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A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [1]

ABSTRACT: In order to establish a strict p53-dependent gene expression profile, p53 negative clones were derived from two TP53+/+ and two TP53-/mut t(4;14) human myeloma cell lines (HMCLs) using CRISPR/Cas9 technology. From the 17 dysregulated genes shared between the 6 clones from the two TP53+/+ myeloma cell lines, we established a 13-gene functional p53 score, involving genes downregulated on p53-silencing. This functional score allowed us to segregate clones, myeloma cell lines and patients’ samples according to the presence or absence of a single or double hit in TP53 gene i.e., chromosomal deletion and/or mutation. The score also distinguished 1,162 cell lines from hematological and solid cancers according to hits in TP53. Moreover, the 13-gene score was predictive of overall survival in two independent cohorts of patients. Among the 13 genes, we showed that p53-regulated BAX expression correlated to, and directly impacted, the MCL1 BH3 mimetic S63845 sensitivity of myeloma cells by modulating the amount of MCL1-BAX complexes. Resistance to cell death induced by p53-silencing was overcome by combining S63845 with venetoclax, although the synergy was significantly lower in p53-deficient versus -proficient clones and patients’ samples. Finally, by using scRNAseq analysis, we further showed in patients’ bone marrow samples that myeloma cells surviving to the BH3 mimetic combination had an about 3-fold lower p53 score. This data established a functional p53 score and showed that p53-mediating BAX expression greatly impacts mitochondria-mediated cell death in myeloma cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE245049 | GEO | 2024/04/04

REPOSITORIES: GEO

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A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [2]

Project description:In order to establish a strict p53-dependent gene expression profile, p53 negative clones were derived from two TP53+/+ and two TP53-/mut t(4;14) human myeloma cell lines (HMCLs) using CRISPR/Cas9 technology. From the 17 dysregulated genes shared between the 6 clones from the two TP53+/+ myeloma cell lines, we established a 13-gene functional p53 score, involving genes downregulated on p53-silencing. This functional score allowed us to segregate clones, myeloma cell lines and patients’ samples according to the presence or absence of a single or double hit in TP53 gene i.e., chromosomal deletion and/or mutation. The score also distinguished 1,162 cell lines from hematological and solid cancers according to hits in TP53. Moreover, the 13-gene score was predictive of overall survival in two independent cohorts of patients. Among the 13 genes, we showed that p53-regulated BAX expression correlated to, and directly impacted, the MCL1 BH3 mimetic S63845 sensitivity of myeloma cells by modulating the amount of MCL1-BAX complexes. Resistance to cell death induced by p53-silencing was overcome by combining S63845 with venetoclax, although the synergy was significantly lower in p53-deficient versus -proficient clones and patients’ samples. Finally, by using scRNAseq analysis, we further showed in patients’ bone marrow samples that myeloma cells surviving to the BH3 mimetic combination had an about 3-fold lower p53 score. This data established a functional p53 score and showed that p53-mediating BAX expression greatly impacts mitochondria-mediated cell death in myeloma cells.

2024-04-04 | GSE245162 | GEO

Putting the STING back into BH3-mimetic drugs for TP53 mutant blood cancers

Project description:TP53-mutant blood cancers remain a major clinical challenge. BH3-mimetic drugs inhibit BCL-2 pro-survival proteins to promote cancer cell apoptosis. Despite acting downstream of TP53, functional TP53 is required for maximal cancer cell killing by BH3-mimetics through an unknown mechanism. Here, we report TP53 can be activated following BH3-mimetic induced mitochondrial outer membrane permeabilization, which leads to induction of BH3-only proteins, thereby potentiating the pro-apoptotic signal. TP53-deficient lymphomas lack this feed-forward loop, providing opportunities for survival and disease relapse after BH3-mimetic treatment. The therapeutic barrier imposed by defects in TP53 could be overcome by direct activation of the cGAS/STING pathway, which promotes apoptosis of blood cancer cells through TP53-independent BH3-only protein upregulation. Combining clinically relevant STING agonists with BH3-mimetics efficiently killed TP53-mutant mouse B lymphoma, human NK/T lymphoma and acute myeloid leukemia cells. This represents a promising therapy regime that can be fast-tracked to tackle TP53-mutant blood cancers in the clinic.

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Transcriptomic changes in SUDHL6 cells upon treatment with S63845 in the presence or abscence of active caspases

Project description:We identified a novel form of caspase-independent cell death (CICD) induced by BH3-mimetics. To characterize the transcriptional changes during CICD and compare these to apoptotic changes, we performed RNA Seq analysis on SUDHL6 lymphoma cells treated with the MCL1 inhibitor S63845 in the presence or abscence of the broad spectrum caspase inhibitor zVAD.fmk.

2024-04-24 | GSE263183 | GEO

A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response

Project description:A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response

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THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors

Project description:Peripheral T-cell lymphomas (PTCL) are aggressive diseases with poor response to chemotherapy and dismal survival. Identification of effective strategies to target PTCL biology represents an urgent need. Here we report that PTCL are sensitive to transcription-targeting drugs, and, in particular, to THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7). The STAT-signaling pathway is highly vulnerable to THZ1 even in PTCL cells that carry the activating STAT3 mutation Y640F. In mutant cells, CDK7 inhibition decreases STAT3 chromatin binding and expression of highly transcribed target genes like MYC, PIM1, MCL1, CD30, IL2RA, CDC25A and IL4R. In surviving cells, THZ1 decreases the expression of STAT-regulated anti-apoptotic BH3 family members MCL1 and BCL-XL sensitizing PTCL cells to BH3 mimetic drugs. Accordingly, the combination of THZ1 and the BH3 mimetic obatoclax improves lymphoma growth control in a primary PTCL ex vivo culture and in two STAT3-mutant PTCL xenografts, delineating a potential targeted agent-based therapeutic option for these patients.

2016-12-15 | GSE79955 | GEO

A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [1]

Project description:A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [1]

| PRJNA1026858 | ENA

A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [2]

Project description:A p53 score derived from TP53 CRISPR/Cas9 HMCLs predicts survival and reveals major role of BAX in BH3 mimetics response [2]

| PRJNA1027285 | ENA

MCL1 inhibitor induces apoptosis in Anaplastic Large Cell Lymphoma and in Primary Effusion Lymphoma

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

Comprehensive profiling and targeting of BCL-2 family members in nasopharyngeal carcinoma

Project description:Nasopharyngeal carcinoma (NPC) is among a small number of solid tumors that are caused by the Epstein-Barr virus (EBV). Recently, BH3 mimetics, a novel class of drugs that inhibit pro-survival proteins of the BCL-2 family, have demonstrated clinical anti-cancer efficacy in hematological malignancies and are being investigated for use in solid tumors. There is known dysregulation of pro-survival pathways, particularly, the intrinsic apoptotic pathway during EBV infection of B cells suggesting NPC may be driven by the same pathways, and thus sensitive to BH3 inhibition. Using immunohistochemistry, we examined the expression of BCL-2 family of proteins (BCL2, MCL1 and BCLxL) in 174 NPC from patients treated with curative intent as well as five NPC cell lines. We subsequently evaluated the anti-tumor efficacy of three BH3 mimetics (ABT-199, ABT-737 and S63845) in NPC cells alone or in combination with cisplatin, a commonly used cytotoxic agent in NPC treatment. BCL-2 was highly expressed in NPC tumors and cells. Despite this, BCL2 inhibition, or BH3 monotherapy was not effective. However, marked sensitivity was observed with the combination S63845 (targeting MCL-1) and cisplatin in NPC43, which had high expression of MCL-1. This combination resulted in upregulation of pro-apoptotic tBID suggesting a priming role of cisplatin and apoptotic potentiation through MCL-1 inhibition. Flow cytometry studies and RNA sequencing of NPC43 cells treated with the combination of cisplatin with S63845 and untreated cells showed death by apoptosis and upregulation in stress response and DNA damage pathways. Our study suggests that combining BH3 mimetics with cisplatin could be an effective treatment strategy for NPC and warrants further investigation

2024-10-01 | GSE235574 | GEO

RNA-seq of S63845 sensitive and resistant myeloma cell lines.

Project description:We performed RNA-seq analysis of in-house generated S63845 sensitive and resistant myeloma cell lines OPM-2 and KMS-12-BM in order to define common events in the acquisition of MCL-1 inhibitor resistance. Our results, however, point to the occurrence of cell line specific, heterogeneous paths to resistance as no common differences were observed. Subsequent experiments rather revealed that the binding kinetics of BH3 family members are a major driver of MCL-1 inhibitor resistance and that individual shifts during the establishment of resistance dependent on the baseline BH3 family profile.

2021-06-05 | GSE176137 | GEO

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