Transcriptional and phenotypic heterogeneity underpinning venetoclax resistance in AML

Abstract The venetoclax BCL2 inhibitor in combination with hypomethylating agents represents a cornerstone of induction therapy for older AML patients, unfit for intensive chemotherapy. Like other targeted therapies, venetoclax-based therapies suffer from innate and acquired resistance. While several mechanisms of resistance have been identified, the heterogeneity of resistance mechanism across patient populations is poorly understood. Here we utilized integrative analysis of transcriptomic and ex-vivo drug response data in AML patients to identify four transcriptionally distinct VEN resistant clusters (VR_C1-4), with distinct phenotypic, genetic and drug response patterns. VR_C1 was characterized by enrichment for differentiated monocytic- and cDC-like blasts, transcriptional activation of PI3K-AKT-mTOR signaling axis, and energy metabolism pathways. They showed sensitivity to mTOR and CDK inhibition. VR_C2 was enriched for NRAS mutations and associated with distinctive transcriptional suppression of HOX expression. VR_C3 was characterized by enrichment for TP53 mutations and higher infiltration by cytotoxic T cells. This cluster showed transcriptional expression of erythroid markers, suggesting tumor cells mimicking erythroid differentiation, activation of JAK-STAT signaling, and sensitivity to JAK inhibition, which in a subset of cases synergized with venetoclax. VR_C4 shared transcriptional similarities with venetoclax-sensitive patients, with modest over-expression of interferon signaling. They were also characterized by high rates of DNMT3A mutations. Finally, we projected venetoclax-resistance states onto single cells profiled from a patient who relapsed under venetoclax therapy capturing multiple resistance states in the tumor and shifts in their abundance under venetoclax selection, suggesting that single tumors may consist of cells mimicking multiple VR_Cs contributing to intra-tumor heterogeneity. Taken together, our results provide a strategy to evaluate inter- and intra-tumor heterogeneity of venetoclax resistance mechanisms and provide insights into approaches to navigate further management of patients who failed therapy with BCL2 inhibitors. Competing Interest Statement J.W.T. has received research support from Acerta, Agios, Aptose, Array, AstraZeneca, Constellation, Genentech, Gilead, Incyte, Janssen, Kronos, Meryx, Petra, Schrodinger, Seattle Genetics, Syros, Takeda, and Tolero and serves on the advisory board for Recludix Pharma. M.K. reports grants from AbbVie, Allogene, Astra Zeneca, Cellectis, Daiichi, Forty Seven, Genentech, Gilead, MEI Pharma, Precision Bio, Rafael Pharmaceutical, Sanofi, Stemline-Menarini; personal fees from AbbVie, AstraZeneca, Auxenion, Genentech, Gilead, F. Hoffman-La Roche, Janssen, MEI Pharma, Sellas, Stemline-Menarini. In addition, Dr. Konopleva has a patent US 7,795,305 B2 CDDO-compounds and combination therapies with royalties paid to Reata Pharm., a patent Combination Therapy with a mutant IDH1 Inhibitor and a BCL-2 licensed to Eli Lilly, and a patent 62/993,166 combination of a mcl-1 inhibitor and midostaurin, uses and pharmaceutical compositions thereof pending to Novartis. G.B.M has received research support from AstraZeneca, Zentalis, Nanostring, Ionis (Provision of tool compounds); is SAB/Consultant: Amphista, Astex, AstraZeneca, Biodyne, BlueDot, Chrysallis Biotechnology, Ellipses Pharma, GSK, ImmunoMET, Infinity, Ionis, Leapfrog Bio, Lilly, Medacorp, Nanostring, Neophore, Nuvectis, Pangea, PDX Pharmaceuticals, Qureator, Roche, Rybodyne, Signalchem Lifesciences, Tarveda, Turbine, Zentalis Pharmaceuticals; has Stock/Options/Financial: Bluedot, Biodyne, Catena Pharmaceuticals, ImmunoMet, Nuvectis, RyboDyne, SignalChem, Tarveda, Turbine; Licensed Technology: HRD assay to Myriad Genetics, DSP patents with Nanostring.