{"gene":"ACP2","run_date":"2026-06-09T22:02:39","timeline":{"discoveries":[{"year":2011,"finding":"Acp2 (lysosomal acid phosphatase 2) acts in concert with Acp5 to dephosphorylate mannose 6-phosphate (Man6P) residues on lysosomal proteins; mice deficient in both Acp2 and Acp5 show accumulation of Man6P-containing proteins in lysosomes. The most abundant substrates identified include Npc2; failure to dephosphorylate Npc2 alters its isoelectric point (ranging 7.0–5.4 depending on phosphatase presence), regulating its interaction with negatively charged lysosomal membranes at acidic pH, and resulting in unesterified cholesterol accumulation in lysosomes of Acp2/Acp5-deficient hepatocytes.","method":"Knockout mouse models (Acp2−/−, Acp5−/−, Acp2/Acp5−/−), 2D Man6P immunoblot analysis, Man6P affinity chromatography, mass spectrometry, cultured hepatocyte lipid analysis","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KO mice, affinity chromatography, MS, immunoblot) in a single rigorous study establishing substrate identity and functional consequence","pmids":["22158965"],"is_preprint":false},{"year":2004,"finding":"A missense mutation (Gly244Glu) in Acp2 renders the lysosomal acid phosphatase enzymatically inactive without affecting transcript stability, causing lysosomal storage body accumulation in cerebellar nucleated cells and leading to disrupted cerebellar cortex cytoarchitecture (loss of granule cell layer, misaligned Purkinje cells, disorganized Bergmann glia) and abnormal hair follicles in nax mice.","method":"Positional cloning, Sanger sequencing, histological analysis, ultrastructural (electron microscopy) analysis of nax mutant mice","journal":"Neurogenetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — positional cloning with missense mutation identification, enzymatic inactivity confirmed, and cellular phenotype established by histology and ultrastructure","pmids":["15503243"],"is_preprint":false},{"year":2017,"finding":"ACP2 is required for the membrane fusion step during influenza A virus entry into host cells. ACP2 knockdown (siRNA) did not affect viral binding to the cell surface or endosomal acidification, but specifically impaired fusion of endosomal and viral membranes, blocking downstream nucleocapsid uncoating and nuclear import of viral ribonucleoproteins. This requirement was specific to influenza viruses (including seasonal A/B and avian H7 subtypes) and was not observed for Ebola or hepatitis C virus.","method":"siRNA knockdown, viral replication assays (multi-cycle growth), viral protein/mRNA quantification, membrane fusion assays, endosomal acidification assay, nuclear import assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA-based KD with multiple orthogonal functional readouts (fusion, uncoating, nuclear import) in a single lab study","pmids":["28272419"],"is_preprint":false},{"year":1995,"finding":"The rat liver low-Mr phosphotyrosine protein phosphatase isoenzyme AcP2 is specifically activated by cGMP (and guanosine), an effect not shared by isoenzyme AcP1. Kinetic analysis showed that cGMP increases the rate of hydrolysis of the covalent enzyme-substrate phosphorylated intermediate formed during catalysis of p-nitrophenyl phosphate hydrolysis.","method":"Kinetic enzyme assays with p-nitrophenyl phosphate substrate, testing heterocyclic compound effects on AcP1 and AcP2 isoenzymes","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro kinetic assay with mechanistic resolution of covalent intermediate step, but single lab and this isoenzyme designation may refer to a different acid phosphatase (low-Mr cytosolic type, not lysosomal ACP2)","pmids":["7827101"],"is_preprint":false},{"year":2021,"finding":"In Acp2 mutant (nax) mice, cerebellar granule cell proliferation is severely reduced. This is associated with downregulation of MYCN protein (at P10) and dysregulation of the SHH signaling pathway, as well as impairment of the protein synthesis machinery, suggesting that Acp2 loss broadly disrupts molecular pathways governing granule cell clonal expansion beyond the SHH-MYCN axis alone.","method":"In vivo/in vitro immunohistochemistry, Western blotting, BrdU proliferation assays, RT-qPCR in nax mutant mice","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (IHC, WB, BrdU, qPCR) in nax KO model, single lab","pmids":["33804256"],"is_preprint":false},{"year":2024,"finding":"Knockdown of ACP2 by siRNA increases VSV∆51 oncolytic virus titers by over 20-fold. RNA sequencing revealed that ACP2 regulates antiviral type I interferon (IFN-1) signaling pathways; its knockdown suppresses IFN-1 responses, thereby enhancing oncolytic virus replication.","method":"High-throughput siRNA screen, viral titer assays, RNA sequencing (in silico pathway analysis), shRNA-encoding engineered virus construct","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — high-throughput screen hit with viral titer validation and in silico pathway analysis, single lab, mechanism inferred from transcriptomics rather than direct functional assay","pmids":["39550388"],"is_preprint":false}],"current_model":"ACP2 encodes a lysosomal acid phosphatase that acts together with ACP5 to dephosphorylate mannose 6-phosphate residues on lysosomal cargo proteins (including Npc2), thereby regulating their charge, membrane interactions, and cholesterol homeostasis; loss-of-function mutations abolish enzymatic activity and cause lysosomal storage, disrupted cerebellar cortex development (impaired granule cell proliferation via the SHH-MYCN axis), and abnormal hair follicle morphology; additionally, ACP2 is required in host cells for the membrane fusion step of influenza virus entry and modulates type I interferon signaling."},"narrative":{"mechanistic_narrative":"ACP2 encodes a lysosomal acid phosphatase that, acting in concert with ACP5, dephosphorylates mannose 6-phosphate (Man6P) residues on lysosomal proteins; combined Acp2/Acp5 deficiency causes accumulation of Man6P-containing proteins in lysosomes [PMID:22158965]. A principal substrate is Npc2, whose dephosphorylation by ACP2/ACP5 shifts its isoelectric point and governs its interaction with negatively charged lysosomal membranes at acidic pH, with loss of this activity producing unesterified cholesterol accumulation in lysosomes [PMID:22158965]. The enzymatic activity is essential for organ development: a Gly244Glu missense mutation abolishes catalytic activity without affecting transcript stability, producing lysosomal storage and disrupting cerebellar cortex architecture and hair follicle morphology in nax mice [PMID:15503243], and Acp2 loss severely reduces cerebellar granule cell proliferation in association with downregulation of MYCN and dysregulation of SHH signaling [PMID:33804256]. Beyond its lysosomal role, ACP2 is required in host cells for the membrane fusion step of influenza A virus entry, acting downstream of binding and endosomal acidification to permit viral membrane fusion, uncoating, and nuclear import of viral ribonucleoproteins [PMID:28272419].","teleology":[{"year":1995,"claim":"Established that a phosphatase activity designated AcP2 is differentially regulated by cGMP, resolving a catalytic step at which regulation acts.","evidence":"in vitro kinetic enzyme assays with p-nitrophenyl phosphate, comparing AcP1 and AcP2 isoenzymes","pmids":["7827101"],"confidence":"Medium","gaps":["This isoenzyme designation may refer to a low-Mr cytosolic phosphatase rather than lysosomal ACP2","No link established to lysosomal substrates or in vivo function"]},{"year":2004,"claim":"Demonstrated that ACP2 enzymatic activity is required for lysosomal homeostasis and tissue architecture, by showing a catalytically inactivating mutation causes storage pathology and developmental defects.","evidence":"positional cloning and Sanger sequencing of nax mutant mice with histological and ultrastructural analysis","pmids":["15503243"],"confidence":"High","gaps":["Did not identify the substrates whose accumulation drives pathology","Mechanism linking storage to cerebellar disorganization unresolved"]},{"year":2011,"claim":"Identified the molecular substrates and biochemical consequence of ACP2 activity, showing it dephosphorylates Man6P on lysosomal proteins including Npc2 to control membrane interaction and cholesterol handling.","evidence":"single, double, and combined Acp2/Acp5 knockout mice with Man6P affinity chromatography, mass spectrometry, 2D immunoblot, and hepatocyte lipid analysis","pmids":["22158965"],"confidence":"High","gaps":["Relative contributions of ACP2 versus ACP5 to individual substrates not fully separated","Does not connect Npc2 dephosphorylation to the cerebellar developmental phenotype"]},{"year":2017,"claim":"Revealed a non-lysosomal-cargo function: ACP2 is specifically required for the membrane fusion step of influenza virus entry, distinguishing fusion from binding and acidification.","evidence":"siRNA knockdown with membrane fusion, endosomal acidification, uncoating, and nuclear import assays","pmids":["28272419"],"confidence":"Medium","gaps":["Molecular target of ACP2 phosphatase activity in the fusion step not identified","siRNA-based, single-lab study without genetic rescue"]},{"year":2021,"claim":"Connected ACP2 loss to a developmental signaling program, showing reduced granule cell proliferation accompanied by MYCN downregulation and SHH pathway dysregulation.","evidence":"immunohistochemistry, Western blot, BrdU proliferation assays, and RT-qPCR in nax mutant mice","pmids":["33804256"],"confidence":"Medium","gaps":["Causal link between lysosomal dysfunction and SHH-MYCN dysregulation not mechanistically demonstrated","Single-lab correlative findings"]},{"year":2024,"claim":"Implicated ACP2 in antiviral interferon signaling, with knockdown suppressing type I IFN responses and enhancing oncolytic virus replication.","evidence":"high-throughput siRNA screen with viral titer assays and RNA sequencing pathway analysis","pmids":["39550388"],"confidence":"Low","gaps":["Mechanism inferred from transcriptomics rather than direct functional assay","No molecular target in the IFN-1 pathway identified","Single-lab screen hit"]},{"year":null,"claim":"How ACP2's lysosomal phosphatase activity mechanistically connects to its roles in viral entry, interferon signaling, and SHH-MYCN-driven cerebellar development remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified substrate explains the non-lysosomal phenotypes","Direct phosphatase targets in viral fusion and IFN pathways unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1266738","term_label":"Developmental Biology","supporting_discovery_ids":[1,4]}],"complexes":[],"partners":["ACP5"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P11117","full_name":"Lysosomal acid phosphatase","aliases":[],"length_aa":423,"mass_kda":48.3,"function":"","subcellular_location":"Lysosome membrane; Lysosome lumen","url":"https://www.uniprot.org/uniprotkb/P11117/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ACP2","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CANX","stoichiometry":0.2},{"gene":"LAMP1","stoichiometry":0.2},{"gene":"STX7","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ACP2","total_profiled":1310},"omim":[{"mim_id":"619732","title":"2-@PHOSPHOXYLOSE PHOSPHATASE 1; PXYLP1","url":"https://www.omim.org/entry/619732"},{"mim_id":"616155","title":"CHARCOT-MARIE-TOOTH DISEASE, AXONAL, TYPE 2S; CMT2S","url":"https://www.omim.org/entry/616155"},{"mim_id":"612034","title":"APC2 REGULATOR OF WNT SIGNALING PATHWAY 2; APC2","url":"https://www.omim.org/entry/612034"},{"mim_id":"610898","title":"SUPRANUCLEAR PALSY, PROGRESSIVE, 3; PSNP3","url":"https://www.omim.org/entry/610898"},{"mim_id":"606362","title":"ACID PHOSPHATASE 4; ACP4","url":"https://www.omim.org/entry/606362"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ACP2"},"hgnc":{"alias_symbol":["LAP"],"prev_symbol":[]},"alphafold":{"accession":"P11117","domains":[{"cath_id":"3.40.50.1240","chopping":"33-157_250-362","consensus_level":"high","plddt":97.1622,"start":33,"end":362}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P11117","model_url":"https://alphafold.ebi.ac.uk/files/AF-P11117-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P11117-F1-predicted_aligned_error_v6.png","plddt_mean":91.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ACP2","jax_strain_url":"https://www.jax.org/strain/search?query=ACP2"},"sequence":{"accession":"P11117","fasta_url":"https://rest.uniprot.org/uniprotkb/P11117.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P11117/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P11117"}},"corpus_meta":[{"pmid":"730175","id":"PMC_730175","title":"Regional mapping of the gene for human lysosomal acid phosphatase (ACP2) using a hybrid clone panel containing segments of human chromosome 11.","date":"1978","source":"Human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/730175","citation_count":49,"is_preprint":false},{"pmid":"22158965","id":"PMC_22158965","title":"Mannose 6 dephosphorylation of lysosomal proteins mediated by acid phosphatases Acp2 and Acp5.","date":"2011","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22158965","citation_count":44,"is_preprint":false},{"pmid":"15503243","id":"PMC_15503243","title":"Mutation in the gene encoding lysosomal acid phosphatase (Acp2) causes cerebellum and skin malformation in mouse.","date":"2004","source":"Neurogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/15503243","citation_count":39,"is_preprint":false},{"pmid":"2835668","id":"PMC_2835668","title":"The Saccharomyces cerevisiae ACP2 gene encodes an essential HMG1-like protein.","date":"1988","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/2835668","citation_count":35,"is_preprint":false},{"pmid":"23780826","id":"PMC_23780826","title":"Spatial and temporal expression of lysosomal acid phosphatase 2 (ACP2) reveals dynamic patterning of the mouse cerebellar cortex.","date":"2013","source":"Cerebellum (London, England)","url":"https://pubmed.ncbi.nlm.nih.gov/23780826","citation_count":20,"is_preprint":false},{"pmid":"24258481","id":"PMC_24258481","title":"Chromosome localization of the genes for ENO1, HK1, ADK, ACP2, MPI, ITPA, ACON1 and α-GAL in the American mink (Mustela vison).","date":"1983","source":"TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik","url":"https://pubmed.ncbi.nlm.nih.gov/24258481","citation_count":19,"is_preprint":false},{"pmid":"3007037","id":"PMC_3007037","title":"Chromosomal mapping of enzyme loci in the domestic cat: GSR to C2, ADA and ITPA to A3, and LDHA-ACP2 to D1.","date":"1986","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/3007037","citation_count":19,"is_preprint":false},{"pmid":"7827101","id":"PMC_7827101","title":"Kinetic studies on rat liver low M(r) phosphotyrosine protein phosphatases. The activation mechanism of the isoenzyme AcP2 by cGMP.","date":"1995","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/7827101","citation_count":19,"is_preprint":false},{"pmid":"28272419","id":"PMC_28272419","title":"Acid phosphatase 2 (ACP2) is required for membrane fusion during influenza virus entry.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/28272419","citation_count":13,"is_preprint":false},{"pmid":"3964226","id":"PMC_3964226","title":"Genetic variation of an acid phosphatase (Acp-2) in the laboratory rat: possible homology with mouse AP-1 and human ACP2.","date":"1986","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/3964226","citation_count":11,"is_preprint":false},{"pmid":"9787802","id":"PMC_9787802","title":"Genetic polymorphism of rabbit (Oryctolagus cuniculus) tissue acid phosphatases (ACP2 and ACP3).","date":"1998","source":"Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9787802","citation_count":8,"is_preprint":false},{"pmid":"33804256","id":"PMC_33804256","title":"Reduced Granule Cell Proliferation and Molecular Dysregulation in the Cerebellum of Lysosomal Acid Phosphatase 2 (ACP2) Mutant Mice.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/33804256","citation_count":6,"is_preprint":false},{"pmid":"39550388","id":"PMC_39550388","title":"High throughput screen identifies lysosomal acid phosphatase 2 (ACP2) to regulate IFN-1 responses to potentiate oncolytic VSV∆51 activity.","date":"2024","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39550388","citation_count":3,"is_preprint":false},{"pmid":"38310198","id":"PMC_38310198","title":"Comprehensive Analysis and Experimental Validation of the Parkinson's Disease Lysosomal Gene ACP2 and Pan-cancer.","date":"2024","source":"Biochemical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38310198","citation_count":2,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.29.685293","title":"Transcriptional condensates at super-enhancers mediate pH-dependent transcriptional control in innate immunity","date":"2025-10-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.29.685293","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8394,"output_tokens":1864,"usd":0.026571,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8786,"output_tokens":2286,"usd":0.05054,"stage2_stop_reason":"end_turn"},"total_usd":0.077111,"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\": 2011,\n      \"finding\": \"Acp2 (lysosomal acid phosphatase 2) acts in concert with Acp5 to dephosphorylate mannose 6-phosphate (Man6P) residues on lysosomal proteins; mice deficient in both Acp2 and Acp5 show accumulation of Man6P-containing proteins in lysosomes. The most abundant substrates identified include Npc2; failure to dephosphorylate Npc2 alters its isoelectric point (ranging 7.0–5.4 depending on phosphatase presence), regulating its interaction with negatively charged lysosomal membranes at acidic pH, and resulting in unesterified cholesterol accumulation in lysosomes of Acp2/Acp5-deficient hepatocytes.\",\n      \"method\": \"Knockout mouse models (Acp2−/−, Acp5−/−, Acp2/Acp5−/−), 2D Man6P immunoblot analysis, Man6P affinity chromatography, mass spectrometry, cultured hepatocyte lipid analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KO mice, affinity chromatography, MS, immunoblot) in a single rigorous study establishing substrate identity and functional consequence\",\n      \"pmids\": [\"22158965\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"A missense mutation (Gly244Glu) in Acp2 renders the lysosomal acid phosphatase enzymatically inactive without affecting transcript stability, causing lysosomal storage body accumulation in cerebellar nucleated cells and leading to disrupted cerebellar cortex cytoarchitecture (loss of granule cell layer, misaligned Purkinje cells, disorganized Bergmann glia) and abnormal hair follicles in nax mice.\",\n      \"method\": \"Positional cloning, Sanger sequencing, histological analysis, ultrastructural (electron microscopy) analysis of nax mutant mice\",\n      \"journal\": \"Neurogenetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — positional cloning with missense mutation identification, enzymatic inactivity confirmed, and cellular phenotype established by histology and ultrastructure\",\n      \"pmids\": [\"15503243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"ACP2 is required for the membrane fusion step during influenza A virus entry into host cells. ACP2 knockdown (siRNA) did not affect viral binding to the cell surface or endosomal acidification, but specifically impaired fusion of endosomal and viral membranes, blocking downstream nucleocapsid uncoating and nuclear import of viral ribonucleoproteins. This requirement was specific to influenza viruses (including seasonal A/B and avian H7 subtypes) and was not observed for Ebola or hepatitis C virus.\",\n      \"method\": \"siRNA knockdown, viral replication assays (multi-cycle growth), viral protein/mRNA quantification, membrane fusion assays, endosomal acidification assay, nuclear import assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA-based KD with multiple orthogonal functional readouts (fusion, uncoating, nuclear import) in a single lab study\",\n      \"pmids\": [\"28272419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"The rat liver low-Mr phosphotyrosine protein phosphatase isoenzyme AcP2 is specifically activated by cGMP (and guanosine), an effect not shared by isoenzyme AcP1. Kinetic analysis showed that cGMP increases the rate of hydrolysis of the covalent enzyme-substrate phosphorylated intermediate formed during catalysis of p-nitrophenyl phosphate hydrolysis.\",\n      \"method\": \"Kinetic enzyme assays with p-nitrophenyl phosphate substrate, testing heterocyclic compound effects on AcP1 and AcP2 isoenzymes\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro kinetic assay with mechanistic resolution of covalent intermediate step, but single lab and this isoenzyme designation may refer to a different acid phosphatase (low-Mr cytosolic type, not lysosomal ACP2)\",\n      \"pmids\": [\"7827101\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In Acp2 mutant (nax) mice, cerebellar granule cell proliferation is severely reduced. This is associated with downregulation of MYCN protein (at P10) and dysregulation of the SHH signaling pathway, as well as impairment of the protein synthesis machinery, suggesting that Acp2 loss broadly disrupts molecular pathways governing granule cell clonal expansion beyond the SHH-MYCN axis alone.\",\n      \"method\": \"In vivo/in vitro immunohistochemistry, Western blotting, BrdU proliferation assays, RT-qPCR in nax mutant mice\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (IHC, WB, BrdU, qPCR) in nax KO model, single lab\",\n      \"pmids\": [\"33804256\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Knockdown of ACP2 by siRNA increases VSV∆51 oncolytic virus titers by over 20-fold. RNA sequencing revealed that ACP2 regulates antiviral type I interferon (IFN-1) signaling pathways; its knockdown suppresses IFN-1 responses, thereby enhancing oncolytic virus replication.\",\n      \"method\": \"High-throughput siRNA screen, viral titer assays, RNA sequencing (in silico pathway analysis), shRNA-encoding engineered virus construct\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — high-throughput screen hit with viral titer validation and in silico pathway analysis, single lab, mechanism inferred from transcriptomics rather than direct functional assay\",\n      \"pmids\": [\"39550388\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ACP2 encodes a lysosomal acid phosphatase that acts together with ACP5 to dephosphorylate mannose 6-phosphate residues on lysosomal cargo proteins (including Npc2), thereby regulating their charge, membrane interactions, and cholesterol homeostasis; loss-of-function mutations abolish enzymatic activity and cause lysosomal storage, disrupted cerebellar cortex development (impaired granule cell proliferation via the SHH-MYCN axis), and abnormal hair follicle morphology; additionally, ACP2 is required in host cells for the membrane fusion step of influenza virus entry and modulates type I interferon signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ACP2 encodes a lysosomal acid phosphatase that, acting in concert with ACP5, dephosphorylates mannose 6-phosphate (Man6P) residues on lysosomal proteins; combined Acp2/Acp5 deficiency causes accumulation of Man6P-containing proteins in lysosomes [#0]. A principal substrate is Npc2, whose dephosphorylation by ACP2/ACP5 shifts its isoelectric point and governs its interaction with negatively charged lysosomal membranes at acidic pH, with loss of this activity producing unesterified cholesterol accumulation in lysosomes [#0]. The enzymatic activity is essential for organ development: a Gly244Glu missense mutation abolishes catalytic activity without affecting transcript stability, producing lysosomal storage and disrupting cerebellar cortex architecture and hair follicle morphology in nax mice [#1], and Acp2 loss severely reduces cerebellar granule cell proliferation in association with downregulation of MYCN and dysregulation of SHH signaling [#4]. Beyond its lysosomal role, ACP2 is required in host cells for the membrane fusion step of influenza A virus entry, acting downstream of binding and endosomal acidification to permit viral membrane fusion, uncoating, and nuclear import of viral ribonucleoproteins [#2].\",\n  \"teleology\": [\n    {\n      \"year\": 1995,\n      \"claim\": \"Established that a phosphatase activity designated AcP2 is differentially regulated by cGMP, resolving a catalytic step at which regulation acts.\",\n      \"evidence\": \"in vitro kinetic enzyme assays with p-nitrophenyl phosphate, comparing AcP1 and AcP2 isoenzymes\",\n      \"pmids\": [\"7827101\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"This isoenzyme designation may refer to a low-Mr cytosolic phosphatase rather than lysosomal ACP2\", \"No link established to lysosomal substrates or in vivo function\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrated that ACP2 enzymatic activity is required for lysosomal homeostasis and tissue architecture, by showing a catalytically inactivating mutation causes storage pathology and developmental defects.\",\n      \"evidence\": \"positional cloning and Sanger sequencing of nax mutant mice with histological and ultrastructural analysis\",\n      \"pmids\": [\"15503243\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the substrates whose accumulation drives pathology\", \"Mechanism linking storage to cerebellar disorganization unresolved\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identified the molecular substrates and biochemical consequence of ACP2 activity, showing it dephosphorylates Man6P on lysosomal proteins including Npc2 to control membrane interaction and cholesterol handling.\",\n      \"evidence\": \"single, double, and combined Acp2/Acp5 knockout mice with Man6P affinity chromatography, mass spectrometry, 2D immunoblot, and hepatocyte lipid analysis\",\n      \"pmids\": [\"22158965\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of ACP2 versus ACP5 to individual substrates not fully separated\", \"Does not connect Npc2 dephosphorylation to the cerebellar developmental phenotype\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed a non-lysosomal-cargo function: ACP2 is specifically required for the membrane fusion step of influenza virus entry, distinguishing fusion from binding and acidification.\",\n      \"evidence\": \"siRNA knockdown with membrane fusion, endosomal acidification, uncoating, and nuclear import assays\",\n      \"pmids\": [\"28272419\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular target of ACP2 phosphatase activity in the fusion step not identified\", \"siRNA-based, single-lab study without genetic rescue\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected ACP2 loss to a developmental signaling program, showing reduced granule cell proliferation accompanied by MYCN downregulation and SHH pathway dysregulation.\",\n      \"evidence\": \"immunohistochemistry, Western blot, BrdU proliferation assays, and RT-qPCR in nax mutant mice\",\n      \"pmids\": [\"33804256\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal link between lysosomal dysfunction and SHH-MYCN dysregulation not mechanistically demonstrated\", \"Single-lab correlative findings\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated ACP2 in antiviral interferon signaling, with knockdown suppressing type I IFN responses and enhancing oncolytic virus replication.\",\n      \"evidence\": \"high-throughput siRNA screen with viral titer assays and RNA sequencing pathway analysis\",\n      \"pmids\": [\"39550388\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Mechanism inferred from transcriptomics rather than direct functional assay\", \"No molecular target in the IFN-1 pathway identified\", \"Single-lab screen hit\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ACP2's lysosomal phosphatase activity mechanistically connects to its roles in viral entry, interferon signaling, and SHH-MYCN-driven cerebellar development remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified substrate explains the non-lysosomal phenotypes\", \"Direct phosphatase targets in viral fusion and IFN pathways unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1266738\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ACP5\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":4,"faith_pct":75.0}}