Chromatin Accessibility Restoration via BRD4 Modulation
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From Analysis:
Epigenetic reprogramming in aging neurons
Investigate mechanisms of epigenetic reprogramming in aging neurons, including DNA methylation changes, histone modification dynamics, chromatin remodeling, and partial reprogramming approaches (e.g., Yamanaka factors) to reverse age-related epigenetic alterations in post-mitotic neurons.
Description
Mechanistic Overview
Chromatin Accessibility Restoration via BRD4 Modulation starts from the claim that modulating BRD4 within the disease context of neurodegeneration can redirect a disease-relevant process. The original description reads: "Molecular Mechanism and Rationale BRD4 functions as a master epigenetic regulator through its unique ability to recognize and bind acetylated histone marks via two tandem bromodomains (BD1 and BD2). The BD1 domain preferentially binds H4K5ac and H4K8ac, while BD2 recognizes H3K14ac and H4K12ac marks that characterize actively transcribed chromatin regions....
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Curated Mechanism Pathway
Curated pathway diagram from expert analysis
flowchart TD
A["Acetylated Histones
H3K27ac, H4K16ac"] --> B["BRD4 Binding
Tandem Bromodomains"]
B --> C["P-TEFb/CDK9 Recruitment"]
C --> D["RNA Pol II Release
from Pausing"]
D --> E["Neuronal Gene Transcription
BDNF, Arc, SYN1, CaMKII"]
F["Aging Process"] --> G["up HDACs Activity"]
F --> H["down BRD4 Protein Levels
25-35% reduction"]
F --> I["BRD4 Mislocalization
to Heterochromatin"]
G --> J["down Histone Acetylation"]
J --> K["down BRD4 Binding Sites"]
H --> L["Aberrant Heterochromatin
at Neuronal Enhancers"]
I --> L
K --> L
L --> M["Silenced Neuronal Genes"]
L --> N["Derepressed LINE-1
Retrotransposons"]
M --> O["down Plasticity
down DNA Repair"]
N --> P["cGAS-STING
Inflammation"]
O --> Q["Neurodegeneration"]
P --> Q
R["Phase 1: Low-dose BETi
Days 1-7"] --> S["Chromatin Clearing
Displace BRD4"]
S --> T["Phase 2: BETi Washout
Days 7-28"]
T --> U["Chromatin Reset
BRD4 Re-engagement"]
U --> V["Restored Neuronal
Transcription Programs"]
classDef central fill:#4fc3f7,stroke:#333,stroke-width:2px
classDef protective fill:#81c784,stroke:#333,stroke-width:2px
classDef pathological fill:#ef5350,stroke:#333,stroke-width:2px
classDef regulatory fill:#ce93d8,stroke:#333,stroke-width:2px
classDef outcomes fill:#ffd54f,stroke:#333,stroke-width:2px
class A,B,C,D central
class E,R,S,T,U,V protective
class F,G,H,I,J,K,L,M,N,O,P,Q pathological
class B regulatory
Dimension Scores
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✓ Supporting Evidence 35
Neutralizing antibodies that target the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein are among the most promising approaches against COVID-191,2. A bispecific IgG1-like molecule (CoV-X2) has been developed on the basis of C121 and C135, two antibodies derived from donors who had recovered from COVID-193. Here we show that CoV-X2 simultaneously binds two independent sites on the RBD and, unlike its parental antibodies, prevents detectable spike binding to the cellular receptor of the virus, angiotensin-converting enzyme 2 (ACE2). Furthermore, CoV-X2 neutralizes wild-type SARS-CoV-2 and its variants of concern, as well as escape mutants generated by the parental monoclonal antibodies. We also found that in a mouse model of SARS-CoV-2 infection with lung inflammation, CoV-X2 protects mice from disease and suppresses viral escape. Thus, the simultaneous targeting of non-overlapping RBD epitopes by IgG-like bispecific antibodies is feasible and effective, and combines the a
Activity-dependent CREB phosphorylation and gene expression are critical for long-term neuronal plasticity. Local signaling at CaV1 channels triggers these events, but how information is relayed onward to the nucleus remains unclear. Here, we report a mechanism that mediates long-distance communication within cells: a shuttle that transports Ca(2+)/calmodulin from the surface membrane to the nucleus. We show that the shuttle protein is γCaMKII, its phosphorylation at Thr287 by βCaMKII protects the Ca(2+)/CaM signal, and CaN triggers its nuclear translocation. Both βCaMKII and CaN act in close proximity to CaV1 channels, supporting their dominance, whereas γCaMKII operates as a carrier, not as a kinase. Upon arrival within the nucleus, Ca(2+)/CaM activates CaMKK and its substrate CaMKIV, the CREB kinase. This mechanism resolves long-standing puzzles about CaM/CaMK-dependent signaling to the nucleus. The significance of the mechanism is emphasized by dysregulation of CaV1, γCaMKII, βCaMK
Patients with EGFR-mutant non-small cell lung cancer achieve variable benefit from targeted therapy, and biomarkers to predict degree of benefit are not in clinical use. EGFR-mutant cancers with high tumor mutational burden demonstrate poorer outcomes on EGFR-targeted therapy. Investigation into the mechanisms underlying this intriguing association is needed.See related article by Offin et al., p. 1063.
The lectin Helix pomatia agglutinin (HPA) recognizes altered glycosylation in solid cancers and the identification of HPA binding partners in tumour tissue and serum is an important aim. Among the many HPA binding proteins, IgA1 has been reported to be the most abundant in liver metastases. In this study, the glycosylation of IgA1 was evaluated using serum samples from patients with breast cancer (BCa) and the utility of IgA1 glycosylation as a biomarker was assessed. Detailed mass spectrometric structural analysis showed an increase in disialo-biantennary N-linked glycans on IgA1 from BCa patients (p < 0.0001: non-core fucosylated; p = 0.0345: core fucosylated) and increased asialo-Thomsen-Friedenreich antigen (TF) and disialo-TF antigens in the O-linked glycan preparations from IgA1 of cancer patients compared with healthy control individuals. An increase in Sambucus nigra binding was observed, suggestive of increased α2,6-linked sialic acid on IgA1 in BCa. Logistic regression analys
A hallmark of chromosome organization is the partition into transcriptionally active A and repressed B compartments, and into topologically associating domains (TADs). Both structures were regarded to be absent from the inactive mouse X chromosome, but to be re-established with transcriptional reactivation and chromatin opening during X-reactivation. Here, we combine a tailor-made mouse iPSC reprogramming system and high-resolution Hi-C to produce a time course combining gene reactivation, chromatin opening and chromosome topology during X-reactivation. Contrary to previous observations, we observe A/B-like compartments on the inactive X harbouring multiple subcompartments. While partial X-reactivation initiates within a compartment rich in X-inactivation escapees, it then occurs rapidly along the chromosome, concomitant with downregulation of Xist. Importantly, we find that TAD formation precedes transcription and initiates from Xist-poor compartments. Here, we show that TAD formation
Endoplasmic reticulum (ER) stress is a major contributor to ethanol-induced neurodegeneration. ER-phagy, the selective elimination of specific ER domains, has emerged as a protective mechanism against ER stress. However, its regulation in ethanol-related neurological disorders remains unclear. Here, we investigated the effects and underlying mechanisms of ethanol on ER-phagy in neuronal cells and ethanol-fed mice. Our findings demonstrate that ethanol-induced ER stress is chronically sustained due to impaired ER-phagy. Among ER-phagy receptors, FAM134A expression was notably reduced by ethanol. Ethanol metabolism contributes to the downregulation of SIRT1 activity, leading to increased acetylation of histone H4 lysine 16 (H4K16ac) and enhanced recruitment of bromodomain-containing protein 4 (BRD4) to the FAM134A promoter. The BRD4/G9a complex-mediated increase in histone H3 lysine 9 dimethylation (H3K9me2) downregulates FAM134A expression by restricting the access of unfolded protein r
A human Tau expressing zebrafish model of progressive supranuclear palsy identifies Brd4 as a regulator of mic… MEDIUM▼
Progressive supranuclear palsy (PSP) is an incurable neurodegenerative disease characterized by 4-repeat (0N/4R)-Tau protein accumulation in CNS neurons. We generated transgenic zebrafish expressing human 0N/4R-Tau to investigate PSP pathophysiology. Tau zebrafish replicated multiple features of PSP, including: decreased survival; hypokinesia; impaired optokinetic responses; neurodegeneration; neuroinflammation; synapse loss; and Tau hyperphosphorylation, misfolding, mislocalization, insolubility, truncation, and oligomerization. Using automated assays, we screened 147 small molecules for activity in rescuing neurological deficits in Tau zebrafish. (+)JQ1, a bromodomain inhibitor, improved hypokinesia, survival, microgliosis, and brain synapse elimination. A heterozygous brd4+/- mutant reducing expression of the bromodomain protein Brd4 similarly rescued these phenotypes. Microglial phagocytosis of synaptic material was decreased by (+)JQ1 in both Tau zebrafish and rat primary cortical
Bromodomains in Human-Immunodeficiency Virus-Associated Neurocognitive Disorders: A Model of Ferroptosis-Induc… MEDIUM▼
Human immunodeficiency virus (HIV)-associated neurocognitive disorders (HAND) comprise a group of illnesses marked by memory and behavioral dysfunction that can occur in up to 50% of HIV patients despite adequate treatment with combination antiretroviral drugs. Iron dyshomeostasis exacerbates HIV-1 infection and plays a major role in Alzheimer's disease pathogenesis. In addition, persons living with HIV demonstrate a high prevalence of neurodegenerative disorders, indicating that HAND provides a unique opportunity to study ferroptosis in these conditions. Both HIV and combination antiretroviral drugs increase the risk of ferroptosis by augmenting ferritin autophagy at the lysosomal level. As many viruses and their proteins exit host cells through lysosomal exocytosis, ferroptosis-driving molecules, iron, cathepsin B and calcium may be released from these organelles. Neurons and glial cells are highly susceptible to ferroptosis and neurodegeneration that engenders white and gray matter
Hair cells (HCs) play crucial roles in perceiving sound, acceleration, and fluid motion. The tonotopic architecture of the sensory epithelium recognizes mechanical stimuli and convert them into electrical signals. The expression and regulation of the genes in the inner ear is very important to keep the sensory organ functional. Our study is the first to investigate the role of the epigenetic reader Brd4 in the mouse inner ear. We demonstrate that HC specific deletion of Brd4 in vivo in the mouse inner ear is sufficient to cause profound hearing loss (HL), degeneration of stereocilia, nerve fibers and HC loss postnatally in mouse; suggesting an important role in hearing function and maintenance.
BET proteins function as histone code readers of acetylated lysins that determine the positive regulation in transcription of genes involved in cell cycle progression, differentiation, inflammation, and many other pathways. In recent years, thanks to the development of BET inhibitors, interest in this protein family has risen for its relevance in brain development and function. For example, experimental evidence has shown that BET modulation affects neuronal activity and the expression of genes involved in learning and memory. In addition, BET inhibition strongly suppresses molecular pathways related to neuroinflammation. These observations suggest that BET modulation may play a critical role in the onset and during the development of diverse neurodegenerative and neuropsychiatric disorders, such as Alzheimer's disease, fragile X syndrome, and Rett syndrome. In this review article, we summarize the most recent evidence regarding the involvement of BET proteins in brain physiology and p
A novel PROTAC molecule dBET1 alleviates pathogenesis of experimental autoimmune encephalomyelitis in mice by … MEDIUM▼
Neuroinflammation and neurodegeneration are hallmarks of multiple sclerosis (MS). Bromodomain-containing protein 4 (BRD4), a bromodomain and extra-terminal domain (BET) protein family member, is indispensable for the transcription of pro-inflammatory genes. Therefore, inhibiting BRD4 may be a prospective therapeutic approach for modulating the inflammatory response and regulating the course of MS. dBET1, a newly synthesized proteolysis-targeting chimera (PROTAC), exhibits effectively degrades of BRD4. However, the precise effects of dBET1 on MS require further investigation. Therefore, we assessed the effect of dBET1 in experimental autoimmune encephalomyelitis (EAE), a typical MS experimental model. Our findings revealed that BRD4 is mainly expressed in astrocytes and neurons of the spinal cords, and is up-regulated in the spinal cords of EAE mice. The dBET1 attenuated lipopolysaccharide-induced expression of astrocytic pro-inflammatory mediators and inhibited deleterious molecular ac
Epigenetic modulation through BET bromodomain inhibitors as a novel therapeutic strategy for progranulin-defic… MEDIUM▼
Frontotemporal dementia (FTD) is a debilitating neurodegenerative disorder with currently no disease-modifying treatment options available. Mutations in GRN are one of the most common genetic causes of FTD, near ubiquitously resulting in progranulin (PGRN) haploinsufficiency. Small molecules that can restore PGRN protein to healthy levels in individuals bearing a heterozygous GRN mutation may thus have therapeutic value. Here, we show that epigenetic modulation through bromodomain and extra-terminal domain (BET) inhibitors (BETi) potently enhance PGRN protein levels, both intracellularly and secreted forms, in human central nervous system (CNS)-relevant cell types, including in microglia-like cells. In terms of potential for disease modification, we show BETi treatment effectively restores PGRN levels in neural cells with a GRN mutation known to cause PGRN haploinsufficiency and FTD. We demonstrate that BETi can rapidly and durably enhance PGRN in neural progenitor cells (NPCs) in a ma
BACKGROUND: Retinal diseases characterized with irreversible loss of retinal nerve cells, such as optic atrophy and retinal degeneration, are the main causes of blindness. Current treatments for these diseases are very limited. An emerging treatment strategy is to induce the reprogramming of Müller glial cells to generate new retinal nerve cells, which could potentially restore vision. MAIN TEXT: Müller glial cells are the predominant glial cells in retinae and play multiple roles to maintain retinal homeostasis. In lower vertebrates, such as in zebrafish, Müller glial cells can undergo cell reprogramming to regenerate new retinal neurons in response to various damage factors, while in mammals, this ability is limited. Interestingly, with proper treatments, Müller glial cells can display the potential for regeneration of retinal neurons in mammalian retinae. Recent studies have revealed that dozens of genetic and epigenetic regulators play a vital role in inducing the reprogramming of
Regulatory T (Treg) cells accumulate into tumors, hindering the success of cancer immunotherapy. Yet, therapeutic targeting of Treg cells shows limited efficacy or leads to autoimmunity. The molecular mechanisms that guide Treg cell stability in tumors remain elusive. In the present study, we identify a cell-intrinsic role of the alarmin interleukin (IL)-33 in the functional stability of Treg cells. Specifically, IL-33-deficient Treg cells demonstrated attenuated suppressive properties in vivo and facilitated tumor regression in a suppression of tumorigenicity 2 receptor (ST2) (IL-33 receptor)-independent fashion. On activation, Il33-/- Treg cells exhibited epigenetic re-programming with increased chromatin accessibility of the Ifng locus, leading to elevated interferon (IFN)-γ production in a nuclear factor (NF)-κB-T-bet-dependent manner. IFN-γ was essential for Treg cell defective function because its ablation restored Il33-/- Treg cell-suppressive properties. Importantly, genetic ab
Lamins are crucial proteins for nuclear functionality. Here, we provide new evidence showing that increased lamin B1 levels contribute to the pathophysiology of Huntington's disease (HD), a CAG repeat-associated neurodegenerative disorder. Through fluorescence-activated nuclear suspension imaging, we show that nucleus from striatal medium-sized spiny and CA1 hippocampal neurons display increased lamin B1 levels, in correlation with altered nuclear morphology and nucleocytoplasmic transport disruption. Moreover, ChIP-sequencing analysis shows an alteration of lamin-associated chromatin domains in hippocampal nuclei, accompanied by changes in chromatin accessibility and transcriptional dysregulation. Supporting lamin B1 alterations as a causal role in mutant huntingtin-mediated neurodegeneration, pharmacological normalization of lamin B1 levels in the hippocampus of the R6/1 mouse model of HD by betulinic acid administration restored nuclear homeostasis and prevented motor and cognitive
AIMS: Vascular calcification (VC) predicts cardiovascular risk in diabetes, chronic kidney disease (CKD) and atherosclerosis patients and is closely linked to the osteogenic transdifferentiation of vascular smooth muscle cells (VSMCs). Our previous work revealed that cGAS-STING signalling pathway in VSMCs increases CKD-associated atherosclerotic plaque vulnerability and recent studies elucidated the involvement of STING in vascular calcification, but its upstream modulation mechanism remains to be elucidated. METHODS AND RESULTS: DNA damage and robust upregulation of STING occurred in high phosphate (Pi)-stimulated VSMCs, calcified aortic tissues from 1,25(OH)2VitD3 (VitD3)-overloaded mice and radial arteries from CKD patients, and these changes were accompanied by the activation of the cGAS‒STING signalling pathway. STING deficiency alleviated vascular calcification in CKD model mice. STING knockdown suppressed calcium deposition and the expression of osteogenic transdifferentiation m
Osteoarthritis (OA) is a common degenerative joint disease with limited disease-modifying therapies. Emerging evidence suggests that epigenetic dysregulation contributes to cartilage degeneration, but effective strategies to selectively target these pathways remain lacking. Here we show that the BRD4/Nav1.7 axis drives inflammatory and metabolic dysfunction in OA. Integrated single-cell and transcriptomic analyses identify BRD4 as a key regulator that enhances Nav1.7 transcription, promoting mitochondrial impairment and catabolic activation in chondrocytes. To therapeutically target this pathway, we develop a biomimetic hydrogel system incorporating chondrocyte membrane-coated nanoparticles for cartilage-specific delivery of a BRD4 proteolysis-targeting chimera (PROTAC), a molecule designed to induce selective protein degradation. This nanoplatform enables efficient intra-articular delivery, immune evasion and targeted retention in cartilage. Treatment suppresses inflammatory responses
Cardiac fibrosis driven by persistent myofibroblast activation is a major contributor to adverse ventricular remodeling and heart failure. Bromodomain and extra-terminal domain (BET) inhibition reduces fibrosis and hypertrophy in preclinical models, but direct targeting of the BET co-activator BRD4 is limited by family homology and potential systemic toxicity. Sertad4 (SERTA domain containing protein 4) is a BRD4-dependent gene induced in activated cardiac fibroblasts, yet its role in cardiac pathology is unknown. Here, we examined Sertad4 expression and function in human heart failure and in murine myocardial infarction (MI). SERTAD4 protein was increased in left ventricular tissue from heart failure patients compared with non-failing controls. In Sertad4/LacZ reporter mice, MI triggered strong Sertad4 activation localized to the infarct scar and border zone, with minimal expression in remote myocardium; single-nucleus RNA sequencing further demonstrated that Sertad4 expression is pre
Postoperative complications such as tumor recurrence, wound infections, and delayed tissue regeneration persist as critical challenges in melanoma management. In this study, we designed a temperature-tunable photothermal immunotherapy hydrogel dressing (Pd/JQ1@SerMA) to overcome these melanoma postoperative complications. Specifically, this immunomodulatory dressing is composed of methacrylic anhydride-modified sericin (SerMA), palladium nanosheets (Pd) with excellent photothermal performance, and the small-molecule BRD4 inhibitor JQ1. The Pd/JQ1@SerMA hydrogel induces immunogenic cell death (ICD) in tumor cells via high-temperature photothermal effects (> 48 °C), while the released JQ1 downregulates interferon-γ-induced programmed death ligand 1 (PD-L1) expression, thereby mitigating acquired immune resistance and enhancing antitumor immunity. The transcriptomic profiling revealed significant activation of tumor-specific immune pathways, including lymphocyte differentiation, T-cell ac
Hsp70-Targeting Chimeras Enable Dual Proteasomal and Lysosomal Degradation of Intracellular and Extracellular … MEDIUM▼
Developing targeted protein degradation (TPD) strategies with disease-specific mechanisms, modularity, and facile designability could ensure drug efficacy and selectivity. Herein, a small-molecule, Hsp70-based targeted protein degradation platform, termed Hsp70TAC, is described that enables tumor-selective degradation of both intracellular and extracellular proteins through distinct cellular pathways. By conjugating protein-of-interest (POI) ligands to Hsp70 inhibitors, Hsp70TACs exploits the chaperone functions of Hsp70 to enable protein degradation through both the ubiquitin-proteasome system and the endocytosis-lysosome pathway. As a proof of concept, Hsp70TACs induced efficient degradation of intracellular Bromodomain Protein 4 (BRD4) via the ubiquitin-proteasome system (DC50 = 0.67 μM) and membrane-bound Programmed Death Ligand 1 (PD-L1) via caveolin-mediated endocytosis-lysosomal processing (DC50 = 0.84 μM). Moreover, Hsp70TACs exploits the elevated expression of Hsp70 in tumor c
Demonstrates BRD4's role in modulating mitochondrial function and gene expression through epigenetic mechanism… MEDIUM▼
Skeletal muscle dysfunction (SMD) associated with Chronic obstructive pulmonary disease (COPD), characterized by muscle atrophy and altered fiber type distribution. High-intensity interval training (HIIT) is increasingly used clinically to improve cardiopulmonary and exercise functions in COPD patients, yet robust scientific evidence and exploration of its molecular mechanisms remain limited. In this research, bioinformatics analysis of GSE datasets revealed the differentially expressed genes in
Explores BRD4 as a therapeutic target in glioblastoma, suggesting potential for epigenetic modulation strategi… MEDIUM▼
Epigenetic dysregulation is increasingly recognized as a key driver of glioblastoma (GBM), with bromodomain-containing protein 4 (BRD4) emerging as a critical regulator of tumor malignancy. GBM is an aggressive brain tumor marked by diffuse infiltration, a population of stem-like cells and multiple resistance mechanisms, which together render it largely incurable. Standard treatment, consisting of surgical resection followed by radiotherapy and temozolomide chemotherapy, confers only limited the
Inflammatory osteolysis is primarily characterized by an extensive macrophage-mediated inflammatory response coupled with osteoclast (OC) formation, triggered by bacterial byproducts and/or environmental stressors. And Osteoarthritis (OA) is one of the most common degenerative diseases in clinical medicine. Currently, anti-inflammatory drugs and intra-articular drug injection are mainly used, but the treatments only relieve symptoms. Punicalagin (PUN), a hydrolyzable tannin derived from pomegran
Develops chemical strategies for BRD4 degradation, demonstrating ongoing interest in targeting BRD4 for therap… MEDIUM▼
This study introduces a divergent synthetic strategy in linkerology using preassembled linkers to generate structural diversity. The approach was validated by developing bromodomain-containing protein 4 (BRD4)-targeting proteolysis-targeting chimeras (PROTACs) based on an "alkyne two-phase strategy," employing the BRD4 inhibitor TK-285 as the binding ligand. In the initial screening phase, alkyne-modified TK-285 derivatives were subjected to click chemistry to optimize linker length and the modi
Restoration of p53 mRNA combined with BRD4 silencing by brain targeted nanocapsules achieves effective combina…▼
Semi-rigid linkers improve the pharmacokinetic properties and therapeutic efficacy of BET PROTACs for cancer t…▼
Design, synthesis and evaluation of novel BRD4 and RIPK3 dual inhibitors as potential anti-inflammatory agents… MODERATE▼
Designing an Osmium(II) Complex to Inhibit the Growth and Recurrence of Tumors by Integrating Photodynamic The… MODERATE▼
✗ Opposing Evidence 10
Protein O-linked β-N-acetylglucosamine modification (O-GlcNAcylation) plays a crucial role in regulating essential cellular processes. The disruption of the homeostasis of O-GlcNAcylation has been linked to various human diseases, including cancer, diabetes, and neurodegeneration. However, there are limited chemical tools for protein- and site-specific O-GlcNAc modification, rendering the precise study of the O-GlcNAcylation challenging. To address this, we have developed heterobifunctional small molecules, named O-GlcNAcylation TArgeting Chimeras (OGTACs), which enable protein-specific O-GlcNAcylation in living cells. OGTACs promote O-GlcNAcylation of proteins such as BRD4, CK2α, and EZH2 in cellulo by recruiting FKBP12F36V-fused O-GlcNAc transferase (OGT), with temporal, magnitude, and reversible control. Overall, the OGTACs represent a promising approach for inducing protein-specific O-GlcNAcylation, thus enabling functional dissection and offering new directions for O-GlcNAc-target
Epigenetic aberration is one of the major driving factors in human cancer, often leading to acquired resistance to chemotherapies. Various small molecule epigenetic modulators have been reported. Nonetheless, outcomes from animal models and clinical trials have underscored the substantial setbacks attributed to pronounced on- and off-target toxicities. To address these challenges, CRISPR/dCas9 technology is emerging as a potent tool for precise modulation of epigenetic mechanism. However, this technology involves co-expressing exogenous epigenetic modulator proteins, which presents technical challenges in preparation and delivery with potential undesirable side effects. Recently, our research demonstrated that Cas9 tagged with the Phe-Cys-Pro-Phe (FCPF)-peptide motif can be specifically targeted by perfluorobiphenyl (PFB) derivatives. Here, we integrated the FCPF-tag into dCas9 and established a chemically inducible platform for epigenome editing, called Chem-CRISPR/dCas9FCPF. We desig
Bromodomain-containing protein 4 (BRD4): a key player in inflammatory bowel disease and potential to inspire e… MEDIUM▼
INTRODUCTION: Inflammatory bowel diseases (IBDs) are debilitating chronic inflammatory disorders with increasing prevalence worldwide. Epigenetic regulator bromodomain-containing protein 4 (BRD4) is critical in controlling gene expression of IBD-associated inflammatory cytokine networks. BRD4 as a promising therapeutic target is also tightly associated with many other diseases, such as airway inflammation and fibrosis, cancers, infectious diseases and central nervous system disorders. AREAS COVERED: This review briefly summarized the critical role of BRD4 in the pathogenesis of IBDs and the current clinical landscape of developing bromodomain and extra terminal domain (BET) inhibitors. The challenges and opportunities as well as future directions of targeting BRD4 inhibition for potential IBD medications were also discussed. EXPERT OPINION: Targeting BRD4 with potent and specific inhibitors may offer novel effective therapeutics for IBD patients, particularly those who are refractory t
BRD4 inhibition paradoxically increases neuroinflammation and microglial activation in neurodegenerative model… STRONG▼
Entomopathogenic fungus Metarhizium anisopliae obtain survival benefit meanwhile promote the nutrient absorption of root as an endophyte. However, little is known concerning molecular mechanisms in the process. We performed the transcriptome sequencing of A. hypogaea roots inoculated M. anisopliae and pathogenic Fusarium axysporum, respectively. There were 81323 unigenes from 132023 transcripts. Total 203 differentially expressed genes (DEGs) respond to the two fungi, including specific 76 and 34 DEGs distributed respectively in M. anisopliae and F. axysporum treatment. KEGG pathway enrichment for DEGs showed the two top2 were signal transductions of plant-pathogen interaction and plant hormone. By qRT-PCR, the mRNA level of 26 genes involved in plant-fungus interaction confirmed the reliability of the RNA-Seq data. The expression pattern of the key DEGs on jasmonic acid (JA) or salicylic acid (SA) signaling pathway presented regulating consistency with JA or SA concentration detected
BRD4-mediated chromatin accessibility in neurons is dependent on continued histone acetylation maintenance; ac… MODERATE▼
In Noonan syndrome (NS) 30-50% of subjects show cognitive deficits of unknown etiology and with no known treatment. Here, we report that knock-in mice expressing either of two NS-associated mutations in Ptpn11, which encodes the nonreceptor protein tyrosine phosphatase Shp2, show hippocampal-dependent impairments in spatial learning and deficits in hippocampal long-term potentiation (LTP). In addition, viral overexpression of an NS-associated allele PTPN11(D61G) in adult mouse hippocampus results in increased baseline excitatory synaptic function and deficits in LTP and spatial learning, which can be reversed by a mitogen-activated protein kinase kinase (MEK) inhibitor. Furthermore, brief treatment with lovastatin reduces activation of the GTPase Ras-extracellular signal-related kinase (Erk) pathway in the brain and normalizes deficits in LTP and learning in adult Ptpn11(D61G/+) mice. Our results demonstrate that increased basal Erk activity and corresponding baseline increases in exci
First-in-human phase I study of the bromodomain and extraterminal motif inhibitor BAY 1238097: emerging pharma… MEDIUM▼
Bromodomain and extraterminal motif (BET) protein inhibition is a promising cancer treatment strategy, notably for targeting MYC- or BRD4-driven diseases. A first-in-human study investigated the safety, pharmacokinetics, maximum tolerated dose and recommended phase II dose of the BET inhibitor BAY 1238097 in patients with advanced malignancies. In this phase I, open-label, non-randomised, multicentre study, patients with cytologically or histologically confirmed advanced refractory malignancies
First-in-human Study of AZD5153, A Small-molecule Inhibitor of Bromodomain Protein 4, in Patients with Relapse… MEDIUM▼
AZD5153, a reversible, bivalent inhibitor of the bromodomain and extraterminal family protein BRD4, has preclinical activity in multiple tumors. This first-in-human, phase I study investigated AZD5153 alone or with olaparib in patients with relapsed/refractory solid tumors or lymphoma. Adults with relapsed tumors intolerant of, or refractory to, prior therapies received escalating doses of oral AZD5153 once daily or twice daily continuously (21-day cycles), or AZD5153 once daily/twice daily cont
Bromodomain inhibitor OTX015 in patients with lymphoma or multiple myeloma: a dose-escalation, open-label, pha… MEDIUM▼
The first-in-class small molecule inhibitor OTX015 (MK-8628) specifically binds to bromodomain motifs BRD2, BRD3, and BRD4 of bromodomain and extraterminal (BET) proteins, inhibiting them from binding to acetylated histones, which occurs preferentially at super-enhancer regions that control oncogene expression. OTX015 is active in haematological preclinical entities including leukaemia, lymphoma, and myeloma. We aimed to establish the recommended dose of OTX015 in patients with haematological ma
Myeloproliferative neoplasm (MPN)-associated myelofibrosis (MF) is characterized by cytopenias, marrow fibrosis, constitutional symptoms, extramedullary hematopoiesis, splenomegaly, and shortened survival. Constitutive activation of the janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling pathway in MF leads to cell proliferation, inhibition of cell death, and clonal expansion of myeloproliferative malignant cells. Fedratinib is a selective oral JAK2 inhibitor recen
The design, synthesis and cellular imaging of a tumor-anchored, potent and cell-permeable BRD4-targeted fluore… MEDIUM▼
Bromodomain 4 (BRD4) proteins play an important role in histone post-translational modifications and facilitate several important physiological and pathological processes, including cancers. The inhibition of BRD4 by small molecule inhibitors shows promise as a therapeutic strategy for cancer treatment. However, their clinical applications were limited, which is largely hampered by off-target effects-induced toxicity. We herein report the design, synthesis, and cellular imaging of a set of tumor
🧬 Theorist Proposes novel mechanisms and generates creative hypotheses ▼
Perfect! Now I have sufficient evidence to generate novel therapeutic hypotheses. Let me create comprehensive, mechanistic hypotheses based on the current literature.
Based on the current research on epigenetic reprogramming in aging neurons, I'll generate novel therapeutic hypotheses that address key knowledge gaps and propose innovative mechanistic approaches:
Novel Therapeutic Hypotheses for Epigenetic Reprogramming in Aging Neurons
1. Temporal TET2-Mediated Hydroxymethylation Cycling
Description: Oscillating TET2 activation through small molecule modulators can restore dy🔍 Skeptic Identifies weaknesses, alternative explanations, and methodological concerns ▼
Critical Evaluation of Therapeutic Hypotheses
Based on my analysis, here are the critical weaknesses and concerns for each hypothesis:
1. Temporal TET2-Mediated Hydroxymethylation Cycling
Specific Weaknesses:
- The hypothesis assumes TET2 can be selectively modulated in neurons without affecting other cell types, but TET2 is essential for hematopoietic stem cell function and immune regulation
- No evidence provided that oscillating TET2 activation is superior to sustained modulation
- The connection between circadian cycles and therapeutic efficacy is correlative, not causal
🎯 Domain Expert Assesses practical feasibility, druggability, and clinical translation ▼
Practical Feasibility Assessment of Neuronal Epigenetic Reprogramming Hypotheses
Based on my analysis of the literature and drug development landscape, here's a comprehensive assessment of the practical feasibility for each therapeutic hypothesis:
1. Temporal TET2-Mediated Hydroxymethylation Cycling
Druggability Assessment: POOR
- Target Challenge: TET2 is notoriously difficult to drug directly. No selective small molecule modulators exist despite years of research
- Mechanism: Requires α-ketoglutarate, ascorbate, and Fe2+ as cofactors - makes selective modulation extremely
⚖ Synthesizer Integrates perspectives and produces final ranked assessments ▼
Price History
| Event | Price | Change | Source | Time | |
|---|---|---|---|---|---|
| 📄 | New Evidence | $0.578 | ▲ 1.5% | evidence_batch_update | 2026-04-13 02:18 |
| 📄 | New Evidence | $0.569 | ▲ 1.7% | evidence_batch_update | 2026-04-13 02:18 |
| ⚖ | Recalibrated | $0.559 | ▲ 1.5% | 2026-04-12 18:34 | |
| ⚖ | Recalibrated | $0.551 | ▼ 1.7% | 2026-04-12 10:15 | |
| ⚖ | Recalibrated | $0.561 | ▼ 2.8% | 2026-04-12 05:13 | |
| ⚖ | Recalibrated | $0.577 | ▼ 0.6% | 2026-04-10 15:58 | |
| ⚖ | Recalibrated | $0.580 | ▲ 0.6% | 2026-04-10 14:28 | |
| ⚖ | Recalibrated | $0.577 | ▼ 2.0% | 2026-04-08 18:39 | |
| ⚖ | Recalibrated | $0.589 | ▲ 3.1% | 2026-04-06 04:04 | |
| ⚖ | Recalibrated | $0.571 | ▼ 0.6% | 2026-04-04 16:38 | |
| ⚖ | Recalibrated | $0.574 | ▼ 1.0% | 2026-04-04 16:02 | |
| 📄 | New Evidence | $0.580 | ▲ 1.3% | evidence_batch_update | 2026-04-04 09:08 |
| ⚖ | Recalibrated | $0.573 | ▼ 6.0% | 2026-04-03 23:46 | |
| 📊 | Score Update | $0.609 | ▲ 29.6% | market_dynamics | 2026-04-03 03:34 |
| 💬 | Debate Round | $0.470 | ▼ 36.9% | market_dynamics | 2026-04-03 01:48 |
Clinical Trials (4) Relevance: 13%
Active
Completed
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Highest Phase
📚 Cited Papers (88)
📙 Related Wiki Pages (15)
📓 Linked Notebooks (1)
📊 Resource Economics & ROI
Cost Ratios
Score Impact
How Economics Pricing Works
Hypotheses receive an efficiency score (0-1) based on how many knowledge graph edges and citations they produce per token of compute spent.
High-efficiency hypotheses (score >= 0.8) get a price premium in the market, pulling their price toward $0.580.
Low-efficiency hypotheses (score < 0.6) receive a discount, pulling their price toward $0.420.
Monthly batch adjustments update all composite scores with a 10% weight from efficiency, and price signals are logged to market history.
Efficiency Price Signals
| Date | Signal Price | Score |
|---|---|---|
| 2026-04-16T20:00 | $0.549 | 0.510 |
Wiki Pages
KG Entities (46)
Dependency Graph (1 upstream, 0 downstream)
Linked Experiments (4)
Related Hypotheses
Estimated Development
🧪 Falsifiable Predictions (2)
Knowledge Subgraph (121 edges)
activates (1)
associated with (4)
co associated with (13)
co discussed (81)
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investigated in (1)
involved in (6)
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participates in (5)
regulates (4)
targets (1)
therapeutic target (5)
Mechanism Pathway for BRD4
Molecular pathway showing key causal relationships underlying this hypothesis
graph TD
BRD4["BRD4"] -->|regulates| chromatin_remodeling["chromatin_remodeling"]
BRD4_1["BRD4"] -->|therapeutic target| neurodegeneration["neurodegeneration"]
BRD4_2["BRD4"] -->|associated with| neurodegeneration_3["neurodegeneration"]
BRD4_4["BRD4"] -->|participates in| Epigenetic_regulation["Epigenetic regulation"]
SIRT3["SIRT3"] -->|co discussed| BRD4_5["BRD4"]
BRD4_6["BRD4"] -->|co discussed| OCT4["OCT4"]
BRD4_7["BRD4"] -->|co discussed| BMAL1["BMAL1"]
BRD4_8["BRD4"] -->|co discussed| SIRT1["SIRT1"]
BRD4_9["BRD4"] -->|co discussed| TET2["TET2"]
BRD4_10["BRD4"] -->|co discussed| SIRT3_11["SIRT3"]
BRD4_12["BRD4"] -->|co discussed| PGC1A["PGC1A"]
TET2_13["TET2"] -->|co discussed| BRD4_14["BRD4"]
HDAC3["HDAC3"] -->|co discussed| BRD4_15["BRD4"]
OCT4_16["OCT4"] -->|co discussed| BRD4_17["BRD4"]
SIRT1_18["SIRT1"] -->|co discussed| BRD4_19["BRD4"]
style BRD4 fill:#ce93d8,stroke:#333,color:#000
style chromatin_remodeling fill:#81c784,stroke:#333,color:#000
style BRD4_1 fill:#ce93d8,stroke:#333,color:#000
style neurodegeneration fill:#ef5350,stroke:#333,color:#000
style BRD4_2 fill:#ce93d8,stroke:#333,color:#000
style neurodegeneration_3 fill:#ef5350,stroke:#333,color:#000
style BRD4_4 fill:#ce93d8,stroke:#333,color:#000
style Epigenetic_regulation fill:#81c784,stroke:#333,color:#000
style SIRT3 fill:#ce93d8,stroke:#333,color:#000
style BRD4_5 fill:#ce93d8,stroke:#333,color:#000
style BRD4_6 fill:#ce93d8,stroke:#333,color:#000
style OCT4 fill:#ce93d8,stroke:#333,color:#000
style BRD4_7 fill:#ce93d8,stroke:#333,color:#000
style BMAL1 fill:#ce93d8,stroke:#333,color:#000
style BRD4_8 fill:#ce93d8,stroke:#333,color:#000
style SIRT1 fill:#ce93d8,stroke:#333,color:#000
style BRD4_9 fill:#ce93d8,stroke:#333,color:#000
style TET2 fill:#ce93d8,stroke:#333,color:#000
style BRD4_10 fill:#ce93d8,stroke:#333,color:#000
style SIRT3_11 fill:#ce93d8,stroke:#333,color:#000
style BRD4_12 fill:#ce93d8,stroke:#333,color:#000
style PGC1A fill:#ce93d8,stroke:#333,color:#000
style TET2_13 fill:#ce93d8,stroke:#333,color:#000
style BRD4_14 fill:#ce93d8,stroke:#333,color:#000
style HDAC3 fill:#ce93d8,stroke:#333,color:#000
style BRD4_15 fill:#ce93d8,stroke:#333,color:#000
style OCT4_16 fill:#ce93d8,stroke:#333,color:#000
style BRD4_17 fill:#ce93d8,stroke:#333,color:#000
style SIRT1_18 fill:#ce93d8,stroke:#333,color:#000
style BRD4_19 fill:#ce93d8,stroke:#333,color:#000
3D Protein Structure
🧬 BRD4 — PDB 3MXF Click to expand 3D viewer
Source Analysis
Epigenetic reprogramming in aging neurons
neurodegeneration | 2026-04-04 | completed
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