Integrated genetic, epigenetic, and immune landscape of mutant AML and higher risk MDS treated with azacitidine.

Background: mutations are associated with an adverse prognosis in acute myeloid leukemia (AML) and higher-risk myelodysplastic syndromes (HR-MDS). However, the integrated genetic, epigenetic, and immunologic landscape of -mutated AML/HR-MDS is not well defined.

Objectives: To define the genetic, epigenetic, and immunologic landscape of mutant and wild-type AML and HR-MDS patients.

Design: analysis of mutant and wild-type patients treated on the randomized FUSION trial with azacitidine ± the anti-PD-L1 antibody durvalumab.

Methods: We performed extensive molecular, epigenetic, and immunologic assays on a well-annotated clinical trial dataset of 61 patients with mutated disease (37 AML, 24 MDS) and 144 wild-type (89 AML, 55 MDS) patients, all of whom received azacitidine-based therapy. A 38 gene-targeted myeloid mutation analysis from screening bone marrow (BM) was performed. DNA methylation arrays, immunophenotyping and immune checkpoint expression by flow cytometry, and gene expression profiles by bulk RNA sequencing were assessed at baseline and serially during the trial.

Results: Global DNA methylation from peripheral blood was independent of mutation and allelic status. AZA therapy led to a statistically significant decrease in global DNA methylation scores independent of mutation status. In BM from mutant patients, we found both a higher T-cell population and upregulation of inhibitory immune checkpoint proteins such as PD-L1 compared to wild-type. RNA sequencing analyses revealed higher expression of the myeloid immune checkpoint gene in mutant samples suggesting a novel therapeutic target.

Conclusion: This integrated analysis of the genetic, epigenetic, and immunophenotypic landscape of mutant AML/HR-MDS suggests that differences in the immune landscape resulting in an immunosuppressive microenvironment rather than epigenetic differences contribute to the poor prognosis of mutant AML/HR-MDS with mono- or multihit mutation status.

Trial Registration: FUSION trial (NCT02775903).