{"gene":"ATP6V1H","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":1993,"finding":"VMA13 (yeast ortholog of ATP6V1H) encodes the 54-kDa subunit of the V-ATPase complex; it is essential for V-ATPase activity but not for assembly or targeting of other subunits (100-, 69-, 60-, 42-, 27-, 17-kDa) to the vacuolar membrane. Deletion of VMA13 yields an inactive, less stable V-ATPase complex.","method":"Null mutant (delta vma13) analysis, vacuolar membrane fractionation, co-purification with active V-ATPase complex, complementation cloning","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — reconstitution by co-purification, null mutant biochemical characterization with multiple orthogonal assays (activity, fractionation, stability), replicated across complementation and deletion approaches","pmids":["8349704"],"is_preprint":false},{"year":2017,"finding":"Loss of ATP6V1H in zebrafish leads to severe reduction in mature calcified bone cells and dramatically increased expression of MMP9 and MMP13; pharmacological inhibition of MMP9/MMP13 significantly restores bone mass, placing ATP6V1H upstream of MMP9/MMP13 in a bone-formation pathway.","method":"CRISPR/Cas9 knockout in zebrafish, small-molecule inhibitor rescue, gene expression analysis","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis via CRISPR KO and pharmacological rescue with two orthogonal readouts (calcified bone cells, MMP expression), single lab","pmids":["28158191"],"is_preprint":false},{"year":2016,"finding":"Haploinsufficiency of ATP6V1H in mice results in increased intracellular pH in osteoclasts, which downregulates TGF-β1 activation, thereby reducing induction of osteoblast formation and causing net bone matrix loss. Bone resorption is also impaired, but the reduction in bone formation exceeds that of resorption.","method":"CRISPR/Cas9 Atp6v1h knockout mice, intracellular pH measurement, TGF-β1 pathway analysis, histology, genome-wide SNP array","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO mouse model with mechanistic pH and TGF-β1 pathway measurements, multiple cellular assays, single lab","pmids":["27924156"],"is_preprint":false},{"year":2018,"finding":"ATP6V1H deficiency in bone marrow stromal cells (BMSCs) reduces proliferation, causes cell cycle arrest, decreases osteogenic differentiation, and increases adipogenic potential; mechanistically, loss of ATP6V1H downregulates TGF-β receptor I and the AP-2 complex subunit β, indicating ATP6V1H regulates BMSC fate via interactions with TGF-β receptor I and AP-2.","method":"Atp6v1h+/- mouse BMSCs, proliferation assays, differentiation assays, qPCR for TGF-β receptor I and AP-2, histological analysis","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, indirect pathway evidence (mRNA level changes), no direct binding/reconstitution for TGF-β receptor I or AP-2 interactions","pmids":["29782852"],"is_preprint":false},{"year":2019,"finding":"In MC3T3-E1 osteoblast-like cells under high-glucose/free-fatty-acid conditions simulating T2DM, ATP6V1H overexpression promotes osteogenic differentiation via inhibition of the Akt/GSK3β signaling pathway, while ATP6V1H knockdown activates this pathway.","method":"Overexpression and knockdown in MC3T3-E1 cells, Alizarin Red staining, western blot for Akt/GSK3β pathway components, CCK8 viability assay","journal":"Organogenesis","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single cell line, pathway placement by western blot without mechanistic reconstitution","pmids":["31272281"],"is_preprint":false},{"year":2022,"finding":"ATP6V1H deficiency in β-cells worsens high-fat-diet-induced glucose intolerance by augmenting endoplasmic reticulum (ER) stress; transcriptome sequencing indicated that alternative splicing of ATP6V1H may be involved in this mechanism.","method":"Atp6v1h+/- mice on HFD, transcriptome sequencing, qPCR, western blot for ER stress markers","journal":"Archives of biochemistry and biophysics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, KO mouse phenotype with transcriptomic pathway inference, no direct reconstitution of ER stress mechanism","pmids":["34990584"],"is_preprint":false},{"year":2024,"finding":"In a simulated microgravity mouse model, Atp6v1h deficiency upregulates Fos, Jun, Src, and multiple integrin subunits. Co-immunoprecipitation demonstrated direct interactions between ATP6V1H and integrin beta 1, beta 3, beta 5, alpha 2b, and alpha 5, indicating ATP6V1H modulates osteoclast activity and bone resorption through the Fos-Jun-Src-Integrin pathway.","method":"Tail-suspension mouse model, micro-CT, transcriptomic sequencing, RT-qPCR, co-immunoprecipitation","journal":"International journal of molecular sciences","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, Co-IP interaction data without reciprocal validation or in vitro reconstitution, pathway placement by transcriptomics","pmids":["38203808"],"is_preprint":false},{"year":2026,"finding":"miR-122-5p directly targets the 3′UTR of ATP6V1H mRNA (validated by dual-luciferase reporter assay), reducing ATP6V1H protein expression, disrupting v-ATPase assembly, and promoting CD36 translocation to the plasma membrane, thereby increasing free fatty acid uptake in hepatocytes.","method":"Dual-luciferase reporter assay (3′UTR targeting), miR-122-5p mimic/inhibitor transfection, western blot, RT-qPCR, exosome co-culture system","journal":"Clinical science (London, England : 1979)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct 3′UTR targeting validated by luciferase assay plus functional rescue with miR-122-5p inhibitor, multiple orthogonal methods, single lab","pmids":["42244364"],"is_preprint":false},{"year":2025,"finding":"In larval zebrafish macrophages, Atp6v1h co-localizes with internalized Aspergillus fumigatus spores in vivo (live imaging). CRISPR/Cas9 knockout of atp6v1h does not impair spore killing but abolishes macrophage-mediated inhibition of spore germination and suppression of extracellular hyphal growth, demonstrating that v-ATPase/Atp6v1h activity specifically controls post-internalization fungal germination rather than spore viability.","method":"Live imaging in zebrafish, CRISPR/Cas9 atp6v1h knockout, co-localization imaging, survival analysis, germination/hyphal growth quantification","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live in vivo imaging plus genetic KO with specific functional dissection (killing vs germination), single lab preprint","pmids":["bio_10.1101_2025.07.14.664761"],"is_preprint":true}],"current_model":"ATP6V1H (subunit H of the V1 domain) is essential for V-ATPase catalytic activity but not for complex assembly; it regulates intracellular/vesicular pH and thereby controls diverse downstream processes including osteoclast-mediated bone remodeling (via TGF-β1, MMP9/MMP13, and integrin/Fos-Jun-Src pathways), osteoblast and bone marrow stromal cell differentiation (via TGF-β receptor I/AP-2 and Akt/GSK3β signaling), β-cell insulin secretion (via ER stress), and macrophage control of fungal germination; additionally, its expression is post-transcriptionally suppressed by miR-122-5p targeting its 3′UTR, which disrupts v-ATPase assembly and promotes CD36-mediated fatty acid uptake."},"narrative":{"mechanistic_narrative":"ATP6V1H encodes a subunit of the V1 domain of the vacuolar H+-ATPase (V-ATPase), the proton pump that acidifies intracellular and vesicular compartments [PMID:8349704]. Studies of the yeast ortholog VMA13 established that this subunit is required for V-ATPase catalytic activity and complex stability but is dispensable for assembly and membrane targeting of the other subunits, so its loss yields an inactive, less stable complex [PMID:8349704]. Through its control of compartmental pH, ATP6V1H governs osteoclast-mediated bone remodeling: haploinsufficiency in mice raises intracellular pH in osteoclasts, downregulating TGF-β1 activation and producing a net loss of bone matrix in which the drop in bone formation exceeds the drop in resorption [PMID:27924156], and loss in zebrafish reduces calcified bone cells with elevated MMP9 and MMP13, whose pharmacological inhibition restores bone mass [PMID:28158191]. In hepatocytes, miR-122-5p directly targets the ATP6V1H 3′UTR to reduce its expression, disrupting V-ATPase assembly and promoting CD36 translocation to the plasma membrane to increase fatty acid uptake [PMID:42244364]. In macrophages, Atp6v1h co-localizes with internalized Aspergillus fumigatus spores and is required specifically to inhibit post-internalization fungal germination rather than to kill spores [PMID:bio_10.1101_2025.07.14.664761].","teleology":[{"year":1993,"claim":"Established the core molecular identity and requirement of the subunit: whether this V-ATPase subunit was needed for pump activity, assembly, or both was unknown until null-mutant analysis dissected its role.","evidence":"Deletion and complementation of yeast VMA13 with vacuolar membrane fractionation and co-purification with the active complex","pmids":["8349704"],"confidence":"High","gaps":["Does not define the human protein's tissue-specific roles","No structural detail on how the subunit confers activity versus stability"]},{"year":2016,"claim":"Connected V-ATPase pH control to bone biology: it was unclear how this subunit's dosage affects skeletal homeostasis, and the work showed osteoclast pH dysregulation suppresses TGF-β1 and uncouples formation from resorption.","evidence":"Atp6v1h+/- knockout mice with intracellular pH measurement and TGF-β1 pathway and histological analysis","pmids":["27924156"],"confidence":"Medium","gaps":["Mechanism linking pH change to TGF-β1 activation not reconstituted","Single lab"]},{"year":2017,"claim":"Placed ATP6V1H upstream of matrix metalloproteinases in bone formation, addressing which effectors mediate its skeletal phenotype.","evidence":"CRISPR/Cas9 zebrafish knockout with MMP9/MMP13 small-molecule inhibitor rescue and expression analysis","pmids":["28158191"],"confidence":"Medium","gaps":["Whether MMP induction is a direct consequence of pH change is not resolved","No biochemical link between subunit and MMP transcription"]},{"year":2018,"claim":"Extended the role to stromal cell fate, testing how the subunit shapes osteogenic versus adipogenic differentiation.","evidence":"Atp6v1h+/- mouse BMSC proliferation and differentiation assays with qPCR for TGF-β receptor I and AP-2","pmids":["29782852"],"confidence":"Low","gaps":["Pathway evidence is mRNA-level only with no direct binding to TGF-β receptor I or AP-2","Single lab"]},{"year":2019,"claim":"Probed signaling placement under metabolic stress, asking which pathway transduces ATP6V1H's effect on osteoblast differentiation in a diabetic-like context.","evidence":"Overexpression/knockdown in MC3T3-E1 cells with Alizarin Red staining and western blot for Akt/GSK3β","pmids":["31272281"],"confidence":"Low","gaps":["Pathway placement by western blot without mechanistic reconstitution","Single cell line, single lab"]},{"year":2022,"claim":"Linked the subunit to metabolic disease via β-cell function, testing whether its loss affects glucose handling.","evidence":"Atp6v1h+/- mice on high-fat diet with transcriptome sequencing and ER stress marker analysis","pmids":["34990584"],"confidence":"Low","gaps":["ER stress mechanism inferred from transcriptomics, not reconstituted","Role of proposed alternative splicing unestablished"]},{"year":2024,"claim":"Proposed direct physical engagement of integrins, addressing whether ATP6V1H acts beyond proton pumping in osteoclast resorption signaling.","evidence":"Simulated microgravity mouse model with transcriptomics and co-immunoprecipitation of ATP6V1H with integrin subunits","pmids":["38203808"],"confidence":"Low","gaps":["Co-IP without reciprocal validation or in vitro reconstitution","Pathway placement by transcriptomics only"]},{"year":2025,"claim":"Defined a host-defense role, distinguishing whether V-ATPase activity controls fungal killing or germination after macrophage internalization.","evidence":"Live imaging and CRISPR/Cas9 atp6v1h knockout in zebrafish macrophages with germination and hyphal growth quantification (preprint)","pmids":["bio_10.1101_2025.07.14.664761"],"confidence":"Medium","gaps":["Preprint, single lab","Molecular link between phagosomal acidification and germination arrest not defined"]},{"year":2026,"claim":"Identified post-transcriptional regulation of ATP6V1H and its consequence for lipid handling, addressing how the subunit is controlled and how its loss alters hepatocyte metabolism.","evidence":"Dual-luciferase 3′UTR reporter assay, miR-122-5p mimic/inhibitor, western blot, and exosome co-culture in hepatocytes","pmids":["42244364"],"confidence":"Medium","gaps":["Mechanism linking disrupted V-ATPase assembly to CD36 translocation not resolved","Single lab"]},{"year":null,"claim":"How a single V-ATPase subunit's pH control is mechanistically transduced into the diverse downstream pathways (TGF-β1, MMPs, integrins, CD36, ER stress) remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of the human complex linking subunit to activity","Direct biochemical chain from acidification to each downstream effector unestablished"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005773","term_label":"vacuole","supporting_discovery_ids":[0]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[8]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0]}],"complexes":["V-ATPase (V1 domain)"],"partners":["ITGB1","ITGB3","ITGB5","ITGA2B","ITGA5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UI12","full_name":"V-type proton ATPase subunit H","aliases":["Nef-binding protein 1","NBP1","Protein VMA13 homolog","V-ATPase 50/57 kDa subunits","Vacuolar proton pump subunit H","Vacuolar proton pump subunit SFD"],"length_aa":483,"mass_kda":55.9,"function":"Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:33065002). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity). Subunit H is essential for V-ATPase activity, but not for the assembly of the complex (By similarity). Involved in the endocytosis mediated by clathrin-coated pits, required for the formation of endosomes (PubMed:12032142)","subcellular_location":"Cytoplasmic vesicle, clathrin-coated vesicle membrane","url":"https://www.uniprot.org/uniprotkb/Q9UI12/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP6V1H","classification":"Common Essential","n_dependent_lines":843,"n_total_lines":1208,"dependency_fraction":0.6978476821192053},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000047249","cell_line_id":"CID001652","localizations":[{"compartment":"vesicles","grade":3},{"compartment":"cytoplasmic","grade":2}],"interactors":[{"gene":"ATP6AP2","stoichiometry":10.0},{"gene":"ATP6V1A","stoichiometry":10.0},{"gene":"ATP6V1B2","stoichiometry":10.0},{"gene":"ATP6V1D","stoichiometry":10.0},{"gene":"ATP6V1E1","stoichiometry":10.0},{"gene":"ATP6V1F","stoichiometry":10.0},{"gene":"ATP6V1G1","stoichiometry":10.0},{"gene":"WDR7","stoichiometry":4.0},{"gene":"ATP6V0A1","stoichiometry":0.2},{"gene":"ATP6V0D1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001652","total_profiled":1310},"omim":[{"mim_id":"608861","title":"ATPase, H+ TRANSPORTING, LYSOSOMAL, 50/57-KD, V1 SUBUNIT H; ATP6V1H","url":"https://www.omim.org/entry/608861"},{"mim_id":"600669","title":"EPILEPSY, IDIOPATHIC GENERALIZED; EIG","url":"https://www.omim.org/entry/600669"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Actin filaments","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATP6V1H"},"hgnc":{"alias_symbol":["CGI-11","SFD","VMA13","SFDalpha","SFDbeta"],"prev_symbol":[]},"alphafold":{"accession":"Q9UI12","domains":[{"cath_id":"1.25.10","chopping":"14-174_195-219","consensus_level":"medium","plddt":92.7906,"start":14,"end":219},{"cath_id":"1.25.10.10","chopping":"222-349","consensus_level":"medium","plddt":93.6272,"start":222,"end":349},{"cath_id":"1.25.40.150","chopping":"376-466","consensus_level":"high","plddt":92.5537,"start":376,"end":466}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UI12","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UI12-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UI12-F1-predicted_aligned_error_v6.png","plddt_mean":87.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP6V1H","jax_strain_url":"https://www.jax.org/strain/search?query=ATP6V1H"},"sequence":{"accession":"Q9UI12","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UI12.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UI12/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UI12"}},"corpus_meta":[{"pmid":"8349704","id":"PMC_8349704","title":"VMA13 encodes a 54-kDa vacuolar H(+)-ATPase subunit required for activity but not assembly of the enzyme complex in Saccharomyces cerevisiae.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8349704","citation_count":131,"is_preprint":false},{"pmid":"28158191","id":"PMC_28158191","title":"ATP6V1H Deficiency Impairs Bone Development through Activation of MMP9 and MMP13.","date":"2017","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28158191","citation_count":48,"is_preprint":false},{"pmid":"27924156","id":"PMC_27924156","title":"Deficiency of ATP6V1H Causes Bone Loss by Inhibiting Bone Resorption and Bone Formation through the TGF-β1 Pathway.","date":"2016","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/27924156","citation_count":43,"is_preprint":false},{"pmid":"21871445","id":"PMC_21871445","title":"Decreased expression of ATP6V1H in type 2 diabetes: a pilot report on the diabetes risk study in Mexican Americans.","date":"2011","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/21871445","citation_count":17,"is_preprint":false},{"pmid":"29751835","id":"PMC_29751835","title":"Genome-wide association study identified ATP6V1H locus influencing cerebrospinal fluid BACE activity.","date":"2018","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29751835","citation_count":15,"is_preprint":false},{"pmid":"29782852","id":"PMC_29782852","title":"ATP6V1H regulates the growth and differentiation of bone marrow stromal cells.","date":"2018","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29782852","citation_count":12,"is_preprint":false},{"pmid":"34990584","id":"PMC_34990584","title":"ATP6V1H deficiency impairs glucose tolerance by augmenting endoplasmic reticulum stress in high fat diet fed mice.","date":"2022","source":"Archives of biochemistry and biophysics","url":"https://pubmed.ncbi.nlm.nih.gov/34990584","citation_count":10,"is_preprint":false},{"pmid":"31272281","id":"PMC_31272281","title":"ATP6V1H facilitates osteogenic differentiation in MC3T3-E1 cells via Akt/GSK3β signaling pathway.","date":"2019","source":"Organogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/31272281","citation_count":9,"is_preprint":false},{"pmid":"38203808","id":"PMC_38203808","title":"Atp6v1h Deficiency Blocks Bone Loss in Simulated Microgravity Mice through the Fos-Jun-Src-Integrin Pathway.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38203808","citation_count":2,"is_preprint":false},{"pmid":"37824389","id":"PMC_37824389","title":"Long Noncoding RNA lnc-TCEA1-3 Affects Osteoclastic Function by Regulating ATP6V1H.","date":"2024","source":"Critical reviews in eukaryotic gene expression","url":"https://pubmed.ncbi.nlm.nih.gov/37824389","citation_count":1,"is_preprint":false},{"pmid":"33787173","id":"PMC_33787173","title":"[Role of ATP6V1H gene in bone metabolism].","date":"2021","source":"Zhongguo gu shang = China journal of orthopaedics and traumatology","url":"https://pubmed.ncbi.nlm.nih.gov/33787173","citation_count":0,"is_preprint":false},{"pmid":"42244364","id":"PMC_42244364","title":"Steatotic Hepatocyte-Derived Exosomes Increase Free Fatty Acids Uptake by Transporting miR-122-5p to Target ATP6V1H-Mediated CD36 Translocation in Hepatocytes.","date":"2026","source":"Clinical science (London, England : 1979)","url":"https://pubmed.ncbi.nlm.nih.gov/42244364","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.14.664761","title":"Macrophage vacuolar ATPase (v-ATPase) function controls  <i>Aspergillus fumigatus</i>  germination and hyphal growth independent of spore killing","date":"2025-07-18","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.14.664761","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8364,"output_tokens":2493,"usd":0.031244,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9696,"output_tokens":2868,"usd":0.06009,"stage2_stop_reason":"end_turn"},"total_usd":0.091334,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1993,\n      \"finding\": \"VMA13 (yeast ortholog of ATP6V1H) encodes the 54-kDa subunit of the V-ATPase complex; it is essential for V-ATPase activity but not for assembly or targeting of other subunits (100-, 69-, 60-, 42-, 27-, 17-kDa) to the vacuolar membrane. Deletion of VMA13 yields an inactive, less stable V-ATPase complex.\",\n      \"method\": \"Null mutant (delta vma13) analysis, vacuolar membrane fractionation, co-purification with active V-ATPase complex, complementation cloning\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — reconstitution by co-purification, null mutant biochemical characterization with multiple orthogonal assays (activity, fractionation, stability), replicated across complementation and deletion approaches\",\n      \"pmids\": [\"8349704\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Loss of ATP6V1H in zebrafish leads to severe reduction in mature calcified bone cells and dramatically increased expression of MMP9 and MMP13; pharmacological inhibition of MMP9/MMP13 significantly restores bone mass, placing ATP6V1H upstream of MMP9/MMP13 in a bone-formation pathway.\",\n      \"method\": \"CRISPR/Cas9 knockout in zebrafish, small-molecule inhibitor rescue, gene expression analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis via CRISPR KO and pharmacological rescue with two orthogonal readouts (calcified bone cells, MMP expression), single lab\",\n      \"pmids\": [\"28158191\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Haploinsufficiency of ATP6V1H in mice results in increased intracellular pH in osteoclasts, which downregulates TGF-β1 activation, thereby reducing induction of osteoblast formation and causing net bone matrix loss. Bone resorption is also impaired, but the reduction in bone formation exceeds that of resorption.\",\n      \"method\": \"CRISPR/Cas9 Atp6v1h knockout mice, intracellular pH measurement, TGF-β1 pathway analysis, histology, genome-wide SNP array\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO mouse model with mechanistic pH and TGF-β1 pathway measurements, multiple cellular assays, single lab\",\n      \"pmids\": [\"27924156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"ATP6V1H deficiency in bone marrow stromal cells (BMSCs) reduces proliferation, causes cell cycle arrest, decreases osteogenic differentiation, and increases adipogenic potential; mechanistically, loss of ATP6V1H downregulates TGF-β receptor I and the AP-2 complex subunit β, indicating ATP6V1H regulates BMSC fate via interactions with TGF-β receptor I and AP-2.\",\n      \"method\": \"Atp6v1h+/- mouse BMSCs, proliferation assays, differentiation assays, qPCR for TGF-β receptor I and AP-2, histological analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect pathway evidence (mRNA level changes), no direct binding/reconstitution for TGF-β receptor I or AP-2 interactions\",\n      \"pmids\": [\"29782852\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In MC3T3-E1 osteoblast-like cells under high-glucose/free-fatty-acid conditions simulating T2DM, ATP6V1H overexpression promotes osteogenic differentiation via inhibition of the Akt/GSK3β signaling pathway, while ATP6V1H knockdown activates this pathway.\",\n      \"method\": \"Overexpression and knockdown in MC3T3-E1 cells, Alizarin Red staining, western blot for Akt/GSK3β pathway components, CCK8 viability assay\",\n      \"journal\": \"Organogenesis\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single cell line, pathway placement by western blot without mechanistic reconstitution\",\n      \"pmids\": [\"31272281\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ATP6V1H deficiency in β-cells worsens high-fat-diet-induced glucose intolerance by augmenting endoplasmic reticulum (ER) stress; transcriptome sequencing indicated that alternative splicing of ATP6V1H may be involved in this mechanism.\",\n      \"method\": \"Atp6v1h+/- mice on HFD, transcriptome sequencing, qPCR, western blot for ER stress markers\",\n      \"journal\": \"Archives of biochemistry and biophysics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, KO mouse phenotype with transcriptomic pathway inference, no direct reconstitution of ER stress mechanism\",\n      \"pmids\": [\"34990584\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In a simulated microgravity mouse model, Atp6v1h deficiency upregulates Fos, Jun, Src, and multiple integrin subunits. Co-immunoprecipitation demonstrated direct interactions between ATP6V1H and integrin beta 1, beta 3, beta 5, alpha 2b, and alpha 5, indicating ATP6V1H modulates osteoclast activity and bone resorption through the Fos-Jun-Src-Integrin pathway.\",\n      \"method\": \"Tail-suspension mouse model, micro-CT, transcriptomic sequencing, RT-qPCR, co-immunoprecipitation\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, Co-IP interaction data without reciprocal validation or in vitro reconstitution, pathway placement by transcriptomics\",\n      \"pmids\": [\"38203808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"miR-122-5p directly targets the 3′UTR of ATP6V1H mRNA (validated by dual-luciferase reporter assay), reducing ATP6V1H protein expression, disrupting v-ATPase assembly, and promoting CD36 translocation to the plasma membrane, thereby increasing free fatty acid uptake in hepatocytes.\",\n      \"method\": \"Dual-luciferase reporter assay (3′UTR targeting), miR-122-5p mimic/inhibitor transfection, western blot, RT-qPCR, exosome co-culture system\",\n      \"journal\": \"Clinical science (London, England : 1979)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct 3′UTR targeting validated by luciferase assay plus functional rescue with miR-122-5p inhibitor, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"42244364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In larval zebrafish macrophages, Atp6v1h co-localizes with internalized Aspergillus fumigatus spores in vivo (live imaging). CRISPR/Cas9 knockout of atp6v1h does not impair spore killing but abolishes macrophage-mediated inhibition of spore germination and suppression of extracellular hyphal growth, demonstrating that v-ATPase/Atp6v1h activity specifically controls post-internalization fungal germination rather than spore viability.\",\n      \"method\": \"Live imaging in zebrafish, CRISPR/Cas9 atp6v1h knockout, co-localization imaging, survival analysis, germination/hyphal growth quantification\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live in vivo imaging plus genetic KO with specific functional dissection (killing vs germination), single lab preprint\",\n      \"pmids\": [\"bio_10.1101_2025.07.14.664761\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"ATP6V1H (subunit H of the V1 domain) is essential for V-ATPase catalytic activity but not for complex assembly; it regulates intracellular/vesicular pH and thereby controls diverse downstream processes including osteoclast-mediated bone remodeling (via TGF-β1, MMP9/MMP13, and integrin/Fos-Jun-Src pathways), osteoblast and bone marrow stromal cell differentiation (via TGF-β receptor I/AP-2 and Akt/GSK3β signaling), β-cell insulin secretion (via ER stress), and macrophage control of fungal germination; additionally, its expression is post-transcriptionally suppressed by miR-122-5p targeting its 3′UTR, which disrupts v-ATPase assembly and promotes CD36-mediated fatty acid uptake.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP6V1H encodes a subunit of the V1 domain of the vacuolar H+-ATPase (V-ATPase), the proton pump that acidifies intracellular and vesicular compartments [#0]. Studies of the yeast ortholog VMA13 established that this subunit is required for V-ATPase catalytic activity and complex stability but is dispensable for assembly and membrane targeting of the other subunits, so its loss yields an inactive, less stable complex [#0]. Through its control of compartmental pH, ATP6V1H governs osteoclast-mediated bone remodeling: haploinsufficiency in mice raises intracellular pH in osteoclasts, downregulating TGF-\\u03b21 activation and producing a net loss of bone matrix in which the drop in bone formation exceeds the drop in resorption [#2], and loss in zebrafish reduces calcified bone cells with elevated MMP9 and MMP13, whose pharmacological inhibition restores bone mass [#1]. In hepatocytes, miR-122-5p directly targets the ATP6V1H 3\\u2032UTR to reduce its expression, disrupting V-ATPase assembly and promoting CD36 translocation to the plasma membrane to increase fatty acid uptake [#7]. In macrophages, Atp6v1h co-localizes with internalized Aspergillus fumigatus spores and is required specifically to inhibit post-internalization fungal germination rather than to kill spores [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 1993,\n      \"claim\": \"Established the core molecular identity and requirement of the subunit: whether this V-ATPase subunit was needed for pump activity, assembly, or both was unknown until null-mutant analysis dissected its role.\",\n      \"evidence\": \"Deletion and complementation of yeast VMA13 with vacuolar membrane fractionation and co-purification with the active complex\",\n      \"pmids\": [\"8349704\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define the human protein's tissue-specific roles\", \"No structural detail on how the subunit confers activity versus stability\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Connected V-ATPase pH control to bone biology: it was unclear how this subunit's dosage affects skeletal homeostasis, and the work showed osteoclast pH dysregulation suppresses TGF-\\u03b21 and uncouples formation from resorption.\",\n      \"evidence\": \"Atp6v1h+/- knockout mice with intracellular pH measurement and TGF-\\u03b21 pathway and histological analysis\",\n      \"pmids\": [\"27924156\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking pH change to TGF-\\u03b21 activation not reconstituted\", \"Single lab\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Placed ATP6V1H upstream of matrix metalloproteinases in bone formation, addressing which effectors mediate its skeletal phenotype.\",\n      \"evidence\": \"CRISPR/Cas9 zebrafish knockout with MMP9/MMP13 small-molecule inhibitor rescue and expression analysis\",\n      \"pmids\": [\"28158191\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether MMP induction is a direct consequence of pH change is not resolved\", \"No biochemical link between subunit and MMP transcription\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended the role to stromal cell fate, testing how the subunit shapes osteogenic versus adipogenic differentiation.\",\n      \"evidence\": \"Atp6v1h+/- mouse BMSC proliferation and differentiation assays with qPCR for TGF-\\u03b2 receptor I and AP-2\",\n      \"pmids\": [\"29782852\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pathway evidence is mRNA-level only with no direct binding to TGF-\\u03b2 receptor I or AP-2\", \"Single lab\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Probed signaling placement under metabolic stress, asking which pathway transduces ATP6V1H's effect on osteoblast differentiation in a diabetic-like context.\",\n      \"evidence\": \"Overexpression/knockdown in MC3T3-E1 cells with Alizarin Red staining and western blot for Akt/GSK3\\u03b2\",\n      \"pmids\": [\"31272281\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Pathway placement by western blot without mechanistic reconstitution\", \"Single cell line, single lab\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked the subunit to metabolic disease via \\u03b2-cell function, testing whether its loss affects glucose handling.\",\n      \"evidence\": \"Atp6v1h+/- mice on high-fat diet with transcriptome sequencing and ER stress marker analysis\",\n      \"pmids\": [\"34990584\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"ER stress mechanism inferred from transcriptomics, not reconstituted\", \"Role of proposed alternative splicing unestablished\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Proposed direct physical engagement of integrins, addressing whether ATP6V1H acts beyond proton pumping in osteoclast resorption signaling.\",\n      \"evidence\": \"Simulated microgravity mouse model with transcriptomics and co-immunoprecipitation of ATP6V1H with integrin subunits\",\n      \"pmids\": [\"38203808\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Co-IP without reciprocal validation or in vitro reconstitution\", \"Pathway placement by transcriptomics only\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a host-defense role, distinguishing whether V-ATPase activity controls fungal killing or germination after macrophage internalization.\",\n      \"evidence\": \"Live imaging and CRISPR/Cas9 atp6v1h knockout in zebrafish macrophages with germination and hyphal growth quantification (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.07.14.664761\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab\", \"Molecular link between phagosomal acidification and germination arrest not defined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified post-transcriptional regulation of ATP6V1H and its consequence for lipid handling, addressing how the subunit is controlled and how its loss alters hepatocyte metabolism.\",\n      \"evidence\": \"Dual-luciferase 3\\u2032UTR reporter assay, miR-122-5p mimic/inhibitor, western blot, and exosome co-culture in hepatocytes\",\n      \"pmids\": [\"42244364\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking disrupted V-ATPase assembly to CD36 translocation not resolved\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single V-ATPase subunit's pH control is mechanistically transduced into the diverse downstream pathways (TGF-\\u03b21, MMPs, integrins, CD36, ER stress) remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of the human complex linking subunit to activity\", \"Direct biochemical chain from acidification to each downstream effector unestablished\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005773\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [8]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"V-ATPase (V1 domain)\"],\n    \"partners\": [\"ITGB1\", \"ITGB3\", \"ITGB5\", \"ITGA2B\", \"ITGA5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}