{"gene":"PPIL1","run_date":"2026-04-28T19:45:44","timeline":{"discoveries":[{"year":1996,"finding":"PPIL1 (hCyPX) was identified as a novel cyclophilin-related protein encoded by a 498-nucleotide ORF (166 amino acids) with ~40% homology to human, bovine, and Drosophila cyclophilins, mapped to chromosome 2p23.3→p23.1.","method":"cDNA cloning, Northern blot, fluorescence in situ hybridization (FISH)","journal":"Cytogenetics and cell genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct chromosomal mapping and cloning; single lab, foundational characterization","pmids":["8978786"],"is_preprint":false},{"year":2001,"finding":"PPIL1 orthologs (CypE in Dictyostelium discoideum and Cyp2 in S. pombe) interact with the SNW/SKIP transcriptional coregulator via its N-terminal region in a cyclosporin A-independent manner, and possess cyclosporin A-sensitive PPIase activity; the SNW proteins act as adaptors for these novel isomerases.","method":"Yeast two-hybrid screen, in vitro PPIase assay, cyclosporin A inhibition assay","journal":"Biochimica et biophysica acta","confidence":"Medium","confidence_rationale":"Tier 2 — two-hybrid plus in vitro activity assay; single lab but two orthogonal methods in two organisms","pmids":["11690648"],"is_preprint":false},{"year":2004,"finding":"PPIL1 is recruited by the spliceosomal/transcriptional coregulator SKIP (SNW/SKIP) into the spliceosome as a prolyl isomerase foldase, suggesting it aids conformational transitions of the gene expression machine.","method":"Review synthesis of experimental data (protein interaction, spliceosomal fractionation)","journal":"Cellular and molecular life sciences : CMLS","confidence":"Low","confidence_rationale":"Tier 3 — review synthesis, no new primary experiment","pmids":["15052407"],"is_preprint":false},{"year":2006,"finding":"PPIL1 exhibits PPIase activity characteristic of the cyclophilin family and stably binds the N-terminal region of SKIP (residues 59–129) via a binding site distinct from the PPIase active site, with a dissociation constant of 1.25×10⁻⁷ M for SKIP-(59-129).","method":"NMR structure determination, GST pulldown, surface plasmon resonance, chemical shift perturbation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — NMR structure plus in vitro binding quantification (SPR) plus mutagenesis-level epitope mapping; single lab with multiple orthogonal methods","pmids":["16595688"],"is_preprint":false},{"year":2006,"finding":"PPIL1 interacts with SNW1/SKIP and stathmin in colon cancer cells; siRNA-mediated knockdown of PPIL1 retards growth of colon cancer cells, implicating PPIL1 in cancer cell proliferation via these partners.","method":"Co-immunoprecipitation, siRNA knockdown, colony formation assay","journal":"Clinical cancer research","confidence":"Medium","confidence_rationale":"Tier 2 — Co-IP plus functional KD with proliferation readout; single lab","pmids":["16397026"],"is_preprint":false},{"year":2009,"finding":"The N-terminal region of SKIP (residues 59–129, SKIPN) is intrinsically disordered and undergoes a disorder-to-order transition upon binding PPIL1; a minimal 21-residue fragment (PBF, residues 59–79) is sufficient for PPIL1 binding via electrostatic and hydrophobic interactions, while the PPIase active site of PPIL1 remains accessible in the complex.","method":"NMR structure of PBF·PPIL1 complex, NMR-based disorder characterization","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — NMR structure with functional epitope mapping; orthologous to prior SPR data; single lab with rigorous structural validation","pmids":["20007319"],"is_preprint":false},{"year":2010,"finding":"Crystal structure of PPIL1 bound to cyclosporine A at 1.15 Å resolution revealed the active site architecture and two Cd²⁺ coordination sites at residues previously implicated in SKIP binding; a 36-residue SKIP epitope (centered on an 8-residue core) suffices for PPIL1 binding, and molecular docking places a SKIP proline in PPIL1's hydrophobic pocket.","method":"X-ray crystallography (SAD phasing), peptide array, GST pulldown, molecular docking","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1 — high-resolution crystal structure combined with biochemical epitope mapping and docking; consistent with prior NMR studies","pmids":["20368803"],"is_preprint":false},{"year":2020,"finding":"Biallelic loss-of-function mutations in PPIL1 cause pontocerebellar hypoplasia with microcephaly (PCHM); PPIL1 forms an active isomerase-substrate interaction with PRP17, but the isomerase activity itself is not required for function; loss of PPIL1 disrupts splicing integrity, predominantly affecting short and high GC-content introns; PPIL1 knockin mice with patient mutations show neuron-specific apoptosis.","method":"Human genetics (WES of 10 families), PPIL1 knockin mouse model, mouse knockout (embryonic lethal), RNA splicing analysis, biochemical interaction assays","journal":"Neuron","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (patient genetics, mouse models, biochemical interaction, transcriptome-wide splicing analysis) across multiple families; strong evidence for non-enzymatic function","pmids":["33220177"],"is_preprint":false},{"year":2022,"finding":"PPIL1 interacts with C3b-α'2 complement fragment through glutamic acid 156 (E156) and aspartic acid 111 (D111) residues of PPIL1; this interaction is required for S1P/S1PR1-driven NLRP3/inflammasome induction and tumor metastasis, and inactivating mutations of C3b-α'2 that prevent PPIL1 association attenuate inflammasome activation and lung colonization in mice.","method":"Inactivating mutations, co-immunoprecipitation, mouse lung colonization/metastasis assays, genetic knockouts (C3aR1⁻/⁻)","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 — specific interaction residues identified with mutation validation plus in vivo functional consequence; single lab","pmids":["36476873"],"is_preprint":false},{"year":2025,"finding":"The proline-rich PxxP motifs of the EWS low-complexity domain (EWSLCD) engage the catalytic face (PPIase active site) of PPIL1 via low-affinity 'fuzzy' complexes; PPIL1 is recruited into EWSLCD phase-separated condensates and alters condensation properties depending on ionic conditions.","method":"NMR titration experiments, phase separation assays, biochemical characterization","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 1–2 — NMR-based structural characterization plus phase separation assays; single lab, moderate evidence","pmids":["40668764"],"is_preprint":false},{"year":2025,"finding":"PPIL1 knockdown in HCC cell lines suppresses proliferation, migration, sphere formation, and tumor initiation; mechanistic studies identify PPIL1 as a regulator of Wnt/β-catenin signaling through transcriptional upregulation of DAAM2.","method":"shRNA knockdown, xenograft mouse models, transcriptome analysis, cell viability and sphere formation assays","journal":"Cancer genomics & proteomics","confidence":"Medium","confidence_rationale":"Tier 2 — KD with multiple phenotypic readouts plus transcriptome-based pathway placement; single lab","pmids":["40883023"],"is_preprint":false}],"current_model":"PPIL1 is a spliceosomal cyclophilin-family peptidyl-prolyl cis/trans isomerase that is recruited into the activated spliceosome (B, B*, and C complexes) through a direct, cyclosporin A-independent interaction with SKIP/SNW1 (via SKIP residues 59–79 engaging a site distinct from the PPIL1 PPIase active site), where it forms an isomerase-substrate complex with PRP17 to support splicing integrity of short, GC-rich introns—a function that is structural rather than enzymatic, as isomerase activity is dispensable; loss of PPIL1 causes neuron-specific apoptosis and pontocerebellar hypoplasia with microcephaly in humans and mice, and PPIL1 also participates in non-spliceosomal interactions including C3b-driven NLRP3 inflammasome signaling (via E156/D111), EWS LCD phase separation (via PxxP-active site contacts), and Wnt/β-catenin/DAAM2 regulation in cancer cells."},"narrative":{"teleology":[{"year":1996,"claim":"Identification of PPIL1 as a novel cyclophilin-family member established that a short (166 aa) PPIase-related protein exists in the human genome at 2p23, opening questions about its specific substrates and cellular role.","evidence":"cDNA cloning, Northern blot, and FISH mapping of hCyPX","pmids":["8978786"],"confidence":"Medium","gaps":["No enzymatic activity demonstrated","No interacting partners or cellular function identified"]},{"year":2001,"claim":"Discovery that PPIL1 orthologs bind the SNW/SKIP coregulator in a cyclosporin A-independent manner while retaining CsA-sensitive PPIase activity revealed a bipartite functionality—enzyme activity and a distinct protein-recruitment interface—and placed PPIL1 in the spliceosomal/transcriptional regulatory axis.","evidence":"Yeast two-hybrid screen and in vitro PPIase assay in Dictyostelium and S. pombe systems","pmids":["11690648"],"confidence":"Medium","gaps":["Binding interface not mapped at residue level","Human PPIL1–SKIP interaction not yet directly demonstrated"]},{"year":2006,"claim":"Structural and biophysical characterization defined two separable surfaces on PPIL1—a PPIase active site and a distinct SKIP-binding face—with nanomolar affinity for SKIP residues 59–129, establishing how PPIL1 can simultaneously bind SKIP and present its catalytic pocket to spliceosomal substrates.","evidence":"NMR structure, SPR (Kd = 1.25 × 10⁻⁷ M), GST pulldown, chemical shift perturbation; X-ray crystallography at 1.15 Å resolution with peptide array and docking","pmids":["16595688","20368803"],"confidence":"High","gaps":["Identity of the PPIase substrate in the spliceosome unknown","Functional significance of isomerase activity untested"]},{"year":2009,"claim":"Demonstration that the SKIP N-terminus is intrinsically disordered and undergoes a disorder-to-order transition upon binding PPIL1, with a minimal 21-residue fragment sufficient, clarified the recruitment mechanism and showed the PPIase active site remains accessible for additional substrates.","evidence":"NMR structure of PBF·PPIL1 complex and disorder characterization","pmids":["20007319"],"confidence":"High","gaps":["In vivo relevance of disorder-to-order transition not tested","No spliceosomal substrate for the free active site identified"]},{"year":2020,"claim":"Human genetics and mouse modeling resolved the key outstanding questions: PPIL1 forms an isomerase–substrate complex with PRP17, but its PPIase catalytic activity is dispensable; loss of PPIL1 disrupts splicing of short, GC-rich introns and causes neuron-specific apoptosis leading to pontocerebellar hypoplasia with microcephaly.","evidence":"WES of 10 families with PCHM, knockin and knockout mouse models, transcriptome-wide splicing analysis, biochemical interaction assays","pmids":["33220177"],"confidence":"High","gaps":["Structural basis for the non-enzymatic PRP17 interaction unresolved","Why neurons are selectively vulnerable unclear","Whether PPIL1 has additional spliceosomal substrates beyond PRP17 unknown"]},{"year":2022,"claim":"Identification of PPIL1 as a C3b-α'2 interactor through E156 and D111 residues revealed a non-spliceosomal role in NLRP3 inflammasome activation and tumor metastasis, broadening PPIL1's functional repertoire to innate immunity.","evidence":"Inactivating mutations, co-immunoprecipitation, mouse lung colonization assays","pmids":["36476873"],"confidence":"Medium","gaps":["Whether PPIase activity is required for C3b interaction not tested","How PPIL1–C3b interaction triggers inflammasome assembly mechanistically unclear","Single-lab finding"]},{"year":2025,"claim":"Two independent studies extended PPIL1's non-spliceosomal roles: its PPIase active site engages EWS low-complexity domain PxxP motifs in fuzzy complexes that modulate phase separation, and it promotes Wnt/β-catenin signaling via DAAM2 upregulation in hepatocellular carcinoma.","evidence":"NMR titration and phase separation assays (EWS); shRNA knockdown, xenograft models, and transcriptome analysis (HCC/DAAM2)","pmids":["40668764","40883023"],"confidence":"Medium","gaps":["Physiological relevance of PPIL1–EWS condensate modulation untested in cells","Whether PPIL1-DAAM2 axis operates through direct interaction or is transcriptionally indirect not resolved","Relationship between spliceosomal and phase-separation roles unclear"]},{"year":null,"claim":"The structural basis for PPIL1's non-enzymatic stabilization of PRP17 within the spliceosome, the mechanism of neuron-selective vulnerability to PPIL1 loss, and the functional integration of its spliceosomal versus non-spliceosomal roles remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of PPIL1–PRP17 complex available","Neuron-specific splicing dependencies of PPIL1 not mapped","Whether spliceosomal and inflammasome/phase-separation functions are coordinated or independent is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,3,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7,10]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[3,5,7]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10]}],"complexes":["spliceosome (B*/C complex)"],"partners":["SNW1","PRP17","STMN1","EWSR1","C3","DAAM2"],"other_free_text":[]},"mechanistic_narrative":"PPIL1 is a spliceosomal cyclophilin-family peptidyl-prolyl cis/trans isomerase that supports pre-mRNA splicing fidelity, particularly of short, GC-rich introns, through a structural rather than enzymatic role within the activated spliceosome. It is recruited to the spliceosome via a direct, cyclosporin A-independent interaction between a site distinct from its PPIase active site and the intrinsically disordered N-terminal region (residues 59–79) of SKIP/SNW1, while its catalytic face engages PRP17 in an isomerase–substrate complex whose prolyl isomerase activity is dispensable for splicing function [PMID:16595688, PMID:20007319, PMID:33220177]. Biallelic loss-of-function mutations in PPIL1 cause pontocerebellar hypoplasia with microcephaly through neuron-specific apoptosis in humans and mice [PMID:33220177]. Beyond splicing, PPIL1 participates in C3b-mediated NLRP3 inflammasome activation via residues E156 and D111 [PMID:36476873], modulates EWS low-complexity domain phase separation through PPIase active-site contacts with PxxP motifs [PMID:40668764], and promotes Wnt/β-catenin signaling through transcriptional upregulation of DAAM2 in hepatocellular carcinoma [PMID:40883023]."},"prefetch_data":{"uniprot":{"accession":"Q9Y3C6","full_name":"Peptidyl-prolyl cis-trans isomerase-like 1","aliases":["Rotamase PPIL1"],"length_aa":166,"mass_kda":18.2,"function":"Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28076346, PubMed:28502770, PubMed:33220177). PPIases accelerate the folding of proteins. Catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides (PubMed:16595688). Catalyzes prolyl peptide bond isomerization in CDC40/PRP17 (PubMed:33220177). Plays an important role in embryonic brain development; this function is independent of its isomerase activity (PubMed:33220177)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y3C6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PPIL1","classification":"Common Essential","n_dependent_lines":974,"n_total_lines":1208,"dependency_fraction":0.8062913907284768},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":0.2},{"gene":"RBM39","stoichiometry":0.2},{"gene":"SF3A1","stoichiometry":0.2},{"gene":"SF3B1","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SNRPB","stoichiometry":0.2},{"gene":"SNRPC","stoichiometry":0.2},{"gene":"SNRPF","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PPIL1","total_profiled":1310},"omim":[{"mim_id":"619302","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 15; PCH15","url":"https://www.omim.org/entry/619302"},{"mim_id":"619301","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 14; PCH14","url":"https://www.omim.org/entry/619301"},{"mim_id":"607596","title":"PONTOCEREBELLAR HYPOPLASIA, TYPE 1A; PCH1A","url":"https://www.omim.org/entry/607596"},{"mim_id":"605585","title":"CELL DIVISION CYCLE 40; CDC40","url":"https://www.omim.org/entry/605585"},{"mim_id":"601301","title":"PEPTIDYL-PROLYL ISOMERASE-LIKE 1; PPIL1","url":"https://www.omim.org/entry/601301"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPIL1"},"hgnc":{"alias_symbol":["CYPL1"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y3C6","domains":[{"cath_id":"2.40.100.10","chopping":"12-163","consensus_level":"high","plddt":95.3449,"start":12,"end":163}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3C6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3C6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3C6-F1-predicted_aligned_error_v6.png","plddt_mean":94.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPIL1","jax_strain_url":"https://www.jax.org/strain/search?query=PPIL1"},"sequence":{"accession":"Q9Y3C6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y3C6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y3C6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3C6"}},"corpus_meta":[{"pmid":"25033284","id":"PMC_25033284","title":"Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease.","date":"2014","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/25033284","citation_count":159,"is_preprint":false},{"pmid":"15052407","id":"PMC_15052407","title":"Transcriptional coregulator SNW/SKIP: the concealed tie of dissimilar pathways.","date":"2004","source":"Cellular and molecular life sciences : CMLS","url":"https://pubmed.ncbi.nlm.nih.gov/15052407","citation_count":71,"is_preprint":false},{"pmid":"33220177","id":"PMC_33220177","title":"Mutations in Spliceosomal Genes PPIL1 and PRP17 Cause Neurodegenerative Pontocerebellar Hypoplasia with Microcephaly.","date":"2020","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/33220177","citation_count":46,"is_preprint":false},{"pmid":"16595688","id":"PMC_16595688","title":"Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP.","date":"2006","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16595688","citation_count":37,"is_preprint":false},{"pmid":"30518120","id":"PMC_30518120","title":"Structural and Functional Insights into Human Nuclear Cyclophilins.","date":"2018","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/30518120","citation_count":35,"is_preprint":false},{"pmid":"25847193","id":"PMC_25847193","title":"Rice cyclophilin OsCYP18-2 is translocated to the nucleus by an interaction with SKIP and enhances drought tolerance in rice and Arabidopsis.","date":"2015","source":"Plant, cell & environment","url":"https://pubmed.ncbi.nlm.nih.gov/25847193","citation_count":35,"is_preprint":false},{"pmid":"20007319","id":"PMC_20007319","title":"A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/20007319","citation_count":32,"is_preprint":false},{"pmid":"16397026","id":"PMC_16397026","title":"Overexpression of peptidyl-prolyl isomerase-like 1 is associated with the growth of colon cancer cells.","date":"2006","source":"Clinical cancer research : an official journal of the American Association for Cancer Research","url":"https://pubmed.ncbi.nlm.nih.gov/16397026","citation_count":31,"is_preprint":false},{"pmid":"36476873","id":"PMC_36476873","title":"Crosstalk between pro-survival sphingolipid metabolism and complement signaling induces inflammasome-mediated tumor metastasis.","date":"2022","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/36476873","citation_count":26,"is_preprint":false},{"pmid":"20368803","id":"PMC_20368803","title":"The crystal structure of PPIL1 bound to cyclosporine A suggests a binding mode for a linear epitope of the SKIP protein.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20368803","citation_count":23,"is_preprint":false},{"pmid":"11690648","id":"PMC_11690648","title":"Cyclophilins of a novel subfamily interact with SNW/SKIP coregulator in Dictyostelium discoideum and Schizosaccharomyces pombe.","date":"2001","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/11690648","citation_count":23,"is_preprint":false},{"pmid":"8978786","id":"PMC_8978786","title":"Cloning, expression and chromosomal mapping of a novel cyclophilin-related gene (PPIL1) from human fetal brain.","date":"1996","source":"Cytogenetics and cell genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8978786","citation_count":18,"is_preprint":false},{"pmid":"25524563","id":"PMC_25524563","title":"The spliceosomal PRP19 complex of trypanosomes.","date":"2015","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25524563","citation_count":15,"is_preprint":false},{"pmid":"27586231","id":"PMC_27586231","title":"Identification of low abundance cyclophilins in human plasma.","date":"2016","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/27586231","citation_count":8,"is_preprint":false},{"pmid":"36636802","id":"PMC_36636802","title":"The spliceophilin CYP18-2 is mainly involved in the splicing of retained introns under heat stress in Arabidopsis.","date":"2023","source":"Journal of integrative plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/36636802","citation_count":6,"is_preprint":false},{"pmid":"39045051","id":"PMC_39045051","title":"Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer's and Parkinson's disease.","date":"2024","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/39045051","citation_count":4,"is_preprint":false},{"pmid":"40668764","id":"PMC_40668764","title":"The Spliceosomal Peptidyl Prolyl Isomerase Like 1 Interacts with the Low-Complexity Domain of the RNA Binding Protein EWS Modulating Its Phase Separation Behavior.","date":"2025","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40668764","citation_count":2,"is_preprint":false},{"pmid":"40883023","id":"PMC_40883023","title":"PPIL1 Drives Hepatocellular Carcinoma Progression and Cancer Stem Cell Self-renewal Through DAAM2-mediated Wnt/β-Catenin Activation.","date":"2025","source":"Cancer genomics & proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/40883023","citation_count":1,"is_preprint":false},{"pmid":"37159429","id":"PMC_37159429","title":"Report of new variants in PPIL1 underlying type 14 pontocerebellar hypoplasia and their associated phenotypic manifestations in two fetuses.","date":"2023","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/37159429","citation_count":1,"is_preprint":false},{"pmid":"33476558","id":"PMC_33476558","title":"Splicing Control of Pontocerebellar Development.","date":"2021","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/33476558","citation_count":1,"is_preprint":false},{"pmid":"38955739","id":"PMC_38955739","title":"[The diagnostic value of inflammation-related genes in bronchopulmonary dysplasia].","date":"2024","source":"Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]","url":"https://pubmed.ncbi.nlm.nih.gov/38955739","citation_count":1,"is_preprint":false},{"pmid":"35236814","id":"PMC_35236814","title":"Nuclear localization of propiece IL-1α in HeLa cells.","date":"2022","source":"Journal of oral science","url":"https://pubmed.ncbi.nlm.nih.gov/35236814","citation_count":1,"is_preprint":false},{"pmid":"41073920","id":"PMC_41073920","title":"Obesity induced by a high-fat diet regulates the MYC‒PPIL1 network in the mediation of asthenozoospermia.","date":"2025","source":"Basic and clinical andrology","url":"https://pubmed.ncbi.nlm.nih.gov/41073920","citation_count":0,"is_preprint":false},{"pmid":"41739400","id":"PMC_41739400","title":"Exploring potential biomarkers of diffuse large B-cell lymphoma through multi-dimensional data.","date":"2026","source":"Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico","url":"https://pubmed.ncbi.nlm.nih.gov/41739400","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":12890,"output_tokens":2689,"usd":0.039503},"stage2":{"model":"claude-opus-4-6","input_tokens":6069,"output_tokens":2238,"usd":0.129442},"total_usd":0.168945,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"PPIL1 (hCyPX) was identified as a novel cyclophilin-related protein encoded by a 498-nucleotide ORF (166 amino acids) with ~40% homology to human, bovine, and Drosophila cyclophilins, mapped to chromosome 2p23.3→p23.1.\",\n      \"method\": \"cDNA cloning, Northern blot, fluorescence in situ hybridization (FISH)\",\n      \"journal\": \"Cytogenetics and cell genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct chromosomal mapping and cloning; single lab, foundational characterization\",\n      \"pmids\": [\"8978786\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"PPIL1 orthologs (CypE in Dictyostelium discoideum and Cyp2 in S. pombe) interact with the SNW/SKIP transcriptional coregulator via its N-terminal region in a cyclosporin A-independent manner, and possess cyclosporin A-sensitive PPIase activity; the SNW proteins act as adaptors for these novel isomerases.\",\n      \"method\": \"Yeast two-hybrid screen, in vitro PPIase assay, cyclosporin A inhibition assay\",\n      \"journal\": \"Biochimica et biophysica acta\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — two-hybrid plus in vitro activity assay; single lab but two orthogonal methods in two organisms\",\n      \"pmids\": [\"11690648\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PPIL1 is recruited by the spliceosomal/transcriptional coregulator SKIP (SNW/SKIP) into the spliceosome as a prolyl isomerase foldase, suggesting it aids conformational transitions of the gene expression machine.\",\n      \"method\": \"Review synthesis of experimental data (protein interaction, spliceosomal fractionation)\",\n      \"journal\": \"Cellular and molecular life sciences : CMLS\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — review synthesis, no new primary experiment\",\n      \"pmids\": [\"15052407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"PPIL1 exhibits PPIase activity characteristic of the cyclophilin family and stably binds the N-terminal region of SKIP (residues 59–129) via a binding site distinct from the PPIase active site, with a dissociation constant of 1.25×10⁻⁷ M for SKIP-(59-129).\",\n      \"method\": \"NMR structure determination, GST pulldown, surface plasmon resonance, chemical shift perturbation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR structure plus in vitro binding quantification (SPR) plus mutagenesis-level epitope mapping; single lab with multiple orthogonal methods\",\n      \"pmids\": [\"16595688\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"PPIL1 interacts with SNW1/SKIP and stathmin in colon cancer cells; siRNA-mediated knockdown of PPIL1 retards growth of colon cancer cells, implicating PPIL1 in cancer cell proliferation via these partners.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, colony formation assay\",\n      \"journal\": \"Clinical cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — Co-IP plus functional KD with proliferation readout; single lab\",\n      \"pmids\": [\"16397026\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"The N-terminal region of SKIP (residues 59–129, SKIPN) is intrinsically disordered and undergoes a disorder-to-order transition upon binding PPIL1; a minimal 21-residue fragment (PBF, residues 59–79) is sufficient for PPIL1 binding via electrostatic and hydrophobic interactions, while the PPIase active site of PPIL1 remains accessible in the complex.\",\n      \"method\": \"NMR structure of PBF·PPIL1 complex, NMR-based disorder characterization\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — NMR structure with functional epitope mapping; orthologous to prior SPR data; single lab with rigorous structural validation\",\n      \"pmids\": [\"20007319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Crystal structure of PPIL1 bound to cyclosporine A at 1.15 Å resolution revealed the active site architecture and two Cd²⁺ coordination sites at residues previously implicated in SKIP binding; a 36-residue SKIP epitope (centered on an 8-residue core) suffices for PPIL1 binding, and molecular docking places a SKIP proline in PPIL1's hydrophobic pocket.\",\n      \"method\": \"X-ray crystallography (SAD phasing), peptide array, GST pulldown, molecular docking\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution crystal structure combined with biochemical epitope mapping and docking; consistent with prior NMR studies\",\n      \"pmids\": [\"20368803\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Biallelic loss-of-function mutations in PPIL1 cause pontocerebellar hypoplasia with microcephaly (PCHM); PPIL1 forms an active isomerase-substrate interaction with PRP17, but the isomerase activity itself is not required for function; loss of PPIL1 disrupts splicing integrity, predominantly affecting short and high GC-content introns; PPIL1 knockin mice with patient mutations show neuron-specific apoptosis.\",\n      \"method\": \"Human genetics (WES of 10 families), PPIL1 knockin mouse model, mouse knockout (embryonic lethal), RNA splicing analysis, biochemical interaction assays\",\n      \"journal\": \"Neuron\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (patient genetics, mouse models, biochemical interaction, transcriptome-wide splicing analysis) across multiple families; strong evidence for non-enzymatic function\",\n      \"pmids\": [\"33220177\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PPIL1 interacts with C3b-α'2 complement fragment through glutamic acid 156 (E156) and aspartic acid 111 (D111) residues of PPIL1; this interaction is required for S1P/S1PR1-driven NLRP3/inflammasome induction and tumor metastasis, and inactivating mutations of C3b-α'2 that prevent PPIL1 association attenuate inflammasome activation and lung colonization in mice.\",\n      \"method\": \"Inactivating mutations, co-immunoprecipitation, mouse lung colonization/metastasis assays, genetic knockouts (C3aR1⁻/⁻)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — specific interaction residues identified with mutation validation plus in vivo functional consequence; single lab\",\n      \"pmids\": [\"36476873\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The proline-rich PxxP motifs of the EWS low-complexity domain (EWSLCD) engage the catalytic face (PPIase active site) of PPIL1 via low-affinity 'fuzzy' complexes; PPIL1 is recruited into EWSLCD phase-separated condensates and alters condensation properties depending on ionic conditions.\",\n      \"method\": \"NMR titration experiments, phase separation assays, biochemical characterization\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1–2 — NMR-based structural characterization plus phase separation assays; single lab, moderate evidence\",\n      \"pmids\": [\"40668764\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PPIL1 knockdown in HCC cell lines suppresses proliferation, migration, sphere formation, and tumor initiation; mechanistic studies identify PPIL1 as a regulator of Wnt/β-catenin signaling through transcriptional upregulation of DAAM2.\",\n      \"method\": \"shRNA knockdown, xenograft mouse models, transcriptome analysis, cell viability and sphere formation assays\",\n      \"journal\": \"Cancer genomics & proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — KD with multiple phenotypic readouts plus transcriptome-based pathway placement; single lab\",\n      \"pmids\": [\"40883023\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPIL1 is a spliceosomal cyclophilin-family peptidyl-prolyl cis/trans isomerase that is recruited into the activated spliceosome (B, B*, and C complexes) through a direct, cyclosporin A-independent interaction with SKIP/SNW1 (via SKIP residues 59–79 engaging a site distinct from the PPIL1 PPIase active site), where it forms an isomerase-substrate complex with PRP17 to support splicing integrity of short, GC-rich introns—a function that is structural rather than enzymatic, as isomerase activity is dispensable; loss of PPIL1 causes neuron-specific apoptosis and pontocerebellar hypoplasia with microcephaly in humans and mice, and PPIL1 also participates in non-spliceosomal interactions including C3b-driven NLRP3 inflammasome signaling (via E156/D111), EWS LCD phase separation (via PxxP-active site contacts), and Wnt/β-catenin/DAAM2 regulation in cancer cells.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PPIL1 is a spliceosomal cyclophilin-family peptidyl-prolyl cis/trans isomerase that supports pre-mRNA splicing fidelity, particularly of short, GC-rich introns, through a structural rather than enzymatic role within the activated spliceosome. It is recruited to the spliceosome via a direct, cyclosporin A-independent interaction between a site distinct from its PPIase active site and the intrinsically disordered N-terminal region (residues 59–79) of SKIP/SNW1, while its catalytic face engages PRP17 in an isomerase–substrate complex whose prolyl isomerase activity is dispensable for splicing function [PMID:16595688, PMID:20007319, PMID:33220177]. Biallelic loss-of-function mutations in PPIL1 cause pontocerebellar hypoplasia with microcephaly through neuron-specific apoptosis in humans and mice [PMID:33220177]. Beyond splicing, PPIL1 participates in C3b-mediated NLRP3 inflammasome activation via residues E156 and D111 [PMID:36476873], modulates EWS low-complexity domain phase separation through PPIase active-site contacts with PxxP motifs [PMID:40668764], and promotes Wnt/β-catenin signaling through transcriptional upregulation of DAAM2 in hepatocellular carcinoma [PMID:40883023].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Identification of PPIL1 as a novel cyclophilin-family member established that a short (166 aa) PPIase-related protein exists in the human genome at 2p23, opening questions about its specific substrates and cellular role.\",\n      \"evidence\": \"cDNA cloning, Northern blot, and FISH mapping of hCyPX\",\n      \"pmids\": [\"8978786\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No enzymatic activity demonstrated\", \"No interacting partners or cellular function identified\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Discovery that PPIL1 orthologs bind the SNW/SKIP coregulator in a cyclosporin A-independent manner while retaining CsA-sensitive PPIase activity revealed a bipartite functionality—enzyme activity and a distinct protein-recruitment interface—and placed PPIL1 in the spliceosomal/transcriptional regulatory axis.\",\n      \"evidence\": \"Yeast two-hybrid screen and in vitro PPIase assay in Dictyostelium and S. pombe systems\",\n      \"pmids\": [\"11690648\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Binding interface not mapped at residue level\", \"Human PPIL1–SKIP interaction not yet directly demonstrated\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Structural and biophysical characterization defined two separable surfaces on PPIL1—a PPIase active site and a distinct SKIP-binding face—with nanomolar affinity for SKIP residues 59–129, establishing how PPIL1 can simultaneously bind SKIP and present its catalytic pocket to spliceosomal substrates.\",\n      \"evidence\": \"NMR structure, SPR (Kd = 1.25 × 10⁻⁷ M), GST pulldown, chemical shift perturbation; X-ray crystallography at 1.15 Å resolution with peptide array and docking\",\n      \"pmids\": [\"16595688\", \"20368803\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the PPIase substrate in the spliceosome unknown\", \"Functional significance of isomerase activity untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstration that the SKIP N-terminus is intrinsically disordered and undergoes a disorder-to-order transition upon binding PPIL1, with a minimal 21-residue fragment sufficient, clarified the recruitment mechanism and showed the PPIase active site remains accessible for additional substrates.\",\n      \"evidence\": \"NMR structure of PBF·PPIL1 complex and disorder characterization\",\n      \"pmids\": [\"20007319\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo relevance of disorder-to-order transition not tested\", \"No spliceosomal substrate for the free active site identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Human genetics and mouse modeling resolved the key outstanding questions: PPIL1 forms an isomerase–substrate complex with PRP17, but its PPIase catalytic activity is dispensable; loss of PPIL1 disrupts splicing of short, GC-rich introns and causes neuron-specific apoptosis leading to pontocerebellar hypoplasia with microcephaly.\",\n      \"evidence\": \"WES of 10 families with PCHM, knockin and knockout mouse models, transcriptome-wide splicing analysis, biochemical interaction assays\",\n      \"pmids\": [\"33220177\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for the non-enzymatic PRP17 interaction unresolved\", \"Why neurons are selectively vulnerable unclear\", \"Whether PPIL1 has additional spliceosomal substrates beyond PRP17 unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of PPIL1 as a C3b-α'2 interactor through E156 and D111 residues revealed a non-spliceosomal role in NLRP3 inflammasome activation and tumor metastasis, broadening PPIL1's functional repertoire to innate immunity.\",\n      \"evidence\": \"Inactivating mutations, co-immunoprecipitation, mouse lung colonization assays\",\n      \"pmids\": [\"36476873\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PPIase activity is required for C3b interaction not tested\", \"How PPIL1–C3b interaction triggers inflammasome assembly mechanistically unclear\", \"Single-lab finding\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Two independent studies extended PPIL1's non-spliceosomal roles: its PPIase active site engages EWS low-complexity domain PxxP motifs in fuzzy complexes that modulate phase separation, and it promotes Wnt/β-catenin signaling via DAAM2 upregulation in hepatocellular carcinoma.\",\n      \"evidence\": \"NMR titration and phase separation assays (EWS); shRNA knockdown, xenograft models, and transcriptome analysis (HCC/DAAM2)\",\n      \"pmids\": [\"40668764\", \"40883023\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Physiological relevance of PPIL1–EWS condensate modulation untested in cells\", \"Whether PPIL1-DAAM2 axis operates through direct interaction or is transcriptionally indirect not resolved\", \"Relationship between spliceosomal and phase-separation roles unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis for PPIL1's non-enzymatic stabilization of PRP17 within the spliceosome, the mechanism of neuron-selective vulnerability to PPIL1 loss, and the functional integration of its spliceosomal versus non-spliceosomal roles remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of PPIL1–PRP17 complex available\", \"Neuron-specific splicing dependencies of PPIL1 not mapped\", \"Whether spliceosomal and inflammasome/phase-separation functions are coordinated or independent is unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 3, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [3, 5, 7]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10]}\n    ],\n    \"complexes\": [\n      \"spliceosome (B*/C complex)\"\n    ],\n    \"partners\": [\n      \"SNW1\",\n      \"PRP17\",\n      \"STMN1\",\n      \"EWSR1\",\n      \"C3\",\n      \"DAAM2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}