{"gene":"STAP1","run_date":"2026-06-10T07:46:42","timeline":{"discoveries":[{"year":1999,"finding":"BRDG1 (STAP1) was identified as a docking protein that acts downstream of the Tec tyrosine kinase. Tec and Pyk2, but not Btk, Bmx, Lyn, Syk, or c-Abl, induced marked tyrosine phosphorylation of BRDG1 in 293 cells. BRDG1 was also directly phosphorylated by Tec in vitro. Efficient phosphorylation required the PH and SH2 domains as well as the kinase domain of Tec. BRDG1 participated in a positive feedback loop by increasing Tec activity. Endogenous BRDG1 underwent tyrosine phosphorylation in response to BCR stimulation in B cells.","method":"Yeast two-hybrid, in vitro kinase assay, co-expression in 293 cells, tyrosine phosphorylation assays, BCR stimulation of B cell line","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — direct in vitro kinase assay plus cell-based phosphorylation assays with multiple kinase specificity controls and endogenous validation in B cells","pmids":["10518561"],"is_preprint":false},{"year":2000,"finding":"Murine STAP-1 was identified as an adaptor protein containing PH and SH2 domains that acts downstream of c-kit in hematopoietic stem cells. In 293 cells, STAP-1 was tyrosine-phosphorylated by activated c-kit. The STAP-1 SH2 domain interacted with tyrosine-phosphorylated proteins including c-kit and STAT5 in vitro. Two-hybrid assay showed STAP-1 bound c-kit and c-fms but not JAK2 or Pyk2.","method":"Yeast two-hybrid screen with c-kit as bait, in vitro binding assay (SH2 domain), tyrosine phosphorylation assay in 293 cells, RT-PCR expression analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus in vitro binding assay and cell-based phosphorylation; single lab, two orthogonal methods","pmids":["10679268"],"is_preprint":false},{"year":2001,"finding":"BRDG1 (STAP1) overexpression strongly augments BCR-mediated activation of CREB but not c-Jun or promoters of c-MYC and BCL-xL. Three isoforms generated by alternative splicing differ in their PH domain; both tyrosine phosphorylation and CREB-activating ability of BRDG1 were isoform-dependent, implicating the PH domain in these functions.","method":"Reporter gene assays (CREB, c-Jun, c-MYC, BCL-xL promoters), overexpression in B cells, alternative splicing analysis, tyrosine phosphorylation assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional reporter assays with isoform-specific deletion analysis; single lab, two orthogonal approaches","pmids":["11716489"],"is_preprint":false},{"year":2008,"finding":"Ectopic expression of STAP-1 in BV-2 microglia changed morphology and cytoskeletal organization, transforming ramified cells to an activated state. STAP-1 overexpression led to interaction with the M-CSF receptor/c-Fms and diminished its ligand-dependent phosphorylation. STAP-1-expressing cells showed strongly reduced migration and increased cytotoxicity against photoreceptor-like cells.","method":"Ectopic STAP-1 expression in BV-2 microglia, morphology and cytoskeletal analysis, co-immunoprecipitation with c-Fms, phosphorylation assay, migration assay, cytotoxicity assay","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — overexpression with multiple functional readouts (morphology, co-IP, phosphorylation, migration, cytotoxicity); single lab","pmids":["19100238"],"is_preprint":false},{"year":2021,"finding":"STAP-1 interacts with BCR-ABL through its SH2 domain and with STAT5a through its PH domain, functioning as a scaffold protein. Binding of STAP-1 to BCR-ABL stabilizes the BCR-ABL protein in CML cells. NFATc1 activates the STAP-1 promoter and induces STAP-1 mRNA expression, linking Ca2+/NFAT signaling to STAP-1 upregulation in CML.","method":"Deletion mutant co-immunoprecipitation, luciferase reporter assay for STAP-1 promoter, western blotting for BCR-ABL protein stability","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — domain-mapping by deletion mutants with co-IP plus promoter reporter assay; single lab, two orthogonal methods","pmids":["33845308"],"is_preprint":false},{"year":2020,"finding":"Whole-body Stap1 knockout mice showed no changes in plasma lipid levels compared with controls. Bone marrow transplant of Stap1-/- marrow into Ldlr-/- mice did not alter plasma lipid levels or atherosclerotic lesions. PBMC from STAP1 variant carriers showed no difference in LDLR mRNA/protein or LDL uptake by HepG2 cells in coculture experiments. These results argue against a direct functional role of STAP1 in LDL cholesterol regulation.","method":"Stap1 knockout mouse model, bone marrow transplantation, coculture assay (PBMCs + HepG2), LDLR mRNA/protein quantification, LDL uptake assay","journal":"Arteriosclerosis, thrombosis, and vascular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal in vivo and in vitro approaches (KO mouse, BMT, coculture) all yielding negative results for lipid regulation; single lab but highly rigorous","pmids":["31996024"],"is_preprint":false},{"year":2023,"finding":"STAP1 overexpression in BV-2 microglia promoted M2-like polarization by increasing ARG1 expression (associated with the IL-6/STAT3 pathway) and inhibited phagocytosis (associated with decreased cofilin and filopodia formation), contributing to glioma malignant progression.","method":"STAP1-overexpressing BV-2 cell line construction, flow cytometry and fluorescence microscopy for phagocytosis, western blotting/immunofluorescence for ARG1 and cofilin, orthotopic/subcutaneous glioma mouse models with bioluminescence imaging","journal":"Journal of neuro-oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — overexpression with multiple functional readouts (phagocytosis, polarization markers, in vivo tumor growth); single lab","pmids":["37462801"],"is_preprint":false},{"year":2025,"finding":"STAP-1 positively upregulates TCR-mediated T cell activation by interacting with LCK and phospholipase C-γ1. A STAP-1-derived peptide (iSP1) that specifically inhibits the STAP-1–LCK interaction suppressed TCR-mediated signal transduction, IL-2 production, and T cell proliferation, and prevented progression of experimental autoimmune encephalomyelitis by inhibiting Th1 and Th17 cell infiltration.","method":"STAP-1-derived inhibitory peptide (iSP1), in vitro binding inhibition assay, IL-2 production assay, T cell proliferation assay, EAE mouse model with Th1/Th17 cell infiltration analysis","journal":"ImmunoHorizons","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — peptide-based binding inhibition with multiple in vitro and in vivo functional readouts; single lab","pmids":["40288812"],"is_preprint":false},{"year":2025,"finding":"In vitro, the gut metabolite IPA increased BV2 microglia myelin debris phagocytosis by inhibiting Stap1 expression, suggesting that STAP1 negatively regulates microglial phagocytic activity.","method":"Stap1 knockdown in BV2 microglia, co-culture with myelin debris, phagocytosis assay","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single preprint, single method (knockdown + phagocytosis assay), no peer review","pmids":["bio_10.1101_2025.11.19.689382"],"is_preprint":true}],"current_model":"STAP1 (BRDG1) is a PH- and SH2-domain-containing adaptor protein expressed predominantly in immune and hematopoietic cells that functions downstream of receptor tyrosine kinases (Tec, c-kit, BCR-ABL) and immune receptors (BCR, TCR) by being phosphorylated on tyrosine residues, scaffolding signaling complexes (including STAT5a and LCK), amplifying kinase activity in a positive feedback manner, activating CREB-dependent transcription, and modulating microglial activation and phagocytosis; it does not regulate plasma LDL cholesterol levels in mouse or human studies."},"narrative":{"mechanistic_narrative":"STAP1 (BRDG1) is a PH- and SH2-domain-containing adaptor/scaffold protein that operates downstream of tyrosine kinases and immune receptors in hematopoietic and immune cells, becoming tyrosine-phosphorylated upon receptor engagement and assembling signaling complexes that amplify kinase output [PMID:10518561, PMID:10679268]. It was first defined as a substrate and positive-feedback amplifier of the Tec tyrosine kinase, phosphorylated directly by Tec in a manner requiring both its own PH and SH2 domains, and undergoing phosphorylation in B cells in response to BCR stimulation [PMID:10518561]; in parallel it acts downstream of c-kit, with its SH2 domain engaging tyrosine-phosphorylated c-kit and STAT5 [PMID:10679268]. Through these domains STAP1 nucleates distinct complexes: its SH2 domain binds BCR-ABL and stabilizes the BCR-ABL protein in CML cells while its PH domain binds STAT5a, with STAP1 itself transcriptionally driven by NFATc1 [PMID:33845308], and in T cells it engages LCK and phospholipase C-γ1 to potentiate TCR signaling, IL-2 production and proliferation [PMID:40288812]. Downstream, STAP1 augments BCR-mediated CREB activation in an isoform- and PH-domain-dependent manner [PMID:11716489], and in microglia its overexpression remodels the cytoskeleton, engages the M-CSF receptor c-Fms, and reprograms activation, migration and phagocytosis [PMID:19100238, PMID:37462801]. A STAP1-derived peptide blocking the STAP1–LCK interaction suppresses TCR signaling and ameliorates experimental autoimmune encephalomyelitis, establishing the scaffold as a tractable immunomodulatory target [PMID:40288812]. Despite its identification as a candidate familial hypercholesterolemia gene, rigorous knockout, bone-marrow transplant, and human variant-carrier studies establish that STAP1 does not regulate plasma LDL cholesterol [PMID:31996024].","teleology":[{"year":1999,"claim":"Established STAP1/BRDG1 as a bona fide docking protein in tyrosine kinase signaling by showing it is a direct Tec substrate that feeds back to amplify Tec activity, defining its core adaptor function.","evidence":"Yeast two-hybrid, in vitro kinase assay, co-expression and phosphorylation assays in 293 cells with kinase specificity controls, and BCR stimulation of B cells","pmids":["10518561"],"confidence":"High","gaps":["Physiological receptor context beyond Tec/BCR not defined","Phosphorylation sites and the structural basis of feedback amplification not mapped"]},{"year":2000,"claim":"Extended STAP1 function to a second kinase axis by showing it acts downstream of c-kit in hematopoietic cells and that its SH2 domain binds phosphorylated c-kit and STAT5, indicating selective receptor coupling.","evidence":"Yeast two-hybrid with c-kit bait, in vitro SH2-domain binding assays, phosphorylation assay in 293 cells, RT-PCR expression analysis","pmids":["10679268"],"confidence":"Medium","gaps":["Interactions shown largely in vitro/heterologous cells","Endogenous c-kit–STAP1 complex and downstream consequence not established"]},{"year":2001,"claim":"Connected STAP1 to a transcriptional output by showing it selectively amplifies BCR-driven CREB activation, and assigned the PH domain a functional role via isoform-dependent activity.","evidence":"Promoter reporter assays (CREB, c-Jun, c-MYC, BCL-xL), overexpression in B cells, alternative splicing and tyrosine phosphorylation analysis","pmids":["11716489"],"confidence":"Medium","gaps":["Mechanism linking STAP1 to CREB not resolved","Overexpression-based; endogenous requirement untested"]},{"year":2008,"claim":"Implicated STAP1 in microglial biology by showing ectopic expression alters cytoskeleton, engages c-Fms, and shifts cells toward an activated, cytotoxic, low-migration phenotype.","evidence":"Ectopic expression in BV-2 microglia, co-IP with c-Fms, phosphorylation, morphology, migration and cytotoxicity assays","pmids":["19100238"],"confidence":"Medium","gaps":["Relies on overexpression in a single cell line","Loss-of-function effect on endogenous microglia not tested"]},{"year":2020,"claim":"Resolved the candidate disease hypothesis by demonstrating, across mouse and human systems, that STAP1 does not regulate plasma LDL cholesterol, redirecting attention to its immune/hematopoietic roles.","evidence":"Stap1 knockout mice, bone marrow transplant into Ldlr-/- mice, PBMC variant-carrier analysis, and PBMC–HepG2 coculture LDL-uptake assays","pmids":["31996024"],"confidence":"High","gaps":["Does not address non-lipid phenotypes of STAP1 loss","Mechanism of original genetic association left unexplained"]},{"year":2021,"claim":"Defined STAP1 as a domain-bipartite scaffold in CML, with SH2-mediated BCR-ABL binding stabilizing the oncoprotein and PH-mediated STAT5a binding, and identified NFATc1 as its transcriptional driver.","evidence":"Deletion-mutant co-immunoprecipitation, STAP1-promoter luciferase reporter, and western blots for BCR-ABL stability","pmids":["33845308"],"confidence":"Medium","gaps":["Mechanism of BCR-ABL stabilization unresolved","Single-lab co-IP without reciprocal/endogenous confirmation"]},{"year":2023,"claim":"Linked STAP1 to tumor-associated immune modulation by showing microglial overexpression promotes M2-like polarization and suppresses phagocytosis, aiding glioma progression.","evidence":"STAP1-overexpressing BV-2 cells, phagocytosis flow cytometry/microscopy, ARG1/cofilin readouts, and orthotopic/subcutaneous glioma mouse models","pmids":["37462801"],"confidence":"Medium","gaps":["Causal molecular link to IL-6/STAT3 and cofilin not mechanistically dissected","Overexpression-based; endogenous loss not tested"]},{"year":2025,"claim":"Established STAP1 as a positive regulator of TCR signaling through LCK and PLC-γ1 binding and provided proof-of-concept that disrupting the STAP1–LCK interaction is therapeutically actionable in autoimmunity.","evidence":"STAP1-derived inhibitory peptide (iSP1), binding-inhibition, IL-2 and proliferation assays, and an EAE mouse model with Th1/Th17 infiltration analysis","pmids":["40288812"],"confidence":"Medium","gaps":["Direct structural definition of the STAP1–LCK interface not provided","Single-lab study; on-target specificity of iSP1 in vivo not fully delineated"]},{"year":null,"claim":"How STAP1 is recruited to specific receptors versus others, the structural basis of its PH/SH2 domain selectivity, and its endogenous loss-of-function physiology across immune cell types remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of STAP1 complexes","Endogenous knockout phenotype in immune cells largely uncharacterized","Phosphorylation-site map and feedback mechanism undefined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1,4,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,4,7]}],"localization":[],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,7]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,4]}],"complexes":[],"partners":["TEC","KIT","STAT5A","BCR-ABL","LCK","PLCG1","CSF1R"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9ULZ2","full_name":"Signal-transducing adaptor protein 1","aliases":["BCR downstream-signaling protein 1","Docking protein BRDG1","Stem cell adaptor protein 1"],"length_aa":295,"mass_kda":34.3,"function":"In BCR signaling, appears to function as a docking protein acting downstream of TEC and participates in a positive feedback loop by increasing the activity of TEC","subcellular_location":"Nucleus; Cytoplasm; Mitochondrion","url":"https://www.uniprot.org/uniprotkb/Q9ULZ2/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/STAP1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/STAP1","total_profiled":1310},"omim":[{"mim_id":"604298","title":"SIGNAL TRANSDUCING ADAPTOR FAMILY MEMBER 1; STAP1","url":"https://www.omim.org/entry/604298"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear bodies","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Tissue enriched","tissue_distribution":"Detected in some","driving_tissues":[{"tissue":"lymphoid tissue","ntpm":47.7}],"url":"https://www.proteinatlas.org/search/STAP1"},"hgnc":{"alias_symbol":["STAP-1","BRDG1"],"prev_symbol":[]},"alphafold":{"accession":"Q9ULZ2","domains":[{"cath_id":"2.30.29.30","chopping":"11-153","consensus_level":"high","plddt":87.1481,"start":11,"end":153},{"cath_id":"3.30.505.10","chopping":"183-259","consensus_level":"high","plddt":86.7301,"start":183,"end":259}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULZ2","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULZ2-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9ULZ2-F1-predicted_aligned_error_v6.png","plddt_mean":78.5},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=STAP1","jax_strain_url":"https://www.jax.org/strain/search?query=STAP1"},"sequence":{"accession":"Q9ULZ2","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9ULZ2.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9ULZ2/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9ULZ2"}},"corpus_meta":[{"pmid":"25035151","id":"PMC_25035151","title":"Mutations in STAP1 are associated with autosomal dominant hypercholesterolemia.","date":"2014","source":"Circulation research","url":"https://pubmed.ncbi.nlm.nih.gov/25035151","citation_count":127,"is_preprint":false},{"pmid":"10518561","id":"PMC_10518561","title":"Molecular cloning of a docking protein, BRDG1, that acts downstream of the Tec tyrosine kinase.","date":"1999","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/10518561","citation_count":49,"is_preprint":false},{"pmid":"10679268","id":"PMC_10679268","title":"Molecular cloning of murine STAP-1, the stem-cell-specific adaptor protein containing PH and SH2 domains.","date":"2000","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/10679268","citation_count":38,"is_preprint":false},{"pmid":"31996024","id":"PMC_31996024","title":"Taking One Step Back in Familial Hypercholesterolemia: STAP1 Does Not Alter Plasma LDL (Low-Density Lipoprotein) Cholesterol in Mice and Humans.","date":"2020","source":"Arteriosclerosis, thrombosis, and vascular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31996024","citation_count":29,"is_preprint":false},{"pmid":"33159017","id":"PMC_33159017","title":"CircGLCE alleviates intervertebral disc degeneration by regulating apoptosis and matrix degradation through the targeting of miR-587/STAP1.","date":"2020","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/33159017","citation_count":22,"is_preprint":false},{"pmid":"19100238","id":"PMC_19100238","title":"Induction of STAP-1 promotes neurotoxic activation of microglia.","date":"2008","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/19100238","citation_count":18,"is_preprint":false},{"pmid":"31809983","id":"PMC_31809983","title":"Predicted pathogenic mutations in STAP1 are not associated with clinically defined familial hypercholesterolemia.","date":"2019","source":"Atherosclerosis","url":"https://pubmed.ncbi.nlm.nih.gov/31809983","citation_count":17,"is_preprint":false},{"pmid":"30308187","id":"PMC_30308187","title":"A rare STAP1 mutation incompletely associated with familial hypercholesterolemia.","date":"2018","source":"Clinica chimica acta; international journal of clinical chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30308187","citation_count":17,"is_preprint":false},{"pmid":"31427613","id":"PMC_31427613","title":"Evaluation of the role of STAP1 in Familial Hypercholesterolemia.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31427613","citation_count":15,"is_preprint":false},{"pmid":"29330417","id":"PMC_29330417","title":"High STAP1 expression in DUX4-rearranged cases is not suitable as therapeutic target in pediatric B-cell precursor acute lymphoblastic leukemia.","date":"2018","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29330417","citation_count":12,"is_preprint":false},{"pmid":"11716489","id":"PMC_11716489","title":"Isoform-dependent interaction of BRDG1 with Tec kinase.","date":"2001","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11716489","citation_count":11,"is_preprint":false},{"pmid":"33845308","id":"PMC_33845308","title":"Positive interactions between STAP-1 and BCR-ABL influence chronic myeloid leukemia cell proliferation and survival.","date":"2021","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/33845308","citation_count":8,"is_preprint":false},{"pmid":"37462801","id":"PMC_37462801","title":"Signal-transducing adaptor protein 1 (STAP1) in microglia promotes the malignant progression of glioma.","date":"2023","source":"Journal of neuro-oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37462801","citation_count":7,"is_preprint":false},{"pmid":"33228548","id":"PMC_33228548","title":"Mice lacking global Stap1 expression do not manifest hypercholesterolemia.","date":"2020","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/33228548","citation_count":3,"is_preprint":false},{"pmid":"32828708","id":"PMC_32828708","title":"Failure of cosegregation between a rare STAP1 missense variant and hypercholesterolemia.","date":"2020","source":"Journal of clinical lipidology","url":"https://pubmed.ncbi.nlm.nih.gov/32828708","citation_count":3,"is_preprint":false},{"pmid":"40288812","id":"PMC_40288812","title":"STAP-1-derived peptide suppresses TCR-mediated T cell activation and ameliorates immune diseases by inhibiting STAP-1-LCK binding.","date":"2025","source":"ImmunoHorizons","url":"https://pubmed.ncbi.nlm.nih.gov/40288812","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.11.19.689382","title":"Gut metabolite IPA alleviates white matter post-ICH injury by enhancing myelin debris phagocytosis via  <i>Stap1</i>  inhibition","date":"2025-11-20","source":"bioRxiv","url":"https://doi.org/10.1101/2025.11.19.689382","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10899,"output_tokens":2758,"usd":0.037033,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9855,"output_tokens":3207,"usd":0.064725,"stage2_stop_reason":"end_turn"},"total_usd":0.101758,"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\": 1999,\n      \"finding\": \"BRDG1 (STAP1) was identified as a docking protein that acts downstream of the Tec tyrosine kinase. Tec and Pyk2, but not Btk, Bmx, Lyn, Syk, or c-Abl, induced marked tyrosine phosphorylation of BRDG1 in 293 cells. BRDG1 was also directly phosphorylated by Tec in vitro. Efficient phosphorylation required the PH and SH2 domains as well as the kinase domain of Tec. BRDG1 participated in a positive feedback loop by increasing Tec activity. Endogenous BRDG1 underwent tyrosine phosphorylation in response to BCR stimulation in B cells.\",\n      \"method\": \"Yeast two-hybrid, in vitro kinase assay, co-expression in 293 cells, tyrosine phosphorylation assays, BCR stimulation of B cell line\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — direct in vitro kinase assay plus cell-based phosphorylation assays with multiple kinase specificity controls and endogenous validation in B cells\",\n      \"pmids\": [\"10518561\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Murine STAP-1 was identified as an adaptor protein containing PH and SH2 domains that acts downstream of c-kit in hematopoietic stem cells. In 293 cells, STAP-1 was tyrosine-phosphorylated by activated c-kit. The STAP-1 SH2 domain interacted with tyrosine-phosphorylated proteins including c-kit and STAT5 in vitro. Two-hybrid assay showed STAP-1 bound c-kit and c-fms but not JAK2 or Pyk2.\",\n      \"method\": \"Yeast two-hybrid screen with c-kit as bait, in vitro binding assay (SH2 domain), tyrosine phosphorylation assay in 293 cells, RT-PCR expression analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus in vitro binding assay and cell-based phosphorylation; single lab, two orthogonal methods\",\n      \"pmids\": [\"10679268\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"BRDG1 (STAP1) overexpression strongly augments BCR-mediated activation of CREB but not c-Jun or promoters of c-MYC and BCL-xL. Three isoforms generated by alternative splicing differ in their PH domain; both tyrosine phosphorylation and CREB-activating ability of BRDG1 were isoform-dependent, implicating the PH domain in these functions.\",\n      \"method\": \"Reporter gene assays (CREB, c-Jun, c-MYC, BCL-xL promoters), overexpression in B cells, alternative splicing analysis, tyrosine phosphorylation assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional reporter assays with isoform-specific deletion analysis; single lab, two orthogonal approaches\",\n      \"pmids\": [\"11716489\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Ectopic expression of STAP-1 in BV-2 microglia changed morphology and cytoskeletal organization, transforming ramified cells to an activated state. STAP-1 overexpression led to interaction with the M-CSF receptor/c-Fms and diminished its ligand-dependent phosphorylation. STAP-1-expressing cells showed strongly reduced migration and increased cytotoxicity against photoreceptor-like cells.\",\n      \"method\": \"Ectopic STAP-1 expression in BV-2 microglia, morphology and cytoskeletal analysis, co-immunoprecipitation with c-Fms, phosphorylation assay, migration assay, cytotoxicity assay\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — overexpression with multiple functional readouts (morphology, co-IP, phosphorylation, migration, cytotoxicity); single lab\",\n      \"pmids\": [\"19100238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"STAP-1 interacts with BCR-ABL through its SH2 domain and with STAT5a through its PH domain, functioning as a scaffold protein. Binding of STAP-1 to BCR-ABL stabilizes the BCR-ABL protein in CML cells. NFATc1 activates the STAP-1 promoter and induces STAP-1 mRNA expression, linking Ca2+/NFAT signaling to STAP-1 upregulation in CML.\",\n      \"method\": \"Deletion mutant co-immunoprecipitation, luciferase reporter assay for STAP-1 promoter, western blotting for BCR-ABL protein stability\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — domain-mapping by deletion mutants with co-IP plus promoter reporter assay; single lab, two orthogonal methods\",\n      \"pmids\": [\"33845308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Whole-body Stap1 knockout mice showed no changes in plasma lipid levels compared with controls. Bone marrow transplant of Stap1-/- marrow into Ldlr-/- mice did not alter plasma lipid levels or atherosclerotic lesions. PBMC from STAP1 variant carriers showed no difference in LDLR mRNA/protein or LDL uptake by HepG2 cells in coculture experiments. These results argue against a direct functional role of STAP1 in LDL cholesterol regulation.\",\n      \"method\": \"Stap1 knockout mouse model, bone marrow transplantation, coculture assay (PBMCs + HepG2), LDLR mRNA/protein quantification, LDL uptake assay\",\n      \"journal\": \"Arteriosclerosis, thrombosis, and vascular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal in vivo and in vitro approaches (KO mouse, BMT, coculture) all yielding negative results for lipid regulation; single lab but highly rigorous\",\n      \"pmids\": [\"31996024\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"STAP1 overexpression in BV-2 microglia promoted M2-like polarization by increasing ARG1 expression (associated with the IL-6/STAT3 pathway) and inhibited phagocytosis (associated with decreased cofilin and filopodia formation), contributing to glioma malignant progression.\",\n      \"method\": \"STAP1-overexpressing BV-2 cell line construction, flow cytometry and fluorescence microscopy for phagocytosis, western blotting/immunofluorescence for ARG1 and cofilin, orthotopic/subcutaneous glioma mouse models with bioluminescence imaging\",\n      \"journal\": \"Journal of neuro-oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — overexpression with multiple functional readouts (phagocytosis, polarization markers, in vivo tumor growth); single lab\",\n      \"pmids\": [\"37462801\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"STAP-1 positively upregulates TCR-mediated T cell activation by interacting with LCK and phospholipase C-γ1. A STAP-1-derived peptide (iSP1) that specifically inhibits the STAP-1–LCK interaction suppressed TCR-mediated signal transduction, IL-2 production, and T cell proliferation, and prevented progression of experimental autoimmune encephalomyelitis by inhibiting Th1 and Th17 cell infiltration.\",\n      \"method\": \"STAP-1-derived inhibitory peptide (iSP1), in vitro binding inhibition assay, IL-2 production assay, T cell proliferation assay, EAE mouse model with Th1/Th17 cell infiltration analysis\",\n      \"journal\": \"ImmunoHorizons\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — peptide-based binding inhibition with multiple in vitro and in vivo functional readouts; single lab\",\n      \"pmids\": [\"40288812\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In vitro, the gut metabolite IPA increased BV2 microglia myelin debris phagocytosis by inhibiting Stap1 expression, suggesting that STAP1 negatively regulates microglial phagocytic activity.\",\n      \"method\": \"Stap1 knockdown in BV2 microglia, co-culture with myelin debris, phagocytosis assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single preprint, single method (knockdown + phagocytosis assay), no peer review\",\n      \"pmids\": [\"bio_10.1101_2025.11.19.689382\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"STAP1 (BRDG1) is a PH- and SH2-domain-containing adaptor protein expressed predominantly in immune and hematopoietic cells that functions downstream of receptor tyrosine kinases (Tec, c-kit, BCR-ABL) and immune receptors (BCR, TCR) by being phosphorylated on tyrosine residues, scaffolding signaling complexes (including STAT5a and LCK), amplifying kinase activity in a positive feedback manner, activating CREB-dependent transcription, and modulating microglial activation and phagocytosis; it does not regulate plasma LDL cholesterol levels in mouse or human studies.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"STAP1 (BRDG1) is a PH- and SH2-domain-containing adaptor/scaffold protein that operates downstream of tyrosine kinases and immune receptors in hematopoietic and immune cells, becoming tyrosine-phosphorylated upon receptor engagement and assembling signaling complexes that amplify kinase output [#0, #1]. It was first defined as a substrate and positive-feedback amplifier of the Tec tyrosine kinase, phosphorylated directly by Tec in a manner requiring both its own PH and SH2 domains, and undergoing phosphorylation in B cells in response to BCR stimulation [#0]; in parallel it acts downstream of c-kit, with its SH2 domain engaging tyrosine-phosphorylated c-kit and STAT5 [#1]. Through these domains STAP1 nucleates distinct complexes: its SH2 domain binds BCR-ABL and stabilizes the BCR-ABL protein in CML cells while its PH domain binds STAT5a, with STAP1 itself transcriptionally driven by NFATc1 [#4], and in T cells it engages LCK and phospholipase C-\\u03b31 to potentiate TCR signaling, IL-2 production and proliferation [#7]. Downstream, STAP1 augments BCR-mediated CREB activation in an isoform- and PH-domain-dependent manner [#2], and in microglia its overexpression remodels the cytoskeleton, engages the M-CSF receptor c-Fms, and reprograms activation, migration and phagocytosis [#3, #6]. A STAP1-derived peptide blocking the STAP1\\u2013LCK interaction suppresses TCR signaling and ameliorates experimental autoimmune encephalomyelitis, establishing the scaffold as a tractable immunomodulatory target [#7]. Despite its identification as a candidate familial hypercholesterolemia gene, rigorous knockout, bone-marrow transplant, and human variant-carrier studies establish that STAP1 does not regulate plasma LDL cholesterol [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established STAP1/BRDG1 as a bona fide docking protein in tyrosine kinase signaling by showing it is a direct Tec substrate that feeds back to amplify Tec activity, defining its core adaptor function.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro kinase assay, co-expression and phosphorylation assays in 293 cells with kinase specificity controls, and BCR stimulation of B cells\",\n      \"pmids\": [\"10518561\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological receptor context beyond Tec/BCR not defined\", \"Phosphorylation sites and the structural basis of feedback amplification not mapped\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Extended STAP1 function to a second kinase axis by showing it acts downstream of c-kit in hematopoietic cells and that its SH2 domain binds phosphorylated c-kit and STAT5, indicating selective receptor coupling.\",\n      \"evidence\": \"Yeast two-hybrid with c-kit bait, in vitro SH2-domain binding assays, phosphorylation assay in 293 cells, RT-PCR expression analysis\",\n      \"pmids\": [\"10679268\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interactions shown largely in vitro/heterologous cells\", \"Endogenous c-kit\\u2013STAP1 complex and downstream consequence not established\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Connected STAP1 to a transcriptional output by showing it selectively amplifies BCR-driven CREB activation, and assigned the PH domain a functional role via isoform-dependent activity.\",\n      \"evidence\": \"Promoter reporter assays (CREB, c-Jun, c-MYC, BCL-xL), overexpression in B cells, alternative splicing and tyrosine phosphorylation analysis\",\n      \"pmids\": [\"11716489\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking STAP1 to CREB not resolved\", \"Overexpression-based; endogenous requirement untested\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Implicated STAP1 in microglial biology by showing ectopic expression alters cytoskeleton, engages c-Fms, and shifts cells toward an activated, cytotoxic, low-migration phenotype.\",\n      \"evidence\": \"Ectopic expression in BV-2 microglia, co-IP with c-Fms, phosphorylation, morphology, migration and cytotoxicity assays\",\n      \"pmids\": [\"19100238\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relies on overexpression in a single cell line\", \"Loss-of-function effect on endogenous microglia not tested\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Resolved the candidate disease hypothesis by demonstrating, across mouse and human systems, that STAP1 does not regulate plasma LDL cholesterol, redirecting attention to its immune/hematopoietic roles.\",\n      \"evidence\": \"Stap1 knockout mice, bone marrow transplant into Ldlr-/- mice, PBMC variant-carrier analysis, and PBMC\\u2013HepG2 coculture LDL-uptake assays\",\n      \"pmids\": [\"31996024\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address non-lipid phenotypes of STAP1 loss\", \"Mechanism of original genetic association left unexplained\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined STAP1 as a domain-bipartite scaffold in CML, with SH2-mediated BCR-ABL binding stabilizing the oncoprotein and PH-mediated STAT5a binding, and identified NFATc1 as its transcriptional driver.\",\n      \"evidence\": \"Deletion-mutant co-immunoprecipitation, STAP1-promoter luciferase reporter, and western blots for BCR-ABL stability\",\n      \"pmids\": [\"33845308\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of BCR-ABL stabilization unresolved\", \"Single-lab co-IP without reciprocal/endogenous confirmation\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linked STAP1 to tumor-associated immune modulation by showing microglial overexpression promotes M2-like polarization and suppresses phagocytosis, aiding glioma progression.\",\n      \"evidence\": \"STAP1-overexpressing BV-2 cells, phagocytosis flow cytometry/microscopy, ARG1/cofilin readouts, and orthotopic/subcutaneous glioma mouse models\",\n      \"pmids\": [\"37462801\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal molecular link to IL-6/STAT3 and cofilin not mechanistically dissected\", \"Overexpression-based; endogenous loss not tested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Established STAP1 as a positive regulator of TCR signaling through LCK and PLC-\\u03b31 binding and provided proof-of-concept that disrupting the STAP1\\u2013LCK interaction is therapeutically actionable in autoimmunity.\",\n      \"evidence\": \"STAP1-derived inhibitory peptide (iSP1), binding-inhibition, IL-2 and proliferation assays, and an EAE mouse model with Th1/Th17 infiltration analysis\",\n      \"pmids\": [\"40288812\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct structural definition of the STAP1\\u2013LCK interface not provided\", \"Single-lab study; on-target specificity of iSP1 in vivo not fully delineated\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How STAP1 is recruited to specific receptors versus others, the structural basis of its PH/SH2 domain selectivity, and its endogenous loss-of-function physiology across immune cell types remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of STAP1 complexes\", \"Endogenous knockout phenotype in immune cells largely uncharacterized\", \"Phosphorylation-site map and feedback mechanism undefined\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1, 4, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 4, 7]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 4]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TEC\", \"KIT\", \"STAT5A\", \"BCR-ABL\", \"LCK\", \"PLCG1\", \"CSF1R\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}