{"gene":"PRELID3B","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2016,"finding":"The yeast Ups2-Mdm35 complex (human ortholog: SLMO2-TRIAP1) functions as a phosphatidylserine (PS)-specific lipid transfer protein in the mitochondrial intermembrane space, enabling PS delivery to the inner mitochondrial membrane where it is decarboxylated to phosphatidylethanolamine (PE) by Psd1. A second pathway shows Psd1 can decarboxylate PS in trans from the outer membrane, independently of Ups2-Mdm35 transfer, requiring MICOS-dependent membrane apposition.","method":"Genetic epistasis (yeast knockouts), lipid transfer assays, mitochondrial fractionation, respiratory measurements, fluorescence microscopy of cristae structure","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (lipid transfer assays, genetic knockouts, functional respiratory readouts, structural imaging) demonstrating the PS-transfer function, independently consistent with Drosophila and human data in other papers","pmids":["27241913"],"is_preprint":false},{"year":2024,"finding":"Drosophila SLMO (ortholog of human SLMO2) specifically transfers phosphatidylserine (PS) from the outer mitochondrial membrane (OMM) to the inner mitochondrial membrane (IMM) within the inner boundary membrane domain, acting in a conserved PSS-SLMO-PISD pathway. This PS transfer is required for mitochondrial morphology maintenance. Knockdown of human SLMO2 confirmed conservation of this role. The putative binding partner dTRIAP was found not to be required for SLMO's role in mitochondrial morphology.","method":"Forward genetic screen in Drosophila, PS transfer assays, fluorescence and electron microscopy of mitochondrial morphology, human SLMO2 knockdown rescue experiments","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — forward genetic screen plus lipid transfer assays plus morphological readouts, with human SLMO2 functional validation; multiple orthogonal methods in one rigorous study","pmids":["39680501"],"is_preprint":false},{"year":2022,"finding":"Molecular dynamics simulations and X-ray crystallography of the PRELID-TRIAP1 protein family (which includes PRELID3B/SLMO2-TRIAP1) revealed that lipid binding is mediated by an extended, water-mediated hydrogen bonding network. A key mutation R53E disrupts this network, causing lipid release from the complex. Lipid transfer assays confirmed that disrupting this network abolishes transfer activity.","method":"Molecular dynamics simulations, X-ray crystallography (apo and lipid-bound forms), mutagenesis (R53E), lipid transfer assays","journal":"Biochimica et biophysica acta. Proteins and proteomics","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure combined with mutagenesis and functional lipid transfer assay in a single study; applies to the PRELID3B/SLMO2-TRIAP1 complex specifically","pmids":["36309326"],"is_preprint":false},{"year":2022,"finding":"In yeast, depletion of Ups2 (ortholog of human PRELID3B/SLMO2) causes overactivation of the Snf1/AMPK pathway, leading to increased mitochondrial ATP production and enhanced quiescence entry. Knockdown of PRELID3B in human Rb1-deficient breast cancer cells decreased cell viability, placing PRELID3B upstream of AMPK signaling and linking its PS-transfer/PE-synthesis function to cellular energy metabolism and cell-cycle regulation.","method":"Yeast knockout (ups2∆), transcriptomic analysis, biochemical AMPK/Snf1 activity assays, genetic epistasis (sak1∆), siRNA knockdown of PRELID3B in human cancer cells, cell viability assay","journal":"FASEB journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods in yeast with human PRELID3B knockdown validation, but human data is limited to viability assay without full mechanistic dissection","pmids":["35639425"],"is_preprint":false},{"year":2025,"finding":"SLMO2 (PRELID3B) physically interacts with TRIAP1 in ovarian cancer cells, and this interaction enhances mitochondrial membrane potential, reduces reactive oxygen species, inhibits autophagy, and suppresses apoptosis. Loss of SLMO2 or TRIAP1 reverses these effects, demonstrated both in vitro and in a xenograft model.","method":"Lentiviral overexpression/knockdown, co-immunoprecipitation (interaction with TRIAP1), flow cytometry (apoptosis, ROS, membrane potential), western blotting, immunofluorescence, transmission electron microscopy, mouse xenograft model","journal":"Histology and histopathology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — reciprocal functional experiments with multiple cellular readouts and in vivo confirmation, but mechanistic pathway details (e.g., direct PS transfer) are inferred rather than directly demonstrated by transfer assay","pmids":["40654025"],"is_preprint":false},{"year":2026,"finding":"PRELID3B was identified as a direct binding target of the ginseng metabolite compound K (CK) and its derivative CKD-4 using unbiased proteome integral solubility alteration and ProTargetMiner proteomics. Both compounds stabilize PRELID3B in cellular thermal shift assays and bind it with Kd of 23 µM (CK) and 5 µM (CKD-4) by biolayer interferometry. Inhibition of PRELID3B by these compounds depletes mitochondrial phospholipids, activates the integrated stress response, and triggers immunomodulatory pathways.","method":"Proteome integral solubility alteration (PISA) assay, ProTargetMiner analysis, cellular thermal shift assay (CETSA), biolayer interferometry, multiomics (lipidomics, transcriptomics), organoid and xenograft models","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal biophysical binding methods and multiomics functional validation, single lab study without independent replication","pmids":["42081720"],"is_preprint":false}],"current_model":"PRELID3B (SLMO2) forms a complex with TRIAP1 in the mitochondrial intermembrane space and functions as a phosphatidylserine (PS)-specific lipid transfer protein that shuttles PS from the outer to the inner mitochondrial membrane, where PS is converted to phosphatidylethanolamine (PE) by phosphatidylserine decarboxylase; this PS-transfer activity, mediated by a water-mediated hydrogen bonding network in the PRELID domain, maintains mitochondrial morphology, membrane potential, and respiratory function, and its loss dysregulates AMPK/Snf1 signaling and promotes apoptosis."},"narrative":{"mechanistic_narrative":"PRELID3B (SLMO2) is a mitochondrial intermembrane-space lipid transfer protein that shuttles phosphatidylserine (PS) from the outer to the inner mitochondrial membrane, where PS is decarboxylated to phosphatidylethanolamine, a pathway conserved from yeast (Ups2-Mdm35) through Drosophila to human and required for maintenance of mitochondrial morphology and respiratory function [PMID:27241913, PMID:39680501]. Lipid binding and transfer depend on an extended, water-mediated hydrogen-bonding network within the PRELID domain; disruption of this network (R53E) releases bound lipid and abolishes transfer activity [PMID:36309326]. PRELID3B partners physically with TRIAP1, and in cancer cells this interaction sustains mitochondrial membrane potential, limits reactive oxygen species, and suppresses autophagy and apoptosis [PMID:40654025]; notably, the Drosophila TRIAP1 ortholog was dispensable for SLMO's role in mitochondrial morphology, indicating the morphology function can proceed independently of the partner [PMID:39680501]. Loss or pharmacological inhibition of PRELID3B depletes mitochondrial phospholipids and links its activity to cellular energy and stress signaling, including overactivation of the Snf1/AMPK pathway and activation of the integrated stress response [PMID:35639425, PMID:42081720]. PRELID3B is a direct binding target of the ginseng metabolite compound K and its derivative CKD-4 [PMID:42081720].","teleology":[{"year":2016,"claim":"Established the core biochemical function: whether the SLMO2-TRIAP1 (yeast Ups2-Mdm35) complex actively moves PS across the mitochondrial intermembrane space to feed inner-membrane PE synthesis.","evidence":"Yeast genetic epistasis, in vitro lipid transfer assays, mitochondrial fractionation, and respiratory and cristae imaging","pmids":["27241913"],"confidence":"High","gaps":["Demonstrated in yeast; human complex function inferred from orthology in this study","Relative contributions of transfer-dependent versus trans-decarboxylation pathways in human cells not quantified"]},{"year":2022,"claim":"Defined the structural basis of lipid handling: how the PRELID domain captures and releases lipid cargo during transfer.","evidence":"X-ray crystallography of apo and lipid-bound complex, molecular dynamics, R53E mutagenesis, and lipid transfer assays","pmids":["36309326"],"confidence":"High","gaps":["Does not resolve how PS is extracted from and inserted into membranes","Lipid head-group selectivity determinants not fully mapped"]},{"year":2022,"claim":"Connected the lipid-transfer function to downstream energy and cell-cycle signaling, placing PRELID3B/Ups2 upstream of AMPK/Snf1.","evidence":"Yeast ups2∆ transcriptomics and AMPK/Snf1 activity assays with sak1∆ epistasis, plus siRNA knockdown and viability assay in Rb1-deficient human cancer cells","pmids":["35639425"],"confidence":"Medium","gaps":["Human data limited to a viability assay without mechanistic dissection of the AMPK link","How phospholipid changes mechanistically activate AMPK/Snf1 not established"]},{"year":2024,"claim":"Confirmed directionality and conservation of PS transfer (OMM to IMM at the inner boundary membrane) and tested partner requirement for the morphology function.","evidence":"Drosophila forward genetic screen, PS transfer assays, electron/fluorescence microscopy, and human SLMO2 knockdown rescue","pmids":["39680501"],"confidence":"High","gaps":["Why dTRIAP is dispensable for morphology while TRIAP1 is functionally important elsewhere unresolved","Spatial mechanism at the inner boundary membrane not structurally defined"]},{"year":2025,"claim":"Showed the PRELID3B-TRIAP1 physical interaction controls mitochondrial fitness and cell survival in a disease (ovarian cancer) context.","evidence":"Co-immunoprecipitation, reciprocal knockdown/overexpression, flow cytometry of apoptosis/ROS/membrane potential, EM, and mouse xenograft","pmids":["40654025"],"confidence":"Medium","gaps":["Direct PS-transfer activity in this setting inferred rather than measured","Whether anti-apoptotic effects are downstream of lipid transfer or a separate function unclear"]},{"year":2026,"claim":"Identified PRELID3B as a druggable direct target whose pharmacological inhibition depletes mitochondrial phospholipids and triggers stress and immunomodulatory responses.","evidence":"PISA and ProTargetMiner proteomics, CETSA, biolayer interferometry, and multiomics in organoid and xenograft models","pmids":["42081720"],"confidence":"Medium","gaps":["Single-lab study without independent replication","Whether compound binding directly blocks PS transfer at the structural level not shown"]},{"year":null,"claim":"How PRELID3B engages source and target membranes for PS extraction/delivery and how its lipid output is mechanistically transduced into AMPK and integrated-stress-response signaling remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the membrane-docking step","Causal chain from phospholipid depletion to AMPK/ISR activation not delineated in human cells"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,1,4]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,5]}],"complexes":[],"partners":["TRIAP1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y3B1","full_name":"PRELI domain containing protein 3B","aliases":["Protein slowmo homolog 2"],"length_aa":194,"mass_kda":21.5,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9Y3B1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PRELID3B","classification":"Common Essential","n_dependent_lines":1194,"n_total_lines":1208,"dependency_fraction":0.9884105960264901},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PRELID3B","total_profiled":1310},"omim":[{"mim_id":"620754","title":"PRELI DOMAIN-CONTAINING PROTEIN 3B; PRELID3B","url":"https://www.omim.org/entry/620754"},{"mim_id":"614943","title":"TP53-REGULATED INHIBITOR OF APOPTOSIS 1; TRIAP1","url":"https://www.omim.org/entry/614943"},{"mim_id":"605733","title":"PRELI DOMAIN-CONTAINING PROTEIN 1; PRELID1","url":"https://www.omim.org/entry/605733"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PRELID3B"},"hgnc":{"alias_symbol":["dJ543J19.5"],"prev_symbol":["C20orf45","SLMO2"]},"alphafold":{"accession":"Q9Y3B1","domains":[{"cath_id":"3.30.530.20","chopping":"1-186","consensus_level":"high","plddt":83.8651,"start":1,"end":186}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3B1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3B1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3B1-F1-predicted_aligned_error_v6.png","plddt_mean":82.06},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PRELID3B","jax_strain_url":"https://www.jax.org/strain/search?query=PRELID3B"},"sequence":{"accession":"Q9Y3B1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y3B1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y3B1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3B1"}},"corpus_meta":[{"pmid":"27241913","id":"PMC_27241913","title":"MICOS and phospholipid transfer by Ups2-Mdm35 organize membrane lipid synthesis in mitochondria.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/27241913","citation_count":130,"is_preprint":false},{"pmid":"22423221","id":"PMC_22423221","title":"A meta-analysis and genome-wide association study of platelet count and mean platelet volume in african americans.","date":"2012","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22423221","citation_count":87,"is_preprint":false},{"pmid":"25254322","id":"PMC_25254322","title":"Platelet count mediates the contribution of a genetic variant in LRRC16A to ARDS risk.","date":"2015","source":"Chest","url":"https://pubmed.ncbi.nlm.nih.gov/25254322","citation_count":40,"is_preprint":false},{"pmid":"25148458","id":"PMC_25148458","title":"Aromatase inhibitor-associated bone fractures: a case-cohort GWAS and functional genomics.","date":"2014","source":"Molecular endocrinology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/25148458","citation_count":37,"is_preprint":false},{"pmid":"33393621","id":"PMC_33393621","title":"Circ_0061012 contributes to IL-22-induced proliferation, migration and invasion in keratinocytes through miR-194-5p/GAB1 axis in psoriasis.","date":"2021","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/33393621","citation_count":28,"is_preprint":false},{"pmid":"35391799","id":"PMC_35391799","title":"Population Genomic Sequencing Delineates Global Landscape of Copy Number Variations that Drive Domestication and Breed Formation of in Chicken.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/35391799","citation_count":22,"is_preprint":false},{"pmid":"39680501","id":"PMC_39680501","title":"SLMO transfers phosphatidylserine between the outer and inner mitochondrial membrane in Drosophila.","date":"2024","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/39680501","citation_count":8,"is_preprint":false},{"pmid":"35639425","id":"PMC_35639425","title":"Mitochondrial phosphatidylethanolamine synthesis affects mitochondrial energy metabolism and quiescence entry through attenuation of Snf1/AMPK signaling in yeast.","date":"2022","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/35639425","citation_count":4,"is_preprint":false},{"pmid":"32724388","id":"PMC_32724388","title":"Identification of long non-coding RNA SCARNA9L as a novel molecular target for colorectal cancer.","date":"2020","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/32724388","citation_count":2,"is_preprint":false},{"pmid":"36309326","id":"PMC_36309326","title":"An intermolecular hydrogen bonded network in the PRELID-TRIAP protein family plays a role in lipid sensing.","date":"2022","source":"Biochimica et biophysica acta. Proteins and proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/36309326","citation_count":2,"is_preprint":false},{"pmid":"30242696","id":"PMC_30242696","title":"Identification of Carassius auratus gibelio liver cell proteins interacting with the GABAA receptor γ2 subunit using a yeast two-hybrid system.","date":"2018","source":"Fish physiology and biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30242696","citation_count":1,"is_preprint":false},{"pmid":"42081720","id":"PMC_42081720","title":"A ginsenoside metabolite and its derivative target PRELID3B against lung cancer cells.","date":"2026","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/42081720","citation_count":0,"is_preprint":false},{"pmid":"40654025","id":"PMC_40654025","title":"SLMO2 inhibits apoptosis in ovarian cancer cells by modulating mitochondrial function via TRIAP1.","date":"2025","source":"Histology and histopathology","url":"https://pubmed.ncbi.nlm.nih.gov/40654025","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8947,"output_tokens":1967,"usd":0.028173,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8984,"output_tokens":2395,"usd":0.052397,"stage2_stop_reason":"end_turn"},"total_usd":0.08057,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2016,\n      \"finding\": \"The yeast Ups2-Mdm35 complex (human ortholog: SLMO2-TRIAP1) functions as a phosphatidylserine (PS)-specific lipid transfer protein in the mitochondrial intermembrane space, enabling PS delivery to the inner mitochondrial membrane where it is decarboxylated to phosphatidylethanolamine (PE) by Psd1. A second pathway shows Psd1 can decarboxylate PS in trans from the outer membrane, independently of Ups2-Mdm35 transfer, requiring MICOS-dependent membrane apposition.\",\n      \"method\": \"Genetic epistasis (yeast knockouts), lipid transfer assays, mitochondrial fractionation, respiratory measurements, fluorescence microscopy of cristae structure\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (lipid transfer assays, genetic knockouts, functional respiratory readouts, structural imaging) demonstrating the PS-transfer function, independently consistent with Drosophila and human data in other papers\",\n      \"pmids\": [\"27241913\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Drosophila SLMO (ortholog of human SLMO2) specifically transfers phosphatidylserine (PS) from the outer mitochondrial membrane (OMM) to the inner mitochondrial membrane (IMM) within the inner boundary membrane domain, acting in a conserved PSS-SLMO-PISD pathway. This PS transfer is required for mitochondrial morphology maintenance. Knockdown of human SLMO2 confirmed conservation of this role. The putative binding partner dTRIAP was found not to be required for SLMO's role in mitochondrial morphology.\",\n      \"method\": \"Forward genetic screen in Drosophila, PS transfer assays, fluorescence and electron microscopy of mitochondrial morphology, human SLMO2 knockdown rescue experiments\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — forward genetic screen plus lipid transfer assays plus morphological readouts, with human SLMO2 functional validation; multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"39680501\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Molecular dynamics simulations and X-ray crystallography of the PRELID-TRIAP1 protein family (which includes PRELID3B/SLMO2-TRIAP1) revealed that lipid binding is mediated by an extended, water-mediated hydrogen bonding network. A key mutation R53E disrupts this network, causing lipid release from the complex. Lipid transfer assays confirmed that disrupting this network abolishes transfer activity.\",\n      \"method\": \"Molecular dynamics simulations, X-ray crystallography (apo and lipid-bound forms), mutagenesis (R53E), lipid transfer assays\",\n      \"journal\": \"Biochimica et biophysica acta. Proteins and proteomics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure combined with mutagenesis and functional lipid transfer assay in a single study; applies to the PRELID3B/SLMO2-TRIAP1 complex specifically\",\n      \"pmids\": [\"36309326\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In yeast, depletion of Ups2 (ortholog of human PRELID3B/SLMO2) causes overactivation of the Snf1/AMPK pathway, leading to increased mitochondrial ATP production and enhanced quiescence entry. Knockdown of PRELID3B in human Rb1-deficient breast cancer cells decreased cell viability, placing PRELID3B upstream of AMPK signaling and linking its PS-transfer/PE-synthesis function to cellular energy metabolism and cell-cycle regulation.\",\n      \"method\": \"Yeast knockout (ups2∆), transcriptomic analysis, biochemical AMPK/Snf1 activity assays, genetic epistasis (sak1∆), siRNA knockdown of PRELID3B in human cancer cells, cell viability assay\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods in yeast with human PRELID3B knockdown validation, but human data is limited to viability assay without full mechanistic dissection\",\n      \"pmids\": [\"35639425\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SLMO2 (PRELID3B) physically interacts with TRIAP1 in ovarian cancer cells, and this interaction enhances mitochondrial membrane potential, reduces reactive oxygen species, inhibits autophagy, and suppresses apoptosis. Loss of SLMO2 or TRIAP1 reverses these effects, demonstrated both in vitro and in a xenograft model.\",\n      \"method\": \"Lentiviral overexpression/knockdown, co-immunoprecipitation (interaction with TRIAP1), flow cytometry (apoptosis, ROS, membrane potential), western blotting, immunofluorescence, transmission electron microscopy, mouse xenograft model\",\n      \"journal\": \"Histology and histopathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — reciprocal functional experiments with multiple cellular readouts and in vivo confirmation, but mechanistic pathway details (e.g., direct PS transfer) are inferred rather than directly demonstrated by transfer assay\",\n      \"pmids\": [\"40654025\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"PRELID3B was identified as a direct binding target of the ginseng metabolite compound K (CK) and its derivative CKD-4 using unbiased proteome integral solubility alteration and ProTargetMiner proteomics. Both compounds stabilize PRELID3B in cellular thermal shift assays and bind it with Kd of 23 µM (CK) and 5 µM (CKD-4) by biolayer interferometry. Inhibition of PRELID3B by these compounds depletes mitochondrial phospholipids, activates the integrated stress response, and triggers immunomodulatory pathways.\",\n      \"method\": \"Proteome integral solubility alteration (PISA) assay, ProTargetMiner analysis, cellular thermal shift assay (CETSA), biolayer interferometry, multiomics (lipidomics, transcriptomics), organoid and xenograft models\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal biophysical binding methods and multiomics functional validation, single lab study without independent replication\",\n      \"pmids\": [\"42081720\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PRELID3B (SLMO2) forms a complex with TRIAP1 in the mitochondrial intermembrane space and functions as a phosphatidylserine (PS)-specific lipid transfer protein that shuttles PS from the outer to the inner mitochondrial membrane, where PS is converted to phosphatidylethanolamine (PE) by phosphatidylserine decarboxylase; this PS-transfer activity, mediated by a water-mediated hydrogen bonding network in the PRELID domain, maintains mitochondrial morphology, membrane potential, and respiratory function, and its loss dysregulates AMPK/Snf1 signaling and promotes apoptosis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PRELID3B (SLMO2) is a mitochondrial intermembrane-space lipid transfer protein that shuttles phosphatidylserine (PS) from the outer to the inner mitochondrial membrane, where PS is decarboxylated to phosphatidylethanolamine, a pathway conserved from yeast (Ups2-Mdm35) through Drosophila to human and required for maintenance of mitochondrial morphology and respiratory function [#0, #1]. Lipid binding and transfer depend on an extended, water-mediated hydrogen-bonding network within the PRELID domain; disruption of this network (R53E) releases bound lipid and abolishes transfer activity [#2]. PRELID3B partners physically with TRIAP1, and in cancer cells this interaction sustains mitochondrial membrane potential, limits reactive oxygen species, and suppresses autophagy and apoptosis [#4]; notably, the Drosophila TRIAP1 ortholog was dispensable for SLMO's role in mitochondrial morphology, indicating the morphology function can proceed independently of the partner [#1]. Loss or pharmacological inhibition of PRELID3B depletes mitochondrial phospholipids and links its activity to cellular energy and stress signaling, including overactivation of the Snf1/AMPK pathway and activation of the integrated stress response [#3, #5]. PRELID3B is a direct binding target of the ginseng metabolite compound K and its derivative CKD-4 [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2016,\n      \"claim\": \"Established the core biochemical function: whether the SLMO2-TRIAP1 (yeast Ups2-Mdm35) complex actively moves PS across the mitochondrial intermembrane space to feed inner-membrane PE synthesis.\",\n      \"evidence\": \"Yeast genetic epistasis, in vitro lipid transfer assays, mitochondrial fractionation, and respiratory and cristae imaging\",\n      \"pmids\": [\"27241913\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Demonstrated in yeast; human complex function inferred from orthology in this study\",\n        \"Relative contributions of transfer-dependent versus trans-decarboxylation pathways in human cells not quantified\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined the structural basis of lipid handling: how the PRELID domain captures and releases lipid cargo during transfer.\",\n      \"evidence\": \"X-ray crystallography of apo and lipid-bound complex, molecular dynamics, R53E mutagenesis, and lipid transfer assays\",\n      \"pmids\": [\"36309326\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not resolve how PS is extracted from and inserted into membranes\",\n        \"Lipid head-group selectivity determinants not fully mapped\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Connected the lipid-transfer function to downstream energy and cell-cycle signaling, placing PRELID3B/Ups2 upstream of AMPK/Snf1.\",\n      \"evidence\": \"Yeast ups2\\u2206 transcriptomics and AMPK/Snf1 activity assays with sak1\\u2206 epistasis, plus siRNA knockdown and viability assay in Rb1-deficient human cancer cells\",\n      \"pmids\": [\"35639425\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Human data limited to a viability assay without mechanistic dissection of the AMPK link\",\n        \"How phospholipid changes mechanistically activate AMPK/Snf1 not established\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Confirmed directionality and conservation of PS transfer (OMM to IMM at the inner boundary membrane) and tested partner requirement for the morphology function.\",\n      \"evidence\": \"Drosophila forward genetic screen, PS transfer assays, electron/fluorescence microscopy, and human SLMO2 knockdown rescue\",\n      \"pmids\": [\"39680501\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Why dTRIAP is dispensable for morphology while TRIAP1 is functionally important elsewhere unresolved\",\n        \"Spatial mechanism at the inner boundary membrane not structurally defined\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showed the PRELID3B-TRIAP1 physical interaction controls mitochondrial fitness and cell survival in a disease (ovarian cancer) context.\",\n      \"evidence\": \"Co-immunoprecipitation, reciprocal knockdown/overexpression, flow cytometry of apoptosis/ROS/membrane potential, EM, and mouse xenograft\",\n      \"pmids\": [\"40654025\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct PS-transfer activity in this setting inferred rather than measured\",\n        \"Whether anti-apoptotic effects are downstream of lipid transfer or a separate function unclear\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified PRELID3B as a druggable direct target whose pharmacological inhibition depletes mitochondrial phospholipids and triggers stress and immunomodulatory responses.\",\n      \"evidence\": \"PISA and ProTargetMiner proteomics, CETSA, biolayer interferometry, and multiomics in organoid and xenograft models\",\n      \"pmids\": [\"42081720\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single-lab study without independent replication\",\n        \"Whether compound binding directly blocks PS transfer at the structural level not shown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PRELID3B engages source and target membranes for PS extraction/delivery and how its lipid output is mechanistically transduced into AMPK and integrated-stress-response signaling remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No structural model of the membrane-docking step\",\n        \"Causal chain from phospholipid depletion to AMPK/ISR activation not delineated in human cells\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TRIAP1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}