{"gene":"PPHLN1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2015,"finding":"Chromosomal translocation t(10;12)(q26;q12) creates an FGFR2-PPHLN1 fusion protein that possesses transforming and oncogenic activity in vitro, inhibitable by a selective FGFR2 inhibitor, establishing PPHLN1 as a fusion partner that contributes to oncogenic FGFR2 activation in intrahepatic cholangiocarcinoma.","method":"RNA- and exome-sequencing to identify fusion; in vitro transformation assays; FGFR2 inhibitor treatment","journal":"Nature communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RNA-seq discovery plus in vitro oncogenicity assays in single study, no structural/reconstitution data","pmids":["25608663"],"is_preprint":false},{"year":2020,"finding":"Biological activity of the FGFR2-PPHLN1 fusion protein requires (1) an active FGFR2-derived tyrosine kinase domain, (2) a dimerization domain contributed by the PPHLN1 moiety, and (3) membrane localization of the fusion protein. The fusion activates MAPK/ERK, JAK/STAT3, and PI3K/AKT signaling pathways.","method":"Soft agar colony formation and focus assays in RIE-1 and NIH3T3 cells using kinase-dead, kinase-activated, and WT constructs; signal peptide deletion and myristylation-signal addition; indirect immunofluorescence; pathway inhibitor treatment","journal":"Translational oncology","confidence":"High","confidence_rationale":"Tier 1-2 / Moderate — multiple orthogonal mutagenesis approaches (kinase-dead, domain deletion, membrane-targeting mutants) with functional readouts in two cell lines, single lab","pmids":["32854034"],"is_preprint":false},{"year":2018,"finding":"PPHLN1 (Periphilin 1) is one of three core components of the HUSH (Human Silencing Hub) complex, together with FAM208A (TASOR) and MPHOSPH8 (MPP8). Vpx/Vpr primate immunodeficiency virus proteins associate with the HUSH complex and degrade its components (including PPHLN1) via the DCAF1/CUL4A/B/proteasome pathway, thereby de-repressing provirus transcription.","method":"Genetic screen identifying HUSH components as Vpx/Vpr mimics; Co-immunoprecipitation of Vpx with HUSH complex; knockdown of FAM208A/PPHLN1; Western blot showing proteasome-dependent degradation; replication kinetics assay","journal":"Nature microbiology","confidence":"High","confidence_rationale":"Tier 2 / Strong — forward genetic screen plus reciprocal Co-IP plus functional knockdown assays; independently replicated by other HUSH complex papers","pmids":["30297740"],"is_preprint":false},{"year":2018,"finding":"PPHLN1, as part of the HUSH complex (with MPP8 and TASOR), is required for silencing of unintegrated retroviral DNA. The DNA-binding protein NP220 recruits the HUSH complex (including PPHLN1), SETDB1, and HDAC1/HDAC4 to unintegrated retroviral DNA to mediate epigenetic silencing.","method":"Genome-wide CRISPR-Cas9 screen; chromatin immunoprecipitation (ChIP); knockout of NP220 with measurement of retroviral replication kinetics","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — genome-wide CRISPR screen plus ChIP demonstrating recruitment, published in top-tier journal with multiple orthogonal methods","pmids":["30487602"],"is_preprint":false},{"year":2025,"finding":"The ERVK3-1 microprotein physically interacts with PPHLN1 (a HUSH complex component) and is essential for transcriptional repression of known HUSH target genes, suggesting PPHLN1 participates in sensing or regulation of target gene expression via interaction with this endogenous retroviral microprotein.","method":"Co-immunoprecipitation of ERVK3-1 microprotein with PPHLN1; loss-of-function of ERVK3-1 with measurement of HUSH target gene expression","journal":"Biochemistry","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — Co-IP plus functional knockdown, single lab, single study","pmids":["40699144"],"is_preprint":false},{"year":2024,"finding":"PPHLN1 is a core subunit of the HuSH complex alongside TASOR and MPP8, and each subunit plays an important role in achieving precise genomic localization to distinct loci for LINE-1 retrotransposon silencing. In silico structure prediction and amino acid substitutions disrupting MPP8 binding to TASOR (and its paralog TASOR2) demonstrated that the relative quantities of HuSH complexes control LINE-1 silencing activity.","method":"In silico protein structure prediction; amino acid substitution/mutagenesis disrupting MPP8-TASOR interactions; functional LINE-1 silencing assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2-3 / Weak — mutagenesis with functional assay but computational structural prediction, preprint, single lab","pmids":["38313255"],"is_preprint":true},{"year":2024,"finding":"PRC1.6 colocalizes with the HUSH complex (including PPHLN1) genome-wide primarily at active promoters, and PRC1.6 binding at a subset of HUSH-silenced genes is dependent on the core HUSH component MPP8, revealing crosstalk between the HUSH complex and PRC1.6 in provirus silencing.","method":"Proximity labeling (C-BERST/dCas9-APEX2); forward genetic screen; genome-wide chromatin profiling (ChIP-seq); loss-of-function experiments","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (proximity labeling, genetic screen, ChIP-seq) but preprint and single lab","pmids":["39026796"],"is_preprint":true},{"year":2025,"finding":"Deficiency of PPHLN1 alone (unlike MPP8 or TASOR deficiency) does NOT trigger colony morphology alteration or defect in exit from pluripotency in mouse embryonic stem cells, indicating PPHLN1 is dispensable for HUSH-mediated regulation of pluripotency exit in this context.","method":"CRISPR-based genome editing knockout of PPHLN1 in mESCs; colony morphology assay; differentiation assays","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean CRISPR KO with defined cellular phenotype but single lab and negative result for PPHLN1 specifically","pmids":["41291012"],"is_preprint":false},{"year":2025,"finding":"The HUSH complex (including PPHLN1) restricts human adenovirus (HAdV) gene expression and replication. To counteract this, adenoviral early proteins E1B-55K and E4orf6 recruit MPP8 for proteasomal degradation via an E3 ubiquitin ligase, and HUSH factors are inhibited through binding to HAdV proteins and subsequent relocalization.","method":"Infection assays with HAdV; co-immunoprecipitation of adenoviral proteins with HUSH components; proteasomal degradation assays; relocalization imaging","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, mechanistic details primarily about MPP8 degradation; PPHLN1 role implied as part of complex but not individually dissected","pmids":["bio_10.1101_2025.02.10.637372"],"is_preprint":true},{"year":2024,"finding":"OTX2 regulates alternative splicing of PPHLN1 in group 3 medulloblastoma as part of a stem cell splicing program; PPHLN1 is expressed in the most primitive rhombic lip stem cells, and targeting PPHLN1 splicing reduces tumor growth and enhances survival in vivo.","method":"OTX2 association with splicing regulators by protein-protein interaction assays; in vivo tumor growth assays with PPHLN1 splicing targeting; survival analysis in animal models","journal":"Nature cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vivo functional validation of PPHLN1 splicing targeting with survival readout, but mechanistic details of PPHLN1 itself are limited; single study","pmids":["39025928"],"is_preprint":false},{"year":2021,"finding":"Both PPHLN1 and its structural homolog BFARv3 interact with RNA-binding/paraspeckle proteins NONO and SFPQ, as confirmed by reciprocal co-immunoprecipitation and proximity ligation assay, suggesting a role for PPHLN1 in RNA metabolism.","method":"Reciprocal co-immunoprecipitation; proximity ligation assay","journal":"Biochimica et biophysica acta. Molecular cell research","confidence":"Low","confidence_rationale":"Tier 3 / Weak — reciprocal Co-IP and PLA confirm interaction but functional consequence of PPHLN1-NONO/SFPQ interaction is not directly tested; single lab","pmids":["34175335"],"is_preprint":false}],"current_model":"PPHLN1 (Periphilin 1) is a core structural subunit of the HUSH (Human Silencing Hub) complex together with TASOR and MPP8, where it contributes to H3K9me3-mediated epigenetic silencing of retrotransposons, unintegrated retroviral DNA, and proviruses; the complex is recruited to target loci partly via NP220, and is antagonized by viral proteins (HIV Vpx/Vpr, adenoviral E1B-55K/E4orf6) that degrade or relocalize its components. Additionally, the PPHLN1 C-terminal region acts as a dimerization domain in the oncogenic FGFR2-PPHLN1 fusion protein found in intrahepatic cholangiocarcinoma, where membrane localization and an active FGFR2 kinase domain are also required for transforming activity."},"narrative":{"mechanistic_narrative":"PPHLN1 (Periphilin 1) is a core structural subunit of the HUSH (Human Silencing Hub) complex, which together with TASOR (FAM208A) and MPP8 (MPHOSPH8) directs H3K9me3-mediated epigenetic silencing of retrotransposons, unintegrated retroviral DNA, and proviruses [PMID:30297740, PMID:30487602]. Recruitment to unintegrated retroviral DNA is mediated by the DNA-binding protein NP220, which brings the HUSH complex together with the SETDB1 methyltransferase and HDAC1/HDAC4 to target loci [PMID:30487602], and the relative stoichiometry of HUSH subunits tunes precise genomic localization for LINE-1 retrotransposon silencing [PMID:38313255]. This silencing activity is antagonized by viral countermeasures: primate immunodeficiency virus Vpx/Vpr proteins associate with HUSH and direct PPHLN1 and other subunits to DCAF1/CUL4-mediated proteasomal degradation to de-repress proviruses [PMID:30297740], and the HUSH complex also restricts human adenovirus, which counteracts it via E1B-55K/E4orf6 [PMID:bio_10.1101_2025.02.10.637372]. Within mouse embryonic stem cells, PPHLN1 is dispensable for HUSH-mediated control of pluripotency exit, unlike MPP8 or TASOR [PMID:41291012]. Independently of its silencing role, the PPHLN1 C-terminal region functions as a dimerization domain in the oncogenic FGFR2-PPHLN1 fusion protein found in intrahepatic cholangiocarcinoma, where transforming activity requires an active FGFR2 kinase domain, the PPHLN1-contributed dimerization domain, and membrane localization, driving MAPK/ERK, JAK/STAT3, and PI3K/AKT signaling [PMID:25608663, PMID:32854034].","teleology":[{"year":2015,"claim":"Established that PPHLN1 can act as an oncogenic fusion partner, framing a disease-relevant role distinct from any silencing function.","evidence":"RNA-/exome-sequencing identifying t(10;12) fusion plus in vitro transformation assays with FGFR2 inhibitor in intrahepatic cholangiocarcinoma","pmids":["25608663"],"confidence":"Medium","gaps":["Which PPHLN1 region drives oncogenicity was not yet defined","No structural or reconstitution data on the fusion","Frequency and clinical scope of the fusion not addressed"]},{"year":2018,"claim":"Defined PPHLN1 as one of three core HUSH subunits and showed its degradation is exploited by viruses to de-repress proviruses, establishing its central role in epigenetic silencing.","evidence":"Forward genetic screen, reciprocal Co-IP of Vpx with HUSH, knockdown of PPHLN1/FAM208A, and proteasome-dependent degradation Western blots","pmids":["30297740"],"confidence":"High","gaps":["Molecular contribution of PPHLN1 to silencing versus TASOR/MPP8 not separated","Structural basis of HUSH assembly not resolved"]},{"year":2018,"claim":"Showed how the HUSH complex is recruited to its targets, answering how PPHLN1-containing HUSH reaches unintegrated retroviral DNA.","evidence":"Genome-wide CRISPR-Cas9 screen and ChIP demonstrating NP220-dependent recruitment of HUSH, SETDB1, and HDAC1/4","pmids":["30487602"],"confidence":"High","gaps":["Direct PPHLN1-NP220 contact not demonstrated","How recruitment is targeted at integrated proviruses versus unintegrated DNA unclear"]},{"year":2021,"claim":"Linked PPHLN1 to RNA-associated paraspeckle proteins, raising a possible role in RNA metabolism beyond chromatin silencing.","evidence":"Reciprocal Co-IP and proximity ligation assay showing PPHLN1 (and homolog BFARv3) interaction with NONO and SFPQ","pmids":["34175335"],"confidence":"Low","gaps":["Functional consequence of PPHLN1-NONO/SFPQ interaction not tested","Single lab, no orthogonal functional validation","Relationship to HUSH silencing not established"]},{"year":2020,"claim":"Dissected the requirements of the FGFR2-PPHLN1 fusion, pinpointing the PPHLN1 moiety as the dimerization module needed for transformation.","evidence":"Soft agar/focus assays with kinase-dead, kinase-active, domain-deletion, and membrane-targeting constructs plus pathway inhibitor treatment in RIE-1 and NIH3T3 cells","pmids":["32854034"],"confidence":"High","gaps":["Structural basis of PPHLN1-mediated dimerization not solved","Single lab; in vivo tumor relevance not tested"]},{"year":2024,"claim":"Showed HUSH subunit stoichiometry controls precise genomic localization for LINE-1 silencing, refining how the complex achieves locus specificity.","evidence":"In silico structure prediction and MPP8-TASOR interface mutagenesis with LINE-1 silencing assays (preprint)","pmids":["38313255"],"confidence":"Medium","gaps":["Computational structure not experimentally confirmed","PPHLN1-specific contribution to localization not isolated","Preprint, single lab"]},{"year":2024,"claim":"Revealed crosstalk between HUSH and PRC1.6 in provirus silencing, broadening the chromatin context of HUSH function.","evidence":"Proximity labeling, genetic screen, and ChIP-seq with loss-of-function (preprint)","pmids":["39026796"],"confidence":"Medium","gaps":["PPHLN1-specific role in PRC1.6 crosstalk not dissected","Preprint, single lab"]},{"year":2024,"claim":"Implicated PPHLN1 alternative splicing in a stem cell program driving group 3 medulloblastoma, suggesting a tumor-relevant role distinct from the FGFR2 fusion.","evidence":"OTX2-splicing regulator interaction assays and in vivo tumor growth/survival assays with PPHLN1 splicing targeting","pmids":["39025928"],"confidence":"Medium","gaps":["Mechanism of the PPHLN1 splice isoform's action not defined","Connection to HUSH silencing function not established"]},{"year":2025,"claim":"Identified an endogenous retroviral microprotein partner of PPHLN1 required for HUSH target repression, hinting at a sensing/regulatory input.","evidence":"Co-IP of ERVK3-1 microprotein with PPHLN1 and loss-of-function with HUSH target gene expression readout","pmids":["40699144"],"confidence":"Medium","gaps":["Direct mechanism by which ERVK3-1 modulates PPHLN1/HUSH unknown","Single study, single lab"]},{"year":2025,"claim":"Demonstrated that PPHLN1 is functionally dispensable for HUSH-mediated pluripotency exit, distinguishing it from TASOR and MPP8 in this context.","evidence":"CRISPR knockout of PPHLN1 in mESCs with colony morphology and differentiation assays","pmids":["41291012"],"confidence":"Medium","gaps":["Whether PPHLN1 is dispensable for retrotransposon silencing in the same system not addressed","Negative result for PPHLN1 specifically, single lab"]},{"year":null,"claim":"The structural basis of PPHLN1 incorporation into HUSH and its precise molecular contribution (versus TASOR/MPP8) to H3K9me3 deposition and locus targeting remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No experimental structure of the PPHLN1-containing HUSH complex","No defined biochemical activity assigned to PPHLN1 itself","Reconciliation of dispensability in pluripotency exit with core-subunit status not established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[2,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[2,3]}],"pathway":[{"term_id":"R-HSA-4839726","term_label":"Chromatin organization","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[1]}],"complexes":["HUSH complex"],"partners":["TASOR","MPP8","NP220","FGFR2","NONO","SFPQ","ERVK3-1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8NEY8","full_name":"Periphilin-1","aliases":["CDC7 expression repressor","CR","Gastric cancer antigen Ga50"],"length_aa":458,"mass_kda":52.7,"function":"RNA-binding component of the HUSH complex, a multiprotein complex that mediates epigenetic repression of mobile genetic elements, such as retroviruses and transposable elements (PubMed:15474462, PubMed:17963697, PubMed:26022416, PubMed:32976585, PubMed:39658355). The HUSH complex mainly represses LINE-1 (L1) retrotransposons that are still capable of transposition (PubMed:32976585, PubMed:39658355). The HUSH complex is recruited to genomic loci rich in H3K9me3 and is probably required to maintain transcriptional silencing by promoting recruitment of SETDB1, a histone methyltransferase that mediates further deposition of H3K9me3, as well as MORC2, a chromatin remodeler that compacts chromatin (PubMed:26022416). The HUSH complex is also involved in the silencing of unintegrated retroviral DNA: some part of the retroviral DNA formed immediately after infection remains unintegrated in the host genome and is transcriptionally repressed (PubMed:30487602). Within the HUSH complex, PPHLN1 acts as a mRNA-binding component, which specifically binds nascent transcripts of mobile genetic elements, enabling HUSH-dependent silencing of transcripts (PubMed:39658355). Contributes to the maintenance of the HUSH complex at chromatin (PubMed:26022416, PubMed:39013473). As part of the HUSH2 complex, promotes epigenetic repression of interferon-stimulated genes (PubMed:33144593, PubMed:39013473). May be involved in epithelial differentiation by contributing to epidermal integrity and barrier formation (PubMed:12853457)","subcellular_location":"Nucleus; Cytoplasm; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q8NEY8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPHLN1","classification":"Not Classified","n_dependent_lines":98,"n_total_lines":1208,"dependency_fraction":0.08112582781456953},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CPSF6","stoichiometry":0.2},{"gene":"HIST2H2BE","stoichiometry":0.2},{"gene":"HMGN5","stoichiometry":0.2},{"gene":"SNRPA","stoichiometry":0.2},{"gene":"SSRP1","stoichiometry":0.2},{"gene":"TOP1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PPHLN1","total_profiled":1310},"omim":[{"mim_id":"621243","title":"TRANSCRIPTION ACTIVATION SUPPRESSOR FAMILY, MEMBER 2; TASOR2","url":"https://www.omim.org/entry/621243"},{"mim_id":"619516","title":"BIFUNCTIONAL APOPTOSIS REGULATOR; BFAR","url":"https://www.omim.org/entry/619516"},{"mim_id":"616661","title":"MORC FAMILY CW-TYPE ZINC FINGER PROTEIN 2; MORC2","url":"https://www.omim.org/entry/616661"},{"mim_id":"615022","title":"ICHTHYOSIS, CONGENITAL, AUTOSOMAL RECESSIVE 7; ARCI7","url":"https://www.omim.org/entry/615022"},{"mim_id":"614349","title":"ZINC FINGER PROTEIN 638; ZNF638","url":"https://www.omim.org/entry/614349"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPHLN1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"Q8NEY8","domains":[{"cath_id":"-","chopping":"413-447","consensus_level":"medium","plddt":91.9734,"start":413,"end":447}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NEY8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NEY8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8NEY8-F1-predicted_aligned_error_v6.png","plddt_mean":56.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPHLN1","jax_strain_url":"https://www.jax.org/strain/search?query=PPHLN1"},"sequence":{"accession":"Q8NEY8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8NEY8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8NEY8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8NEY8"}},"corpus_meta":[{"pmid":"27245147","id":"PMC_27245147","title":"FGFR inhibitors: Effects on cancer cells, tumor microenvironment and whole-body homeostasis (Review).","date":"2016","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/27245147","citation_count":345,"is_preprint":false},{"pmid":"25608663","id":"PMC_25608663","title":"Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma.","date":"2015","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/25608663","citation_count":249,"is_preprint":false},{"pmid":"30297740","id":"PMC_30297740","title":"Primate immunodeficiency virus proteins Vpx and Vpr counteract transcriptional repression of proviruses by the HUSH complex.","date":"2018","source":"Nature microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/30297740","citation_count":110,"is_preprint":false},{"pmid":"30487602","id":"PMC_30487602","title":"NP220 mediates silencing of unintegrated retroviral DNA.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/30487602","citation_count":102,"is_preprint":false},{"pmid":"31899106","id":"PMC_31899106","title":"Functions of FGFR2 corrupted by translocations in intrahepatic cholangiocarcinoma.","date":"2019","source":"Cytokine & growth factor reviews","url":"https://pubmed.ncbi.nlm.nih.gov/31899106","citation_count":56,"is_preprint":false},{"pmid":"26070530","id":"PMC_26070530","title":"Plasma Autoantibodies Associated with Basal-like Breast Cancers.","date":"2015","source":"Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology","url":"https://pubmed.ncbi.nlm.nih.gov/26070530","citation_count":39,"is_preprint":false},{"pmid":"16117785","id":"PMC_16117785","title":"Identification of a novel locus associated with congenital recessive ichthyosis on 12p11.2-q13.","date":"2005","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/16117785","citation_count":24,"is_preprint":false},{"pmid":"39025928","id":"PMC_39025928","title":"A group 3 medulloblastoma stem cell program is maintained by OTX2-mediated alternative splicing.","date":"2024","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/39025928","citation_count":10,"is_preprint":false},{"pmid":"34747541","id":"PMC_34747541","title":"Neuregulin 1 (NRG1) fusion-positive high-grade spindle cell sarcoma: A distinct group of soft tissue tumors with metastatic potential.","date":"2021","source":"Genes, chromosomes & cancer","url":"https://pubmed.ncbi.nlm.nih.gov/34747541","citation_count":8,"is_preprint":false},{"pmid":"39677475","id":"PMC_39677475","title":"Small-cohort GWAS discovery with AI over massive functional genomics knowledge graph.","date":"2024","source":"medRxiv : the preprint server for health sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39677475","citation_count":5,"is_preprint":false},{"pmid":"32854034","id":"PMC_32854034","title":"Oncogenic fusion protein FGFR2-PPHLN1: Requirements for biological activation, and efficacy of inhibitors.","date":"2020","source":"Translational oncology","url":"https://pubmed.ncbi.nlm.nih.gov/32854034","citation_count":3,"is_preprint":false},{"pmid":"40699144","id":"PMC_40699144","title":"The ERVK3-1 Microprotein Interacts with the HUSH Complex.","date":"2025","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/40699144","citation_count":2,"is_preprint":false},{"pmid":"38313255","id":"PMC_38313255","title":"Interplay between Two Paralogous Human Silencing Hub (HuSH) Complexes in Regulating LINE-1 Element Silencing.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38313255","citation_count":2,"is_preprint":false},{"pmid":"39026796","id":"PMC_39026796","title":"PRC1.6 localizes on chromatin with the human silencing hub (HUSH) complex for promoter-specific silencing.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/39026796","citation_count":1,"is_preprint":false},{"pmid":"41291012","id":"PMC_41291012","title":"The HUSH complex facilitates the exit of pluripotency.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/41291012","citation_count":0,"is_preprint":false},{"pmid":"34175335","id":"PMC_34175335","title":"The periphilin 1-like BFAR isoform 3 is highly expressed in transcriptionally silent oocytes and involved in RNA metabolism.","date":"2021","source":"Biochimica et biophysica acta. Molecular cell research","url":"https://pubmed.ncbi.nlm.nih.gov/34175335","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.02.10.637372","title":"Intrinsic immunity against HAdV is achieved by a novel epigenetic silencing complex","date":"2025-02-10","source":"bioRxiv","url":"https://doi.org/10.1101/2025.02.10.637372","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11332,"output_tokens":2994,"usd":0.039453,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10283,"output_tokens":3523,"usd":0.069745,"stage2_stop_reason":"end_turn"},"total_usd":0.109198,"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\": 2015,\n      \"finding\": \"Chromosomal translocation t(10;12)(q26;q12) creates an FGFR2-PPHLN1 fusion protein that possesses transforming and oncogenic activity in vitro, inhibitable by a selective FGFR2 inhibitor, establishing PPHLN1 as a fusion partner that contributes to oncogenic FGFR2 activation in intrahepatic cholangiocarcinoma.\",\n      \"method\": \"RNA- and exome-sequencing to identify fusion; in vitro transformation assays; FGFR2 inhibitor treatment\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RNA-seq discovery plus in vitro oncogenicity assays in single study, no structural/reconstitution data\",\n      \"pmids\": [\"25608663\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Biological activity of the FGFR2-PPHLN1 fusion protein requires (1) an active FGFR2-derived tyrosine kinase domain, (2) a dimerization domain contributed by the PPHLN1 moiety, and (3) membrane localization of the fusion protein. The fusion activates MAPK/ERK, JAK/STAT3, and PI3K/AKT signaling pathways.\",\n      \"method\": \"Soft agar colony formation and focus assays in RIE-1 and NIH3T3 cells using kinase-dead, kinase-activated, and WT constructs; signal peptide deletion and myristylation-signal addition; indirect immunofluorescence; pathway inhibitor treatment\",\n      \"journal\": \"Translational oncology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Moderate — multiple orthogonal mutagenesis approaches (kinase-dead, domain deletion, membrane-targeting mutants) with functional readouts in two cell lines, single lab\",\n      \"pmids\": [\"32854034\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PPHLN1 (Periphilin 1) is one of three core components of the HUSH (Human Silencing Hub) complex, together with FAM208A (TASOR) and MPHOSPH8 (MPP8). Vpx/Vpr primate immunodeficiency virus proteins associate with the HUSH complex and degrade its components (including PPHLN1) via the DCAF1/CUL4A/B/proteasome pathway, thereby de-repressing provirus transcription.\",\n      \"method\": \"Genetic screen identifying HUSH components as Vpx/Vpr mimics; Co-immunoprecipitation of Vpx with HUSH complex; knockdown of FAM208A/PPHLN1; Western blot showing proteasome-dependent degradation; replication kinetics assay\",\n      \"journal\": \"Nature microbiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — forward genetic screen plus reciprocal Co-IP plus functional knockdown assays; independently replicated by other HUSH complex papers\",\n      \"pmids\": [\"30297740\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PPHLN1, as part of the HUSH complex (with MPP8 and TASOR), is required for silencing of unintegrated retroviral DNA. The DNA-binding protein NP220 recruits the HUSH complex (including PPHLN1), SETDB1, and HDAC1/HDAC4 to unintegrated retroviral DNA to mediate epigenetic silencing.\",\n      \"method\": \"Genome-wide CRISPR-Cas9 screen; chromatin immunoprecipitation (ChIP); knockout of NP220 with measurement of retroviral replication kinetics\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — genome-wide CRISPR screen plus ChIP demonstrating recruitment, published in top-tier journal with multiple orthogonal methods\",\n      \"pmids\": [\"30487602\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The ERVK3-1 microprotein physically interacts with PPHLN1 (a HUSH complex component) and is essential for transcriptional repression of known HUSH target genes, suggesting PPHLN1 participates in sensing or regulation of target gene expression via interaction with this endogenous retroviral microprotein.\",\n      \"method\": \"Co-immunoprecipitation of ERVK3-1 microprotein with PPHLN1; loss-of-function of ERVK3-1 with measurement of HUSH target gene expression\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — Co-IP plus functional knockdown, single lab, single study\",\n      \"pmids\": [\"40699144\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PPHLN1 is a core subunit of the HuSH complex alongside TASOR and MPP8, and each subunit plays an important role in achieving precise genomic localization to distinct loci for LINE-1 retrotransposon silencing. In silico structure prediction and amino acid substitutions disrupting MPP8 binding to TASOR (and its paralog TASOR2) demonstrated that the relative quantities of HuSH complexes control LINE-1 silencing activity.\",\n      \"method\": \"In silico protein structure prediction; amino acid substitution/mutagenesis disrupting MPP8-TASOR interactions; functional LINE-1 silencing assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 / Weak — mutagenesis with functional assay but computational structural prediction, preprint, single lab\",\n      \"pmids\": [\"38313255\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PRC1.6 colocalizes with the HUSH complex (including PPHLN1) genome-wide primarily at active promoters, and PRC1.6 binding at a subset of HUSH-silenced genes is dependent on the core HUSH component MPP8, revealing crosstalk between the HUSH complex and PRC1.6 in provirus silencing.\",\n      \"method\": \"Proximity labeling (C-BERST/dCas9-APEX2); forward genetic screen; genome-wide chromatin profiling (ChIP-seq); loss-of-function experiments\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (proximity labeling, genetic screen, ChIP-seq) but preprint and single lab\",\n      \"pmids\": [\"39026796\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Deficiency of PPHLN1 alone (unlike MPP8 or TASOR deficiency) does NOT trigger colony morphology alteration or defect in exit from pluripotency in mouse embryonic stem cells, indicating PPHLN1 is dispensable for HUSH-mediated regulation of pluripotency exit in this context.\",\n      \"method\": \"CRISPR-based genome editing knockout of PPHLN1 in mESCs; colony morphology assay; differentiation assays\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean CRISPR KO with defined cellular phenotype but single lab and negative result for PPHLN1 specifically\",\n      \"pmids\": [\"41291012\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The HUSH complex (including PPHLN1) restricts human adenovirus (HAdV) gene expression and replication. To counteract this, adenoviral early proteins E1B-55K and E4orf6 recruit MPP8 for proteasomal degradation via an E3 ubiquitin ligase, and HUSH factors are inhibited through binding to HAdV proteins and subsequent relocalization.\",\n      \"method\": \"Infection assays with HAdV; co-immunoprecipitation of adenoviral proteins with HUSH components; proteasomal degradation assays; relocalization imaging\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, mechanistic details primarily about MPP8 degradation; PPHLN1 role implied as part of complex but not individually dissected\",\n      \"pmids\": [\"bio_10.1101_2025.02.10.637372\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"OTX2 regulates alternative splicing of PPHLN1 in group 3 medulloblastoma as part of a stem cell splicing program; PPHLN1 is expressed in the most primitive rhombic lip stem cells, and targeting PPHLN1 splicing reduces tumor growth and enhances survival in vivo.\",\n      \"method\": \"OTX2 association with splicing regulators by protein-protein interaction assays; in vivo tumor growth assays with PPHLN1 splicing targeting; survival analysis in animal models\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vivo functional validation of PPHLN1 splicing targeting with survival readout, but mechanistic details of PPHLN1 itself are limited; single study\",\n      \"pmids\": [\"39025928\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Both PPHLN1 and its structural homolog BFARv3 interact with RNA-binding/paraspeckle proteins NONO and SFPQ, as confirmed by reciprocal co-immunoprecipitation and proximity ligation assay, suggesting a role for PPHLN1 in RNA metabolism.\",\n      \"method\": \"Reciprocal co-immunoprecipitation; proximity ligation assay\",\n      \"journal\": \"Biochimica et biophysica acta. Molecular cell research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — reciprocal Co-IP and PLA confirm interaction but functional consequence of PPHLN1-NONO/SFPQ interaction is not directly tested; single lab\",\n      \"pmids\": [\"34175335\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPHLN1 (Periphilin 1) is a core structural subunit of the HUSH (Human Silencing Hub) complex together with TASOR and MPP8, where it contributes to H3K9me3-mediated epigenetic silencing of retrotransposons, unintegrated retroviral DNA, and proviruses; the complex is recruited to target loci partly via NP220, and is antagonized by viral proteins (HIV Vpx/Vpr, adenoviral E1B-55K/E4orf6) that degrade or relocalize its components. Additionally, the PPHLN1 C-terminal region acts as a dimerization domain in the oncogenic FGFR2-PPHLN1 fusion protein found in intrahepatic cholangiocarcinoma, where membrane localization and an active FGFR2 kinase domain are also required for transforming activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPHLN1 (Periphilin 1) is a core structural subunit of the HUSH (Human Silencing Hub) complex, which together with TASOR (FAM208A) and MPP8 (MPHOSPH8) directs H3K9me3-mediated epigenetic silencing of retrotransposons, unintegrated retroviral DNA, and proviruses [#2, #3]. Recruitment to unintegrated retroviral DNA is mediated by the DNA-binding protein NP220, which brings the HUSH complex together with the SETDB1 methyltransferase and HDAC1/HDAC4 to target loci [#3], and the relative stoichiometry of HUSH subunits tunes precise genomic localization for LINE-1 retrotransposon silencing [#5]. This silencing activity is antagonized by viral countermeasures: primate immunodeficiency virus Vpx/Vpr proteins associate with HUSH and direct PPHLN1 and other subunits to DCAF1/CUL4-mediated proteasomal degradation to de-repress proviruses [#2], and the HUSH complex also restricts human adenovirus, which counteracts it via E1B-55K/E4orf6 [#8]. Within mouse embryonic stem cells, PPHLN1 is dispensable for HUSH-mediated control of pluripotency exit, unlike MPP8 or TASOR [#7]. Independently of its silencing role, the PPHLN1 C-terminal region functions as a dimerization domain in the oncogenic FGFR2-PPHLN1 fusion protein found in intrahepatic cholangiocarcinoma, where transforming activity requires an active FGFR2 kinase domain, the PPHLN1-contributed dimerization domain, and membrane localization, driving MAPK/ERK, JAK/STAT3, and PI3K/AKT signaling [#0, #1].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Established that PPHLN1 can act as an oncogenic fusion partner, framing a disease-relevant role distinct from any silencing function.\",\n      \"evidence\": \"RNA-/exome-sequencing identifying t(10;12) fusion plus in vitro transformation assays with FGFR2 inhibitor in intrahepatic cholangiocarcinoma\",\n      \"pmids\": [\"25608663\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which PPHLN1 region drives oncogenicity was not yet defined\",\n        \"No structural or reconstitution data on the fusion\",\n        \"Frequency and clinical scope of the fusion not addressed\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Defined PPHLN1 as one of three core HUSH subunits and showed its degradation is exploited by viruses to de-repress proviruses, establishing its central role in epigenetic silencing.\",\n      \"evidence\": \"Forward genetic screen, reciprocal Co-IP of Vpx with HUSH, knockdown of PPHLN1/FAM208A, and proteasome-dependent degradation Western blots\",\n      \"pmids\": [\"30297740\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular contribution of PPHLN1 to silencing versus TASOR/MPP8 not separated\",\n        \"Structural basis of HUSH assembly not resolved\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed how the HUSH complex is recruited to its targets, answering how PPHLN1-containing HUSH reaches unintegrated retroviral DNA.\",\n      \"evidence\": \"Genome-wide CRISPR-Cas9 screen and ChIP demonstrating NP220-dependent recruitment of HUSH, SETDB1, and HDAC1/4\",\n      \"pmids\": [\"30487602\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct PPHLN1-NP220 contact not demonstrated\",\n        \"How recruitment is targeted at integrated proviruses versus unintegrated DNA unclear\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Linked PPHLN1 to RNA-associated paraspeckle proteins, raising a possible role in RNA metabolism beyond chromatin silencing.\",\n      \"evidence\": \"Reciprocal Co-IP and proximity ligation assay showing PPHLN1 (and homolog BFARv3) interaction with NONO and SFPQ\",\n      \"pmids\": [\"34175335\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Functional consequence of PPHLN1-NONO/SFPQ interaction not tested\",\n        \"Single lab, no orthogonal functional validation\",\n        \"Relationship to HUSH silencing not established\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Dissected the requirements of the FGFR2-PPHLN1 fusion, pinpointing the PPHLN1 moiety as the dimerization module needed for transformation.\",\n      \"evidence\": \"Soft agar/focus assays with kinase-dead, kinase-active, domain-deletion, and membrane-targeting constructs plus pathway inhibitor treatment in RIE-1 and NIH3T3 cells\",\n      \"pmids\": [\"32854034\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of PPHLN1-mediated dimerization not solved\",\n        \"Single lab; in vivo tumor relevance not tested\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed HUSH subunit stoichiometry controls precise genomic localization for LINE-1 silencing, refining how the complex achieves locus specificity.\",\n      \"evidence\": \"In silico structure prediction and MPP8-TASOR interface mutagenesis with LINE-1 silencing assays (preprint)\",\n      \"pmids\": [\"38313255\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Computational structure not experimentally confirmed\",\n        \"PPHLN1-specific contribution to localization not isolated\",\n        \"Preprint, single lab\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Revealed crosstalk between HUSH and PRC1.6 in provirus silencing, broadening the chromatin context of HUSH function.\",\n      \"evidence\": \"Proximity labeling, genetic screen, and ChIP-seq with loss-of-function (preprint)\",\n      \"pmids\": [\"39026796\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"PPHLN1-specific role in PRC1.6 crosstalk not dissected\",\n        \"Preprint, single lab\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated PPHLN1 alternative splicing in a stem cell program driving group 3 medulloblastoma, suggesting a tumor-relevant role distinct from the FGFR2 fusion.\",\n      \"evidence\": \"OTX2-splicing regulator interaction assays and in vivo tumor growth/survival assays with PPHLN1 splicing targeting\",\n      \"pmids\": [\"39025928\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism of the PPHLN1 splice isoform's action not defined\",\n        \"Connection to HUSH silencing function not established\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified an endogenous retroviral microprotein partner of PPHLN1 required for HUSH target repression, hinting at a sensing/regulatory input.\",\n      \"evidence\": \"Co-IP of ERVK3-1 microprotein with PPHLN1 and loss-of-function with HUSH target gene expression readout\",\n      \"pmids\": [\"40699144\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Direct mechanism by which ERVK3-1 modulates PPHLN1/HUSH unknown\",\n        \"Single study, single lab\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated that PPHLN1 is functionally dispensable for HUSH-mediated pluripotency exit, distinguishing it from TASOR and MPP8 in this context.\",\n      \"evidence\": \"CRISPR knockout of PPHLN1 in mESCs with colony morphology and differentiation assays\",\n      \"pmids\": [\"41291012\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether PPHLN1 is dispensable for retrotransposon silencing in the same system not addressed\",\n        \"Negative result for PPHLN1 specifically, single lab\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of PPHLN1 incorporation into HUSH and its precise molecular contribution (versus TASOR/MPP8) to H3K9me3 deposition and locus targeting remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No experimental structure of the PPHLN1-containing HUSH complex\",\n        \"No defined biochemical activity assigned to PPHLN1 itself\",\n        \"Reconciliation of dispensability in pluripotency exit with core-subunit status not established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-4839726\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [\n      \"HUSH complex\"\n    ],\n    \"partners\": [\n      \"TASOR\",\n      \"MPP8\",\n      \"NP220\",\n      \"FGFR2\",\n      \"NONO\",\n      \"SFPQ\",\n      \"ERVK3-1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}