Affinage

CBLN4

Cerebellin-4 · UniProt Q9NTU7

Length
201 aa
Mass
21.8 kDa
Annotated
2026-06-09
44 papers in source corpus 15 papers cited in narrative 15 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 7/7 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

CBLN4 is a secreted N-linked glycoprotein of the C1q/cerebellin family that functions as a trans-synaptic organizer, contributing redundantly with other cerebellins to synapse maintenance and plasticity rather than initial synapse formation (PMID:17331201, PMID:29691328). It is secreted as a glycoprotein and assembles into both homomeric and heteromeric complexes with other cerebellins, and complex subunit composition tunes receptor selectivity—Cbln1/Cbln4 heteromers lose affinity for DCC while gaining affinity for neurexins (PMID:17331201, PMID:22220752). Unlike Cbln1 and Cbln2, Cbln4 binds only weakly to neurexins and is poorly synaptogenic in standard neuronal cultures (PMID:21410790, PMID:21356198), a difference explained by glycosylation: N-linked glycans at an N-terminal site and within the C1q domain mask intrinsic neurexin and GluD2 binding, respectively, and removing these glycans unmasks GluD2 binding sufficient to rescue ataxia in Cbln1-null mice (PMID:29782851). Crystal structures of the Cbln4 C1q-domain homotrimer localize the GluD2-binding divergence to loop CD and define a stable Nrxn1β LNS-domain complex (PMID:28877468). CBLN4 binds selectively to the netrin receptor DCC and its homolog neogenin-1 (NEO1) at membrane-proximal fibronectin domains FN4-6, in a netrin-displaceable manner (PMID:22220752, PMID:24400119). Physiologically, presynaptic CBLN4 anchored via neurexins in entorhinal cortex neurons engages postsynaptic NEO1 (not DCC) in dentate gyrus granule cells to confer long-term potentiation competence without affecting basal transmission (PMID:35544694), and it promotes formation and maintenance of GABAergic connections in hippocampal neurons (PMID:25534236). Cbln4 expression is directly driven by SRY/SOX9 in the developing testis (PMID:19211811) and by Hes1 downstream of NGF in neurons (PMID:25534236), and its mRNA stability is enhanced by METTL14-mediated m6A methylation (PMID:39235700).

Mechanistic history

Synthesis pass · year-by-year structured walk · 13 steps
  1. 2007 Medium

    Established the basic biochemical nature of CBLN4 as a secreted glycoprotein capable of multimerizing with other cerebellins, raising the question of how heteromer composition shapes function.

    Evidence Mammalian heterologous expression with secretion assays, co-IP, and subcellular fractionation

    PMID:17331201

    Open questions at the time
    • Stoichiometry and physiological prevalence of specific heteromers in vivo not defined
    • No receptor binding tested at this stage
  2. 2008 Medium

    Identified DCC as a selective CBLN4 receptor and showed that heteromer composition switches receptor preference between DCC and neurexins, linking subunit assembly to signaling output.

    Evidence Candidate receptor binding/pulldown with netrin displacement competition and Cbln4-null mice

    PMID:22220752

    Open questions at the time
    • Binding site on DCC not mapped
    • Functional consequence of DCC engagement not established
  3. 2011 High

    Distinguished CBLN4 from synaptogenic cerebellins by demonstrating it binds neurexins only weakly and lacks synaptogenic activity in vitro, indicating a divergent functional role.

    Evidence Surface plasmon resonance and in vitro synaptogenesis assays in cortical, hippocampal, and cerebellar neurons across two labs

    PMID:21356198 PMID:21410790

    Open questions at the time
    • Why CBLN4 is non-synaptogenic despite cerebellin homology unresolved at this stage
    • In vivo synaptic role untested
  4. 2014 High

    Defined the molecular CBLN4-DCC interaction surface and extended receptor repertoire to neogenin-1, establishing competitive cross-talk with netrin-1.

    Evidence Extracellular protein microarray screen plus radio-ligand binding competition mapping to FN4-6 domains

    PMID:24400119

    Open questions at the time
    • Cellular/synaptic readout of the CBLN4-DCC/NEO1 interaction not yet shown
    • Affinity hierarchy among receptors not fully resolved
  5. 2017 High

    Provided atomic-resolution structural basis for cerebellin functional divergence, localizing GluD2-binding specificity to loop CD and visualizing the Nrxn1β complex.

    Evidence X-ray crystallography of C1q homotrimers, negative-stain EM, and SPR

    PMID:28877468

    Open questions at the time
    • Structure of the receptor-bound (DCC/NEO1) complex not solved
    • Role of glycosylation not addressed structurally
  6. 2018 High

    Resolved why CBLN4 appears non-synaptogenic by showing N-linked glycosylation masks intrinsic neurexin and GluD2 binding, with deglycosylated CBLN4 functionally substituting for Cbln1 in vivo.

    Evidence Glycosylation-site mutagenesis, in vitro binding, and transgenic rescue of Cbln1-null ataxia

    PMID:29782851

    Open questions at the time
    • Whether glycosylation is dynamically regulated in vivo unknown
    • Cell-type-specific glycoforms not characterized
  7. 2018 Medium

    Defined the in vivo significance of CBLN4 through genetic ablation, showing it acts redundantly with other cerebellins in synapse maintenance rather than initial formation.

    Evidence Single, double, and triple cerebellin knockout mice with synapse density and behavioral phenotyping

    PMID:29691328

    Open questions at the time
    • Specific synapses uniquely dependent on Cbln4 not identified here
    • Molecular partner mediating maintenance not pinpointed
  8. 2022 High

    Established a defined circuit-level function by showing presynaptic CBLN4 signals to postsynaptic neogenin-1 to confer LTP competence at entorhinal cortex→dentate gyrus synapses.

    Evidence Cell-type-specific conditional KOs of presynaptic Cbln4 and postsynaptic NEO1 versus DCC with LTP and basal transmission electrophysiology

    PMID:35544694

    Open questions at the time
    • Downstream NEO1 signaling underlying LTP not defined
    • Generalizability to other circuits untested
  9. 2009 High

    Identified CBLN4 as a direct SRY/SOX9 transcriptional target in the testis, revealing a developmental, non-neuronal regulatory context.

    Evidence Anti-SRY ChIP and transgenic gain/loss-of-function in mouse gonad

    PMID:19211811

    Open questions at the time
    • Functional role of CBLN4 in testis development unknown
    • Downstream effectors not identified
  10. 2014 Medium

    Placed CBLN4 in an NGF/Hes1-controlled program promoting GABAergic connectivity and neuronal survival under amyloid stress.

    Evidence Overexpression, knockdown, and recombinant protein application in cultured hippocampal neurons with GABAergic marker staining and Aβ toxicity rescue

    PMID:25534236

    Open questions at the time
    • In vivo validation of GABAergic role lacking
    • Receptor mediating GABAergic effect not specified
  11. 2024 Medium

    Identified a post-transcriptional control layer, with METTL14-mediated m6A methylation stabilizing CBLN4 mRNA in a neuronal stress model.

    Evidence MeRIP and dual-luciferase reporter assays with CBLN4 overexpression in Aβ-treated SK-N-SH cells

    PMID:39235700

    Open questions at the time
    • m6A sites not mapped at nucleotide resolution
    • In vivo relevance to neural function untested
  12. 2024 Low

    Implicated the GluD1 distal amino-terminal domain as an interaction site for Cbln4-related ligands via a disease-associated GRID1 variant.

    Evidence Site-directed mutagenesis and biochemical complex formation assay (tested directly with Cbln2)

    PMID:37944084

    Open questions at the time
    • Cbln4 interaction inferred from structural similarity, not directly tested
    • Functional consequence of GluD1-Cbln4 binding unknown
  13. 2026 Low

    Nominated neogenin-1 as the principal perinatal postsynaptic receptor mediating CBLN4-dependent somatostatin-interneuron-to-glutamatergic synapse formation in cortex.

    Evidence Single-cell transcriptomics across developmental stages with computational ligand-receptor inference

    PMID:41565644

    Open questions at the time
    • Computational inference without direct binding or functional validation for this interaction
    • Cortical interneuron synapse role not experimentally confirmed

Open questions

Synthesis pass · forward-looking unresolved questions
  • How CBLN4 glycosylation state, heteromer composition, and receptor choice (DCC vs NEO1 vs GluD) are coordinated to specify distinct synaptic functions across brain regions remains unresolved.
  • No structure of CBLN4 bound to DCC/NEO1
  • Downstream intracellular signaling from NEO1 unknown
  • Regulation of glycoform diversity in vivo undefined

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0048018 receptor ligand activity 3 GO:0005198 structural molecule activity 2
Localization
GO:0005576 extracellular region 2 GO:0005886 plasma membrane 2
Pathway
R-HSA-112316 Neuronal System 2 R-HSA-1266738 Developmental Biology 2
Partners
CBLN1DCCGRID2NEO1NRXN1

Evidence

Reading pass · 15 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2007 Cbln2 and Cbln4 are secreted as N-linked glycoproteins when expressed in mammalian heterologous cells. All Cbln family members form not only homomeric but also heteromeric complexes with each other in vitro, and heteromer formation between Cbln1 and Cbln3 modulates each other's trafficking and secretion. Mammalian cell expression, glycoprotein secretion assays, co-immunoprecipitation, subcellular fractionation The European journal of neuroscience Medium 17331201
2008 Cbln4 (but not Cbln1 or Cbln2) binds selectively to the netrin receptor DCC (deleted in colorectal cancer) in a netrin-displaceable fashion. Cbln1/Cbln4 heteromeric complexes have greatly reduced affinity for DCC but increased affinity for neurexins compared to Cbln4 alone, indicating subunit-composition-dependent receptor binding. Candidate receptor-screening binding assay, pulldown, netrin displacement competition assay, generation of Cbln4-null mice Journal of neurochemistry Medium 22220752
2011 Cbln4 does not specifically bind to neurexin α and β isoforms carrying the splice site 4 insert [NRXs(S4+)] and does not induce synaptogenesis in cerebellar, hippocampal, or cortical neurons in vitro, unlike Cbln1 and Cbln2. In vitro synaptogenesis assay, binding assays in cultured neurons The European journal of neuroscience Medium 21356198 21410790
2011 Cbln4 shows only weak interactions with NRXN1α and β-NRXNs as measured by surface plasmon resonance, with binding affinity much lower than Cbln1 or Cbln2, and Cbln4 exhibited little synaptogenic activity in cortical neuron cultures. Surface plasmon resonance, in vitro synaptogenesis assay with cortical neurons Biochemical and biophysical research communications High 21356198
2014 CBLN4 and Netrin-1 are identified as extracellular binding partners of DCC using protein microarray screens. CBLN4 binds to DCC at an overlapping site within membrane-proximal fibronectin domains FN4-6, with Netrin-1 competing with CBLN4 binding and exhibiting ~5-fold higher affinity. CBLN4 also binds to DCC homolog Neogenin-1 (NEO1) with lower affinity than DCC. Extracellular protein microarray screen (>1000 proteins), immunofluorescence, radio-ligand binding competition assay PloS one High 24400119
2017 Crystal structures of the C1q domain homotrimers of Cbln1 and Cbln4 were solved at 2.2 Å and 2.3 Å resolution, respectively. Structural comparison revealed that sequence and structural divergence in loop CD accounts for the difference in GluD2 binding between Cbln1 and Cbln4. Cbln4 was shown to form a stable complex with the LNS domain of Nrxn1β, and negative-stain EM reconstruction suggested Nrxn1β binds to the N-terminal region of Cbln4 through strand β10 of the S4 insert. X-ray crystallography, negative-stain electron microscopy, surface plasmon resonance (stable complex formation) Cell reports High 28877468
2018 Glycosylation of Cbln4 at two N-linked sites attenuates receptor binding: the N-terminal glycosylation site masks neurexin binding, while the C1q domain glycosylation site masks GluD2 binding. Glycosylation mutants (asparagine-to-glutamine) of Cbln4 completely rescued ataxia in Cbln1-null mice in vivo, demonstrating that Cbln4 has intrinsic GluD2 binding that is masked by glycosylation. Site-directed mutagenesis of glycosylation sites, in vitro receptor binding assay, transgenic mouse rescue experiment Brain research High 29782851
2016 Cbln4 is selectively co-expressed with a specific neurexin splice isoform (lacking the SS4 insert) in parvalbumin-positive (PV+) interneurons of the mouse hippocampus. Conditional ablation of neurexin alternative splice insertions selectively in PV+ cells results in elevated hippocampal network activity and learning impairment, placing Cbln4 in a PV-interneuron-specific neurexin signaling pathway. Conditional knockout mouse, electrophysiology, behavioral testing, in situ hybridization, alternative splicing analysis eLife Medium 27960072
2018 Constitutive Cbln4 knockout mice are viable and fertile, and single Cbln4 deletion does not produce the striatal synaptic changes seen in Cbln1-null mice. Combined Cbln1/2/4 triple KO aggravates salience-induced seizures observed in Cbln1/2 double KO, indicating Cbln4 contributes to brain function redundantly with other cerebellins. Cerebellins including Cbln4 are not required for initial synapse formation but contribute to long-term synapse maintenance. Constitutive single, double, and triple knockout mice; synapse density quantification; behavioral phenotyping (motor, seizure) The Journal of neuroscience Medium 29691328
2009 Cbln4 is a direct transcriptional target of SRY and SOX9 in the developing mouse testis. Anti-SRY chromatin immunoprecipitation pulled down a region 7.5 kb upstream of the Cbln4 transcriptional start site. Reducing Sox9 expression in XY mice decreased Cbln4 expression, overexpressing Sox9 in XX mice upregulated Cbln4, and ectopic SRY expression caused ectopic Cbln4 expression. Chromatin immunoprecipitation (ChIP), transgenic mouse overexpression/knockdown, in situ expression analysis Biology of reproduction High 19211811
2014 Cbln4 plays an essential role in the formation and maintenance of inhibitory GABAergic connections in cultured hippocampal neurons. Hes1 transcription factor controls Cbln4 expression downstream of NGF. Overexpression of Cbln4 or application of recombinant Cbln4 increased GABAergic varicosities and rescued neurons from Aβ-induced death; knockdown of Cbln4 reduced GABAergic connections. Cbln4 overexpression and knockdown in cultured hippocampal neurons, recombinant protein application, immunostaining for GABAergic markers (VGAT), Aβ toxicity rescue assay Neurobiology of aging Medium 25534236
2022 Cbln4, expressed presynaptically in entorhinal cortex neurons and bound to neurexins, forms transcellular complexes with postsynaptic neogenin-1 (NEO1) in dentate gyrus granule cells. Presynaptic deletion of Cbln4 or postsynaptic deletion of NEO1 (but not DCC) in dentate granule cells blocked long-term potentiation (LTP) at entorhinal cortex→dentate gyrus synapses without affecting basal synaptic transmission, establishing a Cbln4–neogenin-1 trans-synaptic signaling pathway required for LTP competence. Conditional knockout mice (presynaptic Cbln4 deletion; postsynaptic NEO1 and DCC deletions), electrophysiology (LTP induction and basal synaptic transmission) Proceedings of the National Academy of Sciences of the United States of America High 35544694
2024 A GRID1 variant at a position predicted to interact with Cbln2/Cbln4 disrupts complex formation between GluD1 and Cbln2, identifying the GluD1 distal amino terminal domain as a site of interaction with Cbln4-related ligands. Site-directed mutagenesis of GRID1 variants, biochemical complex formation assay Human molecular genetics Low 37944084
2024 METTL14-mediated m6A methylation improves the stability and expression of CBLN4 mRNA. In Aβ1-42-treated SK-N-SH cells, CBLN4 and METTL14 are both downregulated; overexpression of CBLN4 relieves apoptosis, inflammation, oxidative stress, and ER stress. METTL14 was shown to regulate CBLN4 mRNA stability via m6A modification using MeRIP and dual-luciferase reporter assays. MeRIP (methylated RNA immunoprecipitation), dual-luciferase reporter assay, overexpression in SK-N-SH cells, MTT, flow cytometry, ELISA, Western blot Journal of bioenergetics and biomembranes Medium 39235700
2026 Single-cell transcriptomic analysis across 17 developmental stages identifies NEOGENIN-1 as the principal postsynaptic receptor for CBLN4 during the perinatal period, mediating synapse formation between somatostatin-expressing interneurons and glutamatergic neurons in the mouse cortex. Single-cell transcriptomics across developmental stages, ligand-receptor inference Nature communications Low 41565644

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2011 Cbln family proteins promote synapse formation by regulating distinct neurexin signaling pathways in various brain regions. The European journal of neuroscience 134 21410790
2006 Distinct expression of Cbln family mRNAs in developing and adult mouse brains. The European journal of neuroscience 92 16930405
2016 An alternative splicing switch shapes neurexin repertoires in principal neurons versus interneurons in the mouse hippocampus. eLife 68 27960072
2008 Cbln and C1q family proteins: new transneuronal cytokines. Cellular and molecular life sciences : CMLS 64 18278437
2018 Genetic Ablation of All Cerebellins Reveals Synapse Organizer Functions in Multiple Regions Throughout the Brain. The Journal of neuroscience : the official journal of the Society for Neuroscience 59 29691328
2017 Cerebellins are differentially expressed in selective subsets of neurons throughout the brain. The Journal of comparative neurology 56 28714144
2019 Identification of molecular correlations of RBM8A with autophagy in Alzheimer's disease. Aging 55 31816601
2012 The Cbln family of proteins interact with multiple signaling pathways. Journal of neurochemistry 52 22220752
2014 Defining the ligand specificity of the deleted in colorectal cancer (DCC) receptor. PloS one 48 24400119
2007 Characterization of a transneuronal cytokine family Cbln--regulation of secretion by heteromeric assembly. The European journal of neuroscience 47 17331201
2011 Differential interactions of cerebellin precursor protein (Cbln) subtypes and neurexin variants for synapse formation of cortical neurons. Biochemical and biophysical research communications 46 21356198
2009 The cerebellin 4 precursor gene is a direct target of SRY and SOX9 in mice. Biology of reproduction 40 19211811
2023 GluN2D Subunit in Parvalbumin Interneurons Regulates Prefrontal Cortex Feedforward Inhibitory Circuit and Molecular Networks Relevant to Schizophrenia. Biological psychiatry 34 37004850
2018 Antibiotics suppress colon tumorigenesis through inhibition of aberrant DNA methylation in an azoxymethane and dextran sulfate sodium colitis model. Cancer science 33 30443963
2007 Mapping of Cbln1-like immunoreactivity in adult and developing mouse brain and its localization to the endolysosomal compartment of neurons. The European journal of neuroscience 31 18001291
2019 Genome-wide association study of morbid obesity in Han Chinese. BMC genetics 28 31852448
2014 Cerebellin 4, a synaptic protein, enhances inhibitory activity and resistance of neurons to amyloid-β toxicity. Neurobiology of aging 27 25534236
2022 Transsynaptic cerebellin 4-neogenin 1 signaling mediates LTP in the mouse dentate gyrus. Proceedings of the National Academy of Sciences of the United States of America 25 35544694
2020 DNA methylation analysis with methylation-sensitive high-resolution melting (MS-HRM) reveals gene panel for glioma characteristics. CNS neuroscience & therapeutics 25 32783304
2019 Transcriptional profiling aligned with in situ expression image analysis reveals mosaically expressed molecular markers for GABA neuron sub-groups in the ventral tegmental area. The European journal of neuroscience 25 31374129
2017 Cbln1 and Cbln4 Are Structurally Similar but Differ in GluD2 Binding Interactions. Cell reports 18 28877468
2008 Expression of precerebellins in cultured rat calvaria osteoblast-like cells. International journal of molecular medicine 16 18813864
2009 Precerebellin-related genes and precerebellin 1 peptide in endocrine glands of the rat - pattern of their expression. International journal of molecular medicine 14 19082514
2024 Clinical features, functional consequences, and rescue pharmacology of missense GRID1 and GRID2 human variants. Human molecular genetics 13 37944084
2009 Insulinostatic activity of cerebellin--evidence from in vivo and in vitro studies in rats. Regulatory peptides 12 19481574
2018 Spinal injection of newly identified cerebellin-1 and cerebellin-2 peptides induce mechanical hypersensitivity in mice. Neuropeptides 11 29705514
2023 Glioblastoma survival is associated with distinct proteomic alteration signatures post chemoirradiation in a large-scale proteomic panel. Frontiers in oncology 10 37637066
2008 Investigation of QTL regions on Chromosome 17 for genes associated with meat color in the pig. Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie 10 18717966
2014 Parcellation of cerebellins 1, 2, and 4 among different subpopulations of dorsal horn neurons in mouse spinal cord. The Journal of comparative neurology 9 23853053
2020 Integrated Genome-Wide Methylation and Expression Analyses Reveal Key Regulators in Osteosarcoma. Computational and mathematical methods in medicine 8 32855654
2024 METTL14 inhibits Aβ1-42-induced neuronal injury through regulating the stability of CBLN4 mRNA in Alzheimer's disease. Journal of bioenergetics and biomembranes 7 39235700
2023 Cortical interneurons: fit for function and fit to function? Evidence from development and evolution. Frontiers in neural circuits 7 37215503
2009 Precerebellin-related genes and precerebellin 1 peptide in the adrenal gland of the rat: expression pattern, localization, developmental regulation and effects on corticosteroidogenesis. International journal of molecular medicine 7 19212655
2024 Differential Expression Analysis Identifies Candidate Synaptogenic Molecules for Wiring Direction-Selective Circuits in the Retina. The Journal of neuroscience : the official journal of the Society for Neuroscience 5 38514178
2021 The porcine cerebellin gene family. Gene 3 34274480
2018 Glycosylation of Cblns attenuates their receptor binding. Brain research 3 29782851
2019 [Compound porcine cerebroside and ganglioside relieves brain injury and promotes expression of cerebellin 4 in neonatal mice with intrauterine hypoxia]. Xi bao yu fen zi mian yi xue za zhi = Chinese journal of cellular and molecular immunology 2 31638570
2025 Distinct proteomic CSF profiles in genetic frontotemporal lobar degeneration. Brain : a journal of neurology 1 41343108
2025 Proteomic analysis identifies lipoprotein(a)-associated proteins linked to incident atherosclerotic cardiovascular disease events. medRxiv : the preprint server for health sciences 1 41445622
2026 Uncovering the molecular logic of cortical wiring between neuronal subtypes across development through ligand-receptor inference. Nature communications 0 41565644
2026 Association between systemic redox balance and osteoporosis: prospective evidence, polygenic modification, and proteomic and inflammatory mediation in the UK Biobank. Bone 0 41570964
2026 Structural Architecture and Evolutionary Conservation of Cerebellin-Mediated Trans-Synaptic Signaling. Synapse (New York, N.Y.) 0 41995212
2025 Cell-type specific profiling of human entorhinal cortex at the onset of Alzheimer's disease neuropathology. bioRxiv : the preprint server for biology 0 39803521
2025 Identification of Key Genes in Esketamine's Therapeutic Effects on Perioperative Neurocognitive Disorders via Transcriptome Sequencing. Drug design, development and therapy 0 39974608

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