{"gene":"PPP1R3B","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2017,"finding":"Liver-specific deletion of Ppp1r3b significantly reduced glycogen synthase protein abundance, with remaining protein predominantly phosphorylated and inactive, leading to impaired glucose incorporation into hepatic glycogen, substantially decreased total hepatic glycogen content, and dysregulated fasting energy homeostasis including altered gluconeogenic enzyme expression.","method":"Liver-specific knockout and overexpression mouse models, glycogen content measurement, glycogen synthase activity/phosphorylation assays, isotope tracing","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function mouse genetics with multiple orthogonal metabolic readouts in a single focused study","pmids":["28473467"],"is_preprint":false},{"year":2018,"finding":"Mice lacking PPP1R3B are deficient in hepatic glycogen without change in hepatic triglyceride content, while hepatic overexpression of PPP1R3B causes accumulation of hepatic glycogen and elevated plasma ALT but does not change hepatic triglyceride content, demonstrating that PPP1R3B specifically promotes glycogen storage rather than lipid storage.","method":"Mouse knockout and overexpression models, hepatic glycogen and triglyceride measurements, plasma ALT measurement","journal":"Hepatology (Baltimore, Md.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function in mice with multiple orthogonal metabolic measurements, replicated direction of effect from prior study (PMID:28473467)","pmids":["29266543"],"is_preprint":false},{"year":2024,"finding":"mTORC1 is required for postprandial glycogen synthase activity and glycogenesis in liver via feeding-dependent transcriptional induction of Ppp1r3b; re-expression of Ppp1r3b in livers lacking mTORC1 signaling restores glycogen synthase activity and postprandial glycogen content; mTORC1-dependent transcriptional control of Ppp1r3b is facilitated by FOXO1.","method":"Mouse genetics (liver-specific mTORC1 loss), metabolomics, isotope tracing, viral Ppp1r3b re-expression, glycogen synthase activity assay, transcriptional analysis","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with rescue experiment, isotope tracing, and multiple orthogonal methods in a single rigorous study","pmids":["38290087"],"is_preprint":false},{"year":2021,"finding":"CRISPR/Cas9 engineering of a 105-bp deletion including rs4841132-A in human hepatocarcinoma cells increased PPP1R3B expression, decreased LOC157273 lncRNA, and increased glycogen content; overexpression of PPP1R3B alone increased glycogen but did not decrease LOC157273, indicating the noncoding variant regulates both independently.","method":"CRISPR/Cas9 deletion, PPP1R3B overexpression, LOC157273 knockdown, glycogen measurement in hepatocarcinoma cells","journal":"The Journal of clinical endocrinology and metabolism","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — CRISPR engineering plus overexpression/knockdown dissection with glycogen readout in human cells, single lab with multiple orthogonal methods","pmids":["33231259"],"is_preprint":false},{"year":2020,"finding":"siRNA knockdown of lncRNA LOC157273 in primary human hepatocytes increased PPP1R3B mRNA 1.7-fold and increased glycogen deposition by >50%, identifying LOC157273 as a negative regulator of PPP1R3B expression and hepatocyte glycogen deposition.","method":"siRNA knockdown, RT-PCR, RNA-seq, insulin-stimulated glycogen deposition assay in primary human hepatocytes","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA knockdown with multiple readouts (mRNA, glycogen deposition) in primary human hepatocytes, single lab","pmids":["32754192"],"is_preprint":false},{"year":2025,"finding":"Ppp1r3b overexpression in mice increases liver glycogen stores while Ppp1r3b deletion results in higher liver lipid accumulation, demonstrating that PPP1R3B acts as a metabolic switch shifting hepatic energy storage from lipid to glycogen; deletion-associated lipid accumulation was confirmed by human genetics.","method":"Mouse overexpression and deletion models, hepatic glycogen and lipid measurement, human genetic association with liver fat and plasma lipids","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal gain- and loss-of-function mouse models with metabolic readouts replicated in human genetic data, multiple orthogonal methods","pmids":["40378221"],"is_preprint":false},{"year":2025,"finding":"PPP1R3B promotes M2 macrophage polarization and regulates macrophage glycogen metabolism via phosphorylated STAT3 (p-STAT3), which activates the PPAR-γ/PGC-1α/CD206 anti-inflammatory transcriptional axis in the nucleus and enhances glycogenolysis via the p-GSK-3β/p-PYGL/p-GYS2 axis in mitochondria; PPP1R3B absence accelerates atherosclerotic plaque progression.","method":"PPP1R3B modulation in macrophages, transcriptomic analysis (RNA-seq), high-throughput sequencing, multi-omics pathway analysis, functional polarization assays","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2-3 / Moderate — RNA-seq and functional macrophage assays with pathway dissection in a single lab; mechanistic details of STAT3 dual role inferred from omics with functional validation","pmids":["40984828"],"is_preprint":false},{"year":2019,"finding":"CgPPP1R3B (oyster ortholog) interacts with PPP1 catalytic subunit (CgPPP1C), glycogen synthase (CgGS), and glycogen phosphorylase (CgGP) as shown by Co-IP and yeast two-hybrid; the protein directly binds glycogen molecules in vitro by co-sedimentation; RNAi knockdown of CgPPP1R3B reduced glycogen content in vivo.","method":"Co-immunoprecipitation, yeast two-hybrid, co-sedimentation assay, RNAi knockdown in oyster","journal":"Frontiers in genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal binding assays (Co-IP + Y2H + co-sedimentation) plus in vivo functional knockdown; non-mammalian ortholog study supporting conserved function","pmids":["30853975"],"is_preprint":false},{"year":2006,"finding":"Mouse Ppp1r3b (GL) utilizes two alternative promoters and 5' non-coding exons producing at least three alternatively spliced transcripts encoding identical proteins; GL is expressed in bronchial epithelial cells of embryonic mouse lungs from E12.5 to before birth, suggesting a role in glycogen metabolism during lung development.","method":"RT-PCR, in situ hybridization, alternative promoter/splicing analysis in embryonic mouse lung","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization by in situ hybridization with no functional mechanistic follow-up beyond expression pattern description","pmids":["16949035"],"is_preprint":false}],"current_model":"PPP1R3B (GL) encodes a glycogen-targeting regulatory subunit of protein phosphatase 1 (PP1) that directly binds glycogen, interacts with glycogen synthase and glycogen phosphorylase, promotes glycogen synthase activation by dephosphorylation, and drives postprandial hepatic glycogen synthesis downstream of insulin/mTORC1/FOXO1 signaling; loss of PPP1R3B shifts hepatic energy storage from glycogen to lipid, while its overexpression increases glycogen at the expense of lipid, and in macrophages PPP1R3B additionally regulates glycogen-mediated energy metabolism and M2 polarization via a p-STAT3/PPAR-γ axis."},"narrative":{"mechanistic_narrative":"PPP1R3B (GL) is a glycogen-targeting regulatory subunit of protein phosphatase 1 that governs the partitioning of hepatic energy storage between glycogen and lipid [PMID:28473467, PMID:40378221]. It physically scaffolds the PP1 catalytic subunit together with glycogen synthase and glycogen phosphorylase and binds glycogen directly, thereby coupling phosphatase activity to glycogen particles [PMID:30853975]. In liver, PPP1R3B promotes glycogen synthase activation by dephosphorylation and is required to maintain glycogen synthase protein abundance; its loss leaves the residual enzyme phosphorylated and inactive, impairs glucose incorporation into glycogen, and disrupts fasting energy homeostasis [PMID:28473467]. Reciprocal mouse genetics establish PPP1R3B as a metabolic switch: deletion shifts hepatic storage toward lipid while overexpression drives glycogen accumulation, effects corroborated by human genetic association with liver fat and plasma lipids [PMID:29266543, PMID:40378221]. Postprandial glycogenesis depends on feeding-induced, mTORC1- and FOXO1-driven transcriptional induction of Ppp1r3b, and re-expression of Ppp1r3b restores glycogen synthase activity in livers lacking mTORC1 signaling [PMID:38290087]. PPP1R3B expression is further constrained by the lncRNA LOC157273 and modulated by the noncoding variant rs4841132, which independently regulate PPP1R3B level and hepatocyte glycogen content [PMID:33231259, PMID:32754192]. Beyond hepatocytes, PPP1R3B promotes M2 macrophage polarization and regulates macrophage glycogen metabolism through a p-STAT3/PPAR-γ axis, and its absence accelerates atherosclerotic plaque progression [PMID:40984828].","teleology":[{"year":2017,"claim":"Establishing whether PPP1R3B is functionally required for hepatic glycogen storage, this work showed it controls glycogen synthase abundance and activation state in vivo.","evidence":"Liver-specific knockout/overexpression mice with glycogen content, glycogen synthase activity/phosphorylation assays and isotope tracing","pmids":["28473467"],"confidence":"High","gaps":["Does not resolve the direct biochemical interactions among PP1, glycogen synthase, and glycogen","Mechanism by which PPP1R3B stabilizes glycogen synthase protein not defined"]},{"year":2018,"claim":"Addressing whether PPP1R3B's role is glycogen-specific or general to energy storage, this study showed it selectively promotes glycogen rather than triglyceride accumulation.","evidence":"Reciprocal mouse knockout/overexpression with hepatic glycogen, triglyceride and plasma ALT measurements","pmids":["29266543"],"confidence":"High","gaps":["Did not yet demonstrate the lipid-storage rerouting seen in later models","Cause of elevated ALT on overexpression not mechanistically explained"]},{"year":2019,"claim":"To define the molecular partnerships underlying targeting function, the oyster ortholog was shown to bind the PP1 catalytic subunit, glycogen synthase, glycogen phosphorylase, and glycogen itself.","evidence":"Co-IP, yeast two-hybrid, co-sedimentation and RNAi knockdown in oyster (CgPPP1R3B)","pmids":["30853975"],"confidence":"Medium","gaps":["Interactions demonstrated in a non-mammalian ortholog, not human PPP1R3B","No structural definition of glycogen- or substrate-binding interfaces"]},{"year":2020,"claim":"Identifying upstream regulation, knockdown of lncRNA LOC157273 was shown to derepress PPP1R3B and increase hepatocyte glycogen, framing LOC157273 as a negative regulator.","evidence":"siRNA knockdown with RT-PCR, RNA-seq and insulin-stimulated glycogen assay in primary human hepatocytes","pmids":["32754192"],"confidence":"Medium","gaps":["Single-lab, single-readout direction","Mechanism by which LOC157273 suppresses PPP1R3B transcription unknown"]},{"year":2021,"claim":"Connecting a GWAS noncoding variant to function, CRISPR editing of rs4841132 was shown to raise PPP1R3B and glycogen while independently lowering LOC157273.","evidence":"CRISPR/Cas9 deletion with overexpression/knockdown and glycogen measurement in human hepatocarcinoma cells","pmids":["33231259"],"confidence":"High","gaps":["How the variant locus simultaneously and independently controls two transcripts not resolved","Cell-line context may not reflect primary hepatocyte regulation"]},{"year":2024,"claim":"Placing PPP1R3B in a signaling pathway, this work showed postprandial glycogenesis requires mTORC1/FOXO1-driven transcriptional induction of Ppp1r3b, with re-expression rescuing glycogen synthase activity.","evidence":"Liver-specific mTORC1-loss mice, metabolomics, isotope tracing and viral Ppp1r3b re-expression rescue","pmids":["38290087"],"confidence":"High","gaps":["Direct transcription-factor occupancy at the Ppp1r3b locus not fully defined","Relationship between this signaling axis and LOC157273 regulation unknown"]},{"year":2025,"claim":"Consolidating the storage-partitioning concept, reciprocal mouse models plus human genetics defined PPP1R3B as a switch routing hepatic energy between glycogen and lipid.","evidence":"Mouse overexpression/deletion with glycogen and lipid measurement and human genetic association with liver fat and plasma lipids","pmids":["40378221"],"confidence":"High","gaps":["Mechanism linking reduced glycogen flux to increased lipid synthesis not delineated","Tissue-autonomous versus systemic contributions to lipid phenotype unresolved"]},{"year":2025,"claim":"Extending function beyond hepatocytes, PPP1R3B was shown to drive M2 macrophage polarization and macrophage glycogen metabolism through a p-STAT3/PPAR-γ axis, with loss accelerating atherosclerosis.","evidence":"PPP1R3B modulation in macrophages with RNA-seq, multi-omics pathway analysis and polarization assays","pmids":["40984828"],"confidence":"Medium","gaps":["Dual nuclear/mitochondrial STAT3 role inferred from omics, not biochemically resolved","Direct connection between PPP1R3B phosphatase targeting and STAT3 phosphorylation not established"]},{"year":null,"claim":"How PPP1R3B coordinates its PP1-targeting biochemistry with the macrophage p-STAT3/PPAR-γ signaling role, and the structural basis of its glycogen and substrate engagement in humans, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No human structural model of glycogen/substrate binding","Mechanistic link between glycogen-targeting and STAT3 signaling unestablished"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,7]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,6]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[6]}],"complexes":["PP1-glycogen targeting complex"],"partners":["PPP1CC","GYS2","PYGL"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q86XI6","full_name":"Protein phosphatase 1 regulatory subunit 3B","aliases":["Hepatic glycogen-targeting protein phosphatase 1 regulatory subunit GL","Protein phosphatase 1 regulatory subunit 4","PP1 subunit R4","Protein phosphatase 1 subunit GL","PTG"],"length_aa":285,"mass_kda":32.7,"function":"Acts as a glycogen-targeting subunit for phosphatase PP1. Facilitates interaction of the PP1 with enzymes of the glycogen metabolism and regulates its activity. Suppresses the rate at which PP1 dephosphorylates (inactivates) glycogen phosphorylase and enhances the rate at which it activates glycogen synthase and therefore limits glycogen breakdown. Its activity is inhibited by PYGL, resulting in inhibition of the glycogen synthase and glycogen phosphorylase phosphatase activities of PP1. Dramatically increases basal and insulin-stimulated glycogen synthesis upon overexpression in hepatocytes (By similarity)","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q86XI6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPP1R3B","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PPP1R3B","total_profiled":1310},"omim":[{"mim_id":"610541","title":"PROTEIN PHOSPHATASE 1, REGULATORY SUBUNIT 3B; PPP1R3B","url":"https://www.omim.org/entry/610541"},{"mim_id":"609203","title":"CLAUDIN 23; CLDN23","url":"https://www.omim.org/entry/609203"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"liver","ntpm":135.4},{"tissue":"skeletal muscle","ntpm":89.2}],"url":"https://www.proteinatlas.org/search/PPP1R3B"},"hgnc":{"alias_symbol":["GL","FLJ14005","PPP1R4"],"prev_symbol":[]},"alphafold":{"accession":"Q86XI6","domains":[{"cath_id":"2.60.40.2440","chopping":"111-238","consensus_level":"high","plddt":91.1774,"start":111,"end":238}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86XI6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86XI6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86XI6-F1-predicted_aligned_error_v6.png","plddt_mean":70.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPP1R3B","jax_strain_url":"https://www.jax.org/strain/search?query=PPP1R3B"},"sequence":{"accession":"Q86XI6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86XI6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86XI6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86XI6"}},"corpus_meta":[{"pmid":"23416328","id":"PMC_23416328","title":"Association between variants in or near PNPLA3, GCKR, and PPP1R3B with ultrasound-defined steatosis based on data from the third National Health and Nutrition Examination Survey.","date":"2013","source":"Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association","url":"https://pubmed.ncbi.nlm.nih.gov/23416328","citation_count":134,"is_preprint":false},{"pmid":"23690473","id":"PMC_23690473","title":"Mutated PPP1R3B is recognized by T cells used to treat a melanoma patient who experienced a durable complete tumor regression.","date":"2013","source":"Journal of immunology (Baltimore, Md. : 1950)","url":"https://pubmed.ncbi.nlm.nih.gov/23690473","citation_count":123,"is_preprint":false},{"pmid":"28473467","id":"PMC_28473467","title":"Hepatic protein phosphatase 1 regulatory subunit 3B (Ppp1r3b) promotes hepatic glycogen synthesis and thereby regulates fasting energy homeostasis.","date":"2017","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/28473467","citation_count":59,"is_preprint":false},{"pmid":"29266543","id":"PMC_29266543","title":"Relationship between genetic variation at PPP1R3B and levels of liver glycogen and triglyceride.","date":"2018","source":"Hepatology (Baltimore, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/29266543","citation_count":52,"is_preprint":false},{"pmid":"21947951","id":"PMC_21947951","title":"Association and expression quantitative trait loci (eQTL) analysis of porcine AMBP, GC and PPP1R3B genes with meat quality traits.","date":"2011","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/21947951","citation_count":23,"is_preprint":false},{"pmid":"16907705","id":"PMC_16907705","title":"Examination of PPP1R3B as a candidate gene for the type 2 diabetes and MODY loci on chromosome 8p23.","date":"2006","source":"Annals of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16907705","citation_count":19,"is_preprint":false},{"pmid":"27752939","id":"PMC_27752939","title":"Association between PNPLA3 (rs738409), LYPLAL1 (rs12137855), PPP1R3B (rs4240624), GCKR (rs780094), and elevated transaminase levels in overweight/obese Mexican adults.","date":"2016","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/27752939","citation_count":19,"is_preprint":false},{"pmid":"33231259","id":"PMC_33231259","title":"A Noncoding Variant Near PPP1R3B Promotes Liver Glycogen Storage and MetS, but Protects Against Myocardial Infarction.","date":"2021","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/33231259","citation_count":15,"is_preprint":false},{"pmid":"32754192","id":"PMC_32754192","title":"A Long Non-coding RNA, LOC157273, Is an Effector Transcript at the Chromosome 8p23.1-PPP1R3B Metabolic Traits and Type 2 Diabetes Risk Locus.","date":"2020","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/32754192","citation_count":14,"is_preprint":false},{"pmid":"38290087","id":"PMC_38290087","title":"mTORC1 controls murine postprandial hepatic glycogen synthesis via Ppp1r3b.","date":"2024","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/38290087","citation_count":12,"is_preprint":false},{"pmid":"30853975","id":"PMC_30853975","title":"Association and Functional Analyses Revealed That PPP1R3B Plays an Important Role in the Regulation of Glycogen Content in the Pacific Oyster Crassostrea gigas.","date":"2019","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/30853975","citation_count":11,"is_preprint":false},{"pmid":"29681992","id":"PMC_29681992","title":"Association between the PPP1R3B polymorphisms and serum lipid traits, the risk of coronary artery disease and ischemic stroke in a southern Chinese Han population.","date":"2018","source":"Nutrition & metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/29681992","citation_count":10,"is_preprint":false},{"pmid":"23343124","id":"PMC_23343124","title":"Association of PPP1R3B polymorphisms with blood lipid and C-reactive protein levels in a Chinese population (PPP1R3B C ).","date":"2013","source":"Journal of diabetes","url":"https://pubmed.ncbi.nlm.nih.gov/23343124","citation_count":9,"is_preprint":false},{"pmid":"40984828","id":"PMC_40984828","title":"PPP1R3B Suppresses Atherosclerosis by Promoting the M2 Polarization of Macrophages Through Glycogen Metabolic Reprogramming.","date":"2025","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/40984828","citation_count":6,"is_preprint":false},{"pmid":"40378221","id":"PMC_40378221","title":"Ppp1r3b is a metabolic switch that shifts hepatic energy storage from lipid to glycogen.","date":"2025","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/40378221","citation_count":6,"is_preprint":false},{"pmid":"30629617","id":"PMC_30629617","title":"Increased frequency of rare missense PPP1R3B variants among Danish patients with type 2 diabetes.","date":"2019","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30629617","citation_count":6,"is_preprint":false},{"pmid":"16949035","id":"PMC_16949035","title":"Identification and expression of alternative splice variants of the mouse Ppp1r3b gene in lung epithelial cells.","date":"2006","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16949035","citation_count":4,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11693,"output_tokens":2402,"usd":0.035555,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9646,"output_tokens":3153,"usd":0.063528,"stage2_stop_reason":"end_turn"},"total_usd":0.099083,"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\": 2017,\n      \"finding\": \"Liver-specific deletion of Ppp1r3b significantly reduced glycogen synthase protein abundance, with remaining protein predominantly phosphorylated and inactive, leading to impaired glucose incorporation into hepatic glycogen, substantially decreased total hepatic glycogen content, and dysregulated fasting energy homeostasis including altered gluconeogenic enzyme expression.\",\n      \"method\": \"Liver-specific knockout and overexpression mouse models, glycogen content measurement, glycogen synthase activity/phosphorylation assays, isotope tracing\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function mouse genetics with multiple orthogonal metabolic readouts in a single focused study\",\n      \"pmids\": [\"28473467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Mice lacking PPP1R3B are deficient in hepatic glycogen without change in hepatic triglyceride content, while hepatic overexpression of PPP1R3B causes accumulation of hepatic glycogen and elevated plasma ALT but does not change hepatic triglyceride content, demonstrating that PPP1R3B specifically promotes glycogen storage rather than lipid storage.\",\n      \"method\": \"Mouse knockout and overexpression models, hepatic glycogen and triglyceride measurements, plasma ALT measurement\",\n      \"journal\": \"Hepatology (Baltimore, Md.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal loss-of-function and gain-of-function in mice with multiple orthogonal metabolic measurements, replicated direction of effect from prior study (PMID:28473467)\",\n      \"pmids\": [\"29266543\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"mTORC1 is required for postprandial glycogen synthase activity and glycogenesis in liver via feeding-dependent transcriptional induction of Ppp1r3b; re-expression of Ppp1r3b in livers lacking mTORC1 signaling restores glycogen synthase activity and postprandial glycogen content; mTORC1-dependent transcriptional control of Ppp1r3b is facilitated by FOXO1.\",\n      \"method\": \"Mouse genetics (liver-specific mTORC1 loss), metabolomics, isotope tracing, viral Ppp1r3b re-expression, glycogen synthase activity assay, transcriptional analysis\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with rescue experiment, isotope tracing, and multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"38290087\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CRISPR/Cas9 engineering of a 105-bp deletion including rs4841132-A in human hepatocarcinoma cells increased PPP1R3B expression, decreased LOC157273 lncRNA, and increased glycogen content; overexpression of PPP1R3B alone increased glycogen but did not decrease LOC157273, indicating the noncoding variant regulates both independently.\",\n      \"method\": \"CRISPR/Cas9 deletion, PPP1R3B overexpression, LOC157273 knockdown, glycogen measurement in hepatocarcinoma cells\",\n      \"journal\": \"The Journal of clinical endocrinology and metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — CRISPR engineering plus overexpression/knockdown dissection with glycogen readout in human cells, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"33231259\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"siRNA knockdown of lncRNA LOC157273 in primary human hepatocytes increased PPP1R3B mRNA 1.7-fold and increased glycogen deposition by >50%, identifying LOC157273 as a negative regulator of PPP1R3B expression and hepatocyte glycogen deposition.\",\n      \"method\": \"siRNA knockdown, RT-PCR, RNA-seq, insulin-stimulated glycogen deposition assay in primary human hepatocytes\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA knockdown with multiple readouts (mRNA, glycogen deposition) in primary human hepatocytes, single lab\",\n      \"pmids\": [\"32754192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ppp1r3b overexpression in mice increases liver glycogen stores while Ppp1r3b deletion results in higher liver lipid accumulation, demonstrating that PPP1R3B acts as a metabolic switch shifting hepatic energy storage from lipid to glycogen; deletion-associated lipid accumulation was confirmed by human genetics.\",\n      \"method\": \"Mouse overexpression and deletion models, hepatic glycogen and lipid measurement, human genetic association with liver fat and plasma lipids\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal gain- and loss-of-function mouse models with metabolic readouts replicated in human genetic data, multiple orthogonal methods\",\n      \"pmids\": [\"40378221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPP1R3B promotes M2 macrophage polarization and regulates macrophage glycogen metabolism via phosphorylated STAT3 (p-STAT3), which activates the PPAR-γ/PGC-1α/CD206 anti-inflammatory transcriptional axis in the nucleus and enhances glycogenolysis via the p-GSK-3β/p-PYGL/p-GYS2 axis in mitochondria; PPP1R3B absence accelerates atherosclerotic plaque progression.\",\n      \"method\": \"PPP1R3B modulation in macrophages, transcriptomic analysis (RNA-seq), high-throughput sequencing, multi-omics pathway analysis, functional polarization assays\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Moderate — RNA-seq and functional macrophage assays with pathway dissection in a single lab; mechanistic details of STAT3 dual role inferred from omics with functional validation\",\n      \"pmids\": [\"40984828\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CgPPP1R3B (oyster ortholog) interacts with PPP1 catalytic subunit (CgPPP1C), glycogen synthase (CgGS), and glycogen phosphorylase (CgGP) as shown by Co-IP and yeast two-hybrid; the protein directly binds glycogen molecules in vitro by co-sedimentation; RNAi knockdown of CgPPP1R3B reduced glycogen content in vivo.\",\n      \"method\": \"Co-immunoprecipitation, yeast two-hybrid, co-sedimentation assay, RNAi knockdown in oyster\",\n      \"journal\": \"Frontiers in genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal binding assays (Co-IP + Y2H + co-sedimentation) plus in vivo functional knockdown; non-mammalian ortholog study supporting conserved function\",\n      \"pmids\": [\"30853975\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Mouse Ppp1r3b (GL) utilizes two alternative promoters and 5' non-coding exons producing at least three alternatively spliced transcripts encoding identical proteins; GL is expressed in bronchial epithelial cells of embryonic mouse lungs from E12.5 to before birth, suggesting a role in glycogen metabolism during lung development.\",\n      \"method\": \"RT-PCR, in situ hybridization, alternative promoter/splicing analysis in embryonic mouse lung\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization by in situ hybridization with no functional mechanistic follow-up beyond expression pattern description\",\n      \"pmids\": [\"16949035\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPP1R3B (GL) encodes a glycogen-targeting regulatory subunit of protein phosphatase 1 (PP1) that directly binds glycogen, interacts with glycogen synthase and glycogen phosphorylase, promotes glycogen synthase activation by dephosphorylation, and drives postprandial hepatic glycogen synthesis downstream of insulin/mTORC1/FOXO1 signaling; loss of PPP1R3B shifts hepatic energy storage from glycogen to lipid, while its overexpression increases glycogen at the expense of lipid, and in macrophages PPP1R3B additionally regulates glycogen-mediated energy metabolism and M2 polarization via a p-STAT3/PPAR-γ axis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPP1R3B (GL) is a glycogen-targeting regulatory subunit of protein phosphatase 1 that governs the partitioning of hepatic energy storage between glycogen and lipid [#0, #5]. It physically scaffolds the PP1 catalytic subunit together with glycogen synthase and glycogen phosphorylase and binds glycogen directly, thereby coupling phosphatase activity to glycogen particles [#7]. In liver, PPP1R3B promotes glycogen synthase activation by dephosphorylation and is required to maintain glycogen synthase protein abundance; its loss leaves the residual enzyme phosphorylated and inactive, impairs glucose incorporation into glycogen, and disrupts fasting energy homeostasis [#0]. Reciprocal mouse genetics establish PPP1R3B as a metabolic switch: deletion shifts hepatic storage toward lipid while overexpression drives glycogen accumulation, effects corroborated by human genetic association with liver fat and plasma lipids [#1, #5]. Postprandial glycogenesis depends on feeding-induced, mTORC1- and FOXO1-driven transcriptional induction of Ppp1r3b, and re-expression of Ppp1r3b restores glycogen synthase activity in livers lacking mTORC1 signaling [#2]. PPP1R3B expression is further constrained by the lncRNA LOC157273 and modulated by the noncoding variant rs4841132, which independently regulate PPP1R3B level and hepatocyte glycogen content [#3, #4]. Beyond hepatocytes, PPP1R3B promotes M2 macrophage polarization and regulates macrophage glycogen metabolism through a p-STAT3/PPAR-\\u03b3 axis, and its absence accelerates atherosclerotic plaque progression [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2017,\n      \"claim\": \"Establishing whether PPP1R3B is functionally required for hepatic glycogen storage, this work showed it controls glycogen synthase abundance and activation state in vivo.\",\n      \"evidence\": \"Liver-specific knockout/overexpression mice with glycogen content, glycogen synthase activity/phosphorylation assays and isotope tracing\",\n      \"pmids\": [\"28473467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not resolve the direct biochemical interactions among PP1, glycogen synthase, and glycogen\", \"Mechanism by which PPP1R3B stabilizes glycogen synthase protein not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Addressing whether PPP1R3B's role is glycogen-specific or general to energy storage, this study showed it selectively promotes glycogen rather than triglyceride accumulation.\",\n      \"evidence\": \"Reciprocal mouse knockout/overexpression with hepatic glycogen, triglyceride and plasma ALT measurements\",\n      \"pmids\": [\"29266543\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not yet demonstrate the lipid-storage rerouting seen in later models\", \"Cause of elevated ALT on overexpression not mechanistically explained\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"To define the molecular partnerships underlying targeting function, the oyster ortholog was shown to bind the PP1 catalytic subunit, glycogen synthase, glycogen phosphorylase, and glycogen itself.\",\n      \"evidence\": \"Co-IP, yeast two-hybrid, co-sedimentation and RNAi knockdown in oyster (CgPPP1R3B)\",\n      \"pmids\": [\"30853975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interactions demonstrated in a non-mammalian ortholog, not human PPP1R3B\", \"No structural definition of glycogen- or substrate-binding interfaces\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identifying upstream regulation, knockdown of lncRNA LOC157273 was shown to derepress PPP1R3B and increase hepatocyte glycogen, framing LOC157273 as a negative regulator.\",\n      \"evidence\": \"siRNA knockdown with RT-PCR, RNA-seq and insulin-stimulated glycogen assay in primary human hepatocytes\",\n      \"pmids\": [\"32754192\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab, single-readout direction\", \"Mechanism by which LOC157273 suppresses PPP1R3B transcription unknown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Connecting a GWAS noncoding variant to function, CRISPR editing of rs4841132 was shown to raise PPP1R3B and glycogen while independently lowering LOC157273.\",\n      \"evidence\": \"CRISPR/Cas9 deletion with overexpression/knockdown and glycogen measurement in human hepatocarcinoma cells\",\n      \"pmids\": [\"33231259\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the variant locus simultaneously and independently controls two transcripts not resolved\", \"Cell-line context may not reflect primary hepatocyte regulation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placing PPP1R3B in a signaling pathway, this work showed postprandial glycogenesis requires mTORC1/FOXO1-driven transcriptional induction of Ppp1r3b, with re-expression rescuing glycogen synthase activity.\",\n      \"evidence\": \"Liver-specific mTORC1-loss mice, metabolomics, isotope tracing and viral Ppp1r3b re-expression rescue\",\n      \"pmids\": [\"38290087\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct transcription-factor occupancy at the Ppp1r3b locus not fully defined\", \"Relationship between this signaling axis and LOC157273 regulation unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Consolidating the storage-partitioning concept, reciprocal mouse models plus human genetics defined PPP1R3B as a switch routing hepatic energy between glycogen and lipid.\",\n      \"evidence\": \"Mouse overexpression/deletion with glycogen and lipid measurement and human genetic association with liver fat and plasma lipids\",\n      \"pmids\": [\"40378221\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking reduced glycogen flux to increased lipid synthesis not delineated\", \"Tissue-autonomous versus systemic contributions to lipid phenotype unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extending function beyond hepatocytes, PPP1R3B was shown to drive M2 macrophage polarization and macrophage glycogen metabolism through a p-STAT3/PPAR-\\u03b3 axis, with loss accelerating atherosclerosis.\",\n      \"evidence\": \"PPP1R3B modulation in macrophages with RNA-seq, multi-omics pathway analysis and polarization assays\",\n      \"pmids\": [\"40984828\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Dual nuclear/mitochondrial STAT3 role inferred from omics, not biochemically resolved\", \"Direct connection between PPP1R3B phosphatase targeting and STAT3 phosphorylation not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PPP1R3B coordinates its PP1-targeting biochemistry with the macrophage p-STAT3/PPAR-\\u03b3 signaling role, and the structural basis of its glycogen and substrate engagement in humans, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No human structural model of glycogen/substrate binding\", \"Mechanistic link between glycogen-targeting and STAT3 signaling unestablished\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 6]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"PP1-glycogen targeting complex\"],\n    \"partners\": [\"PPP1CC\", \"GYS2\", \"PYGL\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}