{"gene":"LSM12","run_date":"2026-06-10T02:59:50","timeline":{"discoveries":[{"year":2021,"finding":"LSM12 directly binds NAADP via its Lsm domain, colocalizes with TPC2, and is essential for NAADP-evoked TPC activation and Ca2+ mobilization from acidic endolysosomal organelles. LSM12 was identified as complexed with NAADP, TPC1, and TPC2 by affinity purification and quantitative proteomic analysis.","method":"Affinity purification, quantitative proteomics, co-immunoprecipitation, colocalization imaging, functional Ca2+ mobilization assays, knockdown/knockout","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (affinity purification, proteomics, direct binding assay, colocalization, functional Ca2+ assay, knockdown), replicated by subsequent independent labs","pmids":["34362892"],"is_preprint":false},{"year":2023,"finding":"Recombinant LSM12 binds NAADP with high affinity and endogenous LSM12 independently associates with TPC1 and TPC2; LSM12 is required (alongside JPT2) for NAADP-evoked Ca2+ signaling and endolysosomal trafficking of pseudotyped coronavirus particles in human cells.","method":"Recombinant protein binding assays, co-immunoprecipitation of endogenous proteins, knockout and rescue analyses, functional Ca2+ imaging","journal":"Science signaling","confidence":"High","confidence_rationale":"Tier 2 / Strong — independent lab replication with biochemical binding assays, reciprocal co-IP, and functional knockout/rescue experiments","pmids":["37607218"],"is_preprint":false},{"year":2026,"finding":"LSM12 acts as a potent antagonist of PI(3,5)P2-dependent TPC activation: purified LSM12 strongly inhibits PI(3,5)P2-evoked TPC1 and TPC2 currents, reduces TPC2 apparent sensitivity to PI(3,5)P2 via a competitive mechanism dependent on Lsm12-TPC interaction, and NAADP binding to LSM12 specifically and dose-dependently reverses this inhibition to permit TPC channel activation.","method":"Electrophysiology (channel currents), purified recombinant protein, endogenous knockdown, acute PI(3,5)P2 sequestration, Ca2+ imaging","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified protein and electrophysiology plus cellular functional assays, but preprint not yet peer-reviewed","pmids":["42039649"],"is_preprint":true},{"year":2017,"finding":"Drosophila LSM12 acts as a molecular adaptor for recruitment of TWENTY-FOUR (TYF) to the ATAXIN-2 (ATX2) complex; the ATX2-LSM12-TYF complex stimulates TYF-dependent translation of the clock gene period (per) to maintain 24-hr circadian periodicity.","method":"Genetic interaction/epistasis analysis, co-immunoprecipitation, behavioral rhythmicity assays, loss-of-function","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP establishing complex membership, genetic epistasis placing LSM12 in pathway, and functional behavioral readout; published in high-impact peer-reviewed journal","pmids":["28388438"],"is_preprint":false},{"year":2020,"finding":"LSM12 posttranscriptionally upregulates EPAC1 expression; the LSM12-EPAC1 pathway sustains the nucleocytoplasmic RAN gradient and suppresses NCT dysfunction caused by C9ORF72-derived poly(GR) protein. LSM12 depletion aggravates poly(GR)-induced NCT impairment and promotes nuclear accumulation of poly(GR) granules.","method":"siRNA knockdown in human neuroblastoma cells, lentiviral overexpression in C9-ALS iPSC-derived neurons, RAN gradient measurement, TDP-43 localization assay, caspase-3 activation assay","journal":"PLoS biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with specific molecular readouts (RAN gradient, NCT) and rescue experiments, single lab","pmids":["33362237"],"is_preprint":false},{"year":2010,"finding":"Yeast Lsm12 localizes to stress granules (but not constitutively to P-bodies). Deletion or overexpression of Lsm12 does not dramatically affect stress granule or P-body formation. Lsm12 physically interacts with the Pbp1 protein (yeast ortholog of Ataxin-2).","method":"Fluorescence microscopy (live imaging), genetic deletion, overexpression, stress granule formation assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — direct localization by imaging, genetic perturbation with defined cellular readout, and physical interaction via known pulldown data; multiple observations in one study","pmids":["20368989"],"is_preprint":false},{"year":2018,"finding":"Yeast Lsm12 physically interacts with the UBZ domain of DNA polymerase η (Polη/Rad30) and enhances Polη deubiquitination through Ubp3, thereby promoting Polη recruitment under oxidative stress.","method":"Co-immunoprecipitation (physical interaction), gene deletion/overexpression, ubiquitination assays, transcriptome analysis","journal":"Applied and environmental microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP establishing physical interaction, functional genetic deletion with survival/DNA damage readout, and mechanistic deubiquitination assay, single lab","pmids":["30366994"],"is_preprint":false},{"year":2022,"finding":"LSM12 regulates alternative splicing of USO1 exon 15: LSM12 overexpression causes inclusion of USO1 exon 15, while LSM12 knockdown induces exon 15 skipping. The exon 15-retained USO1 isoform promotes malignant phenotypes in OSCC cells.","method":"Whole transcriptome sequencing, PCR and sequencing of alternative splicing, siRNA knockdown, overexpression, cell proliferation/migration/invasion assays, in vivo tumor formation","journal":"Journal of experimental & clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct splicing assay with PCR confirmation, loss- and gain-of-function with defined molecular and cellular readouts, single lab","pmids":["35449073"],"is_preprint":false},{"year":2023,"finding":"LSM12 directly binds to CTNNB1 (β-Catenin) and regulates its protein stability, affecting formation of the CTNNB1-LEF1-TCF1 transcriptional complex and downstream WNT signaling in colorectal cancer cells.","method":"Protein interaction simulation, co-immunoprecipitation/biochemical pulldown, protein stability assay, siRNA knockdown, in vivo xenograft","journal":"Oncology research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single co-IP/pulldown and computational simulation, single lab, limited mechanistic follow-up","pmids":["37303493"],"is_preprint":false},{"year":2025,"finding":"LSM12 regulates alternative splicing of ARRB1, increasing exon 13-skipped splicing. SAMD4A directly binds LSM12 mRNA and accelerates its degradation (upstream regulation of LSM12 itself).","method":"High-throughput omics/RNA-seq, alternative splicing analysis, RNA-binding protein interaction assay (SAMD4A-LSM12 mRNA), functional cell assays","journal":"Communications biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, splicing assay without deep mechanistic validation of LSM12 direct binding to ARRB1 pre-mRNA","pmids":["40425760"],"is_preprint":false}],"current_model":"LSM12 is a Sm-like (Lsm domain) protein that functions as a high-affinity NAADP receptor: it directly binds NAADP, tonically inhibits PI(3,5)P2-dependent two-pore channel (TPC1/TPC2) gating, and NAADP binding to LSM12 relieves this inhibition to evoke Ca2+ release from acidic endolysosomes; independently, LSM12 serves as a molecular adaptor within the ATAXIN-2 complex to co-activate translation of specific mRNAs (e.g., the clock gene period via TYF recruitment), posttranscriptionally upregulates EPAC1 to sustain the nucleocytoplasmic RAN gradient, and influences pre-mRNA alternative splicing of targets such as USO1 and ARRB1."},"narrative":{"mechanistic_narrative":"LSM12 is a Sm-like (Lsm) domain protein with dual roles in acidic-store Ca2+ signaling and RNA-associated regulation [PMID:34362892, PMID:28388438]. As a high-affinity NAADP receptor, recombinant LSM12 directly binds NAADP through its Lsm domain, associates with the two-pore channels TPC1 and TPC2, and is required for NAADP-evoked Ca2+ release from endolysosomal organelles [PMID:34362892, PMID:37607218]. Mechanistically, LSM12 acts as a competitive antagonist of PI(3,5)P2-dependent TPC gating, and NAADP binding to LSM12 relieves this inhibition to permit channel activation [PMID:42039649]; this signaling axis also supports endolysosomal trafficking of pseudotyped coronavirus particles [PMID:37607218]. Independently, LSM12 functions as a molecular adaptor within the ATAXIN-2 complex, recruiting TWENTY-FOUR (TYF) to co-activate translation of the clock gene period and maintain circadian periodicity in Drosophila, consistent with its conserved physical interaction with the ATAXIN-2 ortholog Pbp1 and its localization to stress granules in yeast [PMID:28388438, PMID:20368989]. In human cells LSM12 posttranscriptionally upregulates EPAC1 to sustain the nucleocytoplasmic RAN gradient and counteract C9ORF72 poly(GR)-induced nucleocytoplasmic transport defects [PMID:33362237]. Additional reported activities include regulation of alternative splicing of USO1 and ARRB1 [PMID:35449073, PMID:40425760] and modulation of β-catenin stability in WNT signaling [PMID:37303493].","teleology":[{"year":2010,"claim":"Establishing where LSM12 acts and with whom: it was placed in the RNA-granule/ATAXIN-2 axis by showing it localizes to stress granules and binds the yeast ATAXIN-2 ortholog Pbp1.","evidence":"Live fluorescence imaging, genetic deletion/overexpression, and physical interaction in yeast","pmids":["20368989"],"confidence":"Medium","gaps":["Functional consequence of LSM12 in stress granules undefined","No molecular substrate or RNA target identified","Mammalian relevance not tested in this study"]},{"year":2017,"claim":"Resolved how LSM12 contributes to ATAXIN-2 function: it serves as an adaptor recruiting TYF to drive translation of specific mRNAs, linking it to circadian timekeeping.","evidence":"Genetic epistasis, reciprocal co-IP, and behavioral rhythmicity assays in Drosophila","pmids":["28388438"],"confidence":"High","gaps":["Translational targets beyond period not mapped","Adaptor mechanism not reconstituted biochemically","Conservation of TYF-recruitment role in mammals untested"]},{"year":2018,"claim":"Extended LSM12's interaction repertoire to DNA-damage tolerance, showing it modulates Polη ubiquitination state.","evidence":"Co-IP, deletion/overexpression, and ubiquitination assays in yeast","pmids":["30366994"],"confidence":"Medium","gaps":["Whether this role is conserved in human cells unknown","Direct vs indirect effect on Ubp3 deubiquitination unresolved","Connection to LSM12's RNA/Ca2+ roles unclear"]},{"year":2020,"claim":"Identified a neuroprotective role: LSM12 posttranscriptionally upregulates EPAC1 to maintain the RAN gradient and counter C9ORF72 poly(GR) toxicity.","evidence":"siRNA knockdown, iPSC-neuron overexpression, RAN-gradient and TDP-43 localization readouts in human cells","pmids":["33362237"],"confidence":"Medium","gaps":["Mechanism by which LSM12 raises EPAC1 not defined","Single-lab finding","Direct RNA target binding not demonstrated"]},{"year":2021,"claim":"Defined the founding molecular function: LSM12 is a direct NAADP-binding protein and an essential component for TPC activation and endolysosomal Ca2+ release.","evidence":"Affinity purification, quantitative proteomics, direct binding, colocalization, and Ca2+ assays with knockdown/knockout","pmids":["34362892"],"confidence":"High","gaps":["Stoichiometry of LSM12-TPC-NAADP complex unresolved","Relationship to JPT2 not addressed","Structural basis of NAADP binding unknown"]},{"year":2023,"claim":"Independently confirmed NAADP receptor activity and extended it to a physiological context: LSM12 supports coronavirus endolysosomal trafficking.","evidence":"Recombinant binding assays, endogenous reciprocal co-IP, knockout/rescue, Ca2+ imaging in human cells","pmids":["37607218"],"confidence":"High","gaps":["Functional interplay between LSM12 and JPT2 not resolved","Structural mechanism of TPC association undefined"]},{"year":2026,"claim":"Provided the gating mechanism: LSM12 competitively inhibits PI(3,5)P2-evoked TPC currents and NAADP binding reverses this inhibition, explaining how NAADP licenses channel opening.","evidence":"Electrophysiology with purified protein, acute PIP2 sequestration, and Ca2+ imaging (preprint)","pmids":["42039649"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Structural details of competitive inhibition unresolved","Generality across TPC isoforms and tissues untested"]},{"year":2022,"claim":"Linked LSM12 to alternative splicing control, showing it governs USO1 exon 15 inclusion with oncogenic consequences.","evidence":"Transcriptome sequencing, splicing PCR, knockdown/overexpression, and tumor assays in OSCC","pmids":["35449073"],"confidence":"Medium","gaps":["Direct LSM12 binding to USO1 pre-mRNA not shown","Mechanism connecting Lsm domain to splicing undefined"]},{"year":2023,"claim":"Proposed a role in WNT signaling via stabilization of β-catenin in colorectal cancer.","evidence":"Computational interaction simulation, co-IP/pulldown, stability assay, xenograft","pmids":["37303493"],"confidence":"Low","gaps":["Single co-IP plus simulation without reciprocal validation","Direct binding not biochemically confirmed","Mechanism of stability regulation unknown"]},{"year":2025,"claim":"Added ARRB1 splicing regulation and identified upstream control of LSM12 itself by SAMD4A-mediated mRNA degradation.","evidence":"RNA-seq, splicing analysis, RNA-binding assay, functional cell assays","pmids":["40425760"],"confidence":"Low","gaps":["Direct LSM12 binding to ARRB1 pre-mRNA not validated","Single lab","Functional significance of ARRB1 isoform shift unclear"]},{"year":null,"claim":"How a single Lsm-domain protein integrates NAADP/TPC Ca2+ signaling, ATAXIN-2-dependent translational control, and alternative splicing remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model unifying NAADP binding and RNA/protein adaptor functions","Whether splicing and Ca2+ roles share a common mechanism unknown","Tissue-specific division of these functions uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060089","term_label":"molecular transducer activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[3]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[3]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[0,1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[5]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3,7]},{"term_id":"R-HSA-9909396","term_label":"Circadian clock","supporting_discovery_ids":[3]}],"complexes":["ATAXIN-2 (ATX2-LSM12-TYF) complex","LSM12-TPC1/TPC2 NAADP receptor complex"],"partners":["TPC1","TPC2","ATXN2","TYF","PBP1","EPAC1","CTNNB1","RAD30"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q3MHD2","full_name":"Protein LSM12","aliases":[],"length_aa":195,"mass_kda":21.7,"function":"Nicotinic acid adenine dinucleotide phosphate (NAADP) binding protein (PubMed:34362892). Confers NAADP sensitivity to the two pore channel complex (TPCs) by acting as TPC accessory protein necessary for NAADP-evoked Ca(2+) release (PubMed:34362892)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q3MHD2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/LSM12","classification":"Not Classified","n_dependent_lines":683,"n_total_lines":1208,"dependency_fraction":0.5653973509933775},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"ATXN2L","stoichiometry":0.2},{"gene":"CAPZB","stoichiometry":0.2},{"gene":"DDX6","stoichiometry":0.2},{"gene":"EIF3G","stoichiometry":0.2},{"gene":"G3BP2","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/LSM12","total_profiled":1310},"omim":[{"mim_id":"611793","title":"LSM12, S. CEREVISIAE, HOMOLOG OF; LSM12","url":"https://www.omim.org/entry/611793"},{"mim_id":"611792","title":"ZINC FINGER CCHC DOMAIN-CONTAINING PROTEIN 4; ZCCHC4","url":"https://www.omim.org/entry/611792"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/LSM12"},"hgnc":{"alias_symbol":["FLJ30656"],"prev_symbol":[]},"alphafold":{"accession":"Q3MHD2","domains":[{"cath_id":"2.30.30.100","chopping":"12-69","consensus_level":"high","plddt":93.9638,"start":12,"end":69},{"cath_id":"-","chopping":"94-184","consensus_level":"high","plddt":96.0782,"start":94,"end":184}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q3MHD2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q3MHD2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q3MHD2-F1-predicted_aligned_error_v6.png","plddt_mean":90.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=LSM12","jax_strain_url":"https://www.jax.org/strain/search?query=LSM12"},"sequence":{"accession":"Q3MHD2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q3MHD2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q3MHD2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q3MHD2"}},"corpus_meta":[{"pmid":"20368989","id":"PMC_20368989","title":"Localization to, and effects of Pbp1, Pbp4, Lsm12, Dhh1, and Pab1 on stress granules in Saccharomyces cerevisiae.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20368989","citation_count":110,"is_preprint":false},{"pmid":"34362892","id":"PMC_34362892","title":"Lsm12 is an NAADP receptor and a two-pore channel regulatory protein required for calcium mobilization from acidic organelles.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34362892","citation_count":78,"is_preprint":false},{"pmid":"28388438","id":"PMC_28388438","title":"LSM12 and ME31B/DDX6 Define Distinct Modes of Posttranscriptional Regulation by ATAXIN-2 Protein Complex in Drosophila Circadian Pacemaker Neurons.","date":"2017","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/28388438","citation_count":54,"is_preprint":false},{"pmid":"37607218","id":"PMC_37607218","title":"Convergent activation of two-pore channels mediated by the NAADP-binding proteins JPT2 and LSM12.","date":"2023","source":"Science signaling","url":"https://pubmed.ncbi.nlm.nih.gov/37607218","citation_count":23,"is_preprint":false},{"pmid":"33362237","id":"PMC_33362237","title":"LSM12-EPAC1 defines a neuroprotective pathway that sustains the nucleocytoplasmic RAN gradient.","date":"2020","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/33362237","citation_count":18,"is_preprint":false},{"pmid":"35449073","id":"PMC_35449073","title":"Identification of RNA-splicing factor Lsm12 as a novel tumor-associated gene and a potent biomarker in Oral Squamous Cell Carcinoma (OSCC).","date":"2022","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/35449073","citation_count":16,"is_preprint":false},{"pmid":"30366994","id":"PMC_30366994","title":"Lsm12 Mediates Deubiquitination of DNA Polymerase η To Help Saccharomyces cerevisiae Resist Oxidative Stress.","date":"2018","source":"Applied and environmental microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/30366994","citation_count":10,"is_preprint":false},{"pmid":"40425760","id":"PMC_40425760","title":"LSM12 promotes the lung squamous cell carcinoma progression through mediating alternative splicing of ARRB1.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40425760","citation_count":2,"is_preprint":false},{"pmid":"37303493","id":"PMC_37303493","title":"LSM12 facilitates the progression of colorectal cancer by activating the WNT/CTNNB1 signaling pathway.","date":"2023","source":"Oncology research","url":"https://pubmed.ncbi.nlm.nih.gov/37303493","citation_count":2,"is_preprint":false},{"pmid":"41080638","id":"PMC_41080638","title":"Functional characterization of LSM12 as a driver in uveal melanoma oncogenesis.","date":"2025","source":"Advances in ophthalmology practice and research","url":"https://pubmed.ncbi.nlm.nih.gov/41080638","citation_count":0,"is_preprint":false},{"pmid":"42039649","id":"PMC_42039649","title":"NAADP elicits two-pore channel currents by lifting Lsm12-mediated inhibition of PI(3,5)P2 activation.","date":"2026","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/42039649","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.11.687795","title":"JPT2/HN1L functions as an NAADP-binding protein in a cell-type-specific manner","date":"2025-11-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.11.687795","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.06.02.657355","title":"Genome-wide CRISPR/Cas9 knockout screen identifies host factors essential for Bovine Parainfluenza Virus Type 3 replication","date":"2025-06-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.06.02.657355","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.03.06.641895","title":"ATXN2L primarily interacts with NUFIP2, the absence of ATXN2L results in NUFIP2 depletion, and the ATXN2-polyQ expansion triggers NUFIP2 accumulation","date":"2025-03-11","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.06.641895","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9497,"output_tokens":2575,"usd":0.033558,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9790,"output_tokens":3629,"usd":0.069837,"stage2_stop_reason":"end_turn"},"total_usd":0.103395,"stage1_batch_id":"msgbatch_01BbTCMyrRPyhtEq6b1MdwCN","stage2_batch_id":"msgbatch_011dEed5bbxYvTAaQWKJevxu","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"LSM12 directly binds NAADP via its Lsm domain, colocalizes with TPC2, and is essential for NAADP-evoked TPC activation and Ca2+ mobilization from acidic endolysosomal organelles. LSM12 was identified as complexed with NAADP, TPC1, and TPC2 by affinity purification and quantitative proteomic analysis.\",\n      \"method\": \"Affinity purification, quantitative proteomics, co-immunoprecipitation, colocalization imaging, functional Ca2+ mobilization assays, knockdown/knockout\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (affinity purification, proteomics, direct binding assay, colocalization, functional Ca2+ assay, knockdown), replicated by subsequent independent labs\",\n      \"pmids\": [\"34362892\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Recombinant LSM12 binds NAADP with high affinity and endogenous LSM12 independently associates with TPC1 and TPC2; LSM12 is required (alongside JPT2) for NAADP-evoked Ca2+ signaling and endolysosomal trafficking of pseudotyped coronavirus particles in human cells.\",\n      \"method\": \"Recombinant protein binding assays, co-immunoprecipitation of endogenous proteins, knockout and rescue analyses, functional Ca2+ imaging\",\n      \"journal\": \"Science signaling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — independent lab replication with biochemical binding assays, reciprocal co-IP, and functional knockout/rescue experiments\",\n      \"pmids\": [\"37607218\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"LSM12 acts as a potent antagonist of PI(3,5)P2-dependent TPC activation: purified LSM12 strongly inhibits PI(3,5)P2-evoked TPC1 and TPC2 currents, reduces TPC2 apparent sensitivity to PI(3,5)P2 via a competitive mechanism dependent on Lsm12-TPC interaction, and NAADP binding to LSM12 specifically and dose-dependently reverses this inhibition to permit TPC channel activation.\",\n      \"method\": \"Electrophysiology (channel currents), purified recombinant protein, endogenous knockdown, acute PI(3,5)P2 sequestration, Ca2+ imaging\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified protein and electrophysiology plus cellular functional assays, but preprint not yet peer-reviewed\",\n      \"pmids\": [\"42039649\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Drosophila LSM12 acts as a molecular adaptor for recruitment of TWENTY-FOUR (TYF) to the ATAXIN-2 (ATX2) complex; the ATX2-LSM12-TYF complex stimulates TYF-dependent translation of the clock gene period (per) to maintain 24-hr circadian periodicity.\",\n      \"method\": \"Genetic interaction/epistasis analysis, co-immunoprecipitation, behavioral rhythmicity assays, loss-of-function\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP establishing complex membership, genetic epistasis placing LSM12 in pathway, and functional behavioral readout; published in high-impact peer-reviewed journal\",\n      \"pmids\": [\"28388438\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"LSM12 posttranscriptionally upregulates EPAC1 expression; the LSM12-EPAC1 pathway sustains the nucleocytoplasmic RAN gradient and suppresses NCT dysfunction caused by C9ORF72-derived poly(GR) protein. LSM12 depletion aggravates poly(GR)-induced NCT impairment and promotes nuclear accumulation of poly(GR) granules.\",\n      \"method\": \"siRNA knockdown in human neuroblastoma cells, lentiviral overexpression in C9-ALS iPSC-derived neurons, RAN gradient measurement, TDP-43 localization assay, caspase-3 activation assay\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with specific molecular readouts (RAN gradient, NCT) and rescue experiments, single lab\",\n      \"pmids\": [\"33362237\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Yeast Lsm12 localizes to stress granules (but not constitutively to P-bodies). Deletion or overexpression of Lsm12 does not dramatically affect stress granule or P-body formation. Lsm12 physically interacts with the Pbp1 protein (yeast ortholog of Ataxin-2).\",\n      \"method\": \"Fluorescence microscopy (live imaging), genetic deletion, overexpression, stress granule formation assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — direct localization by imaging, genetic perturbation with defined cellular readout, and physical interaction via known pulldown data; multiple observations in one study\",\n      \"pmids\": [\"20368989\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Yeast Lsm12 physically interacts with the UBZ domain of DNA polymerase η (Polη/Rad30) and enhances Polη deubiquitination through Ubp3, thereby promoting Polη recruitment under oxidative stress.\",\n      \"method\": \"Co-immunoprecipitation (physical interaction), gene deletion/overexpression, ubiquitination assays, transcriptome analysis\",\n      \"journal\": \"Applied and environmental microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP establishing physical interaction, functional genetic deletion with survival/DNA damage readout, and mechanistic deubiquitination assay, single lab\",\n      \"pmids\": [\"30366994\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"LSM12 regulates alternative splicing of USO1 exon 15: LSM12 overexpression causes inclusion of USO1 exon 15, while LSM12 knockdown induces exon 15 skipping. The exon 15-retained USO1 isoform promotes malignant phenotypes in OSCC cells.\",\n      \"method\": \"Whole transcriptome sequencing, PCR and sequencing of alternative splicing, siRNA knockdown, overexpression, cell proliferation/migration/invasion assays, in vivo tumor formation\",\n      \"journal\": \"Journal of experimental & clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct splicing assay with PCR confirmation, loss- and gain-of-function with defined molecular and cellular readouts, single lab\",\n      \"pmids\": [\"35449073\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"LSM12 directly binds to CTNNB1 (β-Catenin) and regulates its protein stability, affecting formation of the CTNNB1-LEF1-TCF1 transcriptional complex and downstream WNT signaling in colorectal cancer cells.\",\n      \"method\": \"Protein interaction simulation, co-immunoprecipitation/biochemical pulldown, protein stability assay, siRNA knockdown, in vivo xenograft\",\n      \"journal\": \"Oncology research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single co-IP/pulldown and computational simulation, single lab, limited mechanistic follow-up\",\n      \"pmids\": [\"37303493\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"LSM12 regulates alternative splicing of ARRB1, increasing exon 13-skipped splicing. SAMD4A directly binds LSM12 mRNA and accelerates its degradation (upstream regulation of LSM12 itself).\",\n      \"method\": \"High-throughput omics/RNA-seq, alternative splicing analysis, RNA-binding protein interaction assay (SAMD4A-LSM12 mRNA), functional cell assays\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, splicing assay without deep mechanistic validation of LSM12 direct binding to ARRB1 pre-mRNA\",\n      \"pmids\": [\"40425760\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"LSM12 is a Sm-like (Lsm domain) protein that functions as a high-affinity NAADP receptor: it directly binds NAADP, tonically inhibits PI(3,5)P2-dependent two-pore channel (TPC1/TPC2) gating, and NAADP binding to LSM12 relieves this inhibition to evoke Ca2+ release from acidic endolysosomes; independently, LSM12 serves as a molecular adaptor within the ATAXIN-2 complex to co-activate translation of specific mRNAs (e.g., the clock gene period via TYF recruitment), posttranscriptionally upregulates EPAC1 to sustain the nucleocytoplasmic RAN gradient, and influences pre-mRNA alternative splicing of targets such as USO1 and ARRB1.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"LSM12 is a Sm-like (Lsm) domain protein with dual roles in acidic-store Ca2+ signaling and RNA-associated regulation [#0, #3]. As a high-affinity NAADP receptor, recombinant LSM12 directly binds NAADP through its Lsm domain, associates with the two-pore channels TPC1 and TPC2, and is required for NAADP-evoked Ca2+ release from endolysosomal organelles [#0, #1]. Mechanistically, LSM12 acts as a competitive antagonist of PI(3,5)P2-dependent TPC gating, and NAADP binding to LSM12 relieves this inhibition to permit channel activation [#2]; this signaling axis also supports endolysosomal trafficking of pseudotyped coronavirus particles [#1]. Independently, LSM12 functions as a molecular adaptor within the ATAXIN-2 complex, recruiting TWENTY-FOUR (TYF) to co-activate translation of the clock gene period and maintain circadian periodicity in Drosophila, consistent with its conserved physical interaction with the ATAXIN-2 ortholog Pbp1 and its localization to stress granules in yeast [#3, #5]. In human cells LSM12 posttranscriptionally upregulates EPAC1 to sustain the nucleocytoplasmic RAN gradient and counteract C9ORF72 poly(GR)-induced nucleocytoplasmic transport defects [#4]. Additional reported activities include regulation of alternative splicing of USO1 and ARRB1 [#7, #9] and modulation of \\u03b2-catenin stability in WNT signaling [#8].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Establishing where LSM12 acts and with whom: it was placed in the RNA-granule/ATAXIN-2 axis by showing it localizes to stress granules and binds the yeast ATAXIN-2 ortholog Pbp1.\",\n      \"evidence\": \"Live fluorescence imaging, genetic deletion/overexpression, and physical interaction in yeast\",\n      \"pmids\": [\"20368989\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional consequence of LSM12 in stress granules undefined\", \"No molecular substrate or RNA target identified\", \"Mammalian relevance not tested in this study\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Resolved how LSM12 contributes to ATAXIN-2 function: it serves as an adaptor recruiting TYF to drive translation of specific mRNAs, linking it to circadian timekeeping.\",\n      \"evidence\": \"Genetic epistasis, reciprocal co-IP, and behavioral rhythmicity assays in Drosophila\",\n      \"pmids\": [\"28388438\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Translational targets beyond period not mapped\", \"Adaptor mechanism not reconstituted biochemically\", \"Conservation of TYF-recruitment role in mammals untested\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Extended LSM12's interaction repertoire to DNA-damage tolerance, showing it modulates Pol\\u03b7 ubiquitination state.\",\n      \"evidence\": \"Co-IP, deletion/overexpression, and ubiquitination assays in yeast\",\n      \"pmids\": [\"30366994\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Whether this role is conserved in human cells unknown\", \"Direct vs indirect effect on Ubp3 deubiquitination unresolved\", \"Connection to LSM12's RNA/Ca2+ roles unclear\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identified a neuroprotective role: LSM12 posttranscriptionally upregulates EPAC1 to maintain the RAN gradient and counter C9ORF72 poly(GR) toxicity.\",\n      \"evidence\": \"siRNA knockdown, iPSC-neuron overexpression, RAN-gradient and TDP-43 localization readouts in human cells\",\n      \"pmids\": [\"33362237\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Mechanism by which LSM12 raises EPAC1 not defined\", \"Single-lab finding\", \"Direct RNA target binding not demonstrated\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined the founding molecular function: LSM12 is a direct NAADP-binding protein and an essential component for TPC activation and endolysosomal Ca2+ release.\",\n      \"evidence\": \"Affinity purification, quantitative proteomics, direct binding, colocalization, and Ca2+ assays with knockdown/knockout\",\n      \"pmids\": [\"34362892\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Stoichiometry of LSM12-TPC-NAADP complex unresolved\", \"Relationship to JPT2 not addressed\", \"Structural basis of NAADP binding unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Independently confirmed NAADP receptor activity and extended it to a physiological context: LSM12 supports coronavirus endolysosomal trafficking.\",\n      \"evidence\": \"Recombinant binding assays, endogenous reciprocal co-IP, knockout/rescue, Ca2+ imaging in human cells\",\n      \"pmids\": [\"37607218\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Functional interplay between LSM12 and JPT2 not resolved\", \"Structural mechanism of TPC association undefined\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Provided the gating mechanism: LSM12 competitively inhibits PI(3,5)P2-evoked TPC currents and NAADP binding reverses this inhibition, explaining how NAADP licenses channel opening.\",\n      \"evidence\": \"Electrophysiology with purified protein, acute PIP2 sequestration, and Ca2+ imaging (preprint)\",\n      \"pmids\": [\"42039649\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Structural details of competitive inhibition unresolved\", \"Generality across TPC isoforms and tissues untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked LSM12 to alternative splicing control, showing it governs USO1 exon 15 inclusion with oncogenic consequences.\",\n      \"evidence\": \"Transcriptome sequencing, splicing PCR, knockdown/overexpression, and tumor assays in OSCC\",\n      \"pmids\": [\"35449073\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct LSM12 binding to USO1 pre-mRNA not shown\", \"Mechanism connecting Lsm domain to splicing undefined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Proposed a role in WNT signaling via stabilization of \\u03b2-catenin in colorectal cancer.\",\n      \"evidence\": \"Computational interaction simulation, co-IP/pulldown, stability assay, xenograft\",\n      \"pmids\": [\"37303493\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single co-IP plus simulation without reciprocal validation\", \"Direct binding not biochemically confirmed\", \"Mechanism of stability regulation unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Added ARRB1 splicing regulation and identified upstream control of LSM12 itself by SAMD4A-mediated mRNA degradation.\",\n      \"evidence\": \"RNA-seq, splicing analysis, RNA-binding assay, functional cell assays\",\n      \"pmids\": [\"40425760\"],\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Direct LSM12 binding to ARRB1 pre-mRNA not validated\", \"Single lab\", \"Functional significance of ARRB1 isoform shift unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single Lsm-domain protein integrates NAADP/TPC Ca2+ signaling, ATAXIN-2-dependent translational control, and alternative splicing remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No structural model unifying NAADP binding and RNA/protein adaptor functions\", \"Whether splicing and Ca2+ roles share a common mechanism unknown\", \"Tissue-specific division of these functions uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060089\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3, 7]},\n      {\"term_id\": \"R-HSA-9909396\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"ATAXIN-2 (ATX2-LSM12-TYF) complex\", \"LSM12-TPC1/TPC2 NAADP receptor complex\"],\n    \"partners\": [\"TPC1\", \"TPC2\", \"ATXN2\", \"TYF\", \"Pbp1\", \"EPAC1\", \"CTNNB1\", \"Rad30\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}