Lysine-targeting, covalent inhibitors of bromodomain BD1 of BET proteins in live cells and animals
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1194044 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31607354_1.fastq.gz | Fastqsanger.gz | |||
| SRR31607354_2.fastq.gz | Fastqsanger.gz | |||
| SRR31607355_1.fastq.gz | Fastqsanger.gz | |||
| SRR31607355_2.fastq.gz | Fastqsanger.gz | |||
| SRR31607356_1.fastq.gz | Fastqsanger.gz |
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Project description:Bromodomain (BRD) is an epigenetic reader of acetylated lysine. It has emerged as a therapeutic target for cancer and other diseases. Current nonselective BRD inhibitors (BRDis) face several adverse events (i.e. gastrointestinal toxicity and thrombocytopenia), making the development of target covalent inhibitor (TCI) for BD1/2 as a fresh avenue to overcome safety challenges. We report herein a set of activity-based probes (ABPs; P3-P7) based on various lysine-reactive covalent warheads capable of global profiling of ligandable lysine within BRDs in live cells and animals. Chemoproteomic experiments with P7 by utilizing 2-ethynylbenzaldehyde (EBA) identified 16 endogenous BRDs, thus giving a global landscape of ligandable lysines in BRDs. By further introducing EBA and salicylaldehyde into PLX51107 (a non-covalent BRDi), we generated novel irreversible (BDS1-4) and reversible (BDS5-6) lysine-reactive TCIs. Mass spectrometry and X-ray crystallography confirmed the successful covalent engagement between the covalent warhead and lysine near Kac binding site. BDS4 showed 104-fold selectivity for BD1 over BD2 with prolonged anti-cancer effect than non-covalent BRDi. Importantly, BDS4 retained robust activity against fibrosis in cells and animals in comparison to the marginal effect of BD2 inhibitor RVX-208. Our work serves as a useful tool to delineate the distinct function of BD1 and BD2.
2024-12-11 | GSE283487 | GEO
Project description:The evolutionarily conserved BET bromodomain family contain a distinctive tandem bromodomain structure that enables their chromatin binding to facilitate transcription. Whilst first-in-class drugsthat equally inhibit both bromodomains have shown pre-clinicaland clinical efficacy in a range of malignant and inflammatory pathologies, the functional contribution of the first (BD1) and second (BD2) bromodomains to these pathologies remains largely unknown. Here we haveexploited detailedstructuralinsights and our extensivemedicinal chemistry capabilities to develop novel compounds that are exquisitely selectivefor either BD1 or BD2 of the BET proteins. Using thesewell characterised domain-specific inhibitors we show that BD1 is required by all BET proteins to associate with chromatin and maintain established malignant transcriptional programs.Therefore, targeting BD1 alone phenocopies the therapeutic effects of current non-selective BET inhibitorsin models of cancer. Whilst steady state gene expression primarily requires BD1,we find that the rapid increase of gene expression effectedby a wide range of inflammatory stimuli requiresboth BD1 and BD2. Moreover, although BRD4 is the principal member required for the maintenance of established gene expression, efficient gene induction also requires BRD2 and BRD3. Selective inhibition of BD2 is effective in perturbing the recruitment of all the BET proteins for stimulated gene expression and consequently small molecule inhibitors of BD2 amelioratethe immunoinflammatory end organ damage seen in models of inflammatory arthritis, psoriasis and hepatitis. Together,these data provide novel biological and functional insights into this family of key transcriptional regulators. Importantly, they also help refine the future therapeutic approach when targeting the BET proteinsin distinct pathologies such as cancer and immuno-inflammation.
2020-06-17 | GSE138209 | GEO
Project description:The evolutionarily conserved BET bromodomain family contain a distinctive tandem bromodomain structure that enables their chromatin binding to facilitate transcription. Whilst first-in-class drugsthat equally inhibit both bromodomains have shown pre-clinicaland clinical efficacy in a range of malignant and inflammatory pathologies, the functional contribution of the first (BD1) and second (BD2) bromodomains to these pathologies remains largely unknown. Here we haveexploited detailedstructuralinsights and our extensivemedicinal chemistry capabilities to develop novel compounds that are exquisitely selectivefor either BD1 or BD2 of the BET proteins. Using thesewell characterised domain-specific inhibitors we show that BD1 is required by all BET proteins to associate with chromatin and maintain established malignant transcriptional programs.Therefore, targeting BD1 alone phenocopies the therapeutic effects of current non-selective BET inhibitorsin models of cancer. Whilst steady state gene expression primarily requires BD1,we find that the rapid increase of gene expression effectedby a wide range of inflammatory stimuli requiresboth BD1 and BD2. Moreover, although BRD4 is the principal member required for the maintenance of established gene expression, efficient gene induction also requires BRD2 and BRD3. Selective inhibition of BD2 is effective in perturbing the recruitment of all the BET proteins for stimulated gene expression and consequently small molecule inhibitors of BD2 amelioratethe immunoinflammatory end organ damage seen in models of inflammatory arthritis, psoriasis and hepatitis. Together,these data provide novel biological and functional insights into this family of key transcriptional regulators. Importantly, they also help refine the future therapeutic approach when targeting the BET proteinsin distinct pathologies such as cancer and immuno-inflammation.
2020-06-17 | GSE138089 | GEO
Project description:The evolutionarily conserved BET bromodomain family contain a distinctive tandem bromodomain structure that enables their chromatin binding to facilitate transcription. Whilst first-in-class drugsthat equally inhibit both bromodomains have shown pre-clinicaland clinical efficacy in a range of malignant and inflammatory pathologies, the functional contribution of the first (BD1) and second (BD2) bromodomains to these pathologies remains largely unknown. Here we haveexploited detailedstructuralinsights and our extensivemedicinal chemistry capabilities to develop novel compounds that are exquisitely selectivefor either BD1 or BD2 of the BET proteins. Using thesewell characterised domain-specific inhibitors we show that BD1 is required by all BET proteins to associate with chromatin and maintain established malignant transcriptional programs.Therefore, targeting BD1 alone phenocopies the therapeutic effects of current non-selective BET inhibitorsin models of cancer. Whilst steady state gene expression primarily requires BD1,we find that the rapid increase of gene expression effectedby a wide range of inflammatory stimuli requiresboth BD1 and BD2. Moreover, although BRD4 is the principal member required for the maintenance of established gene expression, efficient gene induction also requires BRD2 and BRD3. Selective inhibition of BD2 is effective in perturbing the recruitment of all the BET proteins for stimulated gene expression and consequently small molecule inhibitors of BD2 amelioratethe immunoinflammatory end organ damage seen in models of inflammatory arthritis, psoriasis and hepatitis. Together,these data provide novel biological and functional insights into this family of key transcriptional regulators. Importantly, they also help refine the future therapeutic approach when targeting the BET proteinsin distinct pathologies such as cancer and immuno-inflammation.
2020-06-17 | GSE138084 | GEO
Project description:Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically-defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of MYCN. Genome-wide expression analysis demonstrated downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knock-down phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in three in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma. Significance: Biomarkers of response to small-molecule inhibitors of BET bromodomains, a new compound class with promising anti-cancer activity, have been lacking. Here, we reveal MYCN amplification as a strong genetic predictor of sensitivity to BET bromodomain inhibitors, demonstrate a mechanistic rationale for this finding, and provide a translational framework for clinical trial development of BET bromodomain inhibitors for pediatric patients with MYCN-amplified neuroblastoma. JQ1 is a novel thieno-triazolo-1,4-diazepine, which displaces BET bromodomains from chromatin by competitively binding to the acetyl lysine recognition pocket. BE(2)-C and Kelly cells were treated in triplicate with 1 µM JQ1 or DMSO for 24 hours. RNA was extracted and a decrease in MYCN transcript was confirmed by real time RT-PCR as described above. The samples were profiled using the Affymetrix PrimeView Human Gene Expression Array (Affymetrix) at Beth Israel Deaconess Medical Center (Boston, MA, USA).
2013-02-25 | E-GEOD-43392 | biostudies-arrayexpress
Project description:Bromodomain inhibition comprises a promising therapeutic strategy in cancer, particularly for hematologic malignancies. To date, however, genomic biomarkers to direct clinical translation have been lacking. We conducted a cell-based screen of genetically-defined cancer cell lines using a prototypical inhibitor of BET bromodomains. Integration of genetic features with chemosensitivity data revealed a robust correlation between MYCN amplification and sensitivity to bromodomain inhibition. We characterized the mechanistic and translational significance of this finding in neuroblastoma, a childhood cancer with frequent amplification of MYCN. Genome-wide expression analysis demonstrated downregulation of the MYCN transcriptional program accompanied by suppression of MYCN transcription. Functionally, bromodomain-mediated inhibition of MYCN impaired growth and induced apoptosis in neuroblastoma. BRD4 knock-down phenocopied these effects, establishing BET bromodomains as transcriptional regulators of MYCN. BET inhibition conferred a significant survival advantage in three in vivo neuroblastoma models, providing a compelling rationale for developing BET bromodomain inhibitors in patients with neuroblastoma. Significance: Biomarkers of response to small-molecule inhibitors of BET bromodomains, a new compound class with promising anti-cancer activity, have been lacking. Here, we reveal MYCN amplification as a strong genetic predictor of sensitivity to BET bromodomain inhibitors, demonstrate a mechanistic rationale for this finding, and provide a translational framework for clinical trial development of BET bromodomain inhibitors for pediatric patients with MYCN-amplified neuroblastoma.
2013-02-25 | GSE43392 | GEO
Project description:IL-17-producing T helper (TH17) cells have been selected through evolution for their ability to control fungal and bacterial infections. It is also firmly established that their aberrant generation and activation results in autoimmune conditions. Using a characterized potent and selective small molecule inhibitor, we show that the bromodomain and extra-terminal domain (BET) family of chromatin adaptors plays fundamental and selective roles in human and murine TH17 differentiation from naM-CM-/ve CD4+ T cells, as well as in the activation of previously differentiated TH17 cells. We provide evidence that BET controls TH17 differentiation in a bromodomain-dependent manner through a mechanism that includes the direct regulation of multiple effector TH17-associated cytokines, including IL17, IL21 and GMCSF. We also demonstrate that BET family members Brd2 and Brd4 associate with the Il17 locus in TH17 cells, and that this association requires bromodomains. We recapitulate the critical role of BET bromodomains in TH17 differentiation in vivo and show that therapeutic dosing of the BET inhibitor is efficacious in mouse models of autoimmunity. Our results identify the BET family of proteins as a fundamental link between chromatin signaling and TH17 biology, and support the notion of BET inhibition as a point of therapeutic intervention in autoimmune conditions. 4 samples were analyzed: two conditions in duplicate. Naive T cells were placed in conditions leading to TH17 differentiation, with and without BET inhibitor. RNA was collected at 48 hours.
2013-09-20 | E-GEOD-37270 | biostudies-arrayexpress
Project description:Developmental transitions are guided by master regulatory transcription factors. During adipogenesis, a transcriptional cascade culminates in expression of PPARg and C/EBPa, which orchestrate activation of the adipocyte gene expression program. However, the coactivators controlling PPARg and C/EBPa expression are less well characterized. Here we show the bromodomain-containing protein, BRD4, regulates transcription of PPARg and C/EBPa. Analysis of BRD4 chromatin occupancy reveals that induction of adipogenesis in 3T3L1 fibroblasts provokes dynamic redistribution of BRD4 to de novo super enhancers proximal to genes controlling adipocyte differentiation. BET bromodomain inhibition impedes BRD4 occupancy at these de novo enhancers and disrupts transcription of Pparg and Cebpa, thereby blocking adipogenesis. Furthermore, silencing of these BRD4-occupied distal regulatory elements at the Pparg locus by CRISPRi demonstrates a critical role for these enhancers in the control of Pparg gene expression and adipogenesis in 3T3L1s. Together, these data establish BET bromodomain proteins as time- and context-dependent coactivators of the adipocyte cell state transition.
2018-03-07 | GSE109940 | GEO
Project description:Neural stem cells (NSCs) and progenitor cells (NPCs) are increasingly appreciated to hold great promise for regenerative medicine to treat CNS injuries and neurodegenerative diseases. However, evidence for effective stimulation of neuronal production from endogenous or transplanted NPCs for cell replacement with small molecules remains limited. To identify novel chemical entities/targets for neurogenesis, we had established a NPC phenotypic screen assay and validated it using known small-molecule neurogenesis inducers. Through screening small molecule libraries with annotated targets, we identified BET bromodomain inhibition as a novel mechanism for enhancing neurogenesis. BET bromodomain proteins, Brd2, Brd3, and Brd4 were found to be downregulated in NPCs upon differentiation, while their levels remain unaltered in proliferating NPCs. Consistent with the pharmacological study using bromodomain selective inhibitor (+)-JQ-1, knockdown of each BET protein resulted in an increase in the number of neurons with simultaneous reduction in both astrocytes and oligodendrocytes. Gene expression profiling analysis demonstrated that BET bromodomain inhibition induced a broad but specific transcription program enhancing directed differentiation of NPCs into neurons while suppressing cell cycle progression and gliogenesis. Together, these results highlight a crucial role of BET proteins as promising epigenetic regulators in NPC development and suggest a therapeutic potential of BET inhibitors in treating CNS injury and neurodegenerative diseases. NPCs were treated with (+)-JQ-1 or inactive enantiomer (-)-JQ-1 at 0.2 μM or 0.5 μM for 12 and 24 hrs in differentiation medium. The experiments were carried out in 3 independent preparations of NPCs (triplicates)
2016-07-24 | E-GEOD-77988 | biostudies-arrayexpress