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N/KRAS-mutant AML LSCs Are Resistant to Venetoclax and Drive Clinical Responses
Eirini P Papapetrou,1,2,3,4,5Malgorzata Olszewska,1,2,3,4,5Saul Carcamo,1,5,6Maria Sirenko,7Abhishek Maiti,8Emmanuel Olivier,1,2,3,4,5Manon Jaud,1,2,3,4,5Hager Mansour,1,2,3,4,5Deniz Demircioglu,1,5,6Dan A Landau,9,10Elli Papaemmanuil,7Courtney DiNardo,8Dan Hasson1,5,6Marina Konopleva8,111Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
2Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
3Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
4Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
5Center for Advancement of Blood Cancer Therapies, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
6Bioinformatics for Next Generation Sequencing Shared Resource Facility, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA;
7Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA;
8Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA;
9Cancer Genomics and Evolutionary Dynamics, Weill Cornell Medicine, New York, NY, USA;
10New York Genome Center, New York, NY, USA;
11Department of Oncology, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
The BH3-mimetic drug Venetoclax (VEN) is a selective inhibitor of BCL-2, a key anti-apoptotic protein, which has recently transformed the therapy of acute myeloid leukemia (AML). VEN in combination with hypomethylating agents (HMA) or low-dose cytarabine has now become the standard of care for AML patients who are older or unsuitable to receive intensive chemotherapy and is also currently being evaluated as first-line treatment for AML patients eligible for intensive chemotherapy. However, a sizeable fraction of patients are either refractory to VEN combination therapy or ultimately relapse. Understanding the determinants of resistance and relapse to VEN is therefore of critical importance for clinical decision making and for devising strategies to overcome it.
Efforts to understand the mechanisms of VEN resistance have yielded a number of clinical and laboratory observations with seemingly contradictory findings and have led to conflicting models of resistance. An idea that has gained prominence is that AML with more mature myelomonocytic immunophenotypic features is intrinsically resistant to VEN and that VEN resistance is an inherent property of the monocytic maturation status. However, analyses of other patient cohorts failed to find an association between VEN resistance and monocytic AML.
To address this conundrum, we harnessed two complementary approaches that uniquely allow us to interrogate the impact of mutational status and differentiation stage to VEN sensitivity independently of one another: AML patient-derived induced pluripotent stem cells (iPSCs) and Genotyping of Transcriptomes (GoT). Using in vitro drug sensitivity assays and single-cell transcriptomics in primary and iPSC-derived AML stem cells (LSCs) and monocytic blasts in vivo, as well as reanalysis of clinical trial data from a cohort of 118 patients with newly diagnosed AML prospectively treated with 10-day decitabine DEC and VEN (DEC10-VEN), we provide a unifying mechanistic model of VEN resistance in AML. We find that N/KRAS WT LSCs express high levels of BCL-2 and are the targets of VEN therapy, whose elimination translates into a clinical response. In contrast, monocytic blasts, regardless of RAS genotype, are uniformly VEN-resistant, as they lack expression of BCL-2 and instead rely on MCL-1 expression for survival. However, resistance of the monocytes has no impact on the clinical response, which is instead dependent on the elimination of LSCs – the cells with self-renewal potential that can maintain and regenerate the leukemia. Critically, N/KRAS mutant (MT) LSCs downregulate BCL-2 and upregulate MCL-1 and possibly BCL-xL and are thus resistant to VEN. Therefore, it is the VEN resistance of these N/KRAS MT LSCs, rather than the resistance of the monocytic blasts, that is the determinant of clinical relapse or resistance. We also show that N/KRAS-mutant LSCs produce more monocytic blasts, which can explain previous observations of outgrowth of monocytic AML upon VEN relapse and resistance, as selection of N/KRAS-mutant cells within the LSC compartment would also be accompanied by an increase in their monocytic blast output, with the latter being a byproduct rather than causally impacting the clinical outcome.
Our findings and proposed model explain and reconcile all previously discrepant observations into a unified model of VEN resistance in AML.
This work was supported by US National Institutes of Health (NIH) grants R01CA271418, R01CA260711 and R01CA271331, by a Leukemia and Lymphoma Society (LLS) Scholar Award, by an Edward P Evans Foundation Discovery Research Grant, by an LLS Blood Cancer Discoveries Grant and by a 2021 AACR-MPM Oncology Charitable Foundation Transformative Cancer Research Grant (grant number 21-20-45-PAPA) to EPP. This work was also supported by NIH grant R01CA235622 to MK.