Affinage

MATN3

Matrilin-3 · UniProt O15232

Length
486 aa
Mass
52.8 kDa
Annotated
2026-06-10
34 papers in source corpus 13 papers cited in narrative 13 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 5/5 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

MATN3 (matrilin-3) is a cartilage extracellular matrix protein built from a signal peptide, a von Willebrand factor A (vWFA/A) domain, four EGF repeats, and an alpha-helical coiled-coil region, expressed across cartilage types and by primary chondrocytes as a marker of the differentiated state (PMID:9799608). In the matrix it binds type II and type IX collagen and participates in ECM assembly (PMID:18205203). Dominant mutations clustered in the exon-2 A-domain, especially around the second beta-sheet, cause multiple epiphyseal dysplasia (MED) by misfolding the A-domain so that secretion is blocked and protein is retained intracellularly (PMID:16287128, PMID:15459972); misfolded A-domains associate specifically with the ER chaperone ERp72 and accumulate in dilated rough ER cisternae (PMID:16287128). In vivo, this retention triggers an unfolded protein response, reduces chondrocyte proliferation, and spatially dysregulates apoptosis in the growth plate, disrupting linear bone growth (PMID:17517694), with retained mutant protein forming non-native disulfide-bonded aggregates that co-retain matrilin-1 independently of normal hetero-oligomerization (PMID:22083516). Beyond its structural ECM and disease role, MATN3 delivered via exosomes acts as a signaling ligand: it activates TGF-beta/SMAD/AKT signaling to promote nucleus pulposus proliferation and ECM synthesis (PMID:34136064), modulates the PI3K/AKT/mTOR axis through IL-17A to protect chondrocytes (PMID:37635810), and in gastric cancer drives proliferation and invasion through direct interaction with ASPN (PMID:39301785) and stabilization of EGFR with downstream ELK1/ATG12-mediated autophagy and M2 macrophage polarization (PMID:42163458).

Mechanistic history

Synthesis pass · year-by-year structured walk · 12 steps
  1. 1998 Medium

    Establishing the protein architecture and expression pattern defined MATN3 as a chondrocyte-restricted ECM protein and a candidate differentiation marker.

    Evidence cDNA cloning from cartilage and Northern blot across primary vs. dedifferentiated chondrocytes

    PMID:9799608

    Open questions at the time
    • No functional assay of the encoded protein
    • Role of individual domains not tested
  2. 2000 Medium

    Genomic characterization resolved the gene structure and showed MATN3 lacks the second vWFA domain present in other matrilins, distinguishing its architecture.

    Evidence Genomic cloning, exon mapping, and RNase protection in mouse

    PMID:10656920

    Open questions at the time
    • Functional consequence of single vWFA domain not addressed
    • Splicing feature not linked to disease
  3. 2005 High

    Determining why MED mutations are pathogenic showed that A-domain misfolding blocks secretion and engages the ER chaperone ERp72, establishing a protein-retention disease mechanism.

    Evidence Mammalian secretion assays, reciprocal Co-IP with ERp72, EM and IHC of patient cartilage

    PMID:16287128

    Open questions at the time
    • Did not establish downstream cellular consequences in vivo
    • Mechanism of ERp72-dependent retention not fully defined
  4. 2004 Medium

    Mutation mapping localized MED-causing changes to the exon-2 A-domain beta-sheet region, with one alpha-helix exception, defining the disease-critical region.

    Evidence PCR and direct sequencing of all MATN3 exons in MED patients

    PMID:15459972

    Open questions at the time
    • No functional validation in this study
    • Genotype-phenotype correlation not resolved
  5. 2007 High

    An in vivo knock-in model connected mutant retention to a cellular pathology — UPR activation, reduced proliferation, and dysregulated apoptosis in the growth plate — explaining short-limbed dwarfism.

    Evidence Matn3 MED knock-in mouse with histology, IHC, EM, proliferation and apoptosis readouts

    PMID:17517694

    Open questions at the time
    • Specific UPR effectors driving apoptosis not pinpointed
    • Therapeutic reversibility not tested
  6. 2008 Medium

    Testing individual A-domain mutations distinguished secretion-blocking from non-disruptive variants, showing not all helical mutations act through misfolding.

    Evidence In vitro A-domain secretion, structural assessment, and collagen-binding assays

    PMID:18205203

    Open questions at the time
    • Disease mechanism of p.Lys231Asn unresolved
    • Single-lab in vitro readouts
  7. 2012 High

    Genetic epistasis clarified that mutant retention and aggregation are intrinsic to the misfolded A-domain, not dependent on matrilin-1 hetero-oligomerization.

    Evidence Matn3 V194D x Matn1-null cross with biochemical analysis of disulfide-bonded aggregates and phenotyping

    PMID:22083516

    Open questions at the time
    • Aggregate clearance pathways not defined
    • Other matrilin partners not excluded
  8. 2021 Medium

    Identifying exosomal MATN3 as a signaling cargo revealed a non-structural role: it promotes nucleus pulposus proliferation and ECM synthesis via TGF-beta/SMAD/AKT activation.

    Evidence USC-exosome experiments with MATN3 knockdown, proliferation assays, signaling Western blots, and in vivo IDD model

    PMID:34136064

    Open questions at the time
    • Receptor mediating MATN3-TGF-beta link not identified
    • Single lab
  9. 2023 Medium

    A second exosomal context showed MATN3 modulates the PI3K/AKT/mTOR axis through IL-17A to protect chondrocytes from ECM degradation and autophagy defects in OA.

    Evidence IL-1beta OA cell model, SMSC-Exo with MATN3 overexpression/knockdown, pathway Western blots, DMM in vivo model

    PMID:37635810

    Open questions at the time
    • Direct MATN3 receptor not defined
    • Mechanistic link to IL-17A incomplete
  10. 2024 Medium

    In gastric cancer, MATN3 was shown to act as an oncogenic partner of ASPN, driving proliferation, migration, and invasion via EMT activation.

    Evidence PPI/Co-IP analysis, functional assays, and xenograft co-overexpression model

    PMID:39301785

    Open questions at the time
    • EMT pathway mechanism only sketched
    • ASPN-MATN3 interaction interface unmapped
  11. 2026 Medium

    A defined gastric cancer signaling axis showed exosomal MATN3 stabilizes EGFR, activating ELK1-driven ATG12 autophagy and M2 macrophage polarization for immunosuppression.

    Evidence Co-IP, IF co-localization, ChIP, dual-luciferase, ubiquitination assays, xenograft and macrophage co-culture

    PMID:42163458

    Open questions at the time
    • Not independently replicated
    • Mechanism of EGFR stabilization by MATN3 not fully resolved
  12. 2026 Medium

    A human iPSC MED model expanded the chondrocyte phenotype, linking mutant MATN3 to cholesterol biosynthesis upregulation and lipid droplet accumulation alongside abnormal ECM assembly.

    Evidence hPSC chondrocyte differentiation with CRISPR-edited and patient-derived cells, RNAseq, TEM, IHC

    PMID:41651153

    Open questions at the time
    • Causal link between cholesterol changes and pathology not established
    • UPR induction only modest in this system

Open questions

Synthesis pass · forward-looking unresolved questions
  • How secreted/exosomal MATN3 engages specific cell-surface receptors to trigger TGF-beta, AKT/mTOR, and EGFR signaling, and whether these signaling roles relate mechanistically to its structural ECM function, remains unresolved.
  • No defined MATN3 receptor for its signaling activities
  • Relationship between ECM-assembly role and exosomal signaling role unknown
  • Disease mechanism of non-secretion-blocking variants unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 1 GO:0008092 cytoskeletal protein binding 1
Localization
GO:0005783 endoplasmic reticulum 3 GO:0031012 extracellular matrix 2 GO:0005576 extracellular region 1
Pathway
R-HSA-162582 Signal Transduction 3 R-HSA-1474244 Extracellular matrix organization 2 R-HSA-8953897 Cellular responses to stimuli 2

Evidence

Reading pass · 13 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2005 MED-causing MATN3 mutations in the A-domain cause misfolding of that domain (shown by unfolded conformation of mutant A-domains expressed individually) and prevent secretion of matrilin-3 from mammalian cells; mutant protein is retained intracellularly. Co-immunoprecipitation demonstrated that mutant A-domains associate specifically with ERp72, an ER chaperone involved in disulfide bond formation. Electron microscopy of patient cartilage confirmed intracellular retention in dilated rough ER cisternae. Mammalian cell expression of wild-type and mutant matrilin-3, co-immunoprecipitation with ERp72, electron microscopy and immunohistochemistry of patient cartilage Human mutation High 16287128
2007 In a knock-in mouse model carrying a Matn3 MED mutation, mutant matrilin-3 is retained within the rough ER of chondrocytes and triggers an unfolded protein response (UPR), leading to decreased chondrocyte proliferation and spatially dysregulated apoptosis in the cartilage growth plate, which disrupts linear bone growth and causes short-limbed dwarfism. Mouse knock-in model, histochemistry, immunohistochemistry, electron microscopy, assessment of chondrocyte proliferation and apoptosis in growth plate Human molecular genetics High 17517694
2008 Two alpha-helical A-domain mutations (p.Phe105Ser and p.Ala173Asp) prevent secretion of matrilin-3 A-domain in vitro, similar to beta-sheet mutations. However, a third alpha-helical mutation (p.Lys231Asn) does not prevent A-domain secretion, does not disrupt A-domain structure, and does not inhibit binding to type II or type IX collagen, leaving its disease mechanism unresolved. In vitro A-domain expression and secretion assay, structural assessment, collagen binding assay Human mutation Medium 18205203
2012 Secretion of mutant matrilin-3 (V194D) is not dependent on hetero-oligomerization with matrilin-1; ablation of matrilin-1 expression in Matn3 V194D mice does not alter the proportion of mutant matrilin-3 in the ECM, does not increase intracellular retention, and does not worsen disease severity. Retained mutant matrilin-3 forms non-native disulfide-bonded aggregates through the misfolded A-domain and causes co-retention of matrilin-1. Genetic cross of Matn3 V194D knock-in with Matn1-null mice; histochemistry, biochemistry (disulfide-bonded aggregate analysis), phenotypic assessment Arthritis and rheumatism High 22083516
1998 Human MATN3 encodes a 486 amino acid extracellular matrix protein with the domain architecture: signal peptide, von Willebrand factor A (vWFA) domain, four EGF repeats, and an alpha-helical coiled-coil region. The mRNA is expressed in all cartilage types and by primary (but not dedifferentiated) chondrocytes, suggesting matrilin-3 as a marker of chondrocyte differentiation state. cDNA cloning from cartilage library, sequence analysis, Northern blot / expression in primary vs. dedifferentiated chondrocytes Genomics Medium 9799608
2000 The mouse Matn3 gene comprises 8 exons spanning 23.4 kb; the last intron uses non-canonical AT-AC ends and is spliced by the U12-type spliceosome, a feature conserved in all matrilin genes. Unlike other matrilins, Matn3 lacks a second vWFA domain; the intron that could encode it contains 75% repetitive sequences indicating evolutionary loss. Genomic cloning, exon mapping, RNase protection assay for transcription start sites, SSCP mapping Mammalian genome Medium 10656920
2004 All characterized MED-causing MATN3 mutations cluster within exon 2 encoding the vWFA (A) domain, specifically in and around the 2nd beta-sheet region (amino acids 120-127). One novel mutation (p.F105S) extends the affected region to an alpha-helix of the A-domain, outside the beta-sheet. PCR and direct sequencing of all 8 MATN3 exons in MED patients Human mutation Medium 15459972
2018 An intragenic de novo tandem duplication of exons 2–5 in MATN3 (formed via Alu-Alu mediated recombination) causes multiple epiphyseal dysplasia, establishing intragenic CNV as a novel mutational mechanism for MATN3-related disease. Targeted CNV screening, breakpoint characterization (Alu-Alu fusion identification) Human mutation Low 30080953
2021 Exosomal MATN3 protein from urine-derived stem cells promotes nucleus pulposus cell (NPC) proliferation and ECM synthesis, and alleviates intervertebral disc degeneration in vivo. The mechanism involves MATN3 activating TGF-β signaling, elevating phosphorylation of SMAD and AKT. MATN3 was identified as the required cargo mediating these USC-exosome effects by knockdown experiments. Western blot, CCK-8 proliferation assay, immunofluorescence, in vivo IDD mouse model (CT, MRI, histology), MATN3 knockdown in exosomes Oxidative medicine and cellular longevity Medium 34136064
2023 SMSC-derived exosomal MATN3 suppresses activation of the PI3K/AKT/mTOR signaling pathway through IL-17A, protecting chondrocytes from ECM degradation and autophagy defects in an OA model. In vitro OA model (IL-1β), SMSC-Exo administration, overexpression and knockdown of MATN3, Western blot for PI3K/AKT/mTOR pathway components, in vivo mouse OA model (DMM surgery) Journal of orthopaedic translation Medium 37635810
2024 In gastric cancer, MATN3 interacts directly with ASPN (Co-IP/PPI analysis) and promotes cell proliferation, migration, and invasion; MATN3 knockdown inhibits these behaviors and induces apoptosis. Co-overexpression of MATN3 and ASPN in vivo enhances tumor growth and metastasis, indicating synergistic oncogenic activity through EMT pathway activation. Protein-protein interaction analysis, co-expression analysis, functional assays (proliferation, migration, invasion, apoptosis), in vivo xenograft mouse model Human molecular genetics Medium 39301785
2026 GC-derived exosomal MATN3 interacts with EGFR (confirmed by Co-IP and co-localization by immunofluorescence), enhances EGFR protein stability, activates ELK1 transcription factor, which promotes ATG12-mediated autophagy activation, leading to M2 macrophage polarization and immunosuppressive tumor microenvironment. Mechanistic confirmation by ChIP, dual-luciferase reporter, ubiquitination assay. Co-IP, immunofluorescence co-localization, Western blot, RT-qPCR, ChIP assay, dual-luciferase reporter assay, ubiquitination assay, xenograft mouse model, co-culture of GC-Exo with macrophages Immunology Medium 42163458
2026 In a human pluripotent stem cell (hPSC) model of MED with MATN3 mutations, mutant matrilin-3 causes upregulation of the cholesterol biosynthesis pathway and abnormal ECM matrix assembly, accompanied by distended ER, accumulation of lipid droplets, and increased cholesterol content in chondrocyte pellets. Some UPR marker gene expression was slightly increased. hPSC differentiation to chondrocytes, CRISPR-Cas9 gene editing and patient PBMC reprogramming, RNAseq, transmission electron microscopy, immunohistochemistry Osteoarthritis and cartilage Medium 41651153

Source papers

Stage 0 corpus · 34 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2007 Decreased chondrocyte proliferation and dysregulated apoptosis in the cartilage growth plate are key features of a murine model of epiphyseal dysplasia caused by a matn3 mutation. Human molecular genetics 66 17517694
2005 Multiple epiphyseal dysplasia mutations in MATN3 cause misfolding of the A-domain and prevent secretion of mutant matrilin-3. Human mutation 65 16287128
2021 Exosomal MATN3 of Urine-Derived Stem Cells Ameliorates Intervertebral Disc Degeneration by Antisenescence Effects and Promotes NPC Proliferation and ECM Synthesis by Activating TGF-β. Oxidative medicine and cellular longevity 63 34136064
2004 Novel and recurrent mutations clustered in the von Willebrand factor A domain of MATN3 in multiple epiphyseal dysplasia. Human mutation 47 15459972
2004 Clinical and radiographic findings in multiple epiphyseal dysplasia caused by MATN3 mutations: description of 12 patients. American journal of medical genetics. Part A 42 14994237
1998 Characterization of human matrilin-3 (MATN3). Genomics 35 9799608
2023 MATN3 delivered by exosome from synovial mesenchymal stem cells relieves knee osteoarthritis: Evidence from in vitro and in vivo studies. Journal of orthopaedic translation 26 37635810
2011 Revisit of multiple epiphyseal dysplasia: ethnic difference in genotypes and comparison of radiographic features linked to the COMP and MATN3 genes. American journal of medical genetics. Part A 23 21965141
2008 Novel mutations in exon 2 of MATN3 affect residues within the alpha-helices of the A-domain and can result in the intracellular retention of mutant matrilin-3. Human mutation 18 18205203
2021 Use of Essential Oils for the Control of Anthracnose Disease Caused by Colletotrichum acutatum on Post-Harvest Mangoes of Cat Hoa Loc Variety. Membranes 17 34564536
2018 Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias. Human mutation 15 30080953
2000 Structure and mapping of the mouse matrilin-3 gene (Matn3), a member of a gene family containing a U12-type AT-AC intron. Mammalian genome : official journal of the International Mammalian Genome Society 15 10656920
2014 Comparison of orthopaedic manifestations of multiple epiphyseal dysplasia caused by MATN3 versus COMP mutations: a case control study. BMC musculoskeletal disorders 13 24629099
2021 Hereditary orotic aciduria (HOA): A novel uridine-5-monophosphate synthase (UMPS) mutation. Molecular genetics and metabolism reports 11 33489760
2022 hOA-DN30: a highly effective humanized single-arm MET antibody inducing remission of 'MET-addicted' cancers. Journal of experimental & clinical cancer research : CR 10 35351166
2020 Two new species of Hemiphyllodactylus (Squamata: Gekkonidae) from Hoa Binh Province, Vietnam. Zootaxa 9 33056646
2018 Two new prenylated isoflavones from Maclura cochinchinensis collected in Hoa Binh province Vietnam. Natural product research 9 29468891
2012 Loss of matrilin 1 does not exacerbate the skeletal phenotype in a mouse model of multiple epiphyseal dysplasia caused by a Matn3 V194D mutation. Arthritis and rheumatism 9 22083516
2013 Sarcophaga (Hoa)flexuosa Ho (Diptera: Sarcophagidae): association of sexes using morphological and molecular approaches, and a redefinition of Hoa Rohdendorf. Zootaxa 8 26438923
2012 A haplotype of MATN3 is associated with vertebral fracture in Chinese postmenopausal women: Peking Vertebral Fracture (PK-VF) study. Bone 8 22270056
2018 Characterization of the mature form of a β-defensin-like peptide, Hoa-D1, in the lobster Homarus americanus. Molecular immunology 7 30036799
2014 Hair-inspired crystal growth of HOA in cavities of cellulose matrix via hydrophobic-hydrophilic interface interaction. ACS applied materials & interfaces 7 24865837
2019 Endophytic actinomycetes associated with Cinnamomum cassia Presl in Hoa Binh province, Vietnam: Distribution, antimicrobial activity and, genetic features. The Journal of general and applied microbiology 6 31378748
2012 MATN3 gene polymorphism is associated with osteoarthritis in Chinese Han population: a community-based case-control study. TheScientificWorldJournal 6 22973175
2024 Amino acid metabolism-related genes as potential biomarkers and the role of MATN3 in stomach adenocarcinoma: A bioinformatics, mendelian randomization and experimental validation study. International immunopharmacology 5 39353384
2021 Mosquitoes (Diptera: Culicidae) from Villages and Forest Areas of Rural Communes in Khanh Hoa and Binh Phuoc Provinces, Vietnam. Journal of medical entomology 4 34144599
2024 Investigating MATN3 and ASPN as novel drivers of gastric cancer progression via EMT pathways. Human molecular genetics 3 39301785
2014 Public health assessment of dioxin-contaminated fish at former US airbase, Bien Hoa, Vietnam. International journal of environmental health research 2 25087452
2026 Human pluripotent stem cell model of multiple epiphyseal dysplasia with MATN3 mutation identifies altered matrix organisation and upregulation of the cholesterol biosynthesis pathway. Osteoarthritis and cartilage 0 41651153
2026 Gastric Cancer-Derived Exosomal MATN3 Favours Immunosuppressive Tumour Microenvironment by Activating Autophagy in an EGFR/ELK1/ATG12 Signalling Dependent Manner. Immunology 0 42163458
2025 Regulatory influence of α-Pinene on MATN3 expression in hepatocellular carcinoma: Extending to pan-cancer analysis. PloS one 0 41004439
2025 Phylogenetic analysis of swine influenza viruses circulating in slaughterhouses in Thanh Hoa province, Vietnam, during 2024 and early 2025. Open veterinary journal 0 41036007
2025 A new species of Cyrtodactylus (Squamata, Gekkonidae) from Hon Tre Island in Khanh Hoa Province, Vietnam. ZooKeys 0 41048848
2024 Comparison of waist circumference and waist-to-height ratio as predictors of clustering of cardiovascular risk factors among middle-aged people in rural Khanh Hoa, Vietnam. American journal of human biology : the official journal of the Human Biology Council 0 38470099

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