Modulation of RNA splicing enhances response to BCL2 inhibition in leukemia [eCLIP]
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE199160 | GEO | 2022/10/31
REPOSITORIES: GEO
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Project description:Therapy resistance is a major challenge in the treatment of cancer. Here, we performed CRISPR/Cas9 screens across a broad range of therapies used in acute myeloid leukemia (AML) to identify genomic determinants of drug response. Our screens uncovered a selective dependency on RNA splicing factors whose loss preferentially synergized with the BCL2 inhibitor venetoclax. Loss of the splicing factor RBM10 augmented response to venetoclax in leukemia yet was completely dispensable for normal hematopoiesis. Combined RBM10 and BCL2 inhibition led to mis-splicing and inactivation of the inhibitor of apoptosis XIAP and downregulation of BCL2A1, an anti-apoptotic protein implicated in venetoclax resistance. A novel inhibitor of splicing kinase families CLKs and DYRKs led to intron retention of key splicing factors identified from our screens, synergized with venetoclax, and overcame resistance to BCL2 inhibition. Our findings underscore the central importance of splicing in modulating apoptosis and provide a strategy to improve venetoclax-based treatments.
2022-10-31 | GSE199159 | GEO
Project description:Drug-tolerant “persister” tumor cells underlie the emergence of drug-resistant clones contribute to relapse and disease progression; thus, identifying actionable targets that disable persisters and mitigate relapse are a high priority need. Although the BCL2-targeting agent venetoclax (ABT-199) has shown promising responses in mantle cell and double hit B cell lymphomas, resistance often arises, yet mechanistically how this occurs is unclear. Here we report that ABT-199 resistance can evolve from persister clones that have selective deletions at 18q21 that involve the drug target BCL2 and the apoptotic regulators Noxa (PMAIP1) and TCF4. Notably, reprogramming of super enhancers (SE) in persisters contributes to resistance, where there is a selection for SE-directed overexpression of the apoptotic regulator BCL2A1 and oncogenic transcription factors IKZF1 and FOXC1. At the same time, the SE reprogramming confers an opportunity for overcoming ABT-199 resistance. An unbiased drug screen on a platform that recapitulates the lymphoma microenvironment revealed that persisters are vulnerable to inhibitors of transcription initiation and elongation, and especially so to inhibitors of cyclin-dependent kinase 7 (CDK7) that is essential for transcription initiation. Specifically, CDK7 loss or inhibition eliminated the persister phenotype by disabling SE-driven expression of BCL2A1, IKZF1 and FOXC1. Thus, the co-treatment of ABT-199 with CDK7 inhibitors blocked the evolution of drug resistance, and provoked tumor regression in models of mantle cell lymphoma (MCL) and double hit lymphomas (DHL) that overexpress both MYC and BCL2. Together, these findings establish loss of apoptotic regulators and an adaptive transcriptional response as drug resistance mechanisms in lymphoma, more importantly, establish a rationale for transcription inhibition-based combination strategies to prevent and overcome drug resistance in B cell malignancies toward BCL2 inhibitor.
2020-05-26 | PXD010193 | Pride
Project description:Overexpression of antiapoptotic BCL2 family proteins occurs in various hematologic malignanices and contributes to leukemogenesis by inhibiting the apoptotic machinery of the cells. BH3 mimetics provide an option for medication, with venetoclax as the first drug applied for chronic lymphocytic leukemia and for acute myeloid leukemia. To find additional hematologic entities with ectopic expression of BCL2 family members, we performed expression screening applying the LL-100 panel. Primary effusion lymphoma (PEL) and anaplastic large cell lymphoma (ALCL), 2/22 entities covered by this panel, stood out by high expression of MCL1 and low expression of BCL2. The MCL1 inhibitor AZD-5991 induced apoptosis in both malignancies suggesting that this BH3 mimetic might be efficient as drug for these diseases. The ALCL cell lines also expressed BCLXL and BCL2A1, both contributing to survival of the cells. The combination of specific BH3 mimetics yielded synergistic effects, pointing to a novel strategy for the treatment of ALCL. The PI3K/AKT inhibitor BEZ-235 could also efficiently be applied in combination with AZD-5991, providing an alternative to avoid thrombocytothemia, which is associated with the use of BCLXL inhibitors.
2021-12-31 | E-MTAB-10903 | biostudies-arrayexpress
Project description:Oncogene-driven lung cancers such as those with activating mutations in the epidermal growth factor receptor (EGFR) often harbor additional co-occurring genetic alterations. The significance of most alterations co-occurring with mutant EGFR remains unclear. We report the impact of loss of the mRNA splicing factor RBM10 in human EGFR mutant lung cancer. RBM10 loss decreased EGFR inhibitor efficacy in patient-derived EGFR mutant tumor models. RBM10 regulated mRNA splicing of the mitochondrial apoptotic regulator Bcl-x. Genetic inactivation of RBM10 diminished EGFR inhibitor-mediated apoptosis by altering Bcl-x splicing, decreasing Bcl-xS (pro-apoptotic) and increasing Bcl-xL (anti-apoptotic) levels. Co-inhibition of Bcl-xL and mutant EGFR overcomes resistance induced by RBM10 loss. RBM10 loss was a biomarker of poor response to EGFR inhibitor treatment in clinical samples. Inactivation of the splicing factor RBM10 is a key co-occurring genetic alteration in EGFR mutant tumors that limits EGFR inhibitor efficacy and a potential biomarker of Bcl-xL inhibitor response.
2022-06-04 | GSE199240 | GEO
Project description:Activation of the MYC oncogene is common in B-cell lymphomas, and frequently associated with compensatory events that dampen Myc-induced apoptosis, such as over-expression of anti-apoptotic Bcl2-family proteins. For example, concurrent translocations of MYC and BCL2 in a subset of Diffuse large B-cell lymphoma (DLBCL) lead to the high-grade “double-hit” lymphoma subtype (DHL), characterized by dismal prognosis in the face of current front-line regimens, thus calling for the pursuit of tailored therapeutic strategies. Here, we show that Myc and Bcl2 modulate the sensitivity of B-cells to IACS-010759, a selective inhibitor of mitochondrial respiratory complex I. Myc activation in non-transformed lymphoid precursors suppressed endogenous Bcl2 and sensitized the cells to IACS-010759-induced apoptosis. Treatment with the Bcl2 inhibitor venetoclax also sensitized to IACS-010759, while overexpression of Bcl-2 was protective. IACS-010759 engaged an ATF4-driven Integrated Stress Response (ISR) with dual anti- and pro-apoptotic effects, the latter mediated by the CHOP transcription factor, which contributed to selective killing of Myc-overexpressing cells. In line with the above data, IACS-010759 and venetoclax synergized in killing human DHL cells, and showed strong combinatorial effects in a pre-clinical setting. In a Bcl2-negative Burkitt’s lymphoma cell line, instead, IACS-010759 synergized with the Mcl-1 inhibitor S63845. Altogether, our data point to the combination of IACS-010759 with distinct Bcl2-family inhibitors for therapeutic reactivation of the intrinsic apoptotic pathway in Myc-associated B-cell lymphomas
2022-03-01 | GSE149073 | GEO
Project description:Ventoclax-based combinations are a new standard of care for patients with acute myeloid leukemia (AML) who are not eligible for intensive chemotherapy, but not all patients respond to these treatments, and those who do may relapse. MDM2 inhibitors are promising therapeutics for treating TP53 wild-type tumors, including most de novo AML cases, but clinical trials have shown modest and variable clinical activity. Functional genomic data suggest that venetoclax and the MDM2 inhibitor, idasanutlin, may be ineffective against monocytic leukemia (FAB M4/M5) or leukemia cells with a high immune signature. We hypothesize upregulated myeloid transcription factors and enrichment of certain environmental cues that confer intrinsic and extrinsic drug resistance to these cells. We show that monocytic leukemia cells express a high level of CEBPB and CEBPB overexpression confers drug resistance to a broad range of BH3 mimetics, venetoclax combinations, and MDM2 inhibitors by downregulating CASP3, CASP6, BCL2, and p53 pathway targets, while upregulating MCL1, BCL2A1, and the NFKB/IL1/TNFA pathway. Moreover, leukemia monocytes can extrinsically protect leukemia blasts from venetoclax and MDM2 inhibition by secreting elevated IL1 and TNFA, which drive myelo/monocytic differentiation and upregulate inflammatory cytokines and receptors, including IL1/TNFA pathway in an autoregulatory loop. Remarkably, IL1A/IL1B and TNFA uniquely upregulate CEBPB expression in M4/M5 cells and protect them from apoptosis induced by venetoclax and MDM2 inhibitors. Conversely, TNFA treatment enhances extrinsic apoptosis in M0/M1 leukemia cells. Inhibitors of IRAK or MAPK14 (p38), which block IL1/TNFA signaling, showed synergistic cytotoxicity in M4/M5 AML when combined with venetoclax and idasanutlin. In summary, we described a targetable, positive feedback loop between CEBPB and IL1/TNFA in monocytic leukemia that drives intrinsic and extrinsic drug resistance to BCL2 and MDM2 inhibitors, offering promising therapeutic strategies to enhance treatment efficacy for monocytic leukemia.
2024-10-17 | GSE245597 | GEO
Project description:To assess the synergistic effects of CDK7 inhibitor with Venetoclax, we performed RNA sequencing and gene set enrichment analysis using Venetoclax sensitive and resistant model systems. RNA-sequencing from paired Venetoclax-sensitive and Venetoclax-resistant cells treated with CDK7 inhibitor showed downregulation of genes involved in proliferation and apoptosis. CDK7 inhibitor induces apoptosis in AML cells and combined treatment with Venetoclax led to synergistic effects in overcoming resistance.
2023-07-24 | GSE231745 | GEO
Project description:Acute myeloid leukemias (AML) patients bearing chromosomal rearrangements of KMT2A or MLL gene (KMT2A -r) have poor overall survival. Recently, compounds targeting the KMT2A fusion protein complex, such as DOT1L and Menin inhibitors, have shown promising pre-clinical efficacy. Yet, molecular regulators of the anti-tumor activities of these agents remain poorly studied. UTX is a histone H3K27 demethylase with recurrent loss-of-function mutations in human cancers including leukemia. UTX-null leukemia shows greater resistance to chemotherapy agents. However, the impact of UTX on drug resistance of KMT2A -r AML has not been explored. Through a epigenetic compound screen, we identified a unique role of UTX in the regulation of DOT1L and Menin therapies in KMT2A-r AML. Loss of UTX confers resistance to DOT1L and Menin inhibition in an MLL target gene-independent manner. Mechanistically, We show that UTX is required for activation of myeloid differentiation programs induced by DOT1L inhibition. We also revealed BCL2A1 as a target of UTX. Depletion of UTX increased vulnerability to BCL2 inhibitor venetoclax in vitro and in vivo, and combinational treatment of venetoclax could overcome the therapeutic resistance to DOT1L inhibition caused by UTX loss. Our study provides new insights into the role of UTX in therapeutic responses in KMT2A-r AML.
2022-11-01 | GSE214158 | GEO
Project description:Acute myeloid leukemias (AML) patients bearing chromosomal rearrangements of KMT2A or MLL gene (KMT2A -r) have poor overall survival. Recently, compounds targeting the KMT2A fusion protein complex, such as DOT1L and Menin inhibitors, have shown promising pre-clinical efficacy. Yet, molecular regulators of the anti-tumor activities of these agents remain poorly studied. UTX is a histone H3K27 demethylase with recurrent loss-of-function mutations in human cancers including leukemia. UTX-null leukemia shows greater resistance to chemotherapy agents. However, the impact of UTX on drug resistance of KMT2A -r AML has not been explored. Through a epigenetic compound screen, we identified a unique role of UTX in the regulation of DOT1L and Menin therapies in KMT2A-r AML. Loss of UTX confers resistance to DOT1L and Menin inhibition in an MLL target gene-independent manner. Mechanistically, We show that UTX is required for activation of myeloid differentiation programs induced by DOT1L inhibition. We also revealed BCL2A1 as a target of UTX. Depletion of UTX increased vulnerability to BCL2 inhibitor venetoclax in vitro and in vivo, and combinational treatment of venetoclax could overcome the therapeutic resistance to DOT1L inhibition caused by UTX loss. Our study provides new insights into the role of UTX in therapeutic responses in KMT2A-r AML.
2022-11-01 | GSE214274 | GEO
Project description:Acute myeloid leukemias (AML) patients bearing chromosomal rearrangements of KMT2A or MLL gene (KMT2A -r) have poor overall survival. Recently, compounds targeting the KMT2A fusion protein complex, such as DOT1L and Menin inhibitors, have shown promising pre-clinical efficacy. Yet, molecular regulators of the anti-tumor activities of these agents remain poorly studied. UTX is a histone H3K27 demethylase with recurrent loss-of-function mutations in human cancers including leukemia. UTX-null leukemia shows greater resistance to chemotherapy agents. However, the impact of UTX on drug resistance of KMT2A -r AML has not been explored. Through a epigenetic compound screen, we identified a unique role of UTX in the regulation of DOT1L and Menin therapies in KMT2A-r AML. Loss of UTX confers resistance to DOT1L and Menin inhibition in an MLL target gene-independent manner. Mechanistically, We show that UTX is required for activation of myeloid differentiation programs induced by DOT1L inhibition. We also revealed BCL2A1 as a target of UTX. Depletion of UTX increased vulnerability to BCL2 inhibitor venetoclax in vitro and in vivo, and combinational treatment of venetoclax could overcome the therapeutic resistance to DOT1L inhibition caused by UTX loss. Our study provides new insights into the role of UTX in therapeutic responses in KMT2A-r AML.
2022-11-01 | GSE214275 | GEO