is a member of Scientific Advisory Boards for Kodikaz Therapeutic Solutions, Coherus Biosciences, and Zenshine Pharmaceuticals, and is an inventor on multiple patients related to CD47 cancer immunotherapy licensed to Gilead.
Key Points MEK inhibition rescues T cells from activation-induced cell death in an AML model. MEK inhibitor sensitivity is associated with inflammation pathways and PD-L1 expression.
BCL2 is an antiapoptotic protein commonly expressed in hematologic malignancies. Overexpression of BCL-2 is a poor prognostic factor in acute myeloid leukemia (AML). Venetoclax (ABT-199) is a highly selective BCL2 inhibitor that can induce cell death in multiple leukemia cell lines. Recently, venetoclax received an FDA breakthrough therapy designation for use in combination with hypomethylating agents in treatment-naïve patients with AML who are unfit for intensive chemotherapy. However, venetoclax was only modestly effective as monotherapy in relapsed/refractory AML (19% CR/CRi). The aim of the current study is to integrate genomic and functional screen data to identify biomarkers to predict venetoclax sensitivity and resistance in AML, and to identify potential venetoclax combination treatment strategies. In this study, we investigated approximately 200 AML patient samples and correlated clinical parameters, whole exome sequence data, and RNAseq gene expression data with in vitro drug screening data (drug area under the curve (AUC)) to identify subsets of AML samples with sensitivity or resistance to venetoclax alone and in combinations with 10 small molecular inhibitors (Array-382, dasatinib, JQ-1, idelalisib, quizartinib, palbociclib, panobinostat, ruxolitinib, sorafenib, and trametinib). For gene expression, we observed that venetoclax correlated with 3 gene expression clusters (coefficient frequency: 0.94, 0.80 and 0.71 respectively) among 21 gene expression clusters in AML, associated with innate immune system, neutrophil degranulation, and interleukin-10 signaling. Among the BCL2 gene family, venetoclax AUC positively correlated with BCL2A1 (r=0.59, p<0.0001) and MCL1 (r=0.26, p=0.001) expression, whereas it negatively correlated with BCL2 (r=-0.53, p<0.0001) expression. BCL2A1 is the only BCL2 family gene within all three clusters and correlated the best with venetoclax sensitivity. Interestingly, within the three gene clusters, we observed that cell surface markers CLEC7A (CD369) and CD14 correlated with venetoclax sensitivity (r=0.68 and 0.64, p<0.0001). AML patient samples expressing CD14 detected by flow cytometry also demonstrated reduced venetoclax sensitivity (p=0.005), which could potentially serve as a biomarker to identify venetoclax resistant patients. For cytogenetic categories and mutations, we observed that AML samples harboring PML-RARA translocations, WT1, and FLT3 with IDH1 mutations are more sensitive to venetoclax, and samples with TET2, KRAS, PTPN11 and SF3B1 mutations are more resistant. We validated the effect of WT1, KRAS, and PTPN11 mutations on venetoclax sensitivity by performing drug assays on mouse bone marrow stem cells and/or AML cell lines overexpressing each mutant. Samples harboring PTPN11 mutations demonstrated high MCL1 expression, and PTPN11 mutant-transduced cells remain sensitive to Idasanutlin, which was previously shown to downregulate MCL1 expression. Samples with KRAS mutations demonstrated high BCL2A1 expression, which potentially mediate venetoclax resistance. For venetoclax drug combinations, we observed that venetoclax-trametinib demonstrated a synergistic effect on samples that are sensitive to venetoclax, whereas venetoclax-palbociclib, venetoclax-Array-382, venetoclax-sorafenib, venetoclax-ruxolitinib, venetoclax-dasatinib, and venetoclax-idelalisib are active against samples that are resistant to venetoclax, indicating potential therapeutic combinations. Interestingly, the CDK inhibitor palbociclib demonstrated no effect on the majority of AML samples and does not correlate with the BCL2A1 expression as a single agent, yet shows the most robust synergy with venetoclax, especially on samples that are resistant to venetoclax and with high BCL2A1 expression, indicating a potential synthetic lethal interaction. Venetoclax-palbociclib AUC also negatively correlated with CLEC7A and CD14 expression, indicating that venetoclax-palbociclib could circumvent venetoclax resistance to treat patients with high CLEC7A and/or CD14 expression. In summary, we have identified that CD14 and/or CLEC7A could be used as biomarkers to predict venetoclax sensitivity in AML, and we propose to combine venetoclax and palbociclib to treat patients with a venetoclax resistant profile (high CD14/CLEC7A expression or high BCL2A1 expression, or presence of KRAS mutations). Disclosures Druker: Beta Cat: Membership on an entity's Board of Directors or advisory committees; Fred Hutchinson Cancer Research Center: Research Funding; McGraw Hill: Patents & Royalties; Vivid Biosciences: Membership on an entity's Board of Directors or advisory committees; Oregon Health & Science University: Patents & Royalties; Bristol-Meyers Squibb: Research Funding; GRAIL: Consultancy, Membership on an entity's Board of Directors or advisory committees; ARIAD: Research Funding; Third Coast Therapeutics: Membership on an entity's Board of Directors or advisory committees; Gilead Sciences: Consultancy, Membership on an entity's Board of Directors or advisory committees; Monojul: Consultancy; Novartis Pharmaceuticals: Research Funding; Millipore: Patents & Royalties; Leukemia & Lymphoma Society: Membership on an entity's Board of Directors or advisory committees, Research Funding; ALLCRON: Consultancy, Membership on an entity's Board of Directors or advisory committees; Aileron Therapeutics: Consultancy; Patient True Talk: Consultancy; Cepheid: Consultancy, Membership on an entity's Board of Directors or advisory committees; Henry Stewart Talks: Patents & Royalties; Celgene: Consultancy; Amgen: Membership on an entity's Board of Directors or advisory committees; MolecularMD: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Blueprint Medicines: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees; Aptose Therapeutics: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Majeti:BioMarin: Consultancy; Forty Seven, Inc: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees. Tyner:Incyte: Research Funding; AstraZeneca: Research Funding; Janssen: Research Funding; Takeda: Research Funding; Leap Oncology: Equity Ownership; Seattle Genetics: Research Funding; Genentech: Research Funding; Gilead: Research Funding; Syros: Research Funding; Aptose: Research Funding; Agios: Research Funding.
Many acute myeloid leukemia (AML) patients exhibit hallmarks of immune exhaustion, such as increased myeloid-derived suppressor cells, suppressive regulatory T cells and dysfunctional T cells. Similarly, we have identified the same immune-related features, including exhausted CD8+ T cells (TEx) in a mouse model of AML. Here we show that inhibitors that target bromodomain and extra-terminal domain (BET) proteins affect tumor-intrinsic factors but also rescue T cell exhaustion and ICB resistance. Ex vivo treatment of cells from AML mice and AML patients with BET inhibitors (BETi) reversed CD8+ T cell exhaustion by restoring proliferative capacity and expansion of the more functional precursor-exhausted T cells. This reversal was enhanced by combined BETi and anti-PD1 treatment. BETi synergized with anti-PD1 in vivo, resulting in the reduction of circulating leukemia cells, enrichment of CD8+ T cells in the bone marrow, and increase in expression of Tcf7, Slamf6, and Cxcr5 in CD8+ T cells. Finally, we profiled the epigenomes of in vivo JQ1-treated AML-derived CD8+ T cells by single-cell ATAC-seq and found that JQ1 increases Tcf7 accessibility specifically in Tex cells, suggesting that BETi likely acts mechanistically by relieving repression of progenitor programs in Tex CD8+ T cells and maintaining a pool of anti-PD1 responsive CD8+ T cells.
Summary Drug resistance in chronic myeloid leukaemia (CML) may occur via mutations in the causative BCR::ABL1 fusion or BCR::ABL1‐independent mechanisms. We analysed 48 patients with BCR::ABL1‐independent resistance for the presence of secondary fusion genes by RNA sequencing. We identified 10 of the most frequently detected secondary fusions in 21 patients. Validation studies, cell line models, gene expression analysis and drug screening revealed differences with respect to proliferation rate, differentiation and drug sensitivity. Notably, expression of RUNX1::MECOM led to resistance to ABL1 tyrosine kinase inhibitors in vitro. These results suggest secondary fusions contribute to BCR::ABL1‐independent resistance and may be amenable to combined therapies.
Acute Myeloid Leukemia (AML) is the most common adult leukemia and has a 5-year survival of under 30%. AML is caused by uncontrolled proliferation of myeloid cells resulting from a combination of mutations that affect proliferation, differentiation and epigenetic state. For this reason, drugs targeting epigenetic modifications are being studied in AML. AML cells avoid immune recognition though inhibiting the function of multiple cell types, especially T cells and therefore immune checkpoint blockade presents a promising therapy; however, clinical trials to date have shown very modest efficacy. T cell exhaustion has been shown to be a regulated process involving transcriptional and epigenetic changes. BET proteins, which are chromatin readers, have been implicated in maintaining this exhaustion state. In these studies, we investigated the effects of the BET inhibitor (BETi) JQ1 on T cell exhaustion and checkpoint responsiveness in a murine model of AML and AML patient samples. The AML mouse model bears FLT3-ITD and deletion of TET2 restricted to myeloid lineages and is resistant to anti-PD1 therapy. This mouse model of AML expanded terminally exhausted T cells and impaired proliferative capacity after TCR stimulation. Ex vivo treatment with BETi and anti-PD1 reverses CD8+ T cell exhaustion via rescue of proliferative dysfunction and expansion of more functional precursor exhausted T cells in patient samples and AML splenocytes. Finally, we show that BETi rescues anti-PD1 resistance in vivo and reduces tumor burden in multiple organ sites and enriches CD8+ T cells in the bone marrow. In total, we demonstrate that combining BETi and anti-PD1 therapy in the treatment of AML is a rational strategy to overcome anti-PD1 resistance.
BackgroundAcute Myeloid Leukemia (AML) is the most common adult leukemia and has a very poor prognosis. With a 5-year survival of under 30% (seer.cancer.gov), most people diagnosed with AML will die from the disease. AML is caused by an uncontrolled proliferation of poorly differentiated myeloid precursor cells which results from a combination of three classes of mutations that affect proliferation, differentiation and epigenetic state. For this reason, drugs targeting epigenetic modifications are being actively studied in AML. AML has been shown to avoid immune recognition though inhibiting the function of multiple cell types, especially T cells1 2 and therefore immune checkpoint blockade presents a promising therapy for any immune-targeted strategy; however, clinical trials to date have shown very modest efficacy.3–5 T cell exhaustion in cancer has been shown to be a regulated process involving transcriptional and epigenetic changes.6–9 BRD4 has been shown to be important for maintaining this exhaustion state.10 11 It stands to reason that drugs designed to target epigenetic pathways in tumors will have effects on T cell populations present in the tumor microenvironment. In these studies, we investigated the effects of the BET inhibitor (BETi) JQ1 on T cell exhaustion and checkpoint responsiveness in a murine model of AML.MethodsThe AML mouse model bears FLT3-ITD and deletion of TET2 restricted to the myeloid lineage. For in vitro studies, splenocytes were stimulated with anti-CD3 and either JQ1, anti-PD1 or both and proliferation and differentiation status were assessed by flow cytometry. For in vivo studies, treatment consisted of 2 weeks with JQ1, anti-PD1 or both.ResultsThis mouse model of AML exhibits an expansion of terminally exhausted T cells and impaired proliferative capacity after stimulation through the TCR (figure 1). Ex vivo treatment with BETi and anti-PD1 reverses CD8+ T cell exhaustion via rescue of proliferative dysfunction and expansion of more functional precursor exhausted T cells (TPEx-CD8, PD1+, TCF1+, TIM3-) (figure 2). Finally, we show that BETi synergizes with anti-PD1 in vivo leading to a reduction of tumor cells in multiple organ sites, and enrichment of CD8+ T cells in the bone marrow (figure 3).ConclusionsUsing an AML mouse model that exhibits leukemia-induced immune exhaustion, we demonstrate the pre-clinical efficacy of combining BETi and anti-PD1 therapy in the treatment of AML.ReferencesLamble AJ, Lind EF. Targeting the immune microenvironment in acute myeloid leukemia: a focus on T Cell immunity. Front Oncol 2018;8:213.Lamble AJ, Kosaka Y, Laderas T, Maffit A, Kaempf A, Brady LK, et al. Reversible suppression of T cell function in the bone marrow microenvironment of acute myeloid leukemia. Proc Natl Acad Sci U S A. 2020;117(25):14331–41.Boddu P, Kantarjian H, Garcia-Manero G, Allison J, Sharma P, Daver N. The emerging role of immune checkpoint based approaches in AML and MDS. Leuk Lymphoma 2018;59(4):790–802.Bewersdorf JP, Shallis RM, Zeidan AM. Immune checkpoint inhibition in myeloid malignancies: moving beyond the PD-1/PD-L1 and CTLA-4 pathways. Blood Rev 2020:100709.Daver N, Garcia-Manero G, Basu S, Boddu PC, Alfayez M, Cortes JE, et al. Efficacy, safety, and biomarkers of response to azacitidine and nivolumab in relapsed/Refractory acute myeloid leukemia: a nonrandomized, Open-Label, Phase II Study. Cancer Discov 2019;9(3):370–83.Beltra JC, Manne S, Abdel-Hakeem MS, Kurachi M, Giles JR, Chen Z, et al. Developmental Relationships of Four Exhausted CD8(+) T Cell subsets reveals underlying transcriptional and epigenetic landscape control mechanisms. Immunity 2020;52(5):825–41 e8.Khan O, Giles JR, McDonald S, Manne S, Ngiow SF, Patel KP, et al. TOX transcriptionally and epigenetically programs CD8(+) T cell exhaustion. Nature 2019;571(7764):211–8.Pauken KE, Sammons MA, Odorizzi PM, Manne S, Godec J, Khan O, et al. Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade. Science 2016;354(6316):1160–5.Abdel-Hakeem MS, Manne S, Beltra JC, Stelekati E, Chen Z, Nzingha K, et al. Epigenetic scarring of exhausted T cells hinders memory differentiation upon eliminating chronic antigenic stimulation. Nat Immunol 2021;22(8):1008–19.Milner JJ, Toma C, Quon S, Omilusik K, Scharping NE, Dey A, et al. Bromodomain protein BRD4 directs and sustains CD8 T cell differentiation during infection. J Exp Med 2021;218(8).Kagoya Y, Nakatsugawa M, Yamashita Y, Ochi T, Guo T, Anczurowski M, et al. BET bromodomain inhibition enhances T cell persistence and function in adoptive immunotherapy models. J Clin Invest 2016;126(9):3479–94.Ethics ApprovalThis study has been approved by the OHSU IACUC committee protocol IP00000907 “Immune-based therapeutic approaches for acute myeloid leukemia” Evan Lind PI.Abstract 734 Figure 1T cell exhaustion in the AML mouse model. (A) Cytotoxic T cells show an exhausted phenotype in mice with AML. Spleen cultures from mice with AML or WT controls were stained with antibodies to CD3, CD8, TIM3, PD1, and TCF1. Left shows percent of TPEX CD8 T cells. Right panel shows TEX CD8 T cells. N = 12 animals per group. (B) Proliferative defect in T cells in mice with AML. Splenocytes were labeled with the proliferation dye CFSE. Whole spleen suspensions were stimulated with anti-CD3 or anti-CD3 and anti-CD28 for 3 days. FACs plots show proliferation of T cells in each conditionAbstract 734 Figure 2Treatment with JQ1 results in expansion of T cells with TPEX. (A) Example of proliferation (CFSE dilution) vs TCF-1 expression showing unstimulated, CD3 or CD3+JQ1 120 nM in in vitro 3-day culture. Results gated on CD8 T cells. (B) Summary of T cell proliferation from 4 independent experiments showing the percent proliferation of CD8 T cells with TPEX (PD1+ Tim-3- TCF-1+) (black line) or TEX (PD1+Tim-3+TCF1-) phenotype (red line). Statistics are unpaired T-Test for each treatment condition.Abstract 734 Figure 3In vivo treatment of FTL mice with the BETi JQ1. (A) Schematic overview of treatment protocol. (B) White blood cell counts at pre-treatment, 1 week and 2 weeks after JQ1, PD1 blockade or both. (C) Percent of CD8+ T cells of all CD3-gated T cells in the BM of treated animals. (D) A-C Percent of precursor-exhausted CD8+ T cells as a percent of all T cells in the spleen of treated animals. Results combined from 2 separate experiments n=7. D One experiment n=3.
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