{"gene":"PGBD5","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2015,"finding":"PGBD5 encodes an active DNA transposase that catalyzes cut-and-paste DNA transposition in human cells. This activity requires distinct aspartic acid residues in its transposase domain and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. Transposition occurs genome-wide with precise transposon excision and preference for insertion at TTAA sites.","method":"Transposition assays in human cells; active-site mutagenesis of catalytic aspartic acid residues; whole-genome sequencing of integration sites","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — in-cell transposition assay with active-site mutagenesis and genome-wide sequencing, multiple orthogonal methods in a single rigorous study","pmids":["26406119"],"is_preprint":false},{"year":2017,"finding":"PGBD5 physically associates with genomic PGBD5-specific signal (PSS) sequences and mediates site-specific DNA rearrangements at PSS breakpoints in rhabdoid tumor cells. Ectopic PGBD5 expression in primary immortalized human cells is sufficient to promote cell transformation in vivo. This oncogenic activity requires specific catalytic residues in the transposase domain and functional end-joining (NHEJ) DNA repair.","method":"ChIP/physical association assays with PSS sequences; ectopic expression with catalytic mutants; in vivo transformation assays; assembly-based whole-genome DNA sequencing of rearrangement breakpoints","journal":"Nature genetics","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal methods (ChIP, mutagenesis, in vivo transformation, WGS) in a single rigorous study with functional validation","pmids":["28504702"],"is_preprint":false},{"year":2017,"finding":"PGBD5-induced DNA damage creates a dependency on NHEJ DNA repair; cells deficient in NHEJ cannot tolerate PGBD5 expression. A nuclease activity-deficient PGBD5 mutant does not induce this DNA damage dependency, establishing that the transposase catalytic activity is required. PGBD5-expressing cells accumulate unrepaired DNA damage and undergo apoptosis upon ATR inhibition (AZD6738), identifying a synthetic lethal interaction between PGBD5 transposase activity and ATR-dependent DNA damage signaling.","method":"Functional genetic approaches (NHEJ-deficient mouse and human cells); chemical screen of DNA damage signaling inhibitors; nuclease-dead PGBD5 mutant; endogenous PGBD5 depletion; DNA damage quantification; apoptosis assays","journal":"Science translational medicine","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — epistasis with NHEJ-deficient cells, active-site mutant controls, chemical-genetic screen, and depletion rescue, multiple orthogonal methods","pmids":["29093183"],"is_preprint":false},{"year":2013,"finding":"PGBD5 protein localizes predominantly to the nucleus, but neither DNase I digestion nor high-salt extraction releases it from fractionated mouse brain nuclei, suggesting it does not bind DNA or chromatin in a conventional manner. PGBD5 is preferentially expressed in granule cell lineages of the brain and the CNS.","method":"Subcellular fractionation; DNase I digestion; high-salt extraction of mouse brain nuclei; in situ hybridization data (mouse and human)","journal":"Mobile DNA","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical fractionation with two perturbation conditions (DNase I and high salt), single lab","pmids":["24180413"],"is_preprint":false},{"year":2021,"finding":"Both murine (Mm523) and human (Hs524) PGBD5 isoforms can transpose Tcr-pble (the phylogenetically closest piggyBac-like element to PGBD5) and Ifp2 with similar efficiency. Integration occurs through both proper transposition and improper PGBD5-dependent recombination. PGBD5 recognition of these elements may involve internal palindromic repeats rather than primary sequence of element ends.","method":"Transposition assays in cells using two PGBD5 isoforms and two piggyBac-like elements; phylogenetic analysis; integration site analysis","journal":"Journal of molecular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional transposition assays with two isoforms and two substrates, single lab, multiple element comparisons","pmids":["33539889"],"is_preprint":false},{"year":2024,"finding":"Pgbd5 promotes tumor development in multiple developmentally accurate mouse models of SHH medulloblastoma. Pgbd5-deficient mice do not develop tumors while maintaining normal cerebellar development. Mouse medulloblastomas expressing Pgbd5 have increased somatic structural DNA rearrangements, some carrying PGBD5-specific sequences at their breakpoints, recurrently affecting known tumor suppressors and oncogenes.","method":"Pgbd5-deficient mouse models; mouse models of SHH medulloblastoma; whole-genome sequencing of structural rearrangements; breakpoint sequence analysis","journal":"Science advances","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetically accurate in vivo mouse models with knockout controls, WGS-based structural variant analysis, replicated across multiple tumor models","pmids":["38517960"],"is_preprint":false},{"year":2025,"finding":"EZH2 inhibition induces PGBD5 expression in SMARCB1-deficient epithelioid and rhabdoid tumor cells, promoting DNA damage, at least in part via PGBD5. This creates a synthetic lethal dependency on ATR (but not CHK1) kinase activity, which can be exploited by combined EZH2 and ATR inhibition with improved therapeutic responses in patient-derived tumors in vivo.","method":"Transcriptomic inference; EZH2 inhibitor (tazemetostat) treatment with PGBD5 expression measurement; ATR inhibitor (elimusertib) vs CHK1 inhibitor comparisons; DNA damage assays; patient-derived tumor xenograft models","journal":"The Journal of clinical investigation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mechanistic epistasis (EZH2→PGBD5→ATR dependency) supported by inhibitor selectivity data and in vivo models, single lab","pmids":["40794452"],"is_preprint":false},{"year":2025,"finding":"Human PGBD5 interacts with four species of human piggyBac-like elements (pbles) and promotes their chromosomal integration in cells. PGBD5 binds distinct chromosomal copies of human pbles in a cell type-specific manner and also binds genomic loci containing inverted repeats similar to those in subterminal insect pble ends.","method":"Chromosomal integration assays; chromatin binding assays to endogenous pble copies; cell type comparison experiments","journal":"bioRxiv : the preprint server for biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, binding and integration assays without full biochemical reconstitution or mutagenesis validation","pmids":["40766603"],"is_preprint":true},{"year":2024,"finding":"Knockdown of PGBD5 in glioma cells inhibits migration and invasion, promotes apoptosis, and causes G2/M cell cycle arrest. In vivo, PGBD5 knockdown inhibits Ki67 expression and slows tumor growth. These effects are associated with upregulation of the PPAR signaling pathway, as revealed by transcriptome sequencing.","method":"siRNA knockdown; Transwell migration/invasion assay; flow cytometry (apoptosis, cell cycle); nude mouse tumor transplantation model; transcriptome sequencing","journal":"International journal of oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — loss-of-function with phenotypic readouts and transcriptome-based pathway assignment, single lab, no direct mechanistic epistasis validation of PPAR link","pmids":["38577941"],"is_preprint":false}],"current_model":"PGBD5 is a domesticated piggyBac-family transposase, predominantly expressed in neurons/CNS, that retains active cut-and-paste DNA transposition activity requiring specific catalytic aspartic acid residues and PSS/inverted terminal repeat sequences; in human tumors, this transposase activity drives site-specific genomic rearrangements at PGBD5-specific signal sequences, requires NHEJ for DNA repair of the resulting breaks, and creates a synthetic lethal dependency on ATR kinase—while upstream EZH2 activity represses PGBD5 expression such that EZH2 inhibition de-represses PGBD5 and potentiates ATR inhibitor sensitivity."},"narrative":{"mechanistic_narrative":"PGBD5 is a domesticated piggyBac-family DNA transposase that retains active cut-and-paste transposition activity in human cells, catalyzing precise transposon excision and TTAA-preferential reintegration in a manner dependent on specific catalytic aspartic acid residues and on DNA substrates bearing piggyBac-like inverted terminal repeats [PMID:26406119]. It localizes predominantly to the nucleus and is preferentially expressed in granule cell lineages of the brain and CNS [PMID:24180413], and it recognizes piggyBac-like elements through internal palindromic/inverted-repeat features rather than primary end sequence, mobilizing multiple natural piggyBac-like elements [PMID:33539889]. In tumor cells, PGBD5 physically associates with genomic PGBD5-specific signal (PSS) sequences and drives site-specific structural DNA rearrangements at PSS breakpoints, and its ectopic expression is sufficient to transform primary human cells in vivo; both this oncogenic rearrangement activity and the transformation require intact transposase catalytic residues and functional NHEJ-mediated end joining [PMID:28504702]. The genomic damage PGBD5 generates creates two therapeutically relevant dependencies: cells expressing catalytically active PGBD5 cannot tolerate loss of NHEJ and undergo apoptosis upon ATR inhibition, defining a synthetic-lethal interaction with ATR-dependent DNA-damage signaling [PMID:29093183]. In vivo, Pgbd5 is required for tumor development in developmentally accurate SHH medulloblastoma mouse models, where its activity introduces somatic structural rearrangements—some bearing PGBD5 sequences at breakpoints—that recurrently disrupt tumor suppressors and oncogenes [PMID:38517960]. Upstream, EZH2 represses PGBD5 such that EZH2 inhibition de-represses PGBD5, increases DNA damage, and sensitizes SMARCB1-deficient rhabdoid and epithelioid tumors to ATR (but not CHK1) inhibition [PMID:40794452].","teleology":[{"year":2013,"claim":"Before its enzymatic role was known, the basic localization and expression pattern of PGBD5 had to be established, showing it is a nuclear, neuronally enriched protein with unconventional chromatin association.","evidence":"Subcellular fractionation with DNase I and high-salt extraction of mouse brain nuclei plus in situ hybridization","pmids":["24180413"],"confidence":"Medium","gaps":["Does not define a molecular activity or substrate","Unconventional (non-DNase/non-salt-releasable) nuclear retention left mechanistically unexplained"]},{"year":2015,"claim":"Resolved whether the domesticated PGBD5 retained transposase function by demonstrating it catalyzes bona fide cut-and-paste transposition in human cells, establishing it as an active enzyme rather than an inert relic.","evidence":"In-cell transposition assays, active-site aspartate mutagenesis, and whole-genome integration-site sequencing","pmids":["26406119"],"confidence":"High","gaps":["Did not identify endogenous genomic substrates acted on in vivo","No structural mechanism of catalysis or end recognition"]},{"year":2017,"claim":"Connected the enzymatic activity to disease by showing PGBD5 binds endogenous PSS sequences, drives site-specific rearrangements, and transforms cells—dependent on catalysis and NHEJ.","evidence":"ChIP/physical association to PSS, catalytic mutants, in vivo transformation assays, assembly-based WGS of breakpoints","pmids":["28504702"],"confidence":"High","gaps":["Mechanism by which breaks are channeled to NHEJ not resolved","How PSS recognition differs from transposon end recognition unclear"]},{"year":2017,"claim":"Defined the therapeutic vulnerability created by PGBD5-induced damage, identifying NHEJ dependence and ATR synthetic lethality.","evidence":"NHEJ-deficient cells, nuclease-dead mutant controls, chemical screen of DNA-damage inhibitors, endogenous depletion, ATR inhibitor (AZD6738)","pmids":["29093183"],"confidence":"High","gaps":["Did not establish the in vivo durability of ATR-inhibitor response","Did not address upstream regulation of PGBD5 expression"]},{"year":2021,"claim":"Clarified substrate recognition rules by showing both human and mouse PGBD5 isoforms mobilize the closest natural piggyBac-like elements, likely via internal palindromic repeats.","evidence":"Transposition assays with two isoforms and two piggyBac-like elements, phylogenetics, integration-site analysis","pmids":["33539889"],"confidence":"Medium","gaps":["Internal palindromic repeat dependence inferred, not proven by mutagenesis","Relationship between proper transposition and improper recombination unresolved"]},{"year":2024,"claim":"Established causal in vivo oncogenic requirement for Pgbd5 in a developmentally faithful brain tumor model, linking its rearrangement activity to tumor initiation.","evidence":"Pgbd5-deficient mice, SHH medulloblastoma models, WGS of structural variants and breakpoint analysis","pmids":["38517960"],"confidence":"High","gaps":["Why specific tumor suppressors/oncogenes are recurrently targeted is unexplained","Cell-of-origin determinants of PSS targeting not defined"]},{"year":2024,"claim":"Extended the tumor-promoting role to glioma via loss-of-function phenotypes, with a transcriptome-based link to PPAR signaling.","evidence":"siRNA knockdown, migration/invasion, apoptosis and cell-cycle flow cytometry, xenografts, transcriptome sequencing","pmids":["38577941"],"confidence":"Low","gaps":["PPAR pathway link is correlative transcriptomics without epistatic validation","No demonstration that glioma effects depend on transposase catalytic activity"]},{"year":2025,"claim":"Identified an upstream regulator, showing EZH2 represses PGBD5 and that EZH2 inhibition de-represses it to potentiate ATR-inhibitor sensitivity.","evidence":"Tazemetostat treatment with PGBD5 measurement, ATR (elimusertib) vs CHK1 inhibitor comparison, DNA damage assays, patient-derived xenografts","pmids":["40794452"],"confidence":"Medium","gaps":["Direct vs indirect EZH2 repression of the PGBD5 locus not resolved","DNA damage attributed 'at least in part' to PGBD5, leaving alternative contributors"]},{"year":2025,"claim":"Characterized cell-type-specific binding and mobilization of endogenous human piggyBac-like elements, extending substrate recognition to natural genomic copies.","evidence":"Chromosomal integration and chromatin-binding assays to endogenous pble copies across cell types (preprint)","pmids":["40766603"],"confidence":"Low","gaps":["Preprint without full biochemical reconstitution or mutagenesis validation","Determinants of cell-type-specific binding undefined"]},{"year":null,"claim":"The structural basis of PGBD5 end/PSS recognition and how its breaks are selectively engaged by NHEJ versus other repair pathways remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of catalysis or substrate engagement","Mechanism coupling transposase breaks to NHEJ and ATR signaling not defined","Physiological (non-tumor) function in neurons unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140097","term_label":"catalytic activity, acting on DNA","supporting_discovery_ids":[0,1,4]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[1,7]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[1,5,6]}],"complexes":[],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q8N414","full_name":"PiggyBac transposable element-derived protein 5","aliases":["PiggyBac domain-related protein 5","PiggyBac transposase 5"],"length_aa":524,"mass_kda":58.5,"function":"Transposase that mediates sequence-specific genomic rearrangements (PubMed:26406119, PubMed:28504702). Can induce genomic rearrangements that inactivate the HPRT1 gene (PubMed:27491780)","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q8N414/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PGBD5","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":77,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PIP5K1C","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PGBD5","total_profiled":1310},"omim":[{"mim_id":"621482","title":"NEURODEVELOPMENTAL DISORDER WITH SEIZURES, HYPOTONIA, AND VARIABLE SPASTICITY; NEDSHS","url":"https://www.omim.org/entry/621482"},{"mim_id":"616791","title":"PIGGYBAC TRANSPOSABLE ELEMENT-DERIVED GENE 5; PGBD5","url":"https://www.omim.org/entry/616791"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"brain","ntpm":26.4},{"tissue":"cervix","ntpm":17.0},{"tissue":"pancreas","ntpm":19.1}],"url":"https://www.proteinatlas.org/search/PGBD5"},"hgnc":{"alias_symbol":["DKFZp761A0620","FLJ11413"],"prev_symbol":[]},"alphafold":{"accession":"Q8N414","domains":[{"cath_id":"-","chopping":"118-224_473-516","consensus_level":"high","plddt":94.3323,"start":118,"end":516},{"cath_id":"-","chopping":"249-461","consensus_level":"high","plddt":84.6221,"start":249,"end":461}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N414","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N414-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N414-F1-predicted_aligned_error_v6.png","plddt_mean":80.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PGBD5","jax_strain_url":"https://www.jax.org/strain/search?query=PGBD5"},"sequence":{"accession":"Q8N414","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N414.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N414/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N414"}},"corpus_meta":[{"pmid":"28504702","id":"PMC_28504702","title":"PGBD5 promotes site-specific oncogenic mutations in human tumors.","date":"2017","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28504702","citation_count":70,"is_preprint":false},{"pmid":"26406119","id":"PMC_26406119","title":"Genomic DNA transposition induced by human PGBD5.","date":"2015","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/26406119","citation_count":65,"is_preprint":false},{"pmid":"29093183","id":"PMC_29093183","title":"Therapeutic targeting of PGBD5-induced DNA repair dependency in pediatric solid tumors.","date":"2017","source":"Science translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29093183","citation_count":46,"is_preprint":false},{"pmid":"24180413","id":"PMC_24180413","title":"PGBD5: a neural-specific intron-containing piggyBac transposase domesticated over 500 million years ago and conserved from cephalochordates to humans.","date":"2013","source":"Mobile DNA","url":"https://pubmed.ncbi.nlm.nih.gov/24180413","citation_count":28,"is_preprint":false},{"pmid":"33539889","id":"PMC_33539889","title":"The piggyBac-derived protein 5 (PGBD5) transposes both the closely and the distantly related piggyBac-like elements Tcr-pble and Ifp2.","date":"2021","source":"Journal of molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/33539889","citation_count":10,"is_preprint":false},{"pmid":"38517960","id":"PMC_38517960","title":"Childhood cancer mutagenesis caused by transposase-derived PGBD5.","date":"2024","source":"Science advances","url":"https://pubmed.ncbi.nlm.nih.gov/38517960","citation_count":6,"is_preprint":false},{"pmid":"40794452","id":"PMC_40794452","title":"Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas.","date":"2025","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/40794452","citation_count":3,"is_preprint":false},{"pmid":"38766189","id":"PMC_38766189","title":"Epigenetic targeting of PGBD5-dependent DNA damage in SMARCB1-deficient sarcomas.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38766189","citation_count":2,"is_preprint":false},{"pmid":"39747879","id":"PMC_39747879","title":"CHST3, PGBD5, and SLIT2 can be identified as potential genes for the diagnosis and treatment of osteoporosis and sarcopenia.","date":"2025","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/39747879","citation_count":1,"is_preprint":false},{"pmid":"38577941","id":"PMC_38577941","title":"Knockdown of PGBD5 inhibits the malignant progression of glioma through upregulation of the PPAR pathway.","date":"2024","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/38577941","citation_count":1,"is_preprint":false},{"pmid":"40766603","id":"PMC_40766603","title":"The piggyBac derived transposase 5 (PGBD5) can interact with human piggyBac-like elements.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40766603","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.07.31.667870","title":"The  <i>piggyBac</i>  derived transposase 5 (PGBD5) can interact with human  <i>piggyBac</i>  -like elements","date":"2025-08-02","source":"bioRxiv","url":"https://doi.org/10.1101/2025.07.31.667870","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7922,"output_tokens":2462,"usd":0.030348,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9748,"output_tokens":3187,"usd":0.064208,"stage2_stop_reason":"end_turn"},"total_usd":0.094556,"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\": \"PGBD5 encodes an active DNA transposase that catalyzes cut-and-paste DNA transposition in human cells. This activity requires distinct aspartic acid residues in its transposase domain and specific DNA sequences containing inverted terminal repeats with similarity to piggyBac transposons. Transposition occurs genome-wide with precise transposon excision and preference for insertion at TTAA sites.\",\n      \"method\": \"Transposition assays in human cells; active-site mutagenesis of catalytic aspartic acid residues; whole-genome sequencing of integration sites\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in-cell transposition assay with active-site mutagenesis and genome-wide sequencing, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"26406119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PGBD5 physically associates with genomic PGBD5-specific signal (PSS) sequences and mediates site-specific DNA rearrangements at PSS breakpoints in rhabdoid tumor cells. Ectopic PGBD5 expression in primary immortalized human cells is sufficient to promote cell transformation in vivo. This oncogenic activity requires specific catalytic residues in the transposase domain and functional end-joining (NHEJ) DNA repair.\",\n      \"method\": \"ChIP/physical association assays with PSS sequences; ectopic expression with catalytic mutants; in vivo transformation assays; assembly-based whole-genome DNA sequencing of rearrangement breakpoints\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal methods (ChIP, mutagenesis, in vivo transformation, WGS) in a single rigorous study with functional validation\",\n      \"pmids\": [\"28504702\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PGBD5-induced DNA damage creates a dependency on NHEJ DNA repair; cells deficient in NHEJ cannot tolerate PGBD5 expression. A nuclease activity-deficient PGBD5 mutant does not induce this DNA damage dependency, establishing that the transposase catalytic activity is required. PGBD5-expressing cells accumulate unrepaired DNA damage and undergo apoptosis upon ATR inhibition (AZD6738), identifying a synthetic lethal interaction between PGBD5 transposase activity and ATR-dependent DNA damage signaling.\",\n      \"method\": \"Functional genetic approaches (NHEJ-deficient mouse and human cells); chemical screen of DNA damage signaling inhibitors; nuclease-dead PGBD5 mutant; endogenous PGBD5 depletion; DNA damage quantification; apoptosis assays\",\n      \"journal\": \"Science translational medicine\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — epistasis with NHEJ-deficient cells, active-site mutant controls, chemical-genetic screen, and depletion rescue, multiple orthogonal methods\",\n      \"pmids\": [\"29093183\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"PGBD5 protein localizes predominantly to the nucleus, but neither DNase I digestion nor high-salt extraction releases it from fractionated mouse brain nuclei, suggesting it does not bind DNA or chromatin in a conventional manner. PGBD5 is preferentially expressed in granule cell lineages of the brain and the CNS.\",\n      \"method\": \"Subcellular fractionation; DNase I digestion; high-salt extraction of mouse brain nuclei; in situ hybridization data (mouse and human)\",\n      \"journal\": \"Mobile DNA\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical fractionation with two perturbation conditions (DNase I and high salt), single lab\",\n      \"pmids\": [\"24180413\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Both murine (Mm523) and human (Hs524) PGBD5 isoforms can transpose Tcr-pble (the phylogenetically closest piggyBac-like element to PGBD5) and Ifp2 with similar efficiency. Integration occurs through both proper transposition and improper PGBD5-dependent recombination. PGBD5 recognition of these elements may involve internal palindromic repeats rather than primary sequence of element ends.\",\n      \"method\": \"Transposition assays in cells using two PGBD5 isoforms and two piggyBac-like elements; phylogenetic analysis; integration site analysis\",\n      \"journal\": \"Journal of molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional transposition assays with two isoforms and two substrates, single lab, multiple element comparisons\",\n      \"pmids\": [\"33539889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Pgbd5 promotes tumor development in multiple developmentally accurate mouse models of SHH medulloblastoma. Pgbd5-deficient mice do not develop tumors while maintaining normal cerebellar development. Mouse medulloblastomas expressing Pgbd5 have increased somatic structural DNA rearrangements, some carrying PGBD5-specific sequences at their breakpoints, recurrently affecting known tumor suppressors and oncogenes.\",\n      \"method\": \"Pgbd5-deficient mouse models; mouse models of SHH medulloblastoma; whole-genome sequencing of structural rearrangements; breakpoint sequence analysis\",\n      \"journal\": \"Science advances\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetically accurate in vivo mouse models with knockout controls, WGS-based structural variant analysis, replicated across multiple tumor models\",\n      \"pmids\": [\"38517960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"EZH2 inhibition induces PGBD5 expression in SMARCB1-deficient epithelioid and rhabdoid tumor cells, promoting DNA damage, at least in part via PGBD5. This creates a synthetic lethal dependency on ATR (but not CHK1) kinase activity, which can be exploited by combined EZH2 and ATR inhibition with improved therapeutic responses in patient-derived tumors in vivo.\",\n      \"method\": \"Transcriptomic inference; EZH2 inhibitor (tazemetostat) treatment with PGBD5 expression measurement; ATR inhibitor (elimusertib) vs CHK1 inhibitor comparisons; DNA damage assays; patient-derived tumor xenograft models\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mechanistic epistasis (EZH2→PGBD5→ATR dependency) supported by inhibitor selectivity data and in vivo models, single lab\",\n      \"pmids\": [\"40794452\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Human PGBD5 interacts with four species of human piggyBac-like elements (pbles) and promotes their chromosomal integration in cells. PGBD5 binds distinct chromosomal copies of human pbles in a cell type-specific manner and also binds genomic loci containing inverted repeats similar to those in subterminal insect pble ends.\",\n      \"method\": \"Chromosomal integration assays; chromatin binding assays to endogenous pble copies; cell type comparison experiments\",\n      \"journal\": \"bioRxiv : the preprint server for biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, binding and integration assays without full biochemical reconstitution or mutagenesis validation\",\n      \"pmids\": [\"40766603\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Knockdown of PGBD5 in glioma cells inhibits migration and invasion, promotes apoptosis, and causes G2/M cell cycle arrest. In vivo, PGBD5 knockdown inhibits Ki67 expression and slows tumor growth. These effects are associated with upregulation of the PPAR signaling pathway, as revealed by transcriptome sequencing.\",\n      \"method\": \"siRNA knockdown; Transwell migration/invasion assay; flow cytometry (apoptosis, cell cycle); nude mouse tumor transplantation model; transcriptome sequencing\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — loss-of-function with phenotypic readouts and transcriptome-based pathway assignment, single lab, no direct mechanistic epistasis validation of PPAR link\",\n      \"pmids\": [\"38577941\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PGBD5 is a domesticated piggyBac-family transposase, predominantly expressed in neurons/CNS, that retains active cut-and-paste DNA transposition activity requiring specific catalytic aspartic acid residues and PSS/inverted terminal repeat sequences; in human tumors, this transposase activity drives site-specific genomic rearrangements at PGBD5-specific signal sequences, requires NHEJ for DNA repair of the resulting breaks, and creates a synthetic lethal dependency on ATR kinase—while upstream EZH2 activity represses PGBD5 expression such that EZH2 inhibition de-represses PGBD5 and potentiates ATR inhibitor sensitivity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PGBD5 is a domesticated piggyBac-family DNA transposase that retains active cut-and-paste transposition activity in human cells, catalyzing precise transposon excision and TTAA-preferential reintegration in a manner dependent on specific catalytic aspartic acid residues and on DNA substrates bearing piggyBac-like inverted terminal repeats [#0]. It localizes predominantly to the nucleus and is preferentially expressed in granule cell lineages of the brain and CNS [#3], and it recognizes piggyBac-like elements through internal palindromic/inverted-repeat features rather than primary end sequence, mobilizing multiple natural piggyBac-like elements [#4]. In tumor cells, PGBD5 physically associates with genomic PGBD5-specific signal (PSS) sequences and drives site-specific structural DNA rearrangements at PSS breakpoints, and its ectopic expression is sufficient to transform primary human cells in vivo; both this oncogenic rearrangement activity and the transformation require intact transposase catalytic residues and functional NHEJ-mediated end joining [#1]. The genomic damage PGBD5 generates creates two therapeutically relevant dependencies: cells expressing catalytically active PGBD5 cannot tolerate loss of NHEJ and undergo apoptosis upon ATR inhibition, defining a synthetic-lethal interaction with ATR-dependent DNA-damage signaling [#2]. In vivo, Pgbd5 is required for tumor development in developmentally accurate SHH medulloblastoma mouse models, where its activity introduces somatic structural rearrangements—some bearing PGBD5 sequences at breakpoints—that recurrently disrupt tumor suppressors and oncogenes [#5]. Upstream, EZH2 represses PGBD5 such that EZH2 inhibition de-represses PGBD5, increases DNA damage, and sensitizes SMARCB1-deficient rhabdoid and epithelioid tumors to ATR (but not CHK1) inhibition [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Before its enzymatic role was known, the basic localization and expression pattern of PGBD5 had to be established, showing it is a nuclear, neuronally enriched protein with unconventional chromatin association.\",\n      \"evidence\": \"Subcellular fractionation with DNase I and high-salt extraction of mouse brain nuclei plus in situ hybridization\",\n      \"pmids\": [\"24180413\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not define a molecular activity or substrate\", \"Unconventional (non-DNase/non-salt-releasable) nuclear retention left mechanistically unexplained\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Resolved whether the domesticated PGBD5 retained transposase function by demonstrating it catalyzes bona fide cut-and-paste transposition in human cells, establishing it as an active enzyme rather than an inert relic.\",\n      \"evidence\": \"In-cell transposition assays, active-site aspartate mutagenesis, and whole-genome integration-site sequencing\",\n      \"pmids\": [\"26406119\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify endogenous genomic substrates acted on in vivo\", \"No structural mechanism of catalysis or end recognition\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected the enzymatic activity to disease by showing PGBD5 binds endogenous PSS sequences, drives site-specific rearrangements, and transforms cells—dependent on catalysis and NHEJ.\",\n      \"evidence\": \"ChIP/physical association to PSS, catalytic mutants, in vivo transformation assays, assembly-based WGS of breakpoints\",\n      \"pmids\": [\"28504702\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which breaks are channeled to NHEJ not resolved\", \"How PSS recognition differs from transposon end recognition unclear\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Defined the therapeutic vulnerability created by PGBD5-induced damage, identifying NHEJ dependence and ATR synthetic lethality.\",\n      \"evidence\": \"NHEJ-deficient cells, nuclease-dead mutant controls, chemical screen of DNA-damage inhibitors, endogenous depletion, ATR inhibitor (AZD6738)\",\n      \"pmids\": [\"29093183\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not establish the in vivo durability of ATR-inhibitor response\", \"Did not address upstream regulation of PGBD5 expression\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Clarified substrate recognition rules by showing both human and mouse PGBD5 isoforms mobilize the closest natural piggyBac-like elements, likely via internal palindromic repeats.\",\n      \"evidence\": \"Transposition assays with two isoforms and two piggyBac-like elements, phylogenetics, integration-site analysis\",\n      \"pmids\": [\"33539889\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Internal palindromic repeat dependence inferred, not proven by mutagenesis\", \"Relationship between proper transposition and improper recombination unresolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established causal in vivo oncogenic requirement for Pgbd5 in a developmentally faithful brain tumor model, linking its rearrangement activity to tumor initiation.\",\n      \"evidence\": \"Pgbd5-deficient mice, SHH medulloblastoma models, WGS of structural variants and breakpoint analysis\",\n      \"pmids\": [\"38517960\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why specific tumor suppressors/oncogenes are recurrently targeted is unexplained\", \"Cell-of-origin determinants of PSS targeting not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended the tumor-promoting role to glioma via loss-of-function phenotypes, with a transcriptome-based link to PPAR signaling.\",\n      \"evidence\": \"siRNA knockdown, migration/invasion, apoptosis and cell-cycle flow cytometry, xenografts, transcriptome sequencing\",\n      \"pmids\": [\"38577941\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"PPAR pathway link is correlative transcriptomics without epistatic validation\", \"No demonstration that glioma effects depend on transposase catalytic activity\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified an upstream regulator, showing EZH2 represses PGBD5 and that EZH2 inhibition de-represses it to potentiate ATR-inhibitor sensitivity.\",\n      \"evidence\": \"Tazemetostat treatment with PGBD5 measurement, ATR (elimusertib) vs CHK1 inhibitor comparison, DNA damage assays, patient-derived xenografts\",\n      \"pmids\": [\"40794452\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect EZH2 repression of the PGBD5 locus not resolved\", \"DNA damage attributed 'at least in part' to PGBD5, leaving alternative contributors\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Characterized cell-type-specific binding and mobilization of endogenous human piggyBac-like elements, extending substrate recognition to natural genomic copies.\",\n      \"evidence\": \"Chromosomal integration and chromatin-binding assays to endogenous pble copies across cell types (preprint)\",\n      \"pmids\": [\"40766603\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Preprint without full biochemical reconstitution or mutagenesis validation\", \"Determinants of cell-type-specific binding undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of PGBD5 end/PSS recognition and how its breaks are selectively engaged by NHEJ versus other repair pathways remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of catalysis or substrate engagement\", \"Mechanism coupling transposase breaks to NHEJ and ATR signaling not defined\", \"Physiological (non-tumor) function in neurons unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140097\", \"supporting_discovery_ids\": [0, 1, 4]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [1, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [1, 5, 6]}\n    ],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}