{"gene":"ABHD16A","run_date":"2026-04-28T17:12:37","timeline":{"discoveries":[{"year":2015,"finding":"ABHD16A was identified as a phosphatidylserine (PS) lipase that generates lysophosphatidylserine (lyso-PS) in mammalian systems. Genetic deletion of Abhd16a in mice decreased brain lyso-PS levels, while disruption of ABHD16A in mouse macrophages decreased LPS-induced cytokine production, establishing an ABHD16A-ABHD12 metabolic axis regulating lyso-PS levels in vivo.","method":"Activity-based protein profiling (ABPP), pharmacological inhibition, genetic knockout mice (Abhd16a-/-), lipidomics, cytokine measurements in macrophages","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (ABPP, pharmacology, genetic KO, lipidomics), replicated across cell types and in vivo","pmids":["25580854"],"is_preprint":false},{"year":2014,"finding":"ABHD16A (BAT5) exhibits monoacylglycerol (MAG) lipase activity in vitro, preferentially hydrolyzing long-chain unsaturated MAGs (1-linoleylglycerol, 15d-PGJ2-G) with low-micromolar Km values, with neutral pH optimum and preference for 1(3)- over 2-isomers; it has only marginal diacylglycerol, triacylglycerol, or lysophospholipase activity.","method":"Fluorescent glycerol assay with recombinant human and mouse ABHD16A expressed in HEK293 cells; activity-based protein profiling (ABPP); kinetic characterization; inhibitor profiling","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 — in vitro enzyme assay with recombinant protein, kinetics, substrate specificity, and inhibitor characterization in single rigorous study","pmids":["25290914"],"is_preprint":false},{"year":2020,"finding":"ABHD16A is localized to the endoplasmic reticulum (ER) in mammalian cells, as determined by subcellular organelle fractionation and immunofluorescence microscopy; cerebellar lyso-PS levels are most reduced by Abhd16a knockout, establishing that ER-localized ABHD16A is the primary source of lyso-PS in the cerebellum.","method":"Subcellular organelle fractionation, biochemical assays, immunofluorescence microscopy, immunohistochemistry with Abhd16a knockout mouse controls, mass spectrometry-based lipidomics","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 2 — direct localization with genetic KO controls and functional lipidomic readout, multiple orthogonal methods","pmids":["32462874"],"is_preprint":false},{"year":2022,"finding":"ABHD16A functions as a depalmitoylase that catalyzes the removal of S-palmitoyl groups from IFITM proteins (IFITM1, IFITM2, IFITM3), thereby decreasing their antiviral activity against RNA viruses; ABHD16A also regulates the subcellular localization of IFITM proteins.","method":"Acyl-PEGyl exchange gel shift (APEGS) assay in abhd16a-/- knockout cells and ABHD16A-overexpressing cells; antiviral activity assays","journal":"mBio","confidence":"High","confidence_rationale":"Tier 1–2 — direct biochemical depalmitoylation assay in knockout and overexpression systems with functional antiviral readout","pmids":["36314839"],"is_preprint":false},{"year":2021,"finding":"ABHD16A-generated lyso-PS activates RhoA and downstream LIMK/cofilin signaling cascade through GPR34/Gi subunit, promoting gastric cancer cell invasion and metastasis; miR-4646-5p, derived from intron 3 of ABHD16A with the aid of SRSF2, positively feeds back to regulate ABHD16A expression via PHD3/HIF1A stabilization.","method":"Lipid metabolomics, RhoA/LIMK/cofilin signaling assays, GPR34 pathway analysis, miRNA functional assays, co-immunoprecipitation, invasion/migration assays","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2–3 — multiple assays in a single lab establishing pathway placement with biochemical follow-up","pmids":["33875796"],"is_preprint":false},{"year":2021,"finding":"Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability; immunoblot analysis of fibroblasts from affected individuals confirmed absent or greatly reduced ABHD16A protein, establishing ABHD16A as essential for normal CNS development and function.","method":"Whole-exome sequencing, Sanger validation, immunoblot analysis of patient fibroblasts","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 — patient genetics with protein-level confirmation in multiple families; functional mechanism inferred from established lipase role","pmids":["34587489"],"is_preprint":false},{"year":2024,"finding":"Swine RNF5 (E3 ubiquitin ligase) physically interacts with ABHD16A and ubiquitinates it at residues K3 and K452, targeting it for proteasomal degradation, thereby relieving ABHD16A-mediated depalmitoylation of IFITM1 and restoring its antiviral activity.","method":"AlphaFold2-based protein interaction prediction, co-immunoprecipitation, immunofluorescence, ubiquitination assay, proteasome inhibitor experiments, APEGS depalmitoylation assay, antiviral activity assays","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 — co-IP, ubiquitination assay, site-directed mutagenesis at ubiquitination sites, and functional antiviral readout in single study","pmids":["39601593"],"is_preprint":false},{"year":2025,"finding":"ABHD16A catalyzes the depalmitoylation of IFITM1 in HepG2.215 cells, and CRISPR/Cas9 knockout of ABHD16A enhances anti-HBV activity of IFITM1, demonstrating that ABHD16A-mediated depalmitoylation negatively regulates IFITM1 antiviral function against DNA viruses as well as RNA viruses.","method":"Co-immunoprecipitation, APEGS assay, CRISPR/Cas9 knockout of IFITM1 and ABHD16A, HBV replication assay","journal":"Microbiology spectrum","confidence":"Medium","confidence_rationale":"Tier 2 — direct biochemical depalmitoylation assay combined with genetic KO and functional viral replication readout","pmids":["40434075"],"is_preprint":false},{"year":2025,"finding":"ABHD17A downregulates ABHD16A protein levels, thereby counteracting ABHD16A-mediated depalmitoylation of IFITM1 and increasing IFITM1 S-palmitoylation and antiviral activity; ABHD17A physically interacts with IFITM1 and lacks the DHHC palmitoylating motif, so its effect on IFITM1 palmitoylation is indirect via ABHD16A suppression.","method":"Co-immunoprecipitation, APEGS S-palmitoylation assay, overexpression and knockdown experiments, sequence alignment","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 2–3 — biochemical palmitoylation assay with mechanistic follow-up showing ABHD16A as intermediary, single lab","pmids":["40723864"],"is_preprint":false},{"year":2021,"finding":"IFITM3 interacts directly with ABHD16A (confirmed by yeast two-hybrid) and co-localizes with ABHD16A at the cell membrane; co-expression of IFITM3 and ABHD16A reduces inflammatory cytokine mRNA levels (IL-1β, IL-6, IL-10, TNF-α) compared to single expression, suggesting functional interplay in inflammatory regulation. NOTE: The original paper (PMID:33763481) was subsequently retracted (PMID:35434131).","method":"Yeast two-hybrid, laser confocal co-localization, fluorescent quantitative PCR","journal":"BioMed research international","confidence":"Low","confidence_rationale":"Tier 3 — yeast two-hybrid and co-localization only; paper subsequently retracted","pmids":["33763481","35434131"],"is_preprint":false}],"current_model":"ABHD16A is an ER-localized metabolic serine hydrolase that functions as both a phosphatidylserine lipase (generating immunomodulatory lysophosphatidylserines that signal through GPR34/RhoA/LIMK pathways) and a protein depalmitoylase (removing S-palmitoyl groups from IFITM antiviral proteins to dampen innate immune responses), with its activity regulated by ubiquitin-mediated proteasomal degradation via RNF5, and its loss-of-function in humans causing a hereditary spastic paraplegia with intellectual disability."},"narrative":{"teleology":[{"year":2014,"claim":"Establishing the enzymatic identity of ABHD16A: recombinant protein was shown to possess monoacylglycerol lipase activity with defined substrate preferences, demonstrating it is an active serine hydrolase rather than a catalytically dead member of the α/β-hydrolase family.","evidence":"Fluorescent glycerol assay with recombinant ABHD16A, kinetic characterization, and inhibitor profiling in HEK293 cells","pmids":["25290914"],"confidence":"High","gaps":["Physiological substrate in vivo was not identified; in vitro specificity for MAGs did not predict PS lipase activity","No structural model explaining substrate selectivity"]},{"year":2015,"claim":"Identifying the physiological substrate and metabolic axis: ABHD16A was discovered to be the major PS lipase producing immunomodulatory lyso-PS in vivo, working opposite to ABHD12 which degrades lyso-PS, thereby establishing the ABHD16A–ABHD12 metabolic axis controlling neuroinflammatory lipid signaling.","evidence":"ABPP, Abhd16a knockout mice showing decreased brain lyso-PS, and macrophage cytokine assays","pmids":["25580854"],"confidence":"High","gaps":["Lyso-PS receptor mediating downstream signaling was not identified in this study","Tissue-specific contributions of ABHD16A to lyso-PS pools beyond brain and macrophages were unexplored"]},{"year":2020,"claim":"Resolving subcellular localization: ABHD16A was localized to the endoplasmic reticulum, and the cerebellum was identified as the brain region most dependent on ABHD16A for lyso-PS production, linking ER-resident lipase activity to region-specific lipid metabolism.","evidence":"Subcellular fractionation, immunofluorescence with KO controls, and cerebellar lipidomics in Abhd16a-/- mice","pmids":["32462874"],"confidence":"High","gaps":["How ER-generated lyso-PS reaches the extracellular space or plasma membrane for signaling was not determined","Whether ABHD16A also localizes to other compartments in non-neuronal cells was not resolved"]},{"year":2021,"claim":"Connecting lyso-PS to a specific signaling pathway: ABHD16A-generated lyso-PS was shown to activate RhoA through GPR34/Gi, driving LIMK/cofilin-mediated cancer cell invasion, and a positive feedback loop via an intronic miRNA (miR-4646-5p) sustaining ABHD16A expression was uncovered.","evidence":"Lipid metabolomics, RhoA/LIMK/cofilin signaling assays, GPR34 pathway analysis, and miRNA functional assays in gastric cancer cells","pmids":["33875796"],"confidence":"Medium","gaps":["GPR34 pathway placement relies on a single cancer cell model; generalizability to normal physiology not established","The miR-4646-5p/PHD3/HIF1A feedback loop awaits independent replication"]},{"year":2021,"claim":"Establishing a human disease link: bi-allelic loss-of-function ABHD16A variants were shown to cause hereditary spastic paraplegia with intellectual disability, confirming the gene's essential role in CNS development.","evidence":"Whole-exome sequencing in multiple families with Sanger validation and immunoblot confirmation of absent protein in patient fibroblasts","pmids":["34587489"],"confidence":"Medium","gaps":["Whether disease pathology is driven by lyso-PS deficiency, aberrant palmitoylation, or both was not determined","No rescue experiment was performed to confirm causality beyond genetics"]},{"year":2022,"claim":"Revealing a second enzymatic function: ABHD16A was identified as a depalmitoylase for IFITM proteins, establishing a direct role in innate antiviral immunity by removing S-palmitoyl groups that are required for IFITM antiviral activity.","evidence":"APEGS depalmitoylation assay in ABHD16A knockout and overexpression cells, with functional antiviral readout against RNA viruses","pmids":["36314839"],"confidence":"High","gaps":["Whether depalmitoylase and PS lipase activities use the same catalytic site or represent distinct reaction mechanisms was not addressed","Full spectrum of palmitoylated substrates beyond IFITMs is unknown"]},{"year":2024,"claim":"Identifying a regulatory mechanism for ABHD16A turnover: RNF5-mediated ubiquitination at K3 and K452 targets ABHD16A for proteasomal degradation, providing a mechanism by which cells can restore IFITM1 antiviral function by eliminating the depalmitoylase.","evidence":"Co-immunoprecipitation, ubiquitination assay with site-directed mutagenesis, proteasome inhibitor experiments, and antiviral assays in swine cells","pmids":["39601593"],"confidence":"Medium","gaps":["Demonstrated in swine system; conservation of RNF5-ABHD16A axis in human cells not confirmed","Physiological signals triggering RNF5-mediated degradation of ABHD16A are unknown"]},{"year":2025,"claim":"Extending the depalmitoylase function to DNA viruses and identifying ABHD17A as an indirect regulator: ABHD16A-mediated depalmitoylation of IFITM1 was shown to dampen anti-HBV activity, and ABHD17A was found to counteract ABHD16A by promoting its downregulation rather than by direct palmitoylation of IFITMs.","evidence":"CRISPR/Cas9 knockout of ABHD16A in HepG2.215 cells with HBV replication assay; ABHD17A overexpression/knockdown with APEGS assay","pmids":["40434075","40723864"],"confidence":"Medium","gaps":["Mechanism by which ABHD17A downregulates ABHD16A protein is unresolved","Whether ABHD16A depalmitoylates non-IFITM substrates relevant to viral defense is unknown"]},{"year":null,"claim":"Key unresolved questions include: (1) how the dual enzymatic activities (PS lipase vs. depalmitoylase) are coordinated or regulated in different cellular contexts, (2) the full palmitoyl-proteome regulated by ABHD16A, and (3) whether the hereditary spastic paraplegia phenotype arises from impaired lyso-PS signaling, aberrant protein palmitoylation, or both.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of ABHD16A exists to explain dual substrate specificity","Relative contributions of lipase vs. depalmitoylase activity to CNS disease are not delineated","Comprehensive palmitoyl-proteomics in ABHD16A knockout cells has not been performed"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[3,6,7]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1,2]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,6,7]}],"complexes":[],"partners":["IFITM1","IFITM2","IFITM3","RNF5","ABHD17A","GPR34"],"other_free_text":[]},"mechanistic_narrative":"ABHD16A is a serine hydrolase with dual metabolic functions: it acts as a phosphatidylserine lipase generating lysophosphatidylserine (lyso-PS), and as a protein depalmitoylase that removes S-palmitoyl groups from IFITM antiviral proteins. As a PS lipase localized to the endoplasmic reticulum, ABHD16A is the primary source of lyso-PS in the brain, operating in a metabolic axis with ABHD12 to regulate lyso-PS levels; its lyso-PS product signals through GPR34 to activate RhoA/LIMK/cofilin signaling [PMID:25580854, PMID:32462874, PMID:33875796]. As a depalmitoylase, ABHD16A removes S-palmitoyl modifications from IFITM1, IFITM2, and IFITM3, dampening their antiviral activity against both RNA and DNA viruses; this depalmitoylase function is negatively regulated by RNF5-mediated ubiquitination at K3 and K452, which targets ABHD16A for proteasomal degradation [PMID:36314839, PMID:40434075, PMID:39601593]. Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability [PMID:34587489]."},"prefetch_data":{"uniprot":{"accession":"O95870","full_name":"Phosphatidylserine lipase ABHD16A","aliases":["Alpha/beta hydrolase domain-containing protein 16A","Abhydrolase domain-containing protein 16A","HLA-B-associated transcript 5","hBAT5","Monoacylglycerol lipase ABHD16A","Protein G5"],"length_aa":558,"mass_kda":63.2,"function":"Phosphatidylserine (PS) lipase that mediates the hydrolysis of phosphatidylserine to generate lysophosphatidylserine (LPS) (By similarity). LPS constitutes a class of signaling lipids that regulates immunological and neurological processes (By similarity). Has no activity towards diacylglycerol, triacylglycerol or lysophosphatidylserine lipase (PubMed:25290914). Also has monoacylglycerol lipase activity, with preference for 1-(9Z,12Z-octadecadienoyl)-glycerol (1-LG) and 2-glyceryl-15-deoxy-Delta(12,14)-prostaglandin J2 (15d-PGJ(2)-G) (PubMed:25290914)","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/O95870/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ABHD16A","classification":"Not Classified","n_dependent_lines":14,"n_total_lines":1208,"dependency_fraction":0.011589403973509934},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ABHD16A","total_profiled":1310},"omim":[{"mim_id":"619735","title":"SPASTIC PARAPLEGIA 86, AUTOSOMAL RECESSIVE; SPG86","url":"https://www.omim.org/entry/619735"},{"mim_id":"270800","title":"SPASTIC PARAPLEGIA 5A, AUTOSOMAL RECESSIVE; SPG5A","url":"https://www.omim.org/entry/270800"},{"mim_id":"142620","title":"ABHYDROLASE DOMAIN-CONTAINING PROTEIN 16A, PHOSPHOLIPASE; ABHD16A","url":"https://www.omim.org/entry/142620"},{"mim_id":"142610","title":"G-PATCH DOMAIN- AND ANKYRIN REPEATS-CONTAINING PROTEIN 1; GPANK1","url":"https://www.omim.org/entry/142610"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ABHD16A"},"hgnc":{"alias_symbol":["NG26","D6S82E"],"prev_symbol":["BAT5"]},"alphafold":{"accession":"O95870","domains":[{"cath_id":"-","chopping":"1-17_48-150","consensus_level":"medium","plddt":90.8094,"start":1,"end":150},{"cath_id":"3.40.50","chopping":"158-165_198-420","consensus_level":"medium","plddt":95.4773,"start":158,"end":420},{"cath_id":"-","chopping":"423-440_451-558","consensus_level":"medium","plddt":95.6262,"start":423,"end":558}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O95870","model_url":"https://alphafold.ebi.ac.uk/files/AF-O95870-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O95870-F1-predicted_aligned_error_v6.png","plddt_mean":89.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ABHD16A","jax_strain_url":"https://www.jax.org/strain/search?query=ABHD16A"},"sequence":{"accession":"O95870","fasta_url":"https://rest.uniprot.org/uniprotkb/O95870.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O95870/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O95870"}},"corpus_meta":[{"pmid":"25580854","id":"PMC_25580854","title":"Immunomodulatory lysophosphatidylserines are regulated by ABHD16A and ABHD12 interplay.","date":"2015","source":"Nature chemical biology","url":"https://pubmed.ncbi.nlm.nih.gov/25580854","citation_count":126,"is_preprint":false},{"pmid":"25290914","id":"PMC_25290914","title":"Biochemical and pharmacological characterization of the human lymphocyte antigen B-associated transcript 5 (BAT5/ABHD16A).","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25290914","citation_count":42,"is_preprint":false},{"pmid":"29794032","id":"PMC_29794032","title":"Sequence analysis and structure prediction of ABHD16A and the roles of the ABHD family members in human disease.","date":"2018","source":"Open biology","url":"https://pubmed.ncbi.nlm.nih.gov/29794032","citation_count":33,"is_preprint":false},{"pmid":"33875796","id":"PMC_33875796","title":"Mirtronic miR-4646-5p promotes gastric cancer metastasis by regulating ABHD16A and metabolite lysophosphatidylserines.","date":"2021","source":"Cell death and differentiation","url":"https://pubmed.ncbi.nlm.nih.gov/33875796","citation_count":33,"is_preprint":false},{"pmid":"32462874","id":"PMC_32462874","title":"Mapping the Neuroanatomy of ABHD16A, ABHD12, and Lysophosphatidylserines Provides New Insights into the Pathophysiology of the Human Neurological Disorder PHARC.","date":"2020","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32462874","citation_count":27,"is_preprint":false},{"pmid":"36314839","id":"PMC_36314839","title":"ABHD16A Negatively Regulates the Palmitoylation and Antiviral Function of IFITM Proteins.","date":"2022","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/36314839","citation_count":21,"is_preprint":false},{"pmid":"34587489","id":"PMC_34587489","title":"ABHD16A deficiency causes a complicated form of hereditary spastic paraplegia associated with intellectual disability and cerebral anomalies.","date":"2021","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34587489","citation_count":17,"is_preprint":false},{"pmid":"40723864","id":"PMC_40723864","title":"The Unconventional Role of ABHD17A in Increasing the S-Palmitoylation and Antiviral Activity of IFITM1 by Downregulating ABHD16A.","date":"2025","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/40723864","citation_count":6,"is_preprint":false},{"pmid":"39601593","id":"PMC_39601593","title":"Swine RNF5 positively regulates the antiviral activity of IFITM1 by mediating the degradation of ABHD16A.","date":"2024","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/39601593","citation_count":4,"is_preprint":false},{"pmid":"33763481","id":"PMC_33763481","title":"Human Interferon Inducible Transmembrane Protein 3 (IFITM3) Inhibits Influenza Virus A Replication and Inflammation by Interacting with ABHD16A.","date":"2021","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/33763481","citation_count":4,"is_preprint":false},{"pmid":"37849541","id":"PMC_37849541","title":"Probing the Interactions of Thiazole Abietane Inhibitors with the Human Serine Hydrolases ABHD16A and ABHD12.","date":"2023","source":"ACS medicinal chemistry letters","url":"https://pubmed.ncbi.nlm.nih.gov/37849541","citation_count":3,"is_preprint":false},{"pmid":"8919359","id":"PMC_8919359","title":"Identification of a recombinational breakpoint at the BAT5 locus in three intra-H-2 recombinant inbred mouse strains.","date":"1995","source":"Experimental and clinical immunogenetics","url":"https://pubmed.ncbi.nlm.nih.gov/8919359","citation_count":3,"is_preprint":false},{"pmid":"40434075","id":"PMC_40434075","title":"Depalmitoylase ABHD16A negatively regulates the anti-hepatitis B virus activity of IFITM1.","date":"2025","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/40434075","citation_count":3,"is_preprint":false},{"pmid":"35434131","id":"PMC_35434131","title":"Retracted: Human Interferon Inducible Transmembrane Protein 3 (IFITM3) Inhibits Influenza Virus A Replication and Inflammation by Interacting with ABHD16A.","date":"2022","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/35434131","citation_count":0,"is_preprint":false},{"pmid":"41561502","id":"PMC_41561502","title":"Expansion of the genetic and phenotypic spectrum of hereditary spastic paraplegia caused by ABHD16A gene variants: an integrated analysis based on novel variants and literature review.","date":"2026","source":"Frontiers in pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/41561502","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9726,"output_tokens":2708,"usd":0.034899},"stage2":{"model":"claude-opus-4-6","input_tokens":6034,"output_tokens":2654,"usd":0.14478},"total_usd":0.179679,"stage1_batch_id":"msgbatch_01TqNM6p6FsoMBT2jzQTwKBr","stage2_batch_id":"msgbatch_01Ya473eco8sTHbvRymQaU8o","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"ABHD16A was identified as a phosphatidylserine (PS) lipase that generates lysophosphatidylserine (lyso-PS) in mammalian systems. Genetic deletion of Abhd16a in mice decreased brain lyso-PS levels, while disruption of ABHD16A in mouse macrophages decreased LPS-induced cytokine production, establishing an ABHD16A-ABHD12 metabolic axis regulating lyso-PS levels in vivo.\",\n      \"method\": \"Activity-based protein profiling (ABPP), pharmacological inhibition, genetic knockout mice (Abhd16a-/-), lipidomics, cytokine measurements in macrophages\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (ABPP, pharmacology, genetic KO, lipidomics), replicated across cell types and in vivo\",\n      \"pmids\": [\"25580854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ABHD16A (BAT5) exhibits monoacylglycerol (MAG) lipase activity in vitro, preferentially hydrolyzing long-chain unsaturated MAGs (1-linoleylglycerol, 15d-PGJ2-G) with low-micromolar Km values, with neutral pH optimum and preference for 1(3)- over 2-isomers; it has only marginal diacylglycerol, triacylglycerol, or lysophospholipase activity.\",\n      \"method\": \"Fluorescent glycerol assay with recombinant human and mouse ABHD16A expressed in HEK293 cells; activity-based protein profiling (ABPP); kinetic characterization; inhibitor profiling\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro enzyme assay with recombinant protein, kinetics, substrate specificity, and inhibitor characterization in single rigorous study\",\n      \"pmids\": [\"25290914\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"ABHD16A is localized to the endoplasmic reticulum (ER) in mammalian cells, as determined by subcellular organelle fractionation and immunofluorescence microscopy; cerebellar lyso-PS levels are most reduced by Abhd16a knockout, establishing that ER-localized ABHD16A is the primary source of lyso-PS in the cerebellum.\",\n      \"method\": \"Subcellular organelle fractionation, biochemical assays, immunofluorescence microscopy, immunohistochemistry with Abhd16a knockout mouse controls, mass spectrometry-based lipidomics\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — direct localization with genetic KO controls and functional lipidomic readout, multiple orthogonal methods\",\n      \"pmids\": [\"32462874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ABHD16A functions as a depalmitoylase that catalyzes the removal of S-palmitoyl groups from IFITM proteins (IFITM1, IFITM2, IFITM3), thereby decreasing their antiviral activity against RNA viruses; ABHD16A also regulates the subcellular localization of IFITM proteins.\",\n      \"method\": \"Acyl-PEGyl exchange gel shift (APEGS) assay in abhd16a-/- knockout cells and ABHD16A-overexpressing cells; antiviral activity assays\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — direct biochemical depalmitoylation assay in knockout and overexpression systems with functional antiviral readout\",\n      \"pmids\": [\"36314839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ABHD16A-generated lyso-PS activates RhoA and downstream LIMK/cofilin signaling cascade through GPR34/Gi subunit, promoting gastric cancer cell invasion and metastasis; miR-4646-5p, derived from intron 3 of ABHD16A with the aid of SRSF2, positively feeds back to regulate ABHD16A expression via PHD3/HIF1A stabilization.\",\n      \"method\": \"Lipid metabolomics, RhoA/LIMK/cofilin signaling assays, GPR34 pathway analysis, miRNA functional assays, co-immunoprecipitation, invasion/migration assays\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — multiple assays in a single lab establishing pathway placement with biochemical follow-up\",\n      \"pmids\": [\"33875796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability; immunoblot analysis of fibroblasts from affected individuals confirmed absent or greatly reduced ABHD16A protein, establishing ABHD16A as essential for normal CNS development and function.\",\n      \"method\": \"Whole-exome sequencing, Sanger validation, immunoblot analysis of patient fibroblasts\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — patient genetics with protein-level confirmation in multiple families; functional mechanism inferred from established lipase role\",\n      \"pmids\": [\"34587489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Swine RNF5 (E3 ubiquitin ligase) physically interacts with ABHD16A and ubiquitinates it at residues K3 and K452, targeting it for proteasomal degradation, thereby relieving ABHD16A-mediated depalmitoylation of IFITM1 and restoring its antiviral activity.\",\n      \"method\": \"AlphaFold2-based protein interaction prediction, co-immunoprecipitation, immunofluorescence, ubiquitination assay, proteasome inhibitor experiments, APEGS depalmitoylation assay, antiviral activity assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — co-IP, ubiquitination assay, site-directed mutagenesis at ubiquitination sites, and functional antiviral readout in single study\",\n      \"pmids\": [\"39601593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ABHD16A catalyzes the depalmitoylation of IFITM1 in HepG2.215 cells, and CRISPR/Cas9 knockout of ABHD16A enhances anti-HBV activity of IFITM1, demonstrating that ABHD16A-mediated depalmitoylation negatively regulates IFITM1 antiviral function against DNA viruses as well as RNA viruses.\",\n      \"method\": \"Co-immunoprecipitation, APEGS assay, CRISPR/Cas9 knockout of IFITM1 and ABHD16A, HBV replication assay\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct biochemical depalmitoylation assay combined with genetic KO and functional viral replication readout\",\n      \"pmids\": [\"40434075\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ABHD17A downregulates ABHD16A protein levels, thereby counteracting ABHD16A-mediated depalmitoylation of IFITM1 and increasing IFITM1 S-palmitoylation and antiviral activity; ABHD17A physically interacts with IFITM1 and lacks the DHHC palmitoylating motif, so its effect on IFITM1 palmitoylation is indirect via ABHD16A suppression.\",\n      \"method\": \"Co-immunoprecipitation, APEGS S-palmitoylation assay, overexpression and knockdown experiments, sequence alignment\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — biochemical palmitoylation assay with mechanistic follow-up showing ABHD16A as intermediary, single lab\",\n      \"pmids\": [\"40723864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"IFITM3 interacts directly with ABHD16A (confirmed by yeast two-hybrid) and co-localizes with ABHD16A at the cell membrane; co-expression of IFITM3 and ABHD16A reduces inflammatory cytokine mRNA levels (IL-1β, IL-6, IL-10, TNF-α) compared to single expression, suggesting functional interplay in inflammatory regulation. NOTE: The original paper (PMID:33763481) was subsequently retracted (PMID:35434131).\",\n      \"method\": \"Yeast two-hybrid, laser confocal co-localization, fluorescent quantitative PCR\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — yeast two-hybrid and co-localization only; paper subsequently retracted\",\n      \"pmids\": [\"33763481\", \"35434131\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ABHD16A is an ER-localized metabolic serine hydrolase that functions as both a phosphatidylserine lipase (generating immunomodulatory lysophosphatidylserines that signal through GPR34/RhoA/LIMK pathways) and a protein depalmitoylase (removing S-palmitoyl groups from IFITM antiviral proteins to dampen innate immune responses), with its activity regulated by ubiquitin-mediated proteasomal degradation via RNF5, and its loss-of-function in humans causing a hereditary spastic paraplegia with intellectual disability.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ABHD16A is a serine hydrolase with dual metabolic functions: it acts as a phosphatidylserine lipase generating lysophosphatidylserine (lyso-PS), and as a protein depalmitoylase that removes S-palmitoyl groups from IFITM antiviral proteins. As a PS lipase localized to the endoplasmic reticulum, ABHD16A is the primary source of lyso-PS in the brain, operating in a metabolic axis with ABHD12 to regulate lyso-PS levels; its lyso-PS product signals through GPR34 to activate RhoA/LIMK/cofilin signaling [PMID:25580854, PMID:32462874, PMID:33875796]. As a depalmitoylase, ABHD16A removes S-palmitoyl modifications from IFITM1, IFITM2, and IFITM3, dampening their antiviral activity against both RNA and DNA viruses; this depalmitoylase function is negatively regulated by RNF5-mediated ubiquitination at K3 and K452, which targets ABHD16A for proteasomal degradation [PMID:36314839, PMID:40434075, PMID:39601593]. Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability [PMID:34587489].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing the enzymatic identity of ABHD16A: recombinant protein was shown to possess monoacylglycerol lipase activity with defined substrate preferences, demonstrating it is an active serine hydrolase rather than a catalytically dead member of the α/β-hydrolase family.\",\n      \"evidence\": \"Fluorescent glycerol assay with recombinant ABHD16A, kinetic characterization, and inhibitor profiling in HEK293 cells\",\n      \"pmids\": [\"25290914\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Physiological substrate in vivo was not identified; in vitro specificity for MAGs did not predict PS lipase activity\",\n        \"No structural model explaining substrate selectivity\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identifying the physiological substrate and metabolic axis: ABHD16A was discovered to be the major PS lipase producing immunomodulatory lyso-PS in vivo, working opposite to ABHD12 which degrades lyso-PS, thereby establishing the ABHD16A–ABHD12 metabolic axis controlling neuroinflammatory lipid signaling.\",\n      \"evidence\": \"ABPP, Abhd16a knockout mice showing decreased brain lyso-PS, and macrophage cytokine assays\",\n      \"pmids\": [\"25580854\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Lyso-PS receptor mediating downstream signaling was not identified in this study\",\n        \"Tissue-specific contributions of ABHD16A to lyso-PS pools beyond brain and macrophages were unexplored\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolving subcellular localization: ABHD16A was localized to the endoplasmic reticulum, and the cerebellum was identified as the brain region most dependent on ABHD16A for lyso-PS production, linking ER-resident lipase activity to region-specific lipid metabolism.\",\n      \"evidence\": \"Subcellular fractionation, immunofluorescence with KO controls, and cerebellar lipidomics in Abhd16a-/- mice\",\n      \"pmids\": [\"32462874\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How ER-generated lyso-PS reaches the extracellular space or plasma membrane for signaling was not determined\",\n        \"Whether ABHD16A also localizes to other compartments in non-neuronal cells was not resolved\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connecting lyso-PS to a specific signaling pathway: ABHD16A-generated lyso-PS was shown to activate RhoA through GPR34/Gi, driving LIMK/cofilin-mediated cancer cell invasion, and a positive feedback loop via an intronic miRNA (miR-4646-5p) sustaining ABHD16A expression was uncovered.\",\n      \"evidence\": \"Lipid metabolomics, RhoA/LIMK/cofilin signaling assays, GPR34 pathway analysis, and miRNA functional assays in gastric cancer cells\",\n      \"pmids\": [\"33875796\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"GPR34 pathway placement relies on a single cancer cell model; generalizability to normal physiology not established\",\n        \"The miR-4646-5p/PHD3/HIF1A feedback loop awaits independent replication\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Establishing a human disease link: bi-allelic loss-of-function ABHD16A variants were shown to cause hereditary spastic paraplegia with intellectual disability, confirming the gene's essential role in CNS development.\",\n      \"evidence\": \"Whole-exome sequencing in multiple families with Sanger validation and immunoblot confirmation of absent protein in patient fibroblasts\",\n      \"pmids\": [\"34587489\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether disease pathology is driven by lyso-PS deficiency, aberrant palmitoylation, or both was not determined\",\n        \"No rescue experiment was performed to confirm causality beyond genetics\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealing a second enzymatic function: ABHD16A was identified as a depalmitoylase for IFITM proteins, establishing a direct role in innate antiviral immunity by removing S-palmitoyl groups that are required for IFITM antiviral activity.\",\n      \"evidence\": \"APEGS depalmitoylation assay in ABHD16A knockout and overexpression cells, with functional antiviral readout against RNA viruses\",\n      \"pmids\": [\"36314839\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether depalmitoylase and PS lipase activities use the same catalytic site or represent distinct reaction mechanisms was not addressed\",\n        \"Full spectrum of palmitoylated substrates beyond IFITMs is unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identifying a regulatory mechanism for ABHD16A turnover: RNF5-mediated ubiquitination at K3 and K452 targets ABHD16A for proteasomal degradation, providing a mechanism by which cells can restore IFITM1 antiviral function by eliminating the depalmitoylase.\",\n      \"evidence\": \"Co-immunoprecipitation, ubiquitination assay with site-directed mutagenesis, proteasome inhibitor experiments, and antiviral assays in swine cells\",\n      \"pmids\": [\"39601593\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Demonstrated in swine system; conservation of RNF5-ABHD16A axis in human cells not confirmed\",\n        \"Physiological signals triggering RNF5-mediated degradation of ABHD16A are unknown\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extending the depalmitoylase function to DNA viruses and identifying ABHD17A as an indirect regulator: ABHD16A-mediated depalmitoylation of IFITM1 was shown to dampen anti-HBV activity, and ABHD17A was found to counteract ABHD16A by promoting its downregulation rather than by direct palmitoylation of IFITMs.\",\n      \"evidence\": \"CRISPR/Cas9 knockout of ABHD16A in HepG2.215 cells with HBV replication assay; ABHD17A overexpression/knockdown with APEGS assay\",\n      \"pmids\": [\"40434075\", \"40723864\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which ABHD17A downregulates ABHD16A protein is unresolved\",\n        \"Whether ABHD16A depalmitoylates non-IFITM substrates relevant to viral defense is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Key unresolved questions include: (1) how the dual enzymatic activities (PS lipase vs. depalmitoylase) are coordinated or regulated in different cellular contexts, (2) the full palmitoyl-proteome regulated by ABHD16A, and (3) whether the hereditary spastic paraplegia phenotype arises from impaired lyso-PS signaling, aberrant protein palmitoylation, or both.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of ABHD16A exists to explain dual substrate specificity\",\n        \"Relative contributions of lipase vs. depalmitoylase activity to CNS disease are not delineated\",\n        \"Comprehensive palmitoyl-proteomics in ABHD16A knockout cells has not been performed\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [3, 6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 6, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"IFITM1\",\n      \"IFITM2\",\n      \"IFITM3\",\n      \"RNF5\",\n      \"ABHD17A\",\n      \"GPR34\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}