Single-cell analysis of bone marrow CD8+ T cells in Myeloid Neoplasms predicts response to treatment with Azacitidine

CD8+ T cells are critical players in anti-tumor immunity. In higher-risk myelodysplastic neoplasms (HR-MDS) and acute myeloid leukemia (AML), CD8+ T cells exhibit altered functionality, however whether this affects disease course is poorly understood. Herein, we aimed to identify immune cell signatures in the bone marrow (BM) associated with disease progression and treatment outcomes. In-depth immunophenotypic analysis utilizing mass and flow cytometry on 104 pre-treatment BM samples from patients with myeloid neoplasms, revealed an increased frequency of a CD57+CXCR3+ subset of CD8+ T cells in patients with HR-MDS and AML who failed AZA therapy. Furthermore, increased baseline frequency (>29%) of the CD57+CXCR3+CD8+ T cell subset correlated with poor overall survival. We further engaged scRNA-seq to assess the transcriptional profile of BM CD8+ T cells from treatment-naive patients. We observed an increased abundance of cells within cytotoxic CD8+ T lymphocytes (CTL) cluster in secondary AML compared to HR-MDS. Additionally, response to AZA was positively associated with enrichment of IFN-mediated pathways, whereas enhanced TGF-{beta} signaling signature in CTL clusters was observed in non-responders. Our results support that targeting of CD8+ T cells with inhibitors of TGF-{beta} signaling in combination with AZA is a potential future therapeutic strategy in HR-MDS and AML.