{"gene":"PPDPF","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2008,"finding":"Exdpf (zebrafish ortholog of PPDPF) is a direct transcriptional target of Ptf1a: three consensus Ptf1a binding sites were identified in the exdpf promoter, luciferase assay demonstrated Ptf1a promotes exdpf transcription, and exdpf expression was lost in ptf1a morphants.","method":"Promoter analysis, luciferase reporter assay, antisense morpholino knockdown in zebrafish","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (promoter binding site identification, luciferase assay, morpholino KD) in a single rigorous study","pmids":["19067490"],"is_preprint":false},{"year":2008,"finding":"Exdpf (zebrafish ortholog of PPDPF) is required for exocrine pancreas cell proliferation; knockdown causes lineage-specific cell cycle arrest (not apoptosis) mediated by upregulation of p21(Cip), p27(Kip), and cyclin G1.","method":"Antisense morpholino knockdown in zebrafish, real-time PCR for cell cycle inhibitor genes","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KD with defined cellular phenotype and molecular mechanism, multiple orthogonal methods in one rigorous study","pmids":["19067490"],"is_preprint":false},{"year":2008,"finding":"Exdpf is genetically downstream of retinoic acid (RA) signaling in exocrine pancreas development: exdpf knockdown abolished RA-induced ectopic cpa expression, and exdpf mRNA injection rescued endogenous cpa expression in embryos treated with a RA signaling inhibitor.","method":"Genetic epistasis via morpholino knockdown and mRNA rescue in zebrafish with RA pathway manipulation","journal":"PLoS biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with gain- and loss-of-function experiments, multiple conditions tested","pmids":["19067490"],"is_preprint":false},{"year":2022,"finding":"PPDPF promotes STAT3 hyperactivation by interfering with the STAT3-PTPN1 interaction, leading to increased BMPR2 transcription and inhibition of apoptosis in lung adenocarcinoma.","method":"Co-immunoprecipitation, in vitro and in vivo loss-of-function assays, transcriptional analysis","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — mechanistic pathway placement via co-IP and KD, single lab with multiple readouts","pmids":["35906391"],"is_preprint":false},{"year":2022,"finding":"PPDPF interacts with BABAM2 and blocks MDM2-mediated ubiquitination of BABAM2, thereby stabilizing BABAM2 and promoting radioresistance in non-small cell lung cancer cells.","method":"Co-immunoprecipitation, ubiquitination assay, KO and overexpression in lung cancer cells and KL mouse model","journal":"International journal of biological sciences","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP, ubiquitination assay, and in vivo mouse model, single lab","pmids":["34975328"],"is_preprint":false},{"year":2022,"finding":"PPDPF can bind GTP and transfer GTP to SOS1, thereby enhancing SOS1 GEF activity and promoting KRAS activation in pancreatic ductal adenocarcinoma; mutations at GTP-binding sites of PPDPF or critical SOS1-PPDPF interaction residues severely impair GEF activity and tumor-promoting effects.","method":"GTP-binding assay, GEF activity assay, site-directed mutagenesis, co-immunoprecipitation, in vitro and in vivo overexpression/KO, KRASG12D genetic mouse model","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro biochemical assays (GTP binding, GEF activity), active-site mutagenesis, and in vivo genetic mouse models, multiple orthogonal methods","pmids":["36453576"],"is_preprint":false},{"year":2023,"finding":"PPDPF interacts with RIPK1 and recruits the E3 ligase TRIM21, which catalyzes K63-linked ubiquitination of RIPK1 at K140, thereby activating NF-κB signaling and suppressing hepatocellular carcinoma development.","method":"Co-immunoprecipitation, ubiquitination assay with site-specific (K140) mutant, liver-specific KO and overexpression mouse models (DEN-induced HCC)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — biochemical ubiquitination assays with specific lysine mutant, co-IP of complex, and in vivo mouse models, multiple orthogonal methods","pmids":["37027301"],"is_preprint":false},{"year":2023,"finding":"PPDPF interacts with CK1α, disrupting its binding to Axin and disassociating the β-catenin destruction complex, thereby decreasing β-catenin phosphorylation and activating the Wnt/β-catenin pathway in colorectal cancer.","method":"Co-immunoprecipitation, phosphorylation assays, intestinal epithelium-specific KO with organoid and AOM/DSS mouse models","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — co-IP of protein complex disruption, phosphorylation readout, and multiple in vivo mouse models, single rigorous study with multiple orthogonal methods","pmids":["37477088"],"is_preprint":false},{"year":2023,"finding":"PPDPF is phosphorylated at Tyr16 and Tyr17 by IL6/JAK2 inflammatory signaling, which stabilizes the PPDPF protein.","method":"Phosphorylation site mapping, mutational analysis, IL6/JAK2 pathway manipulation","journal":"EMBO reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — specific phosphorylation sites identified with mutagenesis, single lab","pmids":["37477088"],"is_preprint":false},{"year":2025,"finding":"PPDPF functions as a thiol-disulfide oxidoreductase that maintains cellular NAD+ levels by supporting nicotinamide mononucleotide adenylyl transferase (NMNAT) activity; PPDPF deficiency impairs NAD+ and mitochondrial homeostasis in proximal tubule cells.","method":"Enzymatic activity assay (thiol-disulfide oxidoreductase), NAD+ level measurement, NMNAT activity assay, PPDPF KO mouse models (aging, chemical exposure, obstruction)","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct enzymatic characterization, defined substrate (NMNAT), multiple KO mouse models with functional readouts","pmids":["40106551"],"is_preprint":false},{"year":2025,"finding":"PPDPF prevents the interaction between MCCA and MCCB subunits of the methylcrotonyl-CoA carboxylase complex, thereby inhibiting leucine catabolism and activating mTORC1 signaling in cholangiocarcinoma.","method":"SILAC metabolic labeling screen, metabolic flux analysis, co-immunoprecipitation, PPDPF KO mouse model","journal":"Oncogene","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — SILAC screen plus metabolic flux analysis plus co-IP plus in vivo mouse model, multiple orthogonal methods","pmids":["40025229"],"is_preprint":false},{"year":2025,"finding":"PPDPF protein stability is regulated by ubiquitination: ARIH2 (E3 ligase) and OTUD4 (deubiquitinase) cooperatively control PPDPF ubiquitination and stability under amino acid starvation conditions.","method":"Ubiquitination assay, co-immunoprecipitation with ARIH2 and OTUD4","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP and ubiquitination assay identifying writer/eraser, single lab","pmids":["40025229"],"is_preprint":false},{"year":2025,"finding":"PPDPF interferes with c-Myc–GSK3β interaction, enhancing c-Myc protein stability and thereby upregulating CD24 expression to promote immune escape from macrophage phagocytosis in esophageal squamous cell carcinoma.","method":"GST-pulldown, co-immunoprecipitation, immunoblotting, fluorescence microscopy-based phagocytosis assay, flow cytometry, KO mouse models","journal":"Journal for immunotherapy of cancer","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — GST-pulldown, reciprocal co-IP, functional phagocytosis assay, and in vivo mouse models, multiple orthogonal methods","pmids":["40774693"],"is_preprint":false},{"year":2024,"finding":"PPDPF interacts with PCCA (a subunit of propionyl-CoA carboxylase) and inhibits PCCA-PCCB binding, thereby blocking methionine catabolism via the C-Vomit pathway and increasing methionine and SAM levels in esophageal squamous cell carcinoma.","method":"Mass spectrometry, co-immunoprecipitation, metabolite measurement in vitro and in vivo","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — mass spectrometry interaction discovery, co-IP, and metabolic measurements, single lab","pmids":["39694223"],"is_preprint":false},{"year":2025,"finding":"PPDPF knockout in human embryonic stem cells differentiated toward the pancreatic lineage shows only a very modest effect on pancreatic progenitor development in vitro and does not affect lineage specification upon orthotopic transplantation in vivo, indicating PPDPF is NOT a key regulator of human pancreas development (in contrast to its zebrafish ortholog).","method":"CRISPR/Cas9 knockout in hESCs, pancreatic differentiation protocol, orthotopic transplantation in vivo","journal":"PLoS genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR KO with in vitro and in vivo differentiation assay; negative result replicated across multiple conditions in single study","pmids":["40193385"],"is_preprint":false}],"current_model":"PPDPF (also known as EXDPF/C20orf149) is a multifunctional protein with enzymatic activity as a thiol-disulfide oxidoreductase that supports NMNAT-mediated NAD+ homeostasis; it acts as a GTP-binding factor that transfers GTP to SOS1 to enhance its GEF activity and activate RAS signaling; it modulates multiple signaling pathways by disrupting protein–protein interactions (CK1α–Axin to activate Wnt/β-catenin, STAT3–PTPN1 to hyperactivate STAT3, c-Myc–GSK3β to stabilize c-Myc, MCCA–MCCB to block leucine catabolism, PCCA–PCCB to block methionine catabolism); it scaffolds ubiquitination complexes (recruiting TRIM21 to K63-ubiquitinate RIPK1 at K140 for NF-κB activation; blocking MDM2-mediated ubiquitination of BABAM2); and its own stability is regulated by phosphorylation (JAK2 at Tyr16/Tyr17) and ubiquitination (ARIH2/OTUD4), while in zebrafish it is transcriptionally controlled by Ptf1a downstream of retinoic acid signaling."},"narrative":{"mechanistic_narrative":"PPDPF (EXDPF/C20orf149) is a small multifunctional adaptor and enzyme that couples developmental, metabolic, and oncogenic signaling, and was first defined as a Ptf1a-regulated, retinoic-acid-dependent driver of exocrine pancreas cell proliferation in zebrafish, where its loss triggers cell-cycle arrest through induction of p21, p27, and cyclin G1 [PMID:19067490]. Its best-characterized biochemical activities are direct: PPDPF binds GTP and transfers it to SOS1 to enhance SOS1 GEF activity and KRAS activation, with GTP-binding and SOS1-interaction mutants abolishing this function [PMID:36453576], and it acts as a thiol-disulfide oxidoreductase that supports NMNAT activity to maintain NAD+ and mitochondrial homeostasis [PMID:40106551]. A recurring mechanistic theme is that PPDPF modulates signaling by disrupting or scaffolding specific protein-protein interactions: it interferes with the CK1α–Axin interaction to dismantle the β-catenin destruction complex and activate Wnt/β-catenin [PMID:37477088], blocks STAT3–PTPN1 binding to hyperactivate STAT3 [PMID:35906391], disrupts c-Myc–GSK3β association to stabilize c-Myc and drive CD24-mediated immune escape [PMID:40774693], and prevents assembly of the metabolic carboxylase pairs MCCA–MCCB and PCCA–PCCB to block leucine and methionine catabolism and feed mTORC1 and SAM pools [PMID:40025229, PMID:39694223]. PPDPF also scaffolds ubiquitination events, recruiting TRIM21 to catalyze K63-linked ubiquitination of RIPK1 at K140 to activate NF-κB [PMID:37027301] and blocking MDM2-mediated ubiquitination of BABAM2 to confer radioresistance [PMID:34975328]. Its own abundance is controlled post-translationally, being stabilized by IL6/JAK2-mediated phosphorylation at Tyr16/Tyr17 [PMID:37477088] and by the opposing actions of the E3 ligase ARIH2 and deubiquitinase OTUD4 under amino acid starvation [PMID:40025229]. Notably, the developmental role is not conserved: PPDPF knockout in human embryonic stem cells has only a modest effect on pancreatic progenitor development and does not alter lineage specification in vivo [PMID:40193385].","teleology":[{"year":2008,"claim":"Established the first biological role and upstream regulation of PPDPF, placing its zebrafish ortholog as a retinoic-acid/Ptf1a-controlled effector of exocrine pancreas proliferation.","evidence":"Promoter binding-site analysis, luciferase reporter, morpholino knockdown, mRNA rescue, and cell-cycle gene profiling in zebrafish","pmids":["19067490"],"confidence":"High","gaps":["Molecular activity of the protein itself was not defined","Whether the proliferation role generalizes beyond exocrine pancreas was untested"]},{"year":2022,"claim":"Defined PPDPF as a direct GTP-binding factor that potentiates SOS1 GEF activity, providing a concrete biochemical mechanism for its RAS-pathway and tumor-promoting effects.","evidence":"GTP-binding and GEF activity assays, active-site mutagenesis, co-IP, and KRASG12D mouse models in pancreatic ductal adenocarcinoma","pmids":["36453576"],"confidence":"High","gaps":["Structural basis of GTP transfer to SOS1 not resolved","Whether this activity operates outside pancreatic cancer is unclear"]},{"year":2022,"claim":"Showed PPDPF acts as an interaction modulator and ubiquitination regulator in lung cancer, interfering with STAT3-PTPN1 and protecting BABAM2 from MDM2.","evidence":"Co-IP, ubiquitination assays, knockout/overexpression, and lung cancer mouse models","pmids":["35906391","34975328"],"confidence":"Medium","gaps":["Direct vs indirect nature of the disruption not fully resolved","Single-lab mechanistic placement"]},{"year":2023,"claim":"Generalized the protein-interaction-disruption and scaffolding model across cancers, linking PPDPF to Wnt/β-catenin activation and to TRIM21-dependent K63-ubiquitination of RIPK1 for NF-κB signaling, and identified JAK2 phosphorylation as a stabilizing input.","evidence":"Co-IP, site-specific ubiquitination assays (RIPK1 K140), phosphorylation-site mapping, organoid and tissue-specific KO mouse models","pmids":["37027301","37477088"],"confidence":"High","gaps":["How one small protein selects among many distinct partners is unexplained","Stoichiometry and structural mode of complex disruption unknown"]},{"year":2024,"claim":"Extended the interaction-disruption mechanism into amino acid metabolism, with PPDPF blocking PCCA-PCCB assembly to elevate methionine and SAM.","evidence":"Mass spectrometry, co-IP, and metabolite measurements in esophageal squamous cell carcinoma","pmids":["39694223"],"confidence":"Medium","gaps":["Direct binding interface with PCCA not mapped","Single-lab finding"]},{"year":2025,"claim":"Defined an intrinsic enzymatic activity (thiol-disulfide oxidoreductase) supporting NMNAT and NAD+ homeostasis, and added further metabolic and immune-evasion mechanisms plus a writer/eraser pair controlling PPDPF stability.","evidence":"Enzymatic and NMNAT activity assays, SILAC and metabolic flux analysis, GST-pulldown, ubiquitination assays, and multiple KO mouse models","pmids":["40106551","40025229","40774693"],"confidence":"High","gaps":["How thiol-disulfide oxidoreductase activity reconciles with the GTP-binding and adaptor activities is unknown","Whether a single domain mediates all these functions is unresolved"]},{"year":2025,"claim":"Revealed that the developmental role is not conserved in humans, with PPDPF dispensable for human pancreatic lineage specification, sharpening interpretation of the original zebrafish phenotype.","evidence":"CRISPR/Cas9 knockout in hESCs with pancreatic differentiation and orthotopic transplantation","pmids":["40193385"],"confidence":"Medium","gaps":["Functional compensation in human cells not ruled out","Does not address PPDPF roles in adult/disease tissues"]},{"year":null,"claim":"How a single small protein integrates a thiol-disulfide oxidoreductase activity, GTP binding, and a broad set of protein-interaction-disruption events into a coherent structural and regulatory logic remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure of PPDPF or its complexes reported in the corpus","Determinants of partner selectivity unknown","Relationship between enzymatic and adaptor functions unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[3,5,7,10,12,13]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[4,6]}],"localization":[],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[3,5,7,12]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[9,10,13]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,6,8,11]}],"complexes":[],"partners":["SOS1","CK1Α","STAT3","PTPN1","RIPK1","TRIM21","BABAM2","MCCA"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H3Y8","full_name":"Pancreatic progenitor cell differentiation and proliferation factor","aliases":["Exocrine differentiation and proliferation factor"],"length_aa":114,"mass_kda":11.8,"function":"Probable regulator of exocrine pancreas development","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9H3Y8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPDPF","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PPDPF","total_profiled":1310},"omim":[],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Microtubules","reliability":"Approved"},{"location":"Nucleoli","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPDPF"},"hgnc":{"alias_symbol":["dJ697K14.9","exdpf"],"prev_symbol":["C20orf149"]},"alphafold":{"accession":"Q9H3Y8","domains":[],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H3Y8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H3Y8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H3Y8-F1-predicted_aligned_error_v6.png","plddt_mean":59.84},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPDPF","jax_strain_url":"https://www.jax.org/strain/search?query=PPDPF"},"sequence":{"accession":"Q9H3Y8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H3Y8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H3Y8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H3Y8"}},"corpus_meta":[{"pmid":"30954221","id":"PMC_30954221","title":"Circular RNA circ-FOXM1 facilitates cell progression as ceRNA to target PPDPF and MACC1 by sponging miR-1304-5p in non-small cell lung cancer.","date":"2019","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/30954221","citation_count":72,"is_preprint":false},{"pmid":"19067490","id":"PMC_19067490","title":"Exdpf is a key regulator of exocrine pancreas development controlled by retinoic acid and ptf1a in zebrafish.","date":"2008","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/19067490","citation_count":40,"is_preprint":false},{"pmid":"37027301","id":"PMC_37027301","title":"PPDPF suppresses the development of hepatocellular carcinoma through TRIM21-mediated ubiquitination of RIPK1.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37027301","citation_count":20,"is_preprint":false},{"pmid":"35906391","id":"PMC_35906391","title":"PPDPF promotes lung adenocarcinoma progression via inhibiting apoptosis and NK cell-mediated cytotoxicity through STAT3.","date":"2022","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/35906391","citation_count":18,"is_preprint":false},{"pmid":"36453576","id":"PMC_36453576","title":"PPDPF Promotes the Development of Mutant KRAS-Driven Pancreatic Ductal Adenocarcinoma by Regulating the GEF Activity of SOS1.","date":"2022","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/36453576","citation_count":14,"is_preprint":false},{"pmid":"34975328","id":"PMC_34975328","title":"PPDPF Promotes the Progression and acts as an Antiapoptotic Protein in Non-Small Cell Lung Cancer.","date":"2022","source":"International journal of biological sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34975328","citation_count":13,"is_preprint":false},{"pmid":"34041032","id":"PMC_34041032","title":"The Exocrine Differentiation and Proliferation Factor (EXDPF) Gene Promotes Ovarian Cancer Tumorigenesis by Up-Regulating DNA Replication Pathway.","date":"2021","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/34041032","citation_count":12,"is_preprint":false},{"pmid":"37477088","id":"PMC_37477088","title":"Phosphorylation of PPDPF via IL6-JAK2 activates the Wnt/β-catenin pathway in colorectal cancer.","date":"2023","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/37477088","citation_count":11,"is_preprint":false},{"pmid":"40106551","id":"PMC_40106551","title":"PPDPF preserves integrity of proximal tubule by modulating NMNAT activity in chronic kidney diseases.","date":"2025","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/40106551","citation_count":4,"is_preprint":false},{"pmid":"40025229","id":"PMC_40025229","title":"PPDPF-mediated regulation of BCAA metabolism enhances mTORC1 activity and drives cholangiocarcinoma progression.","date":"2025","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/40025229","citation_count":3,"is_preprint":false},{"pmid":"40774693","id":"PMC_40774693","title":"PPDPF promotes the progression of esophageal squamous cell carcinoma via c-Myc/CD24 axis.","date":"2025","source":"Journal for immunotherapy of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/40774693","citation_count":1,"is_preprint":false},{"pmid":"39694223","id":"PMC_39694223","title":"PPDPF promotes esophageal squamous cell carcinoma progression by blocking PCCA binding to PCCB and inhibiting methionine catabolism.","date":"2024","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/39694223","citation_count":0,"is_preprint":false},{"pmid":"40193385","id":"PMC_40193385","title":"PPDPF is not a key regulator of human pancreas development.","date":"2025","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40193385","citation_count":0,"is_preprint":false},{"pmid":"41984037","id":"PMC_41984037","title":"Chemoresistance and Immune Suppression in Gastric Cancer Are Driven by PPDPF Overexpression.","date":"2026","source":"Chemical biology & drug design","url":"https://pubmed.ncbi.nlm.nih.gov/41984037","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9013,"output_tokens":3544,"usd":0.0401,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":11185,"output_tokens":3124,"usd":0.067013,"stage2_stop_reason":"end_turn"},"total_usd":0.107113,"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\": 2008,\n      \"finding\": \"Exdpf (zebrafish ortholog of PPDPF) is a direct transcriptional target of Ptf1a: three consensus Ptf1a binding sites were identified in the exdpf promoter, luciferase assay demonstrated Ptf1a promotes exdpf transcription, and exdpf expression was lost in ptf1a morphants.\",\n      \"method\": \"Promoter analysis, luciferase reporter assay, antisense morpholino knockdown in zebrafish\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (promoter binding site identification, luciferase assay, morpholino KD) in a single rigorous study\",\n      \"pmids\": [\"19067490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Exdpf (zebrafish ortholog of PPDPF) is required for exocrine pancreas cell proliferation; knockdown causes lineage-specific cell cycle arrest (not apoptosis) mediated by upregulation of p21(Cip), p27(Kip), and cyclin G1.\",\n      \"method\": \"Antisense morpholino knockdown in zebrafish, real-time PCR for cell cycle inhibitor genes\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KD with defined cellular phenotype and molecular mechanism, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"19067490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Exdpf is genetically downstream of retinoic acid (RA) signaling in exocrine pancreas development: exdpf knockdown abolished RA-induced ectopic cpa expression, and exdpf mRNA injection rescued endogenous cpa expression in embryos treated with a RA signaling inhibitor.\",\n      \"method\": \"Genetic epistasis via morpholino knockdown and mRNA rescue in zebrafish with RA pathway manipulation\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with gain- and loss-of-function experiments, multiple conditions tested\",\n      \"pmids\": [\"19067490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PPDPF promotes STAT3 hyperactivation by interfering with the STAT3-PTPN1 interaction, leading to increased BMPR2 transcription and inhibition of apoptosis in lung adenocarcinoma.\",\n      \"method\": \"Co-immunoprecipitation, in vitro and in vivo loss-of-function assays, transcriptional analysis\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — mechanistic pathway placement via co-IP and KD, single lab with multiple readouts\",\n      \"pmids\": [\"35906391\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PPDPF interacts with BABAM2 and blocks MDM2-mediated ubiquitination of BABAM2, thereby stabilizing BABAM2 and promoting radioresistance in non-small cell lung cancer cells.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, KO and overexpression in lung cancer cells and KL mouse model\",\n      \"journal\": \"International journal of biological sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP, ubiquitination assay, and in vivo mouse model, single lab\",\n      \"pmids\": [\"34975328\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PPDPF can bind GTP and transfer GTP to SOS1, thereby enhancing SOS1 GEF activity and promoting KRAS activation in pancreatic ductal adenocarcinoma; mutations at GTP-binding sites of PPDPF or critical SOS1-PPDPF interaction residues severely impair GEF activity and tumor-promoting effects.\",\n      \"method\": \"GTP-binding assay, GEF activity assay, site-directed mutagenesis, co-immunoprecipitation, in vitro and in vivo overexpression/KO, KRASG12D genetic mouse model\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro biochemical assays (GTP binding, GEF activity), active-site mutagenesis, and in vivo genetic mouse models, multiple orthogonal methods\",\n      \"pmids\": [\"36453576\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPDPF interacts with RIPK1 and recruits the E3 ligase TRIM21, which catalyzes K63-linked ubiquitination of RIPK1 at K140, thereby activating NF-κB signaling and suppressing hepatocellular carcinoma development.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay with site-specific (K140) mutant, liver-specific KO and overexpression mouse models (DEN-induced HCC)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — biochemical ubiquitination assays with specific lysine mutant, co-IP of complex, and in vivo mouse models, multiple orthogonal methods\",\n      \"pmids\": [\"37027301\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPDPF interacts with CK1α, disrupting its binding to Axin and disassociating the β-catenin destruction complex, thereby decreasing β-catenin phosphorylation and activating the Wnt/β-catenin pathway in colorectal cancer.\",\n      \"method\": \"Co-immunoprecipitation, phosphorylation assays, intestinal epithelium-specific KO with organoid and AOM/DSS mouse models\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — co-IP of protein complex disruption, phosphorylation readout, and multiple in vivo mouse models, single rigorous study with multiple orthogonal methods\",\n      \"pmids\": [\"37477088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PPDPF is phosphorylated at Tyr16 and Tyr17 by IL6/JAK2 inflammatory signaling, which stabilizes the PPDPF protein.\",\n      \"method\": \"Phosphorylation site mapping, mutational analysis, IL6/JAK2 pathway manipulation\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — specific phosphorylation sites identified with mutagenesis, single lab\",\n      \"pmids\": [\"37477088\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPDPF functions as a thiol-disulfide oxidoreductase that maintains cellular NAD+ levels by supporting nicotinamide mononucleotide adenylyl transferase (NMNAT) activity; PPDPF deficiency impairs NAD+ and mitochondrial homeostasis in proximal tubule cells.\",\n      \"method\": \"Enzymatic activity assay (thiol-disulfide oxidoreductase), NAD+ level measurement, NMNAT activity assay, PPDPF KO mouse models (aging, chemical exposure, obstruction)\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct enzymatic characterization, defined substrate (NMNAT), multiple KO mouse models with functional readouts\",\n      \"pmids\": [\"40106551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPDPF prevents the interaction between MCCA and MCCB subunits of the methylcrotonyl-CoA carboxylase complex, thereby inhibiting leucine catabolism and activating mTORC1 signaling in cholangiocarcinoma.\",\n      \"method\": \"SILAC metabolic labeling screen, metabolic flux analysis, co-immunoprecipitation, PPDPF KO mouse model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — SILAC screen plus metabolic flux analysis plus co-IP plus in vivo mouse model, multiple orthogonal methods\",\n      \"pmids\": [\"40025229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPDPF protein stability is regulated by ubiquitination: ARIH2 (E3 ligase) and OTUD4 (deubiquitinase) cooperatively control PPDPF ubiquitination and stability under amino acid starvation conditions.\",\n      \"method\": \"Ubiquitination assay, co-immunoprecipitation with ARIH2 and OTUD4\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP and ubiquitination assay identifying writer/eraser, single lab\",\n      \"pmids\": [\"40025229\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPDPF interferes with c-Myc–GSK3β interaction, enhancing c-Myc protein stability and thereby upregulating CD24 expression to promote immune escape from macrophage phagocytosis in esophageal squamous cell carcinoma.\",\n      \"method\": \"GST-pulldown, co-immunoprecipitation, immunoblotting, fluorescence microscopy-based phagocytosis assay, flow cytometry, KO mouse models\",\n      \"journal\": \"Journal for immunotherapy of cancer\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — GST-pulldown, reciprocal co-IP, functional phagocytosis assay, and in vivo mouse models, multiple orthogonal methods\",\n      \"pmids\": [\"40774693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPDPF interacts with PCCA (a subunit of propionyl-CoA carboxylase) and inhibits PCCA-PCCB binding, thereby blocking methionine catabolism via the C-Vomit pathway and increasing methionine and SAM levels in esophageal squamous cell carcinoma.\",\n      \"method\": \"Mass spectrometry, co-immunoprecipitation, metabolite measurement in vitro and in vivo\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — mass spectrometry interaction discovery, co-IP, and metabolic measurements, single lab\",\n      \"pmids\": [\"39694223\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPDPF knockout in human embryonic stem cells differentiated toward the pancreatic lineage shows only a very modest effect on pancreatic progenitor development in vitro and does not affect lineage specification upon orthotopic transplantation in vivo, indicating PPDPF is NOT a key regulator of human pancreas development (in contrast to its zebrafish ortholog).\",\n      \"method\": \"CRISPR/Cas9 knockout in hESCs, pancreatic differentiation protocol, orthotopic transplantation in vivo\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR KO with in vitro and in vivo differentiation assay; negative result replicated across multiple conditions in single study\",\n      \"pmids\": [\"40193385\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPDPF (also known as EXDPF/C20orf149) is a multifunctional protein with enzymatic activity as a thiol-disulfide oxidoreductase that supports NMNAT-mediated NAD+ homeostasis; it acts as a GTP-binding factor that transfers GTP to SOS1 to enhance its GEF activity and activate RAS signaling; it modulates multiple signaling pathways by disrupting protein–protein interactions (CK1α–Axin to activate Wnt/β-catenin, STAT3–PTPN1 to hyperactivate STAT3, c-Myc–GSK3β to stabilize c-Myc, MCCA–MCCB to block leucine catabolism, PCCA–PCCB to block methionine catabolism); it scaffolds ubiquitination complexes (recruiting TRIM21 to K63-ubiquitinate RIPK1 at K140 for NF-κB activation; blocking MDM2-mediated ubiquitination of BABAM2); and its own stability is regulated by phosphorylation (JAK2 at Tyr16/Tyr17) and ubiquitination (ARIH2/OTUD4), while in zebrafish it is transcriptionally controlled by Ptf1a downstream of retinoic acid signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPDPF (EXDPF/C20orf149) is a small multifunctional adaptor and enzyme that couples developmental, metabolic, and oncogenic signaling, and was first defined as a Ptf1a-regulated, retinoic-acid-dependent driver of exocrine pancreas cell proliferation in zebrafish, where its loss triggers cell-cycle arrest through induction of p21, p27, and cyclin G1 [#0, #1, #2]. Its best-characterized biochemical activities are direct: PPDPF binds GTP and transfers it to SOS1 to enhance SOS1 GEF activity and KRAS activation, with GTP-binding and SOS1-interaction mutants abolishing this function [#5], and it acts as a thiol-disulfide oxidoreductase that supports NMNAT activity to maintain NAD+ and mitochondrial homeostasis [#9]. A recurring mechanistic theme is that PPDPF modulates signaling by disrupting or scaffolding specific protein-protein interactions: it interferes with the CK1\\u03b1\\u2013Axin interaction to dismantle the \\u03b2-catenin destruction complex and activate Wnt/\\u03b2-catenin [#7], blocks STAT3\\u2013PTPN1 binding to hyperactivate STAT3 [#3], disrupts c-Myc\\u2013GSK3\\u03b2 association to stabilize c-Myc and drive CD24-mediated immune escape [#12], and prevents assembly of the metabolic carboxylase pairs MCCA\\u2013MCCB and PCCA\\u2013PCCB to block leucine and methionine catabolism and feed mTORC1 and SAM pools [#10, #13]. PPDPF also scaffolds ubiquitination events, recruiting TRIM21 to catalyze K63-linked ubiquitination of RIPK1 at K140 to activate NF-\\u03baB [#6] and blocking MDM2-mediated ubiquitination of BABAM2 to confer radioresistance [#4]. Its own abundance is controlled post-translationally, being stabilized by IL6/JAK2-mediated phosphorylation at Tyr16/Tyr17 [#8] and by the opposing actions of the E3 ligase ARIH2 and deubiquitinase OTUD4 under amino acid starvation [#11]. Notably, the developmental role is not conserved: PPDPF knockout in human embryonic stem cells has only a modest effect on pancreatic progenitor development and does not alter lineage specification in vivo [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established the first biological role and upstream regulation of PPDPF, placing its zebrafish ortholog as a retinoic-acid/Ptf1a-controlled effector of exocrine pancreas proliferation.\",\n      \"evidence\": \"Promoter binding-site analysis, luciferase reporter, morpholino knockdown, mRNA rescue, and cell-cycle gene profiling in zebrafish\",\n      \"pmids\": [\"19067490\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular activity of the protein itself was not defined\", \"Whether the proliferation role generalizes beyond exocrine pancreas was untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Defined PPDPF as a direct GTP-binding factor that potentiates SOS1 GEF activity, providing a concrete biochemical mechanism for its RAS-pathway and tumor-promoting effects.\",\n      \"evidence\": \"GTP-binding and GEF activity assays, active-site mutagenesis, co-IP, and KRASG12D mouse models in pancreatic ductal adenocarcinoma\",\n      \"pmids\": [\"36453576\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of GTP transfer to SOS1 not resolved\", \"Whether this activity operates outside pancreatic cancer is unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Showed PPDPF acts as an interaction modulator and ubiquitination regulator in lung cancer, interfering with STAT3-PTPN1 and protecting BABAM2 from MDM2.\",\n      \"evidence\": \"Co-IP, ubiquitination assays, knockout/overexpression, and lung cancer mouse models\",\n      \"pmids\": [\"35906391\", \"34975328\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect nature of the disruption not fully resolved\", \"Single-lab mechanistic placement\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Generalized the protein-interaction-disruption and scaffolding model across cancers, linking PPDPF to Wnt/\\u03b2-catenin activation and to TRIM21-dependent K63-ubiquitination of RIPK1 for NF-\\u03baB signaling, and identified JAK2 phosphorylation as a stabilizing input.\",\n      \"evidence\": \"Co-IP, site-specific ubiquitination assays (RIPK1 K140), phosphorylation-site mapping, organoid and tissue-specific KO mouse models\",\n      \"pmids\": [\"37027301\", \"37477088\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How one small protein selects among many distinct partners is unexplained\", \"Stoichiometry and structural mode of complex disruption unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the interaction-disruption mechanism into amino acid metabolism, with PPDPF blocking PCCA-PCCB assembly to elevate methionine and SAM.\",\n      \"evidence\": \"Mass spectrometry, co-IP, and metabolite measurements in esophageal squamous cell carcinoma\",\n      \"pmids\": [\"39694223\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct binding interface with PCCA not mapped\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined an intrinsic enzymatic activity (thiol-disulfide oxidoreductase) supporting NMNAT and NAD+ homeostasis, and added further metabolic and immune-evasion mechanisms plus a writer/eraser pair controlling PPDPF stability.\",\n      \"evidence\": \"Enzymatic and NMNAT activity assays, SILAC and metabolic flux analysis, GST-pulldown, ubiquitination assays, and multiple KO mouse models\",\n      \"pmids\": [\"40106551\", \"40025229\", \"40774693\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How thiol-disulfide oxidoreductase activity reconciles with the GTP-binding and adaptor activities is unknown\", \"Whether a single domain mediates all these functions is unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Revealed that the developmental role is not conserved in humans, with PPDPF dispensable for human pancreatic lineage specification, sharpening interpretation of the original zebrafish phenotype.\",\n      \"evidence\": \"CRISPR/Cas9 knockout in hESCs with pancreatic differentiation and orthotopic transplantation\",\n      \"pmids\": [\"40193385\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional compensation in human cells not ruled out\", \"Does not address PPDPF roles in adult/disease tissues\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single small protein integrates a thiol-disulfide oxidoreductase activity, GTP binding, and a broad set of protein-interaction-disruption events into a coherent structural and regulatory logic remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure of PPDPF or its complexes reported in the corpus\", \"Determinants of partner selectivity unknown\", \"Relationship between enzymatic and adaptor functions unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [3, 5, 7, 10, 12, 13]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [4, 6]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [3, 5, 7, 12]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [9, 10, 13]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 6, 8, 11]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"SOS1\", \"CK1\\u03b1\", \"STAT3\", \"PTPN1\", \"RIPK1\", \"TRIM21\", \"BABAM2\", \"MCCA\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":5,"faith_total":6,"faith_pct":83.33333333333333}}