{"gene":"PPP6R1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2010,"finding":"The C. elegans PP6 ortholog PPH-6 and its associated regulatory subunit SAPS-1 (ortholog of PPP6R1) form a complex that is required for cortical actomyosin contractility and proper spindle positioning in one-cell embryos. The complex regulates organization of cortical non-muscle myosin II (NMY-2) and contributes to cytokinesis by stimulating actomyosin contractility. PPH-6/SAPS-1 is also required for cortical localization of GPR-1/2 and LIN-5, positive regulators of spindle pole pulling forces during anaphase.","method":"RNAi knockdown of pph-6 and saps-1 in C. elegans embryos; live imaging of cortical NMY-2 and spindle positioning; localization of GPR-1/2 and LIN-5","journal":"Development (Cambridge, England)","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal live-imaging and genetic approaches in a well-controlled model organism, with distinct phenotypic readouts for actomyosin contractility and spindle positioning","pmids":["20040490"],"is_preprint":false},{"year":2016,"finding":"The PP6 complex (PPH-6/SAPS-1 in C. elegans; PPP6C/PP6 in human cells) associates with Aurora A kinase (AIR-1 in C. elegans). PPH-6-SAPS-1 negatively regulates Aurora A localization at the cell cortex, and Aurora A acts downstream of PPH-6-SAPS-1 in modulating spindle positioning. In human cells, both Aurora A and PP6 phosphatase subunit PPP6C are necessary for spindle positioning and cortical localization of NuMA and dynein during mitosis.","method":"Co-immunoprecipitation of PPH-6/SAPS-1 with AIR-1 in C. elegans; acute inactivation of AIR-1 during mitosis; epistasis analysis; RNAi/knockdown in human cells; live imaging of NuMA and dynein cortical localization","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, genetic epistasis, and functional rescue across two organisms with multiple orthogonal methods","pmids":["27335426"],"is_preprint":false},{"year":2014,"finding":"PP6 holoenzyme, including regulatory subunit PPP6R1, physically interacts with the PB1 and PB2 subunits of the influenza A virus RNA-dependent RNA polymerase (RdRP). siRNA-mediated knockdown of the PP6 catalytic subunit (PPP6C) in infected cells reduces viral RNA accumulation and attenuates virus growth, indicating PP6 positively regulates RdRP activity.","method":"Affinity purification (Strep-tag on PB2) followed by label-free quantitative mass spectrometry from infected human cells; direct binding assay between PP6 subunits and PB1/PB2; siRNA knockdown of PPP6C with viral RNA accumulation and growth assays","journal":"Journal of virology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — affinity purification-MS plus direct binding assay plus siRNA functional readout, but direct interaction with PPP6R1 specifically was identified by MS without independent confirmation of PPP6R1's specific contribution","pmids":["25187537"],"is_preprint":false},{"year":2017,"finding":"PP6 exerts negative control at multiple steps of NF-κB signaling. The PP6 catalytic subunit and the PPP6R1 regulatory subunit are expressed at especially high levels in hematopoietic cells and lymphoid tissues. Conditional knockout of PP6c or PPP6R1 (SAPS1) genes revealed distinctive effects on development of and signaling in lymphocytes.","method":"Conditional gene knockout in mice; analysis of lymphocyte development and NF-κB signaling; expression analysis in hematopoietic tissues","journal":"Biochemical Society transactions","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined cellular phenotypes, but review/perspective article summarizing multiple studies; single-lab findings","pmids":["28620030"],"is_preprint":false},{"year":2018,"finding":"PPP6R1 (SAPS1) interacts with Slfn2. This interaction leads to reduced type I IFN-induced activation of NF-κB signaling and results in reduced expression of interferon-stimulated genes (ISGs). Targeted disruption of Slfn2 increased ISG transcription and enhanced antiviral responses, consistent with Slfn2 using PPP6R1 to dampen NF-κB-dependent ISG expression.","method":"Co-immunoprecipitation of Slfn2 with PPP6R1; Slfn2 gene knockout mice; NF-κB pathway activation assays; ISG expression analysis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP interaction plus KO phenotype with defined NF-κB pathway readout, single lab","pmids":["29866656"],"is_preprint":false},{"year":2019,"finding":"PPP6R1/SAPS1 is required for the cellular DNA damage response. SAPS1-null mice and cells are radiosensitive. Loss of SAPS1 impairs dephosphorylation of DNA damage/repair markers γH2AX, p53, and Kap1 after ionizing radiation. These findings confirm that recognition of DNA-PKcs is mediated by the SAPS1 PP6 regulatory subunit.","method":"SAPS1 null mouse generation; whole-body irradiation survival studies; clonogenic survival assays; western blotting of γH2AX, p53, and Kap1 dephosphorylation kinetics in null vs. wild-type cells","journal":"DNA repair","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo KO mouse with whole-organism and cellular phenotypes, multiple DNA damage marker readouts, confirmatory of prior cell-line knockdown results","pmids":["31751917"],"is_preprint":false},{"year":2024,"finding":"PP6 holoenzyme components PPP6R1, PPP6R2, and PPP6R3 have redundant roles in regulating TAK1 inhibitor-induced PANoptosis (RIPK1-dependent lytic cell death). Combined depletion of all three regulatory subunits is required to block TAK1i-induced cell death. Mechanistically, PPP6C and its regulatory subunits promote the pro-death S166 auto-phosphorylation of RIPK1 and reduce the pro-survival S321 phosphorylation of RIPK1.","method":"CRISPR screen for cell death regulators; individual and combined siRNA/CRISPR depletion of PPP6R1/2/3 and PPP6C; phosphorylation state analysis of RIPK1 at S166 and S321 by western blot","journal":"BMC biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CRISPR screen plus targeted validation with specific phosphorylation site readouts; single lab, redundancy requires combined depletion to observe effect","pmids":["38807188"],"is_preprint":false},{"year":2020,"finding":"In C. elegans, PP6 complex constituents PPH-6 and SAPS-1 contribute to host defense during aging, apparently without affecting DAF-16 (FoxO) transcriptional activity, distinguishing the PP6 complex from PP2A and PP4 complexes in this context.","method":"Reverse genetics (RNAi) of C. elegans orthologs of human PP6 subunits in postreproductive adults; pathogen infection survival assays; DAF-16 transcriptional reporter assays","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 3 / Weak — RNAi knockdown with survival phenotype and negative DAF-16 reporter result; single lab, single method per readout","pmids":["33315870"],"is_preprint":false}],"current_model":"PPP6R1 (SAPS1) is a conserved regulatory subunit of the PP6 serine/threonine phosphatase holoenzyme that, together with the catalytic subunit PPP6C, forms heterotrimeric complexes responsible for dephosphorylating substrates involved in DNA damage repair (including DNA-PKcs, γH2AX, p53, Kap1), spindle positioning via regulation of cortical actomyosin and Aurora A kinase, NF-κB-dependent immune signaling, RIPK1-dependent PANoptosis (by modulating RIPK1 phosphorylation at S166 and S321), and influenza A virus RdRP activity; in lymphocytes, PPP6R1 expression is especially high and its loss disrupts lymphocyte development and signaling."},"narrative":{"mechanistic_narrative":"PPP6R1 (SAPS1) is a conserved regulatory subunit of the PP6 serine/threonine phosphatase holoenzyme that, in partnership with the catalytic subunit PPP6C, directs substrate-specific dephosphorylation across cell division, DNA repair, and immune signaling [PMID:20040490, PMID:31751917]. In dividing cells, the PP6 (PPH-6/SAPS-1) complex governs spindle positioning by controlling cortical actomyosin contractility and by negatively regulating Aurora A kinase localization at the cell cortex, with downstream effects on cortical recruitment of NuMA and dynein [PMID:20040490, PMID:27335426]. In the DNA damage response, PPP6R1 is the regulatory subunit that mediates recognition of DNA-PKcs and is required for timely dephosphorylation of γH2AX, p53, and Kap1 after ionizing radiation; its loss renders cells and mice radiosensitive [PMID:31751917]. PPP6R1 also functions in immune and cell-death signaling: it exerts negative control over NF-κB signaling and, through interaction with Slfn2, dampens type I IFN-induced NF-κB activation and interferon-stimulated gene expression [PMID:28620030, PMID:29866656]. Acting redundantly with PPP6R2 and PPP6R3, PPP6R1 tunes RIPK1-dependent PANoptosis by promoting pro-death RIPK1 S166 autophosphorylation while reducing pro-survival S321 phosphorylation [PMID:38807188]. PP6 containing PPP6R1 additionally binds the PB1 and PB2 subunits of the influenza A virus RNA-dependent RNA polymerase and positively supports viral RdRP activity [PMID:25187537]. PPP6R1 is expressed at especially high levels in hematopoietic and lymphoid tissues, where its loss disrupts lymphocyte development and signaling [PMID:28620030].","teleology":[{"year":2010,"claim":"Established that SAPS1/PPP6R1, as a PP6 regulatory subunit, has a cell-division function by linking the PP6 complex to cortical actomyosin organization and spindle positioning.","evidence":"RNAi of pph-6 and saps-1 in C. elegans embryos with live imaging of cortical NMY-2, spindle positioning, and GPR-1/2 and LIN-5 localization","pmids":["20040490"],"confidence":"High","gaps":["Direct phosphatase substrates at the cortex not identified","Mechanism by which the complex regulates GPR-1/2 and LIN-5 localization unresolved","Conducted in C. elegans embryos; human PPP6R1 contribution inferred"]},{"year":2014,"claim":"Showed that PP6 including PPP6R1 physically engages the influenza A RdRP and positively supports viral replication, extending PP6 function to host-pathogen interaction.","evidence":"Strep-tag affinity purification-MS from infected human cells, direct binding assays with PB1/PB2, and PPP6C siRNA knockdown with viral RNA/growth readouts","pmids":["25187537"],"confidence":"Medium","gaps":["PPP6R1-specific functional contribution not separated from PPP6C","Phosphorylation substrate on the RdRP not defined","Direct PPP6R1–PB1/PB2 binding identified by MS without independent confirmation"]},{"year":2016,"claim":"Defined the Aurora A axis by demonstrating that PP6/SAPS-1 binds and negatively regulates Aurora A cortical localization, placing Aurora A downstream of the complex in spindle positioning.","evidence":"Co-IP of PPH-6/SAPS-1 with AIR-1, acute AIR-1 inactivation and epistasis in C. elegans, plus knockdown and NuMA/dynein imaging in human cells","pmids":["27335426"],"confidence":"High","gaps":["Whether Aurora A is a direct PP6 dephosphorylation substrate not established","Cortical dephosphorylation targets controlling NuMA/dynein unknown"]},{"year":2017,"claim":"Connected PPP6R1 to NF-κB-dependent immune signaling and lymphocyte biology, showing tissue-selective high expression and loss-of-function developmental phenotypes.","evidence":"Conditional knockout of PP6c or PPP6R1 in mice with lymphocyte development and NF-κB signaling analyses (perspective summarizing studies)","pmids":["28620030"],"confidence":"Medium","gaps":["Specific NF-κB pathway substrates of PP6 not identified","Single-lab findings summarized in a review","Step(s) of NF-κB signaling under PP6 control not fully mapped"]},{"year":2018,"claim":"Provided a molecular partner (Slfn2) through which PPP6R1 restrains type I IFN-induced NF-κB activation and ISG expression.","evidence":"Co-IP of Slfn2 with PPP6R1, Slfn2 knockout mice, and NF-κB activation and ISG expression assays","pmids":["29866656"],"confidence":"Medium","gaps":["Direct dephosphorylation target downstream of the Slfn2–PPP6R1 interaction not defined","Reciprocal validation and structural basis of the interaction not shown"]},{"year":2019,"claim":"Confirmed PPP6R1 as the substrate-targeting subunit for the DNA damage response, mediating DNA-PKcs recognition and dephosphorylation of repair markers in vivo.","evidence":"SAPS1-null mice, whole-body irradiation survival, clonogenic assays, and dephosphorylation kinetics of γH2AX, p53, and Kap1","pmids":["31751917"],"confidence":"High","gaps":["Direct enzyme-substrate kinetics on individual markers not reconstituted","How PPP6R1 recognizes DNA-PKcs structurally not resolved"]},{"year":2020,"claim":"Distinguished PP6 (PPH-6/SAPS-1) from PP2A and PP4 in aging host defense and showed the effect is independent of DAF-16/FoxO transcription.","evidence":"RNAi of C. elegans PP6 orthologs in postreproductive adults with pathogen survival assays and DAF-16 reporters","pmids":["33315870"],"confidence":"Low","gaps":["Single-lab RNAi with one method per readout","Effector pathway downstream of PP6 in host defense unknown","Relevance to mammalian PPP6R1 untested"]},{"year":2024,"claim":"Placed PPP6R1 in RIPK1-dependent PANoptosis, showing redundancy with PPP6R2/R3 and a phospho-site-specific influence on RIPK1.","evidence":"CRISPR screen plus individual/combined depletion of PPP6R1/2/3 and PPP6C, with RIPK1 S166 and S321 phosphorylation readouts","pmids":["38807188"],"confidence":"Medium","gaps":["Whether RIPK1 is a direct PP6 substrate not established","Functional redundancy obscures PPP6R1-specific role","Single-lab findings"]},{"year":null,"claim":"How a single regulatory subunit, PPP6R1, selects among such diverse substrates (DNA-PKcs/repair markers, Aurora A/cortical factors, NF-κB components, RIPK1, viral RdRP) and is itself spatially and temporally regulated remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of PPP6R1 substrate recognition","Determinants of context-specific substrate targeting unknown","Direct enzyme-substrate relationships largely inferred rather than reconstituted"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[5,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,5]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,1]}],"pathway":[{"term_id":"R-HSA-73894","term_label":"DNA Repair","supporting_discovery_ids":[5]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3,4]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[6]}],"complexes":["PP6 phosphatase holoenzyme"],"partners":["PPP6C","AURKA","RIPK1","SLFN2","PB1","PB2","PPP6R2","PPP6R3"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UPN7","full_name":"Serine/threonine-protein phosphatase 6 regulatory subunit 1","aliases":["SAPS domain family member 1"],"length_aa":881,"mass_kda":96.7,"function":"Regulatory subunit of protein phosphatase 6 (PP6). May function as a scaffolding PP6 subunit. Involved in the PP6-mediated dephosphorylation of NFKBIE opposing its degradation in response to TNF","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9UPN7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPP6R1","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000105063","cell_line_id":"CID001614","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"vesicles","grade":2}],"interactors":[{"gene":"ANKRD28","stoichiometry":10.0},{"gene":"PPP6C","stoichiometry":10.0},{"gene":"PPP6R3","stoichiometry":4.0},{"gene":"ANKRD52","stoichiometry":0.2},{"gene":"ANKRD44","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001614","total_profiled":1310},"omim":[{"mim_id":"610875","title":"PROTEIN PHOSPHATASE 6, REGULATORY SUBUNIT 1; PPP6R1","url":"https://www.omim.org/entry/610875"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Cytosol","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPP6R1"},"hgnc":{"alias_symbol":["SAP190"],"prev_symbol":["KIAA1115","SAPS1"]},"alphafold":{"accession":"Q9UPN7","domains":[{"cath_id":"1.25.40","chopping":"352-418_426-518","consensus_level":"medium","plddt":93.2186,"start":352,"end":518}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UPN7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UPN7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UPN7-F1-predicted_aligned_error_v6.png","plddt_mean":67.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPP6R1","jax_strain_url":"https://www.jax.org/strain/search?query=PPP6R1"},"sequence":{"accession":"Q9UPN7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UPN7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UPN7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UPN7"}},"corpus_meta":[{"pmid":"25187537","id":"PMC_25187537","title":"Interactome analysis of the influenza A virus transcription/replication machinery identifies protein phosphatase 6 as a cellular factor required for efficient virus replication.","date":"2014","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/25187537","citation_count":54,"is_preprint":false},{"pmid":"11812212","id":"PMC_11812212","title":"Individual acid aspartic proteinases (Saps) 1-6 of Candida albicans are not essential for invasion and colonization of the gastrointestinal tract in mice.","date":"2002","source":"Microbial pathogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/11812212","citation_count":48,"is_preprint":false},{"pmid":"20040490","id":"PMC_20040490","title":"Regulation of cortical contractility and spindle positioning by the protein phosphatase 6 PPH-6 in one-cell stage C. elegans embryos.","date":"2010","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/20040490","citation_count":47,"is_preprint":false},{"pmid":"27335426","id":"PMC_27335426","title":"Aurora A kinase regulates proper spindle positioning in C. elegans and in human cells.","date":"2016","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/27335426","citation_count":45,"is_preprint":false},{"pmid":"28620030","id":"PMC_28620030","title":"Functions of protein phosphatase-6 in NF-κB signaling and in lymphocytes.","date":"2017","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/28620030","citation_count":38,"is_preprint":false},{"pmid":"38807188","id":"PMC_38807188","title":"The protein phosphatase PP6 promotes RIPK1-dependent PANoptosis.","date":"2024","source":"BMC biology","url":"https://pubmed.ncbi.nlm.nih.gov/38807188","citation_count":32,"is_preprint":false},{"pmid":"29866656","id":"PMC_29866656","title":"Slfn2 Regulates Type I Interferon Responses by Modulating the NF-κB Pathway.","date":"2018","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29866656","citation_count":14,"is_preprint":false},{"pmid":"31751917","id":"PMC_31751917","title":"Deletion of the SAPS1 subunit of protein phosphatase 6 in mice increases radiosensitivity and impairs the cellular DNA damage response.","date":"2019","source":"DNA repair","url":"https://pubmed.ncbi.nlm.nih.gov/31751917","citation_count":8,"is_preprint":false},{"pmid":"17974505","id":"PMC_17974505","title":"Promiscuous T cell epitope prediction of Candida albicans secretory aspartyl protienase family of proteins.","date":"2007","source":"Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/17974505","citation_count":6,"is_preprint":false},{"pmid":"39051243","id":"PMC_39051243","title":"Saps1-3 Antigens in Candida albicans: Differential Modulation Following Exposure to Soluble Proteins, Mammalian Cells, and Infection in Mice.","date":"2024","source":"Infectious disease reports","url":"https://pubmed.ncbi.nlm.nih.gov/39051243","citation_count":1,"is_preprint":false},{"pmid":"40956397","id":"PMC_40956397","title":"Endocrine disruptors and male infertility: multi-omics identification of key genes in non-obstructive azoospermia.","date":"2025","source":"Journal of assisted reproduction and genetics","url":"https://pubmed.ncbi.nlm.nih.gov/40956397","citation_count":1,"is_preprint":false},{"pmid":"38473795","id":"PMC_38473795","title":"Analysis of the Association between Copy Number Variation and Ventricular Fibrillation in ST-Elevation Acute Myocardial Infarction.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/38473795","citation_count":1,"is_preprint":false},{"pmid":"33315870","id":"PMC_33315870","title":"The PP2A/4/6 subfamily of phosphoprotein phosphatases regulates DAF-16 and confers resistance to environmental stress in postreproductive adult C. elegans.","date":"2020","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/33315870","citation_count":1,"is_preprint":false},{"pmid":"40577224","id":"PMC_40577224","title":"Study on the synthesis, structural characterization, and anti-hepatoma cell proliferation effects of sulfated alfalfa polysaccharides.","date":"2025","source":"Journal of Asian natural products research","url":"https://pubmed.ncbi.nlm.nih.gov/40577224","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9086,"output_tokens":2510,"usd":0.032454,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9649,"output_tokens":3342,"usd":0.065897,"stage2_stop_reason":"end_turn"},"total_usd":0.098351,"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\": 2010,\n      \"finding\": \"The C. elegans PP6 ortholog PPH-6 and its associated regulatory subunit SAPS-1 (ortholog of PPP6R1) form a complex that is required for cortical actomyosin contractility and proper spindle positioning in one-cell embryos. The complex regulates organization of cortical non-muscle myosin II (NMY-2) and contributes to cytokinesis by stimulating actomyosin contractility. PPH-6/SAPS-1 is also required for cortical localization of GPR-1/2 and LIN-5, positive regulators of spindle pole pulling forces during anaphase.\",\n      \"method\": \"RNAi knockdown of pph-6 and saps-1 in C. elegans embryos; live imaging of cortical NMY-2 and spindle positioning; localization of GPR-1/2 and LIN-5\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal live-imaging and genetic approaches in a well-controlled model organism, with distinct phenotypic readouts for actomyosin contractility and spindle positioning\",\n      \"pmids\": [\"20040490\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"The PP6 complex (PPH-6/SAPS-1 in C. elegans; PPP6C/PP6 in human cells) associates with Aurora A kinase (AIR-1 in C. elegans). PPH-6-SAPS-1 negatively regulates Aurora A localization at the cell cortex, and Aurora A acts downstream of PPH-6-SAPS-1 in modulating spindle positioning. In human cells, both Aurora A and PP6 phosphatase subunit PPP6C are necessary for spindle positioning and cortical localization of NuMA and dynein during mitosis.\",\n      \"method\": \"Co-immunoprecipitation of PPH-6/SAPS-1 with AIR-1 in C. elegans; acute inactivation of AIR-1 during mitosis; epistasis analysis; RNAi/knockdown in human cells; live imaging of NuMA and dynein cortical localization\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, genetic epistasis, and functional rescue across two organisms with multiple orthogonal methods\",\n      \"pmids\": [\"27335426\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PP6 holoenzyme, including regulatory subunit PPP6R1, physically interacts with the PB1 and PB2 subunits of the influenza A virus RNA-dependent RNA polymerase (RdRP). siRNA-mediated knockdown of the PP6 catalytic subunit (PPP6C) in infected cells reduces viral RNA accumulation and attenuates virus growth, indicating PP6 positively regulates RdRP activity.\",\n      \"method\": \"Affinity purification (Strep-tag on PB2) followed by label-free quantitative mass spectrometry from infected human cells; direct binding assay between PP6 subunits and PB1/PB2; siRNA knockdown of PPP6C with viral RNA accumulation and growth assays\",\n      \"journal\": \"Journal of virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — affinity purification-MS plus direct binding assay plus siRNA functional readout, but direct interaction with PPP6R1 specifically was identified by MS without independent confirmation of PPP6R1's specific contribution\",\n      \"pmids\": [\"25187537\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PP6 exerts negative control at multiple steps of NF-κB signaling. The PP6 catalytic subunit and the PPP6R1 regulatory subunit are expressed at especially high levels in hematopoietic cells and lymphoid tissues. Conditional knockout of PP6c or PPP6R1 (SAPS1) genes revealed distinctive effects on development of and signaling in lymphocytes.\",\n      \"method\": \"Conditional gene knockout in mice; analysis of lymphocyte development and NF-κB signaling; expression analysis in hematopoietic tissues\",\n      \"journal\": \"Biochemical Society transactions\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined cellular phenotypes, but review/perspective article summarizing multiple studies; single-lab findings\",\n      \"pmids\": [\"28620030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PPP6R1 (SAPS1) interacts with Slfn2. This interaction leads to reduced type I IFN-induced activation of NF-κB signaling and results in reduced expression of interferon-stimulated genes (ISGs). Targeted disruption of Slfn2 increased ISG transcription and enhanced antiviral responses, consistent with Slfn2 using PPP6R1 to dampen NF-κB-dependent ISG expression.\",\n      \"method\": \"Co-immunoprecipitation of Slfn2 with PPP6R1; Slfn2 gene knockout mice; NF-κB pathway activation assays; ISG expression analysis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP interaction plus KO phenotype with defined NF-κB pathway readout, single lab\",\n      \"pmids\": [\"29866656\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PPP6R1/SAPS1 is required for the cellular DNA damage response. SAPS1-null mice and cells are radiosensitive. Loss of SAPS1 impairs dephosphorylation of DNA damage/repair markers γH2AX, p53, and Kap1 after ionizing radiation. These findings confirm that recognition of DNA-PKcs is mediated by the SAPS1 PP6 regulatory subunit.\",\n      \"method\": \"SAPS1 null mouse generation; whole-body irradiation survival studies; clonogenic survival assays; western blotting of γH2AX, p53, and Kap1 dephosphorylation kinetics in null vs. wild-type cells\",\n      \"journal\": \"DNA repair\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo KO mouse with whole-organism and cellular phenotypes, multiple DNA damage marker readouts, confirmatory of prior cell-line knockdown results\",\n      \"pmids\": [\"31751917\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"PP6 holoenzyme components PPP6R1, PPP6R2, and PPP6R3 have redundant roles in regulating TAK1 inhibitor-induced PANoptosis (RIPK1-dependent lytic cell death). Combined depletion of all three regulatory subunits is required to block TAK1i-induced cell death. Mechanistically, PPP6C and its regulatory subunits promote the pro-death S166 auto-phosphorylation of RIPK1 and reduce the pro-survival S321 phosphorylation of RIPK1.\",\n      \"method\": \"CRISPR screen for cell death regulators; individual and combined siRNA/CRISPR depletion of PPP6R1/2/3 and PPP6C; phosphorylation state analysis of RIPK1 at S166 and S321 by western blot\",\n      \"journal\": \"BMC biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CRISPR screen plus targeted validation with specific phosphorylation site readouts; single lab, redundancy requires combined depletion to observe effect\",\n      \"pmids\": [\"38807188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"In C. elegans, PP6 complex constituents PPH-6 and SAPS-1 contribute to host defense during aging, apparently without affecting DAF-16 (FoxO) transcriptional activity, distinguishing the PP6 complex from PP2A and PP4 complexes in this context.\",\n      \"method\": \"Reverse genetics (RNAi) of C. elegans orthologs of human PP6 subunits in postreproductive adults; pathogen infection survival assays; DAF-16 transcriptional reporter assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — RNAi knockdown with survival phenotype and negative DAF-16 reporter result; single lab, single method per readout\",\n      \"pmids\": [\"33315870\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPP6R1 (SAPS1) is a conserved regulatory subunit of the PP6 serine/threonine phosphatase holoenzyme that, together with the catalytic subunit PPP6C, forms heterotrimeric complexes responsible for dephosphorylating substrates involved in DNA damage repair (including DNA-PKcs, γH2AX, p53, Kap1), spindle positioning via regulation of cortical actomyosin and Aurora A kinase, NF-κB-dependent immune signaling, RIPK1-dependent PANoptosis (by modulating RIPK1 phosphorylation at S166 and S321), and influenza A virus RdRP activity; in lymphocytes, PPP6R1 expression is especially high and its loss disrupts lymphocyte development and signaling.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPP6R1 (SAPS1) is a conserved regulatory subunit of the PP6 serine/threonine phosphatase holoenzyme that, in partnership with the catalytic subunit PPP6C, directs substrate-specific dephosphorylation across cell division, DNA repair, and immune signaling [#0, #5]. In dividing cells, the PP6 (PPH-6/SAPS-1) complex governs spindle positioning by controlling cortical actomyosin contractility and by negatively regulating Aurora A kinase localization at the cell cortex, with downstream effects on cortical recruitment of NuMA and dynein [#0, #1]. In the DNA damage response, PPP6R1 is the regulatory subunit that mediates recognition of DNA-PKcs and is required for timely dephosphorylation of \\u03b3H2AX, p53, and Kap1 after ionizing radiation; its loss renders cells and mice radiosensitive [#5]. PPP6R1 also functions in immune and cell-death signaling: it exerts negative control over NF-\\u03baB signaling and, through interaction with Slfn2, dampens type I IFN-induced NF-\\u03baB activation and interferon-stimulated gene expression [#3, #4]. Acting redundantly with PPP6R2 and PPP6R3, PPP6R1 tunes RIPK1-dependent PANoptosis by promoting pro-death RIPK1 S166 autophosphorylation while reducing pro-survival S321 phosphorylation [#6]. PP6 containing PPP6R1 additionally binds the PB1 and PB2 subunits of the influenza A virus RNA-dependent RNA polymerase and positively supports viral RdRP activity [#2]. PPP6R1 is expressed at especially high levels in hematopoietic and lymphoid tissues, where its loss disrupts lymphocyte development and signaling [#3].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established that SAPS1/PPP6R1, as a PP6 regulatory subunit, has a cell-division function by linking the PP6 complex to cortical actomyosin organization and spindle positioning.\",\n      \"evidence\": \"RNAi of pph-6 and saps-1 in C. elegans embryos with live imaging of cortical NMY-2, spindle positioning, and GPR-1/2 and LIN-5 localization\",\n      \"pmids\": [\"20040490\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct phosphatase substrates at the cortex not identified\", \"Mechanism by which the complex regulates GPR-1/2 and LIN-5 localization unresolved\", \"Conducted in C. elegans embryos; human PPP6R1 contribution inferred\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed that PP6 including PPP6R1 physically engages the influenza A RdRP and positively supports viral replication, extending PP6 function to host-pathogen interaction.\",\n      \"evidence\": \"Strep-tag affinity purification-MS from infected human cells, direct binding assays with PB1/PB2, and PPP6C siRNA knockdown with viral RNA/growth readouts\",\n      \"pmids\": [\"25187537\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"PPP6R1-specific functional contribution not separated from PPP6C\", \"Phosphorylation substrate on the RdRP not defined\", \"Direct PPP6R1\\u2013PB1/PB2 binding identified by MS without independent confirmation\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Defined the Aurora A axis by demonstrating that PP6/SAPS-1 binds and negatively regulates Aurora A cortical localization, placing Aurora A downstream of the complex in spindle positioning.\",\n      \"evidence\": \"Co-IP of PPH-6/SAPS-1 with AIR-1, acute AIR-1 inactivation and epistasis in C. elegans, plus knockdown and NuMA/dynein imaging in human cells\",\n      \"pmids\": [\"27335426\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether Aurora A is a direct PP6 dephosphorylation substrate not established\", \"Cortical dephosphorylation targets controlling NuMA/dynein unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected PPP6R1 to NF-\\u03baB-dependent immune signaling and lymphocyte biology, showing tissue-selective high expression and loss-of-function developmental phenotypes.\",\n      \"evidence\": \"Conditional knockout of PP6c or PPP6R1 in mice with lymphocyte development and NF-\\u03baB signaling analyses (perspective summarizing studies)\",\n      \"pmids\": [\"28620030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific NF-\\u03baB pathway substrates of PP6 not identified\", \"Single-lab findings summarized in a review\", \"Step(s) of NF-\\u03baB signaling under PP6 control not fully mapped\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided a molecular partner (Slfn2) through which PPP6R1 restrains type I IFN-induced NF-\\u03baB activation and ISG expression.\",\n      \"evidence\": \"Co-IP of Slfn2 with PPP6R1, Slfn2 knockout mice, and NF-\\u03baB activation and ISG expression assays\",\n      \"pmids\": [\"29866656\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct dephosphorylation target downstream of the Slfn2\\u2013PPP6R1 interaction not defined\", \"Reciprocal validation and structural basis of the interaction not shown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Confirmed PPP6R1 as the substrate-targeting subunit for the DNA damage response, mediating DNA-PKcs recognition and dephosphorylation of repair markers in vivo.\",\n      \"evidence\": \"SAPS1-null mice, whole-body irradiation survival, clonogenic assays, and dephosphorylation kinetics of \\u03b3H2AX, p53, and Kap1\",\n      \"pmids\": [\"31751917\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct enzyme-substrate kinetics on individual markers not reconstituted\", \"How PPP6R1 recognizes DNA-PKcs structurally not resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Distinguished PP6 (PPH-6/SAPS-1) from PP2A and PP4 in aging host defense and showed the effect is independent of DAF-16/FoxO transcription.\",\n      \"evidence\": \"RNAi of C. elegans PP6 orthologs in postreproductive adults with pathogen survival assays and DAF-16 reporters\",\n      \"pmids\": [\"33315870\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single-lab RNAi with one method per readout\", \"Effector pathway downstream of PP6 in host defense unknown\", \"Relevance to mammalian PPP6R1 untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed PPP6R1 in RIPK1-dependent PANoptosis, showing redundancy with PPP6R2/R3 and a phospho-site-specific influence on RIPK1.\",\n      \"evidence\": \"CRISPR screen plus individual/combined depletion of PPP6R1/2/3 and PPP6C, with RIPK1 S166 and S321 phosphorylation readouts\",\n      \"pmids\": [\"38807188\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RIPK1 is a direct PP6 substrate not established\", \"Functional redundancy obscures PPP6R1-specific role\", \"Single-lab findings\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How a single regulatory subunit, PPP6R1, selects among such diverse substrates (DNA-PKcs/repair markers, Aurora A/cortical factors, NF-\\u03baB components, RIPK1, viral RdRP) and is itself spatially and temporally regulated remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of PPP6R1 substrate recognition\", \"Determinants of context-specific substrate targeting unknown\", \"Direct enzyme-substrate relationships largely inferred rather than reconstituted\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [5, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 5]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-73894\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"complexes\": [\"PP6 phosphatase holoenzyme\"],\n    \"partners\": [\"PPP6C\", \"AURKA\", \"RIPK1\", \"SLFN2\", \"PB1\", \"PB2\", \"PPP6R2\", \"PPP6R3\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}