Selective HDAC3 Inhibition with Cognitive Enhancement

Target: HDAC3 Composite Score: 0.779 Price: $0.77▲38.2% Citation Quality: Pending neurodegeneration Status: promoted
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✓ All Quality Gates Passed
Evidence Strength Pending (0%)
48
Citations
3
Debates
34
Supporting
8
Opposing
Quality Report Card click to collapse
B+
Composite: 0.779
Top 5% of 1875 hypotheses
T1 Established
Multi-source converged and validated
T0 Axiom requires manual override only
B+ Mech. Plausibility 15% 0.75 Top 23%
A Evidence Strength 15% 0.80 Top 5%
A Novelty 12% 0.85 Top 20%
B+ Feasibility 12% 0.70 Top 36%
A Impact 12% 0.80 Top 34%
B+ Druggability 10% 0.75 Top 27%
C+ Safety Profile 8% 0.55 Top 47%
B Competition 6% 0.60 Top 56%
B+ Data Availability 5% 0.75 Top 26%
B+ Reproducibility 5% 0.70 Top 24%
Evidence
34 supporting | 8 opposing
Citation quality: 100%
Debates
1 session A+
Avg quality: 0.95
Convergence
1.00 A+ 30 related hypothesis share this target

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.

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Description

Mechanistic Overview


Selective HDAC3 Inhibition with Cognitive Enhancement starts from the claim that modulating HDAC3 within the disease context of neurodegeneration can redirect a disease-relevant process. The original description reads: "Molecular Mechanism and Rationale Histone deacetylase 3 (HDAC3) represents a critical epigenetic regulator that orchestrates chromatin remodeling through targeted deacetylation of lysine residues on histone tails, particularly H3K27 and H4K16. In the aging brain, HDAC3 exhibits a paradoxical dual role that has confounded therapeutic development efforts. The molecular mechanism underlying selective HDAC3 inhibition centers on exploiting age-related changes in neuronal HDAC3 localization and co-factor interactions.

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Curated Mechanism Pathway

Curated pathway diagram from expert analysis

graph TD
    A["Aging Brain
Neurons"] -->|"cytoplasmic translocation"| B["Cytoplasmic
HDAC3"] A -->|"maintained in nucleus"| C["Nuclear HDAC3-
NCoR/SMRT
Complexes"] D["Hyperphosphorylated
Tau Ser202/Thr205"] -->|"pathological binding"| B E["Amyloid-beta
Oligomers"] -->|"aberrant interaction"| B B -->|"allosteric modification"| F["Modified HDAC3
Zinc-binding
Pocket"] G["Age-selective
HDAC3 Inhibitor"] -->|"preferential binding"| F G -.->|"spares normal function"| C F -->|"selective inhibition"| H["Reduced Pathological
Deacetylation
Activity"] C -->|"maintains homeostasis"| I["Physiological H3K27
and H4K16
Deacetylation"] H -->|"restores acetylation"| J["Increased Histone
H3K27ac and
H4K16ac"] J -->|"chromatin remodeling"| K["Open Chromatin
Structure at
Memory Loci"] K -->|"transcriptional activation"| L["Enhanced CREB-
mediated Gene
Expression"] L -->|"upregulation"| M["Memory-associated
Genes: BDNF,
Arc, Fos"] M -->|"synaptic enhancement"| N["Increased Synaptic
Plasticity and
LTP Formation"] N -->|"functional improvement"| O["Enhanced Memory
Consolidation and
Retrieval"] I -->|"preserves normal"| P["Baseline Neuronal
Transcriptional
Programs"] H -->|"reduces tau pathology"| Q["Decreased Tau
Hyperphosphorylation
and Aggregation"] Q -->|"neuroprotection"| R["Reduced Neuronal
Death and Cognitive
Decline"] O -->|"therapeutic outcome"| S["Cognitive
Enhancement in
Neurodegeneration"] R -->|"disease modification"| S classDef normal fill:#4fc3f7,stroke:#2196f3 classDef therapeutic fill:#81c784,stroke:#4caf50 classDef pathology fill:#ef5350,stroke:#f44336 classDef outcome fill:#ffd54f,stroke:#ff9800 classDef molecular fill:#ce93d8,stroke:#9c27b0 class A,C,I,P normal class G,H,L therapeutic class B,D,E,F,Q pathology class O,R,S outcome class J,K,M,N molecular

GTEx v10 Brain Expression

JSON

Median TPM across 13 brain regions for HDAC3 from GTEx v10.

Cerebellum76.6 Cerebellar Hemisphere75.9 Cortex33.6 Frontal Cortex BA931.7 Nucleus accumbens basal ganglia27.8 Hypothalamus24.1 Anterior cingulate cortex BA2423.6 Caudate basal ganglia21.8 Substantia nigra19.7 Putamen basal ganglia19.3 Spinal cord cervical c-118.1 Hippocampus17.7 Amygdala17.1median TPM (GTEx v10)

Dimension Scores

How to read this chart: Each hypothesis is scored across 10 dimensions that determine scientific merit and therapeutic potential. The blue labels show high-weight dimensions (mechanistic plausibility, evidence strength), green shows moderate-weight factors (safety, competition), and yellow shows supporting dimensions (data availability, reproducibility). Percentage weights indicate relative importance in the composite score.
Mechanistic 0.75 (15%) Evidence 0.80 (15%) Novelty 0.85 (12%) Feasibility 0.70 (12%) Impact 0.80 (12%) Druggability 0.75 (10%) Safety 0.55 (8%) Competition 0.60 (6%) Data Avail. 0.75 (5%) Reproducible 0.70 (5%) KG Connect 0.78 (8%) 0.779 composite
42 citations 42 with PMID 35 medium Validation: 100% 34 supporting / 8 opposing
For (34)
27
8
(8) Against
High Medium Low
High Medium Low
Evidence Matrix — sortable by strength/year, click Abstract to expand
Evidence Types
7
18
17
MECH 7CLIN 18GENE 17EPID 0
ClaimStanceCategorySourceStrength ↕Year ↕Quality ↕PMIDsAbstract
HDAC3 has dual roles in brain functionSupportingGENEExp Biol Med (M… MEDIUM20200.33PMID:32486848
HDAC inhibitors improve learning consolidation in …SupportingGENEMol Cell Neuros… MEDIUM20080.33PMID:18638560
Selective chemical modulation favors oligodendrocy…SupportingGENEChem Biol MEDIUM20140.33PMID:24954007
Histone acetylation significantly impacts neurobeh…SupportingGENEEpigenomics MEDIUM20240.33PMID:38321930
Melatonin attenuates chronic sleep deprivation-ind…SupportingCLINCNS Neurosci Th… MEDIUM20240.33PMID:37721401
Microbiota-derived butyrate restricts tuft cell di…SupportingGENEImmunity MEDIUM20240.33PMID:38295798
HDAC3 aberration-incurred GPX4 suppression drives …SupportingGENERedox Biol MEDIUM20230.33PMID:37890360
HDAC3 deficiency protects against acute lung injur…SupportingGENERedox Biol MEDIUM20230.33PMID:37244125
HDAC3 inhibition ameliorates ischemia/reperfusion-…SupportingCLINTheranostics MEDIUM20200.33PMID:32863951
Deletion of myeloid HDAC3 promotes efferocytosis t…SupportingCLINJ Neuroinflamma… MEDIUM20240.48PMID:38997746
A phenotypic screening platform for identifying ch…SupportingGENENat Neurosci MEDIUM20240.60PMID:38378993
NKAPL facilitates transcription pause-release and …SupportingGENENat Commun MEDIUM20250.60PMID:39824811
Epigenetic regulation of general anesthesia-induce…SupportingGENEOncotarget MEDIUM20170.33PMID:28086213-
Ketogenic diet attenuates neuroinflammation and in…SupportingCLINFood Funct MEDIUM20230.33PMID:37466915
HDAC3 Inhibition Alleviates High-Glucose-Induced R…SupportingMECHBiomed Res Int MEDIUM20220.33PMID:36046456
Selective toxicity by HDAC3 in neurons: regulation…SupportingCLINJ Neurosci MEDIUM20110.54PMID:21289184
Determination of Slow-Binding HDAC Inhibitor Poten…SupportingCLINACS Med Chem Le… MEDIUM20220.33PMID:35586419
Targeting HDAC3 Activity with RGFP966 Protects Aga…SupportingCLINJ Ocul Pharmaco… MEDIUM20180.33PMID:29211617
Histone deacetylase-1 (HDAC1) is a molecular switc…SupportingCLINJ Biol Chem MEDIUM20120.49PMID:22918830
HOX Code-Based Stratification Reveals RUNX1T1-HDAC…SupportingCLINCancer Lett MEDIUM20260.33PMID:41912135
Microglial HDAC3 inhibits the migration of CD8-pos…SupportingGENECell Biosci MEDIUM20260.59PMID:41888851-
EXPRESS: Identification of Acetylation-Related Mol…SupportingCLINMol Pain MEDIUM20260.33PMID:41876476
Myeloid HDAC3 deletion protects against traumatic …SupportingGENECell Death Disc… MEDIUM20260.59PMID:41851071
LncRNA SNHG5 promotes macrophage lipid accumulatio…SupportingGENEBiochim Biophys… MEDIUM20260.59PMID:41844502
The paper suggests GABA can suppress HDAC2/3 in as…SupportingCLINFoods MEDIUM20260.33PMID:41829110
Demonstrates GR/HDAC3's role in regulating co…SupportingMECHFASEB J MEDIUM20260.33PMID:41837847
Discovery of a HDAC3 degrader with anti-inflammato…SupportingMECHJ Med Chem MEDIUM20260.33PMID:41812251
PROTAC-Based HDAC Degradation: A Paradigm Shift in…OpposingCLINChemMedChem MEDIUM20250.33PMID:41160773
Epigenetic Modulation and Neuroprotective Effects …OpposingGENEGenes (Basel) MEDIUM20250.33PMID:41153431
Epigenetic therapy meets targeted protein degradat…OpposingCLINFuture Med Chem MEDIUM20250.33PMID:40667573
Understanding the Role of Histone Deacetylase and …OpposingCLINCurr Neuropharm… MEDIUM20220.33PMID:34151764
The Two Faces of HDAC3: Neuroinflammation in Disea…OpposingGENEEpigenomics MEDIUM20240.33PMID:39513228
Deficiency of histone deacetylases 3 in macrophage…OpposingGENEArthritis Res T… MEDIUM20240.33PMID:38711064
Targeting HDAC3 Suppresses Ferroptosis and Demyeli…OpposingCLINCNS Neurosci Th… MEDIUM20250.33PMID:40485011
Histone deacetylase 3 as a novel therapeutic targe…OpposingCLINLeukemia MEDIUM20140.33PMID:23913134
SATB2 Mediates H3K9 Delactylation by Recruiting HD…SupportingMECHAdv Sci (Weinh)-20260.33PMID:41736683-
HDAC3 mediates retinal endothelial cell metabolic …SupportingMECHActa Pharmacol …-20260.33PMID:41023273-
β-Hydroxybutyrate improves glymphatic system funct…SupportingMECHActa Pharmacol …-20260.33PMID:41535708-
Histone deacetylases: Function in tumor developmen…SupportingCLINOncol Lett-20260.33PMID:41783166-
Metabolomics identifies riboflavin as a therapeuti…SupportingCLINJ Nutr Biochem-20260.33PMID:41352543-
Regulatory B Cells at the Crossroads of Epigenetic…SupportingGENEClin Rev Allerg… MODERATE2026-PMID:41949720-
Histone decrotonylation plays a distinct role in H…SupportingMECHSci Adv MODERATE2026-PMID:41961925-
Legacy Card View — expandable citation cards

Supporting Evidence 34

HDAC3 has dual roles in brain function MEDIUM
Exp Biol Med (Maywood) · 2020 · PMID:32486848 · Q:0.33
ABSTRACT

Brain development and degeneration are highly complex processes that are regulated by a large number of molecules and signaling pathways the identities of which are being unraveled. Accumulating evidence points to histone deacetylases and epigenetic mechanisms as being important regulators of these processes. In this review, we describe that histone deacetylase-3 (HDAC3) is a particularly crucial regulator of both neurodevelopment and neurodegeneration. In addition, HDAC3 regulates memory formation, synaptic plasticity, and the cognitive impairment associated with normal aging. Understanding how HDAC3 functions contributes to the normal development and functioning of the brain while also promoting neurodegeneration could lead to the development of therapeutic approaches for neurodevelopmental, neuropsychiatric, and neurodegenerative disorders.

HDAC inhibitors improve learning consolidation in neurodegeneration models MEDIUM
Mol Cell Neurosci · 2008 · PMID:18638560 · Q:0.33
ABSTRACT

Histone deacetylases (HDAC) are enzymes that maintain chromatin in a condensate state, related with absence of transcription. We have studied the role of HDAC on learning and memory processes. Both eyeblink classical conditioning (EBCC) and object recognition memory (ORM) induced an increase in histone H3 acetylation (Ac-H3). Systemic treatment with HDAC inhibitors improved cognitive processes in EBCC and in ORM tests. Immunohistochemistry and gene expression analyses indicated that administration of HDAC inhibitors decreased the stimulation threshold for Ac-H3, and gene expression to reach the levels required for learning and memory. Finally, we evaluated the effect of systemic administration of HDAC inhibitors to mice models of neurodegeneration and aging. HDAC inhibitors reversed learning and consolidation deficits in ORM in these models. These results point out HDAC inhibitors as candidate agents for the palliative treatment of learning and memory impairments in aging and in neurod

Selective chemical modulation favors oligodendrocyte lineage progression MEDIUM
Chem Biol · 2014 · PMID:24954007 · Q:0.33
ABSTRACT

Lysine acetylation regulates gene expression through modulating protein-protein interactions in chromatin. Chemical inhibition of acetyl-lysine binding bromodomains of the major chromatin regulators BET (bromodomain and extraterminal domain) proteins has been shown to effectively block cell proliferation in cancer and inflammation. However, whether selective inhibition of individual BET bromodomains has distinctive functional consequences remains only partially understood. In this study, we show that selective chemical inhibition of the first bromodomain of BET proteins using our small-molecule inhibitor, Olinone, accelerated the progression of mouse primary oligodendrocyte progenitors toward differentiation, whereas inhibition of both bromodomains of BET proteins hindered differentiation. This effect was target specific, as it was not detected in cells treated with inactive analogs and independent of any effect on proliferation. Therefore, selective chemical modulation of individual b

Histone acetylation significantly impacts neurobehavioral changes in neurodegenerative disorders MEDIUM
Epigenomics · 2024 · PMID:38321930 · Q:0.33
ABSTRACT

Recent genomics and epigenetic advances have empowered the exploration of DNA/RNA methylation and histone modifications crucial for gene expression in response to stress, aging and disease. Interest in understanding neuronal plasticity's epigenetic mechanisms, influencing brain rewiring amid development, aging and neurodegenerative disorders, continues to grow. Histone acetylation dysregulation, a commonality in diverse brain disorders, has become a therapeutic focus. Histone acetyltransferases and histone deacetylases have emerged as promising targets for neurodegenerative disorder treatment. This review delves into histone acetylation regulation, potential therapies and future perspectives for disorders like Alzheimer's, Parkinson's and Huntington's. Exploring genetic-environmental interplay through models and studies reveals molecular changes, behavioral insights and early intervention possibilities targeting the epigenome in at-risk individuals. Scientists have made progress in und

Melatonin attenuates chronic sleep deprivation-induced cognitive deficits and HDAC3-Bmal1/clock interruption. MEDIUM
CNS Neurosci Ther · 2024 · PMID:37721401 · Q:0.33
ABSTRACT

BACKGROUND AND AIMS: Sleep is predicted as a key modulator of cognition, but the underlying mechanisms are poorly understood. In this study, we investigated the effects of melatonin on chronic rapid eye movement sleep deprivation (CRSD)-induced cognitive impairment and circadian dysfunction in rat models. METHODS: Thirty-six Sprague-Dawley male rats were divided into three groups: CRSD with saline treatment, CRSD with chronic melatonin injection (20 mg/kg/day), and non-sleep-deprived control. The cognitive behavioral tests as well as the expression of clocks and HDAC3 were evaluated in all groups. RESULTS: CRSD significantly reduced recognition index in novel object location, increased escape latency and distance traveling in Morris water maze while melatonin treatment attenuated CRSD-induced hippocampal-dependent spatial learning and memory deficits. Furthermore, the mRNAs of brain and muscle aryl hydrocarbon receptor nuclear translocator-like 1(Bmal1) and circadian locomotor output c

Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestin… MEDIUM
Microbiota-derived butyrate restricts tuft cell differentiation via histone deacetylase 3 to modulate intestinal type 2 immunity.
Immunity · 2024 · PMID:38295798 · Q:0.33
ABSTRACT

Tuft cells in mucosal tissues are key regulators of type 2 immunity. Here, we examined the impact of the microbiota on tuft cell biology in the intestine. Succinate induction of tuft cells and type 2 innate lymphoid cells was elevated with loss of gut microbiota. Colonization with butyrate-producing bacteria or treatment with butyrate suppressed this effect and reduced intestinal histone deacetylase activity. Epithelial-intrinsic deletion of the epigenetic-modifying enzyme histone deacetylase 3 (HDAC3) inhibited tuft cell expansion in vivo and impaired type 2 immune responses during helminth infection. Butyrate restricted stem cell differentiation into tuft cells, and inhibition of HDAC3 in adult mice and human intestinal organoids blocked tuft cell expansion. Collectively, these data define a HDAC3 mechanism in stem cells for tuft cell differentiation that is dampened by a commensal metabolite, revealing a pathway whereby the microbiota calibrate intestinal type 2 immunity.

HDAC3 aberration-incurred GPX4 suppression drives renal ferroptosis and AKI-CKD progression. MEDIUM
Redox Biol · 2023 · PMID:37890360 · Q:0.33
ABSTRACT

Acute kidney injury (AKI) progression to chronic kidney disease (CKD) represents a unique renal disease setting characterized by early renal cellular injury and regulated cell death, and later renal fibrosis, of which the critical role and nature of ferroptosis are only partially understood. Here, we report that renal tubular epithelial ferroptosis caused by HDAC3 (histone deacetylase 3) aberration and the resultant GPX4 suppression drives AKI-CKD progression. In mouse models of AKI-CKD transition induced by nephrotoxic aristolochic acid (AA) and folic acid (FA), renal tubular epithelial ferroptosis occurred early that coincided with preferential HDAC3 elevation and marked suppression of a core anti-ferroptosis enzyme GPX4 (glutathione peroxidase 4). Intriguingly, genetic Hdac3 knockout or administration of a HDAC3-selective inhibitor RGFP966 effectively mitigated the GPX4 suppression, ferroptosis and the fibrosis-associated renal functional loss. In cultured tubular epithelial cells,

HDAC3 deficiency protects against acute lung injury by maintaining epithelial barrier integrity through preser… MEDIUM
HDAC3 deficiency protects against acute lung injury by maintaining epithelial barrier integrity through preserving mitochondrial quality control.
Redox Biol · 2023 · PMID:37244125 · Q:0.33
ABSTRACT

Sepsis is one common cause of acute lung injury (ALI) and acute respiratory distress syndrome (ARDS), which is closely associated with high mortality in intensive care units (ICU). Histone deacetylase 3 (HDAC3) serves as an important epigenetic modifying enzyme which could affect chromatin structure and transcriptional regulation. Here, we explored the effects of HDAC3 in type II alveolar epithelial cells (AT2) on lipopolysaccharide (LPS)-induced ALI and shed light on potential molecular mechanisms. We generated ALI mouse model with HDAC3 conditional knockout mice (Sftpc-cre; Hdac3f/f) in AT2 and the roles of HDAC3 in ALI and epithelial barrier integrity were investigated in LPS-treated AT2. The levels of HDAC3 were significantly upregulated in lung tissues from mice with sepsis and in LPS-treated AT2. HDAC3 deficiency in AT2 not only decreased inflammation, apoptosis, and oxidative stress, but also maintained epithelial barrier integrity. Meanwhile, HDAC3 deficiency in LPS-treated AT2

HDAC3 inhibition ameliorates ischemia/reperfusion-induced brain injury by regulating the microglial cGAS-STING… MEDIUM
HDAC3 inhibition ameliorates ischemia/reperfusion-induced brain injury by regulating the microglial cGAS-STING pathway.
Theranostics · 2020 · PMID:32863951 · Q:0.33
ABSTRACT

Rationale: It is known that neuroinflammation plays a critical and detrimental role in the development of cerebral ischemia/reperfusion (I/R), but the regulation of the cyclic GMP-AMP synthase (cGAS)-mediated innate immune response in I/R-induced neuroinflammation is largely unexplored. This study aimed to investigate the function and regulatory mechanism of cGAS in I/R-induced neuroinflammation and brain injury, and to identify possible strategies for the treatment of ischemic stroke. Methods: To demonstrate that microglial histone deacetylase 3 (HDAC3) regulates the microglial cGAS-stimulator of interferon genes (cGAS-STING) pathway and is involved in I/R-induced neuroinflammation and brain injury, a series of cell biological, molecular, and biochemical approaches were utilized. These approaches include transient middle cerebral artery occlusion (tMCAO), real-time polymerase chain reaction (PCR), RNA sequencing, western blot, co-immunoprecipitation, chromosome-immunoprecipitation, en

Deletion of myeloid HDAC3 promotes efferocytosis to ameliorate retinal ischemic injury. MEDIUM
J Neuroinflammation · 2024 · PMID:38997746 · Q:0.48
ABSTRACT

Ischemia-induced retinopathy is a hallmark finding of common visual disorders including diabetic retinopathy (DR) and central retinal artery and vein occlusions. Treatments for ischemic retinopathies fail to improve clinical outcomes and the design of new therapies will depend on understanding the underlying disease mechanisms. Histone deacetylases (HDACs) are an enzyme class that removes acetyl groups from histone and non-histone proteins, thereby regulating gene expression and protein function. HDACs have been implicated in retinal neurovascular injury in preclinical studies in which nonspecific HDAC inhibitors mitigated retinal injury. Histone deacetylase 3 (HDAC3) is a class I histone deacetylase isoform that plays a central role in the macrophage inflammatory response. We recently reported that myeloid cells upregulate HDAC3 in a mouse model of retinal ischemia-reperfusion (IR) injury. However, whether this cellular event is an essential contributor to retinal IR injury is unknown

A phenotypic screening platform for identifying chemical modulators of astrocyte reactivity. MEDIUM
Nat Neurosci · 2024 · PMID:38378993 · Q:0.60
ABSTRACT

Disease, injury and aging induce pathological reactive astrocyte states that contribute to neurodegeneration. Modulating reactive astrocytes therefore represent an attractive therapeutic strategy. Here we describe the development of an astrocyte phenotypic screening platform for identifying chemical modulators of astrocyte reactivity. Leveraging this platform for chemical screening, we identify histone deacetylase 3 (HDAC3) inhibitors as effective suppressors of pathological astrocyte reactivity. We demonstrate that HDAC3 inhibition reduces molecular and functional characteristics of reactive astrocytes in vitro. Transcriptional and chromatin mapping studies show that HDAC3 inhibition disarms pathological astrocyte gene expression and function while promoting the expression of genes associated with beneficial astrocytes. Administration of RGFP966, a small molecule HDAC3 inhibitor, blocks reactive astrocyte formation and promotes neuroprotection in vivo in mice. Collectively, these resu

NKAPL facilitates transcription pause-release and bridges elongation to initiation during meiosis exit. MEDIUM
Nat Commun · 2025 · PMID:39824811 · Q:0.60
ABSTRACT

Transcription elongation, especially RNA polymerase II (Pol II) pause-release, is less studied than transcription initiation in regulating gene expression during meiosis. It is also unclear how transcription elongation interplays with transcription initiation. Here, we show that depletion of NKAPL, a testis-specific protein distantly related to RNA splicing factors, causes male infertility in mice by blocking the meiotic exit and downregulating haploid genes. NKAPL binds to promoter-associated nascent transcripts and co-localizes with DNA-RNA hybrid R-loop structures at GAA-rich loci to enhance R-loop formation and facilitate Pol II pause-release. NKAPL depletion prolongs Pol II pauses and stalls the SOX30/HDAC3 transcription initiation complex on the chromatin. Genetic variants in NKAPL are associated with azoospermia in humans, while mice carrying an NKAPL frameshift mutation (M349fs) show defective meiotic exit and transcriptomic changes similar to NKAPL depletion. These findings id

Epigenetic regulation of general anesthesia-induced neonatal neurodegeneration. MEDIUM
Oncotarget · 2017 · PMID:28086213 · Q:0.33
Ketogenic diet attenuates neuroinflammation and induces conversion of M1 microglia to M2 in an EAE model of mu… MEDIUM
Ketogenic diet attenuates neuroinflammation and induces conversion of M1 microglia to M2 in an EAE model of multiple sclerosis by regulating the NF-κB/NLRP3 pathway and inhibiting HDAC3 and P2X7R activation.
Food Funct · 2023 · PMID:37466915 · Q:0.33
ABSTRACT

Multiple sclerosis (MS) is an autoimmune disorder characterized by demyelination and neurodegeneration in the central nervous system (CNS); severe symptoms lead MS patients to use complementary treatments. Ketogenic diet (KD) shows wide neuroprotective effects, but the precise mechanisms underlying the therapeutic activity of KD in MS are unclear. The present study established a continuous 24 days experimental autoimmune encephalomyelitis (EAE) mouse model with or without KD. The changes in motor function, pathological hallmarks of EAE, the status of microglia, neuroinflammatory response and intracellular signaling pathways in mice were detected by the rotarod test, histological analysis, real-time PCR (RT-PCR) and western blotting. Our results showed that KD could prevent motor deficiency, reduce clinical scores, inhibit demyelination, improve pathological lesions and suppress microglial activation in the spinal cord of EAE mice. Meanwhile, KD shifted microglial polarization toward th

HDAC3 Inhibition Alleviates High-Glucose-Induced Retinal Ganglion Cell Death through Inhibiting Inflammasome A… MEDIUM
HDAC3 Inhibition Alleviates High-Glucose-Induced Retinal Ganglion Cell Death through Inhibiting Inflammasome Activation.
Biomed Res Int · 2022 · PMID:36046456 · Q:0.33
ABSTRACT

PURPOSE: The exact effects of histone deacetylase 3 (HDAC3) inhibition in DR related retinal ganglion cells (RGCs) death remained unclear. This study is aimed at detecting the influence of HDAC3 on the high-glucose-induced retinal ganglion cell death. METHODS: The retinal HDAC3 expression in DR of different time points was analyzed by immunohistochemical assay and western blot. Besides, the expression of HDAC3 and both retinal thickness and RGC loss were analyzed. The effects of HDAC3 inhibitor on cell viability, oxidative stress, and apoptosis in high-glucose- (HG-) treated RGCs were analyzed. Both inflammatory and antioxidative factors were detected by ELISA. RESULTS: Advanced effects of HDAC3 inhibition on the expression of NLRP3 inflammasome were detected using western blots. High HDAC3 expression was detected only in the late DR mice (4 months of diabetes duration) but not early DR mice (2 months of diabetes duration). The immunohistochemical assay showed that HDAC3 expression was

Selective toxicity by HDAC3 in neurons: regulation by Akt and GSK3beta. MEDIUM
J Neurosci · 2011 · PMID:21289184 · Q:0.54
ABSTRACT

Although it is well established that pharmacological inhibitors of classical histone deacetylases (HDACs) are protective in various in vivo models of neurodegenerative disease, the identity of the neurotoxic HDAC(s) that these inhibitors target to exert their protective effects has not been resolved. We find that HDAC3 is a protein with strong neurotoxic activity. Forced expression of HDAC3 induces death of otherwise healthy rat cerebellar granule neurons, whereas shRNA-mediated suppression of its expression protects against low-potassium-induced neuronal death. Forced expression of HDAC3 also promotes the death of rat cortical neurons and hippocampally derived HT22 cells, but has no effect on the viability of primary kidney fibroblasts or the HEK293 and HeLa cell lines. This suggests that the toxic effect of HDAC3 is cell selective and that neurons are sensitive to it. Neurotoxicity by HDAC3 is inhibited by treatment with IGF-1 as well as by the expression of a constitutively active f

Determination of Slow-Binding HDAC Inhibitor Potency and Subclass Selectivity. MEDIUM
ACS Med Chem Lett · 2022 · PMID:35586419 · Q:0.33
ABSTRACT

Histone deacetylases (HDACs) 1-3 regulate chromatin structure and gene expression. These three enzymes are targets for cancer chemotherapy and have been studied for the treatment of immune disorders and neurodegeneration, but there is a lack of selective pharmacological tool compounds to unravel their individual roles. Potent inhibitors of HDACs 1-3 often display slow-binding kinetics, which causes a delay in inhibitor-enzyme equilibration and may affect assay readout. Here we compare the potencies and selectivities of slow-binding inhibitors measured by discontinuous and continuous assays. We find that entinostat, a clinical candidate, inhibits HDACs 1-3 by a two-step slow-binding mechanism with lower potencies than previously reported. In addition, we show that RGFP966, commercialized as an HDAC3-selective probe, is a slow-binding inhibitor with inhibitor constants of 57, 31, and 13 nM against HDACs 1-3, respectively. These data highlight the need for thorough kinetic investigation i

Targeting HDAC3 Activity with RGFP966 Protects Against Retinal Ganglion Cell Nuclear Atrophy and Apoptosis Aft… MEDIUM
Targeting HDAC3 Activity with RGFP966 Protects Against Retinal Ganglion Cell Nuclear Atrophy and Apoptosis After Optic Nerve Injury.
J Ocul Pharmacol Ther · 2018 · PMID:29211617 · Q:0.33
ABSTRACT

PURPOSE: HDAC3 regulates nuclear atrophy as an early response to axonal injury in retinal ganglion cells (RGCs) following optic nerve crush (ONC). Since conditional knockout of Hdac3 prevents nuclear atrophy post ONC, HDAC3 selective inhibition with RGFP966 through localized and systemic dosing of RGFP966 is necessary for application to acute and chronic models of optic nerve injury. METHODS: C57BL/6 mice were injected intravitreally with 1-10 μM RGFP966 immediately following ONC, and retinas were analyzed at 5, 7, and 14 days for metrics of nuclear atrophy and cell loss. Mice were similarly assessed after intraperitoneal (IP) injections with RGFP966 doses of 2-10 mg/kg, and eyes were harvested at 5, 14, and 28 days after ONC. H&E and BrdU staining were used to analyze toxicity to off-target tissues after 14 days of daily treatment with RGFP966. RESULTS: A single intravitreal injection of RGFP966 prevented histone deacetylation, heterochromatin formation, apoptosis, and DNA damage at 5

Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death. MEDIUM
J Biol Chem · 2012 · PMID:22918830 · Q:0.49
ABSTRACT

Both neuroprotective and neurotoxic roles have previously been described for histone deacetylase-1 (HDAC1). Here we report that HDAC1 expression is elevated in vulnerable brain regions of two mouse models of neurodegeneration, the R6/2 model of Huntington disease and the Ca(2+)/calmodulin-dependent protein kinase (CaMK)/p25 double-transgenic model of tauopathic degeneration, suggesting a role in promoting neuronal death. Indeed, elevating HDAC1 expression by ectopic expression promotes the death of otherwise healthy cerebellar granule neurons and cortical neurons in culture. The neurotoxic effect of HDAC1 requires interaction and cooperation with HDAC3, which has previously been shown to selectively induce the death of neurons. HDAC1-HDAC3 interaction is greatly elevated under conditions of neurodegeneration both in vitro and in vivo. Furthermore, the knockdown of HDAC3 suppresses HDAC1-induced neurotoxicity, and the knockdown of HDAC1 suppresses HDAC3 neurotoxicity. As described previously for HDAC3, the neurotoxic effect of HDAC1 is inhibited by treatment with IGF-1, the expression of Akt, or the inhibition of glycogen synthase kinase 3β (GSK3β). In addition to HDAC3, HDAC1 has been shown to interact with histone deacetylase-related protein (HDRP), a truncated form of HDAC9, whose expression is down-regulated during neuronal death. In contrast to HDAC3, the interaction between HDRP and HDAC1 protects neurons from death, an effect involving acquisition of the deacetylase act

HOX Code-Based Stratification Reveals RUNX1T1-HDAC Reprogramming as a Targetable Driver of Lineage Plasticity … MEDIUM
HOX Code-Based Stratification Reveals RUNX1T1-HDAC Reprogramming as a Targetable Driver of Lineage Plasticity Across Cancers.
Cancer Lett · 2026 · PMID:41912135 · Q:0.33
ABSTRACT

Cancer remains a leading cause of death worldwide, with lineage plasticity emerging as a hallmark that drives therapy resistance and tumor progression by enabling cancer cells to alter identity and evade targeted therapies. Although genomic and transcriptomic aberrations correlate with lineage plasticity, the absence of scalable cross-cancer markers to rapidly identify plastic subtypes has limited predictive utility. Homeobox (HOX) genes encode transcription factors that define tissue identity through distinct expression patterns, or HOX codes, within specific lineages. By analyzing multi-omics data encompassing 39 HOX genes across more than 80,000 RNA-seq samples across 23 cancer types spanning 114 cancer subtypes, we found that HOX code expression robustly stratifies lineage-constrained and lineage-plastic states at a cross-cancer level. This framework revealed previously unrecognized lineage-plastic subtypes in prostate cancer, lung cancer, and acute myeloid leukemia (AML), each dis

Microglial HDAC3 inhibits the migration of CD8-positive T cell in the development of EAE by restraining the ex… MEDIUM
Microglial HDAC3 inhibits the migration of CD8-positive T cell in the development of EAE by restraining the expression of CCL5.
Cell Biosci · 2026 · PMID:41888851 · Q:0.59
EXPRESS: Identification of Acetylation-Related Molecular Signatures in Knee Osteoarthritis Patients with Signi… MEDIUM
EXPRESS: Identification of Acetylation-Related Molecular Signatures in Knee Osteoarthritis Patients with Significant Response to Warm-Needle Acupuncture Using Machine-Learning Approaches.
Mol Pain · 2026 · PMID:41876476 · Q:0.33
ABSTRACT

OBJECTIVE: This study aims to delineate remodeling effects of acetylation-related gene expression in knee osteoarthritis (KOA) patients markedly responsive to warm-needle acupuncture (WNA) and identify key genes and immunoregulatory mechanisms. METHODS: A prospective self-paired design recruited 34 KOA patients to donate whole-blood samples before and after WNA treatment and further enroll them to perform transcriptome sequencing. Differential expression analysis identified acetylation-related genes followed by enrichment and protein-protein interaction analyses. Key genes were extracted via feature selection based on LASSO and SVM-RFE methods and further used to establish and validate a multigene logistic regression model. Consensus clustering was implemented to divide two acetylation subtypes (ACEcluster A/B) and further explore their immune characteristics by ssGSEA and immune-cell infiltration profiling. RESULTS: After treatment, samples exhibited global up-regulation of acetylatio

Myeloid HDAC3 deletion protects against traumatic optic injury. MEDIUM
Cell Death Discov · 2026 · PMID:41851071 · Q:0.59
ABSTRACT

Traumatic optic neuropathy (TON) occurs due to trauma to the optic nerve, resulting in blindness. Current management focuses primarily on supportive care, highlighting an urgent need to identify novel treatment targets. Neuronal expression of the enzyme histone deacetylase 3 (HDAC3) has been previously implicated in retinal ganglion cell (RGC) degeneration after optic nerve crush (ONC), a model of TON. Here we investigated the role of myeloid HDAC3 (i.e., HDAC3 expressed in microglia and macrophages) in RGC loss, axonal degeneration, and efferocytosis, a reparative process by which phagocytic myeloid cells engulf apoptotic cells. ONC injury was performed on myeloid-specific HDAC3 knockout (KO) and floxed control mice. Neurodegeneration and efferocytosis assays were assessed using retina flatmount immunolabeling and confocal imaging. RGC function was evaluated using pattern electroretinography (PERG). Axonal sprouting was quantified by anterograde transport of cholera toxin B injected intravitreally. Myelin debris clearance was assessed in optic nerves in vivo and in vitro using bone-marrow-derived macrophages isolated from myeloid HDAC3 KO and control mice. Myeloid HDAC3 deletion preserved RGC and improved axonal regeneration after ONC, together with improved retinal function assessed by PERG. Furthermore, the deletion of HDAC3 enhanced the phagocytic function of myeloid cells to effectively remove apoptotic cells and myelin debris, both in vivo and in vitro. These protective

LncRNA SNHG5 promotes macrophage lipid accumulation and aggravates atherosclerosis by targeting the miR-216a-5… MEDIUM
LncRNA SNHG5 promotes macrophage lipid accumulation and aggravates atherosclerosis by targeting the miR-216a-5p/HDAC3/ABCA1 axis.
Biochim Biophys Acta Mol Cell Biol Lipids · 2026 · PMID:41844502 · Q:0.59
ABSTRACT

Long noncoding RNA small nucleolar RNA host gene 5 (SNHG5) has been implicated in cell death, glucose homeostasis, and tumor progression, yet its role in atherosclerosis (AS) remains unclear. In this study, SNHG5 expression was markedly elevated in aortic tissues of high-fat diet-fed apoE-/- mice and in ox-LDL-stimulated THP-1 macrophages. Lentiviral-mediated SNHG5 silencing in vivo reduced plaque burden, attenuated lipid deposition, increased collagen content, and decreased systemic inflammation. Moreover, SNHG5 knockdown increased plasma HDL-C and promoted reverse cholesterol transport. In mouse peritoneal macrophages and THP-1-derived foam cells, SNHG5 silencing enhanced cholesterol efflux to lipid-free apoA-I without affecting uptake, accompanied by upregulation of ABCA1. LXRα expression remained unchanged, whereas HDAC3 was downregulated; HDAC3 overexpression reversed the effects of SNHG5 knockdown on ABCA1 expression, cholesterol efflux, and foam cell formation. Subcellular fract

The paper suggests GABA can suppress HDAC2/3 in astrocytes, which aligns with the hypothesis of targeted HDAC3… MEDIUM
The paper suggests GABA can suppress HDAC2/3 in astrocytes, which aligns with the hypothesis of targeted HDAC3 inhibition for neuroinflammation reduction.
Foods · 2026 · PMID:41829110 · Q:0.33
ABSTRACT

As a widely available dietary supplement, γ-Aminobutyric acid (GABA) exhibits potential for early intervention against Alzheimer's disease (AD). This study demonstrates that GABA alleviates AD neuroinflammation, and its suppression of astrocytic pro-inflammatory cytokine expression through histone deacetylase (HDAC2/3) inhibition contributes to this effect. Here, in both the cerebral cortex of AD mice and Aβ-exposed U251 cells, pro-inflammatory cytokines and HDAC2/3 expression levels were elevat

Demonstrates GR/HDAC3's role in regulating cognitive signaling pathways, supporting the hypothesis's molecular… MEDIUM
Demonstrates GR/HDAC3's role in regulating cognitive signaling pathways, supporting the hypothesis's molecular mechanism.
FASEB J · 2026 · PMID:41837847 · Q:0.33
ABSTRACT

Prenatal hypoxia (PH) is a common pregnancy complication that can lead to cognitive impairment in the offspring, but the underlying mechanisms remain unclear. In this study, we established a model of PH by exposing C57 mice to hypoxia (10.5% oxygen) environment from gestational day (GD) 12.5-17.5. We found that PH resulted in cognitive impairment and reduced hippocampal neurogenesis in male offspring compared to control offspring. Mechanistically, PH is a form of prenatal stress that promotes pl

Discovery of a HDAC3 degrader with anti-inflammatory activity provides additional evidence for targeted HDAC3 … MEDIUM
Discovery of a HDAC3 degrader with anti-inflammatory activity provides additional evidence for targeted HDAC3 modulation.
J Med Chem · 2026 · PMID:41812251 · Q:0.33
ABSTRACT

Histone deacetylase 3 (HDAC3) plays a pivotal role in inflammation by regulating transcriptional programs and promoting NLRP3 inflammasome activation. Here, we report the discovery of GS-1, a covalent HDAC3 degrader derived from a previously reported 18β-glycyrrhetinic acid derivative A18 via structural optimization. It selectively degraded HDAC3 in THP-1 cells, with minimal enzymatic HDAC inhibition and low cytotoxicity. LC-MS/MS analysis revealed covalent modification at Lys367, and molecular

SATB2 Mediates H3K9 Delactylation by Recruiting HDAC3 to Repress LCN2 and Inhibit Lung Tumor Growth and Metast…
SATB2 Mediates H3K9 Delactylation by Recruiting HDAC3 to Repress LCN2 and Inhibit Lung Tumor Growth and Metastasis.
Adv Sci (Weinh) · 2026 · PMID:41736683 · Q:0.33
HDAC3 mediates retinal endothelial cell metabolic reprogramming and angiogenesis.
Acta Pharmacol Sin · 2026 · PMID:41023273 · Q:0.33
β-Hydroxybutyrate improves glymphatic system function and alleviates cerebral edema in mice after ischemic str…
β-Hydroxybutyrate improves glymphatic system function and alleviates cerebral edema in mice after ischemic stroke.
Acta Pharmacol Sin · 2026 · PMID:41535708 · Q:0.33
Histone deacetylases: Function in tumor development and therapeutic prospects (Review).
Oncol Lett · 2026 · PMID:41783166 · Q:0.33
Metabolomics identifies riboflavin as a therapeutic agent for acute pancreatitis.
J Nutr Biochem · 2026 · PMID:41352543 · Q:0.33
Regulatory B Cells at the Crossroads of Epigenetic Control and Immune Homeostasis MODERATE
Clin Rev Allergy Immunol · 2026 · PMID:41949720
Histone decrotonylation plays a distinct role in HIV latency MODERATE
Sci Adv · 2026 · PMID:41961925

Opposing Evidence 8

PROTAC-Based HDAC Degradation: A Paradigm Shift in Targeted Epigenetic Therapies MEDIUM
ChemMedChem · 2025 · PMID:41160773 · Q:0.33
ABSTRACT

Proteolysis-targeting chimeras (PROTACs) have emerged as an excellent strategy for targeted protein degradation by the ubiquitin-proteasome system. Traditional inhibitors suppress the enzymatic activity, but the PROTACs utilize the method of total degradation of protein, promising prolonged and target-specific therapeutic efficacy. Histone deacetylases (HDACs) are epigenetic regulators, implicated in most cancers, neurodegeneration, and other inflammatory diseases. Therefore, HDAC-PROTAC development provides a unique approach to overcome the limitations of conventional HDAC inhibitors, including off-target effects, short duration of action, and resistance mechanisms. Recent advancements in HDAC-PROTACs lead to the design of selective degraders for specific isoforms of HDACs, including HDAC3, HDAC4, HDAC6, and HDAC8, representing superior efficacy in preclinical studies. This review highlights the progress of HDAC-targeting PROTACs, focusing on structural optimization, selectivity enhancements, and therapeutic applications with their degradation potential. However, various challenges include poor pharmacokinetics and bioavailability, and limited in vivo validation for further safety, efficacy analysis. Further research and optimization efforts will be pivotal in translating HDAC-PROTACs into clinically viable therapies for cancer and other epigenetic disorders.

Epigenetic Modulation and Neuroprotective Effects of Neurofabine-C in a Transgenic Model of Alzheimer's Diseas… MEDIUM
Epigenetic Modulation and Neuroprotective Effects of Neurofabine-C in a Transgenic Model of Alzheimer's Disease
Genes (Basel) · 2025 · PMID:41153431 · Q:0.33
ABSTRACT

Background: Currently, there are limited therapeutic or preventative strategies for neurodegenerative disorders due to the challenges in alleviating the progressive neuronal loss and neuroinflammation which are the primary characteristics of these diseases, ultimately leading to cell death and functional impairment. Cocoa-derived flavanols (Theobroma cacao) have been studied as potential bioactive compounds to modify and reverse various inflammation-associated diseases because of their remarkable antioxidant properties and capacity to modulate metabolic imbalance and reactive inflammatory responses. The faba bean (Vicia faba) extract obtained through nondenaturing biotechnological processes is a potent dopamine (DA) enhancer that has shown promising results as a neuroprotective agent against degeneration. Objective: This study will examine the synergistic effects of Neurofabine-C, a hybrid compound derived from cocoa and faba bean extracts, on various brain biomarkers in mice related to inflammatory, metabolic, and neurodegenerative processes. Methods: A triple-transgenic mouse model of neurodegeneration was treated with Neurofabine-C, and biomolecular data were obtained by performing biochemical and immunohistochemical analysis. Results: Neurofabine-C prevented neuronal degeneration (NeuN), mitigated the neuro-inflammatory processes triggered (decreased expression of reactive astrocytes (GFAP)), and induced an increase in neurogenesis in the treated cortical mice brain (PAX6

Epigenetic therapy meets targeted protein degradation: HDAC-PROTACs in cancer treatment MEDIUM
Future Med Chem · 2025 · PMID:40667573 · Q:0.33
ABSTRACT

Epigenetic therapy and targeted protein degradation have converged in the development of histone deacetylases (HDACs)-targeting proteolysis-targeting chimeras (PROTACs), offering a novel approach to cancer treatment. Unlike traditional HDAC inhibitors, HDAC-PROTACs facilitate selective degradation of HDACs via the ubiquitin-proteasome system, effectively eliminating both enzymatic and scaffolding functions. These bifunctional molecules recruit HDACs to E3 ligases, triggering ubiquitination and subsequent proteasomal degradation. PROTACs demonstrate catalytic activity, requiring lower dosages while sustaining prolonged effects compared to inhibitors. Advances in PROTAC chemistry have led to the development of selective degraders targeting distinct HDAC classes. Class I HDAC-targeting PROTACs, such as PROTAC 1 and PROTAC 2, induce robust degradation of HDAC1-3 with nanomolar DC50 values, showing promising anti-cancer activity. Similarly, class IIa and IIb HDAC PROTACs, including selective HDAC4 and HDAC6 degraders, exhibit potent anti-proliferative effects in leukemia, lymphoma, and multiple myeloma models. Despite these advancements, challenges persist in optimizing selectivity, linker design, and bioavailability while mitigating off-target effects. Future strategies include enhancing tumor-specific delivery, refining ligand-E3 ligase compatibility, and integrating combination therapies to overcome resistance. This review explores the mechanistic insights, therapeutic potentia

Understanding the Role of Histone Deacetylase and their Inhibitors in Neurodegenerative Disorders: Current Tar… MEDIUM
Understanding the Role of Histone Deacetylase and their Inhibitors in Neurodegenerative Disorders: Current Targets and Future Perspective.
Curr Neuropharmacol · 2022 · PMID:34151764 · Q:0.33
ABSTRACT

Neurodegenerative diseases are a group of pathological conditions that cause motor incordination (jerking movements), cognitive and memory impairments result from degeneration of neurons in a specific area of the brain. Oxidative stress, mitochondrial dysfunction, excitotoxicity, neuroinflammation, neurochemical imbalance and histone deacetylase enzymes (HDAC) are known to play a crucial role in neurodegeneration. HDAC is classified into four categories (class I, II, III and class IV) depending upon their location and functions. HDAC1 and 2 are involved in neurodegeneration, while HDAC3-11 and class III HDACs are beneficial as neuroprotective. HDACs are localized in different parts of the brain- HDAC1 (hippocampus and cortex), HDAC2 (nucleus), HDAC3, 4, 5, 7 and 9 (nucleus and cytoplasm), HDAC6 & HDAC7 (cytoplasm) and HDAC11 (Nucleus, cornus ammonis 1 and spinal cord). In pathological conditions, HDAC up-regulates glutamate, phosphorylation of tau, and glial fibrillary acidic proteins while down-regulating BDNF, Heat shock protein 70 and Gelsolin. Class III HDACs are divided into seven sub-classes (SIRT1-SIRT7). Sirtuins are localized in the different parts of the brain and neuron -Sirt1 (nucleus), Sirt2 (cortex, striatum, hippocampus and spinal cord), Sirt3 (mitochondria and cytoplasm), Sirt4, Sirt5 & Sirt6 (mitochondria), Sirt7 (nucleus) and Sirt8 (nucleolus). SIRTs (1, 3, 4, and 6) are involved in neuronal survival, proliferation and modulating stress response, and SIRT2 i

The Two Faces of HDAC3: Neuroinflammation in Disease and Neuroprotection in Recovery. MEDIUM
Epigenomics · 2024 · PMID:39513228 · Q:0.33
ABSTRACT

Histone deacetylase 3 (HDAC3) is a critical regulator of gene expression, influencing a variety of cellular processes in the central nervous system. As such, dysfunction of this enzyme may serve as a key driver in the pathophysiology of various neuropsychiatric disorders and neurodegenerative diseases. HDAC3 plays a crucial role in regulating neuroinflammation, and is now widely recognized as a major contributor to neurological conditions, as well as in promoting neuroprotective recovery following brain injury, hemorrhage and stroke. Emerging evidence suggests that pharmacological inhibition of HDAC3 can mitigate behavioral and neuroimmune deficits in various brain diseases and disorders, offering a promising therapeutic strategy. Understanding HDAC3 in the healthy brain lays the necessary foundation to define and resolve its dysfunction in a disease state. This review explores the mechanisms of HDAC3 in various cell types and its involvement in disease pathology, emphasizing the potential of HDAC3 inhibition to address neuroimmune, gene expression and behavioral deficits in a range of neurodegenerative and neuropsychiatric conditions. Histone deacetylase 3 (HDAC3) is an essential enzyme that helps regulate gene expression in the brain, influencing a variety of processes critical for brain health. Dysfunction of this enzyme may contribute to various brain disorders and diseases, including Alzheimer's disease, Parkinson's disease, Huntington's disease, spinal cord injury, stro

Deficiency of histone deacetylases 3 in macrophage alleviates monosodium urate crystals-induced gouty inflamma… MEDIUM
Deficiency of histone deacetylases 3 in macrophage alleviates monosodium urate crystals-induced gouty inflammation in mice
Arthritis Res Ther · 2024 · PMID:38711064 · Q:0.33
ABSTRACT

BACKGROUND: Gout is caused by monosodium urate (MSU) crystals deposition to trigger immune response. A recent study suggested that inhibition of Class I Histone deacetylases (HDACs) can significantly reduce MSU crystals-induced inflammation. However, which one of HDACs members in response to MSU crystals was still unknown. Here, we investigated the roles of HDAC3 in MSU crystals-induced gouty inflammation. METHODS: Macrophage specific HDAC3 knockout (KO) mice were used to investigate inflammatory profiles of gout in mouse models in vivo, including ankle arthritis, foot pad arthritis and subcutaneous air pouch model. In the in vitro experiments, bone marrow-derived macrophages (BMDMs) from mice were treated with MSU crystals to assess cytokines, potential target gene and protein. RESULTS: Deficiency of HDAC3 in macrophage not only reduced MSU-induced foot pad and ankle joint swelling but also decreased neutrophils trafficking and IL-1β release in air pouch models. In addition, the levels of inflammatory genes related to TLR2/4/NF-κB/IL-6/STAT3 signaling pathway were significantly decreased in BMDMs from HDAC3 KO mice after MSU treatment. Moreover, RGFP966, selective inhibitor of HDAC3, inhibited IL-6 and TNF-α production in BMDMs treated with MSU crystals. Besides, HDAC3 deficiency shifted gene expression from pro-inflammatory macrophage (M1) to anti-inflammatory macrophage (M2) in BMDMs after MSU challenge. CONCLUSIONS: Deficiency of HDAC3 in macrophage alleviates MSU crystal

Targeting HDAC3 Suppresses Ferroptosis and Demyelination in White Matter Injury by Restoring PDK4-Mediated Iro… MEDIUM
Targeting HDAC3 Suppresses Ferroptosis and Demyelination in White Matter Injury by Restoring PDK4-Mediated Iron Homeostasis
CNS Neurosci Ther · 2025 · PMID:40485011 · Q:0.33
ABSTRACT

AIM: White matter injury (WMI), characterized by white matter degeneration and iron deposition, contributes to neurological dysfunction. Histone deacetylase 3 (HDAC3) is implicated in neurodegenerative processes, yet its role in WMI-associated ferroptosis remains unclear. METHODS: Clinical assessments in WMI patients revealed correlations between serum iron, α-synuclein, and antioxidant levels and MRI-confirmed white matter degeneration. In a cuprizone-induced demyelination mouse model, white matter integrity, oligodendrocyte dysfunction, iron accumulation, and lipid peroxidation were evaluated through behavioral testing, histological staining, and biochemical analyses. To identify potential molecular targets of HDAC3-mediated ferroptosis, CUT&Tag sequencing was performed. The involvement of this pathway was further validated in vitro using iron overload assays and in vivo through HDAC3 overexpression via AAV vectors. RESULTS: In the present study, HDAC3 expression was elevated following demyelination and was suppressed by RGFP966 treatment. Brain MRI findings from clinical patients and histological analyses in CPZ-treated mice revealed disrupted iron metabolism following white matter injury, likely driven by increased iron deposition and lipid peroxidation in the affected regions. HDAC3 inhibition alleviated oligodendrocyte lineage dysfunction, preserved myelin integrity, and mitigated cognitive and motor deficits induced by demyelination. CUT&Tag sequencing suggested that t

Histone deacetylase 3 as a novel therapeutic target in multiple myeloma MEDIUM
Leukemia · 2014 · PMID:23913134 · Q:0.33
ABSTRACT

Histone deacetylases (HDACs) represent novel molecular targets for the treatment of various types of cancers, including multiple myeloma (MM). Many HDAC inhibitors have already shown remarkable antitumor activities in the preclinical setting; however, their clinical utility is limited because of unfavorable toxicities associated with their broad range HDAC inhibitory effects. Isoform-selective HDAC inhibition may allow for MM cytotoxicity without attendant side effects. In this study, we demonstrated that HDAC3 knockdown and a small-molecule HDAC3 inhibitor BG45 trigger significant MM cell growth inhibition via apoptosis, evidenced by caspase and poly (ADP-ribose) polymerase cleavage. Importantly, HDAC3 inhibition downregulates phosphorylation (tyrosine 705 and serine 727) of signal transducers and activators of transcription 3 (STAT3). Neither interleukin-6 nor bone marrow stromal cells overcome this inhibitory effect of HDAC3 inhibition on phospho-STAT3 and MM cell growth. Moreover, HDAC3 inhibition also triggers hyperacetylation of STAT3, suggesting crosstalk signaling between phosphorylation and acetylation of STAT3. Importantly, inhibition of HDAC3, but not HDAC1 or 2, significantly enhances bortezomib-induced cytotoxicity. Finally, we confirm that BG45 alone and in combination with bortezomib trigger significant tumor growth inhibition in vivo in a murine xenograft model of human MM. Our results indicate that HDAC3 represents a promising therapeutic target, and validate

Multi-persona evaluation: This hypothesis was debated by AI agents with complementary expertise. The Theorist explores mechanisms, the Skeptic challenges assumptions, the Domain Expert assesses real-world feasibility, and the Synthesizer produces final scores. Expand each card to see their arguments.
Gap Analysis | 4 rounds | 2026-04-02 | View Analysis
🧬 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

0.250.500.75 evidence: evidence_update (2026-04-02T16:38)evidence: market_dynamics (2026-04-02T17:18)debate: debate_engine (2026-04-02T17:18)evidence: market_dynamics_seed (2026-04-02T18:16)evidence: market_dynamics (2026-04-02T19:27)debate: market_dynamics (2026-04-02T21:15)debate: market_dynamics (2026-04-02T22:43)score_update: market_dynamics (2026-04-02T23:28)score_update: market_dynamics (2026-04-02T23:31)score_update: market_dynamics (2026-04-03T00:32)debate: market_dynamics (2026-04-03T00:49)evidence: evidence_batch_update (2026-04-03T01:06)evidence: evidence_batch_update (2026-04-03T01:06)evidence: market_dynamics (2026-04-03T01:46)debate: market_dynamics (2026-04-03T02:18)evidence: market_dynamics (2026-04-03T04:08)evidence: evidence_batch_update (2026-04-04T09:08)evidence: evidence_batch_update (2026-04-13T02:18)evidence: evidence_batch_update (2026-04-13T02:18) 1.00 0.00 2026-04-022026-04-122026-04-27 Market PriceScoreevidencedebate 227 events
7d Trend
Falling
7d Momentum
▼ 4.2%
Volatility
Medium
0.0230
Events (7d)
4
⚡ Price Movement Log Recent 15 events
Event Price Change Source Time
📄 New Evidence $0.582 ▲ 1.7% evidence_batch_update 2026-04-13 02:18
📄 New Evidence $0.572 ▲ 1.6% evidence_batch_update 2026-04-13 02:18
Recalibrated $0.563 ▼ 1.7% 2026-04-12 10:15
Recalibrated $0.573 ▼ 2.7% 2026-04-12 05:13
Recalibrated $0.588 ▼ 0.5% 2026-04-10 15:58
Recalibrated $0.591 ▲ 0.6% 2026-04-10 14:28
Recalibrated $0.588 ▼ 1.7% 2026-04-08 18:39
Recalibrated $0.598 ▲ 1.4% 2026-04-06 04:04
Recalibrated $0.590 ▼ 0.6% 2026-04-04 16:38
Recalibrated $0.593 ▼ 1.3% 2026-04-04 16:02
📄 New Evidence $0.601 ▲ 1.6% evidence_batch_update 2026-04-04 09:08
Recalibrated $0.591 ▼ 22.5% 2026-04-03 23:46
📄 New Evidence $0.763 ▲ 4.5% market_dynamics 2026-04-03 04:08
💬 Debate Round $0.730 ▲ 25.8% market_dynamics 2026-04-03 02:18
📄 New Evidence $0.580 ▼ 1.2% market_dynamics 2026-04-03 01:46

📚 Cited Papers (84)

Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death.
The Journal of biological chemistry (2012) · PMID:22918830
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Figure 1
The cytosolic DNA-sensing pathway is upregulated in microglia after cerebral ischemia/reperfusion (I/R). ( A ) Kyoto encyclopedia of genes and genomes (KEGG) analysis of the upreg...
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Figure 2
Figure 2
The cytosolic DNA sensor cGAS is activated after cerebral ischemia/reperfusion. ( A ) The mRNA level of cGAS in primary microglia isolated from brain tissue 3 h post-tMCAO (9 mice...
pmc_api
Selective toxicity by HDAC3 in neurons: regulation by Akt and GSK3beta.
The Journal of neuroscience : the official journal of the Society for Neuroscience (2011) · PMID:21289184
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Classification of HDAC super families.
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HDACs and SIRTs mediated pathological mechanism of Alzheimer’s disease. Histone proteins present in nucleus accumbens and cortex causes mutation on ataxin 1 through chronic stress....
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Selective toxicity by HDAC3 in neurons: regulation by Akt and GSK3beta.
The Journal of neuroscience : the official journal of the Society for Neuroscience (2011) · PMID:21289184
No extracted figures yet
Histone deacetylase-1 (HDAC1) is a molecular switch between neuronal survival and death.
The Journal of biological chemistry (2012) · PMID:22918830
No extracted figures yet

📅 Citation Freshness Audit

Freshness score = exp(-age×ln2/5): halves every 5 years. Green >0.6, Amber 0.3–0.6, Red <0.3.

No citation freshness data yet. Export bibliography — run scripts/audit_citation_freshness.py to populate.

⚔ Arena Performance

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📊 Resource Economics & ROI

High Efficiency Resource Efficiency Score
0.90
69.6th percentile (776 hypotheses)
Tokens Used
7,281
KG Edges Generated
1,117
Citations Produced
48

Cost Ratios

Cost per KG Edge
55.16 tokens
Lower is better (baseline: 2000)
Cost per Citation
173.36 tokens
Lower is better (baseline: 1000)
Cost per Score Point
9799.46 tokens
Tokens / composite_score

Score Impact

Efficiency Boost to Composite
+0.090
10% weight of efficiency score
Adjusted Composite
0.869

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$0.5520.512

📋 Reviews View all →

Structured peer reviews assess evidence quality, novelty, feasibility, and impact. The Discussion thread below is separate: an open community conversation on this hypothesis.

💬 Discussion

No DepMap CRISPR Chronos data found for HDAC3.

Run python3 scripts/backfill_hypothesis_depmap.py to populate.

No curated ClinVar variants loaded for this hypothesis.

Run scripts/backfill_clinvar_variants.py to fetch P/LP/VUS variants.

🔍 Search ClinVar for HDAC3 →
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⚖️ Governance History

No governance decisions recorded for this hypothesis.

Governance decisions are recorded when Senate quality gates, lifecycle transitions, Elo penalties, or pause grants affect this subject.

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Wiki Pages

Adrenal Chromaffin Cells in NeurodegenerationcellSynaptic Biomarkers in NeurodegenerationbiomarkerGlutamate - Excitotoxicity and Neurodegeneration BbiomarkerExosomal miR-155 in NeurodegenerationbiomarkerMDS 2026 — Fluid Biomarker Advances in NeurodegeneeventNeuroimaging Biomarkers for NeurodegenerationbiomarkerBlood-Based Biomarkers for NeurodegenerationbiomarkerCSF Neurofilament Light Chain (NfL) in NeurodegenebiomarkerDNA Methylation Biomarkers in NeurodegenerationbiomarkerExosomal Biomarkers in NeurodegenerationbiomarkerIL-6 (Interleukin-6) in NeurodegenerationbiomarkerLiquid Biopsy in NeurodegenerationbiomarkerCell-Free DNA Biomarkers in NeurodegenerationbiomarkerMetabolomic Biomarkers in NeurodegenerationbiomarkerAlpha-1 Adrenergic Receptor Neurons in Neurodegenecell

KG Entities (91)

AMPKAPOEAPOE4APPATG5ATG7ApoE mimeticsApoE3Astrocyte reactivity signalingBDNFBMAL1BRD4C1QCD33CDK5CREBBPCSF1RDLG4DNA_methylationEpigenetic regulation

Dependency Graph (1 upstream, 2 downstream)

Depends On
HDAC3-Selective Inhibition for Clock Resetrefines (0.5)
Depended On By
Astrocyte-Mediated Neuronal Epigenetic Rescuebuilds_on (0.6)Chromatin Accessibility Restoration via BRD4 Modulationbuilds_on (0.6)

Linked Experiments (7)

Epigenetic clocks association with brain aging patterns in older womenexploratory | tests | 0.90Animal Model Comparison for Neurodegenerative Disease Therapeuticsclinical | tests | 0.40Epigenetic Dysregulation in Huntington's Disease — Therapeutic Targetingvalidation | tests | 0.40Mechanism: Why Does Amyloid Removal Only Slow Decline 27%?clinical | tests | 0.40Epigenetic Dysregulation Validation in Parkinson's Diseaseclinical | tests | 0.40Proposed experiment from debate on Epigenetic clocks and biological aging in neufalsification | tests | 0.40Epigenetic Regulation Dysfunction in Alzheimer's and Parkinson's Diseaseclinical | tests | 0.40

Related Hypotheses

HDAC3-Selective Inhibition for Clock Reset
Score: 0.710 | neurodegeneration
HDAC3-Dependent A1 Astrocyte Commitment Window
Score: 0.611 | neurodegeneration
Gut Microbiome Remodeling to Prevent Systemic NLRP3 Priming in Neurodegeneration
Score: 0.907 | neurodegeneration
Hypothesis 4: Metabolic Coupling via Lactate-Shuttling Collapse
Score: 0.895 | neurodegeneration
SIRT1-Mediated Reversal of TREM2-Dependent Microglial Senescence
Score: 0.893 | neurodegeneration

Estimated Development

Estimated Cost
$0
Timeline
4.5 years

🧪 Falsifiable Predictions (2)

2 total 0 confirmed 0 falsified
Selective pharmacological inhibition of HDAC3 using RGFP966 (10 mg/kg, daily i.p.) for 4 weeks will produce at least a 25% improvement in hippocampal-dependent spatial memory consolidation in aged (18-22 month) 3xTg-AD mice, as measured by reduced latency to find the hidden platform during probe trial sessions in the Morris water maze.
pending conf: 0.72
Expected outcome: Target quadrant occupancy ≥40% (vs. expected chance level of 25%) in HDAC3-inhibited aged mice, representing a statistically significant (p<0.05) improvement with Cohen's d effect size ≥0.6 compared to vehicle-treated age-matched controls.
Falsified by: No statistically significant difference (p≥0.05) between RGFP966-treated and vehicle-treated groups in Morris water maze probe trial performance after 4 weeks of treatment; or performance improvements <15% above vehicle controls; or presence of adverse effects causing motor/sensory deficits that confound interpretation.
Method: Model system: 3xTg-AD mice (aged 18-22 months, n≥12 per group); Compound: RGFP966 (selective HDAC3 inhibitor, 10 mg/kg daily i.p.); Duration: 4 weeks of continuous treatment; Outcome measures: Morris water maze acquisition and probe trial performance, followed by histological verification of HDAC3 target engagement (nuclear H3K27ac/H4K16ac levels in hippocampal CA1 neurons via ChIP-qPCR); Timeframe: Experiment completable within 6 months including behavioral testing and tissue analysis.
Selective HDAC3 inhibition will restore age-associated deficits in hippocampal histone acetylation by increasing H3K27ac and H4K16ac occupancy at promoters of memory-related genes (c-Fos, Bdnf exon IV, Arc, and Creb) to levels comparable to young adult (3-6 month) mice, as quantified by chromatin immunoprecipitation sequencing (ChIP-seq).
pending conf: 0.68
Expected outcome: H3K27ac and H4K16ac signal enrichment ≥1.8-fold increase at promoters of c-Fos, Bdnf exon IV, Arc, and Creb in aged mice receiving HDAC3 inhibitor vs. aged vehicle controls, achieving acetylation levels that fall within 80% of young adult baseline values.
Falsified by: H3K27ac/H4K16ac enrichment at memory-related gene promoters shows no significant change (fold-change <1.2) in HDAC3-inhibited aged mice compared to vehicle controls; OR acetylation levels remain >50% below young adult baseline despite treatment; OR off-target changes in acetylation of non-memory genes suggest non-selective HDAC inhibition.
Method: Model system: C57BL/6J mice (young adults 3-6 months, n=8; aged 18-22 months, n=12 per treatment group); Compound: RGFP966 (10 mg/kg daily i.p.) or vehicle (DMSO/PBS) for 4 weeks; Tissue collection: Hippocampal tissue following behavioral testing; Analysis: ChIP-seq for H3K27ac (Abcam ab4729) and H4K16ac (Active Motif #61231) at gene promoters (±2kb from TSS) with bioinformatics validation using HOMER and DESeq2; Timeframe: 8-10 months for complete molecular characterization including behavioral correlates.

Knowledge Subgraph (153 edges)

activates (1)

OCT4cellular_reprogramming

associated with (4)

SIRT1SIRT3SIRT3neurodegenerationSIRT1neurodegenerationBRD4neurodegeneration

causal extracted (1)

sess_SDA-2026-04-04-gap-epigenetic-reprog-b685190eprocessed

causes (7)

agingmetabolic-epigenetic couplingtrained immunityneurodegenerationinflammatory epigenetic scarstrained immunitychromatin velocityepigenetic rejuvenationinflammatory epigenetic scarsneurodegeneration
▸ Show 2 more

co associated with (13)

BRD4OCT4HDAC3SIRT1BRD4HDAC3HDAC3OCT4SIRT1TET2
▸ Show 8 more

co discussed (81)

APPSIRT1PARP1SIRT1PARP1SIRT3BDNFSYN1DLG4PARP1
▸ Show 76 more
DLG4SYN1PARP1SYN1PSEN1TAUNGFTAUATG5MDM2ATG7MDM2ATG7TAUSIRT1SIRT6SIRT3TAUAPOE4SIRT3DLG4GRIN2BSIRT3BRD4SIRT3OCT4SIRT3BMAL1SIRT3HDAC3SIRT3SIRT1SIRT3TET2BRD4OCT4BRD4BMAL1BRD4SIRT1BRD4TET2OCT4BMAL1OCT4HDAC3OCT4SIRT1OCT4TET2BMAL1HDAC3HDAC3SIRT1BRD4SIRT3OCT4SIRT3SIRT1HDAC3HDAC3BMAL1BRD4PGC1AOCT4PGC1APGC1ASIRT3PGC1AHDAC3PGC1ATET2PGC1ABMAL1TET2OCT4TET2SIRT1TET2SIRT3TET2BRD4HDAC3OCT4HDAC3SIRT3HDAC3BRD4OCT4BRD4SIRT1BRD4BMAL1SIRT3BMAL1BRD4TET2PGC1AHDAC3PGC1APGC1AOCT4PGC1ABRD4BDNFHDACHDACNGFGDNFHDACHDACTAUAPOE4HDACCD33HDACHDACTREM2CDK5HDACATG5HDACATG7HDACHDACLAMP1CSF1RHDACAMPKSIRT6AMPKTET2HDACSIRT3HDACBRD4HDACOCT4BRD4HDACOCT4HDACSIRT1HDACSIRT3HDACPGC1AHDACHDACPGC1AC1QSIRT3

controls (1)

chromatin velocity modulatorschromatin state transitions

depends on (1)

synaptic plasticitycompartmentalized chromatin

disrupts (1)

agingglial-neuronal epigenetic cross-talk

enables (1)

histone_acetylationmemory_formation

inhibits (2)

histone demethylase inhibitorstrained immunityKDM1A inhibitorstrained immunity

investigated in (1)

diseases-huntingtonsh-4bb7fd8c

involved in (6)

SIRT1sirtuin_1___nad__metabolism___deacetylationHDAC3classical_complement_cascadeBRD4epigenetic_regulationSIRT3sirtuin_3___mitochondrial_deacetylationTET2epigenetic_regulation
▸ Show 1 more

modulates (6)

cholesterol_metabolismhistone_acetylationSIRT1metabolic oscillatorschromatin-modifying metabolitesneuronal chromatin accessibilityKDM1AneuroinflammationNAD+ precursorsepigenetic clock
▸ Show 1 more

participates in (5)

SIRT1Sirtuin-1 / NAD+ metabolism / deacetylationBRD4Epigenetic regulationSIRT3Sirtuin-3 / mitochondrial deacetylationOCT4Epigenetic regulationHDACAstrocyte reactivity signaling

prevents (2)

autophagy enhancersepigenetic scarsautophagy enhancersinflammatory epigenetic scars

protective against (1)

ApoE3neurodegeneration

regulates (12)

TET2DNA_methylationSIRT1chromatin_remodelingBRD4chromatin_remodelingSIRT3mitochondriaAPOEcholesterol_metabolism
▸ Show 7 more

targets (1)

SIRT1neurodegeneration

therapeutic target (5)

HDAC3neurodegenerationBRD4neurodegenerationSIRT3neurodegenerationTET2neurodegenerationOCT4neurodegeneration

therapeutic target for (1)

ApoE mimeticsmetabolic-epigenetic coupling

Mechanism Pathway for HDAC3

Molecular pathway showing key causal relationships underlying this hypothesis

graph TD
    HDAC3["HDAC3"] -->|therapeutic target| neurodegeneration["neurodegeneration"]
    SIRT3["SIRT3"] -->|co discussed| HDAC3_1["HDAC3"]
    OCT4["OCT4"] -->|co discussed| HDAC3_2["HDAC3"]
    BMAL1["BMAL1"] -->|co discussed| HDAC3_3["HDAC3"]
    HDAC3_4["HDAC3"] -->|co discussed| SIRT1["SIRT1"]
    SIRT1_5["SIRT1"] -->|co discussed| HDAC3_6["HDAC3"]
    HDAC3_7["HDAC3"] -->|co discussed| BMAL1_8["BMAL1"]
    PGC1A["PGC1A"] -->|co discussed| HDAC3_9["HDAC3"]
    HDAC3_10["HDAC3"] -->|co discussed| OCT4_11["OCT4"]
    HDAC3_12["HDAC3"] -->|co discussed| SIRT3_13["SIRT3"]
    HDAC3_14["HDAC3"] -->|co discussed| BRD4["BRD4"]
    HDAC3_15["HDAC3"] -->|co discussed| PGC1A_16["PGC1A"]
    HDAC3_17["HDAC3"] -->|co associated with| SIRT1_18["SIRT1"]
    BRD4_19["BRD4"] -->|co associated with| HDAC3_20["HDAC3"]
    HDAC3_21["HDAC3"] -->|co associated with| OCT4_22["OCT4"]
    style HDAC3 fill:#ce93d8,stroke:#333,color:#000
    style neurodegeneration fill:#ef5350,stroke:#333,color:#000
    style SIRT3 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_1 fill:#ce93d8,stroke:#333,color:#000
    style OCT4 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_2 fill:#ce93d8,stroke:#333,color:#000
    style BMAL1 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_3 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_4 fill:#ce93d8,stroke:#333,color:#000
    style SIRT1 fill:#ce93d8,stroke:#333,color:#000
    style SIRT1_5 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_6 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_7 fill:#ce93d8,stroke:#333,color:#000
    style BMAL1_8 fill:#ce93d8,stroke:#333,color:#000
    style PGC1A fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_9 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_10 fill:#ce93d8,stroke:#333,color:#000
    style OCT4_11 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_12 fill:#ce93d8,stroke:#333,color:#000
    style SIRT3_13 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_14 fill:#ce93d8,stroke:#333,color:#000
    style BRD4 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_15 fill:#ce93d8,stroke:#333,color:#000
    style PGC1A_16 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_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
    style HDAC3_20 fill:#ce93d8,stroke:#333,color:#000
    style HDAC3_21 fill:#ce93d8,stroke:#333,color:#000
    style OCT4_22 fill:#ce93d8,stroke:#333,color:#000

3D Protein Structure

🧬 HDAC3 — PDB 4A69 Click to expand 3D viewer

Experimental structure from RCSB PDB | Powered by Mol* | Rotate: click+drag | Zoom: scroll | Reset: right-click

Source Analysis

Epigenetic reprogramming in aging neurons

neurodegeneration | 2026-04-04 | completed

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Same Analysis (5)

Chromatin Accessibility Restoration via BRD4 Modulation
Score: 0.77 · BRD4
Chromatin Remodeling-Mediated Nutrient Sensing Restoration
Score: 0.76 · SMARCA4
Metabolic NAD+ Salvage Pathway Enhancement Through NAMPT Overexpressio
Score: 0.75 · NAMPT
Astrocyte-Mediated Neuronal Epigenetic Rescue
Score: 0.73 · HDAC
Mitochondrial-Nuclear Epigenetic Cross-Talk Restoration
Score: 0.70 · SIRT3
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