{"gene":"PSME2","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2001,"finding":"PA28α and PA28β form a heteropolymer that binds to both ends of the 20S proteasome; double knockout mice showed decreased ATP-dependent proteolytic activities, indicating 'hybrid proteasomes' (containing PA28αβ) contribute to protein degradation. PA28α/β is not required for antigen presentation in general but is essential for processing specific antigens such as the melanoma antigen TRP2-derived peptide.","method":"Genetic knockout (PA28α/β double KO mice), biochemical proteolytic activity assays, antigen presentation assays with ovalbumin and TRP2 peptide, influenza A virus infection model","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean double-KO mouse model with multiple functional readouts (proteolytic activity, specific antigen processing), replicated across multiple antigen systems","pmids":["11689430"],"is_preprint":false},{"year":2000,"finding":"PA28β alone (without PA28α) can enhance MHC class I antigen presentation of the MCMV pp89 epitope, but this effect is due to increased PA28αβ heterodimer formation rather than PA28β acting independently. PA28α can act alone, whereas PA28β's observed effect requires formation of PA28αβ complexes.","method":"Stable transfection of PA28β alone or PA28αβ together in mouse B8 cells; northern blot and immunoprecipitation to assess complex formation; MHC class I antigen presentation assay","journal":"Molecular immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal immunoprecipitation plus functional antigen presentation assay, single lab, two orthogonal methods","pmids":["10781831"],"is_preprint":false},{"year":2013,"finding":"N-α-acetyltransferase 10 protein (Naa10p) physically associates with PA28β (PSME2) and also interacts with PA28α in a PA28β-dependent manner. Naa10p negatively regulates PA28-dependent chymotrypsin-like 28S proteasome activity in cancer cells and in a cell-free reconstituted system with purified proteins. This suppression is independent of Naa10p acetyltransferase activity.","method":"Co-immunoprecipitation, cell-free reconstitution with purified proteins, proteasome chymotrypsin-like activity assay, acetyltransferase-dead mutant of Naa10p","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with purified proteins plus mutagenesis (acetyltransferase-dead mutant), complemented by co-IP in cells; single lab but multiple orthogonal methods","pmids":["23624078"],"is_preprint":false},{"year":2016,"finding":"Genetic deletion of PA28α and PA28β protected diabetic mice from renal and retinal microvascular injury; this protection was associated with diminished expression of OPN and MCP-1 in glomeruli. Peptides that inhibit binding of PA28 to the 20S proteasome suppressed PA28-mediated OPN expression under high-glucose conditions in mesangial cells, demonstrating that PA28 binding to the 20S proteasome is required for high-glucose-induced OPN upregulation.","method":"PA28α/β double-KO mouse model (STZ-induced diabetes), peptide inhibition of PA28–20S proteasome binding, cultured mesangial cells and retinal pericytes from KO mice under high glucose, immunohistochemistry for OPN and MCP-1","journal":"International journal of nephrology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic KO plus peptide inhibitor targeting PA28–20S interaction, two complementary approaches in one study; single lab","pmids":["27830089"],"is_preprint":false},{"year":2012,"finding":"Knockdown of PA28β (PSME2) in gastric cancer cells enhanced cell invasion, while overexpression inhibited invasion. Proteomics comparison revealed that PA28β knockdown significantly upregulated CLIC1, and subsequent knockdown of CLIC1 rescued the enhanced invasion caused by PA28β knockdown, placing CLIC1 downstream of PA28β in the regulation of gastric cancer cell invasiveness.","method":"siRNA knockdown and overexpression of PA28β, Transwell invasion assay, proteomics profiling (2D gel/MS), siRNA knockdown of CLIC1, IHC of patient tissue samples","journal":"Journal of cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis by double knockdown (PA28β then CLIC1) with functional rescue, complemented by proteomics; single lab","pmids":["22173998"],"is_preprint":false},{"year":2021,"finding":"Knockdown of PSME2 in clear cell renal cell carcinoma cell lines (CAKI-1 and 786-O) reduced invasive ability and enhanced autophagy. PSME2 was found to regulate ccRCC invasion by inhibiting BNIP3-mediated autophagy.","method":"siRNA knockdown of PSME2, Transwell invasion assay, western blot, immunofluorescence, transmission electron microscopy for autophagy, RT-qPCR","journal":"International journal of oncology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — loss-of-function with defined phenotypic readout and pathway placement (BNIP3-mediated autophagy), multiple orthogonal detection methods; single lab","pmids":["34779489"],"is_preprint":false},{"year":2025,"finding":"Knockdown of PSME2 in ESCC cells induced autophagy through the IL-6/STAT3 signaling pathway, leading to cell death resistance. Combined inhibition of PSME2 and STAT3 inhibitor WP1066 or autophagy inhibitor chloroquine suppressed tumor growth in vivo, indicating PSME2 promotes malignant progression by suppressing autophagy via IL-6/STAT3.","method":"siRNA knockdown of PSME2, STAT3 inhibitor (WP1066), autophagy inhibitor (chloroquine), in vitro proliferation/migration/invasion assays, in vivo subcutaneous tumor xenograft in nude mice","journal":"Life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro and in vivo loss-of-function with pharmacological pathway dissection; single lab, pathway placement via inhibitor rescue","pmids":["40404117"],"is_preprint":false},{"year":2025,"finding":"PSME2 silencing in LPS-treated colonic cells restored claudin-1 (tight junction protein) expression, reduced inflammatory cytokines (IL-6, IL-10, TNF-α), and enhanced autophagy (increased LC3-II/LC3-I, reduced p62). Chloroquine treatment (autophagy inhibitor) reversed the protective effects of PSME2 silencing on barrier integrity, demonstrating that PSME2 disrupts intestinal barrier function by suppressing autophagy.","method":"PSME2 siRNA knockdown in LPS-stimulated colonic cells, chloroquine autophagy inhibition, western blot for claudin-1/LC3/p62, cytokine measurement, DSS-induced colitis mouse model","journal":"Open life sciences","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — loss-of-function with pharmacological rescue (chloroquine), multiple molecular readouts; single lab","pmids":["41211066"],"is_preprint":false},{"year":1999,"finding":"The mouse genome contains two chromosomal loci for PA28β (PSME2): the canonical IFNγ-inducible PMSE2 gene with intron-exon structure, and a second retrotransposon-derived copy (PMSE2b) inserted into a LINE1 element and driven by a LINE1 F-type monomer promoter (shown by luciferase assay), constitutively expressed and encoding an identical protein.","method":"Genomic Southern blot, luciferase reporter assay for promoter activity, cDNA cloning and sequencing","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter assay directly demonstrates LINE1 promoter drives PSME2b expression; single lab with functional and structural evidence","pmids":["10222192"],"is_preprint":false}],"current_model":"PSME2 (PA28β) is a subunit of the PA28αβ heteropolymeric proteasome activator that binds the 20S proteasome to stimulate its peptidase activities; while PA28β alone can form complexes only via PA28αβ heterodimers, the PA28αβ complex is required for processing specific antigens (e.g., TRP2) but not for general antigen presentation, regulates protein degradation in 'hybrid proteasomes,' promotes high-glucose-induced OPN/MCP-1 expression in perivascular cells through 20S proteasome binding, and its activity is negatively regulated by Naa10p binding in a manner independent of acetyltransferase activity; in cancer cells, PSME2 suppresses autophagy (via BNIP3 and IL-6/STAT3 pathways) and modulates invasion at least partly through regulation of CLIC1 expression."},"narrative":{"mechanistic_narrative":"PSME2 (PA28β) is a subunit of the interferon-γ-inducible PA28αβ proteasome activator, which binds both ends of the 20S proteasome to form 'hybrid proteasomes' that contribute to ATP-dependent protein degradation and to the processing of specific antigens such as the melanoma TRP2-derived peptide, while being dispensable for general antigen presentation [PMID:11689430]. PA28β does not function autonomously: its apparent activity in enhancing MHC class I antigen presentation reflects its incorporation into PA28αβ heterodimers rather than independent action [PMID:10781831]. PA28-dependent chymotrypsin-like proteasome activity is negatively regulated by Naa10p, which physically associates with PA28β and, through it, with PA28α, in a manner independent of Naa10p acetyltransferase activity [PMID:23624078]. Binding of PA28 to the 20S proteasome is required for high-glucose-induced upregulation of OPN and MCP-1 in renal mesangial cells, linking the activator to diabetic microvascular injury [PMID:27830089]. In cancer and epithelial-barrier contexts, PSME2 suppresses autophagy and restrains it through BNIP3 and the IL-6/STAT3 axis, thereby promoting tumor cell survival and invasion and disrupting intestinal barrier integrity [PMID:34779489, PMID:40404117, PMID:41211066], and it modulates gastric cancer invasiveness at least partly by repressing CLIC1 [PMID:22173998].","teleology":[{"year":2000,"claim":"Established that PA28β cannot drive proteasome-dependent antigen presentation on its own, resolving whether the two PA28 subunits act independently.","evidence":"Stable transfection of PA28β alone versus PA28αβ in mouse B8 cells with reciprocal immunoprecipitation and an MHC class I antigen presentation assay for the MCMV pp89 epitope","pmids":["10781831"],"confidence":"Medium","gaps":["Does not quantify the stoichiometry of PA28αβ assembly required for activity","Single epitope tested in one cell system"]},{"year":2001,"claim":"Defined the in vivo role of PA28αβ by showing it forms hybrid proteasomes contributing to proteolysis and is specifically required for processing certain antigens but not for general antigen presentation.","evidence":"PA28α/β double-knockout mice with biochemical proteolytic activity assays, ovalbumin and TRP2 antigen presentation assays, and influenza A infection","pmids":["11689430"],"confidence":"High","gaps":["Does not define which antigen structural features make processing PA28αβ-dependent","Mechanism by which hybrid proteasomes enhance proteolysis not resolved at the structural level"]},{"year":2013,"claim":"Identified a negative regulator of the activator by showing Naa10p binds PA28β and suppresses PA28-dependent chymotrypsin-like activity independently of its acetyltransferase function.","evidence":"Co-immunoprecipitation in cancer cells, cell-free reconstitution with purified proteins, proteasome chymotrypsin-like activity assay, and an acetyltransferase-dead Naa10p mutant","pmids":["23624078"],"confidence":"High","gaps":["Structural basis of Naa10p–PA28β interaction unknown","Physiological contexts where this regulation operates not defined"]},{"year":2012,"claim":"Connected PSME2 to cancer cell invasion by placing CLIC1 downstream as a mediator, addressing how the activator influences tumor behavior.","evidence":"siRNA knockdown and overexpression of PA28β in gastric cancer cells, Transwell invasion assays, 2D-gel/MS proteomics, and CLIC1 knockdown rescue","pmids":["22173998"],"confidence":"Medium","gaps":["How PSME2 represses CLIC1 mechanistically is not shown","Single lab and cancer type"]},{"year":2016,"claim":"Linked PA28–20S binding to a disease phenotype by demonstrating it is required for high-glucose-induced OPN/MCP-1 expression and diabetic microvascular injury.","evidence":"PA28α/β double-KO STZ-diabetic mice, peptide inhibition of PA28–20S binding in mesangial cells and pericytes, and immunohistochemistry for OPN/MCP-1","pmids":["27830089"],"confidence":"Medium","gaps":["Substrates degraded by PA28-bound proteasome to drive OPN expression not identified","Single lab"]},{"year":2025,"claim":"Consolidated PSME2 as a suppressor of autophagy across cancer and epithelial contexts, defining BNIP3 and IL-6/STAT3 as the pathways through which it restrains autophagy to promote survival, invasion, and barrier disruption.","evidence":"siRNA knockdown of PSME2 in ccRCC, ESCC, and LPS-treated colonic cells with autophagy readouts (LC3, p62, TEM), STAT3 inhibitor WP1066 and chloroquine rescue, and in vivo xenograft and DSS-colitis models","pmids":["34779489","40404117","41211066"],"confidence":"Medium","gaps":["Whether autophagy suppression depends on PSME2's proteasome-activator function is not established","Direct molecular link between PSME2 and BNIP3 or IL-6/STAT3 not defined"]},{"year":null,"claim":"How PSME2's canonical role as a 20S proteasome activator mechanistically connects to its autophagy-suppressing and invasion-modulating activities in disease remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model linking proteasome activation to autophagy regulation","Direct degradation substrates underlying disease phenotypes not identified","Whether PA28α is co-required for the cancer/epithelial phenotypes untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,2,3]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,2]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[5,6,7]}],"complexes":["PA28αβ proteasome activator","20S proteasome (hybrid proteasome)"],"partners":["PSME1","NAA10"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UL46","full_name":"Proteasome activator complex subunit 2","aliases":["11S regulator complex subunit beta","REG-beta","Activator of multicatalytic protease subunit 2","Proteasome activator 28 subunit beta","PA28b","PA28beta"],"length_aa":239,"mass_kda":27.4,"function":"Implicated in immunoproteasome assembly and required for efficient antigen processing. The PA28 activator complex enhances the generation of class I binding peptides by altering the cleavage pattern of the proteasome","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9UL46/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PSME2","classification":"Not Classified","n_dependent_lines":105,"n_total_lines":1208,"dependency_fraction":0.0869205298013245},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000100911","cell_line_id":"CID000133","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":2}],"interactors":[{"gene":"PSME1","stoichiometry":10.0},{"gene":"PSMB1","stoichiometry":0.2},{"gene":"PSMA5","stoichiometry":0.2},{"gene":"PSMA2","stoichiometry":0.2},{"gene":"PSMA4","stoichiometry":0.2},{"gene":"PSMC3","stoichiometry":0.2},{"gene":"PSMD6","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000133","total_profiled":1310},"omim":[{"mim_id":"612024","title":"OTU DOMAIN-CONTAINING PROTEIN 7A; OTUD7A","url":"https://www.omim.org/entry/612024"},{"mim_id":"602161","title":"PROTEASOME ACTIVATOR SUBUNIT 2; PSME2","url":"https://www.omim.org/entry/602161"},{"mim_id":"600654","title":"PROTEASOME ACTIVATOR SUBUNIT 1; PSME1","url":"https://www.omim.org/entry/600654"},{"mim_id":"147574","title":"INTERFERON REGULATORY FACTOR 9; IRF9","url":"https://www.omim.org/entry/147574"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PSME2"},"hgnc":{"alias_symbol":["PA28beta"],"prev_symbol":[]},"alphafold":{"accession":"Q9UL46","domains":[{"cath_id":"1.20.120.180","chopping":"16-55_97-229","consensus_level":"high","plddt":97.7475,"start":16,"end":229}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UL46","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UL46-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UL46-F1-predicted_aligned_error_v6.png","plddt_mean":91.81},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PSME2","jax_strain_url":"https://www.jax.org/strain/search?query=PSME2"},"sequence":{"accession":"Q9UL46","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UL46.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UL46/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UL46"}},"corpus_meta":[{"pmid":"11689430","id":"PMC_11689430","title":"Immunoproteasome assembly and antigen presentation in mice lacking both PA28alpha and PA28beta.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11689430","citation_count":133,"is_preprint":false},{"pmid":"22173998","id":"PMC_22173998","title":"PA28β regulates cell invasion of gastric cancer via modulating the expression of chloride intracellular channel 1.","date":"2012","source":"Journal of cellular biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22173998","citation_count":34,"is_preprint":false},{"pmid":"38385075","id":"PMC_38385075","title":"PSME2 offers value as a biomarker of M1 macrophage infiltration in pan-cancer and inhibits osteosarcoma malignant phenotypes.","date":"2024","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38385075","citation_count":23,"is_preprint":false},{"pmid":"34779489","id":"PMC_34779489","title":"Increased expression of PSME2 is associated with clear cell renal cell carcinoma invasion by regulating BNIP3‑mediated autophagy.","date":"2021","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34779489","citation_count":21,"is_preprint":false},{"pmid":"16901544","id":"PMC_16901544","title":"Molecular cloning of proteasome activator PA28-beta subunit of large yellow croaker (Pseudosciana crocea) and its coordinated up-regulation with MHC class I alpha-chain and beta 2-microglobulin in poly I:C-treated fish.","date":"2006","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/16901544","citation_count":20,"is_preprint":false},{"pmid":"10222192","id":"PMC_10222192","title":"A second gene encoding the mouse proteasome activator PA28beta subunit is part of a LINE1 element and is driven by a LINE1 promoter.","date":"1999","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/10222192","citation_count":18,"is_preprint":false},{"pmid":"29020885","id":"PMC_29020885","title":"Identification of PA28β as a potential novel biomarker in human esophageal squamous cell carcinoma.","date":"2017","source":"Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29020885","citation_count":16,"is_preprint":false},{"pmid":"23624078","id":"PMC_23624078","title":"N-α-acetyltransferase 10 protein is a negative regulator of 28S proteasome through interaction with PA28β.","date":"2013","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/23624078","citation_count":16,"is_preprint":false},{"pmid":"20140627","id":"PMC_20140627","title":"Potential roles for PA28beta in gastric adenocarcinoma development and diagnosis.","date":"2010","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/20140627","citation_count":14,"is_preprint":false},{"pmid":"27830089","id":"PMC_27830089","title":"Proteasome Activators, PA28α and PA28β, Govern Development of Microvascular Injury in Diabetic Nephropathy and Retinopathy.","date":"2016","source":"International journal of nephrology","url":"https://pubmed.ncbi.nlm.nih.gov/27830089","citation_count":11,"is_preprint":false},{"pmid":"14597164","id":"PMC_14597164","title":"Cloning and sequence analysis of cDNA for the proteasome activator PA28-beta subunit of flounder (Paralichthys olivaceus).","date":"2003","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/14597164","citation_count":11,"is_preprint":false},{"pmid":"10781831","id":"PMC_10781831","title":"PA28alphabeta double and PA28beta single transfectant mouse B8 cell lines reveal enhanced presentation of a mouse cytomegalovirus (MCMV) pp89 MHC class I epitope.","date":"2000","source":"Molecular immunology","url":"https://pubmed.ncbi.nlm.nih.gov/10781831","citation_count":10,"is_preprint":false},{"pmid":"15373739","id":"PMC_15373739","title":"Sequence characterization, polymorphism and chromosomal localizations of the porcine PSME1 and PSME2 genes.","date":"2004","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/15373739","citation_count":9,"is_preprint":false},{"pmid":"36583022","id":"PMC_36583022","title":"PSME2 identifies immune-hot tumors in breast cancer and associates with well therapeutic response to immunotherapy.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36583022","citation_count":7,"is_preprint":false},{"pmid":"23916540","id":"PMC_23916540","title":"Genomic structural characterization and transcriptional expression analysis of proteasome activator PA28α and PA28β subunits from Oplegnathus fasciatus.","date":"2013","source":"Fish & shellfish immunology","url":"https://pubmed.ncbi.nlm.nih.gov/23916540","citation_count":4,"is_preprint":false},{"pmid":"37430323","id":"PMC_37430323","title":"YWHAH, a member of 14-3-3 family proteins, and PSME2, the proteasome activator subunit 2, are key host factors of Japanese encephalitis virus infection.","date":"2023","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/37430323","citation_count":2,"is_preprint":false},{"pmid":"40404117","id":"PMC_40404117","title":"PSME2 promotes malignant progression through autophagy modulation via IL-6/STAT3 signaling pathway in esophageal squamous cell carcinoma.","date":"2025","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/40404117","citation_count":1,"is_preprint":false},{"pmid":"41035633","id":"PMC_41035633","title":"Immunoproteasome components LMP2, PSME1, and PSME2 as novel tissue biomarkers predicting response and survival in neoadjuvant chemoimmunotherapy for resectable NSCLC.","date":"2025","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/41035633","citation_count":1,"is_preprint":false},{"pmid":"41211066","id":"PMC_41211066","title":"PSME2 exacerbates ulcerative colitis by disrupting intestinal barrier function and promoting autophagy-dependent inflammation.","date":"2025","source":"Open life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/41211066","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11638,"output_tokens":2634,"usd":0.037212,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10057,"output_tokens":2499,"usd":0.05638,"stage2_stop_reason":"end_turn"},"total_usd":0.093592,"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\": 2001,\n      \"finding\": \"PA28α and PA28β form a heteropolymer that binds to both ends of the 20S proteasome; double knockout mice showed decreased ATP-dependent proteolytic activities, indicating 'hybrid proteasomes' (containing PA28αβ) contribute to protein degradation. PA28α/β is not required for antigen presentation in general but is essential for processing specific antigens such as the melanoma antigen TRP2-derived peptide.\",\n      \"method\": \"Genetic knockout (PA28α/β double KO mice), biochemical proteolytic activity assays, antigen presentation assays with ovalbumin and TRP2 peptide, influenza A virus infection model\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean double-KO mouse model with multiple functional readouts (proteolytic activity, specific antigen processing), replicated across multiple antigen systems\",\n      \"pmids\": [\"11689430\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"PA28β alone (without PA28α) can enhance MHC class I antigen presentation of the MCMV pp89 epitope, but this effect is due to increased PA28αβ heterodimer formation rather than PA28β acting independently. PA28α can act alone, whereas PA28β's observed effect requires formation of PA28αβ complexes.\",\n      \"method\": \"Stable transfection of PA28β alone or PA28αβ together in mouse B8 cells; northern blot and immunoprecipitation to assess complex formation; MHC class I antigen presentation assay\",\n      \"journal\": \"Molecular immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal immunoprecipitation plus functional antigen presentation assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"10781831\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"N-α-acetyltransferase 10 protein (Naa10p) physically associates with PA28β (PSME2) and also interacts with PA28α in a PA28β-dependent manner. Naa10p negatively regulates PA28-dependent chymotrypsin-like 28S proteasome activity in cancer cells and in a cell-free reconstituted system with purified proteins. This suppression is independent of Naa10p acetyltransferase activity.\",\n      \"method\": \"Co-immunoprecipitation, cell-free reconstitution with purified proteins, proteasome chymotrypsin-like activity assay, acetyltransferase-dead mutant of Naa10p\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with purified proteins plus mutagenesis (acetyltransferase-dead mutant), complemented by co-IP in cells; single lab but multiple orthogonal methods\",\n      \"pmids\": [\"23624078\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Genetic deletion of PA28α and PA28β protected diabetic mice from renal and retinal microvascular injury; this protection was associated with diminished expression of OPN and MCP-1 in glomeruli. Peptides that inhibit binding of PA28 to the 20S proteasome suppressed PA28-mediated OPN expression under high-glucose conditions in mesangial cells, demonstrating that PA28 binding to the 20S proteasome is required for high-glucose-induced OPN upregulation.\",\n      \"method\": \"PA28α/β double-KO mouse model (STZ-induced diabetes), peptide inhibition of PA28–20S proteasome binding, cultured mesangial cells and retinal pericytes from KO mice under high glucose, immunohistochemistry for OPN and MCP-1\",\n      \"journal\": \"International journal of nephrology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic KO plus peptide inhibitor targeting PA28–20S interaction, two complementary approaches in one study; single lab\",\n      \"pmids\": [\"27830089\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Knockdown of PA28β (PSME2) in gastric cancer cells enhanced cell invasion, while overexpression inhibited invasion. Proteomics comparison revealed that PA28β knockdown significantly upregulated CLIC1, and subsequent knockdown of CLIC1 rescued the enhanced invasion caused by PA28β knockdown, placing CLIC1 downstream of PA28β in the regulation of gastric cancer cell invasiveness.\",\n      \"method\": \"siRNA knockdown and overexpression of PA28β, Transwell invasion assay, proteomics profiling (2D gel/MS), siRNA knockdown of CLIC1, IHC of patient tissue samples\",\n      \"journal\": \"Journal of cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis by double knockdown (PA28β then CLIC1) with functional rescue, complemented by proteomics; single lab\",\n      \"pmids\": [\"22173998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Knockdown of PSME2 in clear cell renal cell carcinoma cell lines (CAKI-1 and 786-O) reduced invasive ability and enhanced autophagy. PSME2 was found to regulate ccRCC invasion by inhibiting BNIP3-mediated autophagy.\",\n      \"method\": \"siRNA knockdown of PSME2, Transwell invasion assay, western blot, immunofluorescence, transmission electron microscopy for autophagy, RT-qPCR\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — loss-of-function with defined phenotypic readout and pathway placement (BNIP3-mediated autophagy), multiple orthogonal detection methods; single lab\",\n      \"pmids\": [\"34779489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Knockdown of PSME2 in ESCC cells induced autophagy through the IL-6/STAT3 signaling pathway, leading to cell death resistance. Combined inhibition of PSME2 and STAT3 inhibitor WP1066 or autophagy inhibitor chloroquine suppressed tumor growth in vivo, indicating PSME2 promotes malignant progression by suppressing autophagy via IL-6/STAT3.\",\n      \"method\": \"siRNA knockdown of PSME2, STAT3 inhibitor (WP1066), autophagy inhibitor (chloroquine), in vitro proliferation/migration/invasion assays, in vivo subcutaneous tumor xenograft in nude mice\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro and in vivo loss-of-function with pharmacological pathway dissection; single lab, pathway placement via inhibitor rescue\",\n      \"pmids\": [\"40404117\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PSME2 silencing in LPS-treated colonic cells restored claudin-1 (tight junction protein) expression, reduced inflammatory cytokines (IL-6, IL-10, TNF-α), and enhanced autophagy (increased LC3-II/LC3-I, reduced p62). Chloroquine treatment (autophagy inhibitor) reversed the protective effects of PSME2 silencing on barrier integrity, demonstrating that PSME2 disrupts intestinal barrier function by suppressing autophagy.\",\n      \"method\": \"PSME2 siRNA knockdown in LPS-stimulated colonic cells, chloroquine autophagy inhibition, western blot for claudin-1/LC3/p62, cytokine measurement, DSS-induced colitis mouse model\",\n      \"journal\": \"Open life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — loss-of-function with pharmacological rescue (chloroquine), multiple molecular readouts; single lab\",\n      \"pmids\": [\"41211066\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"The mouse genome contains two chromosomal loci for PA28β (PSME2): the canonical IFNγ-inducible PMSE2 gene with intron-exon structure, and a second retrotransposon-derived copy (PMSE2b) inserted into a LINE1 element and driven by a LINE1 F-type monomer promoter (shown by luciferase assay), constitutively expressed and encoding an identical protein.\",\n      \"method\": \"Genomic Southern blot, luciferase reporter assay for promoter activity, cDNA cloning and sequencing\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter assay directly demonstrates LINE1 promoter drives PSME2b expression; single lab with functional and structural evidence\",\n      \"pmids\": [\"10222192\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PSME2 (PA28β) is a subunit of the PA28αβ heteropolymeric proteasome activator that binds the 20S proteasome to stimulate its peptidase activities; while PA28β alone can form complexes only via PA28αβ heterodimers, the PA28αβ complex is required for processing specific antigens (e.g., TRP2) but not for general antigen presentation, regulates protein degradation in 'hybrid proteasomes,' promotes high-glucose-induced OPN/MCP-1 expression in perivascular cells through 20S proteasome binding, and its activity is negatively regulated by Naa10p binding in a manner independent of acetyltransferase activity; in cancer cells, PSME2 suppresses autophagy (via BNIP3 and IL-6/STAT3 pathways) and modulates invasion at least partly through regulation of CLIC1 expression.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PSME2 (PA28β) is a subunit of the interferon-γ-inducible PA28αβ proteasome activator, which binds both ends of the 20S proteasome to form 'hybrid proteasomes' that contribute to ATP-dependent protein degradation and to the processing of specific antigens such as the melanoma TRP2-derived peptide, while being dispensable for general antigen presentation [#0]. PA28β does not function autonomously: its apparent activity in enhancing MHC class I antigen presentation reflects its incorporation into PA28αβ heterodimers rather than independent action [#1]. PA28-dependent chymotrypsin-like proteasome activity is negatively regulated by Naa10p, which physically associates with PA28β and, through it, with PA28α, in a manner independent of Naa10p acetyltransferase activity [#2]. Binding of PA28 to the 20S proteasome is required for high-glucose-induced upregulation of OPN and MCP-1 in renal mesangial cells, linking the activator to diabetic microvascular injury [#3]. In cancer and epithelial-barrier contexts, PSME2 suppresses autophagy and restrains it through BNIP3 and the IL-6/STAT3 axis, thereby promoting tumor cell survival and invasion and disrupting intestinal barrier integrity [#5, #6, #7], and it modulates gastric cancer invasiveness at least partly by repressing CLIC1 [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Established that PA28β cannot drive proteasome-dependent antigen presentation on its own, resolving whether the two PA28 subunits act independently.\",\n      \"evidence\": \"Stable transfection of PA28β alone versus PA28αβ in mouse B8 cells with reciprocal immunoprecipitation and an MHC class I antigen presentation assay for the MCMV pp89 epitope\",\n      \"pmids\": [\"10781831\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not quantify the stoichiometry of PA28αβ assembly required for activity\", \"Single epitope tested in one cell system\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Defined the in vivo role of PA28αβ by showing it forms hybrid proteasomes contributing to proteolysis and is specifically required for processing certain antigens but not for general antigen presentation.\",\n      \"evidence\": \"PA28α/β double-knockout mice with biochemical proteolytic activity assays, ovalbumin and TRP2 antigen presentation assays, and influenza A infection\",\n      \"pmids\": [\"11689430\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define which antigen structural features make processing PA28αβ-dependent\", \"Mechanism by which hybrid proteasomes enhance proteolysis not resolved at the structural level\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified a negative regulator of the activator by showing Naa10p binds PA28β and suppresses PA28-dependent chymotrypsin-like activity independently of its acetyltransferase function.\",\n      \"evidence\": \"Co-immunoprecipitation in cancer cells, cell-free reconstitution with purified proteins, proteasome chymotrypsin-like activity assay, and an acetyltransferase-dead Naa10p mutant\",\n      \"pmids\": [\"23624078\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of Naa10p–PA28β interaction unknown\", \"Physiological contexts where this regulation operates not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connected PSME2 to cancer cell invasion by placing CLIC1 downstream as a mediator, addressing how the activator influences tumor behavior.\",\n      \"evidence\": \"siRNA knockdown and overexpression of PA28β in gastric cancer cells, Transwell invasion assays, 2D-gel/MS proteomics, and CLIC1 knockdown rescue\",\n      \"pmids\": [\"22173998\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How PSME2 represses CLIC1 mechanistically is not shown\", \"Single lab and cancer type\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Linked PA28–20S binding to a disease phenotype by demonstrating it is required for high-glucose-induced OPN/MCP-1 expression and diabetic microvascular injury.\",\n      \"evidence\": \"PA28α/β double-KO STZ-diabetic mice, peptide inhibition of PA28–20S binding in mesangial cells and pericytes, and immunohistochemistry for OPN/MCP-1\",\n      \"pmids\": [\"27830089\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Substrates degraded by PA28-bound proteasome to drive OPN expression not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Consolidated PSME2 as a suppressor of autophagy across cancer and epithelial contexts, defining BNIP3 and IL-6/STAT3 as the pathways through which it restrains autophagy to promote survival, invasion, and barrier disruption.\",\n      \"evidence\": \"siRNA knockdown of PSME2 in ccRCC, ESCC, and LPS-treated colonic cells with autophagy readouts (LC3, p62, TEM), STAT3 inhibitor WP1066 and chloroquine rescue, and in vivo xenograft and DSS-colitis models\",\n      \"pmids\": [\"34779489\", \"40404117\", \"41211066\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether autophagy suppression depends on PSME2's proteasome-activator function is not established\", \"Direct molecular link between PSME2 and BNIP3 or IL-6/STAT3 not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PSME2's canonical role as a 20S proteasome activator mechanistically connects to its autophagy-suppressing and invasion-modulating activities in disease remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model linking proteasome activation to autophagy regulation\", \"Direct degradation substrates underlying disease phenotypes not identified\", \"Whether PA28α is co-required for the cancer/epithelial phenotypes untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [5, 6, 7]}\n    ],\n    \"complexes\": [\"PA28αβ proteasome activator\", \"20S proteasome (hybrid proteasome)\"],\n    \"partners\": [\"PSME1\", \"NAA10\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":5,"faith_total":5,"faith_pct":100.0}}