{"gene":"FNDC3A","run_date":"2026-06-09T23:54:44","timeline":{"discoveries":[{"year":2006,"finding":"FNDC3A is required for adhesion between spermatids and Sertoli cells in the seminiferous epithelium; loss-of-function (deletion of Fndc3a in sys mice) causes defective spermatid-Sertoli adhesion and male sterility, confirmed by genetic complementation with a specific Fndc3a mutation.","method":"Genetic complementation analysis in mice; loss-of-function deletion mapping; immunohistochemistry","journal":"Developmental biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic complementation with specific allele, replicated in two independent mouse models (deletion and point mutation), clear cellular phenotype","pmids":["16904100"],"is_preprint":false},{"year":2006,"finding":"FNDC3A protein localizes to the acrosome of spermatids (steps 2–10) and later to cytoplasmic vesicular structures in elongate spermatids (step 12); it also localizes to Leydig cells in mouse testis. The protein contains a hydrophobic C-terminus similar to tail-anchored proteins, suggesting ER membrane localization.","method":"Immunohistochemical staining of mouse testis sections","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization by IHC in multiple developmental stages, single lab, no functional rescue tied to localization domain","pmids":["16904100"],"is_preprint":false},{"year":2008,"finding":"In human odontoblasts, FNDC3A (HUGO) protein localizes to Golgi vesicles, suggesting a role in collagen and glycosaminoglycan synthesis in these cells.","method":"Immunohistochemistry and subcellular localization in odontoblasts","journal":"Journal of dental research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method (IHC/localization), no functional follow-up","pmids":["18218838"],"is_preprint":false},{"year":2018,"finding":"The Drosophila FNDC3 ortholog MTGO physically and genetically interacts with CCT3, a subunit of the TRiC/CCT chaperonin complex; a CCT3 mutation that reduces binding to MTGO phenocopies NMJ branching and growth defects seen in mtgo null mutants, establishing a functional complex between FNDC3 and the chaperonin.","method":"Physical interaction (co-immunoprecipitation/pulldown), genetic epistasis (double mutants), transgenic rescue (neuronal-specific expression)","journal":"Developmental biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — physical interaction plus genetic epistasis in single lab, ortholog (Drosophila), two orthogonal methods","pmids":["30539716"],"is_preprint":false},{"year":2019,"finding":"Loss of fndc3a in zebrafish (hypomorphic CRISPR/Cas9 mutant) causes ECM alterations, defects in actinotrichia formation, and disrupted epidermal cell organization, implicating FNDC3A in ECM regulation during fin development and regeneration.","method":"CRISPR/Cas9 loss-of-function in zebrafish; gene expression profiling; phenotypic analysis of fin development and regeneration","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean CRISPR KO with defined cellular/tissue phenotype and ECM characterization, single lab","pmids":["31527654"],"is_preprint":false},{"year":2020,"finding":"FNDC3A is an ER membrane-resident protein that interacts with FAM46C (TENT5C), anchoring FAM46C to the cytoplasmic face of the ER. This FAM46C/FNDC3A complex modulates secretion routes (increasing lysosome exocytosis), impairs autophagy, and promotes accumulation of intracellular protein aggregates leading to apoptosis in multiple myeloma cells.","method":"Co-immunoprecipitation; biochemical fractionation; knockdown and overexpression of FNDC3A with defined phenotypic readouts (aggregates, apoptosis, autophagy flux)","journal":"Cancer research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal biochemical interaction, loss-of-function and gain-of-function with multiple phenotypic readouts, independently replicated in companion paper (PMID:32966780)","pmids":["32963011","32966780"],"is_preprint":false},{"year":2020,"finding":"FAM46C activity and its interaction with FNDC3A proteins is regulated by p62: the ZZ domain of the autophagic receptor p62 binds FAM46C and sequesters it in p62+ aggregates, preventing its association with FNDC3A and thereby limiting its poly(A) polymerase activity toward ER-targeted mRNAs.","method":"Co-immunoprecipitation; domain-mapping mutagenesis; confocal imaging of p62 aggregates; mRNA stabilization assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — mechanistic dissection of p62/FAM46C/FNDC3 circuit with biochemical interaction mapping, domain mutagenesis, and functional mRNA assays; replicated across two labs","pmids":["32966780","32963011"],"is_preprint":false},{"year":2024,"finding":"Recombinant FNDC3A (10 ng/mL) added to bovine granulosa cells decreases IGF1-dependent progesterone secretion, reduces IGF1-dependent lactate secretion and GLUT3/GLUT4 mRNA abundance, and increases Akt phosphorylation, suggesting FNDC3A acts as an extracellular adipokine modulating IGF1 signaling and granulosa cell metabolism. FNDC3A protein is also present in follicular fluid associated with extracellular vesicles.","method":"In vitro granulosa cell culture with recombinant FNDC3A; hormone/metabolite assays; western blot (pAkt); qPCR; extracellular vesicle isolation","journal":"Reproduction (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean in vitro functional assay with recombinant protein and multiple readouts, single lab, bovine model","pmids":["38513348"],"is_preprint":false},{"year":2025,"finding":"FNDC3A knockdown in triple-negative breast cancer cell lines suppresses EMT, invasion, and cancer stemness, and RNA-seq revealed concomitant inhibition of YAP1 and its target genes, placing FNDC3A upstream of the YAP1 pathway in TNBC.","method":"siRNA knockdown; invasion/migration assays; RNA-seq; stemness assays","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — loss-of-function with transcriptomic pathway placement, single lab, no rescue experiment or direct YAP1 interaction shown","pmids":["40120859"],"is_preprint":false},{"year":2026,"finding":"A member-specific C-terminal region of TENT5/FAM46 proteins (including TENT5C/FAM46C) is necessary and sufficient for binding to ER-transmembrane FNDC3 proteins and for ER localization. Mutations in this C-terminal region of TENT5C found in multiple myeloma impair FNDC3 binding or protein stability, reducing immunoglobulin production and tumor-suppressive activity.","method":"Systematic mutagenesis; transcriptomic and proteomic profiling; co-immunoprecipitation; localization assays","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — systematic mutagenesis defining necessary and sufficient domain, combined with proteomic/transcriptomic profiling and functional readouts in disease-relevant context","pmids":["42247288"],"is_preprint":false}],"current_model":"FNDC3A is an ER transmembrane protein that serves as an anchor and functional partner for the TENT5/FAM46 family of non-canonical poly(A) polymerases (particularly FAM46C/TENT5C), recruiting them to the cytoplasmic face of the ER via a specific C-terminal interaction domain; this complex regulates ER-targeted mRNA stabilization, secretory output, lysosome exocytosis, and autophagy, while in the testis FNDC3A is required for spermatid–Sertoli cell adhesion, and in other contexts it modulates ECM organization, YAP1-dependent invasion, and IGF1 signaling."},"narrative":{"mechanistic_narrative":"FNDC3A is an endoplasmic reticulum transmembrane protein that functions both as a membrane anchor for cytoplasmic effector enzymes and as a tissue-level mediator of cell adhesion and extracellular matrix organization [PMID:16904100, PMID:32963011, PMID:32966780]. Its best-defined molecular role is to recruit the TENT5/FAM46 family of non-canonical poly(A) polymerases—notably FAM46C/TENT5C—to the cytoplasmic face of the ER, where the FNDC3A/FAM46C complex stabilizes ER-targeted mRNAs and shapes the secretory output of the cell, increasing lysosome exocytosis, impairing autophagy, and driving accumulation of intracellular protein aggregates and apoptosis in multiple myeloma cells [PMID:32963011, PMID:32966780]. Binding is mediated by a member-specific C-terminal region of TENT5C that is necessary and sufficient for FNDC3 association and ER localization; multiple myeloma mutations in this region disrupt FNDC3 binding or TENT5C stability and abrogate its tumor-suppressive, immunoglobulin-promoting activity [PMID:42247288]. This circuit is gated by the autophagic receptor p62, whose ZZ domain sequesters FAM46C in aggregates and prevents its productive engagement with FNDC3A [PMID:32966780, PMID:32963011]. Beyond this complex, FNDC3A is genetically required for spermatid–Sertoli cell adhesion in the testis, where its loss causes male sterility [PMID:16904100], and it regulates extracellular matrix and epidermal organization during zebrafish fin development and regeneration [PMID:31527654]. FNDC3A loss in triple-negative breast cancer cells suppresses EMT, invasion, and stemness with concomitant inhibition of the YAP1 transcriptional program [PMID:40120859], and recombinant FNDC3A acts extracellularly on bovine granulosa cells to dampen IGF1-dependent progesterone and lactate secretion [PMID:38513348].","teleology":[{"year":2006,"claim":"Established the first in vivo function of FNDC3A by showing it is genetically required for a specific cell–cell adhesion event, defining the protein as essential for male fertility rather than merely expressed in testis.","evidence":"Loss-of-function deletion mapping and genetic complementation with a specific Fndc3a allele in sys mice, with immunohistochemistry","pmids":["16904100"],"confidence":"High","gaps":["Molecular mechanism of adhesion not defined","No identified binding partner mediating spermatid–Sertoli attachment","Subcellular site of action versus membrane topology not resolved functionally"]},{"year":2006,"claim":"Localized FNDC3A to acrosomal and cytoplasmic vesicular structures and noted a tail-anchor-like hydrophobic C-terminus, providing the first structural clue that the protein is membrane-associated.","evidence":"Immunohistochemical staining of staged mouse testis sections","pmids":["16904100"],"confidence":"Medium","gaps":["ER membrane insertion inferred from sequence, not demonstrated","Localization not tied to function by domain rescue"]},{"year":2008,"claim":"Extended FNDC3A expression to a secretory cell type by localizing it to Golgi vesicles in odontoblasts, hinting at a role in matrix biosynthesis.","evidence":"Immunohistochemistry and subcellular localization in human odontoblasts","pmids":["18218838"],"confidence":"Low","gaps":["Single lab, single method (IHC) with no functional follow-up","Golgi versus ER localization not reconciled with later ER residency data","No demonstrated link to collagen or glycosaminoglycan synthesis"]},{"year":2018,"claim":"Connected an FNDC3 ortholog to chaperonin function by showing a physical and genetic interaction with the TRiC/CCT subunit CCT3 governing neuronal morphogenesis.","evidence":"Co-IP/pulldown, genetic epistasis with double mutants, and neuronal rescue of Drosophila mtgo phenotypes","pmids":["30539716"],"confidence":"Medium","gaps":["Demonstrated in Drosophila ortholog only","Relationship between CCT3 interaction and the mammalian ER/FAM46C role unknown","Direct binding interface not mapped"]},{"year":2019,"claim":"Defined a developmental ECM function by showing FNDC3A loss disrupts actinotrichia and epidermal organization, implicating the protein in matrix regulation beyond testis adhesion.","evidence":"Hypomorphic CRISPR/Cas9 mutant in zebrafish with gene-expression profiling and fin development/regeneration phenotyping","pmids":["31527654"],"confidence":"Medium","gaps":["Molecular targets in ECM not identified","Connection to ER/secretory function not established","Hypomorphic allele leaves null phenotype undefined"]},{"year":2020,"claim":"Resolved the central molecular function: FNDC3A is an ER membrane protein that anchors the poly(A) polymerase FAM46C/TENT5C to the cytoplasmic ER face, coupling the complex to secretion, lysosome exocytosis, autophagy, and aggregate-driven apoptosis.","evidence":"Reciprocal co-IP, biochemical fractionation, and knockdown/overexpression with aggregate, apoptosis, and autophagy-flux readouts in multiple myeloma cells, replicated in a companion study","pmids":["32963011","32966780"],"confidence":"High","gaps":["Stoichiometry and structure of the FNDC3A–FAM46C complex unknown","Which ER-targeted mRNAs are regulated not comprehensively defined","Generality beyond myeloma cells untested"]},{"year":2020,"claim":"Showed the FNDC3A–FAM46C circuit is regulated by p62, whose ZZ domain sequesters FAM46C and blocks its FNDC3A association and poly(A) polymerase activity, embedding the complex in autophagic/proteostatic control.","evidence":"Co-IP, domain-mapping mutagenesis, confocal imaging of p62 aggregates, and mRNA-stabilization assays across two labs","pmids":["32966780","32963011"],"confidence":"High","gaps":["Signals controlling p62-mediated sequestration not defined","Whether FNDC3A itself is regulated by p62 unknown"]},{"year":2024,"claim":"Identified an extracellular, adipokine-like role: recombinant FNDC3A suppresses IGF1-dependent steroidogenesis and metabolism in granulosa cells and is carried in follicular-fluid extracellular vesicles.","evidence":"In vitro bovine granulosa cell culture with recombinant FNDC3A, hormone/metabolite assays, pAkt western blot, qPCR, and EV isolation","pmids":["38513348"],"confidence":"Medium","gaps":["Receptor mediating extracellular FNDC3A action unidentified","Reconciliation of secreted/EV form with ER-transmembrane topology unclear","Single lab, bovine model"]},{"year":2025,"claim":"Placed FNDC3A upstream of the YAP1 oncogenic program by showing its knockdown suppresses EMT, invasion, and stemness in triple-negative breast cancer.","evidence":"siRNA knockdown with invasion/migration and stemness assays plus RNA-seq pathway analysis","pmids":["40120859"],"confidence":"Medium","gaps":["No rescue experiment","Direct FNDC3A–YAP1 interaction not shown","Mechanism linking ER anchor function to YAP1 regulation unknown"]},{"year":2026,"claim":"Defined the binding determinant: a member-specific C-terminal region of TENT5/FAM46 proteins is necessary and sufficient for FNDC3 binding and ER localization, and myeloma mutations there disrupt the interaction and tumor-suppressive output.","evidence":"Systematic mutagenesis with transcriptomic/proteomic profiling, co-IP, and localization assays","pmids":["42247288"],"confidence":"High","gaps":["Reciprocal FNDC3A binding domain not mapped at residue level","Structure of the interaction interface unresolved","Whether other FNDC3 family members bind distinct TENT5 members untested"]},{"year":null,"claim":"How the ER-anchoring/mRNA-stabilization function mechanistically connects to the organismal roles in cell adhesion, ECM organization, YAP1-driven invasion, and extracellular IGF1 modulation remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking ER-resident FAM46C anchoring to secreted/adhesive functions","FNDC3A receptor/effector for its extracellular activities unknown","Full repertoire of FNDC3A-regulated transcripts and secretory cargo undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[5,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,9]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[5,9]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[2]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[6]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5,6]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5,9]}],"complexes":[],"partners":["FAM46C","CCT3","SQSTM1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y2H6","full_name":"Fibronectin type-III domain-containing protein 3A","aliases":["Human gene expressed in odontoblasts"],"length_aa":1198,"mass_kda":131.9,"function":"Mediates spermatid-Sertoli adhesion during spermatogenesis","subcellular_location":"Golgi apparatus membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y2H6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/FNDC3A","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CCDC47","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/FNDC3A","total_profiled":1310},"omim":[{"mim_id":"615794","title":"FIBRONECTIN TYPE III DOMAIN-CONTAINING PROTEIN 3A; FNDC3A","url":"https://www.omim.org/entry/615794"},{"mim_id":"609416","title":"MICRO RNA 17; MIR17","url":"https://www.omim.org/entry/609416"},{"mim_id":"600114","title":"CHAPERONIN CONTAINING T-COMPLEX POLYPEPTIDE 1, SUBUNIT 3; CCT3","url":"https://www.omim.org/entry/600114"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Centrosome","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/FNDC3A"},"hgnc":{"alias_symbol":["bA203I16.5","KIAA0970"],"prev_symbol":["FNDC3"]},"alphafold":{"accession":"Q9Y2H6","domains":[{"cath_id":"-","chopping":"32-97","consensus_level":"high","plddt":56.3494,"start":32,"end":97},{"cath_id":"2.60.40.10","chopping":"265-287_305-365","consensus_level":"high","plddt":84.8174,"start":265,"end":365},{"cath_id":"2.60.40.10","chopping":"369-464","consensus_level":"medium","plddt":89.6173,"start":369,"end":464},{"cath_id":"2.60.40.10","chopping":"470-558","consensus_level":"high","plddt":87.4675,"start":470,"end":558},{"cath_id":"2.60.40.10","chopping":"566-656","consensus_level":"high","plddt":93.7066,"start":566,"end":656},{"cath_id":"2.60.40.10","chopping":"668-753","consensus_level":"medium","plddt":92.5695,"start":668,"end":753},{"cath_id":"2.60.40.10","chopping":"765-846","consensus_level":"medium","plddt":91.6487,"start":765,"end":846},{"cath_id":"2.60.40.10","chopping":"856-945","consensus_level":"medium","plddt":88.5118,"start":856,"end":945},{"cath_id":"2.60.40.10","chopping":"956-972_984-1041","consensus_level":"medium","plddt":88.4907,"start":956,"end":1041},{"cath_id":"2.60.40.10","chopping":"1053-1144","consensus_level":"medium","plddt":84.9912,"start":1053,"end":1144}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y2H6-F1-predicted_aligned_error_v6.png","plddt_mean":77.69},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=FNDC3A","jax_strain_url":"https://www.jax.org/strain/search?query=FNDC3A"},"sequence":{"accession":"Q9Y2H6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y2H6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y2H6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y2H6"}},"corpus_meta":[{"pmid":"16904100","id":"PMC_16904100","title":"FNDC3A is required for adhesion between spermatids and Sertoli cells.","date":"2006","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/16904100","citation_count":57,"is_preprint":false},{"pmid":"32966780","id":"PMC_32966780","title":"The Interaction of the Tumor Suppressor FAM46C with p62 and FNDC3 Proteins Integrates Protein and Secretory Homeostasis.","date":"2020","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/32966780","citation_count":39,"is_preprint":false},{"pmid":"32963011","id":"PMC_32963011","title":"FAM46C and FNDC3A Are Multiple Myeloma Tumor Suppressors That Act in Concert to Impair Clearing of Protein Aggregates and Autophagy.","date":"2020","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/32963011","citation_count":38,"is_preprint":false},{"pmid":"31527654","id":"PMC_31527654","title":"ECM alterations in Fndc3a (Fibronectin Domain Containing Protein 3A) deficient zebrafish cause temporal fin development and regeneration defects.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31527654","citation_count":14,"is_preprint":false},{"pmid":"30539716","id":"PMC_30539716","title":"Miles to go (mtgo) encodes FNDC3 proteins that interact with the chaperonin subunit CCT3 and are required for NMJ branching and growth in Drosophila.","date":"2018","source":"Developmental biology","url":"https://pubmed.ncbi.nlm.nih.gov/30539716","citation_count":12,"is_preprint":false},{"pmid":"18218838","id":"PMC_18218838","title":"HUGO (FNDC3A): a new gene overexpressed in human odontoblasts.","date":"2008","source":"Journal of dental research","url":"https://pubmed.ncbi.nlm.nih.gov/18218838","citation_count":10,"is_preprint":false},{"pmid":"38513348","id":"PMC_38513348","title":"Exosomal or follicular FNDC3A decreases FOLR1 mRNA abundance and progesterone and lactate synthesis in bovine granulosa cells.","date":"2024","source":"Reproduction (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/38513348","citation_count":4,"is_preprint":false},{"pmid":"40521987","id":"PMC_40521987","title":"LncRNA SNHG14 Regulated by ZNF460 Promotes Gastric Cancer Progression and Metastasis by Targeting the miR-206/FNDC3A Axis.","date":"2025","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40521987","citation_count":4,"is_preprint":false},{"pmid":"36254247","id":"PMC_36254247","title":"Microarray expression profiling of fndc3a zebrafish mutants.","date":"2022","source":"microPublication biology","url":"https://pubmed.ncbi.nlm.nih.gov/36254247","citation_count":1,"is_preprint":false},{"pmid":"40120859","id":"PMC_40120859","title":"Silencing of fibronectin type III domain-containing protein 3A (FNDC3A) attenuates epithelial-to-mesenchymal transition (EMT), cancer invasion, and stemness in triple-negative breast cancer (TNBC).","date":"2025","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/40120859","citation_count":0,"is_preprint":false},{"pmid":"42247288","id":"PMC_42247288","title":"The C-terminal region of TENT5 proteins drives ER-associated mRNA polyadenylation via FNDC3 interaction.","date":"2026","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/42247288","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.07.13.24310153","title":"Proteome-wide Mendelian randomization study implicates inflammaging biomarkers in retinal vasculature, cardiometabolic diseases and longevity","date":"2024-07-14","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.13.24310153","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8302,"output_tokens":2491,"usd":0.031135,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9644,"output_tokens":3758,"usd":0.071085,"stage2_stop_reason":"end_turn"},"total_usd":0.10222,"stage1_batch_id":"msgbatch_01AsR7g8dGTEiEw9U83bJeWn","stage2_batch_id":"msgbatch_01YV5ZyxtFNUZEjxRcpd9jzb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2006,\n      \"finding\": \"FNDC3A is required for adhesion between spermatids and Sertoli cells in the seminiferous epithelium; loss-of-function (deletion of Fndc3a in sys mice) causes defective spermatid-Sertoli adhesion and male sterility, confirmed by genetic complementation with a specific Fndc3a mutation.\",\n      \"method\": \"Genetic complementation analysis in mice; loss-of-function deletion mapping; immunohistochemistry\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic complementation with specific allele, replicated in two independent mouse models (deletion and point mutation), clear cellular phenotype\",\n      \"pmids\": [\"16904100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"FNDC3A protein localizes to the acrosome of spermatids (steps 2–10) and later to cytoplasmic vesicular structures in elongate spermatids (step 12); it also localizes to Leydig cells in mouse testis. The protein contains a hydrophobic C-terminus similar to tail-anchored proteins, suggesting ER membrane localization.\",\n      \"method\": \"Immunohistochemical staining of mouse testis sections\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization by IHC in multiple developmental stages, single lab, no functional rescue tied to localization domain\",\n      \"pmids\": [\"16904100\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In human odontoblasts, FNDC3A (HUGO) protein localizes to Golgi vesicles, suggesting a role in collagen and glycosaminoglycan synthesis in these cells.\",\n      \"method\": \"Immunohistochemistry and subcellular localization in odontoblasts\",\n      \"journal\": \"Journal of dental research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (IHC/localization), no functional follow-up\",\n      \"pmids\": [\"18218838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The Drosophila FNDC3 ortholog MTGO physically and genetically interacts with CCT3, a subunit of the TRiC/CCT chaperonin complex; a CCT3 mutation that reduces binding to MTGO phenocopies NMJ branching and growth defects seen in mtgo null mutants, establishing a functional complex between FNDC3 and the chaperonin.\",\n      \"method\": \"Physical interaction (co-immunoprecipitation/pulldown), genetic epistasis (double mutants), transgenic rescue (neuronal-specific expression)\",\n      \"journal\": \"Developmental biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — physical interaction plus genetic epistasis in single lab, ortholog (Drosophila), two orthogonal methods\",\n      \"pmids\": [\"30539716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Loss of fndc3a in zebrafish (hypomorphic CRISPR/Cas9 mutant) causes ECM alterations, defects in actinotrichia formation, and disrupted epidermal cell organization, implicating FNDC3A in ECM regulation during fin development and regeneration.\",\n      \"method\": \"CRISPR/Cas9 loss-of-function in zebrafish; gene expression profiling; phenotypic analysis of fin development and regeneration\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean CRISPR KO with defined cellular/tissue phenotype and ECM characterization, single lab\",\n      \"pmids\": [\"31527654\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FNDC3A is an ER membrane-resident protein that interacts with FAM46C (TENT5C), anchoring FAM46C to the cytoplasmic face of the ER. This FAM46C/FNDC3A complex modulates secretion routes (increasing lysosome exocytosis), impairs autophagy, and promotes accumulation of intracellular protein aggregates leading to apoptosis in multiple myeloma cells.\",\n      \"method\": \"Co-immunoprecipitation; biochemical fractionation; knockdown and overexpression of FNDC3A with defined phenotypic readouts (aggregates, apoptosis, autophagy flux)\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal biochemical interaction, loss-of-function and gain-of-function with multiple phenotypic readouts, independently replicated in companion paper (PMID:32966780)\",\n      \"pmids\": [\"32963011\", \"32966780\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"FAM46C activity and its interaction with FNDC3A proteins is regulated by p62: the ZZ domain of the autophagic receptor p62 binds FAM46C and sequesters it in p62+ aggregates, preventing its association with FNDC3A and thereby limiting its poly(A) polymerase activity toward ER-targeted mRNAs.\",\n      \"method\": \"Co-immunoprecipitation; domain-mapping mutagenesis; confocal imaging of p62 aggregates; mRNA stabilization assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — mechanistic dissection of p62/FAM46C/FNDC3 circuit with biochemical interaction mapping, domain mutagenesis, and functional mRNA assays; replicated across two labs\",\n      \"pmids\": [\"32966780\", \"32963011\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Recombinant FNDC3A (10 ng/mL) added to bovine granulosa cells decreases IGF1-dependent progesterone secretion, reduces IGF1-dependent lactate secretion and GLUT3/GLUT4 mRNA abundance, and increases Akt phosphorylation, suggesting FNDC3A acts as an extracellular adipokine modulating IGF1 signaling and granulosa cell metabolism. FNDC3A protein is also present in follicular fluid associated with extracellular vesicles.\",\n      \"method\": \"In vitro granulosa cell culture with recombinant FNDC3A; hormone/metabolite assays; western blot (pAkt); qPCR; extracellular vesicle isolation\",\n      \"journal\": \"Reproduction (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean in vitro functional assay with recombinant protein and multiple readouts, single lab, bovine model\",\n      \"pmids\": [\"38513348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"FNDC3A knockdown in triple-negative breast cancer cell lines suppresses EMT, invasion, and cancer stemness, and RNA-seq revealed concomitant inhibition of YAP1 and its target genes, placing FNDC3A upstream of the YAP1 pathway in TNBC.\",\n      \"method\": \"siRNA knockdown; invasion/migration assays; RNA-seq; stemness assays\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — loss-of-function with transcriptomic pathway placement, single lab, no rescue experiment or direct YAP1 interaction shown\",\n      \"pmids\": [\"40120859\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"A member-specific C-terminal region of TENT5/FAM46 proteins (including TENT5C/FAM46C) is necessary and sufficient for binding to ER-transmembrane FNDC3 proteins and for ER localization. Mutations in this C-terminal region of TENT5C found in multiple myeloma impair FNDC3 binding or protein stability, reducing immunoglobulin production and tumor-suppressive activity.\",\n      \"method\": \"Systematic mutagenesis; transcriptomic and proteomic profiling; co-immunoprecipitation; localization assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — systematic mutagenesis defining necessary and sufficient domain, combined with proteomic/transcriptomic profiling and functional readouts in disease-relevant context\",\n      \"pmids\": [\"42247288\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"FNDC3A is an ER transmembrane protein that serves as an anchor and functional partner for the TENT5/FAM46 family of non-canonical poly(A) polymerases (particularly FAM46C/TENT5C), recruiting them to the cytoplasmic face of the ER via a specific C-terminal interaction domain; this complex regulates ER-targeted mRNA stabilization, secretory output, lysosome exocytosis, and autophagy, while in the testis FNDC3A is required for spermatid–Sertoli cell adhesion, and in other contexts it modulates ECM organization, YAP1-dependent invasion, and IGF1 signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"FNDC3A is an endoplasmic reticulum transmembrane protein that functions both as a membrane anchor for cytoplasmic effector enzymes and as a tissue-level mediator of cell adhesion and extracellular matrix organization [#0, #5]. Its best-defined molecular role is to recruit the TENT5/FAM46 family of non-canonical poly(A) polymerases—notably FAM46C/TENT5C—to the cytoplasmic face of the ER, where the FNDC3A/FAM46C complex stabilizes ER-targeted mRNAs and shapes the secretory output of the cell, increasing lysosome exocytosis, impairing autophagy, and driving accumulation of intracellular protein aggregates and apoptosis in multiple myeloma cells [#5]. Binding is mediated by a member-specific C-terminal region of TENT5C that is necessary and sufficient for FNDC3 association and ER localization; multiple myeloma mutations in this region disrupt FNDC3 binding or TENT5C stability and abrogate its tumor-suppressive, immunoglobulin-promoting activity [#9]. This circuit is gated by the autophagic receptor p62, whose ZZ domain sequesters FAM46C in aggregates and prevents its productive engagement with FNDC3A [#6]. Beyond this complex, FNDC3A is genetically required for spermatid–Sertoli cell adhesion in the testis, where its loss causes male sterility [#0], and it regulates extracellular matrix and epidermal organization during zebrafish fin development and regeneration [#4]. FNDC3A loss in triple-negative breast cancer cells suppresses EMT, invasion, and stemness with concomitant inhibition of the YAP1 transcriptional program [#8], and recombinant FNDC3A acts extracellularly on bovine granulosa cells to dampen IGF1-dependent progesterone and lactate secretion [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established the first in vivo function of FNDC3A by showing it is genetically required for a specific cell–cell adhesion event, defining the protein as essential for male fertility rather than merely expressed in testis.\",\n      \"evidence\": \"Loss-of-function deletion mapping and genetic complementation with a specific Fndc3a allele in sys mice, with immunohistochemistry\",\n      \"pmids\": [\"16904100\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular mechanism of adhesion not defined\", \"No identified binding partner mediating spermatid–Sertoli attachment\", \"Subcellular site of action versus membrane topology not resolved functionally\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Localized FNDC3A to acrosomal and cytoplasmic vesicular structures and noted a tail-anchor-like hydrophobic C-terminus, providing the first structural clue that the protein is membrane-associated.\",\n      \"evidence\": \"Immunohistochemical staining of staged mouse testis sections\",\n      \"pmids\": [\"16904100\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"ER membrane insertion inferred from sequence, not demonstrated\", \"Localization not tied to function by domain rescue\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Extended FNDC3A expression to a secretory cell type by localizing it to Golgi vesicles in odontoblasts, hinting at a role in matrix biosynthesis.\",\n      \"evidence\": \"Immunohistochemistry and subcellular localization in human odontoblasts\",\n      \"pmids\": [\"18218838\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single lab, single method (IHC) with no functional follow-up\", \"Golgi versus ER localization not reconciled with later ER residency data\", \"No demonstrated link to collagen or glycosaminoglycan synthesis\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Connected an FNDC3 ortholog to chaperonin function by showing a physical and genetic interaction with the TRiC/CCT subunit CCT3 governing neuronal morphogenesis.\",\n      \"evidence\": \"Co-IP/pulldown, genetic epistasis with double mutants, and neuronal rescue of Drosophila mtgo phenotypes\",\n      \"pmids\": [\"30539716\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Demonstrated in Drosophila ortholog only\", \"Relationship between CCT3 interaction and the mammalian ER/FAM46C role unknown\", \"Direct binding interface not mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined a developmental ECM function by showing FNDC3A loss disrupts actinotrichia and epidermal organization, implicating the protein in matrix regulation beyond testis adhesion.\",\n      \"evidence\": \"Hypomorphic CRISPR/Cas9 mutant in zebrafish with gene-expression profiling and fin development/regeneration phenotyping\",\n      \"pmids\": [\"31527654\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular targets in ECM not identified\", \"Connection to ER/secretory function not established\", \"Hypomorphic allele leaves null phenotype undefined\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved the central molecular function: FNDC3A is an ER membrane protein that anchors the poly(A) polymerase FAM46C/TENT5C to the cytoplasmic ER face, coupling the complex to secretion, lysosome exocytosis, autophagy, and aggregate-driven apoptosis.\",\n      \"evidence\": \"Reciprocal co-IP, biochemical fractionation, and knockdown/overexpression with aggregate, apoptosis, and autophagy-flux readouts in multiple myeloma cells, replicated in a companion study\",\n      \"pmids\": [\"32963011\", \"32966780\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and structure of the FNDC3A–FAM46C complex unknown\", \"Which ER-targeted mRNAs are regulated not comprehensively defined\", \"Generality beyond myeloma cells untested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed the FNDC3A–FAM46C circuit is regulated by p62, whose ZZ domain sequesters FAM46C and blocks its FNDC3A association and poly(A) polymerase activity, embedding the complex in autophagic/proteostatic control.\",\n      \"evidence\": \"Co-IP, domain-mapping mutagenesis, confocal imaging of p62 aggregates, and mRNA-stabilization assays across two labs\",\n      \"pmids\": [\"32966780\", \"32963011\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signals controlling p62-mediated sequestration not defined\", \"Whether FNDC3A itself is regulated by p62 unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified an extracellular, adipokine-like role: recombinant FNDC3A suppresses IGF1-dependent steroidogenesis and metabolism in granulosa cells and is carried in follicular-fluid extracellular vesicles.\",\n      \"evidence\": \"In vitro bovine granulosa cell culture with recombinant FNDC3A, hormone/metabolite assays, pAkt western blot, qPCR, and EV isolation\",\n      \"pmids\": [\"38513348\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Receptor mediating extracellular FNDC3A action unidentified\", \"Reconciliation of secreted/EV form with ER-transmembrane topology unclear\", \"Single lab, bovine model\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Placed FNDC3A upstream of the YAP1 oncogenic program by showing its knockdown suppresses EMT, invasion, and stemness in triple-negative breast cancer.\",\n      \"evidence\": \"siRNA knockdown with invasion/migration and stemness assays plus RNA-seq pathway analysis\",\n      \"pmids\": [\"40120859\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No rescue experiment\", \"Direct FNDC3A–YAP1 interaction not shown\", \"Mechanism linking ER anchor function to YAP1 regulation unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined the binding determinant: a member-specific C-terminal region of TENT5/FAM46 proteins is necessary and sufficient for FNDC3 binding and ER localization, and myeloma mutations there disrupt the interaction and tumor-suppressive output.\",\n      \"evidence\": \"Systematic mutagenesis with transcriptomic/proteomic profiling, co-IP, and localization assays\",\n      \"pmids\": [\"42247288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Reciprocal FNDC3A binding domain not mapped at residue level\", \"Structure of the interaction interface unresolved\", \"Whether other FNDC3 family members bind distinct TENT5 members untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the ER-anchoring/mRNA-stabilization function mechanistically connects to the organismal roles in cell adhesion, ECM organization, YAP1-driven invasion, and extracellular IGF1 modulation remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking ER-resident FAM46C anchoring to secreted/adhesive functions\", \"FNDC3A receptor/effector for its extracellular activities unknown\", \"Full repertoire of FNDC3A-regulated transcripts and secretory cargo undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [5, 9]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"FAM46C\", \"CCT3\", \"SQSTM1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":6,"faith_total":6,"faith_pct":100.0}}