{"gene":"PADI1","run_date":"2026-06-10T05:19:53","timeline":{"discoveries":[{"year":2021,"finding":"PADI1 (and PADI3) citrullinate pyruvate kinase M2 (PKM2) at R106, reprogramming cross-talk between PKM2 ligands: lowering sensitivity to inhibitors Tryptophan, Alanine, and Phenylalanine while promoting activation by Serine, thereby bypassing normal physiological regulation by low Serine levels to promote excessive glycolysis and reduced cell proliferation.","method":"Mass spectrometry identification of citrullination site, biochemical activity assays, cancer cell knockdown/overexpression with glycolysis readouts, hypoxia induction experiments","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — direct biochemical identification of citrullination site on PKM2 by MS, functional reconstitution of enzymatic activity change, multiple orthogonal methods (MS, metabolic assays, KD/OE) in single rigorous study","pmids":["33741961"],"is_preprint":false},{"year":2007,"finding":"Transcription factors MZF1 and Sp1/Sp3 bind the PADI1 promoter and drive its expression in human keratinocytes; MZF1 or Sp1 siRNA knockdown reduces PADI1 expression, and MZF1 expression increases in parallel with PAD1 during keratinocyte differentiation.","method":"Promoter deletion/luciferase reporter assays, site-directed mutagenesis of MZF1/Sp1 binding sites, chromatin immunoprecipitation (ChIP), siRNA knockdown with quantitative RT-PCR","journal":"The Journal of investigative dermatology","confidence":"High","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, reporter assays, mutagenesis, siRNA KD) in a single focused study on PADI1 transcriptional regulation","pmids":["17851584"],"is_preprint":false},{"year":2021,"finding":"PADI1 knockdown suppresses cell migration and invasion in pancreatic ductal adenocarcinoma (PAAD) cells and activates the ERK1/2-p38 signaling pathway; MEK1/2 inhibitor treatment attenuates the effects of PADI1 knockdown on migration, invasion, and EMT, placing PADI1 upstream of ERK1/2-p38 signaling.","method":"siRNA knockdown and cDNA overexpression in PAAD cell lines, wound-healing assay, Transwell invasion assay, western blot, MEK1/2 inhibitor epistasis","journal":"Journal of gastrointestinal oncology","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — single lab, pathway placement via pharmacological epistasis and KD/OE but no direct biochemical substrate identification","pmids":["34295566"],"is_preprint":false},{"year":2025,"finding":"PADI1 knockdown in trophoblast cells inhibits TG-induced endoplasmic reticulum stress (ERS) and apoptosis by downregulating ERS markers (IRE1α, XBP1, CHOP, ATF6, GRP78) through activation of the FAK/ERK1/2 signaling pathway; FAK/ERK1/2 inhibition blocks the pro-survival effects of PADI1 knockdown, placing PADI1 upstream of FAK/ERK1/2 in trophoblast ERS regulation.","method":"siRNA knockdown in HTR-8 and Swan-71 trophoblast cells, thapsigargin-induced ERS model, western blot for ERS markers, FAK/ERK1/2 pathway inhibitor epistasis, cell viability and migration assays","journal":"Tissue & cell","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — single lab, pharmacological epistasis with KD, multiple pathway markers assessed but no direct biochemical substrate identification for PADI1","pmids":["40424721"],"is_preprint":false}],"current_model":"PADI1 is a calcium-dependent peptidylarginine deiminase that citrullinates specific arginine residues on substrate proteins (including PKM2 R106) to reprogramme their activity; its expression in keratinocytes is driven by transcription factors MZF1 and Sp1/Sp3, and it modulates cancer cell glycolysis, migration/invasion, and trophoblast endoplasmic reticulum stress through downstream ERK1/2-p38 and FAK/ERK1/2 signaling pathways."},"narrative":{"mechanistic_narrative":"PADI1 is a calcium-dependent peptidylarginine deiminase that reprogrammes substrate protein function through site-specific citrullination, with broad consequences for cell metabolism, migration, and stress signaling [PMID:33741961]. Biochemically, PADI1 citrullinates pyruvate kinase M2 (PKM2) at R106, altering allosteric cross-talk among PKM2 ligands — lowering sensitivity to the inhibitors tryptophan, alanine, and phenylalanine while enhancing serine-driven activation — so that PKM2 bypasses normal regulation by low serine and drives excessive glycolysis [PMID:33741961]. In keratinocytes, PADI1 transcription is driven by the transcription factors MZF1 and Sp1/Sp3, which bind its promoter, and MZF1 rises in parallel with PADI1 during differentiation [PMID:17851584]. Beyond its biochemical activity, PADI1 acts upstream of MAPK cascades in disease contexts: it promotes pancreatic ductal adenocarcinoma migration, invasion, and EMT via ERK1/2-p38 signaling [PMID:34295566], and it drives endoplasmic reticulum stress and apoptosis in trophoblast cells through the FAK/ERK1/2 pathway [PMID:40424721]. Apart from the PKM2 R106 site, additional direct substrates underlying these signaling phenotypes have not been identified in the available corpus.","teleology":[{"year":2007,"claim":"Established how PADI1 expression is controlled, identifying the transcriptional inputs that couple it to keratinocyte differentiation.","evidence":"Promoter deletion/luciferase reporters, binding-site mutagenesis, ChIP, and siRNA knockdown in human keratinocytes","pmids":["17851584"],"confidence":"High","gaps":["Does not address PADI1 enzymatic substrates or catalytic mechanism","Regulation outside keratinocyte differentiation not examined","No link drawn between transcriptional control and downstream citrullination targets"]},{"year":2021,"claim":"Defined a direct molecular substrate and catalytic consequence for PADI1, showing that citrullination of PKM2 R106 reprogrammes allosteric ligand cross-talk to drive glycolysis.","evidence":"Mass spectrometry site mapping, biochemical activity assays, and knockdown/overexpression with metabolic readouts in cancer cells under hypoxia","pmids":["33741961"],"confidence":"High","gaps":["Whether PKM2 is the principal substrate driving phenotypes in other cell types is unknown","No structural model of the PADI1-PKM2 interaction","Calcium-dependence and regulation of PADI1 catalytic activity in vivo not detailed"]},{"year":2021,"claim":"Placed PADI1 upstream of a MAPK cascade in cancer cell motility, linking its activity to migration, invasion, and EMT.","evidence":"siRNA knockdown/cDNA overexpression in PAAD cells with wound-healing, Transwell, western blot, and MEK1/2 inhibitor epistasis","pmids":["34295566"],"confidence":"Medium","gaps":["No direct citrullination substrate identified to connect PADI1 enzymatic activity to ERK1/2-p38 activation","Pathway placement rests on pharmacological epistasis from a single lab","Whether catalytic activity is required for the phenotype is untested"]},{"year":2025,"claim":"Extended PADI1's signaling role to trophoblast ER stress, showing it acts upstream of FAK/ERK1/2 to promote stress-induced apoptosis.","evidence":"siRNA knockdown in HTR-8 and Swan-71 cells, thapsigargin-induced ERS model, ERS marker western blots, and FAK/ERK1/2 inhibitor epistasis","pmids":["40424721"],"confidence":"Medium","gaps":["No biochemical substrate identified linking PADI1 to FAK/ERK1/2","Single-lab pharmacological epistasis without catalytic-dead controls","Physiological relevance to placental disease not established"]},{"year":null,"claim":"Whether the diverse signaling phenotypes (ERK1/2-p38, FAK/ERK1/2) depend on PADI1's deiminase activity and which citrullinated substrates mediate them remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No substrate beyond PKM2 R106 identified for the signaling phenotypes","Catalytic requirement for migration/invasion and ERS phenotypes untested","No structural data on PADI1 substrate recognition"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0]}],"localization":[],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3]}],"complexes":[],"partners":["PKM2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9ULC6","full_name":"Protein-arginine deiminase type-1","aliases":["Peptidylarginine deiminase I","Protein-arginine deiminase type I"],"length_aa":663,"mass_kda":74.7,"function":"Catalyzes the deimination of arginine residues of proteins","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9ULC6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PADI1","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/PADI1","total_profiled":1310},"omim":[{"mim_id":"616284","title":"FILAGGRIN FAMILY MEMBER 2; FLG2","url":"https://www.omim.org/entry/616284"},{"mim_id":"610363","title":"PEPTIDYLARGININE DEIMINASE, TYPE VI; PADI6","url":"https://www.omim.org/entry/610363"},{"mim_id":"607935","title":"PEPTIDYLARGININE DEIMINASE, TYPE II; PADI2","url":"https://www.omim.org/entry/607935"},{"mim_id":"607934","title":"PEPTIDYLARGININE DEIMINASE, TYPE I; PADI1","url":"https://www.omim.org/entry/607934"},{"mim_id":"606755","title":"PEPTIDYLARGININE DEIMINASE, TYPE III; PADI3","url":"https://www.omim.org/entry/606755"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"esophagus","ntpm":84.3}],"url":"https://www.proteinatlas.org/search/PADI1"},"hgnc":{"alias_symbol":["HPAD10","PDI1","PDI","PAD1"],"prev_symbol":[]},"alphafold":{"accession":"Q9ULC6","domains":[{"cath_id":"2.60.40.1860","chopping":"7-116","consensus_level":"high","plddt":89.6138,"start":7,"end":116},{"cath_id":"2.60.40.1700","chopping":"123-292","consensus_level":"high","plddt":94.8725,"start":123,"end":292},{"cath_id":"3.75.10.10","chopping":"296-656","consensus_level":"medium","plddt":96.6144,"start":296,"end":656}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULC6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULC6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULC6-F1-predicted_aligned_error_v6.png","plddt_mean":94.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PADI1","jax_strain_url":"https://www.jax.org/strain/search?query=PADI1"},"sequence":{"accession":"Q9ULC6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULC6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULC6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULC6"}},"corpus_meta":[{"pmid":"33741961","id":"PMC_33741961","title":"Citrullination of pyruvate kinase M2 by PADI1 and PADI3 regulates glycolysis and cancer cell proliferation.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/33741961","citation_count":56,"is_preprint":false},{"pmid":"1761527","id":"PMC_1761527","title":"Molecular structure of a yeast gene, PDI1, encoding protein disulfide isomerase that is essential for cell growth.","date":"1991","source":"Journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/1761527","citation_count":55,"is_preprint":false},{"pmid":"31730668","id":"PMC_31730668","title":"N-glycosylation of the protein disulfide isomerase Pdi1 ensures full Ustilago maydis virulence.","date":"2019","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/31730668","citation_count":40,"is_preprint":false},{"pmid":"8385117","id":"PMC_8385117","title":"Functional replacement of the Saccharomyces cerevisiae Trg1/Pdi1 protein by members of the mammalian protein disulfide isomerase family.","date":"1993","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8385117","citation_count":38,"is_preprint":false},{"pmid":"17851584","id":"PMC_17851584","title":"Crucial roles of MZF1 and Sp1 in the transcriptional regulation of the peptidylarginine deiminase type I gene (PADI1) in human keratinocytes.","date":"2007","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/17851584","citation_count":29,"is_preprint":false},{"pmid":"27053108","id":"PMC_27053108","title":"A Complex of Htm1 and the Oxidoreductase Pdi1 Accelerates Degradation of Misfolded Glycoproteins.","date":"2016","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/27053108","citation_count":27,"is_preprint":false},{"pmid":"34587346","id":"PMC_34587346","title":"Ero1-Pdi1 module-catalysed dimerization of a nucleotide sugar transporter, FonNst2, regulates virulence of Fusarium oxysporum on watermelon.","date":"2021","source":"Environmental microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/34587346","citation_count":22,"is_preprint":false},{"pmid":"34295566","id":"PMC_34295566","title":"PADI1 contributes to EMT in PAAD by activating the ERK1/2-p38 signaling pathway.","date":"2021","source":"Journal of gastrointestinal oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34295566","citation_count":17,"is_preprint":false},{"pmid":"32912692","id":"PMC_32912692","title":"Pichia pastoris Protein Disulfide Isomerase (PDI1) promoter for heterologous protein production and its sequence characterization.","date":"2020","source":"Enzyme and microbial technology","url":"https://pubmed.ncbi.nlm.nih.gov/32912692","citation_count":13,"is_preprint":false},{"pmid":"30427898","id":"PMC_30427898","title":"Protein Disulfide Isomerase (PDI1-1) differential expression and modification in Mexican malting barley cultivars.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/30427898","citation_count":8,"is_preprint":false},{"pmid":"36816748","id":"PMC_36816748","title":"Next generation oncolytic viruses expressing PADI1 and TIMP2 exhibit anti-tumor activity against melanoma in nude and humanized mouse models.","date":"2023","source":"Molecular therapy oncolytics","url":"https://pubmed.ncbi.nlm.nih.gov/36816748","citation_count":8,"is_preprint":false},{"pmid":"29321956","id":"PMC_29321956","title":"An amebic protein disulfide isomerase (PDI) complements the yeast PDI1 mutation but is unable to support cell viability under ER or thermal stress.","date":"2017","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/29321956","citation_count":5,"is_preprint":false},{"pmid":"40424721","id":"PMC_40424721","title":"PADI1 aggravates endoplasmic reticulum stress in trophoblast cells by inhibiting the FAK-ERK signaling pathway.","date":"2025","source":"Tissue & cell","url":"https://pubmed.ncbi.nlm.nih.gov/40424721","citation_count":1,"is_preprint":false},{"pmid":"42151978","id":"PMC_42151978","title":"Evaluation of recombinant trypsinogen and chymotrypsinogen production in Komagataella phaffii through co-expression of HAC1 and PDI1.","date":"2026","source":"Microbial cell factories","url":"https://pubmed.ncbi.nlm.nih.gov/42151978","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.10.17.618908","title":"Initiation of ERAD by the bifunctional complex of Mnl1 mannosidase and protein disulfide isomerase","date":"2024-10-17","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.17.618908","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.08.21.609038","title":"Reexamining the essentiality of Pdi1 in yeast – A  <i>PDI1</i>  knockout is viable in  <i>Komagataella phaffii</i>  and still produces recombinant disulfide bonded proteins","date":"2024-08-21","source":"bioRxiv","url":"https://doi.org/10.1101/2024.08.21.609038","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9579,"output_tokens":1274,"usd":0.023924,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7886,"output_tokens":2008,"usd":0.044815,"stage2_stop_reason":"end_turn"},"total_usd":0.068739,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2021,\n      \"finding\": \"PADI1 (and PADI3) citrullinate pyruvate kinase M2 (PKM2) at R106, reprogramming cross-talk between PKM2 ligands: lowering sensitivity to inhibitors Tryptophan, Alanine, and Phenylalanine while promoting activation by Serine, thereby bypassing normal physiological regulation by low Serine levels to promote excessive glycolysis and reduced cell proliferation.\",\n      \"method\": \"Mass spectrometry identification of citrullination site, biochemical activity assays, cancer cell knockdown/overexpression with glycolysis readouts, hypoxia induction experiments\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — direct biochemical identification of citrullination site on PKM2 by MS, functional reconstitution of enzymatic activity change, multiple orthogonal methods (MS, metabolic assays, KD/OE) in single rigorous study\",\n      \"pmids\": [\"33741961\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Transcription factors MZF1 and Sp1/Sp3 bind the PADI1 promoter and drive its expression in human keratinocytes; MZF1 or Sp1 siRNA knockdown reduces PADI1 expression, and MZF1 expression increases in parallel with PAD1 during keratinocyte differentiation.\",\n      \"method\": \"Promoter deletion/luciferase reporter assays, site-directed mutagenesis of MZF1/Sp1 binding sites, chromatin immunoprecipitation (ChIP), siRNA knockdown with quantitative RT-PCR\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, reporter assays, mutagenesis, siRNA KD) in a single focused study on PADI1 transcriptional regulation\",\n      \"pmids\": [\"17851584\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"PADI1 knockdown suppresses cell migration and invasion in pancreatic ductal adenocarcinoma (PAAD) cells and activates the ERK1/2-p38 signaling pathway; MEK1/2 inhibitor treatment attenuates the effects of PADI1 knockdown on migration, invasion, and EMT, placing PADI1 upstream of ERK1/2-p38 signaling.\",\n      \"method\": \"siRNA knockdown and cDNA overexpression in PAAD cell lines, wound-healing assay, Transwell invasion assay, western blot, MEK1/2 inhibitor epistasis\",\n      \"journal\": \"Journal of gastrointestinal oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — single lab, pathway placement via pharmacological epistasis and KD/OE but no direct biochemical substrate identification\",\n      \"pmids\": [\"34295566\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PADI1 knockdown in trophoblast cells inhibits TG-induced endoplasmic reticulum stress (ERS) and apoptosis by downregulating ERS markers (IRE1α, XBP1, CHOP, ATF6, GRP78) through activation of the FAK/ERK1/2 signaling pathway; FAK/ERK1/2 inhibition blocks the pro-survival effects of PADI1 knockdown, placing PADI1 upstream of FAK/ERK1/2 in trophoblast ERS regulation.\",\n      \"method\": \"siRNA knockdown in HTR-8 and Swan-71 trophoblast cells, thapsigargin-induced ERS model, western blot for ERS markers, FAK/ERK1/2 pathway inhibitor epistasis, cell viability and migration assays\",\n      \"journal\": \"Tissue & cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — single lab, pharmacological epistasis with KD, multiple pathway markers assessed but no direct biochemical substrate identification for PADI1\",\n      \"pmids\": [\"40424721\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PADI1 is a calcium-dependent peptidylarginine deiminase that citrullinates specific arginine residues on substrate proteins (including PKM2 R106) to reprogramme their activity; its expression in keratinocytes is driven by transcription factors MZF1 and Sp1/Sp3, and it modulates cancer cell glycolysis, migration/invasion, and trophoblast endoplasmic reticulum stress through downstream ERK1/2-p38 and FAK/ERK1/2 signaling pathways.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PADI1 is a calcium-dependent peptidylarginine deiminase that reprogrammes substrate protein function through site-specific citrullination, with broad consequences for cell metabolism, migration, and stress signaling [#0]. Biochemically, PADI1 citrullinates pyruvate kinase M2 (PKM2) at R106, altering allosteric cross-talk among PKM2 ligands — lowering sensitivity to the inhibitors tryptophan, alanine, and phenylalanine while enhancing serine-driven activation — so that PKM2 bypasses normal regulation by low serine and drives excessive glycolysis [#0]. In keratinocytes, PADI1 transcription is driven by the transcription factors MZF1 and Sp1/Sp3, which bind its promoter, and MZF1 rises in parallel with PADI1 during differentiation [#1]. Beyond its biochemical activity, PADI1 acts upstream of MAPK cascades in disease contexts: it promotes pancreatic ductal adenocarcinoma migration, invasion, and EMT via ERK1/2-p38 signaling [#2], and it drives endoplasmic reticulum stress and apoptosis in trophoblast cells through the FAK/ERK1/2 pathway [#3]. Apart from the PKM2 R106 site, additional direct substrates underlying these signaling phenotypes have not been identified in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2007,\n      \"claim\": \"Established how PADI1 expression is controlled, identifying the transcriptional inputs that couple it to keratinocyte differentiation.\",\n      \"evidence\": \"Promoter deletion/luciferase reporters, binding-site mutagenesis, ChIP, and siRNA knockdown in human keratinocytes\",\n      \"pmids\": [\"17851584\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Does not address PADI1 enzymatic substrates or catalytic mechanism\",\n        \"Regulation outside keratinocyte differentiation not examined\",\n        \"No link drawn between transcriptional control and downstream citrullination targets\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined a direct molecular substrate and catalytic consequence for PADI1, showing that citrullination of PKM2 R106 reprogrammes allosteric ligand cross-talk to drive glycolysis.\",\n      \"evidence\": \"Mass spectrometry site mapping, biochemical activity assays, and knockdown/overexpression with metabolic readouts in cancer cells under hypoxia\",\n      \"pmids\": [\"33741961\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether PKM2 is the principal substrate driving phenotypes in other cell types is unknown\",\n        \"No structural model of the PADI1-PKM2 interaction\",\n        \"Calcium-dependence and regulation of PADI1 catalytic activity in vivo not detailed\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Placed PADI1 upstream of a MAPK cascade in cancer cell motility, linking its activity to migration, invasion, and EMT.\",\n      \"evidence\": \"siRNA knockdown/cDNA overexpression in PAAD cells with wound-healing, Transwell, western blot, and MEK1/2 inhibitor epistasis\",\n      \"pmids\": [\"34295566\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct citrullination substrate identified to connect PADI1 enzymatic activity to ERK1/2-p38 activation\",\n        \"Pathway placement rests on pharmacological epistasis from a single lab\",\n        \"Whether catalytic activity is required for the phenotype is untested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Extended PADI1's signaling role to trophoblast ER stress, showing it acts upstream of FAK/ERK1/2 to promote stress-induced apoptosis.\",\n      \"evidence\": \"siRNA knockdown in HTR-8 and Swan-71 cells, thapsigargin-induced ERS model, ERS marker western blots, and FAK/ERK1/2 inhibitor epistasis\",\n      \"pmids\": [\"40424721\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No biochemical substrate identified linking PADI1 to FAK/ERK1/2\",\n        \"Single-lab pharmacological epistasis without catalytic-dead controls\",\n        \"Physiological relevance to placental disease not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the diverse signaling phenotypes (ERK1/2-p38, FAK/ERK1/2) depend on PADI1's deiminase activity and which citrullinated substrates mediate them remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No substrate beyond PKM2 R106 identified for the signaling phenotypes\",\n        \"Catalytic requirement for migration/invasion and ERS phenotypes untested\",\n        \"No structural data on PADI1 substrate recognition\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"PKM2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":4,"faith_total":4,"faith_pct":100.0}}