{"gene":"ATP11A","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2021,"finding":"ATP11A translocates phosphatidylserine (PtdSer), but not phosphatidylcholine (PtdCho), from the outer to the inner leaflet of plasma membranes, maintaining asymmetric PtdSer distribution. A Q84E substitution in the first transmembrane segment causes aberrant PtdCho flipping; molecular dynamics simulations showed this mutation allows PtdCho binding at the substrate entry site. Aberrant PtdCho flipping decreased PtdCho in the outer leaflet and increased sphingomyelin, altering cell growth, cholesterol homeostasis, and sensitivity to sphingomyelinase.","method":"In vitro flippase activity assays, molecular dynamics simulations, MALDI-IMS, knockin mouse model","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal methods including functional assay, structural simulation, mutagenesis, and in vivo mouse model in a single rigorous study","pmids":["34403372"],"is_preprint":false},{"year":2022,"finding":"ATP11A (and ATP11C) function as flippases at the plasma membrane to translocate phosphatidylserine from the outer to inner leaflet. Atp11a-null mouse embryos die at ~E14.5 with thin-walled heart ventricles. Atp11a is expressed in mouse placenta (but not Atp11c), and its loss causes poor development of the labyrinthine layer with unfused trophoblasts (syncytiotrophoblast formation failure). In BeWo cells, combined loss of ATP11A and ATP11C eliminated PS flipping and cell fusion upon forskolin treatment.","method":"Knockout mouse model, immunohistochemistry, electron microscopy, TUNEL assay, PS flippase assay in BeWo cells, siRNA knockdown","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO mouse with defined cellular phenotype, orthogonal methods (histology, EM, functional flippase assay), replicated in cell model","pmids":["35476530"],"is_preprint":false},{"year":2020,"finding":"ATP11A localizes to the Golgi and plasma membrane when co-expressed with its beta-subunit TMEM30A. Residues Y300 and D913 (corresponding to functionally critical residues in the related flippase ATP8A2) are required for correct Golgi/plasma membrane localization and PS flippase activity; Y300F mutation also reduces ATP11A expression levels.","method":"Mutagenesis, fluorescence microscopy (subcellular localization), PS flippase activity assay, co-expression with TMEM30A","journal":"BioMed research international","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis plus functional flippase assay and localization, single lab study","pmids":["32596364"],"is_preprint":false},{"year":2023,"finding":"A 5500 bp deletion in ATP11A activates a cryptic splice site forming an alternative last exon, causing the altered C-terminus to lose flippase activity for phosphatidylserine. Atp11a is expressed in fibers and synaptic contacts of the auditory nerve and cochlear nucleus in mice; conditional Atp11a knockout mice show progressive reduction of spiral ganglion neuron compound action potential, recapitulating auditory neuropathy.","method":"Whole-genome sequencing, in vitro functional flippase assay, immunohistochemistry, conditional knockout mouse model, auditory electrophysiology","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — in vitro functional assay demonstrating loss of flippase activity, conditional KO mouse with defined electrophysiological phenotype, immunohistochemical localization, multiple orthogonal methods","pmids":["36300302"],"is_preprint":false},{"year":2022,"finding":"ATP11A binds specifically to the Numb PRRL isoform (by immunoprecipitation), positively regulates Numb PRRL, Snail2, and ZEB1 protein expression, and promotes epithelial-to-mesenchymal transition (EMT) in pancreatic cancer cells via a TGFβ-dependent Numb PRRL–ZEB1/Snail2 pathway. Knockdown of Numb PRRL suppresses the ATP11A-mediated enhancement of ZEB1/Snail2.","method":"Immunoprecipitation, Western blot, overexpression/knockdown, rescue assay, invasion/migration assays","journal":"PeerJ","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single Co-IP plus rescue experiments, single lab, multiple functional assays but no in vitro reconstitution","pmids":["35345586"],"is_preprint":false},{"year":2025,"finding":"Genetic ablation of Atp11a in mouse uterine epithelium causes loss of tight junctions, disrupted luminal epithelial morphology, incomplete luminal epithelial cell specification (retention of gland-restricted FOXA2 marker), and depletion of gland progenitor cells (SOX9, PAX8, LGR5, PROM1). This results in uterine receptivity deficits and frequent pregnancy failure. Heterozygous Atp11a loss increases incidence of abnormal placental trophoblast differentiation and developmental heart defects in embryos.","method":"Conditional knockout mouse, immunofluorescence, transcriptional profiling, morphological analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Moderate — clean conditional KO with multiple defined cellular phenotypes and transcriptional readouts, single lab but multiple orthogonal methods","pmids":["40261925"],"is_preprint":false},{"year":2025,"finding":"Loss-of-function atp11a mutant zebrafish display reduced stereocilia in the larval ear and reduced hair cells in sensory neuromasts. Photoreceptors in atp11a mutants show reduced outer segments (worsened by light exposure) and mitochondrial fission with increased mitochondrial number, suggesting defects in energy homeostasis.","method":"Loss-of-function zebrafish mutant, confocal microscopy, hair cell counting, electron/fluorescence microscopy of mitochondria","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean loss-of-function model with defined cellular phenotypes in multiple tissues, single lab","pmids":["40223426"],"is_preprint":false},{"year":2024,"finding":"ATP11A promotes migration, invasion, proliferation, and EMT in gastric cancer cells by inactivating the Hippo pathway, as evidenced by changes in Hippo pathway markers upon ATP11A knockdown/overexpression.","method":"Transwell/wound healing/CCK8/colony formation assays, Western blot for EMT and Hippo pathway markers, siRNA knockdown and overexpression","journal":"Journal of Cancer","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method set (Western blot pathway markers), no direct mechanistic link between flippase activity and Hippo pathway established","pmids":["39247595"],"is_preprint":false},{"year":2005,"finding":"Overexpression of ATP11A confers protection of Bcr/Abl-positive lymphoblastic leukemia cells against farnesyltransferase inhibitors (SCH66336/lonafarnib, FTI-276, GGTI-298) and imatinib mesylate, while siRNA-mediated knockdown of endogenous ATP11A sensitizes cells to these drugs.","method":"Overexpression, siRNA knockdown, drug sensitivity assays","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — reciprocal gain- and loss-of-function experiments with clear drug sensitivity readout, single lab but bidirectional evidence","pmids":["15860663"],"is_preprint":false}],"current_model":"ATP11A is a P4-type ATPase flippase that, in complex with its beta-subunit TMEM30A, translocates phosphatidylserine (and phosphatidylethanolamine) from the outer to the inner leaflet of the plasma membrane to maintain phospholipid asymmetry; its substrate specificity is determined by transmembrane residues (notably Q84, Y300, D913), and its activity is required for syncytiotrophoblast formation in the placenta, spiral ganglion neuron function in the auditory system, uterine epithelial integrity, and photoreceptor/hair cell maintenance, while gain-of-function or loss-of-function mutations cause aberrant lipid distribution with downstream consequences for cell signaling, EMT, and neurological function."},"narrative":{"mechanistic_narrative":"ATP11A is a P4-type ATPase phospholipid flippase that translocates phosphatidylserine from the outer to the inner leaflet of the plasma membrane to establish and maintain transbilayer lipid asymmetry [PMID:34403372, PMID:35476530]. Its substrate selectivity is dictated by transmembrane residues: a Q84E substitution opens the substrate entry site to phosphatidylcholine, producing aberrant PtdCho flipping that depletes outer-leaflet PtdCho, raises sphingomyelin, and perturbs cholesterol homeostasis and cell growth [PMID:34403372], while residues Y300 and D913 are required for flippase activity and for correct Golgi and plasma membrane localization in complex with its beta-subunit TMEM30A [PMID:32596364]. This flippase activity is developmentally essential across multiple tissues: ATP11A (with ATP11C) drives the phosphatidylserine exposure needed for syncytiotrophoblast fusion in the placental labyrinth, and Atp11a-null embryos die with thin-walled heart ventricles [PMID:35476530]; conditional loss disrupts uterine epithelial integrity, gland progenitor specification, and pregnancy success [PMID:40261925]; and it sustains spiral ganglion neurons of the auditory nerve, where loss-of-function causes auditory neuropathy in mice and humans carrying a splice-altering deletion that abolishes PtdSer flipping [PMID:36300302]. In zebrafish, loss of atp11a reduces stereocilia and sensory hair cells and impairs photoreceptor outer segments with mitochondrial fission defects, linking flippase activity to sensory cell maintenance and energy homeostasis [PMID:40223426]. Beyond its lipid-transport role, ATP11A is reported to bind the Numb PRRL isoform and promote epithelial-to-mesenchymal transition in pancreatic cancer cells [PMID:35345586].","teleology":[{"year":2005,"claim":"Before its biochemical activity was defined, ATP11A was linked to a cellular phenotype: its expression level modulates leukemia cell survival under targeted-drug pressure, establishing it as a functionally relevant gene.","evidence":"Overexpression and siRNA knockdown with drug sensitivity assays in Bcr/Abl-positive lymphoblastic leukemia cells","pmids":["15860663"],"confidence":"Medium","gaps":["No mechanism connecting ATP11A to drug resistance proposed","Flippase activity not yet established as the relevant function","No in vivo validation"]},{"year":2020,"claim":"Established that ATP11A requires its beta-subunit TMEM30A and specific transmembrane residues (Y300, D913) for both correct Golgi/plasma membrane trafficking and phosphatidylserine flippase activity, defining structural determinants of function.","evidence":"Mutagenesis, fluorescence localization, and PS flippase assays with TMEM30A co-expression","pmids":["32596364"],"confidence":"Medium","gaps":["Single-lab study","Mechanism by which residues couple transport to localization not resolved","No structural model"]},{"year":2021,"claim":"Defined the substrate specificity logic of ATP11A by showing it selectively flips phosphatidylserine and that a single Q84E mutation at the substrate entry site permits aberrant phosphatidylcholine flipping with downstream effects on membrane lipid composition and cell physiology.","evidence":"In vitro flippase assays, molecular dynamics simulations, MALDI-IMS, and a knockin mouse model","pmids":["34403372"],"confidence":"High","gaps":["Physiological context where Q84-type gain-of-function arises not defined","Full transport cycle structure not resolved"]},{"year":2022,"claim":"Showed that ATP11A flippase activity is developmentally essential, driving phosphatidylserine-dependent syncytiotrophoblast fusion in the placenta and being required for embryonic survival.","evidence":"Atp11a-null mouse embryos, histology, EM, TUNEL, and PS flippase/fusion assays in BeWo cells with siRNA","pmids":["35476530"],"confidence":"High","gaps":["Molecular link between PS exposure and the fusion machinery not detailed","Cause of cardiac ventricular defect not mechanistically resolved"]},{"year":2022,"claim":"Proposed a non-canonical role for ATP11A in cancer, binding the Numb PRRL isoform to drive a TGFβ-dependent Numb–ZEB1/Snail2 EMT program.","evidence":"Co-immunoprecipitation, Western blot, overexpression/knockdown and rescue, invasion/migration assays in pancreatic cancer cells","pmids":["35345586"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal validation","Whether the interaction depends on flippase activity is unknown","Direct versus indirect binding not established"]},{"year":2023,"claim":"Connected loss of ATP11A flippase activity to human auditory neuropathy, identifying a deletion that creates a cryptic last exon abolishing PtdSer transport and recapitulating the phenotype in conditional knockout mice.","evidence":"Whole-genome sequencing, in vitro flippase assay, immunohistochemistry, conditional KO mouse, and auditory electrophysiology","pmids":["36300302"],"confidence":"High","gaps":["How PS asymmetry loss leads to spiral ganglion neuron dysfunction not defined","Cell-autonomous versus systemic contribution not separated"]},{"year":2025,"claim":"Extended ATP11A's essential role to uterine biology, showing its loss disrupts epithelial tight junctions, gland progenitor specification, and receptivity, causing pregnancy failure.","evidence":"Conditional uterine knockout mouse, immunofluorescence, transcriptional profiling, morphological analysis","pmids":["40261925"],"confidence":"High","gaps":["Mechanism linking phospholipid asymmetry to junction and progenitor defects unresolved","Whether defects are flippase-dependent not formally tested"]},{"year":2025,"claim":"Demonstrated conservation of ATP11A's requirement in sensory cell and photoreceptor maintenance, linking its loss to defective stereocilia, hair cells, outer segments, and mitochondrial energy homeostasis.","evidence":"Loss-of-function zebrafish mutant with confocal/EM imaging and mitochondrial analysis","pmids":["40223426"],"confidence":"Medium","gaps":["Mechanistic link between flippase activity and mitochondrial fission unknown","Single-lab study","Whether mitochondrial phenotype is primary or secondary unclear"]},{"year":2024,"claim":"Reported that ATP11A promotes gastric cancer cell migration, invasion and EMT via Hippo pathway inactivation.","evidence":"Migration/invasion/proliferation assays and Western blot of EMT and Hippo markers with knockdown/overexpression in gastric cancer cells","pmids":["39247595"],"confidence":"Low","gaps":["No direct mechanistic link between flippase activity and Hippo signaling established","Single method set (pathway-marker Westerns)","No in vivo validation"]},{"year":null,"claim":"How ATP11A's phospholipid-flipping activity is mechanistically coupled to its diverse tissue-specific roles — EMT signaling, mitochondrial homeostasis, junction integrity, and neuronal function — remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No causal chain from membrane PS asymmetry to downstream signaling pathways","Whether cancer-associated functions require catalytic activity untested","No high-resolution structure of the ATP11A–TMEM30A complex"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,2]},{"term_id":"GO:0005215","term_label":"transporter activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,5]},{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0,1]}],"complexes":[],"partners":["TMEM30A","NUMB"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P98196","full_name":"Phospholipid-transporting ATPase IH","aliases":["ATPase IS","ATPase class VI type 11A","P4-ATPase flippase complex alpha subunit ATP11A"],"length_aa":1134,"mass_kda":129.8,"function":"Catalytic component of a P4-ATPase flippase complex which catalyzes the hydrolysis of ATP coupled to the transport of aminophospholipids, phosphatidylserines (PS) and phosphatidylethanolamines (PE), from the outer to the inner leaflet of the plasma membrane (PubMed:25315773, PubMed:25947375, PubMed:26567335, PubMed:29799007, PubMed:30018401, PubMed:36300302). Does not show flippase activity toward phosphatidylcholine (PC) (PubMed:34403372). Contributes to the maintenance of membrane lipid asymmetry with a specific role in morphogenesis of muscle cells. In myoblasts, mediates PS enrichment at the inner leaflet of plasma membrane, triggering PIEZO1-dependent Ca2+ influx and Rho GTPases signal transduction, subsequently leading to the assembly of cortical actomyosin fibers and myotube formation (PubMed:29799007). May be involved in the uptake of farnesyltransferase inhibitor drugs, such as lonafarnib","subcellular_location":"Cell membrane; Early endosome; Recycling endosome; Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/P98196/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP11A","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/ATP11A","total_profiled":1310},"omim":[{"mim_id":"620384","title":"AUDITORY NEUROPATHY, AUTOSOMAL DOMINANT 2; AUNA2","url":"https://www.omim.org/entry/620384"},{"mim_id":"619851","title":"LEUKODYSTROPHY, HYPOMYELINATING, 24; HLD24","url":"https://www.omim.org/entry/619851"},{"mim_id":"619810","title":"DEAFNESS, AUTOSOMAL DOMINANT 84; DFNA84","url":"https://www.omim.org/entry/619810"},{"mim_id":"614211","title":"DEAFNESS, AUTOSOMAL DOMINANT 33; DFNA33","url":"https://www.omim.org/entry/614211"},{"mim_id":"609129","title":"AUDITORY NEUROPATHY, AUTOSOMAL DOMINANT 1; AUNA1","url":"https://www.omim.org/entry/609129"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Vesicles","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATP11A"},"hgnc":{"alias_symbol":["ATPIH","ATPIS","KIAA1021"],"prev_symbol":[]},"alphafold":{"accession":"P98196","domains":[{"cath_id":"2.70.150.10","chopping":"147-279","consensus_level":"high","plddt":83.9486,"start":147,"end":279},{"cath_id":"-","chopping":"363-376_875-1121","consensus_level":"high","plddt":88.278,"start":363,"end":1121},{"cath_id":"3.40.50.1000","chopping":"396-420_667-736_756-859","consensus_level":"high","plddt":84.1865,"start":396,"end":859},{"cath_id":"3.40.1110.10","chopping":"428-446_468-487_512-665","consensus_level":"high","plddt":85.602,"start":428,"end":665}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P98196","model_url":"https://alphafold.ebi.ac.uk/files/AF-P98196-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P98196-F1-predicted_aligned_error_v6.png","plddt_mean":82.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP11A","jax_strain_url":"https://www.jax.org/strain/search?query=ATP11A"},"sequence":{"accession":"P98196","fasta_url":"https://rest.uniprot.org/uniprotkb/P98196.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P98196/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P98196"}},"corpus_meta":[{"pmid":"34403372","id":"PMC_34403372","title":"A sublethal ATP11A mutation associated with neurological deterioration causes aberrant phosphatidylcholine flipping in plasma membranes.","date":"2021","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/34403372","citation_count":37,"is_preprint":false},{"pmid":"20043114","id":"PMC_20043114","title":"ATP11A is a novel predictive marker for metachronous metastasis of colorectal cancer.","date":"2010","source":"Oncology reports","url":"https://pubmed.ncbi.nlm.nih.gov/20043114","citation_count":26,"is_preprint":false},{"pmid":"15860663","id":"PMC_15860663","title":"Resistance to farnesyltransferase inhibitors in Bcr/Abl-positive lymphoblastic leukemia by increased expression of a novel ABC transporter homolog ATP11a.","date":"2005","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/15860663","citation_count":26,"is_preprint":false},{"pmid":"35476530","id":"PMC_35476530","title":"Inefficient development of syncytiotrophoblasts in the Atp11a-deficient mouse placenta.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/35476530","citation_count":25,"is_preprint":false},{"pmid":"35278131","id":"PMC_35278131","title":"Autosomal dominant non-syndromic hearing loss maps to DFNA33 (13q34) and co-segregates with splice and frameshift variants in ATP11A, a phospholipid flippase gene.","date":"2022","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35278131","citation_count":19,"is_preprint":false},{"pmid":"35345586","id":"PMC_35345586","title":"ATP11A promotes EMT by regulating Numb PRRL in pancreatic cancer cells.","date":"2022","source":"PeerJ","url":"https://pubmed.ncbi.nlm.nih.gov/35345586","citation_count":15,"is_preprint":false},{"pmid":"36300302","id":"PMC_36300302","title":"A mutation in ATP11A causes autosomal-dominant auditory neuropathy type 2.","date":"2023","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36300302","citation_count":10,"is_preprint":false},{"pmid":"32596364","id":"PMC_32596364","title":"Disease Mutation Study Identifies Critical Residues for Phosphatidylserine Flippase ATP11A.","date":"2020","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/32596364","citation_count":6,"is_preprint":false},{"pmid":"40261925","id":"PMC_40261925","title":"Phospholipid flippase ATP11A brokers uterine epithelial integrity and function.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40261925","citation_count":4,"is_preprint":false},{"pmid":"32344036","id":"PMC_32344036","title":"Expression of three P4-phospholipid flippases-atp11a, atp11b, and atp11c in zebrafish (Danio rerio).","date":"2020","source":"Gene expression patterns : GEP","url":"https://pubmed.ncbi.nlm.nih.gov/32344036","citation_count":4,"is_preprint":false},{"pmid":"40185629","id":"PMC_40185629","title":"De novo heterozygous missense variants in ATP11A are associated with refractory focal epilepsy.","date":"2025","source":"Journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40185629","citation_count":4,"is_preprint":false},{"pmid":"33808877","id":"PMC_33808877","title":"DNA Methylation at ATP11A cg11702988 Is a Biomarker of Lung Disease Severity in Cystic Fibrosis: A Longitudinal Study.","date":"2021","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/33808877","citation_count":4,"is_preprint":false},{"pmid":"39247595","id":"PMC_39247595","title":"ATP11A Promotes Epithelial-mesenchymal Transition in Gastric Cancer Cells via the Hippo Pathway.","date":"2024","source":"Journal of Cancer","url":"https://pubmed.ncbi.nlm.nih.gov/39247595","citation_count":1,"is_preprint":false},{"pmid":"40223426","id":"PMC_40223426","title":"The P4-phospholipid flippase Atp11a is required for maintenance of eye and ear structure in zebrafish.","date":"2025","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/40223426","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.07.13.24310305","title":"Context-specific eQTLs reveal causal genes underlying shared genetic architecture of critically ill COVID-19 and idiopathic pulmonary fibrosis","date":"2024-07-14","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.13.24310305","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9520,"output_tokens":2481,"usd":0.032888,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9687,"output_tokens":3332,"usd":0.065867,"stage2_stop_reason":"end_turn"},"total_usd":0.098755,"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\": 2021,\n      \"finding\": \"ATP11A translocates phosphatidylserine (PtdSer), but not phosphatidylcholine (PtdCho), from the outer to the inner leaflet of plasma membranes, maintaining asymmetric PtdSer distribution. A Q84E substitution in the first transmembrane segment causes aberrant PtdCho flipping; molecular dynamics simulations showed this mutation allows PtdCho binding at the substrate entry site. Aberrant PtdCho flipping decreased PtdCho in the outer leaflet and increased sphingomyelin, altering cell growth, cholesterol homeostasis, and sensitivity to sphingomyelinase.\",\n      \"method\": \"In vitro flippase activity assays, molecular dynamics simulations, MALDI-IMS, knockin mouse model\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal methods including functional assay, structural simulation, mutagenesis, and in vivo mouse model in a single rigorous study\",\n      \"pmids\": [\"34403372\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ATP11A (and ATP11C) function as flippases at the plasma membrane to translocate phosphatidylserine from the outer to inner leaflet. Atp11a-null mouse embryos die at ~E14.5 with thin-walled heart ventricles. Atp11a is expressed in mouse placenta (but not Atp11c), and its loss causes poor development of the labyrinthine layer with unfused trophoblasts (syncytiotrophoblast formation failure). In BeWo cells, combined loss of ATP11A and ATP11C eliminated PS flipping and cell fusion upon forskolin treatment.\",\n      \"method\": \"Knockout mouse model, immunohistochemistry, electron microscopy, TUNEL assay, PS flippase assay in BeWo cells, siRNA knockdown\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO mouse with defined cellular phenotype, orthogonal methods (histology, EM, functional flippase assay), replicated in cell model\",\n      \"pmids\": [\"35476530\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ATP11A localizes to the Golgi and plasma membrane when co-expressed with its beta-subunit TMEM30A. Residues Y300 and D913 (corresponding to functionally critical residues in the related flippase ATP8A2) are required for correct Golgi/plasma membrane localization and PS flippase activity; Y300F mutation also reduces ATP11A expression levels.\",\n      \"method\": \"Mutagenesis, fluorescence microscopy (subcellular localization), PS flippase activity assay, co-expression with TMEM30A\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis plus functional flippase assay and localization, single lab study\",\n      \"pmids\": [\"32596364\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A 5500 bp deletion in ATP11A activates a cryptic splice site forming an alternative last exon, causing the altered C-terminus to lose flippase activity for phosphatidylserine. Atp11a is expressed in fibers and synaptic contacts of the auditory nerve and cochlear nucleus in mice; conditional Atp11a knockout mice show progressive reduction of spiral ganglion neuron compound action potential, recapitulating auditory neuropathy.\",\n      \"method\": \"Whole-genome sequencing, in vitro functional flippase assay, immunohistochemistry, conditional knockout mouse model, auditory electrophysiology\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — in vitro functional assay demonstrating loss of flippase activity, conditional KO mouse with defined electrophysiological phenotype, immunohistochemical localization, multiple orthogonal methods\",\n      \"pmids\": [\"36300302\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ATP11A binds specifically to the Numb PRRL isoform (by immunoprecipitation), positively regulates Numb PRRL, Snail2, and ZEB1 protein expression, and promotes epithelial-to-mesenchymal transition (EMT) in pancreatic cancer cells via a TGFβ-dependent Numb PRRL–ZEB1/Snail2 pathway. Knockdown of Numb PRRL suppresses the ATP11A-mediated enhancement of ZEB1/Snail2.\",\n      \"method\": \"Immunoprecipitation, Western blot, overexpression/knockdown, rescue assay, invasion/migration assays\",\n      \"journal\": \"PeerJ\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single Co-IP plus rescue experiments, single lab, multiple functional assays but no in vitro reconstitution\",\n      \"pmids\": [\"35345586\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Genetic ablation of Atp11a in mouse uterine epithelium causes loss of tight junctions, disrupted luminal epithelial morphology, incomplete luminal epithelial cell specification (retention of gland-restricted FOXA2 marker), and depletion of gland progenitor cells (SOX9, PAX8, LGR5, PROM1). This results in uterine receptivity deficits and frequent pregnancy failure. Heterozygous Atp11a loss increases incidence of abnormal placental trophoblast differentiation and developmental heart defects in embryos.\",\n      \"method\": \"Conditional knockout mouse, immunofluorescence, transcriptional profiling, morphological analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional KO with multiple defined cellular phenotypes and transcriptional readouts, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"40261925\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Loss-of-function atp11a mutant zebrafish display reduced stereocilia in the larval ear and reduced hair cells in sensory neuromasts. Photoreceptors in atp11a mutants show reduced outer segments (worsened by light exposure) and mitochondrial fission with increased mitochondrial number, suggesting defects in energy homeostasis.\",\n      \"method\": \"Loss-of-function zebrafish mutant, confocal microscopy, hair cell counting, electron/fluorescence microscopy of mitochondria\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean loss-of-function model with defined cellular phenotypes in multiple tissues, single lab\",\n      \"pmids\": [\"40223426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ATP11A promotes migration, invasion, proliferation, and EMT in gastric cancer cells by inactivating the Hippo pathway, as evidenced by changes in Hippo pathway markers upon ATP11A knockdown/overexpression.\",\n      \"method\": \"Transwell/wound healing/CCK8/colony formation assays, Western blot for EMT and Hippo pathway markers, siRNA knockdown and overexpression\",\n      \"journal\": \"Journal of Cancer\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method set (Western blot pathway markers), no direct mechanistic link between flippase activity and Hippo pathway established\",\n      \"pmids\": [\"39247595\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Overexpression of ATP11A confers protection of Bcr/Abl-positive lymphoblastic leukemia cells against farnesyltransferase inhibitors (SCH66336/lonafarnib, FTI-276, GGTI-298) and imatinib mesylate, while siRNA-mediated knockdown of endogenous ATP11A sensitizes cells to these drugs.\",\n      \"method\": \"Overexpression, siRNA knockdown, drug sensitivity assays\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — reciprocal gain- and loss-of-function experiments with clear drug sensitivity readout, single lab but bidirectional evidence\",\n      \"pmids\": [\"15860663\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATP11A is a P4-type ATPase flippase that, in complex with its beta-subunit TMEM30A, translocates phosphatidylserine (and phosphatidylethanolamine) from the outer to the inner leaflet of the plasma membrane to maintain phospholipid asymmetry; its substrate specificity is determined by transmembrane residues (notably Q84, Y300, D913), and its activity is required for syncytiotrophoblast formation in the placenta, spiral ganglion neuron function in the auditory system, uterine epithelial integrity, and photoreceptor/hair cell maintenance, while gain-of-function or loss-of-function mutations cause aberrant lipid distribution with downstream consequences for cell signaling, EMT, and neurological function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP11A is a P4-type ATPase phospholipid flippase that translocates phosphatidylserine from the outer to the inner leaflet of the plasma membrane to establish and maintain transbilayer lipid asymmetry [#0, #1]. Its substrate selectivity is dictated by transmembrane residues: a Q84E substitution opens the substrate entry site to phosphatidylcholine, producing aberrant PtdCho flipping that depletes outer-leaflet PtdCho, raises sphingomyelin, and perturbs cholesterol homeostasis and cell growth [#0], while residues Y300 and D913 are required for flippase activity and for correct Golgi and plasma membrane localization in complex with its beta-subunit TMEM30A [#2]. This flippase activity is developmentally essential across multiple tissues: ATP11A (with ATP11C) drives the phosphatidylserine exposure needed for syncytiotrophoblast fusion in the placental labyrinth, and Atp11a-null embryos die with thin-walled heart ventricles [#1]; conditional loss disrupts uterine epithelial integrity, gland progenitor specification, and pregnancy success [#5]; and it sustains spiral ganglion neurons of the auditory nerve, where loss-of-function causes auditory neuropathy in mice and humans carrying a splice-altering deletion that abolishes PtdSer flipping [#3]. In zebrafish, loss of atp11a reduces stereocilia and sensory hair cells and impairs photoreceptor outer segments with mitochondrial fission defects, linking flippase activity to sensory cell maintenance and energy homeostasis [#6]. Beyond its lipid-transport role, ATP11A is reported to bind the Numb PRRL isoform and promote epithelial-to-mesenchymal transition in pancreatic cancer cells [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Before its biochemical activity was defined, ATP11A was linked to a cellular phenotype: its expression level modulates leukemia cell survival under targeted-drug pressure, establishing it as a functionally relevant gene.\",\n      \"evidence\": \"Overexpression and siRNA knockdown with drug sensitivity assays in Bcr/Abl-positive lymphoblastic leukemia cells\",\n      \"pmids\": [\"15860663\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No mechanism connecting ATP11A to drug resistance proposed\", \"Flippase activity not yet established as the relevant function\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established that ATP11A requires its beta-subunit TMEM30A and specific transmembrane residues (Y300, D913) for both correct Golgi/plasma membrane trafficking and phosphatidylserine flippase activity, defining structural determinants of function.\",\n      \"evidence\": \"Mutagenesis, fluorescence localization, and PS flippase assays with TMEM30A co-expression\",\n      \"pmids\": [\"32596364\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study\", \"Mechanism by which residues couple transport to localization not resolved\", \"No structural model\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the substrate specificity logic of ATP11A by showing it selectively flips phosphatidylserine and that a single Q84E mutation at the substrate entry site permits aberrant phosphatidylcholine flipping with downstream effects on membrane lipid composition and cell physiology.\",\n      \"evidence\": \"In vitro flippase assays, molecular dynamics simulations, MALDI-IMS, and a knockin mouse model\",\n      \"pmids\": [\"34403372\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological context where Q84-type gain-of-function arises not defined\", \"Full transport cycle structure not resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed that ATP11A flippase activity is developmentally essential, driving phosphatidylserine-dependent syncytiotrophoblast fusion in the placenta and being required for embryonic survival.\",\n      \"evidence\": \"Atp11a-null mouse embryos, histology, EM, TUNEL, and PS flippase/fusion assays in BeWo cells with siRNA\",\n      \"pmids\": [\"35476530\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link between PS exposure and the fusion machinery not detailed\", \"Cause of cardiac ventricular defect not mechanistically resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Proposed a non-canonical role for ATP11A in cancer, binding the Numb PRRL isoform to drive a TGFβ-dependent Numb–ZEB1/Snail2 EMT program.\",\n      \"evidence\": \"Co-immunoprecipitation, Western blot, overexpression/knockdown and rescue, invasion/migration assays in pancreatic cancer cells\",\n      \"pmids\": [\"35345586\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP without reciprocal validation\", \"Whether the interaction depends on flippase activity is unknown\", \"Direct versus indirect binding not established\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected loss of ATP11A flippase activity to human auditory neuropathy, identifying a deletion that creates a cryptic last exon abolishing PtdSer transport and recapitulating the phenotype in conditional knockout mice.\",\n      \"evidence\": \"Whole-genome sequencing, in vitro flippase assay, immunohistochemistry, conditional KO mouse, and auditory electrophysiology\",\n      \"pmids\": [\"36300302\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How PS asymmetry loss leads to spiral ganglion neuron dysfunction not defined\", \"Cell-autonomous versus systemic contribution not separated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended ATP11A's essential role to uterine biology, showing its loss disrupts epithelial tight junctions, gland progenitor specification, and receptivity, causing pregnancy failure.\",\n      \"evidence\": \"Conditional uterine knockout mouse, immunofluorescence, transcriptional profiling, morphological analysis\",\n      \"pmids\": [\"40261925\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking phospholipid asymmetry to junction and progenitor defects unresolved\", \"Whether defects are flippase-dependent not formally tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated conservation of ATP11A's requirement in sensory cell and photoreceptor maintenance, linking its loss to defective stereocilia, hair cells, outer segments, and mitochondrial energy homeostasis.\",\n      \"evidence\": \"Loss-of-function zebrafish mutant with confocal/EM imaging and mitochondrial analysis\",\n      \"pmids\": [\"40223426\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic link between flippase activity and mitochondrial fission unknown\", \"Single-lab study\", \"Whether mitochondrial phenotype is primary or secondary unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Reported that ATP11A promotes gastric cancer cell migration, invasion and EMT via Hippo pathway inactivation.\",\n      \"evidence\": \"Migration/invasion/proliferation assays and Western blot of EMT and Hippo markers with knockdown/overexpression in gastric cancer cells\",\n      \"pmids\": [\"39247595\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct mechanistic link between flippase activity and Hippo signaling established\", \"Single method set (pathway-marker Westerns)\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ATP11A's phospholipid-flipping activity is mechanistically coupled to its diverse tissue-specific roles — EMT signaling, mitochondrial homeostasis, junction integrity, and neuronal function — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No causal chain from membrane PS asymmetry to downstream signaling pathways\", \"Whether cancer-associated functions require catalytic activity untested\", \"No high-resolution structure of the ATP11A–TMEM30A complex\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0005215\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 5]},\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TMEM30A\", \"NUMB\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}