Transcriptome Profiling of Immune Response to Dendritic/AML Fusion Vaccine

Introduction In a clinical trial of patients vaccinated after chemotherapy-induced remission with patient-derived AML cells fused with autologous dendritic cells (DC/AML fusions) we demonstrated durable AML-specific immunity. 71% of patients sustained long-term remission from AML at 55-91 months (responders) while those who experienced relapse had recurrence at 2-26 months (non-responders). Objectives We performed genomic analysis of the marrow microenvironment to identify factors associated with durable remission after vaccination. Methods RNA sequencing was done using banked formalin-fixed paraffin embedded (FFPE) marrow at serial time points. Ingenuity Pathways IPA 9.0 was used to define pathways and upstream regulators. To characterize the cellular components, single cell RNA-seq was performed on fresh frozen aspirates with cell cluster annotation performed by Single Cell Wizard software and peripheral blood was used for TCR clonal diversity by NGS. Results Heatmaps depict significant (p-value ≤0.01 and fold change ≥2) differential gene expression both pre- and post-vaccination in responders compared to non-responders. Prior to vaccination there was inhibition of TGF-β in responders. Notable upregulated pathways in responders after vaccination (p value Conclusion In a cohort of AML patients treated with DC/AML fusions, we found distinct gene signatures amongst patients with long term remisison vs those with early relapse. The transcriptomes indicate a microenvironment in which TGF-β-mediated immunosuppression is inhibited after chemotherapy and in which interleukins, B cell and macrophage signaling are activated are associated with vaccine response, and have potential for combinatorial therapeutic strategies. T cell costimulation and activation are key components of response with NK cells and DC activation playing a supporting role. A durable oligoclonal T cell expansion suggests vaccine is capable of enhancing the T cell repertroie which could provide a unique opportunity to identify target antigens by TCR-epitope pairing.