gene

CX3CR1

Entity Detail — Knowledge Graph Node

Understanding Entity Pages

This page aggregates everything SciDEX knows about CX3CR1: 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.

1306Connections

12Hypotheses

13Analyses

50Outgoing

50Incoming

10Experiments

15Debates

Summary

CX3CR1 is a gene implicated in neurodegeneration research. Key relationships include: activates, associated with, regulates. Associated with ALS, ALZHEIMER'S DISEASE, Aging. Connected to 552 entities in the SciDEX knowledge graph.

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🧬 Gene Info

Gene Symbol	CX3CR1
Full Name	CX3C Chemokine Receptor 1
Chromosome	3p21.31
Protein Type	Gpcr
Target Class	Gpcr
Function	GPCR antagonist modulating microglial activation and neuroinflammation
Mechanism of Action	GPCR antagonist modulating microglial activation and neuroinflammation
Primary Expression	Microglia, Monocytes, NK cells, T cells
Druggability	Low (0.44)
Clinical Stage	Phase II
Pathways	Complement, Immune Response, Neuroinflammatory, Oxidative Stress, Synaptic Plasticity
UniProt ID	P41597
NCBI Gene ID	1524
Ensembl ID	ENSG00000168329
OMIM	601470
GeneCards	CX3CR1
Human Protein Atlas	CX3CR1
Associated Diseases	Aging, Als, Alzheimer, Alzheimer's disease
Known Drugs/Compounds	Baicalein
Interactions	AGING, AKT, ALZHEIMER, ALZHEIMER'S DISEASE, AMPK, AMYLOID
SciDEX Target	View Target Profile (7 clinical trials)
SciDEX Hypotheses	Optogenetic Microglial Deactivation via Engineered CX3CR1 Promoter Methylation Disrupts Neuron-Microg CX3CR1 Agonism Enhances Microglial Phagocytosis of (+2 more)
KG Connections	1298 knowledge graph edges
Databases	GeneCards HPA STRING

🔮 Predicted Structure: CX3CR1 — AlphaFold P49238 Click to expand

AI-predicted structure from AlphaFold | Powered by Mol*

Wiki Pages (6)

Knowledge base pages for this entity

Canonical Page

Pathway Diagram

flowchart TD
    CX3CR1(["CX3CR1"])
    CX3CL1(["CX3CL1"])
    FKN(["FKN"])
    Fractalkine(["Fractalkine"])
    Hematoma_Resolution("Hematoma Resolution")
    h_ba3a948a["h-ba3a948a"]
    h_782b40b1["h-782b40b1"]
    Als["Als"]
    Microglial_Inflammatory_Response("Microglial Inflammatory Response")
    Synaptic_Pruning("Synaptic Pruning")
    A_["Abeta"]
    Neurological_Function("Neurological Function")

    CX3CL1 -->|"binds"| CX3CR1
    FKN -->|"activates"| CX3CR1
    CX3CR1 -->|"binds"| Fractalkine
    CX3CR1 -->|"involved in"| Hematoma_Resolution
    h_ba3a948a -->|"therapeutic target"| CX3CR1
    h_782b40b1 -->|"therapeutic target"| CX3CR1
    h_ba3a948a -->|"targets gene"| CX3CR1
    h_782b40b1 -->|"targets gene"| CX3CR1
    CX3CR1 -.->|"inhibits"| Als
    CX3CR1 -.->|"inhibits"| Microglial_Inflammatory_Response
    CX3CR1 -->|"regulates"| Synaptic_Pruning
    CX3CR1 -->|"involved in"| Synaptic_Pruning
    CX3CR1 -->|"associated with"| A_
    CX3CR1 -->|"associated with"| Neurological_Function
    h_ba3a948a -->|"targets"| CX3CR1

    style CX3CR1 fill:#006494,stroke:#4fc3f7,stroke-width:3px,color:#e0e0e0

Outgoing (838)

Target	Relation	Type	Str
benchmark_ot_ad_answer_key:CX3CR1	data_in	dataset_row	0.00
ds-db4a006ea647	provides_data_for	dataset	1.00
ds-f2c28aed24a7	provides_data_for	dataset	1.00
Favorable Survival	associated_with	phenotype	0.95
hematoma resolution	promotes	process	0.90
hematoma resolution	enhances	process	0.90
border-associated macrophages	expressed_in	cell_type	0.90
microglia	activates	cell_type	0.90
ACTIVITY-DEPENDENT SYNAPSE REMOVAL	regulates	biological_process	0.90
PPARΓ	modulates	protein	0.85
AΒ PHAGOCYTOSIS	regulates	biological_process	0.85
Schizophrenia	biomarker_for	disease	0.85
Lipid Droplet Accumulation	involved_in	process	0.85
microglial inflammatory response	suppresses	process	0.85
Microglial Inflammatory Response	inhibits	process	0.85
Als	inhibits	disease	0.85
Immune cell infiltration	regulates	process	0.80
neuroinflammation	activates	disease	0.80
neuroinflammation	regulates	disease	0.80
microglia	associated_with	cell_type	0.80
neurodegenerative diseases	implicated_in	disease	0.80
microglia	inhibits	cell_type	0.80
microglia	biomarker_for	cell_type	0.80
neurodegenerative disease	implicated_in	disease	0.80
microglia	expressed_in	cell_type	0.80
MICROGLIA	inhibits	cell_type	0.80
MICROGLIA	activates	cell_type	0.80
fractalkine_signaling	mediates	pathway	0.80
microglial_activation	controls	pathway	0.80
Neuroinflammation	activates	disease	0.75
Inflammation	implicated_in	disease	0.75
Aging	activates	disease	0.75
Alzheimer	activates	disease	0.75
Aging	associated_with	disease	0.75
Alzheimer	regulates	disease	0.75
Inflammation	regulates	disease	0.75
Als	interacts_with	disease	0.75
Carcinoma	activates	disease	0.75
SYNAPSE	associated_with	gene	0.75
Tumor	activates	disease	0.75
Als	associated_with	disease	0.75
Inflammation	activates	disease	0.75
Inflammation	inhibits	disease	0.75
Inflammation	associated_with	disease	0.75
Cancer	inhibits	disease	0.75
COGNITIVE DECLINE	exacerbates	phenotype	0.70
NEURON	exacerbates	cell_type	0.70
TAU	exacerbates	protein	0.70
COGNITIVE DECLINE	treats	phenotype	0.70
AMYLOID	causes	protein	0.70

Incoming (468)

Source	Relation	Type	Str
benchmark_ot_ad_answer_key:CX3CR1	data_in	dataset_row	0.00
ds-db4a006ea647	data_in	dataset	1.00
ALZHEIMER'S DISEASE	associated_with	disease	1.00
ds-f2c28aed24a7	data_in	dataset	1.00
MICROGLIA	inhibits	gene	0.98
FKN	binds	protein	0.95
Cx3Cl1	binds	protein	0.95
h-782b40b1	targets_gene	hypothesis	0.90
h-ba3a948a	targets_gene	hypothesis	0.90
h-494861d2	targets_gene	hypothesis	0.90
TNF	associated_with	gene	0.90
MICROGLIA	expresses	gene	0.90
FRACTALKINE	activates	protein	0.90
MICROGLIA	associated_with	gene	0.82
h-ba3a948a	targets	hypothesis	0.80
h-782b40b1	targets	hypothesis	0.80
HCRTR2	modulates_via_microglia	gene	0.80
AMYLOID	associated_with	gene	0.74
PARKINSON'S DISEASE	associated_with	disease	0.74
ALZHEIMER	regulates	gene	0.70
TNF	activates	gene	0.70
CCR2	associated_with	gene	0.70
ALZHEIMER	activates	gene	0.70
TREM2	synergizes_with	gene	0.70
h-494861d2	targets	hypothesis	0.70
NF-KB	associated_with	protein	0.66
IL-6	associated_with	gene	0.66
MICROGLIA	activates	gene	0.66
ALS	associated_with	gene	0.66
APOE	associated_with	gene	0.65
NEUROINFLAMMATION	mediated_by	process	0.65
MICROGLIA	treats	cell_type	0.65
INFLAMMATION	exacerbates	phenotype	0.65
ASTROCYTE	reduces	cell_type	0.65
h-019c56c1	targets	hypothesis	0.65
ASTROCYTE	associated_with	gene	0.65
CD33	associated_with	gene	0.65
AMPK	associated_with	gene	0.65
CX3CL1	stabilizes	gene	0.65
CTSS	activates	gene	0.60
FOS	activates	gene	0.60
CTSL	activates	gene	0.60
TLR4	inhibits	gene	0.60
FOSB	activates	gene	0.60
CD4	regulates	gene	0.60
P2X7	activates	gene	0.60
TREM2	inhibits	gene	0.60
LGALS3	contributes_to	gene	0.60
CX3CL1	activates	gene	0.60
CTSB	activates	gene	0.60

Targeting Hypotheses (12)

Hypotheses where this entity is a therapeutic target

Hypothesis	Score	Disease	Analysis
CX3CR1-TREM2 Integration for Synapse Pruning Normalization	0.776	neurodegeneration	TREM2 agonism vs antagonism in DAM micro
Optogenetic Microglial Deactivation via Engineered Inhibitor	0.655	neurodegeneration	Synaptic pruning by microglia in early A
CX3CR1 Promoter Methylation Disrupts Neuron-Microglia Cross-	0.640	developmental neurobiology	Do perinatal immune challenges create pe
CX3CR1 Agonism Enhances Microglial Phagocytosis of Extracell	0.630	neurodegeneration	Investigate prion-like spreading of tau
CX3CR1-Targeted HDAC3 Knockdown in Microglia via AAV9 Delive	0.620	pharmacology	How can CNS-selective HDAC/DNMT inhibito

CX3CR1-Negative Trem2-High Microglial Subset Mediates Female	0.570	neuroinflammation	How do regional, age, and sex-dependent
Fractalkine Axis Amplification via CX3CR1 Positive Allosteri	0.563	neurodegeneration	Synaptic pruning by microglia in early A
Soluble CX3CL1 cleavage by ADAM proteases disengages fractal	0.540	neurodegeneration	Synaptic pruning by microglia in neurode
CX3CR1-Targeted AntimiR-155 Oligonucleotides for Microglial	0.530	pharmacology	How can CNS-selective HDAC/DNMT inhibito
CX3CR1 PET with Nano-bodies for Microglial Surveillance Stat	0.500	biomarkers	What biomarkers can reliably detect micr
GluN2B-Regulated Microglial Phagocytosis of Tau Aggregates v	0.491	neuroscience	Circuit-level neural dynamics in neurode
TREM2 Agonism with CX3CR1 Antagonism for Microglial Homeosta	0.105	neurodegeneration	Neuroinflammation Biomarker Panel for Ea

Mentioning Analyses (13)

Scientific analyses that reference this entity

Experiments (10)

Experimental studies targeting or related to this entity

Experiment	Type	Disease	Score	Feasibility	Model	Status	Est. Cost
Proposed experiment from debate on Synaptic pruning by microglia in ea	falsification	Neuroinflammation	0.400	0.50	mouse	proposed	$240,000
Proposed experiment from debate on Microglia activate astrocytes via I	falsification	Neurodegeneration	0.400	0.50	cell_line	proposed	$100,000
TREM2 Function in Alzheimer's Disease — From Risk Variant to Therapeut	validation	Alzheimer's Disease	0.400	0.50	human	proposed	$2,960,000
s:** - GPR32 knockout in microglia should worsen neuroinflammation if	falsification	Neuroinflammation	0.400	0.50	cell_line	proposed	$80,000
DLB Treatment Response Biomarkers — Predicting Cholinesterase Inhibito	clinical	Neurodegeneration	0.400	0.50	human	proposed	$6,550,000
FTD Microglia Role: Protective vs Destructive Mechanism Study	validation	Neuroinflammation	0.400	0.50	human	proposed	$2,960,000
Microglial Aging and Immune Memory in Neurodegeneration — Training the	validation	Alzheimer's Disease	0.400	0.50	human	proposed	$2,960,000
Microglial Contributions to Huntington's Disease Pathogenesis	validation	Neuroinflammation	0.400	0.50	human	proposed	$2,960,000
Microglial TREM2 Agonist In Vivo Efficacy	validation	Alzheimer's Disease	0.400	0.50	mouse	proposed	$360,000
TREM2 Agonist Therapy for Parkinson's Disease — Experimental Design	validation	Parkinson's Disease	0.400	0.50	mouse	proposed	$280,000

Related Papers (20)

Scientific publications cited in analyses involving this entity

Title & PMID	Authors	Journal	Year	Citations
Reducing microglial lipid load enhances β amyloid phagocytosis in an Alzheimer's [PMID:39908361]	Wu X, Miller JA, Lee BTK, Wang Y, Ruedl	Sci Adv	2025	1
Fractalkine Enhances Hematoma Resolution and Improves Neurological Function via [PMID:37465997]	Chen X, He X, Xu F, Xu N, Sharifi NH, Zh	Stroke	2023	1
Microglia-Mediated Neuroinflammation: A Potential Target for the Treatment of Ca [PMID:35642214]	Wang M, Pan W, Xu Y, Zhang J, Wan J, Jia	J Inflamm Res	2022	1
CX3CL1/CX3CR1 signaling targets for the treatment of neurodegenerative diseases. [PMID:34492237]	Subbarayan MS, Joly-Amado A, Bickford PC	Pharmacol Ther	2022	1
Microglia in neurodegeneration. [PMID:30258234]	Hickman S, Izzy S, Sen P, Morsett L, El	Nat Neurosci	2018	1
How neuroinflammation contributes to neurodegeneration. [PMID:27540165]	Ransohoff RM	Science	2016	1
CX3CL1/CX3CR1 axis dysregulation contributes to epileptogenic mechanisms in foca [PMID:41863015]	Lei Lei; Shengyu Yang; Yinchao Li; Jiaha	Acta neuropathologica communic	2026	0
Constitutive expression of CX3CR1-BAC-Cre introduces minimal off-target effects [PMID:41924777]	Mroue-Ruiz FH, Desai B, Garvin MM, Shehu	Biochemical and biophysical re	2026	0
Systems-level molecular and immunological evidence identifies Th17/Treg modulati [PMID:41788408]	["Li X", "Li X", "Chen S", "Wang L", "Xi	Frontiers in aging neuroscienc	2026	0
Multimodal tumor thermal therapy enhances antitumor immunity by expanding tumor- [PMID:41799205]	["Wang S", "Wang Y", "Zhang Y", "Zhang Z	Theranostics	2026	0
Spatiotemporal dynamic regulation of the CX3CL1-CX3CR1 axis: A double-edged swor [PMID:41564496]	Liang J, Zhu W, Pan R, Wei S, Zhang S et	Cytokine Growth Factor Rev	2026	0
Peripheral cancer attenuates amyloid pathology in Alzheimer's disease via cystat [PMID:41576952]	Li X, Tang X, Zeng J, Duan L, Hou Z et a	Cell	2026	0
[Corrigendum] Influence of aspirin on the CX3CL1/CX3CR1 signaling pathway in acu [PMID:41930567]	Zhang Z, Yang W, Ying R, Shi Y, Jiang H	Int J Mol Med	2026	0
CX3CR1-T280M polymorphism and end-stage renal disease development in chronic kid [PMID:41932952]	Matteo Gatti; Ivano Baragetti; Andrea Ba	Scientific reports	2026	0
SYK-dependent lipid handling in monocyte-derived macrophages governs functional [PMID:41831796]	["Zhao Y", "Hu H", "Wang J", "Hu Y", "Ya	Brain research bulletin	2026	0
Microglial Lag3 Drives α-Synuclein-induced Neurotoxic Activated (A1) Astrocytes [PMID:41542562]	["Yang X", "Kumbhar R", "Seo B", "Ha S",	bioRxiv : the preprint server	2026	0
Conserved ductular reaction mechanisms in biliary atresia and PSC derived from s [PMID:41903685]	Schofield A, Kamath BM, MacParland SA, T	Cellular and molecular gastroe	2026	0
Identification of suicide brain transcriptomic signatures using meta-analysis of [PMID:41916959]	Sokolov AV, Lafta MS, Jokinen J, Schiöth	Translational psychiatry	2026	0
Helper T cells and chemokines in elderly asthma - Mechanisms of airway inflammat [PMID:41805218]	["Wu Y"]	Biomolecules & biomedicine	2026	0
Identification of metabolism and inflammation-related biomarkers and potential d [PMID:41781900]	["Chen Y", "Zhang M", "Qiao L", "Lu F",	BMC psychiatry	2026	0

Debates (15)

Multi-agent debates referencing this entity

CX3CR1

Understanding Entity Pages

Summary

Wiki Pages (6)

CX3CR1 Modulation Therapy for Neurodegeneration

CX3CR1 PET Imaging — Microglia-Targeted Neuroimaging

CX3CR1 Modulation Therapy

CX3CR1 — CX3C Chemokine Receptor 1

CX3CR1 Protein (Fractalkine Receptor)

CX3CR1-Expressing Neurons

Pathway Diagram

Outgoing (838)

Incoming (468)

Targeting Hypotheses (12)

Mentioning Analyses (13)

Why do clinical manifestations overlap despite distinct underlying etiologies in

Investigate prion-like spreading of tau pathology through connected brain region

Neuroinflammation and microglial priming in early Alzheimer's Disease

Tau propagation mechanisms and therapeutic interception points

Gene expression changes in aging mouse brain predicting neurodegenerative vulner

Cell type vulnerability in Alzheimers Disease (SEA-AD transcriptomic data)

Cell type vulnerability in Alzheimer's Disease (SEA-AD data - v2)

SEA-AD Gene Expression Profiling — Allen Brain Cell Atlas

Sleep disruption as cause and consequence of neurodegeneration

Synaptic pruning by microglia in early AD

Senolytic therapy for age-related neurodegeneration

Microglia-astrocyte crosstalk amplification loops in neurodegeneration

TREM2 agonism vs antagonism in DAM microglia

Experiments (10)

Related Papers (20)

Debates (15)

Investigate prion-like spreading of tau pathology through connected brain region

Investigate prion-like spreading of tau pathology through connected brain region

Investigate mechanistic links between early microglial priming states, neuroinfl

Investigate mechanistic links between early microglial priming states, neuroinfl

The abstract notes that clinical presentations overlap across different myelopat

Microglia activate astrocytes via IL-1alpha/TNF/C1q, and reactive astrocytes fee

Senolytics targeting p16/p21+ senescent astrocytes and microglia may reduce SASP

Sleep disruption as cause and consequence of neurodegeneration

Synaptic pruning by microglia in early AD

Tau propagation mechanisms and therapeutic interception points