{"gene":"SPIDR","run_date":"2026-06-10T07:46:40","timeline":{"discoveries":[{"year":2013,"finding":"SPIDR (scaffolding protein involved in DNA repair) independently interacts with both BLM helicase and RAD51, and promotes the formation of a BLM/RAD51-containing complex. Depletion of SPIDR increases sister chromatid exchange rates and causes defects in homologous recombination, establishing SPIDR as a scaffold linking BLM and RAD51 in a multifunctional DNA-processing complex.","method":"Co-immunoprecipitation, siRNA depletion with sister chromatid exchange assay, HR reporter assay, DNA damage sensitivity assays, immunofluorescence foci analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP identifying two binding partners, multiple orthogonal functional assays (SCE, HR reporter, damage sensitivity, foci), replicated by subsequent independent studies","pmids":["23509288"],"is_preprint":false},{"year":2021,"finding":"SPIDR functions as part of the SWS1-SWSAP1-SPIDR complex to control distinct types of homology-directed repair (HDR). This complex is required for stable RAD51 assembly at DNA damage sites, is critical for inter-homolog HDR (the first mitotic factor identified specifically for this function), drives high-level sister chromatid exchange, promotes long-range loss of heterozygosity, and is required for the poor growth phenotype of BLM-deficient cells. Genetic epistasis shows SWSAP1 loss prolongs Blm-mutant embryo survival.","method":"CRISPR/Cas9 knockout, genetic epistasis in mouse models, HDR pathway-specific reporter assays, RAD51 foci analysis, sister chromatid exchange assay","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods including KO mouse models, epistasis analysis, pathway-specific HDR assays, and RAD51 foci quantification across multiple labs","pmids":["34253720"],"is_preprint":false},{"year":2019,"finding":"SPIDR interacts with SWS1 and SWSAP1 (the human Shu complex) and also with PDS5B, forming a complex that functions in the same genetic pathway upon DNA damage. This complex promotes RAD51 recruitment to DNA repair foci, regulates replication fork restart after stalling, and is required for normal sister chromatid exchange levels.","method":"Co-immunoprecipitation, CRISPR/Cas9 deletion of SWS1 and SWSAP1, RAD51 foci analysis, sister chromatid exchange assay, DNA damage sensitivity assay (MMS, MMC)","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP identifying novel complex members, CRISPR KO with multiple orthogonal functional readouts, genetic epistasis established","pmids":["31665741"],"is_preprint":false},{"year":2023,"finding":"SPIDR regulates the assembly or stability of RAD51/DMC1 nucleoprotein filaments on ssDNA during meiosis. Knockout of Spidr in male mice causes complete meiotic arrest with defects in synapsis and crossover formation, leading to male infertility. In females, Spidr loss causes subfertility, and this is partially rescued by ablation of the DNA damage checkpoint kinase CHK2 in females but not males.","method":"Conditional knockout mouse model, meiotic spread analysis, RAD51/DMC1 foci immunofluorescence, synapsis analysis, genetic epistasis with CHK2 knockout","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo KO mouse model with defined cellular phenotypes, multiple orthogonal readouts, genetic epistasis with checkpoint kinase","pmids":["36938872"],"is_preprint":false},{"year":2017,"finding":"A biallelic stop-gain mutation in SPIDR (c.839G>A, p.W280*) alters homologous recombination activity in human patient cells, resulting in accumulation of 53BP1-labeled DSBs post-ionizing radiation and γH2AX-labeled damage during unperturbed growth, establishing SPIDR as required for HR in vivo in humans.","method":"Whole-exome sequencing, EGFP-based DSB repair pathway assay, 53BP1 and γH2AX immunofluorescence in patient blood-derived cells","journal":"The Journal of clinical endocrinology and metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human loss-of-function variant with functional HR assay and DNA damage marker analysis, single lab, patient cells only","pmids":["27967308"],"is_preprint":false},{"year":2021,"finding":"A homozygous nonsense variant in SPIDR (c.814C>T, R272*) in a human patient causes chromosomal instability manifesting as increased mitomycin C-induced DNA breaks and aberrant metaphases, consistent with impairment of the RAD51 pathway. Notably, sister chromatid exchanges were normal (unlike BLM pathway defects), indicating SPIDR's primary in vivo role is through RAD51 rather than BLM.","method":"Targeted next-generation sequencing, mitomycin C-induced chromosome breakage assay, metaphase analysis, sister chromatid exchange assay in patient cells","journal":"Clinical genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — human loss-of-function variant with mechanistically informative negative SCE result and positive chromosome instability assay, single lab, patient cells","pmids":["34697795"],"is_preprint":false},{"year":2024,"finding":"NRF1 transcription factor activates SPIDR transcription by binding to a super enhancer (SE) region of SPIDR (confirmed by ChIP-qPCR). SPIDR depletion in HCC cells increases reactive oxygen species, malondialdehyde, and γH2AX levels, and decreases SOD levels and cell proliferation under oxidative stress; overexpression of SPIDR partially rescues effects of NRF1 silencing, placing SPIDR downstream of NRF1 in oxidative stress response.","method":"ChIP-qPCR for NRF1 binding and H3K27ac at SPIDR SE, siRNA knockdown, SPIDR overexpression rescue, ROS/MDA/SOD/γH2AX assays, JQ1 BET inhibitor treatment","journal":"BMC gastroenterology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP-qPCR for direct transcription factor binding plus epistasis rescue experiment, single lab, multiple functional readouts","pmids":["38438958"],"is_preprint":false}],"current_model":"SPIDR is a scaffolding protein that forms part of the SWS1-SWSAP1-SPIDR complex, physically bridging BLM helicase and RAD51/DMC1 recombinases to coordinate homologous recombination (HR): it promotes stable assembly of RAD51 (and DMC1 during meiosis) at DNA damage sites, facilitates inter-homolog HDR, drives sister chromatid exchange, and is essential for meiotic synapsis and crossover formation in male mice; its transcription is activated by NRF1 via a super enhancer, and loss-of-function mutations in humans cause chromosomal instability, primary ovarian insufficiency, and gonadal dysgenesis."},"narrative":{"mechanistic_narrative":"SPIDR (scaffolding protein involved in DNA repair) is a scaffold that coordinates homologous recombination by physically and independently bridging BLM helicase and the RAD51 recombinase, promoting assembly of a BLM/RAD51-containing complex; its depletion elevates sister chromatid exchange and impairs HR [PMID:23509288]. SPIDR operates as part of the SWS1–SWSAP1–SPIDR complex (the human Shu complex), additionally engaging PDS5B, and this complex is required for stable RAD51 loading at damage sites, controls distinct homology-directed repair outcomes including inter-homolog HDR, regulates replication fork restart after stalling, and underlies the poor growth of BLM-deficient cells [PMID:34253720, PMID:31665741]. During meiosis SPIDR governs assembly or stability of RAD51/DMC1 nucleoprotein filaments on ssDNA, and its loss in male mice causes complete meiotic arrest with synapsis and crossover defects, while female subfertility is partially rescued by ablation of the checkpoint kinase CHK2 [PMID:36938872]. Biallelic loss-of-function mutations in humans impair HR and produce chromosomal instability, with one nonsense variant leaving sister chromatid exchange normal, indicating SPIDR acts in vivo chiefly through the RAD51 rather than the BLM arm [PMID:27967308, PMID:34697795]. SPIDR transcription is activated by NRF1 binding a super enhancer, placing SPIDR downstream of NRF1 in the oxidative stress response [PMID:38438958].","teleology":[{"year":2013,"claim":"Established that a single protein could physically couple BLM helicase to RAD51, answering how these recombination factors are co-assembled into one DNA-processing complex.","evidence":"Reciprocal Co-IP, siRNA depletion with SCE and HR reporter assays, damage sensitivity and foci analysis in human cells","pmids":["23509288"],"confidence":"High","gaps":["Did not define which domains of SPIDR bind BLM versus RAD51","No in vivo or organismal phenotype established"]},{"year":2017,"claim":"Demonstrated SPIDR is required for HR in humans, connecting the molecular scaffold to a disease-relevant DNA repair defect.","evidence":"Whole-exome sequencing of a biallelic stop-gain variant plus EGFP DSB repair assay and 53BP1/γH2AX immunofluorescence in patient cells","pmids":["27967308"],"confidence":"Medium","gaps":["Single lab, patient cells only","Did not separate BLM-dependent from RAD51-dependent contributions"]},{"year":2019,"claim":"Placed SPIDR within a defined SWS1–SWSAP1 (Shu) complex with PDS5B, clarifying the protein assembly through which it promotes RAD51 recruitment and fork restart.","evidence":"Co-IP, CRISPR deletion of SWS1/SWSAP1, RAD51 foci, SCE, and MMS/MMC sensitivity with epistasis","pmids":["31665741"],"confidence":"High","gaps":["Stoichiometry and architecture of the complex not resolved","Mechanism of PDS5B linkage to RAD51 loading unclear"]},{"year":2021,"claim":"Resolved the pathway-specific function of the complex, identifying it as the first mitotic factor specific to inter-homolog HDR and genetically epistatic to BLM.","evidence":"CRISPR KO, mouse genetic epistasis with Blm, pathway-specific HDR reporters, RAD51 foci and SCE assays","pmids":["34253720"],"confidence":"High","gaps":["Biochemical mechanism distinguishing inter-homolog from inter-sister repair not defined"]},{"year":2021,"claim":"Showed that a human SPIDR null variant produces chromosomal instability with normal SCE, dissecting SPIDR's primary in vivo role toward RAD51 rather than BLM.","evidence":"Targeted NGS, mitomycin C breakage and metaphase analysis, and SCE assay in patient cells","pmids":["34697795"],"confidence":"Medium","gaps":["Single patient/lab","Discordance with cell-line SCE phenotypes not mechanistically reconciled"]},{"year":2023,"claim":"Extended SPIDR function to meiosis, showing it controls RAD51/DMC1 filament assembly required for synapsis and crossover formation in vivo.","evidence":"Conditional KO mouse, meiotic spreads, RAD51/DMC1 foci, synapsis analysis, CHK2 epistasis","pmids":["36938872"],"confidence":"High","gaps":["Why CHK2 ablation rescues females but not males is unexplained","Direct biochemical effect on filament nucleation versus stabilization not separated"]},{"year":2024,"claim":"Identified upstream transcriptional control, showing NRF1 drives SPIDR expression via a super enhancer to support an oxidative stress response.","evidence":"ChIP-qPCR for NRF1/H3K27ac, siRNA knockdown, overexpression rescue, ROS/MDA/SOD/γH2AX assays with JQ1 in HCC cells","pmids":["38438958"],"confidence":"Medium","gaps":["Single lab/cell-type context","How HR scaffolding relates mechanistically to ROS handling not established"]},{"year":null,"claim":"The structural basis of how SPIDR simultaneously engages BLM, RAD51/DMC1, and the SWS1–SWSAP1–PDS5B complex, and how it biases repair toward inter-homolog HDR, remains unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of SPIDR or its complexes","Domain-level mapping of partner-binding interfaces absent","Mechanism coupling transcriptional control to repair output unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,2]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[0,1,2,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,2,4]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[0,1,2,4,5]},{"term_id":"R-HSA-1474165","term_label":"Reproduction","supporting_discovery_ids":[3]}],"complexes":["SWS1-SWSAP1-SPIDR (Shu) complex","BLM/RAD51-containing complex"],"partners":["BLM","RAD51","SWS1","SWSAP1","PDS5B","DMC1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q14159","full_name":"DNA repair-scaffolding protein","aliases":["Scaffolding protein involved in DNA repair"],"length_aa":915,"mass_kda":100.3,"function":"Plays a role in DNA double-strand break (DBS) repair via homologous recombination (HR). Serves as a scaffolding protein that helps to promote the recruitment of DNA-processing enzymes like the helicase BLM and recombinase RAD51 to site of DNA damage, and hence contributes to maintain genomic integrity","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q14159/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SPIDR","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/SPIDR","total_profiled":1310},"omim":[{"mim_id":"619665","title":"OVARIAN DYSGENESIS 9; ODG9","url":"https://www.omim.org/entry/619665"},{"mim_id":"615384","title":"SCAFFOLDING PROTEIN INVOLVED IN DNA REPAIR; SPIDR","url":"https://www.omim.org/entry/615384"},{"mim_id":"615383","title":"FIDGETIN-LIKE PROTEIN 1; FIGNL1","url":"https://www.omim.org/entry/615383"},{"mim_id":"604610","title":"RECQ PROTEIN-LIKE 3; RECQL3","url":"https://www.omim.org/entry/604610"},{"mim_id":"233300","title":"OVARIAN DYSGENESIS 1; ODG1","url":"https://www.omim.org/entry/233300"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SPIDR"},"hgnc":{"alias_symbol":[],"prev_symbol":["KIAA0146"]},"alphafold":{"accession":"Q14159","domains":[{"cath_id":"2.40.50.120","chopping":"298-321_338-389","consensus_level":"medium","plddt":83.5568,"start":298,"end":389},{"cath_id":"2.40.50.140","chopping":"462-495_514-581_599-626","consensus_level":"high","plddt":86.0792,"start":462,"end":626},{"cath_id":"2.40.50.140","chopping":"641-743","consensus_level":"high","plddt":82.3078,"start":641,"end":743},{"cath_id":"-","chopping":"776-802_829-903","consensus_level":"high","plddt":87.2257,"start":776,"end":903}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14159","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q14159-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q14159-F1-predicted_aligned_error_v6.png","plddt_mean":61.97},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SPIDR","jax_strain_url":"https://www.jax.org/strain/search?query=SPIDR"},"sequence":{"accession":"Q14159","fasta_url":"https://rest.uniprot.org/uniprotkb/Q14159.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q14159/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q14159"}},"corpus_meta":[{"pmid":"23509288","id":"PMC_23509288","title":"Scaffolding protein SPIDR/KIAA0146 connects the Bloom syndrome helicase with homologous recombination repair.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/23509288","citation_count":61,"is_preprint":false},{"pmid":"27967308","id":"PMC_27967308","title":"A Biallelic Mutation in the Homologous Recombination Repair Gene SPIDR Is Associated With Human Gonadal Dysgenesis.","date":"2017","source":"The Journal of clinical endocrinology and metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/27967308","citation_count":45,"is_preprint":false},{"pmid":"34253720","id":"PMC_34253720","title":"Distinct pathways of homologous recombination controlled by the SWS1-SWSAP1-SPIDR complex.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34253720","citation_count":38,"is_preprint":false},{"pmid":"31665741","id":"PMC_31665741","title":"The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31665741","citation_count":36,"is_preprint":false},{"pmid":"31624232","id":"PMC_31624232","title":"Circ-Spidr enhances axon regeneration after peripheral nerve injury.","date":"2019","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/31624232","citation_count":36,"is_preprint":false},{"pmid":"40701149","id":"PMC_40701149","title":"SPIDR enables multiplexed mapping of RNA-protein interactions and uncovers a mechanism for selective translational suppression upon cell stress.","date":"2025","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/40701149","citation_count":17,"is_preprint":false},{"pmid":"36938872","id":"PMC_36938872","title":"SPIDR is required for homologous recombination during mammalian meiosis.","date":"2023","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/36938872","citation_count":13,"is_preprint":false},{"pmid":"34697795","id":"PMC_34697795","title":"A SPIDR homozygous nonsense pathogenic variant in isolated primary ovarian insufficiency with chromosomal instability.","date":"2021","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/34697795","citation_count":12,"is_preprint":false},{"pmid":"37333139","id":"PMC_37333139","title":"SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37333139","citation_count":10,"is_preprint":false},{"pmid":"23603433","id":"PMC_23603433","title":"Instability at the FRA8I common fragile site disrupts the genomic integrity of the KIAA0146, CEBPD and PRKDC genes in colorectal cancer.","date":"2013","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/23603433","citation_count":10,"is_preprint":false},{"pmid":"29661129","id":"PMC_29661129","title":"SPIDR: small-molecule peptide-influenced drug repurposing.","date":"2018","source":"BMC bioinformatics","url":"https://pubmed.ncbi.nlm.nih.gov/29661129","citation_count":9,"is_preprint":false},{"pmid":"38438958","id":"PMC_38438958","title":"Nuclear respiratory factor 1 regulates super enhancer-controlled SPIDR to protect hepatocellular carcinoma cells from oxidative stress.","date":"2024","source":"BMC gastroenterology","url":"https://pubmed.ncbi.nlm.nih.gov/38438958","citation_count":2,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7954,"output_tokens":2111,"usd":0.027763,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9140,"output_tokens":2640,"usd":0.05585,"stage2_stop_reason":"end_turn"},"total_usd":0.083613,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"SPIDR (scaffolding protein involved in DNA repair) independently interacts with both BLM helicase and RAD51, and promotes the formation of a BLM/RAD51-containing complex. Depletion of SPIDR increases sister chromatid exchange rates and causes defects in homologous recombination, establishing SPIDR as a scaffold linking BLM and RAD51 in a multifunctional DNA-processing complex.\",\n      \"method\": \"Co-immunoprecipitation, siRNA depletion with sister chromatid exchange assay, HR reporter assay, DNA damage sensitivity assays, immunofluorescence foci analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP identifying two binding partners, multiple orthogonal functional assays (SCE, HR reporter, damage sensitivity, foci), replicated by subsequent independent studies\",\n      \"pmids\": [\"23509288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"SPIDR functions as part of the SWS1-SWSAP1-SPIDR complex to control distinct types of homology-directed repair (HDR). This complex is required for stable RAD51 assembly at DNA damage sites, is critical for inter-homolog HDR (the first mitotic factor identified specifically for this function), drives high-level sister chromatid exchange, promotes long-range loss of heterozygosity, and is required for the poor growth phenotype of BLM-deficient cells. Genetic epistasis shows SWSAP1 loss prolongs Blm-mutant embryo survival.\",\n      \"method\": \"CRISPR/Cas9 knockout, genetic epistasis in mouse models, HDR pathway-specific reporter assays, RAD51 foci analysis, sister chromatid exchange assay\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods including KO mouse models, epistasis analysis, pathway-specific HDR assays, and RAD51 foci quantification across multiple labs\",\n      \"pmids\": [\"34253720\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SPIDR interacts with SWS1 and SWSAP1 (the human Shu complex) and also with PDS5B, forming a complex that functions in the same genetic pathway upon DNA damage. This complex promotes RAD51 recruitment to DNA repair foci, regulates replication fork restart after stalling, and is required for normal sister chromatid exchange levels.\",\n      \"method\": \"Co-immunoprecipitation, CRISPR/Cas9 deletion of SWS1 and SWSAP1, RAD51 foci analysis, sister chromatid exchange assay, DNA damage sensitivity assay (MMS, MMC)\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP identifying novel complex members, CRISPR KO with multiple orthogonal functional readouts, genetic epistasis established\",\n      \"pmids\": [\"31665741\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SPIDR regulates the assembly or stability of RAD51/DMC1 nucleoprotein filaments on ssDNA during meiosis. Knockout of Spidr in male mice causes complete meiotic arrest with defects in synapsis and crossover formation, leading to male infertility. In females, Spidr loss causes subfertility, and this is partially rescued by ablation of the DNA damage checkpoint kinase CHK2 in females but not males.\",\n      \"method\": \"Conditional knockout mouse model, meiotic spread analysis, RAD51/DMC1 foci immunofluorescence, synapsis analysis, genetic epistasis with CHK2 knockout\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo KO mouse model with defined cellular phenotypes, multiple orthogonal readouts, genetic epistasis with checkpoint kinase\",\n      \"pmids\": [\"36938872\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"A biallelic stop-gain mutation in SPIDR (c.839G>A, p.W280*) alters homologous recombination activity in human patient cells, resulting in accumulation of 53BP1-labeled DSBs post-ionizing radiation and γH2AX-labeled damage during unperturbed growth, establishing SPIDR as required for HR in vivo in humans.\",\n      \"method\": \"Whole-exome sequencing, EGFP-based DSB repair pathway assay, 53BP1 and γH2AX immunofluorescence in patient blood-derived cells\",\n      \"journal\": \"The Journal of clinical endocrinology and metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human loss-of-function variant with functional HR assay and DNA damage marker analysis, single lab, patient cells only\",\n      \"pmids\": [\"27967308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"A homozygous nonsense variant in SPIDR (c.814C>T, R272*) in a human patient causes chromosomal instability manifesting as increased mitomycin C-induced DNA breaks and aberrant metaphases, consistent with impairment of the RAD51 pathway. Notably, sister chromatid exchanges were normal (unlike BLM pathway defects), indicating SPIDR's primary in vivo role is through RAD51 rather than BLM.\",\n      \"method\": \"Targeted next-generation sequencing, mitomycin C-induced chromosome breakage assay, metaphase analysis, sister chromatid exchange assay in patient cells\",\n      \"journal\": \"Clinical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — human loss-of-function variant with mechanistically informative negative SCE result and positive chromosome instability assay, single lab, patient cells\",\n      \"pmids\": [\"34697795\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NRF1 transcription factor activates SPIDR transcription by binding to a super enhancer (SE) region of SPIDR (confirmed by ChIP-qPCR). SPIDR depletion in HCC cells increases reactive oxygen species, malondialdehyde, and γH2AX levels, and decreases SOD levels and cell proliferation under oxidative stress; overexpression of SPIDR partially rescues effects of NRF1 silencing, placing SPIDR downstream of NRF1 in oxidative stress response.\",\n      \"method\": \"ChIP-qPCR for NRF1 binding and H3K27ac at SPIDR SE, siRNA knockdown, SPIDR overexpression rescue, ROS/MDA/SOD/γH2AX assays, JQ1 BET inhibitor treatment\",\n      \"journal\": \"BMC gastroenterology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP-qPCR for direct transcription factor binding plus epistasis rescue experiment, single lab, multiple functional readouts\",\n      \"pmids\": [\"38438958\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SPIDR is a scaffolding protein that forms part of the SWS1-SWSAP1-SPIDR complex, physically bridging BLM helicase and RAD51/DMC1 recombinases to coordinate homologous recombination (HR): it promotes stable assembly of RAD51 (and DMC1 during meiosis) at DNA damage sites, facilitates inter-homolog HDR, drives sister chromatid exchange, and is essential for meiotic synapsis and crossover formation in male mice; its transcription is activated by NRF1 via a super enhancer, and loss-of-function mutations in humans cause chromosomal instability, primary ovarian insufficiency, and gonadal dysgenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SPIDR (scaffolding protein involved in DNA repair) is a scaffold that coordinates homologous recombination by physically and independently bridging BLM helicase and the RAD51 recombinase, promoting assembly of a BLM/RAD51-containing complex; its depletion elevates sister chromatid exchange and impairs HR [#0]. SPIDR operates as part of the SWS1–SWSAP1–SPIDR complex (the human Shu complex), additionally engaging PDS5B, and this complex is required for stable RAD51 loading at damage sites, controls distinct homology-directed repair outcomes including inter-homolog HDR, regulates replication fork restart after stalling, and underlies the poor growth of BLM-deficient cells [#1, #2]. During meiosis SPIDR governs assembly or stability of RAD51/DMC1 nucleoprotein filaments on ssDNA, and its loss in male mice causes complete meiotic arrest with synapsis and crossover defects, while female subfertility is partially rescued by ablation of the checkpoint kinase CHK2 [#3]. Biallelic loss-of-function mutations in humans impair HR and produce chromosomal instability, with one nonsense variant leaving sister chromatid exchange normal, indicating SPIDR acts in vivo chiefly through the RAD51 rather than the BLM arm [#4, #5]. SPIDR transcription is activated by NRF1 binding a super enhancer, placing SPIDR downstream of NRF1 in the oxidative stress response [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Established that a single protein could physically couple BLM helicase to RAD51, answering how these recombination factors are co-assembled into one DNA-processing complex.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA depletion with SCE and HR reporter assays, damage sensitivity and foci analysis in human cells\",\n      \"pmids\": [\"23509288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which domains of SPIDR bind BLM versus RAD51\", \"No in vivo or organismal phenotype established\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrated SPIDR is required for HR in humans, connecting the molecular scaffold to a disease-relevant DNA repair defect.\",\n      \"evidence\": \"Whole-exome sequencing of a biallelic stop-gain variant plus EGFP DSB repair assay and 53BP1/\\u03b3H2AX immunofluorescence in patient cells\",\n      \"pmids\": [\"27967308\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, patient cells only\", \"Did not separate BLM-dependent from RAD51-dependent contributions\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placed SPIDR within a defined SWS1–SWSAP1 (Shu) complex with PDS5B, clarifying the protein assembly through which it promotes RAD51 recruitment and fork restart.\",\n      \"evidence\": \"Co-IP, CRISPR deletion of SWS1/SWSAP1, RAD51 foci, SCE, and MMS/MMC sensitivity with epistasis\",\n      \"pmids\": [\"31665741\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry and architecture of the complex not resolved\", \"Mechanism of PDS5B linkage to RAD51 loading unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Resolved the pathway-specific function of the complex, identifying it as the first mitotic factor specific to inter-homolog HDR and genetically epistatic to BLM.\",\n      \"evidence\": \"CRISPR KO, mouse genetic epistasis with Blm, pathway-specific HDR reporters, RAD51 foci and SCE assays\",\n      \"pmids\": [\"34253720\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism distinguishing inter-homolog from inter-sister repair not defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showed that a human SPIDR null variant produces chromosomal instability with normal SCE, dissecting SPIDR's primary in vivo role toward RAD51 rather than BLM.\",\n      \"evidence\": \"Targeted NGS, mitomycin C breakage and metaphase analysis, and SCE assay in patient cells\",\n      \"pmids\": [\"34697795\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single patient/lab\", \"Discordance with cell-line SCE phenotypes not mechanistically reconciled\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Extended SPIDR function to meiosis, showing it controls RAD51/DMC1 filament assembly required for synapsis and crossover formation in vivo.\",\n      \"evidence\": \"Conditional KO mouse, meiotic spreads, RAD51/DMC1 foci, synapsis analysis, CHK2 epistasis\",\n      \"pmids\": [\"36938872\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why CHK2 ablation rescues females but not males is unexplained\", \"Direct biochemical effect on filament nucleation versus stabilization not separated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified upstream transcriptional control, showing NRF1 drives SPIDR expression via a super enhancer to support an oxidative stress response.\",\n      \"evidence\": \"ChIP-qPCR for NRF1/H3K27ac, siRNA knockdown, overexpression rescue, ROS/MDA/SOD/\\u03b3H2AX assays with JQ1 in HCC cells\",\n      \"pmids\": [\"38438958\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab/cell-type context\", \"How HR scaffolding relates mechanistically to ROS handling not established\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The structural basis of how SPIDR simultaneously engages BLM, RAD51/DMC1, and the SWS1–SWSAP1–PDS5B complex, and how it biases repair toward inter-homolog HDR, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No structural model of SPIDR or its complexes\", \"Domain-level mapping of partner-binding interfaces absent\", \"Mechanism coupling transcriptional control to repair output unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 2]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [0, 1, 2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [0, 1, 2, 4, 5]},\n      {\"term_id\": \"R-HSA-1474165\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"SWS1-SWSAP1-SPIDR (Shu) complex\",\n      \"BLM/RAD51-containing complex\"\n    ],\n    \"partners\": [\n      \"BLM\",\n      \"RAD51\",\n      \"SWS1\",\n      \"SWSAP1\",\n      \"PDS5B\",\n      \"DMC1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}