Single-cell polyfunctional proteomics of CD4 cells from patients with AML predicts responses to anti–PD-1–based therapy

Abstract

Acute myeloid leukemia (AML) remains a difficult disease to treat disease. In a phase 2 clinical trial in patients with relapsed/refractory AML, combining the hypomethylating agent, azacitidine, with the PD-1 checkpoint inhibitor, nivolumab, demonstrated encouraging response rates (33%), median event-free, and overall survival, compared with a historical cohort of contemporary patients treated with azacitidine-based therapies, with an acceptable safety profile. Biomarkers of response are yet to be determined. In this study, we leveraged a multiplexed immune assay to assess the functional states of CD41 and CD81 cells at a single-cell level in pretherapy bone marrows in 16 patients with relapsed/refractory AML treated with azacitidine/ nivolumab. Effector CD41 but not CD81 cells had distinct polyfunctional groups and were associated with responses and better outcomes. Further evaluation of the polyfunctional strength index composition across cell types revealed that interferon-gamma (IFN-g) and tumor necrosis factor-alpha (TNF-a) were the major drivers of enhanced polyfunctionality index of pretherapy CD41 subset, whereas Granzyme B, IFN-g, MIP-1b, and TNF-a drove the nonsignificantly enhanced pretreatment Polyfunctional Strength Index of CD81 subset in the responders. Single-cell polyfunctional assays were predictive of response in AML and may have a potential role as a biomarker in the wider sphere of immunotherapy.