enzyme

HDAC

Entity Detail — Knowledge Graph Node

Understanding Entity Pages

This page aggregates everything SciDEX knows about HDAC: its mechanistic relationships (Knowledge Graph edges), hypotheses targeting it, analyses mentioning it, and supporting scientific papers. The interactive graph below shows its immediate neighbors. All content is AI-synthesized from peer-reviewed literature.

691Connections

8Hypotheses

10Analyses

50Outgoing

50Incoming

Summary

HDAC is an entity related to neurodegeneration research. Key relationships include: inhibits, activates, co discussed. Associated with ALS, ALZHEIMER'S DISEASE, Aging. Connected to 104 entities in the SciDEX knowledge graph.

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🔬 Protein Info

Gene Symbol	HDAC
Pathways	Amyloid, Blood-Brain Barrier, Epigenetic, Pi3K/Akt, Wnt
GeneCards	HDAC
Human Protein Atlas	HDAC
Alzheimer's Disease (AD)	~6.5 million Americans, $321 billion annual cost[@alzheimers2024]
Parkinson's Disease (PD)	~1 million Americans, $52 billion annual cost[@parkinsons2024]
Huntington's Disease (HD)	~41,000 Americans[@huntingtons2024]
ALS	~30,000 Americans[@als2024]
HDAC6 inhibitors	Promote clearance of α-synuclein and tau via autophagy[@simes2022]
Class I HDACs	Reduce neuroinflammation and improve synaptic plasticity[@liu2020]
Sirtuin activators	Enhance mitochondrial function and stress resistance[@singh2023]
Associated Diseases	ALS, Alzheimer, Alzheimer's disease, Amyotrophic Lateral Sclerosis, Autoimmune
Known Drugs/Compounds	HDAC inhibitors, aducanumab, lecanemab, rapamycin, donanemab, valproic acid
Interactions	PI3K, ANXIETY, HDAC3, BDNF, Β-HYDROXYBUTYRATE, DEPRESSION
SciDEX Hypotheses	Astrocyte-Mediated Neuronal Epigenetic Rescue
KG Connections	691 knowledge graph edges
Databases	GeneCards UniProt NCBI Gene HPA STRING

Wiki Pages (21)

Knowledge base pages for this entity

Canonical Page

Pathway Diagram

graph TD
    HDAC["HDAC"] -.->|"inhibits"| Gene_Expression["Gene Expression"]
    HDAC["HDAC"] -->|"modulates"| Chromatin_Structure["Chromatin Structure"]
    HDAC["HDAC"] -->|"involved in"| Nervous_System["Nervous System"]
    HDAC["HDAC"] -->|"regulates"| Histone_Lysine_Acetylation["Histone Lysine Acetylation"]
    HDAC["HDAC"] -->|"involved in"| Pathological_Processes["Pathological Processes"]
    HDAC["HDAC"] -->|"contributes to"| Cognitive_Decline["Cognitive Decline"]
    HDAC_Inhibitors["HDAC Inhibitors"] -.->|"inhibits"| HDAC["HDAC"]
    Butyrate["Butyrate"] -.->|"inhibits"| HDAC["HDAC"]
    h_8fe389e8["h-8fe389e8"] -->|"targets"| HDAC["HDAC"]
    AND["AND"] -->|"activates"| HDAC["HDAC"]
    style HDAC fill:#006494,stroke:#4fc3f7,stroke-width:2px,color:#e0e0e0

Outgoing (450)

Target	Relation	Type	Str
chromatin architecture	modulates	process	0.95
gene transcription	regulates	process	0.95
HDAC inhibitors	therapeutic_target	drug	0.95
epigenetic regulation	participates_in	pathway	0.80
Alzheimer's disease	inhibits	disease	0.70
Alzheimer's disease	treats	disease	0.70
cortex	expressed_in	brain_region	0.70
oxidative stress response	participates_in	pathway	0.70
neural stem cells	inhibits	cell_type	0.70
aging	inhibits	disease	0.70
Fibrosis	activates	disease	0.65
ALS	associated_with	disease	0.65
Tumor	associated_with	disease	0.65
Ms	activates	disease	0.65
Anxiety	activates	disease	0.65
Depression	activates	disease	0.65
Aging	inhibits	disease	0.65
ALS	inhibits	disease	0.65
Alzheimer	inhibits	disease	0.65
Inflammation	inhibits	disease	0.65
Neuroinflammation	inhibits	disease	0.65
Alzheimer	regulates	disease	0.65
Cancer	inhibits	disease	0.65
Obesity	activates	disease	0.65
ALS	activates	disease	0.65
Dementia	activates	disease	0.65
Alzheimer	activates	disease	0.65
Tumor	activates	disease	0.65
Cancer	activates	disease	0.65
Stroke	activates	disease	0.65
Hypertension	activates	disease	0.65
Cardiovascular	activates	disease	0.65
Diabetes	activates	disease	0.65
Autoimmune	activates	disease	0.65
Als	activates	disease	0.65
Als	inhibits	disease	0.65
Tumor	contributes_to	disease	0.65
Parkinson	inhibits	disease	0.65
Autoimmune	inhibits	disease	0.65
Als	therapeutic_target	disease	0.65
Tumor	therapeutic_target	disease	0.65
Carcinoma	activates	disease	0.65
Neuroinflammation	implicated_in	disease	0.65
Neurodegeneration	contributes_to	disease	0.65
Huntington	regulates	disease	0.65
Inflammation	implicated_in	disease	0.65
Parkinson	regulates	disease	0.65
Ms	therapeutic_target	disease	0.65
Ms	expressed_in	disease	0.65
Parkinson	activates	disease	0.65

Incoming (241)

Source	Relation	Type	Str
h-8fe389e8	targets_gene	hypothesis	0.90
h-8fe389e8	targets	hypothesis	0.80
ALZHEIMER'S DISEASE	inhibits	gene	0.74
ALZHEIMER'S DISEASE	associated_with	disease	0.74
IL-6	associated_with	gene	0.66
TNF	associated_with	gene	0.66
GDNF	activates	gene	0.65
HK2	activates	gene	0.60
GENES	inhibits	gene	0.60
TRKB	activates	gene	0.60
HDAC2	activates	gene	0.60
EXERCISE	activates	gene	0.60
ALZHEIMER	inhibits	gene	0.60
NEURODEGENERATIVE DISEASES	inhibits	gene	0.60
ALZHEIMER	regulates	gene	0.60
LRP6	expressed_in	gene	0.60
ALZHEIMER'S DISEASE	activates	gene	0.60
ALZHEIMER	activates	gene	0.60
TNF	activates	gene	0.60
TNF-Α	activates	gene	0.60
CYTOKINES	activates	gene	0.60
PI3K	regulates	gene	0.60
AND	inhibits	gene	0.60
METTL3	activates	gene	0.60
HK2	inhibits	gene	0.60
TP53	inhibits	gene	0.60
E2F7	contributes_to	gene	0.60
RB1	inhibits	gene	0.60
CANCER	inhibits	gene	0.60
YAP	inhibits	gene	0.60
PARKINSON'S DISEASE	inhibits	gene	0.60
PARKINSON	inhibits	gene	0.60
MITOCHONDRIAL DYSFUNCTION	inhibits	gene	0.60
HDAC6	inhibits	gene	0.60
INFLAMMATION	inhibits	gene	0.60
APOPTOSIS	inhibits	gene	0.60
AND	activates	gene	0.60
BCL-2	inhibits	gene	0.60
NF-ΚB	inhibits	gene	0.60
HDAC3	activates	gene	0.60
STAT3	inhibits	gene	0.60
HDAC1	inhibits	gene	0.60
ROS	inhibits	gene	0.60
CYCLIN D1	inhibits	gene	0.60
DNA	inhibits	gene	0.60
AND	therapeutic_target	gene	0.60
WNT	therapeutic_target	gene	0.60
NF2	therapeutic_target	gene	0.60
VEGF	therapeutic_target	gene	0.60
MMP2	activates	gene	0.60

Targeting Hypotheses (8)

Hypotheses where this entity is a therapeutic target

Hypothesis	Score	Disease	Analysis
HDAC6 Selective Inhibition to Restore Acetylation Balance an	0.577	structural biology	What is the atomic-resolution structure
Selective HDAC3 Inhibition with Cognitive Enhancement	0.563	neurodegeneration	Epigenetic reprogramming in aging neuron
HDAC6 Activation as SCFA-Mediated Neuroprotective Mechanism	0.537	neurodegeneration	Do SCFAs directly modulate α-synuclein a
Astrocyte-Mediated Neuronal Epigenetic Rescue	0.479	neurodegeneration	Epigenetic reprogramming in aging neuron
HDAC6 Inhibition for Dual Restoration of Microtubule Stabili	0.459	neurodegeneration	Which tau PTMs are both disease-specific

HDAC3-Selective Inhibition for Clock Reset	0.459	neurodegeneration	Epigenetic clocks and biological aging i
MITF Acts as the Primary Transcriptional Effector Downstream	0.444	neurodegeneration	How does HDAC1/2 deletion specifically e
HDAC2-Specific Repression of PU.1 Pioneer Factor Target Site	0.415	neurodegeneration	How does HDAC1/2 deletion specifically e

Mentioning Analyses (10)

Scientific analyses that reference this entity

Related Papers (20)

Scientific publications cited in analyses involving this entity

Title & PMID	Authors	Journal	Year	Citations
Effect of Electronic Prescribing Compared to Paper-Based (Handwritten) Prescribi [PMID:34433219]	Aluga D, Nnyanzi LA, King N, Okolie EA,	Appl Clin Inform	2021	1
Structurally diverse sesquiterpenoids from the aerial parts of Artemisia annua ( [PMID:32891001]	Qin DP, Li HB, Pang QQ, Huang YX, Pan DB	Bioorg Chem	2020	1
Mycobacterium Abscessus: A Rare Cause of Peri-Ductal Mastitis in Endemic Regions [PMID:32580856]	Shaikh A, Vohra LM	J Coll Physicians Surg Pak	2020	1
The scanning ion conductance microscope for cellular physiology. [PMID:23086993]	Lab MJ, Bhargava A, Wright PT, Gorelik J	Am J Physiol Heart Circ Physio	2013	1
Telomere dysfunction causes sustained inflammation in chronic obstructive pulmon [PMID:21885626]	Amsellem V, Gary-Bobo G, Marcos E, Maitr	Am J Respir Crit Care Med	2011	1
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's diseas [PMID:21102463]	Franke A, McGovern DP, Barrett JC, Wang	Nat Genet	2010	1
Discovery of a Covalent HDAC3 Degrader with Excellent Anti-Inflammatory Activity [PMID:41812251]	["Qin H", "Shi Y", "Liu R", "Wang B", "G	Journal of medicinal chemistry	2026	0
Myeloid HDAC3 deletion protects against traumatic optic injury. [PMID:41851071]	Shahror RA, Morris CA, Cunningham A, Chu	Cell death discovery	2026	0
HDAC3 mediates retinal endothelial cell metabolic reprogramming and angiogenesis [PMID:41023273]	Mitchell CD, Morris CA, Wild M, Cunningh	Acta Pharmacol Sin	2026	0
Metabolomics identifies riboflavin as a therapeutic agent for acute pancreatitis [PMID:41352543]	Shi Y, Peng J	J Nutr Biochem	2026	0
β-Hydroxybutyrate improves glymphatic system function and alleviates cerebral ed [PMID:41535708]	Yu MJ, Xiong RQ, Wu JW, Li YC, Xie JX et	Acta Pharmacol Sin	2026	0
SATB2 Mediates H3K9 Delactylation by Recruiting HDAC3 to Repress LCN2 and Inhibi [PMID:41736683]	Wen T, Yang L, Cai S, Liu Y, Fan J et al	Adv Sci (Weinh)	2026	0
Histone deacetylases: Function in tumor development and therapeutic prospects (R [PMID:41783166]	Lin R, Zhang Y, Li H, Liang F	Oncol Lett	2026	0
Regulatory B Cells at the Crossroads of Epigenetic Control and Immune Homeostasi [PMID:41949720]	Angappulige DH, Ballard DJ, Thomas CJ, X	Clin Rev Allergy Immunol	2026	0
Histone decrotonylation plays a distinct role in HIV latency. [PMID:41961925]	Li X, Li D, Tang Y, Nearing M, Varco-Mer	Sci Adv	2026	0
LncRNA SNHG5 promotes macrophage lipid accumulation and aggravates atheroscleros [PMID:41844502]	Liu X, Wang HH, Lan XY, Sun SY, Xu XD, H	Biochimica et biophysica acta.	2026	0
HOX code-based stratification reveals RUNX1T1-HDAC reprogramming as a targetable [PMID:41912135]	Jiang Y, Cheng S, Zhang CY, Jin X, Li L,	Cancer letters	2026	0
Microglial HDAC3 inhibits the migration of CD8-positive T cell in the developmen [PMID:41888851]	Che N, Zhang Y, Wang B, Wu H, Mao Z, Yua	Cell & bioscience	2026	0
GR/HDAC3 Regulates Npas4 Signaling Pathway and Mediates Cognitive Impairment in [PMID:41837847]	Zhao Z, Song Y, Yu X, Gao Q, Wang B, Sun	FASEB journal : official publi	2026	0
EXPRESS: Identification of Acetylation-Related Molecular Signatures in Knee Oste [PMID:41876476]	Wang J, Xu B, Yoon DE, Xu S, Xia S, Xu J	Molecular pain	2026	0

HDAC

Understanding Entity Pages

Summary

Wiki Pages (21)

HDAC Inhibitors for Neurodegeneration — Investment Landscape

Personalized Treatment Plan — Atypical Parkinsonism (CBS/PSP)

Section 148: Advanced Nutritional Biochemistry in CBS/PSP

Therapeutics

NPM1 Gene

Frontotemporal Dementia (FTD)

Pathway Diagram

Outgoing (450)

Incoming (241)

Targeting Hypotheses (8)

Mentioning Analyses (10)

What molecular mechanisms mediate HDAC9's effects on Aβ deposition and synaptic

What molecular mechanisms mediate HDAC9's effects on Aβ deposition and synaptic

How does HDAC1/2 deletion specifically enhance microglial amyloid phagocytosis c

What is the optimal therapeutic window during preclinical AD for epigenetic repr

Epigenetic reprogramming in aging neurons

CRISPR-based therapeutic approaches for neurodegenerative diseases

Circuit-level neural dynamics in neurodegeneration

Epigenetic clocks and biological aging in neurodegeneration

Sleep disruption as cause and consequence of neurodegeneration

What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's

Related Papers (20)

HDAC

Understanding Entity Pages

Summary

Wiki Pages (21)

HDAC Inhibitors for Neurodegeneration — Investment Landscape

Personalized Treatment Plan — Atypical Parkinsonism (CBS/PSP)

Section 148: Advanced Nutritional Biochemistry in CBS/PSP

Therapeutics

NPM1 Gene

Frontotemporal Dementia (FTD)

Oligodendrocytes

Rapamycin ALS Trial - mTOR Inhibition for Amyotrophic Lateral Sclerosis

nf1-protein

Epigenetic Dysregulation in Neurodegeneration

Epigenetic Dysregulation Comparison -- AD/PD/ALS/FTD/HD

Epigenetic Alterations in Alzheimer's Disease

Clinical Trials Dashboard

CREB Signaling in Neurodegeneration

Machado-Joseph Disease (Spinocerebellar Ataxia Type 3)

Neuronal Ceroid Lipofuscinosis (NCL)

vitamin-d-therapy-neurodegeneration

MACF1 — Microtubule-actin crosslinking factor 1

Gene-Mechanism-Therapy Causal Chains

Tauopathies

NPAS3 Gene

Pathway Diagram

Outgoing (450)

Incoming (241)

Targeting Hypotheses (8)

Mentioning Analyses (10)

What molecular mechanisms mediate HDAC9's effects on Aβ deposition and synaptic

What molecular mechanisms mediate HDAC9's effects on Aβ deposition and synaptic

How does HDAC1/2 deletion specifically enhance microglial amyloid phagocytosis c

What is the optimal therapeutic window during preclinical AD for epigenetic repr

Epigenetic reprogramming in aging neurons

CRISPR-based therapeutic approaches for neurodegenerative diseases

Circuit-level neural dynamics in neurodegeneration

Epigenetic clocks and biological aging in neurodegeneration

Sleep disruption as cause and consequence of neurodegeneration

What are the mechanisms by which gut microbiome dysbiosis influences Parkinson's

Related Papers (20)