriched CD8 and MAIT versus cytotoxic T lymphocyte (CD8 CTL) signatures demonstrated highest enrichment for pathways involved in leukocyte differentiation, calcium signaling, and cytokine production. scTCR clonotype assessment revealed more shared clonotypes with the terminally effector CD8 CTL cells following PD-1 blockade. Following treatment, novel clones represented 38.7% (39/101) of total clones, followed by contracted clones (32.6%) and expanded (28.7%) clones. However, 76.9% and 72.4% of novel and expanded clones were contributed by the responders. On the other hand, non-responders contributed only 5% and 3.4% of the novel and expanded clones, respectively. Conclusion: We identified a CD8 continuum in BMs of patients with AML. The response to combined azacitidine/nivolumab is driven by emergence of novel clones and expansion of prior clones demonstrating T cell plasticity and adaptability. Our results demonstrate that the subverted T cells can be reinvigorated via PD-1 blockade and elicit responses in AML and warrants further functional characterization of GZMK expressing lymphocytes in mediating antileukemic responses.

This abstract is also being presented as PO059.

Citation Format: Hussein A. Abbas, Dapeng Hao, Katarzyna Tomczak, Praveen Barrodia, Jin Seon Im, Patrick K. Reville, Gheath Al-Atrash, Jing Ning, Maomao Ding, Jairo T. Mathews, Latasha Little, Jianhua Zhang, Sreyashi Basu, Marina Konopleva, Guillermo Garcia-Manero, Michael R. Green, Padmanee Sharma, James P. Allison, Steven M. Kornblau, Kunal Rai, Linghua Wang, Naval Daver, Andrew Futreal. Single-cell profiling of acute myeloid leukemia (AML) and its microenvironment reveals a CD8 continuum and adaptable T cell plasticity in response to PD-1 blockade-based therapy [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PR003.