{"gene":"ABHD16A","run_date":"2026-06-09T22:02:37","timeline":{"discoveries":[{"year":2015,"finding":"ABHD16A is a phosphatidylserine (PS) lipase that generates lysophosphatidylserine (lyso-PS) in mammalian systems. Genetic knockout of Abhd16a in mice decreases brain lyso-PS levels, opposite to the elevation seen in Abhd12-/- mice. In mouse macrophages, disruption of ABHD16A decreases lyso-PS and lipopolysaccharide-induced cytokine production, placing ABHD16A upstream of ABHD12 in an lyso-PS biosynthesis-degradation axis.","method":"Activity-based protein profiling (ABPP), pharmacological inhibition, genetic knockout mice (Abhd16a-/-, Abhd12-/-), lipid mass spectrometry, cytokine measurements in macrophages","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (ABPP, pharmacological inhibitor, genetic KO) replicated across cell and in vivo contexts, defining enzymatic activity and pathway position","pmids":["25580854"],"is_preprint":false},{"year":2014,"finding":"ABHD16A (BAT5) is a catalytically active serine hydrolase with monoacylglycerol (MAG) lipase activity in vitro, preferring long-chain unsaturated MAGs (1-linoleylglycerol, 15d-PGJ2-G; low-micromolar Km). It shows only marginal diacylglycerol, triacylglycerol, or lysophospholipase activity. The enzyme has a neutral pH optimum and preference for 1(3)- vs 2-MAG isomers. Beta-lactone-based lipase inhibitors and the HSL inhibitor C7600 inhibit it at nanomolar concentrations.","method":"Activity-based protein profiling (ABPP), fluorescent glycerol substrate assay, inhibitor profiling (IC50 measurements), recombinant expression in HEK293 cells","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay with substrate panel and inhibitor SAR, single lab, multiple biochemical methods","pmids":["25290914"],"is_preprint":false},{"year":2020,"finding":"ABHD16A is localized to the endoplasmic reticulum (ER) in mammalian cells, as demonstrated by subcellular organelle fractionation and immunofluorescence microscopy. In the murine brain, ABHD16A and ABHD12 localize to distinct regions and cell types in the cerebellum. Cerebellar lyso-PS levels are most reduced by ABHD16A deletion and most elevated by ABHD12 deletion, establishing functional cross-talk between the two lipases specifically in the cerebellum.","method":"Subcellular organelle fractionation, immunofluorescence high-resolution microscopy, immunohistochemistry with genetic KO controls, quantitative mass spectrometry of lyso-PS in brain regions","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (fractionation, immunofluorescence, IHC with KO controls, MS lipidomics) in a single rigorous study establishing ER localization and regional functional consequence","pmids":["32462874"],"is_preprint":false},{"year":2021,"finding":"ABHD16A, acting as a PS lipase, generates lyso-PS in gastric cancer cells, which stimulates RhoA and the downstream LIMK/cofilin cascade through GPR34/Gi signaling, promoting cancer cell invasion and metastasis.","method":"ABHD16A overexpression/knockdown, lyso-PS measurement, RhoA/LIMK/cofilin pathway analysis, GPR34/Gi pharmacological dissection, cell invasion assays","journal":"Cell death and differentiation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic manipulation combined with lipidomics and downstream pathway analysis, single lab, multiple methods linking ABHD16A enzymatic activity to a signaling cascade","pmids":["33875796"],"is_preprint":false},{"year":2022,"finding":"ABHD16A functions as a depalmitoylase that catalyzes the depalmitoyl reaction on S-palmitoylated IFITM proteins (IFITM1, IFITM2, IFITM3), thereby decreasing their S-palmitoylation levels and reducing their antiviral activity against RNA viruses. ABHD16A also regulates subcellular localization of IFITM proteins.","method":"Acyl-PEGyl exchange gel shift (APEGS) assay for palmitoylation detection, ABHD16A knockout cells (abhd16a-/-), ABHD16A overexpression, antiviral activity assays, immunofluorescence for localization","journal":"mBio","confidence":"High","confidence_rationale":"Tier 1 / Strong — enzymatic depalmitoylation activity demonstrated biochemically (APEGS) in both KO and overexpression systems across three species, with functional antiviral readout","pmids":["36314839"],"is_preprint":false},{"year":2024,"finding":"Swine RNF5 (E3 ubiquitin ligase) interacts with ABHD16A and targets it for ubiquitination at residues K3 and K452, leading to proteasomal degradation of ABHD16A. This degradation attenuates ABHD16A-mediated depalmitoylation of IFITM1, thereby restoring IFITM1 antiviral activity.","method":"AlphaFold2-based protein-protein interaction prediction, co-immunoprecipitation, immunofluorescence, ubiquitination assays, proteasome inhibitor experiments, ABHD16A KO/overexpression with antiviral readouts","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and functional ubiquitination assays with site identification (K3, K452), single lab, multiple methods","pmids":["39601593"],"is_preprint":false},{"year":2025,"finding":"ABHD17A physically interacts with IFITM1 and indirectly increases its S-palmitoylation by downregulating ABHD16A expression, thereby counteracting ABHD16A-mediated depalmitoylation of IFITM1 and enhancing IFITM1 antiviral activity.","method":"Co-immunoprecipitation, Western blotting for ABHD16A protein levels, APEGS assay for palmitoylation, antiviral activity assays","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — single lab, co-IP plus functional assay, but the mechanism of ABHD17A-mediated ABHD16A downregulation is incompletely resolved in the abstract","pmids":["40723864"],"is_preprint":false},{"year":2025,"finding":"ABHD16A catalyzes depalmitoylation of IFITM1 in hepatocytes (HepG2.215 cells), and this depalmitoylation negatively regulates IFITM1 anti-HBV activity. CRISPR/Cas9 knockout of ABHD16A increased IFITM1 palmitoylation and enhanced restriction of HBV replication.","method":"Co-immunoprecipitation, APEGS palmitoylation assay, CRISPR/Cas9 knockout of ABHD16A and IFITM1, HBV replication assay","journal":"Microbiology spectrum","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical depalmitoylation assay combined with genetic KO and functional viral replication readout, single lab","pmids":["40434075"],"is_preprint":false},{"year":2021,"finding":"IFITM3 interacts with ABHD16A (confirmed by yeast two-hybrid), and they co-localize at the cell membrane. Co-expression of IFITM3 and ABHD16A modulates inflammatory cytokine production (IL-1β, IL-6, IL-10, TNF-α) in response to influenza A virus infection. NOTE: The original paper (PMID:33763481) was retracted (PMID:35434131); findings should be interpreted with caution.","method":"Yeast two-hybrid, laser confocal co-localization, fluorescence quantitative PCR for cytokines, overexpression in HEK293 cells","journal":"BioMed research international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — yeast two-hybrid and co-localization only, single lab, and the paper was subsequently retracted","pmids":["33763481"],"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 showed little to no ABHD16A protein, establishing that loss of the PS lipase is the molecular basis of this neurological disorder.","method":"Whole-exome sequencing, Sanger sequencing validation, immunoblot analysis on patient fibroblasts","journal":"American journal of human genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — protein-level confirmation in patient fibroblasts combined with genetic evidence from 11 individuals, establishing disease causality; mechanism inferred from prior enzymatic characterization","pmids":["34587489"],"is_preprint":false}],"current_model":"ABHD16A is an endoplasmic reticulum-localized α/β-hydrolase that functions primarily as a phosphatidylserine lipase, generating lysophosphatidylserine (lyso-PS) in vivo; it works antagonistically with the lyso-PS lipase ABHD12 to dynamically regulate lyso-PS levels in the brain and immune cells, with downstream consequences for TLR-mediated cytokine production and GPR34/RhoA/LIMK signaling. In addition, ABHD16A acts as a depalmitoylase that removes palmitate from IFITM antiviral proteins, reducing their activity and membrane localization, and is itself regulated by ubiquitin-mediated proteasomal degradation via RNF5. Loss of ABHD16A function in humans causes a complicated hereditary spastic paraplegia with intellectual disability."},"narrative":{"mechanistic_narrative":"ABHD16A is an endoplasmic reticulum-localized serine hydrolase of the α/β-hydrolase family that acts as a phosphatidylserine lipase, generating lysophosphatidylserine (lyso-PS) in mammalian brain and immune cells [PMID:25580854, PMID:32462874]. In vitro it is a catalytically active lipase with monoacylglycerol hydrolase activity, preferring long-chain unsaturated monoacylglycerols at a neutral pH optimum, and is inhibited by β-lactone and HSL inhibitors at nanomolar concentrations [PMID:25290914]. ABHD16A works upstream of and antagonistically to the lyso-PS lipase ABHD12 to set steady-state lyso-PS levels: its deletion lowers brain and cerebellar lyso-PS whereas ABHD12 loss raises it, defining a biosynthesis–degradation axis with regional specificity in the cerebellum [PMID:25580854, PMID:32462874]. Lyso-PS produced by ABHD16A is signaling-competent, stimulating RhoA and the downstream LIMK/cofilin cascade through GPR34/Gi to drive gastric cancer cell invasion [PMID:33875796], and supports lipopolysaccharide-induced cytokine production in macrophages [PMID:25580854]. Independently of its lipase role, ABHD16A functions as a depalmitoylase that removes palmitate from S-palmitoylated IFITM antiviral proteins (IFITM1/2/3), reducing their palmitoylation, membrane localization, and antiviral activity against RNA viruses and HBV [PMID:36314839, PMID:40434075]; this activity is itself controlled by RNF5-mediated ubiquitination at K3 and K452 leading to proteasomal degradation of ABHD16A [PMID:39601593]. Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability, with patient fibroblasts showing little to no ABHD16A protein [PMID:34587489].","teleology":[{"year":2014,"claim":"Established that ABHD16A (BAT5) is a bona fide catalytically active serine hydrolase, answering whether the protein had intrinsic lipase activity and defining its in vitro substrate preference.","evidence":"ABPP, fluorescent glycerol substrate assays, inhibitor SAR, and recombinant expression in HEK293 cells","pmids":["25290914"],"confidence":"Medium","gaps":["In vitro MAG hydrolase activity did not establish the physiological substrate","No cellular or in vivo lipid context provided","Phosphatidylserine was not yet identified as the substrate"]},{"year":2015,"claim":"Identified phosphatidylserine as the physiological substrate and placed ABHD16A upstream of ABHD12 in a lyso-PS biosynthesis–degradation axis, resolving the in vivo function and pathway position.","evidence":"ABPP, pharmacological inhibition, Abhd16a-/- and Abhd12-/- mice, brain lipid mass spectrometry, and macrophage cytokine measurements","pmids":["25580854"],"confidence":"High","gaps":["Subcellular site of lyso-PS generation not yet localized","Downstream lyso-PS receptors/signaling not defined","Mechanism of antagonism with ABHD12 not structurally resolved"]},{"year":2020,"claim":"Localized ABHD16A to the ER and demonstrated region- and cell-type-specific functional cross-talk with ABHD12 in the cerebellum, connecting enzymatic activity to anatomical context.","evidence":"Subcellular fractionation, immunofluorescence, immunohistochemistry with KO controls, and quantitative lyso-PS lipidomics across brain regions","pmids":["32462874"],"confidence":"High","gaps":["Does not explain how spatially distinct lipases coordinate lyso-PS pools","No link to a neurological phenotype yet","Receptor-level signaling consequences not addressed"]},{"year":2021,"claim":"Connected ABHD16A-generated lyso-PS to a defined signaling output, showing it activates GPR34/Gi/RhoA/LIMK/cofilin to promote cancer cell invasion.","evidence":"ABHD16A overexpression/knockdown, lyso-PS measurement, pathway dissection, and invasion assays in gastric cancer cells","pmids":["33875796"],"confidence":"Medium","gaps":["Single tumor context","Direct receptor engagement by ABHD16A-derived lyso-PS not biochemically isolated","In vivo metastasis dependence on ABHD16A not fully established"]},{"year":2021,"claim":"Established ABHD16A as the molecular cause of a Mendelian neurological disorder, linking loss of the PS lipase to disease in humans.","evidence":"Whole-exome sequencing of 11 affected individuals, Sanger validation, and immunoblot of patient fibroblasts showing loss of protein","pmids":["34587489"],"confidence":"Medium","gaps":["Pathophysiology linking lyso-PS dysregulation to spastic paraplegia not mechanistically demonstrated","Mechanism inferred from prior enzymatic work rather than directly tested in neurons","Genotype-phenotype correlation limited"]},{"year":2022,"claim":"Revealed a second, lipase-independent activity—ABHD16A depalmitoylates IFITM antiviral proteins—expanding its substrate scope beyond phospholipids to protein S-acylation.","evidence":"APEGS palmitoylation assay in ABHD16A KO and overexpression cells across species, with antiviral and localization readouts","pmids":["36314839"],"confidence":"High","gaps":["Structural basis distinguishing lipase vs depalmitoylase activity unresolved","Whether ER localization governs IFITM access not addressed","Endogenous regulation of the depalmitoylase activity not yet defined"]},{"year":2024,"claim":"Defined how ABHD16A's depalmitoylase activity is itself regulated, showing RNF5-mediated ubiquitination at K3/K452 drives its proteasomal degradation to restore IFITM antiviral function.","evidence":"AlphaFold2 interaction prediction, co-IP, ubiquitination assays with site mapping, proteasome inhibition, and antiviral readouts","pmids":["39601593"],"confidence":"Medium","gaps":["Single-lab co-IP-based interaction","Physiological stimulus triggering RNF5-mediated degradation unclear","Conservation of K3/K452 regulation in human cells not established"]},{"year":2025,"claim":"Extended the ABHD16A–IFITM regulatory network, showing ABHD17A counteracts ABHD16A by downregulating its expression and confirming ABHD16A depalmitoylation negatively regulates IFITM1 anti-HBV activity in hepatocytes.","evidence":"Co-IP, Western blotting, APEGS assays, CRISPR/Cas9 KO, and viral replication assays in HepG2.215 cells","pmids":["40723864","40434075"],"confidence":"Medium","gaps":["Mechanism of ABHD17A-mediated ABHD16A downregulation incompletely resolved","Single-lab studies","Interplay between depalmitoylase and lipase functions in vivo untested"]},{"year":null,"claim":"How ABHD16A reconciles its two distinct catalytic activities (PS lipase vs IFITM depalmitoylase) and how lyso-PS dysregulation produces the neurological disease phenotype remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model distinguishing the two activities","Neuronal mechanism connecting lyso-PS to spastic paraplegia not demonstrated","Tissue-specific balance between lipase and depalmitoylase roles unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,7]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,4]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5]}],"complexes":[],"partners":["ABHD12","IFITM1","IFITM3","RNF5","ABHD17A","GPR34"],"other_free_text":[]}},"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":127,"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":"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":35,"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":"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":23,"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":5,"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":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":"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},{"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}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10495,"output_tokens":2931,"usd":0.037725,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10207,"output_tokens":3470,"usd":0.068892,"stage2_stop_reason":"end_turn"},"total_usd":0.106617,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"ABHD16A is a phosphatidylserine (PS) lipase that generates lysophosphatidylserine (lyso-PS) in mammalian systems. Genetic knockout of Abhd16a in mice decreases brain lyso-PS levels, opposite to the elevation seen in Abhd12-/- mice. In mouse macrophages, disruption of ABHD16A decreases lyso-PS and lipopolysaccharide-induced cytokine production, placing ABHD16A upstream of ABHD12 in an lyso-PS biosynthesis-degradation axis.\",\n      \"method\": \"Activity-based protein profiling (ABPP), pharmacological inhibition, genetic knockout mice (Abhd16a-/-, Abhd12-/-), lipid mass spectrometry, cytokine measurements in macrophages\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (ABPP, pharmacological inhibitor, genetic KO) replicated across cell and in vivo contexts, defining enzymatic activity and pathway position\",\n      \"pmids\": [\"25580854\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"ABHD16A (BAT5) is a catalytically active serine hydrolase with monoacylglycerol (MAG) lipase activity in vitro, preferring long-chain unsaturated MAGs (1-linoleylglycerol, 15d-PGJ2-G; low-micromolar Km). It shows only marginal diacylglycerol, triacylglycerol, or lysophospholipase activity. The enzyme has a neutral pH optimum and preference for 1(3)- vs 2-MAG isomers. Beta-lactone-based lipase inhibitors and the HSL inhibitor C7600 inhibit it at nanomolar concentrations.\",\n      \"method\": \"Activity-based protein profiling (ABPP), fluorescent glycerol substrate assay, inhibitor profiling (IC50 measurements), recombinant expression in HEK293 cells\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay with substrate panel and inhibitor SAR, single lab, multiple biochemical methods\",\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 demonstrated by subcellular organelle fractionation and immunofluorescence microscopy. In the murine brain, ABHD16A and ABHD12 localize to distinct regions and cell types in the cerebellum. Cerebellar lyso-PS levels are most reduced by ABHD16A deletion and most elevated by ABHD12 deletion, establishing functional cross-talk between the two lipases specifically in the cerebellum.\",\n      \"method\": \"Subcellular organelle fractionation, immunofluorescence high-resolution microscopy, immunohistochemistry with genetic KO controls, quantitative mass spectrometry of lyso-PS in brain regions\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (fractionation, immunofluorescence, IHC with KO controls, MS lipidomics) in a single rigorous study establishing ER localization and regional functional consequence\",\n      \"pmids\": [\"32462874\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ABHD16A, acting as a PS lipase, generates lyso-PS in gastric cancer cells, which stimulates RhoA and the downstream LIMK/cofilin cascade through GPR34/Gi signaling, promoting cancer cell invasion and metastasis.\",\n      \"method\": \"ABHD16A overexpression/knockdown, lyso-PS measurement, RhoA/LIMK/cofilin pathway analysis, GPR34/Gi pharmacological dissection, cell invasion assays\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic manipulation combined with lipidomics and downstream pathway analysis, single lab, multiple methods linking ABHD16A enzymatic activity to a signaling cascade\",\n      \"pmids\": [\"33875796\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ABHD16A functions as a depalmitoylase that catalyzes the depalmitoyl reaction on S-palmitoylated IFITM proteins (IFITM1, IFITM2, IFITM3), thereby decreasing their S-palmitoylation levels and reducing their antiviral activity against RNA viruses. ABHD16A also regulates subcellular localization of IFITM proteins.\",\n      \"method\": \"Acyl-PEGyl exchange gel shift (APEGS) assay for palmitoylation detection, ABHD16A knockout cells (abhd16a-/-), ABHD16A overexpression, antiviral activity assays, immunofluorescence for localization\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — enzymatic depalmitoylation activity demonstrated biochemically (APEGS) in both KO and overexpression systems across three species, with functional antiviral readout\",\n      \"pmids\": [\"36314839\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Swine RNF5 (E3 ubiquitin ligase) interacts with ABHD16A and targets it for ubiquitination at residues K3 and K452, leading to proteasomal degradation of ABHD16A. This degradation attenuates ABHD16A-mediated depalmitoylation of IFITM1, thereby restoring IFITM1 antiviral activity.\",\n      \"method\": \"AlphaFold2-based protein-protein interaction prediction, co-immunoprecipitation, immunofluorescence, ubiquitination assays, proteasome inhibitor experiments, ABHD16A KO/overexpression with antiviral readouts\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and functional ubiquitination assays with site identification (K3, K452), single lab, multiple methods\",\n      \"pmids\": [\"39601593\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ABHD17A physically interacts with IFITM1 and indirectly increases its S-palmitoylation by downregulating ABHD16A expression, thereby counteracting ABHD16A-mediated depalmitoylation of IFITM1 and enhancing IFITM1 antiviral activity.\",\n      \"method\": \"Co-immunoprecipitation, Western blotting for ABHD16A protein levels, APEGS assay for palmitoylation, antiviral activity assays\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — single lab, co-IP plus functional assay, but the mechanism of ABHD17A-mediated ABHD16A downregulation is incompletely resolved in the abstract\",\n      \"pmids\": [\"40723864\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ABHD16A catalyzes depalmitoylation of IFITM1 in hepatocytes (HepG2.215 cells), and this depalmitoylation negatively regulates IFITM1 anti-HBV activity. CRISPR/Cas9 knockout of ABHD16A increased IFITM1 palmitoylation and enhanced restriction of HBV replication.\",\n      \"method\": \"Co-immunoprecipitation, APEGS palmitoylation assay, CRISPR/Cas9 knockout of ABHD16A and IFITM1, HBV replication assay\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical depalmitoylation assay combined with genetic KO and functional viral replication readout, single lab\",\n      \"pmids\": [\"40434075\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"IFITM3 interacts with ABHD16A (confirmed by yeast two-hybrid), and they co-localize at the cell membrane. Co-expression of IFITM3 and ABHD16A modulates inflammatory cytokine production (IL-1β, IL-6, IL-10, TNF-α) in response to influenza A virus infection. NOTE: The original paper (PMID:33763481) was retracted (PMID:35434131); findings should be interpreted with caution.\",\n      \"method\": \"Yeast two-hybrid, laser confocal co-localization, fluorescence quantitative PCR for cytokines, overexpression in HEK293 cells\",\n      \"journal\": \"BioMed research international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — yeast two-hybrid and co-localization only, single lab, and the paper was subsequently retracted\",\n      \"pmids\": [\"33763481\"],\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 showed little to no ABHD16A protein, establishing that loss of the PS lipase is the molecular basis of this neurological disorder.\",\n      \"method\": \"Whole-exome sequencing, Sanger sequencing validation, immunoblot analysis on patient fibroblasts\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — protein-level confirmation in patient fibroblasts combined with genetic evidence from 11 individuals, establishing disease causality; mechanism inferred from prior enzymatic characterization\",\n      \"pmids\": [\"34587489\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ABHD16A is an endoplasmic reticulum-localized α/β-hydrolase that functions primarily as a phosphatidylserine lipase, generating lysophosphatidylserine (lyso-PS) in vivo; it works antagonistically with the lyso-PS lipase ABHD12 to dynamically regulate lyso-PS levels in the brain and immune cells, with downstream consequences for TLR-mediated cytokine production and GPR34/RhoA/LIMK signaling. In addition, ABHD16A acts as a depalmitoylase that removes palmitate from IFITM antiviral proteins, reducing their activity and membrane localization, and is itself regulated by ubiquitin-mediated proteasomal degradation via RNF5. Loss of ABHD16A function in humans causes a complicated hereditary spastic paraplegia with intellectual disability.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ABHD16A is an endoplasmic reticulum-localized serine hydrolase of the α/β-hydrolase family that acts as a phosphatidylserine lipase, generating lysophosphatidylserine (lyso-PS) in mammalian brain and immune cells [#0, #2]. In vitro it is a catalytically active lipase with monoacylglycerol hydrolase activity, preferring long-chain unsaturated monoacylglycerols at a neutral pH optimum, and is inhibited by β-lactone and HSL inhibitors at nanomolar concentrations [#1]. ABHD16A works upstream of and antagonistically to the lyso-PS lipase ABHD12 to set steady-state lyso-PS levels: its deletion lowers brain and cerebellar lyso-PS whereas ABHD12 loss raises it, defining a biosynthesis–degradation axis with regional specificity in the cerebellum [#0, #2]. Lyso-PS produced by ABHD16A is signaling-competent, stimulating RhoA and the downstream LIMK/cofilin cascade through GPR34/Gi to drive gastric cancer cell invasion [#3], and supports lipopolysaccharide-induced cytokine production in macrophages [#0]. Independently of its lipase role, ABHD16A functions as a depalmitoylase that removes palmitate from S-palmitoylated IFITM antiviral proteins (IFITM1/2/3), reducing their palmitoylation, membrane localization, and antiviral activity against RNA viruses and HBV [#4, #7]; this activity is itself controlled by RNF5-mediated ubiquitination at K3 and K452 leading to proteasomal degradation of ABHD16A [#5]. Bi-allelic loss-of-function variants in ABHD16A cause hereditary spastic paraplegia with intellectual disability, with patient fibroblasts showing little to no ABHD16A protein [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that ABHD16A (BAT5) is a bona fide catalytically active serine hydrolase, answering whether the protein had intrinsic lipase activity and defining its in vitro substrate preference.\",\n      \"evidence\": \"ABPP, fluorescent glycerol substrate assays, inhibitor SAR, and recombinant expression in HEK293 cells\",\n      \"pmids\": [\"25290914\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"In vitro MAG hydrolase activity did not establish the physiological substrate\", \"No cellular or in vivo lipid context provided\", \"Phosphatidylserine was not yet identified as the substrate\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified phosphatidylserine as the physiological substrate and placed ABHD16A upstream of ABHD12 in a lyso-PS biosynthesis–degradation axis, resolving the in vivo function and pathway position.\",\n      \"evidence\": \"ABPP, pharmacological inhibition, Abhd16a-/- and Abhd12-/- mice, brain lipid mass spectrometry, and macrophage cytokine measurements\",\n      \"pmids\": [\"25580854\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Subcellular site of lyso-PS generation not yet localized\", \"Downstream lyso-PS receptors/signaling not defined\", \"Mechanism of antagonism with ABHD12 not structurally resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Localized ABHD16A to the ER and demonstrated region- and cell-type-specific functional cross-talk with ABHD12 in the cerebellum, connecting enzymatic activity to anatomical context.\",\n      \"evidence\": \"Subcellular fractionation, immunofluorescence, immunohistochemistry with KO controls, and quantitative lyso-PS lipidomics across brain regions\",\n      \"pmids\": [\"32462874\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Does not explain how spatially distinct lipases coordinate lyso-PS pools\", \"No link to a neurological phenotype yet\", \"Receptor-level signaling consequences not addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connected ABHD16A-generated lyso-PS to a defined signaling output, showing it activates GPR34/Gi/RhoA/LIMK/cofilin to promote cancer cell invasion.\",\n      \"evidence\": \"ABHD16A overexpression/knockdown, lyso-PS measurement, pathway dissection, and invasion assays in gastric cancer cells\",\n      \"pmids\": [\"33875796\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single tumor context\", \"Direct receptor engagement by ABHD16A-derived lyso-PS not biochemically isolated\", \"In vivo metastasis dependence on ABHD16A not fully established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Established ABHD16A as the molecular cause of a Mendelian neurological disorder, linking loss of the PS lipase to disease in humans.\",\n      \"evidence\": \"Whole-exome sequencing of 11 affected individuals, Sanger validation, and immunoblot of patient fibroblasts showing loss of protein\",\n      \"pmids\": [\"34587489\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Pathophysiology linking lyso-PS dysregulation to spastic paraplegia not mechanistically demonstrated\", \"Mechanism inferred from prior enzymatic work rather than directly tested in neurons\", \"Genotype-phenotype correlation limited\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a second, lipase-independent activity—ABHD16A depalmitoylates IFITM antiviral proteins—expanding its substrate scope beyond phospholipids to protein S-acylation.\",\n      \"evidence\": \"APEGS palmitoylation assay in ABHD16A KO and overexpression cells across species, with antiviral and localization readouts\",\n      \"pmids\": [\"36314839\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Structural basis distinguishing lipase vs depalmitoylase activity unresolved\", \"Whether ER localization governs IFITM access not addressed\", \"Endogenous regulation of the depalmitoylase activity not yet defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined how ABHD16A's depalmitoylase activity is itself regulated, showing RNF5-mediated ubiquitination at K3/K452 drives its proteasomal degradation to restore IFITM antiviral function.\",\n      \"evidence\": \"AlphaFold2 interaction prediction, co-IP, ubiquitination assays with site mapping, proteasome inhibition, and antiviral readouts\",\n      \"pmids\": [\"39601593\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Single-lab co-IP-based interaction\", \"Physiological stimulus triggering RNF5-mediated degradation unclear\", \"Conservation of K3/K452 regulation in human cells not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended the ABHD16A–IFITM regulatory network, showing ABHD17A counteracts ABHD16A by downregulating its expression and confirming ABHD16A depalmitoylation negatively regulates IFITM1 anti-HBV activity in hepatocytes.\",\n      \"evidence\": \"Co-IP, Western blotting, APEGS assays, CRISPR/Cas9 KO, and viral replication assays in HepG2.215 cells\",\n      \"pmids\": [\"40723864\", \"40434075\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"Mechanism of ABHD17A-mediated ABHD16A downregulation incompletely resolved\", \"Single-lab studies\", \"Interplay between depalmitoylase and lipase functions in vivo untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ABHD16A reconciles its two distinct catalytic activities (PS lipase vs IFITM depalmitoylase) and how lyso-PS dysregulation produces the neurological disease phenotype remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\"No structural model distinguishing the two activities\", \"Neuronal mechanism connecting lyso-PS to spastic paraplegia not demonstrated\", \"Tissue-specific balance between lipase and depalmitoylase roles unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 7]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ABHD12\", \"IFITM1\", \"IFITM3\", \"RNF5\", \"ABHD17A\", \"GPR34\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}