# Microglial CX3CR1 deficiency regulates the selective vulnerability of cone photoreceptors via STAT3/CCL–ACKR1 signaling in the mouse retina

**Authors:** Rong Li, Jing Zhang, Qiong Wang, Jun-Qi Fan, Bin Lin

PMC · DOI: 10.1038/s12276-025-01618-7 · Experimental & Molecular Medicine · 2026-01-15

## TL;DR

The study shows how a lack of CX3CR1 in microglia causes specific cone cell death in the retina through inflammation and signaling pathways, offering a potential treatment target for neurodegenerative diseases.

## Contribution

The study identifies a novel mechanism involving microglial CX3CR1 deficiency and STAT3/CCL–ACKR1 signaling in the selective vulnerability of cone photoreceptors.

## Key findings

- Microglial CX3CR1 deficiency activates STAT3 signaling, leading to proinflammatory responses in microglia and astrocytes.
- Cone photoreceptor vulnerability is mediated through CCL and ACKR1 signaling, with NF-κB upregulating ACKR1 in cones.
- Cxcl1-dominant microglia interact with astrocytes via BMP2, increasing STAT3 and chemokine production, which worsens cone loss.

## Abstract

Selective neuronal vulnerability is a common feature of neurodegenerative disorders. However, the molecular mechanisms that drive this selective vulnerability are not fully understood. Here we observed that microglial CX3CR1 interference induced proinflammatory responses in microglia and astrocytes that were correlated with the selective vulnerability of cone photoreceptors in the mouse retina. Via proteomic analysis, we identified STAT3 as a potential downstream target by which CX3CR1 mediates microglial neurotoxicity. Moreover, single-cell RNA sequencing analysis revealed that CX3CR1-deficient microglia exhibit eight distinct transcriptomic phenotypes. At the mechanistic level, our data revealed that the involvement of Tnf-dominant microglia occurred mainly via microglia‒cone interactions through CCLs and their receptor, atypical chemokine receptor 1 (Ackr1), whose expression was upregulated primarily in cones through NF-κB signaling, leading to selective cone loss. In addition, we found that Cxcl1-dominant microglia primarily communicated with astrocytes via the Bmp2–Bmpr1a/Bmpr1b pair, leading to increased STAT3 levels and, consequently, elevated CCL and CXCL production in astrocytes, which in turn contributed to further cone loss through Ackr1. Overall, our data demonstrate that microglial CX3CR1 deficiency induces selective cone cell death via activation of the STAT3/CCL–ACKR1 signaling pathway, and that targeting CX3CR1/STAT3 could represent a therapeutic strategy to reduce microglial neurotoxicity.

This study explores why certain neurons in the brain are more vulnerable in degenerative contexts such as Alzheimer’s disease. The study investigates the role of CX3CL1/CX3CR1 signaling in selective neuronal vulnerability in the retina, an extension of the brain. They found that CX3CR1 deficiency in microglia activates STAT3 signaling, triggering proinflammatory responses in both microglia and astrocytes. This neuroinflammation, mediated by chemokines such as CCL and CXCL, specifically targets cone photoreceptors primarily expressing Ackr1, leading to their selective vulnerability and loss. These findings demonstrate that the CX3CR1/STAT3 pathway is a key mechanism driving selective neuronal damage, suggesting it as a promising therapeutic target for mitigating microglia-mediated neurotoxicity in neurological disorders.

This summary was initially drafted using artificial intelligence, then revised and fact-checked by the author.

## Linked entities

- **Genes:** CX3CR1 (C-X3-C motif chemokine receptor 1) [NCBI Gene 1524], STAT3 (signal transducer and activator of transcription 3) [NCBI Gene 6774], CRYGC (crystallin gamma C) [NCBI Gene 1420], ACKR1 (atypical chemokine receptor 1 (Duffy blood group)) [NCBI Gene 2532], TNF (tumor necrosis factor) [NCBI Gene 7124], CXCL1 (C-X-C motif chemokine ligand 1) [NCBI Gene 2919], BMP2 (bone morphogenetic protein 2) [NCBI Gene 650], BMPR1A (bone morphogenetic protein receptor type 1A) [NCBI Gene 657], BMPR1B (bone morphogenetic protein receptor type 1B) [NCBI Gene 658], NFKB1 (nuclear factor kappa B subunit 1) [NCBI Gene 4790]
- **Diseases:** Alzheimer’s disease (MONDO:0004975)
- **Species:** Mus musculus (taxon 10090)

## Full-text entities

- **Genes:** Ptgs2 (prostaglandin-endoperoxide synthase 2) [NCBI Gene 19225] {aka COX2, Cox-2, PES-2, PGHS-2, PHS II, PHS-2}, Gnat1 (G protein subunit alpha transducin 1) [NCBI Gene 14685] {aka Gnat-1, Hg1f, Ird1, Ird2, Tralpha, irdc}, Ggta1 (glycoprotein galactosyltransferase alpha 1, 3) [NCBI Gene 14594] {aka GALT, Gal, Ggta, Ggta-1, alpha Gal, alpha3GalT}, Il1b (interleukin 1 beta) [NCBI Gene 16176] {aka IL-1beta, Il-1b}, Jam3 (junction adhesion molecule 3) [NCBI Gene 83964] {aka 1110002N23Rik, JAM-3, JAM-C, Jcam3}, Fos (Fos proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 14281] {aka D12Rfj1, c-fos, cFos}, Tnfrsf1a (tumor necrosis factor receptor superfamily, member 1a) [NCBI Gene 21937] {aka CD120a, FPF, TNF-R, TNF-R-I, TNF-R1, TNF-R55}, Il13 (interleukin 13) [NCBI Gene 16163] {aka Il-13}, Fth1 (ferritin heavy polypeptide 1) [NCBI Gene 14319] {aka FHC, Fth, HFt, MFH}, Gnb1 (guanine nucleotide binding protein (G protein), beta 1) [NCBI Gene 14688] {aka Gnb-1, Hg2a}, Itgam (integrin alpha M) [NCBI Gene 16409] {aka CD11b/CD18, CR3, CR3A, Cd11b, F730045J24Rik, Ly-40}, Kdm6b (KDM1 lysine (K)-specific demethylase 6B) [NCBI Gene 216850] {aka 1700064E03Rik, Jmjd3}, S100a10 (S100 calcium binding protein A10 (calpactin)) [NCBI Gene 20194] {aka 42C, CAL12, CLP11, Cal1l, p10, p11}, Cnga1 (cyclic nucleotide gated channel alpha 1) [NCBI Gene 12788] {aka Cncg}, Edn1 (endothelin 1) [NCBI Gene 13614] {aka ET-1, PPET1, preproET}, Iigp1 (interferon inducible GTPase 1) [NCBI Gene 60440] {aka 2900074L10Rik, Ifgga1, Iigp, Irga6}, Fbln5 (fibulin 5) [NCBI Gene 23876] {aka A55, DANCE, EVEC}, Nr2e3 (nuclear receptor subfamily 2, group E, member 3) [NCBI Gene 23958] {aka A930035N01Rik, PNR, RNR, rd7}, Ifrd1 (interferon-related developmental regulator 1) [NCBI Gene 15982] {aka Ifnl, PC4, Tis7}, Pdc (phosducin) [NCBI Gene 20028] {aka Rpr-1, Rpr1}, Fosl2 (fos-like antigen 2) [NCBI Gene 14284] {aka Fra-2}, Cx3cr1 (C-X3-C motif chemokine receptor 1) [NCBI Gene 13051] {aka mCX3CR1}, Tyrobp (TYRO protein tyrosine kinase binding protein) [NCBI Gene 22177] {aka DAP12, KARAP, Ly83}, F11r (F11 receptor) [NCBI Gene 16456] {aka 9130004G24, ESTM33, JAM, JAM-1, JAM-A, Jcam}, Ackr1 (atypical chemokine receptor 1 (Duffy blood group)) [NCBI Gene 13349] {aka CCBP1, CD234, Darc, Dfy, ESTM35, FY}, Ier2 (immediate early response 2) [NCBI Gene 15936] {aka Ch1, Pip92}, Gabrb3 (GABRB3, gamma-aminobutyric acid type A receptor subunit beta 3) [NCBI Gene 14402] {aka A230092K12Rik, Cp1, Gabrb-3, beta3}, Tnf (tumor necrosis factor) [NCBI Gene 21926] {aka DIF, TNF-a, TNF-alpha, TNFSF2, TNFalpha, Tnfa}, Prnp (prion protein) [NCBI Gene 19122] {aka CD230, PrP, PrP<C>, PrPC, PrPSc, Prn-i}, Adgre1 (adhesion G protein-coupled receptor E1) [NCBI Gene 13733] {aka DD7A5-7, EGF-TM7, Emr1, F4/80, Gpf480, Ly71}, Ednrb (endothelin receptor type B) [NCBI Gene 13618] {aka ET-B, ET-BR, ETR-b, ETb, Sox10m1}, Ccr5 (C-C motif chemokine receptor 5) [NCBI Gene 12774] {aka AM4-7, CD195, Cmkbr5}, Arid5a (AT-rich interaction domain 5A) [NCBI Gene 214855] {aka D430024K22Rik, Mrf1}, Isg15 (ISG15 ubiquitin-like modifier) [NCBI Gene 100038882] {aka G1p2, IGI15, IP17, Irfp, UCRP}, Ifit3 (interferon-induced protein with tetratricopeptide repeats 3) [NCBI Gene 15959] {aka Ifi49, P49}, Rho (rhodopsin) [NCBI Gene 212541] {aka Noerg1, Opn2, Ops, RP4}, Arr3 (arrestin 3, retinal) [NCBI Gene 170735] {aka Arr4, Car, Carfl, Carr}, Plekho2 (pleckstrin homology domain containing, family O member 2) [NCBI Gene 102595] {aka Plekhq1}, Lgals3 (lectin, galactose binding, soluble 3) [NCBI Gene 16854] {aka GBP, L-34, Mac-2, gal3}, Ccr1 (C-C motif chemokine receptor 1) [NCBI Gene 12768] {aka Cmkbr1, Mip-1a-R}, Ptprc (protein tyrosine phosphatase receptor type C) [NCBI Gene 19264] {aka B220, CD45R, Cd45, L-CA, Ly-5, Lyt-4}, Lgals9 (lectin, galactose binding, soluble 9) [NCBI Gene 16859] {aka LGALS35, Lgals5, gal-9, galectin-9}, Mcl1 (myeloid cell leukemia sequence 1) [NCBI Gene 17210] {aka Gm52627, Mcl-1}, Ccl2 (C-C motif chemokine ligand 2) [NCBI Gene 20296] {aka HC11, JE, MCAF, MCP-1, MCP1, SMC-CF}, Ccr2 (C-C motif chemokine receptor 2) [NCBI Gene 12772] {aka Cc-ckr-2, Ccr2a, Ccr2b, Ckr2, Ckr2a, Ckr2b}, Mcm3 (minichromosome maintenance complex component 3) [NCBI Gene 17215] {aka Mcmd, P1, P1-MCM3, p1.m}, Casp3 (caspase 3) [NCBI Gene 12367] {aka A830040C14Rik, AC-3, CASP-3, CC3, CPP-32, CPP32}, Jun (Jun proto-oncogene, AP-1 transcription factor subunit) [NCBI Gene 16476] {aka AP-1, Junc, c-jun}, Spag9 (sperm associated antigen 9) [NCBI Gene 70834] {aka 3110018C07Rik, 4733401I23Rik, 4831406C20Rik, JIP-4, JLP, JSAP2}, Fkbp5 (FK506 binding protein 5) [NCBI Gene 14229] {aka D17Ertd592e, Dit1, FKBP-5, FKBP51}, Tmsb10 (thymosin beta 10) [NCBI Gene 19240] {aka Ptmb10, Tb10}, Mcm2 (minichromosome maintenance complex component 2) [NCBI Gene 17216] {aka BM28, CDCL1, Mcmd2, mKIAA0030}, Cd68 (CD68 antigen) [NCBI Gene 12514] {aka Lamp4, Scard1, gp110}, H2-Aa (histocompatibility 2, class II antigen A, alpha) [NCBI Gene 14960] {aka Aalpha, H-2Aa, H2Aa, I-Aalpha, IAalpha, Ia-1}, Actb (actin, beta) [NCBI Gene 11461] {aka Actx, E430023M04Rik, beta-actin}, Apc (APC, WNT signaling pathway regulator) [NCBI Gene 11789] {aka CC1, Min, mAPC}, S100b (S100 protein, beta polypeptide, neural) [NCBI Gene 20203] {aka Bpb}, Cxcl12 (C-X-C motif chemokine ligand 12) [NCBI Gene 20315] {aka Pbsf, Scyb12, Sdf1, Tlsf, Tpar1}, H2-T23 (histocompatibility 2, T region locus 23) [NCBI Gene 15040] {aka 37b, 37c, H-2T23, H2-K1, H2-Qa1, Qa-1}, Gfap (glial fibrillary acidic protein) [NCBI Gene 14580]
- **Diseases:** Parkinson's disease (MESH:D010300), cone photoreceptor degeneration (MESH:C566719), amyotrophic lateral sclerosis (MESH:D000690), Inflammation (MESH:D007249), multiple sclerosis (MESH:D009103), retinal degenerative diseases (MESH:D012164), blindness (MESH:D001766), brain diseases (MESH:D001927), retinitis pigmentosa (MESH:D012174), photoreceptor (MESH:D012173), cognitive deficits (MESH:D003072), proinflammatory factors (MESH:D005171), inflammatory cytokines (MESH:D000080424), spinal cord injury (MESH:D013119), AD (MESH:D000544), neurological disorders (MESH:D009461), toxicity (MESH:D064420), inherited retinal degenerative diseases (MESH:D020271), OPL (MESH:D018318), neurotoxicity (MESH:D020258), neuronal damage (MESH:D009410), age-related macular degeneration (MESH:D008268), neuroinflammation (MESH:D000090862), cone photoreceptor (MESH:D000077765), ischemic stroke (MESH:D002544), neurodegeneration (MESH:D019636), infection (MESH:D007239), traumatic brain injury (MESH:D000070642)
- **Chemicals:** Alexa Fluor 555 (MESH:C000608607), dithiothreitol (MESH:D004229), xylazine (MESH:D014991), isothiocyanate (MESH:C037152), CO2 (MESH:D002245), polyvinylidene difluoride (MESH:C024865), sucrose (MESH:D013395), reactive oxygen species (MESH:D017382), EDTA (MESH:D004492), propidium iodide (MESH:D011419), streptomycin (MESH:D013307), penicillin (MESH:D010406), paraformaldehyde (MESH:C003043), Triton X-100 (MESH:D017830), Hypromellose (MESH:D065347), peptides (MESH:D010455), acetonitrile (MESH:C032159), Alexa Fluor 594 (-), PI (MESH:D010716), ketamine hydrochloride (MESH:D007649), formic acid (MESH:C030544), CCLs (MESH:D002433), GlutaMAX (MESH:C054122), methanol (MESH:D000432), TFA (MESH:D014269), SDS (MESH:D012967), N-2 (MESH:D009584), calcium (MESH:D002118), Alexa Fluor 488 (MESH:C000711379), TRIzol (MESH:C411644)
- **Species:** Homo sapiens (human, species) [taxon 9606], Mus musculus (house mouse, species) [taxon 10090], Rattus norvegicus (brown rat, species) [taxon 10116], Gallus gallus (bantam, species) [taxon 9031]
- **Cell lines:** 661W — Mus musculus (Mouse), Transformed cell line (CVCL_6240), aMG_3 — Mus musculus (Mouse), Hybridoma (CVCL_C6V6), /6J — Homo sapiens (Human), Cutaneous melanoma, Cancer cell line (CVCL_W797), ACM-2 — Homo sapiens (Human), Colon carcinoma, Cancer cell line (CVCL_A628), C57BL/6J — Mus musculus (Mouse), Transformed cell line (CVCL_C0MW), BV2 — Mus musculus (Mouse), Transformed cell line (CVCL_0182), ACM-1 — Mus musculus (Mouse), Hybridoma (CVCL_C7RB), IMA2.1 — Mus musculus (Mouse), Transformed cell line (CVCL_X370)

## Full text

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## Figures

9 figures with captions in the complete paper: https://tomesphere.com/paper/PMC12868684/full.md

## References

5 references — full list in the complete paper: https://tomesphere.com/paper/PMC12868684/full.md

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Source: https://tomesphere.com/paper/PMC12868684