Bromodomain And Extraterminal Motif Proteins Research Articles

Abstract C109: INTASYL™ PH-894 self-delivering RNAi targeting BRD4 enhances the antigenicity of melanoma cells through MART-1 upregulation

Abstract Background: BRD4 is a member of the family of bromodomain and extra-terminal motif (BET) proteins that act as epigenetic readers and regulators of gene transcription. BRD4 has been shown to be significantly upregulated in cancer including melanoma, with preclinical data supporting BRD4 inhibition as a promising therapeutic target. However, clinical translation of BRD4 inhibitors (BRD4i) has remained elusive. Current small molecule inhibitors of BET proteins are not specific to BRD4 as demonstrated by their inhibition of other members of the BET protein family. Additionally, systemic approaches must overcome a narrow therapeutic window. The INTASYL™ platform is a self-delivering RNAi technology that imparts small molecule-like properties to interfering RNAs, providing efficient delivery to target cells without need for specialized formulations or drug delivery systems. PH-894 is an INTASYL compound that silences BRD4 mRNA. PH-894 has been shown to specifically silence BRD4 mRNA and provide robust direct and abscopal antitumor efficacy in vivo when administered intratumorally (IT). Therefore, IT PH-894 holds promise to realize the therapeutic potential of BRD4 inhibition by avoiding toxicities associated with systemic delivery of small molecule BET inhibitors. Here, we explored the impact of PH-894 mediated BRD4 inhibition on antigenicity of melanoma tumor cells. Specifically, expression of the melanoma tumor-associated antigen MART-1 was studied following PH-894 treatment. Methods: SK-MEL-5 melanoma cells were treated for 72 hours with PH-894 or a non-targeting control (NTC) INTASYL compound. After 72 hours (Day 3), PH-894 was washed out and cells were replated in media containing no INTAYSL compound for the duration of the experiment. Cells were collected for analysis of both BRD4 and MART-1 mRNA and protein from Day 3 through Day 7. Results: PH-894 provided robust silencing of BRD4 mRNA and protein in SK-MEL-5 melanoma cells. Furthermore, PH-894 treatment resulted in a statistically significant upregulation of MART-1 mRNA and protein in these cells. BRD4 silencing and MART-1 upregulation persisted through at least 7 days post-treatment with PH-894. Conclusions: This study demonstrates the ability of PH-894 to efficiently silence BRD4 and upregulate MART-1, thereby increasing the antigenicity of melanoma cells. Local treatment with PH-894 is a potential strategy to decrease BRD4 expression and increase immune response to cancer cells while reducing toxicities associated with systemic BETi. This study supports further development of PH-894 for injectable solid tumor indications such as melanoma. Citation Format: Brianna Rivest, Melissa Maxwell, Andrew Boone, Benjamin Cuiffo, Dingxue Yan, James Cardia. INTASYL™ PH-894 self-delivering RNAi targeting BRD4 enhances the antigenicity of melanoma cells through MART-1 upregulation [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr C109.

Streamlined DNA-encoded small molecule library screening and validation for the discovery of novel chemotypes targeting BET proteins

Targeting aberrant epigenetic programs that drive tumorigenesis is a promising approach to cancer therapy. DNA-encoded library (DEL) screening is a core platform technology increasingly used to identify drugs that bind to protein targets. Here, we use DEL screening against bromodomain and extra-terminal motif (BET) proteins to identify inhibitors with new chemotypes, and successfully identified BBC1115 as a selective BET inhibitor. While BBC1115 does not structurally resemble OTX-015, a clinically active pan-BET inhibitor, our intensive biological characterization revealed that BBC1115 binds to BET proteins, including BRD4, and suppresses aberrant cell fate programs. Phenotypically, BBC1115-mediated BET inhibition impaired proliferation in acute myeloid leukemia, pancreatic, colorectal, and ovarian cancer cells invitro. Moreover, intravenous administration of BBC1115 inhibited subcutaneous tumor xenograft growth with minimal toxicity and favorable pharmacokinetic properties invivo. Since epigenetic regulations are ubiquitously distributed across normal and malignant cells, it will be critical to evaluate if BBC1115 affects normal cell function. Nonetheless, our study shows integrating DEL-based small-molecule compound screening and multi-step biological validation represents a reliable strategy to discover new chemotypes with selectivity, efficacy, and safety profiles for targeting proteins involved in epigenetic regulation in human malignancies.

Reset of Inflammatory Priming of Joint Tissue and Reduction of the Severity of Arthritis Flares by Bromodomain Inhibition.

We have recently shown that priming of synovial fibroblasts (SFs) drives arthritis flares. Pathogenic priming of SFs is essentially mediated by epigenetic reprogramming. Bromodomain and extraterminal motif (BET) proteins translate epigenetic changes into transcription. Here, we used a BET inhibitor (I-BET151) to target inflammatory tissue priming and to reduce flare severity in a murine experimental arthritis model. BALB/c mice were treated by intraperitoneal injection or by local injection in the paw with I-BET151, which blocks the interaction of BET proteins with acetylated histones. We assessed the effects of I-BET151 on acute arthritis and/or inflammatory tissue priming in a model of repeated injections of monosodium urate crystals or zymosan into the mouse paw. I-BET151 was given before arthritis induction, at peak inflammation, or after healing of the first arthritis bout. We performed transcriptomic (RNA-Seq), epigenomic (ATAC-Seq), and functional (invasion, cytokine production, migration, senescence, metabolic flux) analyses of murine and human SFs treated with I-BET151 in vitro or in vivo. Systemic I-BET151 administration did not affect acute inflammation but abolished inflammatory tissue priming and diminished flare severity in both preventive and therapeutic treatment settings. I-BET151 was also effective when applied locally in the joint. BET inhibition also inhibited osteoclast differentiation, while macrophage activation in the joint was not affected. Flare reduction after BET inhibition was mediated, at least in part, by rolling back the primed transcriptional, metabolic, and pathogenic phenotype of SFs. Inflammatory tissue priming is dependent on transcriptional regulation by BET proteins, making them promising therapeutic targets for prevention of arthritis flares in previously affected joints.

NUT Carcinoma-An Underdiagnosed Malignancy.

NUT carcinoma (NC) is a rare and highly aggressive malignancy with a dismal prognosis and a median survival of 6–9 months only. Although very few cases of NC are reported each year, the true prevalence is estimated to be much higher, with NC potentially widely underdiagnosed due to the lack of awareness. NC primarily occurs in midline structures including thorax, head, and neck; however, other sites such as pancreas and kidney are also affected, albeit at lower frequencies. NC is characterized by a single translocation involving the NUTM1 (NUT midline carcinoma family member 1) gene and different partner genes. The resulting fusion proteins initiate tumorigenesis through a mechanism involving BET (bromo-domain and extra-terminal motif) proteins such as Bromodomain-containing protein 4 (BRD4) and inordinate acetylation of chromatin, leading to the dysregulation of growth and differentiation genes. While no clinical characteristics are specific for NC, some histologic features can be indicative; therefore, patients with these tumor characteristics should be routinely tested for NUTM1. The diagnosis of NC using immunohistochemistry with a highly specific antibody is straightforward. There are currently no standard-of-care treatment options for patients with NC. However, novel therapies specifically addressing the unique tumorigenic mechanism are under investigation, including BET inhibitors. This review aims to raise awareness of this underdiagnosed cancer entity and provide all patients the opportunity to be properly diagnosed and referred to a clinical study.

Exploiting Transcription-Replication Conflicts As a Novel Therapeutic Intervention in Multiple Myeloma

Multiple myeloma (MM) is the second most frequent hematological malignancy, characterized by the accumulation of malignant plasma cells (PCs) within the bone marrow. To date, there is no definitive treatment for this pathology and a majority of patients will invariably relapse. Antibody secretion, the key biological function of PCs, is maintained in malignant PCs meaning that these cells display an elevated transcriptional stress. Besides, malignant PCs face oncogene-induced replication stress concomitantly with cell cycle deregulation. Consequently, transcription and replication in malignant PCs need to be tightly coordinated to avoid too much interferences that would increase replication stress and genomic instability. A failure to cope with these transcription/replication conflicts (TRCs) could have a significant impact on mutagenesis involved in MM development. Importantly, these effects might open the therapeutic possibility of TRCs enhancement to specifically kill malignant PCs.Based on these observations, we identified a signature of 13 TRCs resolution factors significantly overexpressed in MM patients. Considering the potent role of TRCs resolution in MM cell adaptation to replication stress, we sought to identify the TRCs resolution factors that are associated with a poor outcome in MM. High expression of 9 out of the 13 TRCs resolution factors significantly overexpressed in malignant PCs are associated with a poor outcome in MM (TT2 cohort, n = 345). We gathered the prognostic value of these 9 genes within a Gene Expression Profile (GEP)-based TRC resolution score (TRC score). High TRC score is associated with a poor outcome in two independent cohorts of newly diagnosed MM patients treated by high dose therapy and autologous stem cell transplantation (Arkansas, TT2 cohort, n = 345; CoMMpass cohort, n = 674) (Fig.1A). Interestingly, we investigated the link between the TRC score and the MM cells drug response using our collection of human myeloma cell lines (HMCLs), and identified that HMCLs with high TRC score values are significantly more sensitive to Panobinostat histone deacetylase inhibitor, currently used in MM treatment at relapse (n = 11, p value < 0.05). Histone acetylation has been shown to promote R-loop formation that constitutes obstacles to replication fork progression. Using primary MM cells from patients (n = 12) co-cultured with their bone marrow microenvironment, we found that a high TRC score value is associated with a higher toxicity of Panobinostat (p value < 0.01). Therefore, the TRC score allows the identification of a MM patients subgroup with a poor outcome that could benefit from Panobinostat treatment.Interestingly, TRCs are promoted by R-loop formation and G-quadruplex (G4) stabilizers treatment. R-loops are formed by the reannealing of the nascent RNA with the template DNA (called an RNA:DNA hybrid). G4s are four-stranded secondary DNA structures, constituted of stacked guanine tetrads. Both structures are formed during transcription in G-rich DNA regions and can represent a barrier for replication fork progression if unscheduled. G4s can stabilize R-loops which have been shown to mediate DNA damage induced by G4 stabilizers. Interestingly, treatment with the G4 stabilizer Pyridostatin (PDS) was associated with significant toxicity on HMCLs (n = 15) (Fig.1B), and on primary MM cells of patients cocultured with their bone marrow microenvironment (n = 5, p value < 0.05). Interestingly, the combination of PDS and Panobinostat has a synergistic effect in HMCLs. We also found a correlation between HMCLs TRC score and the response to two Bromodomain and Extra-Terminal motif (BET) proteins inhibitors, I-BET-762 and RVX-208. The synergistic effect of PDS combination with I-BET-762 was validated in vitro. BET proteins inhibition has been shown to increase R-loop formation and DNA damage. Furthermore, we used inducible RNase H expression in HMCLs to specifically degrade RNA:DNA hybrids. RNase H expression resulted in a significant reduction of DNA damage response after PDS treatment (Fig.1C). Our results underline that spontaneous replication stress and genomic instability are related to R-loop formation and TRCs in MM cells.Altogether, these results emphasize the therapeutic potential of TRCs targeting in MM using G4 stabilizers alone or in combination with current treatments. [Display omitted] DisclosuresVincent: Janssen: Membership on an entity's Board of Directors or advisory committees; Celgene: Membership on an entity's Board of Directors or advisory committees; Takeda: Membership on an entity's Board of Directors or advisory committees. Cartron: Roche, Celgene-BMS: Consultancy; Danofi, Gilead, Novartis, Jansen, Roche, Celgene-BMS, Abbvie, Takeda: Honoraria. Herbaux: Roche: Honoraria; Janssen: Honoraria; Takeda: Honoraria, Research Funding; Abbvie: Honoraria, Research Funding. Moreaux: Diag2Tec: Consultancy.

CG223, a novel BET inhibitor, exerts TGF-β1-mediated antifibrotic effects in a murine model of bleomycin-induced pulmonary fibrosis

Pulmonary fibrosis is a progressive disease with poor prognosis and limited therapeutic options. In this study, we evaluated the potential therapeutic effects of CG223, a novel inhibitor of bromodomain and extra-terminal motif (BET) proteins, on pulmonary fibrosis by focusing on the transforming growth factor-β1 (TGF-β1) pathway. In a murine model of bleomycin-induced pulmonary fibrosis, CG223 attenuated fibrosis while reducing the infiltration of inflammatory cells into the lungs. Fibroblasts expressing BRD4, a member of the BET protein family, were enriched in the tissue regions corresponding to bleomycin-induced fibrotic lesions. Additionally, pulmonary fibroblasts isolated from bleomycin-instilled mice showed a significantly increased association of BRD4 with the promoters of two pro-fibrotic genes linked to the entry into the TGF-β1 autocrine/paracrine loop, thrombospondin 1 (Thbs1) and integrin β3 (Itgb3), as well as with the promoter of a myofibroblast marker gene, actin alpha 2 (Acta2). Subsequent in vitro studies with murine primary lung fibroblasts showed that the mRNA induction of Thbs1, Itgb3, and Acta2 by TGF-β1 can be inhibited by CG223 in a dose-dependent manner. Taken together, CG223-induced BRD4 inhibition suppressed lung fibrogenesis by affecting multiple genes, including those involved in the triggering of the TGF-β1 autocrine/paracrine loop.

The Clinical BET Inhibitor, GS-5829, Is Active Against Chronic Lymphocytic Leukemia As Single Agent and in Combination with B-Cell Receptor Signaling Inhibitors

The Clinical BET Inhibitor, GS-5829, Is Active Against Chronic Lymphocytic Leukemia As Single Agent and in Combination with B-Cell Receptor Signaling Inhibitors

A quinazoline-based bromodomain inhibitor, CN210, ameliorates indomethacin-induced ileitis in mice by inhibiting inflammatory cytokine expression.

Inhibitors of bromodomain and extra-terminal motif (BET) proteins are emerging epigenetic therapeutics that suppress gene expressions that drive cancer and inflammation. The present study examined anti-inflammatory effects of a quinazoline-based BET inhibitor, CN210, in a murine ileitis model. CN210 was given orally 30 min before and 24 h after a subcutaneous administration of indomethacin. Macroscopic and histological evidences of ileitis, mucosal myeloperoxidase (MPO) activity and cytokine expressions were evaluated 48 h after the indomethacin administration. To further characterize the anti-inflammatory pathways modulated by CN210, its effects on RAW264 cells treated with lipopolysaccharide (LPS) were investigated. Competitive ligand binding and docking studies of CN210 to CREB-binding protein (CBP) and p300 were also performed. Oral administration of CN210 significantly reduced the severity of ileitis, normalized both proinflammatory MPO activity and concomitant cytokine expressions induced by indomethacin administration. Furthermore, CN210 attenuated the expression of cytokines and reversed the activation of nuclear factor κB (NF-κB) and mitogen-activated protein kinases (MAPK) induced by LPS. Competitive ligand binding assays showed that CN210 bound to the bromodomains of two paralogous histone acetyltransferases, CBP and p300, in addition to the bromodomains of BET proteins. Docking studies of CN210 to the bromodomains of CBP and p300 showed a similarity to the binding mode of SGC-CBP30, a specific CBP/p300 inhibitor. CN210 ameliorates indomethacin-induced ileitis by inhibiting the expression of inflammatory cytokines through the attenuation of NF-κB and MAPK pathways. CN210 thus represents a new mode of therapy for non-steroidal anti-inflammatory drug-induced ileitis and inflammatory bowel disease.

INTASYL self-delivering RNAi therapy specifically dual-targeting BRD4 and PD-1 to elicit complete tumor responses and evidence of synergy in a subcutaneous Hepa1-6 model of murine hepatoma in C57BL/6N mice.

e14537 Background: The therapeutic potential of targeting bromodomain and extra-terminal motif (BET) protein BRD4 is supported by promising preclinical data in multiple cancer contexts. However, clinical trials of BET inhibitors (BETi) have overall shown limited clinical efficacy and only passable safety profiles as monotherapy. BET proteins are now also understood to control a wide range of immunoregulatory pathways. Preclinical data suggests a synergistic impact with immune checkpoint blockade (ICB) targeting PD-1. Trials assessing the potential of BETi in rational combination with ICB are underway. The INTASYL platform is a self-delivering RNAi technology enabling efficient delivery into target cells without need for specialized drug delivery systems. INTASYL provides specific, robust, and durable on-target gene silencing. Furthermore, INTASYL moieties targeting multiple specific targets can be formulated together, providing a highly versatile platform for providing multi-targeted combination therapy in a single drug substance. Methods: Here we assessed the efficacy of mouse/human BRD4-targeting INTASYL PH-894 as monotherapy or co-formulated with mouse PD-1 targeting INTASYL mPH-762, in treating a subcutaneous Hepa1-6 model of murine hepatoma in C57BL/6N mice. On-target, specific silencing of BRD4 and PD-1 was demonstrated in vitro. In vivo, mice bearing tumors of ̃150 mm3 (N = 12/arm) were treated intratumorally on Days 1, 3, 7, 10 &amp; 14 with of PH-894 or mPH-762 as single-agent, or PH-894/mPH-762 in combination at sub-optimal doses (0.1 mg/INTASYL/dose), or with PH-894/mPH-762 at half-suboptimal dose (0.05mg/INTASYL/dose) to assess potential synergistic impacts. Positive control groups received systemic (IP) (+)-JQ-1 (13.33mg/dose; qdx5), anti-mouse PD-1 antibody (75 µg; Days 1, 3, 7, 10, 14), or both treatments. Negative control animals received vehicle only. Tumor volumes and body weights were recorded longitudinally. Results: Compared to vehicle, suboptimal (+)-JQ-1, anti-PD-1, PH-894 or mPH-762 each elicited tumor control but not resolution as expected; while treatment with suboptimal PH-894/mPH-762 combo produced complete response (CR) in 75% (9/12) mice, outperforming combination treatment with (+)-JQ-1 and anti-PD-1 mAb [CR 58% (7/12) of mice]. Treatment with half-suboptimal doses of PH-894/mPH-762 resulted in CR for 42% (5/12) mice and tumor control exceeding that elicited by each monotherapy, suggesting potential synergy of the dual-targeting formulation. Tumors were isolated for mechanistic analyses of immune and tumor cells. Conclusions: These data demonstrate proof-of-concept of the therapeutic potential of rational dual-targeted INTASYL provided as single formulation in vivo, suggesting potential for meaningful clinical therapeutic impact.

BET inhibitors repress expression of interferon-stimulated genes and synergize with HDAC inhibitors in glioblastoma.

BackgroundThe development of rational combination therapies is key to overcome inherent treatment resistance of glioblastoma (GBM). We aim at identifying new druggable targets by disturbing GBM cells with inhibitors of bromodomain and extra-terminal motif (BET) proteins to reveal cancer-relevant vulnerabilities that may sensitize to a second drug. BET proteins are epigenetic modulators and have been associated with proto-oncogene overexpression in cancer.MethodsA GBM-derived sphere-line was treated with the BET inhibitor (BETi) JQ1 over a time-course of 48 hours, followed by RNA-sequencing. Four chromatin marks were investigated by chromatin immunoprecipitation followed by sequencing (ChIP-seq). Signatures of interest were functionally validated in vitro and in orthotopic xenografts. Combination therapies were evaluated for synergistic effects.ResultsCancer-relevant pathways significantly modulated by JQ1 comprised interferon alpha (IFN-α) response genes and response signatures to histone deacetylase inhibitors (HDACi). The IFN-signature was reminiscent of a GBM-derived IFN-signature comprising CD274 (PD-L1). Functional pathway analysis suggested that JQ1 was acting directly on the transcriptional level of IFN-response genes and not via the canonical JAK/STAT pathway. This was in line with JQ1 modulated expression and BRD4 and Pol II occupancy at IFN-signature genes, supporting a direct mechanistic interaction. Finally, we showed that combining HDACi with JQ1 acts synergistically in reducing cell viability of GS-lines.ConclusionsOur approach identified BETi-induced vulnerabilities in cancer-relevant pathways, potentially amenable to synergistic combinatorial therapy, such as combination with HDACi. The direct inhibitory effect of BETi on IFN-responsive genes in GBM cells, including CD274, indicates modulation of the tumor immune landscape and warrants further studies.

77232 The role of the bromodomain and extra-terminal motif (BET) family of proteins in head and neck cancer tumorigenic phenotype

ABSTRACT IMPACT: Understanding the biology underpinning head and neck cancer invasion and metastasis could lead to novel targeted therapies that are both effective and tolerable for patients with this debilitating disease. OBJECTIVES/GOALS: The bromodomain and extra-terminal (BET) family of epigenetic regulators has been implicated in the tumorigenesis of various cancers. In head and neck squamous cell carcinoma (HNSCC), the majority of morbidity is due to invasion and metastasis, so there is special interest in understanding the development of these phenotypes in HNSCC cells. METHODS/STUDY POPULATION: Stable SCC9 knockdown cell lines were generated by infecting cells with a lentivirus encoding Cas9-KRAB and a lentivirus encoding gRNA targeting each of the candidate BET proteins: BRD2, BRD3, BRD4, and BRDT. Knockdown was confirmed by qRT-PCR. Next, standard assays for proliferation (CellTiter-glo), invasion (Matrigel), and migration (scratch-wound healing assay) were performed for all candidate knockdowns and compared to a non-target control. RESULTS/ANTICIPATED RESULTS: Proliferation assay results revealed that BRD4 knockdown had a significant negative effect on the proliferative capacity of SCC9 cells in vitro. Similarly, BRD4 knockdown SCC9 cell lines were less invasive and less migratory. Interestingly, knockdown of BRD2, BRD3, and BRDT had no effect on proliferation, invasiveness, or migration. DISCUSSION/SIGNIFICANCE OF FINDINGS: We have identified BRD4 as a key driver of the HNSCC tumorigenic phenotype. In the future, we plan to investigate the role of JQ1, a pan-BET inhibitor, on HNSCC cell phenotypes. Additionally, we will identify the downstream targets of BRD4, which may serve as potential therapeutic targets for both HNSCC as well as other cancers more broadly.

Comparative structure-function analysis of bromodomain and extraterminal motif (BET) proteins in a gene-complementation system

The widely expressed bromodomain and extraterminal motif (BET) proteins bromodomain-containing protein 2 (BRD2), BRD3, and BRD4 are multifunctional transcriptional regulators that bind acetylated chromatin via their conserved tandem bromodomains. Small molecules that target BET bromodomains are being tested for various diseases but typically do not discern between BET family members. Genomic distributions and protein partners of BET proteins have been described, but the basis for differences in BET protein function within a given lineage remains unclear. By establishing a gene knockout-rescue system in a Brd2-null erythroblast cell line, here we compared a series of mutant and chimeric BET proteins for their ability to modulate cell growth, differentiation, and gene expression. We found that the BET N-terminal halves bearing the bromodomains convey marked differences in protein stability but do not account for specificity in BET protein function. Instead, when BET proteins were expressed at comparable levels, their specificity was largely determined by the C-terminal half. Remarkably, a chimeric BET protein comprising the N-terminal half of the structurally similar short BRD4 isoform (BRD4S) and the C-terminal half of BRD2 functioned similarly to intact BRD2. We traced part of the BRD2-specific activity to a previously uncharacterized short segment predicted to harbor a coiled-coil (CC) domain. Deleting the CC segment impaired BRD2's ability to restore growth and differentiation, and the CC region functioned in conjunction with the adjacent ET domain to impart BRD2-like activity onto BRD4S. In summary, our results identify distinct BET protein domains that regulate protein turnover and biological activities.

Targeting bromodomain-containing proteins to prevent spontaneous preterm birth.

Preterm birth is a global healthcare challenge. Spontaneous preterm birth (sPTB) is commonly caused by inflammation, yet there are currently no effective therapies available. The Bromodomain and Extra-Terminal motif (BET) proteins, Bromodomain-containing protein (Brd) 2 (Brd2), Brd3 and Brd4 regulate inflammation in non-gestational tissues. The roles of Brd2-4 in human pregnancy are unknown. Using human and mouse models, the present study has identified the Brd proteins part of the process by which inflammation induces parturition. Using human clinical samples, we demonstrate that labor and infection increase the expression of Brds in the uterus and fetal membranes. In primary human myometrial, amnion and decidual cells, we found that global Brd protein inhibition, as well as selective inhibition of Brds, suppressed inflammation-induced expression of mediators involved in myometrial contractions and rupture of fetal membranes. Importantly, studies in the mouse model demonstrate that the pan-Brd inhibitor JQ1 reduced intrauterine inflammation induced by bacterial endotoxin LPS as well as decreasing the effectiveness of LPS to induce parturition. These results implicate BET proteins as novel therapeutic targets for reducing inflammation associated with spontaneous preterm labor.

TNF-induced inflammatory genes escape repression in fibroblast-like synoviocytes: transcriptomic and epigenomic analysis

ObjectiveWe investigated genome-wide changes in gene expression and chromatin remodelling induced by tumour necrosis factor (TNF) in fibroblast-like synoviocytes (FLS) and macrophages to better understand the contribution of FLS to...

BET Inhibition Improves NASH and Liver Fibrosis

Non-alcoholic fatty liver disease (NAFLD) is a leading form of chronic liver disease with large unmet need. Non-alcoholic steatohepatitis (NASH), a progressive variant of NAFLD, can lead to fibrosis, cirrhosis, and hepatocellular carcinoma. To identify potential new therapeutics for NASH, we used a computational approach based on Connectivity Map (CMAP) analysis, which pointed us to bromodomain and extra-terminal motif (BET) inhibitors for treating NASH. To experimentally validate this hypothesis, we tested a small-molecule inhibitor of the BET family of proteins, GSK1210151A (I-BET151), in the STAM mouse NASH model at two different dosing timepoints (onset of NASH and progression to fibrosis). I-BET151 decreased the non-alcoholic fatty liver disease activity score (NAS), a clinical endpoint for assessing the severity of NASH, as well as progression of liver fibrosis and interferon-γ expression. Transcriptional characterization of these mice through RNA-sequencing was consistent with predictions from the CMAP analysis of a human NASH signature and pointed to alterations in molecular mechanisms related to interferon signaling and cholesterol biosynthesis, as well as reversal of gene expression patterns linked to fibrotic markers. Altogether, these results suggest that inhibition of BET proteins may present a novel therapeutic opportunity in the treatment of NASH and liver fibrosis.

Highlights from Recent Cancer Literature

Highlights from Recent Cancer Literature

The BET Protein BRD2 Cooperates with CTCF to Enforce Transcriptional and Architectural Boundaries

Bromodomain and extraterminal motif (BET) proteins are pharmacologic targets for the treatment of diverse diseases, yet the roles of individual BET family members remain unclear. We find that BRD2, but not BRD4, co-localizes with the architectural/insulator protein CCCTC-binding factor (CTCF) genome-wide. CTCF recruits BRD2 to co-bound sites whereas BRD2 is dispensable for CTCF occupancy. Disruption of a CTCF/BRD2-occupied element positioned between two unrelated genes enables regulatory influence to spread from one gene to another, suggesting that CTCF and BRD2 form a transcriptional boundary. Accordingly, single-molecule mRNA fluorescence insitu hybridization (FISH) reveals that, upon site-specific CTCF disruption or BRD2 depletion, expression of the two genes becomes increasingly correlated. HiC shows that BRD2 depletion weakens boundaries co-occupied by CTCF and BRD2, but not those that lack BRD2. These findings indicate that BRD2 supports boundary activity, and they raise the possibility that pharmacologic BET inhibitors can influence gene expression in part by perturbing domain boundary function.

Bdf1 Bromodomains Are Essential for Meiosis and the Expression of Meiotic-Specific Genes.

Bromodomain and Extra-terminal motif (BET) proteins play a central role in transcription regulation and chromatin signalling pathways. They are present in unicellular eukaryotes and in this study, the role of the BET protein Bdf1 has been explored in Saccharomyces cerevisiae. Mutation of Bdf1 bromodomains revealed defects on both the formation of spores and the meiotic progression, blocking cells at the exit from prophase, before the first meiotic division. This phenotype is associated with a massive deregulation of the transcription of meiotic genes and Bdf1 bromodomains are required for appropriate expression of the key meiotic transcription factor NDT80 and almost all the Ndt80-inducible genes, including APC complex components. Bdf1 notably accumulates on the promoter of Ndt80 and its recruitment is dependent on Bdf1 bromodomains. In addition, the ectopic expression of NDT80 during meiosis partially bypasses this dependency. Finally, purification of Bdf1 partners identified two independent complexes with Bdf2 or the SWR complex, neither of which was required to complete sporulation. Taken together, our results unveil a new role for Bdf1 –working independently from its predominant protein partners Bdf2 and the SWR1 complex–as a regulator of meiosis-specific genes.

The Role of Bromodomain and Extraterminal Motif (BET) Proteins in Chromatin Structure.

Bromodomain and extraterminal motif (BET) proteins have been widely investigated for their roles in gene regulation and their potential as therapeutic targets in cancer. Pharmacologic BET inhibitors target the conserved bromodomain-acetyllysine interaction and do not distinguish between BRD2, BRD3, and BRD4. Thus, comparatively little is known regarding the distinct roles played by individual family members, as well as the underlying mechanisms that drive the transcriptional effects of BET inhibitors. Here we review studies regarding the contributions of BET proteins to genome structure and function, including recent work identifying a role for BRD2 as a component of functional and physical chromatin domain boundaries. We also discuss directions of future studies aimed at providing insights into broader architectural functions of BET proteins and their roles in chromatin domain boundary formation.

Bromodomain and Extra-Terminal Motif Proteins (BETs) Mediate 5-Azacitidine Resistance in Myeloid Leukemia through Recruitment of an Active RNA Polymerase II Complex

Background: BETs are evolutionarily conserved proteins that specifically bind to acetyl-lysines on histones and other proteins to recruit transcriptional machinery and influence gene expression (Shi and Vakoc. 2014 Mol Cell 54, 728-736). Small molecules that target BETs, such as JQ1 and I-BET, can effectively inhibit the growth of midline carcinoma cells that have a BRD4-NUT gene fusionas well as leukemia cells, such as AML, which have a diverse genetic background and do not have BRD4 rearrangements. DNA methyltransferase (DNMT) inhibitors, such as azacitidine (5-AZA) and decitabine, have been proven effective in some patients with hematologic malignancies including AML and MDS. However, the detailed mechanisms underlying the selectivity and resistance of these epigenetic-modifying drugs remain elusive. Our previous genome-wide epigenetic profiling data have demonstrated epigenetic inactivation of the SPI1/PU.1 pathway in cytogenetically normal MDS with erythroid predominance (Cheng et al. 2013 Leukemia 27, 1291-1300). This study aims to elucidate the role of chromatin structure in the regulation of response to epigenetic drugs in MDS and AML.Methods: Co-immunoprecipitation (co-IP) coupled with RNase/DNase digestion, super-resolution two-photon stimulated-emission depletion (STED) confocal microscopy, high-throughput sequencing and chromatin conformation capture (3C) were used.Results: Our data demonstrate that GATA1 and SPI1/PU.1, erythroid- vs. myeloid-determining transcription factors (TFs), selectively interact with specific sets of DNA/histone modifiers, such as TET2, DNMTs and EZH2, to form distinct lineage-specific, drug-responsive chromatin structures at specific gene loci. The interactions between the TFs, DNA/histone modifiers and chromatin structures are highly sensitive to RNase and DNase digestions, i.e., dependent on native chromatin environment. Our experiments show that hnRNPK, a conserved factor in the heterogeneous nuclear RNA-binding protein (hnRNP) complexes, directly interact with the lineage-determining TFs and DNA/histone modifiers as well as RNAs/DNAs to form distinct chromatin-structures in MDS/AML cells. Epigenetic drugs, such as 5-AZA, efficiently disrupt the hnRNPK-mediated chromatin structures in 5-AZA-sensitive MDS/AML cells, but not in 5-AZA-resistant MDS/AML cells. Our data demonstrate a marked (~4-6 fold) increase in BRD4, BRD2 and DNMT1 in the 5-AZA-resistant MDS/AML cell lines compared to the 5-AZA-sensitive MDS/AML cell lines. Strikingly, a massive amount of BRD4-associated RNA polymerase II (pol-II) is observed in the 5-AZA-resistant MDS/AML cells, but not in the 5-AZA-senstive MDS/AML, and there is approximately 70-80 fold increase in BRD4-associated pol-II, but not in BRD4-associated GATA1, in the 5-AZA-resistant cells compared to the 5-AZA-sensitive cells. Such BRD4-associated pol-II is almost exclusively in a processive pol-II complex that is associated with the phosphorylated C-terminal domain (S2p/S5p-CTD) of pol-II, and sensitive to JQ1. Furthermore, JQ1 significantly decreases the interactions between BRD4 and lineage-determining TFs GATA1 and SPI1/PU.1, in the 5-AZA-sensitive MDS/AML cells, but not in the 5-AZA-resistant MDS/AML cells. A very low concentration (0.01 uM) of JQ1 can re-sensitize the 5-AZA-resistant MDS/AML cell lines and completely reverse the drug resistance to 5-AZA, suggesting a BET-mediated 5-AZA-resistance in those cells. Genome-wide chromatin immunoprecipitation coupled with high-throughput sequencing has been carried out to map the BRD4-associated RNA pol-II at the genome-wide level in the 5-AZA resistant and sensitive MDS/AML cells. Our experiments using clinical specimens demonstrate a positive correlation between MDS/AML progression and increase in expression of hnRNPK, BRD2 and BRD4, confirming their importance and clinical relevance.Conclusion: Our study has revealed a novel drug resistance mechanism that operates through BET-mediated recruitment of an active pol-II complex and induction of drug-responsive chromatin structural changes in MDS/AML cells (Fig 1). Such BET-mediated changes in pol-II complexes and chromatin structure could become useful biomarkers to predict drug responses, leading to rational designs and actionable targets to reprogram therapeutic drug susceptibility for more effective therapy in MDS and AML. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.