{"gene":"SH3PXD2B","run_date":"2026-04-28T20:42:07","timeline":{"discoveries":[{"year":2009,"finding":"Tks4 (SH3PXD2B) is tyrosine phosphorylated by Src and localizes to rosettes of podosomes in Src-transformed fibroblasts; loss of Tks4 results in incomplete podosome formation, inhibited ECM degradation, and failure to recruit MT1-MMP to podosomes. Tyrosine phosphorylation sites of Tks4 are required for efficient rescue of both phenotypes.","method":"shRNA knockdown, mouse embryo fibroblasts from Tks4-null mice, rescue experiments with wild-type and phosphorylation-site mutants, ECM degradation assay, immunofluorescence localization","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (KO MEFs, shRNA, rescue with mutagenesis, ECM assay, localization), replicated across systems","pmids":["19144821"],"is_preprint":false},{"year":2009,"finding":"SH3PXD2B localizes to podosomes in Src-transfected fibroblasts and, through its last (fourth) SH3 domain, associates with ADAM15, a transmembrane member of the ADAM metalloproteinase family.","method":"Immunofluorescence localization in Src-transfected fibroblasts; co-immunoprecipitation/pulldown demonstrating SH3 domain-mediated interaction with ADAM15","journal":"Mammalian genome","confidence":"Medium","confidence_rationale":"Tier 3 — single pulldown/interaction assay identifying binding partner and domain, single lab","pmids":["19669234"],"is_preprint":false},{"year":2011,"finding":"SH3PXD2B forms a complex with Src (is phosphorylated by Src) and forms a complex with cortactin via the C-terminal region of cortactin; SH3PXD2B co-localizes with cortactin to Src-induced podosomes, EGF-induced membrane ruffles, and lamellipodia. Loss of SH3PXD2B inhibits EGF-induced lamellipodia/membrane ruffle formation and reduces cell spreading.","method":"Co-immunoprecipitation of SH3PXD2B with Src and cortactin, immunofluorescence co-localization, siRNA knockdown with phenotypic readout (cell spreading and lamellipodia formation assays)","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2/3 — reciprocal Co-IP with two partners plus KD with defined cellular phenotype, single lab","pmids":["21886807"],"is_preprint":false},{"year":2010,"finding":"Loss-of-function mutations in SH3PXD2B (encoding the TKS4 podosome adaptor protein) cause Frank-Ter Haar syndrome, establishing TKS4's essential role in embryonic skeletal, cardiovascular, and ocular development through its podosome/invadopodia function.","method":"Homozygosity mapping, sequencing of SH3PXD2B in FTHS families, identification of five homozygous mutations; phenotypic analysis of Tks4-null mice recapitulating FTHS features","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 — genetic epistasis linking SH3PXD2B loss-of-function to FTHS phenotype confirmed in multiple families and mouse KO model","pmids":["20137777"],"is_preprint":false},{"year":2020,"finding":"Loss of sh3pxd2b in zebrafish (pretzel mutant) causes dermal and musculoskeletal fibrosis rather than the severe skeletal abnormalities seen in mmp14a/b knockouts, indicating that SH3PXD2B-dependent podosome function is specifically required for collagen/ECM remodeling and prevention of fibrosis, and that sh3pxd2b and mmp14 act in distinct spatiotemporal contexts for ECM remodeling.","method":"sh3pxd2b loss-of-function zebrafish mutant (pretzel) with histological analysis of fibrosis; comparison to mmp14a/b knockout zebrafish by genetic epistasis/phenotypic analysis","journal":"Biology open","confidence":"Medium","confidence_rationale":"Tier 2 — genetic loss-of-function with defined fibrotic phenotype and comparative epistasis with mmp14 knockout, single lab","pmids":["33234702"],"is_preprint":false},{"year":2024,"finding":"Mass spectrometry pulldown identified interacting partners of SH3PXD2B relevant to cell migration; SH3PXD2B knockdown inhibited breast cancer and lung cancer cell migration, and its upregulation promoted migration, implicating the SH3 domains in driving epithelial-to-mesenchymal transition.","method":"Mass spectrometry pulldown of SH3PXD2B interactors, immunoblotting validation, immunofluorescence, shRNA knockdown and overexpression with migration assay, in vivo bioluminescent IVIS metastasis imaging","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 — preprint, single lab, pulldown with partial mechanistic validation","pmids":["bio_10.1101_2024.10.16.618596"],"is_preprint":true}],"current_model":"SH3PXD2B (TKS4) is a Src-phosphorylated scaffold/adaptor protein that localizes to podosomes and invadopodia via its N-terminal PX domain and four SH3 domains; it is required for complete podosome assembly, recruitment of MT1-MMP to podosomes, pericellular ECM degradation, and EGF-induced lamellipodia formation through interactions with Src, cortactin, and ADAM15, and its loss causes defective collagen remodeling and fibrosis in vivo, underlying Frank-Ter Haar syndrome."},"narrative":{"teleology":[{"year":2009,"claim":"Establishing SH3PXD2B as a Src substrate required for podosome integrity and ECM degradation resolved how invadopodia/podosome scaffolding depends on tyrosine phosphorylation-driven adaptor recruitment.","evidence":"shRNA knockdown and Tks4-null MEFs with rescue by WT and phospho-mutant constructs, ECM degradation assays, immunofluorescence for MT1-MMP recruitment","pmids":["19144821"],"confidence":"High","gaps":["Identity of the kinase-specific phosphotyrosine sites required for each downstream function not fully mapped","Mechanism by which SH3PXD2B recruits MT1-MMP to podosomes not defined at the structural level","Relative contributions of the PX domain versus SH3 domains to podosome targeting not dissected"]},{"year":2009,"claim":"Identification of ADAM15 as a binding partner of the fourth SH3 domain extended the podosome scaffold model to include transmembrane metalloproteinases beyond MT1-MMP.","evidence":"Co-immunoprecipitation and SH3 domain pulldown in Src-transfected fibroblasts","pmids":["19669234"],"confidence":"Medium","gaps":["Functional consequence of the SH3PXD2B–ADAM15 interaction on ECM degradation not tested","No reciprocal validation or endogenous co-IP reported","Whether ADAM15 localizes to podosomes in an SH3PXD2B-dependent manner is untested"]},{"year":2010,"claim":"Linking SH3PXD2B loss-of-function to Frank-Ter Haar syndrome established a direct developmental requirement for podosome-mediated ECM remodeling in skeletal, cardiac, and ocular morphogenesis.","evidence":"Homozygosity mapping and sequencing in multiple FTHS families identifying five homozygous mutations; Tks4-null mice recapitulating FTHS phenotypes","pmids":["20137777"],"confidence":"High","gaps":["Cell-type-specific contributions of SH3PXD2B to each affected organ system not resolved","Whether residual podosome function from TKS5 (SH3PXD2A) partially compensates in FTHS patients is unknown"]},{"year":2011,"claim":"Demonstrating that SH3PXD2B complexes with both Src and cortactin and is required for EGF-induced lamellipodia broadened its role from a podosome-restricted scaffold to a general actin-based protrusion regulator.","evidence":"Reciprocal co-immunoprecipitation of SH3PXD2B with Src and cortactin; siRNA knockdown with lamellipodia formation and cell spreading assays","pmids":["21886807"],"confidence":"Medium","gaps":["Whether SH3PXD2B directly bridges Src to cortactin or forms separate binary complexes is unresolved","Signaling intermediates between EGF receptor and SH3PXD2B activation not identified"]},{"year":2020,"claim":"Zebrafish sh3pxd2b mutants revealed that SH3PXD2B-dependent podosome function is specifically required for collagen remodeling and fibrosis prevention, acting in a pathway distinct from MMP14.","evidence":"sh3pxd2b loss-of-function zebrafish (pretzel) with histological fibrosis analysis and phenotypic comparison to mmp14a/b knockouts","pmids":["33234702"],"confidence":"Medium","gaps":["Molecular basis for the distinct spatiotemporal requirements of SH3PXD2B versus MMP14 in ECM remodeling is undefined","Whether fibrosis arises from failed collagen turnover or aberrant collagen deposition is not distinguished","Rescue experiments with mammalian SH3PXD2B in zebrafish not performed"]},{"year":null,"claim":"Key unresolved questions include the structural basis of SH3PXD2B scaffold assembly at podosomes, the full inventory of SH3 domain-dependent interactors, and how SH3PXD2B coordinates with TKS5 to regulate invadopodia versus podosomes in different cell types.","evidence":"","pmids":[],"confidence":"Low","gaps":["No high-resolution structural data for SH3PXD2B or its domain complexes","Functional redundancy versus division of labor with TKS5/SH3PXD2A not systematically tested","Role in cancer cell invasion established only at preprint level without peer-reviewed validation"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[0,2]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,2]}],"complexes":[],"partners":["SRC","CTTN","ADAM15","MMP14"],"other_free_text":[]},"mechanistic_narrative":"SH3PXD2B (TKS4) is a Src-phosphorylated scaffold protein that drives podosome assembly, ECM degradation, and cell migration through its PX domain and four SH3 domains. It localizes to podosomes in Src-transformed cells, where it is required for complete podosome rosette formation and recruitment of MT1-MMP; its tyrosine phosphorylation by Src is essential for these functions [PMID:19144821]. SH3PXD2B interacts with cortactin and ADAM15 at podosomes and EGF-induced lamellipodia, and its loss impairs lamellipodia formation, cell spreading, and pericellular collagen remodeling, leading to fibrosis in vivo [PMID:21886807, PMID:33234702]. Loss-of-function mutations in SH3PXD2B cause Frank-Ter Haar syndrome, a developmental disorder affecting skeletal, cardiovascular, and ocular tissues, as confirmed by human genetics and recapitulation in Tks4-null mice [PMID:20137777]."},"prefetch_data":{"uniprot":{"accession":"A1X283","full_name":"SH3 and PX domain-containing protein 2B","aliases":["Adapter protein HOFI","Factor for adipocyte differentiation 49","Tyrosine kinase substrate with four SH3 domains"],"length_aa":911,"mass_kda":101.6,"function":"Adapter protein involved in invadopodia and podosome formation and extracellular matrix degradation. Binds matrix metalloproteinases (ADAMs), NADPH oxidases (NOXs) and phosphoinositides. Acts as an organizer protein that allows NOX1- or NOX3-dependent reactive oxygen species (ROS) generation and ROS localization. Plays a role in mitotic clonal expansion during the immediate early stage of adipocyte differentiation (By similarity)","subcellular_location":"Cytoplasm; Cell projection, podosome","url":"https://www.uniprot.org/uniprotkb/A1X283/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SH3PXD2B","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SH3PXD2B","total_profiled":1310},"omim":[{"mim_id":"613293","title":"SH3 AND PX DOMAINS-CONTAINING PROTEIN 2B; SH3PXD2B","url":"https://www.omim.org/entry/613293"},{"mim_id":"277950","title":"WINCHESTER SYNDROME; WNCHRS","url":"https://www.omim.org/entry/277950"},{"mim_id":"249420","title":"FRANK-TER HAAR SYNDROME; FTHS","url":"https://www.omim.org/entry/249420"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Plasma membrane","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SH3PXD2B"},"hgnc":{"alias_symbol":["FLJ20831"],"prev_symbol":["KIAA1295"]},"alphafold":{"accession":"A1X283","domains":[{"cath_id":"3.30.1520.10","chopping":"8-130","consensus_level":"high","plddt":86.9041,"start":8,"end":130},{"cath_id":"2.30.30.40","chopping":"155-216","consensus_level":"medium","plddt":75.8584,"start":155,"end":216},{"cath_id":"2.30.30.40","chopping":"219-279","consensus_level":"medium","plddt":81.7264,"start":219,"end":279},{"cath_id":"2.30.30.40","chopping":"373-428","consensus_level":"high","plddt":84.8857,"start":373,"end":428},{"cath_id":"2.30.30.40","chopping":"855-910","consensus_level":"high","plddt":83.6198,"start":855,"end":910}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/A1X283","model_url":"https://alphafold.ebi.ac.uk/files/AF-A1X283-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-A1X283-F1-predicted_aligned_error_v6.png","plddt_mean":55.91},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SH3PXD2B","jax_strain_url":"https://www.jax.org/strain/search?query=SH3PXD2B"},"sequence":{"accession":"A1X283","fasta_url":"https://rest.uniprot.org/uniprotkb/A1X283.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/A1X283/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/A1X283"}},"corpus_meta":[{"pmid":"19144821","id":"PMC_19144821","title":"The novel adaptor protein Tks4 (SH3PXD2B) is required for functional podosome formation.","date":"2009","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/19144821","citation_count":153,"is_preprint":false},{"pmid":"20137777","id":"PMC_20137777","title":"Disruption of the podosome adaptor protein TKS4 (SH3PXD2B) causes the skeletal dysplasia, eye, and cardiac abnormalities of Frank-Ter Haar Syndrome.","date":"2010","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/20137777","citation_count":82,"is_preprint":false},{"pmid":"21282566","id":"PMC_21282566","title":"Anterior segment dysgenesis and early-onset glaucoma in nee mice with mutation of Sh3pxd2b.","date":"2011","source":"Investigative ophthalmology & visual science","url":"https://pubmed.ncbi.nlm.nih.gov/21282566","citation_count":52,"is_preprint":false},{"pmid":"19669234","id":"PMC_19669234","title":"The podosomal-adaptor protein SH3PXD2B is essential for normal postnatal development.","date":"2009","source":"Mammalian genome : official journal of the International Mammalian Genome Society","url":"https://pubmed.ncbi.nlm.nih.gov/19669234","citation_count":47,"is_preprint":false},{"pmid":"21886807","id":"PMC_21886807","title":"The homolog of the five SH3-domain protein (HOFI/SH3PXD2B) regulates lamellipodia formation and cell spreading.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21886807","citation_count":34,"is_preprint":false},{"pmid":"24105366","id":"PMC_24105366","title":"Mutations in SH3PXD2B cause Borrone dermato-cardio-skeletal syndrome.","date":"2013","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/24105366","citation_count":30,"is_preprint":false},{"pmid":"21818352","id":"PMC_21818352","title":"Sh3pxd2b mice are a model for craniofacial dysmorphology and otitis media.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21818352","citation_count":29,"is_preprint":false},{"pmid":"28694206","id":"PMC_28694206","title":"Identification of two novel SH3PXD2B gene mutations in Frank-Ter Haar syndrome by exome sequencing: Case report and review of the literature.","date":"2017","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/28694206","citation_count":16,"is_preprint":false},{"pmid":"22509100","id":"PMC_22509100","title":"Localization of SH3PXD2B in human eyes and detection of rare variants in patients with anterior segment diseases and glaucoma.","date":"2012","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/22509100","citation_count":10,"is_preprint":false},{"pmid":"37211344","id":"PMC_37211344","title":"Comprehensive bioinformatics and experimental analysis of SH3PXD2B reveals its carcinogenic effect in gastric carcinoma.","date":"2023","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/37211344","citation_count":5,"is_preprint":false},{"pmid":"39660974","id":"PMC_39660974","title":"Identification of a novel SH3PXD2B::FER fusion in a case of plexiform myofibroblastic tumor and review of the literature.","date":"2024","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/39660974","citation_count":4,"is_preprint":false},{"pmid":"35205281","id":"PMC_35205281","title":"The Role of the Disrupted Podosome Adaptor Protein (SH3PXD2B) in Frank-Ter Haar Syndrome.","date":"2022","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/35205281","citation_count":4,"is_preprint":false},{"pmid":"33234702","id":"PMC_33234702","title":"The novel zebrafish model pretzel demonstrates a central role for SH3PXD2B in defective collagen remodelling and fibrosis in Frank-Ter Haar syndrome.","date":"2020","source":"Biology open","url":"https://pubmed.ncbi.nlm.nih.gov/33234702","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.16.618596","title":"Unlocking the role of SH3PXD2B in epithelial-to-mesenchymal transition driving Breast Cancer Lung Metastasis","date":"2024-10-18","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.16.618596","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8710,"output_tokens":1687,"usd":0.025718},"stage2":{"model":"claude-opus-4-6","input_tokens":4926,"output_tokens":1841,"usd":0.105982},"total_usd":0.1317,"stage1_batch_id":"msgbatch_011rkcQdVV1RaFq9XhcG6df6","stage2_batch_id":"msgbatch_01RzgrJafdF4EWHhj5mNi6dh","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2009,\n      \"finding\": \"Tks4 (SH3PXD2B) is tyrosine phosphorylated by Src and localizes to rosettes of podosomes in Src-transformed fibroblasts; loss of Tks4 results in incomplete podosome formation, inhibited ECM degradation, and failure to recruit MT1-MMP to podosomes. Tyrosine phosphorylation sites of Tks4 are required for efficient rescue of both phenotypes.\",\n      \"method\": \"shRNA knockdown, mouse embryo fibroblasts from Tks4-null mice, rescue experiments with wild-type and phosphorylation-site mutants, ECM degradation assay, immunofluorescence localization\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KO MEFs, shRNA, rescue with mutagenesis, ECM assay, localization), replicated across systems\",\n      \"pmids\": [\"19144821\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"SH3PXD2B localizes to podosomes in Src-transfected fibroblasts and, through its last (fourth) SH3 domain, associates with ADAM15, a transmembrane member of the ADAM metalloproteinase family.\",\n      \"method\": \"Immunofluorescence localization in Src-transfected fibroblasts; co-immunoprecipitation/pulldown demonstrating SH3 domain-mediated interaction with ADAM15\",\n      \"journal\": \"Mammalian genome\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single pulldown/interaction assay identifying binding partner and domain, single lab\",\n      \"pmids\": [\"19669234\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"SH3PXD2B forms a complex with Src (is phosphorylated by Src) and forms a complex with cortactin via the C-terminal region of cortactin; SH3PXD2B co-localizes with cortactin to Src-induced podosomes, EGF-induced membrane ruffles, and lamellipodia. Loss of SH3PXD2B inhibits EGF-induced lamellipodia/membrane ruffle formation and reduces cell spreading.\",\n      \"method\": \"Co-immunoprecipitation of SH3PXD2B with Src and cortactin, immunofluorescence co-localization, siRNA knockdown with phenotypic readout (cell spreading and lamellipodia formation assays)\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — reciprocal Co-IP with two partners plus KD with defined cellular phenotype, single lab\",\n      \"pmids\": [\"21886807\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Loss-of-function mutations in SH3PXD2B (encoding the TKS4 podosome adaptor protein) cause Frank-Ter Haar syndrome, establishing TKS4's essential role in embryonic skeletal, cardiovascular, and ocular development through its podosome/invadopodia function.\",\n      \"method\": \"Homozygosity mapping, sequencing of SH3PXD2B in FTHS families, identification of five homozygous mutations; phenotypic analysis of Tks4-null mice recapitulating FTHS features\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic epistasis linking SH3PXD2B loss-of-function to FTHS phenotype confirmed in multiple families and mouse KO model\",\n      \"pmids\": [\"20137777\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Loss of sh3pxd2b in zebrafish (pretzel mutant) causes dermal and musculoskeletal fibrosis rather than the severe skeletal abnormalities seen in mmp14a/b knockouts, indicating that SH3PXD2B-dependent podosome function is specifically required for collagen/ECM remodeling and prevention of fibrosis, and that sh3pxd2b and mmp14 act in distinct spatiotemporal contexts for ECM remodeling.\",\n      \"method\": \"sh3pxd2b loss-of-function zebrafish mutant (pretzel) with histological analysis of fibrosis; comparison to mmp14a/b knockout zebrafish by genetic epistasis/phenotypic analysis\",\n      \"journal\": \"Biology open\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function with defined fibrotic phenotype and comparative epistasis with mmp14 knockout, single lab\",\n      \"pmids\": [\"33234702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Mass spectrometry pulldown identified interacting partners of SH3PXD2B relevant to cell migration; SH3PXD2B knockdown inhibited breast cancer and lung cancer cell migration, and its upregulation promoted migration, implicating the SH3 domains in driving epithelial-to-mesenchymal transition.\",\n      \"method\": \"Mass spectrometry pulldown of SH3PXD2B interactors, immunoblotting validation, immunofluorescence, shRNA knockdown and overexpression with migration assay, in vivo bioluminescent IVIS metastasis imaging\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — preprint, single lab, pulldown with partial mechanistic validation\",\n      \"pmids\": [\"bio_10.1101_2024.10.16.618596\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"SH3PXD2B (TKS4) is a Src-phosphorylated scaffold/adaptor protein that localizes to podosomes and invadopodia via its N-terminal PX domain and four SH3 domains; it is required for complete podosome assembly, recruitment of MT1-MMP to podosomes, pericellular ECM degradation, and EGF-induced lamellipodia formation through interactions with Src, cortactin, and ADAM15, and its loss causes defective collagen remodeling and fibrosis in vivo, underlying Frank-Ter Haar syndrome.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"SH3PXD2B (TKS4) is a Src-phosphorylated scaffold protein that drives podosome assembly, ECM degradation, and cell migration through its PX domain and four SH3 domains. It localizes to podosomes in Src-transformed cells, where it is required for complete podosome rosette formation and recruitment of MT1-MMP; its tyrosine phosphorylation by Src is essential for these functions [PMID:19144821]. SH3PXD2B interacts with cortactin and ADAM15 at podosomes and EGF-induced lamellipodia, and its loss impairs lamellipodia formation, cell spreading, and pericellular collagen remodeling, leading to fibrosis in vivo [PMID:21886807, PMID:33234702]. Loss-of-function mutations in SH3PXD2B cause Frank-Ter Haar syndrome, a developmental disorder affecting skeletal, cardiovascular, and ocular tissues, as confirmed by human genetics and recapitulation in Tks4-null mice [PMID:20137777].\",\n  \"teleology\": [\n    {\n      \"year\": 2009,\n      \"claim\": \"Establishing SH3PXD2B as a Src substrate required for podosome integrity and ECM degradation resolved how invadopodia/podosome scaffolding depends on tyrosine phosphorylation-driven adaptor recruitment.\",\n      \"evidence\": \"shRNA knockdown and Tks4-null MEFs with rescue by WT and phospho-mutant constructs, ECM degradation assays, immunofluorescence for MT1-MMP recruitment\",\n      \"pmids\": [\"19144821\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Identity of the kinase-specific phosphotyrosine sites required for each downstream function not fully mapped\",\n        \"Mechanism by which SH3PXD2B recruits MT1-MMP to podosomes not defined at the structural level\",\n        \"Relative contributions of the PX domain versus SH3 domains to podosome targeting not dissected\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Identification of ADAM15 as a binding partner of the fourth SH3 domain extended the podosome scaffold model to include transmembrane metalloproteinases beyond MT1-MMP.\",\n      \"evidence\": \"Co-immunoprecipitation and SH3 domain pulldown in Src-transfected fibroblasts\",\n      \"pmids\": [\"19669234\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Functional consequence of the SH3PXD2B–ADAM15 interaction on ECM degradation not tested\",\n        \"No reciprocal validation or endogenous co-IP reported\",\n        \"Whether ADAM15 localizes to podosomes in an SH3PXD2B-dependent manner is untested\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Linking SH3PXD2B loss-of-function to Frank-Ter Haar syndrome established a direct developmental requirement for podosome-mediated ECM remodeling in skeletal, cardiac, and ocular morphogenesis.\",\n      \"evidence\": \"Homozygosity mapping and sequencing in multiple FTHS families identifying five homozygous mutations; Tks4-null mice recapitulating FTHS phenotypes\",\n      \"pmids\": [\"20137777\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Cell-type-specific contributions of SH3PXD2B to each affected organ system not resolved\",\n        \"Whether residual podosome function from TKS5 (SH3PXD2A) partially compensates in FTHS patients is unknown\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Demonstrating that SH3PXD2B complexes with both Src and cortactin and is required for EGF-induced lamellipodia broadened its role from a podosome-restricted scaffold to a general actin-based protrusion regulator.\",\n      \"evidence\": \"Reciprocal co-immunoprecipitation of SH3PXD2B with Src and cortactin; siRNA knockdown with lamellipodia formation and cell spreading assays\",\n      \"pmids\": [\"21886807\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether SH3PXD2B directly bridges Src to cortactin or forms separate binary complexes is unresolved\",\n        \"Signaling intermediates between EGF receptor and SH3PXD2B activation not identified\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Zebrafish sh3pxd2b mutants revealed that SH3PXD2B-dependent podosome function is specifically required for collagen remodeling and fibrosis prevention, acting in a pathway distinct from MMP14.\",\n      \"evidence\": \"sh3pxd2b loss-of-function zebrafish (pretzel) with histological fibrosis analysis and phenotypic comparison to mmp14a/b knockouts\",\n      \"pmids\": [\"33234702\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Molecular basis for the distinct spatiotemporal requirements of SH3PXD2B versus MMP14 in ECM remodeling is undefined\",\n        \"Whether fibrosis arises from failed collagen turnover or aberrant collagen deposition is not distinguished\",\n        \"Rescue experiments with mammalian SH3PXD2B in zebrafish not performed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include the structural basis of SH3PXD2B scaffold assembly at podosomes, the full inventory of SH3 domain-dependent interactors, and how SH3PXD2B coordinates with TKS5 to regulate invadopodia versus podosomes in different cell types.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No high-resolution structural data for SH3PXD2B or its domain complexes\",\n        \"Functional redundancy versus division of labor with TKS5/SH3PXD2A not systematically tested\",\n        \"Role in cancer cell invasion established only at preprint level without peer-reviewed validation\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"SRC\",\n      \"CTTN\",\n      \"ADAM15\",\n      \"MMP14\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}