{"gene":"SNX9","run_date":"2026-06-10T07:46:37","timeline":{"discoveries":[{"year":2005,"finding":"SNX9 binds directly to dynamin-1 and dynamin-2, stimulates dynamin assembly, potentiates dynamin's basal GTPase activity, and stimulates assembly-stimulated GTPase activity on liposomes. SNX9 is transiently recruited to clathrin-coated pits during late stages of vesicle formation coinciding with dynamin recruitment, and siRNA-mediated knockdown of SNX9 inhibits transferrin internalization in HeLa cells.","method":"Direct binding assays, GTPase activity assays on liposomes, TIRF microscopy in live cells, siRNA knockdown with transferrin internalization readout","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro reconstitution of dynamin stimulation, live-cell TIRF microscopy, and functional KD with defined endocytic readout; multiple orthogonal methods in a single rigorous study","pmids":["15703209"],"is_preprint":false},{"year":1999,"finding":"SNX9 (SH3PX1) interacts with the cytoplasmic domains of the metalloprotease disintegrins MDC9 (ADAM9) and MDC15 via its SH3 domain, as established by yeast two-hybrid, bacterial fusion protein pulldowns, and co-immunoprecipitation from eukaryotic cells. Both proteins preferentially bind the precursor but not the processed form of MDC9 and MDC15.","method":"Yeast two-hybrid, GST-fusion protein pulldowns, co-immunoprecipitation from COS-7 cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and pulldown with two orthogonal methods, single lab","pmids":["10531379"],"is_preprint":false},{"year":2008,"finding":"SNX9 deforms plasma membranes and liposomes into narrow tubules via its BAR and PX domains plus low-complexity (LC) domain; it recruits N-WASP and dynamin 2 to these tubules via its SH3 domain. The LC domain binds the Arp2/3 complex. SNX9 binds PtdIns(4)P-5-kinases via its PX domain and stimulates their kinase activity, suggesting a positive feedback loop regulating phosphoinositide levels at endocytic sites.","method":"In vitro liposome tubulation assays, domain truncation/mutation analysis, co-immunoprecipitation, kinase activity assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple in vitro reconstitution assays with domain mutants, kinase activity assay, and cell-based co-IP; multiple orthogonal methods","pmids":["18388313"],"is_preprint":false},{"year":2002,"finding":"SNX9 (SH3PX1) interacts with ACK2 via the ACK2 proline-rich domain and SNX9 SH3 domain. ACK2, clathrin, and SNX9 form a complex in cells. ACK2 mediates EGF-stimulated tyrosine phosphorylation of SNX9, and co-expression of ACK2 with SNX9 leads to constitutive SNX9 phosphorylation. Together ACK2 and SNX9 promote EGF receptor degradation.","method":"Co-immunoprecipitation, kinase-dead mutant ACK2(K158R) to block phosphorylation, EGF receptor degradation assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP with kinase-dead mutant validation and functional EGF receptor degradation readout, single lab","pmids":["11799118"],"is_preprint":false},{"year":2005,"finding":"SNX9 SH3 domain binds synaptojanin-1 at multiple sites within its proline-rich region, and binds ACK1 at a single dominant site (residues 920–955). In the presence of SNX9, synaptojanin colocalizes with ACK1-containing vesicles, indicating SNX9 acts as an adaptor linking synaptojanin-1 to ACK1.","method":"In vivo biotinylated GST-SH3 domain blot overlays, synthetic peptide arrays, co-immunofluorescence localization","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay with peptide array mapping and colocalization, single lab with two methods","pmids":["16137687"],"is_preprint":false},{"year":2006,"finding":"Dimerization of SNX9 (SH3PX1) mediated by its BAR/coiled-coil domain at the C-terminus is required for ACK2-catalyzed and EGF-stimulated tyrosine phosphorylation of SNX9, interaction with ACK2, and proper intracellular localization. Truncation of as few as 13 C-terminal residues abolishes dimerization, phosphorylation, ACK2 binding, and normal localization.","method":"Domain truncation mutagenesis, co-immunoprecipitation, intracellular localization assays","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic truncation mutants with multiple functional readouts, single lab","pmids":["16316319"],"is_preprint":false},{"year":2010,"finding":"SNX18 and SNX9 can form a heterodimer, colocalize in tubular membrane structures, and are functionally redundant in clathrin-mediated endocytosis. Both interact with dynamin and stimulate its basal GTPase activity, and both interact with N-WASP and synaptojanin. TIRF microscopy shows SNX18 is transiently recruited to clathrin-coated pits coinciding with dynamin and SNX9.","method":"Co-immunoprecipitation, GTPase activity assay, siRNA knockdown with transferrin uptake readout, TIRF microscopy","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (GTPase assay, Co-IP, TIRF, functional KD) in a single lab","pmids":["20427313"],"is_preprint":false},{"year":2013,"finding":"On curved membranes containing both PI(3)P and PI(4,5)P2, SNX9 acts as a specific adaptor replacing toca-1 to mobilize N-WASP and the Arp2/3 complex for actin polymerization, bypassing the requirement for toca-1 in a Cdc42-dependent manner.","method":"Cell-free reconstitution of actin polymerization on liposomes with defined lipid compositions","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Moderate — cell-free reconstitution with defined lipid compositions and systematic component omission; single lab but rigorous in vitro approach","pmids":["23589871"],"is_preprint":false},{"year":2012,"finding":"SNX9 is required for progression through mitosis: siRNA depletion induces multinucleation (cytokinesis failure), disrupts MRLC(S19) localization during ingression, blocks recruitment of Rab11-positive recycling endosomes to the intracellular bridge, and disrupts Golgi localization during cytokinesis. SNX9 depletion also delays chromosome alignment and segregation during metaphase without blocking transferrin uptake, indicating a non-endocytic mitotic role.","method":"siRNA knockdown, time-lapse microscopy, immunofluorescence localization, transferrin uptake assay","journal":"Journal of cell science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA with time-lapse and multiple localization readouts distinguishing endocytic and non-endocytic roles, single lab","pmids":["22718350"],"is_preprint":false},{"year":2010,"finding":"The bacterial effector EspF binds SNX9 and exploits SNX9's membrane-deforming activity to promote EPEC invasion of intestinal epithelial cells. Invasion requires the SNX9 lipid-binding domains and the EspF SNX9-binding domain, as well as clathrin-coated pit assembly, but is independent of dynamin activity.","method":"Point mutagenesis of SNX9 lipid-binding domains, EspF truncation analysis, pharmacological inhibition of CCP assembly and dynamin, bacterial invasion assay","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple mutants and inhibitors with functional invasion readout, single lab","pmids":["20088948"],"is_preprint":false},{"year":2016,"finding":"SNX9 controls activation of RhoA and Cdc42 GTPases, regulates cell motility via RhoA-ROCK and N-WASP pathways, and is required for RhoGTPase-dependent clathrin-independent endocytosis. SNX9 can functionally substitute for GRAF1 (a RhoGAP) in this pathway, establishing SNX9 as a multifunctional scaffold coordinating endocytosis and invasion.","method":"SNX9 knockdown with RhoA/Cdc42 activation assays, cell invasion assay, clathrin-independent endocytosis assay, rescue with GRAF1","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with multiple pathway readouts and functional substitution experiment, single lab","pmids":["26960793"],"is_preprint":false},{"year":2018,"finding":"SNX9 interacts with ADAM9 and regulates ADAM9 protein levels at the cell surface. Single SNX9 knockdown increased ADAM9 levels at the plasma membrane and enhanced shedding of EphB4 (an ADAM9 substrate). Double knockdown of SNX9 and SNX18 was required to significantly decrease ADAM9 internalization, demonstrating redundancy for internalization but a non-redundant SNX9 role in controlling total ADAM9 levels.","method":"Co-immunoprecipitation, siRNA knockdown (single and double), cell-surface ADAM9 quantification, EphB4 shedding assay","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP, redundancy dissected by double KD, functional shedding assay, single lab","pmids":["29622675"],"is_preprint":false},{"year":2019,"finding":"In Drosophila, SH3PX1 (SNX9 ortholog) acts in an endocytosis-autophagy network including Dynamin, Rab5, Rab7, and Atg proteins to promote lysosomal degradation of ligand-activated EGFRs. Loss of SH3PX1 stabilizes EGFRs and routes them via Rab11-dependent recycling endosomes back to the plasma membrane, hyperactivating ERK, calcium signaling, and ER stress to stimulate intestinal stem cell proliferation.","method":"Genetic screen, epistasis with endocytic/autophagic pathway genes, Rab11-dependent recycling assay, ERK pathway readout in Drosophila ISCs","journal":"Developmental cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with multiple pathway components and functional readouts, Drosophila model","pmids":["31006650"],"is_preprint":false},{"year":2020,"finding":"SNX9 is an endogenous component of filopodia. Antibodies targeting SNX9 caused shorter filopodia-like structures in vitro. SNX9 is found at specialized filopodia in Xenopus development and at filopodia hijacked during Chlamydia cell entry.","method":"Phage display phenotypic antibody screen, in vitro filopodia-like structure assay, immunolocalization in Xenopus and during Chlamydia infection","journal":"The Journal of cell biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — phage display functional screen combined with in vivo localization and pathogen entry model, single lab","pmids":["32328641"],"is_preprint":false},{"year":2022,"finding":"Upon CD28 triggering, SNX9 is recruited to CD28 clusters at the immunological synapse and generates membrane tubulation from CD28 clusters (shown by 3D correlative light and electron microscopy). SNX9 regulates the stability of CD28 clusters, CD28 phosphorylation, and IL-2 cytokine production.","method":"3D correlative light and electron microscopy (CLEM), super-resolution microscopy, CD28 phosphorylation assay, IL-2 production assay","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — CLEM showing tubulation from CD28 clusters with functional signaling readouts, single lab","pmids":["35050850"],"is_preprint":false},{"year":2022,"finding":"The crystal structure of SNX9 SH3 in complex with an eastern equine encephalitis virus (EEEV) nsP3 peptide reveals that the length and composition of the n-Src loop determines specificity for an unusual RxAPxxP class I SH3 binding motif (with Ala instead of Pro/Leu at the hydrophobic position). The HTLV-1 Gag polyprotein also contains this motif, and it is required for efficient HTLV-1 infection.","method":"X-ray crystal structure of SH3–peptide complex, mutagenesis of binding interface residues, affinity measurements, viral infection assay","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with mutagenesis and functional viral infection readout, single lab but Tier 1 method","pmids":["35390274"],"is_preprint":false},{"year":2023,"finding":"SNX9 deletion in CD8 T cells decreases PLCγ1, Ca2+, and NFATc2-mediated TCR signaling downstream of TCR/CD28 stimulation and reduces expression of exhaustion transcription factors NR4A1/3 and TOX, resulting in enhanced memory differentiation, IFNγ secretion, and improved CAR-T anti-tumor efficacy in vivo.","method":"Pooled CRISPR-Cas9 screen, individual gene knockout validation, calcium flux assay, NFATc2 signaling readout, adoptive transfer in vivo tumor model","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — CRISPR screen validated individually with multiple signaling readouts plus in vivo functional assay, replicated across multiple T cell contexts","pmids":["36732507"],"is_preprint":false},{"year":2022,"finding":"In Drosophila, Sh3px1 (SNX9 ortholog) facilitates selective autophagy of the TAK1/TAB2 (Tak1/Tab2) kinase complex by interacting with Tab2 and the autophagy protein Atg8a, thereby targeting the complex to the autophagy platform and preventing constitutive activation of the IMD innate immune pathway.","method":"Co-immunoprecipitation, genetic epistasis in Drosophila IMD pathway, autophagy flux assays","journal":"Cell reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP and genetic epistasis with defined pathway readout in Drosophila, single lab","pmids":["35081354"],"is_preprint":false},{"year":2018,"finding":"Drosophila Nedd4-long (dNedd4Lo) directly binds SH3PX1 (SNX9 ortholog) via the SH3PX1 SH3 domain interacting with a proline-rich sequence in the dNedd4Lo Middle region. Postsynaptic overexpression of dNedd4Lo reduces SH3PX1 levels at the subsynaptic reticulum and impairs presynaptic neurotransmitter release at the neuromuscular junction.","method":"In vitro binding assay, co-immunoprecipitation in S2 cells, in vivo overexpression with immunofluorescence and electrophysiology","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding validated in vitro and in cells with functional synaptic readout, single lab","pmids":["30518551"],"is_preprint":false},{"year":2020,"finding":"SNX9 interacts directly with YAP and increases LATS1-mediated phosphorylation of YAP, resulting in cytoplasmic retention of YAP, decreased YAP/TEAD4 transcriptional activity, and suppression of Hippo target gene expression and cyst development in polycystic kidney disease cells.","method":"Co-immunoprecipitation, YAP phosphorylation assay, transcriptional reporter assay, gain- and loss-of-function in ADPKD cell lines and Pkd1-/- mice","journal":"Frontiers in cell and developmental biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-IP with functional readouts but single lab, single paper with no independent validation of the direct interaction mechanism","pmids":["32974348"],"is_preprint":false},{"year":2024,"finding":"SNX9 (and SNX18) act as cargo adaptors for β-arrestin-independent GPCR endocytosis. SNX9 is recruited to CXCR4 at the plasma membrane and interacts directly with the receptor's carboxyl-terminal tail in a phosphorylation-dependent manner to promote agonist-stimulated CXCR4 endocytosis.","method":"siRNA knockdown of SNX9/SNX18 and β-arrestins with CXCR4 internalization assay, co-immunoprecipitation of SNX9 with CXCR4 C-tail","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — receptor internalization assay with KD and direct binding assay, single lab with two methods","pmids":["39511325"],"is_preprint":false},{"year":2025,"finding":"SNX9 forms a complex with NUMB (Ex3-containing isoform) at the plasma membrane and recruits p53 in a SNX9-dependent manner. This complex is internalized and trafficked to multivesicular bodies for exosomal secretion of p53, requiring both SNX9 and NUMB.","method":"Co-immunoprecipitation, live-cell imaging, exosome isolation and p53 tracking, SNX9 knockdown with functional p53 trafficking readout","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint, single lab, co-IP and imaging without independent replication","pmids":["bio_10.1101_2025.08.16.670648"],"is_preprint":true},{"year":2025,"finding":"The SNX9 PX domain uses a non-canonical interface to selectively bind and sequester PI(3,4)P2 over PI(4,5)P2 during macropinocytic membrane ruffling. Mutational disruption of this non-canonical interface abolishes PI(3,4)P2 protection, demonstrating that SNX9 protects PI(3,4)P2 from hydrolysis. Actin assembly by SNX9 requires the combined PX-BAR and SH3 domain network; SNX9 can build both branched and bundled actin networks.","method":"Biolayer interferometry, cell-free reconstitution, live-cell imaging, molecular dynamics simulations, cryo-electron tomography, mutagenesis of PX domain residues","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — multiple orthogonal methods including in vitro reconstitution, cryo-ET, and mutagenesis in a single preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.03.26.645564"],"is_preprint":true},{"year":2025,"finding":"In B cells, SNX9 promotes the association of PI3K with CD19 in an AIM2-dependent manner, facilitating downstream PI3K-AKT signaling, and is involved in BCR/CD19 endocytosis and antigen uptake via SNX9-WASP interaction.","method":"IP-MS to identify SNX9 as AIM2 interactor, co-immunoprecipitation, BCR endocytosis assay, AIM2 knockout mice","journal":"Cell death and differentiation","confidence":"Low","confidence_rationale":"Tier 3 / Weak — IP-MS hit with co-IP and functional assay, single lab, mechanism not fully dissected for SNX9 specifically","pmids":["41437148"],"is_preprint":false},{"year":2026,"finding":"ZG16 physically interacts with SNX9 and recruits the E3 ubiquitin ligase ITCH to promote ubiquitin-proteasome-dependent degradation of SNX9.","method":"IP-LC/MS, co-immunoprecipitation, GST pulldown, ubiquitination assay","journal":"Hepatology international","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-IP and pulldown identifying ubiquitination machinery, single lab, mechanism partially characterized","pmids":["41781795"],"is_preprint":false},{"year":2026,"finding":"RAB40C promotes SNX9 degradation via the ubiquitin-proteasome pathway; silencing RAB40C increases SNX9 expression and influences Hippo signaling pathway target proteins.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown with proliferation/invasion readouts","journal":"Central-European journal of immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — co-IP and functional knockdown, single lab, limited mechanistic detail in abstract","pmids":["42245125"],"is_preprint":false},{"year":2025,"finding":"SNX9 PX-BAR domain binds more PI(4,5)P2 and PI(3)P-containing liposomes than PI(3,4)P2 liposomes in terms of total binding capacity despite similar affinities. Actin assembly by SNX9 on membranes requires both PX-BAR and SH3 domain interactions.","method":"Biolayer interferometry, cell-free actin reconstitution, superresolution microscopy (3D-dSTORM)","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution and biophysical binding assays with superresolution imaging, single lab","pmids":["40105919"],"is_preprint":false}],"current_model":"SNX9 is a multidomain scaffold protein (SH3-PX-BAR) that is transiently recruited to clathrin-coated pits during late-stage vesicle formation, where it directly binds and stimulates dynamin GTPase activity to drive membrane scission; simultaneously, its SH3 domain recruits N-WASP and synaptojanin to coordinate actin polymerization via the Arp2/3 complex, while its PX-BAR domain senses and deforms phosphoinositide-rich membranes (PI(4,5)P2, PI(3)P, and PI(3,4)P2) into tubules; beyond clathrin-mediated endocytosis, SNX9 regulates RhoGTPase-dependent clathrin-independent endocytosis, acts as a cargo adaptor for β-arrestin-independent GPCR internalization, promotes filopodium biogenesis, coordinates membrane remodeling at the immunological synapse to regulate CD28 signaling, mediates T cell exhaustion downstream of TCR/CD28 stimulation by modulating PLCγ1-Ca2+-NFATc2 signaling, and is subject to tyrosine phosphorylation by ACK2 and ubiquitin-proteasome degradation mediated by ITCH and RAB40C."},"narrative":{"mechanistic_narrative":"SNX9 is a multidomain SH3-PX-BAR scaffold that couples membrane deformation to actin dynamics during the late stages of clathrin-mediated endocytosis [PMID:15703209, PMID:18388313]. Through its PX and BAR domains it senses and tubulates phosphoinositide-rich membranes, while its SH3 domain recruits the actin machinery: SNX9 binds and stimulates dynamin GTPase activity to drive vesicle scission [PMID:15703209], recruits N-WASP and dynamin to membrane tubules, engages the Arp2/3 complex via its low-complexity domain, and binds and stimulates PtdIns(4)P-5-kinases to reinforce local phosphoinositide synthesis [PMID:18388313]. On membranes bearing both PI(3)P and PI(4,5)P2, SNX9 acts as an adaptor that mobilizes N-WASP/Arp2/3 actin polymerization in a Cdc42-dependent manner [PMID:23589871], and its PX domain uses a non-canonical interface to selectively bind PI(3,4)P2 during macropinocytic ruffling [PMID:bio_10.1101_2025.03.26.645564]. C-terminal BAR/coiled-coil-mediated dimerization is required for its proper localization and regulation [PMID:16316319]. SNX9 functions partially redundantly with its paralog SNX18, which also heterodimerizes with it and shares dynamin, N-WASP, and synaptojanin interactions [PMID:20427313, PMID:29622675]. Beyond canonical endocytosis, SNX9 supports RhoA/Cdc42-dependent clathrin-independent endocytosis and cell motility [PMID:26960793], filopodium biogenesis [PMID:32328641], cytokinesis and mitotic progression [PMID:22718350], and acts as a cargo adaptor for beta-arrestin-independent GPCR internalization by binding the phosphorylated CXCR4 C-tail [PMID:39511325]. In immune cells, SNX9 is recruited to CD28 clusters at the immunological synapse to generate membrane tubulation and regulate CD28 signaling and IL-2 production [PMID:35050850], and it modulates TCR/CD28-driven PLCγ1-Ca2+-NFATc2 signaling to promote CD8 T cell exhaustion, such that its deletion enhances memory differentiation and CAR-T anti-tumor efficacy [PMID:36732507]. SNX9 also serves as a host factor exploited by pathogens and viruses, including the EPEC effector EspF and an unusual RxAPxxP SH3-binding motif present in EEEV nsP3 and HTLV-1 Gag [PMID:20088948, PMID:35390274].","teleology":[{"year":1999,"claim":"The first identified SNX9 partners established it as an SH3-domain adaptor engaging the cytoplasmic tails of ADAM-family metalloprotease disintegrins, hinting at a role in membrane-protein trafficking.","evidence":"Yeast two-hybrid, GST pulldown, and co-IP from COS-7 cells showing SH3-mediated binding to MDC9/ADAM9 and MDC15 precursors","pmids":["10531379"],"confidence":"Medium","gaps":["Functional consequence of the interaction was not defined","Did not address endocytic or membrane-remodeling activity"]},{"year":2002,"claim":"Linking SNX9 to ACK2 and clathrin revealed it as a tyrosine-phosphorylated component of receptor downregulation, connecting it to growth-factor receptor degradation.","evidence":"Co-IP, kinase-dead ACK2(K158R) mutant, and EGF receptor degradation assay","pmids":["11799118"],"confidence":"Medium","gaps":["Functional role of SNX9 phosphorylation not resolved","Did not establish mechanism of EGFR degradation"]},{"year":2005,"claim":"Biochemical and live-cell work established the core endocytic function: SNX9 directly stimulates dynamin GTPase activity and is recruited to clathrin-coated pits at the scission stage, with knockdown blocking transferrin uptake.","evidence":"In vitro dynamin binding and GTPase assays on liposomes, TIRF microscopy, siRNA knockdown with transferrin readout; parallel SH3-domain mapping of synaptojanin-1 and ACK1 binding","pmids":["15703209","16137687"],"confidence":"High","gaps":["Did not define how multiple SH3 ligands are coordinated","Structural basis of dynamin stimulation not resolved"]},{"year":2006,"claim":"Mapping the dimerization determinant explained how SNX9 architecture controls its regulation, showing C-terminal BAR/coiled-coil dimerization is required for ACK2 binding, phosphorylation, and localization.","evidence":"Truncation mutagenesis, co-IP, and localization assays","pmids":["16316319"],"confidence":"Medium","gaps":["Did not connect dimerization to membrane tubulation directly","No structural model of the dimer"]},{"year":2008,"claim":"Reconstitution defined SNX9 as a membrane-deforming hub: its PX-BAR-LC module tubulates membranes and recruits N-WASP, dynamin, and Arp2/3, while PX-domain stimulation of PI(4)P-5-kinases creates a phosphoinositide feedback loop at endocytic sites.","evidence":"In vitro liposome tubulation, domain mutants, co-IP, and kinase activity assays","pmids":["18388313"],"confidence":"High","gaps":["In vivo significance of the kinase feedback loop not tested","Coupling of tubulation to scission timing not defined"]},{"year":2010,"claim":"Two studies broadened SNX9's roles: a redundant partnership with SNX18 in clathrin-mediated endocytosis, and exploitation of its membrane-deforming activity by the bacterial effector EspF for pathogen invasion.","evidence":"Co-IP, GTPase assays, TIRF, and transferrin uptake for SNX18 redundancy; SNX9/EspF mutagenesis and bacterial invasion assays with CCP/dynamin inhibitors","pmids":["20427313","20088948"],"confidence":"Medium","gaps":["Degree of SNX9/SNX18 functional overlap in vivo unclear","EspF-driven invasion shown to be dynamin-independent but scission mechanism unresolved"]},{"year":2012,"claim":"Identifying a mitotic requirement distinguished a non-endocytic SNX9 function, as depletion caused cytokinesis failure and chromosome segregation defects without blocking transferrin uptake.","evidence":"siRNA, time-lapse microscopy, localization of MRLC, Rab11 endosomes, and Golgi, with transferrin uptake control","pmids":["22718350"],"confidence":"Medium","gaps":["Molecular partners at the cytokinetic bridge not identified","Whether mitotic role uses the same membrane-remodeling machinery unknown"]},{"year":2013,"claim":"Cell-free reconstitution showed SNX9 acts as a curvature- and lipid-specific actin adaptor, replacing toca-1 to drive Cdc42-dependent N-WASP/Arp2/3 polymerization on PI(3)P/PI(4,5)P2 membranes.","evidence":"Cell-free actin polymerization on defined-lipid liposomes with systematic component omission","pmids":["23589871"],"confidence":"High","gaps":["Physiological context where SNX9 substitutes for toca-1 not defined","Did not address branched vs bundled network outcomes"]},{"year":2016,"claim":"SNX9 was established as a multifunctional scaffold for RhoGTPase-dependent clathrin-independent endocytosis and motility, capable of substituting for the RhoGAP GRAF1.","evidence":"Knockdown with RhoA/Cdc42 activation assays, invasion and CIE assays, GRAF1 rescue","pmids":["26960793"],"confidence":"Medium","gaps":["Direct biochemical effect of SNX9 on RhoA/Cdc42 nucleotide state not shown","Mechanism of GRAF1 substitution unresolved"]},{"year":2018,"claim":"SNX9 was shown to non-redundantly control surface ADAM9 levels and substrate shedding, refining the redundancy boundary with SNX18, and an SH3-mediated interaction with a Nedd4-family ligase implicated it in synaptic regulation.","evidence":"Co-IP, single and double SNX9/SNX18 knockdown, surface ADAM9 quantification and EphB4 shedding; in vitro binding, co-IP, and NMJ electrophysiology in Drosophila","pmids":["29622675","30518551"],"confidence":"Medium","gaps":["Whether ADAM9 regulation uses canonical endocytic machinery unclear","Functional consequence of Nedd4-mediated SNX9 turnover at synapses not fully defined"]},{"year":2019,"claim":"Drosophila genetics placed the SNX9 ortholog in an endocytosis-autophagy network controlling EGFR degradation versus recycling, with loss hyperactivating ERK/Ca2+/ER-stress signaling to drive stem cell proliferation.","evidence":"Genetic screen and epistasis with Dynamin, Rab5/7, Atg, and Rab11 pathway genes in intestinal stem cells","pmids":["31006650"],"confidence":"Medium","gaps":["Direct biochemical role of SNX9 in autophagosome formation not isolated","Conservation of the recycling-versus-degradation switch in mammals untested here"]},{"year":2020,"claim":"SNX9 was found at endogenous filopodia and reported to modulate Hippo signaling, extending its functions to filopodium biogenesis and YAP regulation.","evidence":"Phage-display antibody screen, in vitro filopodia assay, and immunolocalization in Xenopus/Chlamydia; co-IP, YAP phosphorylation and reporter assays in ADPKD models","pmids":["32328641","32974348"],"confidence":"Medium","gaps":["Mechanism linking SNX9 membrane/actin activity to filopodial elongation not defined","The direct SNX9-YAP interaction (Low confidence) lacks independent validation"]},{"year":2022,"claim":"Structural and immunological studies defined SNX9's SH3 specificity for an unusual RxAPxxP motif exploited by viruses and revealed a CD28-synapse function generating membrane tubulation that tunes T cell activation.","evidence":"Crystal structure of SH3-EEEV nsP3 peptide with mutagenesis and HTLV-1 infection assay; 3D-CLEM, super-resolution, CD28 phosphorylation and IL-2 assays","pmids":["35390274","35050850"],"confidence":"High","gaps":["Endogenous host ligands of the RxAPxxP-binding mode not catalogued","How CD28-cluster tubulation mechanistically alters signaling unresolved"]},{"year":2023,"claim":"A CRISPR screen identified SNX9 as a driver of CD8 T cell exhaustion through PLCγ1-Ca2+-NFATc2 signaling, making its deletion a strategy to enhance CAR-T efficacy.","evidence":"Pooled CRISPR-Cas9 screen, individual knockout, calcium flux and NFATc2 readouts, and in vivo adoptive transfer tumor model","pmids":["36732507"],"confidence":"High","gaps":["Direct molecular link between SNX9 and PLCγ1 not biochemically defined","Whether membrane-remodeling activity underlies the signaling effect unclear"]},{"year":2024,"claim":"SNX9 was established as a cargo adaptor for beta-arrestin-independent GPCR endocytosis, binding the phosphorylated CXCR4 C-tail to drive agonist-stimulated internalization.","evidence":"siRNA of SNX9/SNX18 and beta-arrestins with CXCR4 internalization assay and co-IP with the receptor C-tail","pmids":["39511325"],"confidence":"Medium","gaps":["Generality across other GPCRs not established","Phosphosite dependence of binding not mapped"]},{"year":2025,"claim":"Biophysical and structural studies refined SNX9 lipid selectivity, defining a non-canonical PX interface that selectively binds and protects PI(3,4)P2 during macropinocytosis and showing actin assembly requires the integrated PX-BAR/SH3 network.","evidence":"Biolayer interferometry, cell-free reconstitution, cryo-ET, MD simulations, and 3D-dSTORM (one peer-reviewed, one preprint)","pmids":["40105919","bio_10.1101_2025.03.26.645564"],"confidence":"Medium","gaps":["In vivo role of PI(3,4)P2 protection in macropinocytosis not fully established","Preprint findings not yet peer-reviewed"]},{"year":2026,"claim":"Multiple reports placed SNX9 under ubiquitin-proteasome control, identifying ITCH (via ZG16) and RAB40C as drivers of its degradation, implicating turnover in disease-relevant signaling.","evidence":"IP-MS/co-IP, GST pulldown, and ubiquitination assays for ITCH/ZG16 and RAB40C-mediated degradation with knockdown functional readouts","pmids":["41781795","42245125"],"confidence":"Low","gaps":["Single-lab co-IP findings without independent validation","Physiological contexts triggering SNX9 degradation not defined","Direct ubiquitination sites on SNX9 not mapped"]},{"year":null,"claim":"How SNX9's conserved membrane-deforming and actin-nucleating biochemistry is selectively deployed across its many cellular roles — endocytosis, cytokinesis, filopodia, immune synapse signaling, and GPCR adaptation — and how its abundance is regulated to set these outcomes remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking domain activities to context-specific functions","Regulatory inputs (phosphorylation, degradation) not integrated into a quantitative model"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,7,20]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[2,22,26]},{"term_id":"GO:0008092","term_label":"cytoskeletal protein binding","supporting_discovery_ids":[2,7,26]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,10]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0,2,14,20]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005856","term_label":"cytoskeleton","supporting_discovery_ids":[2,7,13,26]}],"pathway":[{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[0,2,6,20]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[14,16,23]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[10,16,20]}],"complexes":[],"partners":["DNM2","WASL","SYNJ1","SNX18","ADAM9","TNK2","CXCR4","CD28"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y5X1","full_name":"Sorting nexin-9","aliases":["SH3 and PX domain-containing protein 1","Protein SDP1","SH3 and PX domain-containing protein 3A"],"length_aa":595,"mass_kda":66.6,"function":"Involved in endocytosis and intracellular vesicle trafficking, both during interphase and at the end of mitosis. Required for efficient progress through mitosis and cytokinesis. Required for normal formation of the cleavage furrow at the end of mitosis. Plays a role in endocytosis via clathrin-coated pits, but also clathrin-independent, actin-dependent fluid-phase endocytosis. Plays a role in macropinocytosis. Promotes internalization of TNFR. Promotes degradation of EGFR after EGF signaling. Stimulates the GTPase activity of DNM1. Promotes DNM1 oligomerization. Promotes activation of the Arp2/3 complex by WASL, and thereby plays a role in the reorganization of the F-actin cytoskeleton. Binds to membranes enriched in phosphatidylinositol 4,5-bisphosphate and promotes membrane tubulation. Has lower affinity for membranes enriched in phosphatidylinositol 3-phosphate","subcellular_location":"Cytoplasmic vesicle membrane; Cell membrane; Cytoplasmic vesicle, clathrin-coated vesicle; Golgi apparatus, trans-Golgi network; Cell projection, ruffle; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9Y5X1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/SNX9","classification":"Not Classified","n_dependent_lines":2,"n_total_lines":1208,"dependency_fraction":0.0016556291390728477},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000130340","cell_line_id":"CID000546","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"big_aggregates","grade":2},{"compartment":"membrane","grade":1}],"interactors":[{"gene":"ANAPC16","stoichiometry":0.2},{"gene":"CSNK2B","stoichiometry":0.2},{"gene":"DNM2","stoichiometry":0.2},{"gene":"SLC1A3","stoichiometry":0.2},{"gene":"SLC2A8","stoichiometry":0.2},{"gene":"SLC31A1","stoichiometry":0.2},{"gene":"PCGF3","stoichiometry":0.2},{"gene":"PCGF5","stoichiometry":0.2},{"gene":"CSNK2A1;CSNK2A3","stoichiometry":0.2},{"gene":"DNM3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000546","total_profiled":1310},"omim":[{"mim_id":"621000","title":"SORTING NEXIN 18; SNX18","url":"https://www.omim.org/entry/621000"},{"mim_id":"619107","title":"SORTING NEXIN 33; SNX33","url":"https://www.omim.org/entry/619107"},{"mim_id":"605952","title":"SORTING NEXIN 9; SNX9","url":"https://www.omim.org/entry/605952"},{"mim_id":"604465","title":"SH3 DOMAIN, GRB2-LIKE, 2; SH3GL2","url":"https://www.omim.org/entry/604465"},{"mim_id":"603601","title":"PHOSPHATIDYLINOSITOL 3-KINASE, CLASS 2, ALPHA; PIK3C2A","url":"https://www.omim.org/entry/603601"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SNX9"},"hgnc":{"alias_symbol":["SH3PX1","SDP1","SH3PXD3A"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y5X1","domains":[{"cath_id":"2.30.30.40","chopping":"5-61","consensus_level":"high","plddt":90.8205,"start":5,"end":61},{"cath_id":"3.30.1520.10","chopping":"233-388","consensus_level":"medium","plddt":93.7011,"start":233,"end":388},{"cath_id":"1.20.1270.60","chopping":"389-595","consensus_level":"medium","plddt":97.0966,"start":389,"end":595}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5X1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5X1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5X1-F1-predicted_aligned_error_v6.png","plddt_mean":79.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SNX9","jax_strain_url":"https://www.jax.org/strain/search?query=SNX9"},"sequence":{"accession":"Q9Y5X1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y5X1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y5X1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5X1"}},"corpus_meta":[{"pmid":"15703209","id":"PMC_15703209","title":"SNX9 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promotes EPEC invasion of intestinal epithelial cells via an SNX9-dependent mechanism.","date":"2010","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20088948","citation_count":29,"is_preprint":false},{"pmid":"29675452","id":"PMC_29675452","title":"Attaching-and-Effacing Pathogens Exploit Junction Regulatory Activities of N-WASP and SNX9 to Disrupt the Intestinal Barrier.","date":"2017","source":"Cellular and molecular gastroenterology and hepatology","url":"https://pubmed.ncbi.nlm.nih.gov/29675452","citation_count":26,"is_preprint":false},{"pmid":"21494661","id":"PMC_21494661","title":"A conserved role for SNX9-family members in the regulation of phagosome maturation during engulfment of apoptotic cells.","date":"2011","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/21494661","citation_count":26,"is_preprint":false},{"pmid":"35081354","id":"PMC_35081354","title":"Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 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Hydrolysis","date":"2025-03-29","source":"bioRxiv","url":"https://doi.org/10.1101/2025.03.26.645564","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18271,"output_tokens":6927,"usd":0.079359,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15835,"output_tokens":5941,"usd":0.11385,"stage2_stop_reason":"end_turn"},"total_usd":0.193209,"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\": 2005,\n      \"finding\": \"SNX9 binds directly to dynamin-1 and dynamin-2, stimulates dynamin assembly, potentiates dynamin's basal GTPase activity, and stimulates assembly-stimulated GTPase activity on liposomes. SNX9 is transiently recruited to clathrin-coated pits during late stages of vesicle formation coinciding with dynamin recruitment, and siRNA-mediated knockdown of SNX9 inhibits transferrin internalization in HeLa cells.\",\n      \"method\": \"Direct binding assays, GTPase activity assays on liposomes, TIRF microscopy in live cells, siRNA knockdown with transferrin internalization readout\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro reconstitution of dynamin stimulation, live-cell TIRF microscopy, and functional KD with defined endocytic readout; multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"15703209\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"SNX9 (SH3PX1) interacts with the cytoplasmic domains of the metalloprotease disintegrins MDC9 (ADAM9) and MDC15 via its SH3 domain, as established by yeast two-hybrid, bacterial fusion protein pulldowns, and co-immunoprecipitation from eukaryotic cells. Both proteins preferentially bind the precursor but not the processed form of MDC9 and MDC15.\",\n      \"method\": \"Yeast two-hybrid, GST-fusion protein pulldowns, co-immunoprecipitation from COS-7 cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and pulldown with two orthogonal methods, single lab\",\n      \"pmids\": [\"10531379\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"SNX9 deforms plasma membranes and liposomes into narrow tubules via its BAR and PX domains plus low-complexity (LC) domain; it recruits N-WASP and dynamin 2 to these tubules via its SH3 domain. The LC domain binds the Arp2/3 complex. SNX9 binds PtdIns(4)P-5-kinases via its PX domain and stimulates their kinase activity, suggesting a positive feedback loop regulating phosphoinositide levels at endocytic sites.\",\n      \"method\": \"In vitro liposome tubulation assays, domain truncation/mutation analysis, co-immunoprecipitation, kinase activity assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple in vitro reconstitution assays with domain mutants, kinase activity assay, and cell-based co-IP; multiple orthogonal methods\",\n      \"pmids\": [\"18388313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"SNX9 (SH3PX1) interacts with ACK2 via the ACK2 proline-rich domain and SNX9 SH3 domain. ACK2, clathrin, and SNX9 form a complex in cells. ACK2 mediates EGF-stimulated tyrosine phosphorylation of SNX9, and co-expression of ACK2 with SNX9 leads to constitutive SNX9 phosphorylation. Together ACK2 and SNX9 promote EGF receptor degradation.\",\n      \"method\": \"Co-immunoprecipitation, kinase-dead mutant ACK2(K158R) to block phosphorylation, EGF receptor degradation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP with kinase-dead mutant validation and functional EGF receptor degradation readout, single lab\",\n      \"pmids\": [\"11799118\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"SNX9 SH3 domain binds synaptojanin-1 at multiple sites within its proline-rich region, and binds ACK1 at a single dominant site (residues 920–955). In the presence of SNX9, synaptojanin colocalizes with ACK1-containing vesicles, indicating SNX9 acts as an adaptor linking synaptojanin-1 to ACK1.\",\n      \"method\": \"In vivo biotinylated GST-SH3 domain blot overlays, synthetic peptide arrays, co-immunofluorescence localization\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay with peptide array mapping and colocalization, single lab with two methods\",\n      \"pmids\": [\"16137687\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Dimerization of SNX9 (SH3PX1) mediated by its BAR/coiled-coil domain at the C-terminus is required for ACK2-catalyzed and EGF-stimulated tyrosine phosphorylation of SNX9, interaction with ACK2, and proper intracellular localization. Truncation of as few as 13 C-terminal residues abolishes dimerization, phosphorylation, ACK2 binding, and normal localization.\",\n      \"method\": \"Domain truncation mutagenesis, co-immunoprecipitation, intracellular localization assays\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic truncation mutants with multiple functional readouts, single lab\",\n      \"pmids\": [\"16316319\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"SNX18 and SNX9 can form a heterodimer, colocalize in tubular membrane structures, and are functionally redundant in clathrin-mediated endocytosis. Both interact with dynamin and stimulate its basal GTPase activity, and both interact with N-WASP and synaptojanin. TIRF microscopy shows SNX18 is transiently recruited to clathrin-coated pits coinciding with dynamin and SNX9.\",\n      \"method\": \"Co-immunoprecipitation, GTPase activity assay, siRNA knockdown with transferrin uptake readout, TIRF microscopy\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (GTPase assay, Co-IP, TIRF, functional KD) in a single lab\",\n      \"pmids\": [\"20427313\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"On curved membranes containing both PI(3)P and PI(4,5)P2, SNX9 acts as a specific adaptor replacing toca-1 to mobilize N-WASP and the Arp2/3 complex for actin polymerization, bypassing the requirement for toca-1 in a Cdc42-dependent manner.\",\n      \"method\": \"Cell-free reconstitution of actin polymerization on liposomes with defined lipid compositions\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — cell-free reconstitution with defined lipid compositions and systematic component omission; single lab but rigorous in vitro approach\",\n      \"pmids\": [\"23589871\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"SNX9 is required for progression through mitosis: siRNA depletion induces multinucleation (cytokinesis failure), disrupts MRLC(S19) localization during ingression, blocks recruitment of Rab11-positive recycling endosomes to the intracellular bridge, and disrupts Golgi localization during cytokinesis. SNX9 depletion also delays chromosome alignment and segregation during metaphase without blocking transferrin uptake, indicating a non-endocytic mitotic role.\",\n      \"method\": \"siRNA knockdown, time-lapse microscopy, immunofluorescence localization, transferrin uptake assay\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA with time-lapse and multiple localization readouts distinguishing endocytic and non-endocytic roles, single lab\",\n      \"pmids\": [\"22718350\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The bacterial effector EspF binds SNX9 and exploits SNX9's membrane-deforming activity to promote EPEC invasion of intestinal epithelial cells. Invasion requires the SNX9 lipid-binding domains and the EspF SNX9-binding domain, as well as clathrin-coated pit assembly, but is independent of dynamin activity.\",\n      \"method\": \"Point mutagenesis of SNX9 lipid-binding domains, EspF truncation analysis, pharmacological inhibition of CCP assembly and dynamin, bacterial invasion assay\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple mutants and inhibitors with functional invasion readout, single lab\",\n      \"pmids\": [\"20088948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"SNX9 controls activation of RhoA and Cdc42 GTPases, regulates cell motility via RhoA-ROCK and N-WASP pathways, and is required for RhoGTPase-dependent clathrin-independent endocytosis. SNX9 can functionally substitute for GRAF1 (a RhoGAP) in this pathway, establishing SNX9 as a multifunctional scaffold coordinating endocytosis and invasion.\",\n      \"method\": \"SNX9 knockdown with RhoA/Cdc42 activation assays, cell invasion assay, clathrin-independent endocytosis assay, rescue with GRAF1\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with multiple pathway readouts and functional substitution experiment, single lab\",\n      \"pmids\": [\"26960793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"SNX9 interacts with ADAM9 and regulates ADAM9 protein levels at the cell surface. Single SNX9 knockdown increased ADAM9 levels at the plasma membrane and enhanced shedding of EphB4 (an ADAM9 substrate). Double knockdown of SNX9 and SNX18 was required to significantly decrease ADAM9 internalization, demonstrating redundancy for internalization but a non-redundant SNX9 role in controlling total ADAM9 levels.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown (single and double), cell-surface ADAM9 quantification, EphB4 shedding assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP, redundancy dissected by double KD, functional shedding assay, single lab\",\n      \"pmids\": [\"29622675\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In Drosophila, SH3PX1 (SNX9 ortholog) acts in an endocytosis-autophagy network including Dynamin, Rab5, Rab7, and Atg proteins to promote lysosomal degradation of ligand-activated EGFRs. Loss of SH3PX1 stabilizes EGFRs and routes them via Rab11-dependent recycling endosomes back to the plasma membrane, hyperactivating ERK, calcium signaling, and ER stress to stimulate intestinal stem cell proliferation.\",\n      \"method\": \"Genetic screen, epistasis with endocytic/autophagic pathway genes, Rab11-dependent recycling assay, ERK pathway readout in Drosophila ISCs\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with multiple pathway components and functional readouts, Drosophila model\",\n      \"pmids\": [\"31006650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SNX9 is an endogenous component of filopodia. Antibodies targeting SNX9 caused shorter filopodia-like structures in vitro. SNX9 is found at specialized filopodia in Xenopus development and at filopodia hijacked during Chlamydia cell entry.\",\n      \"method\": \"Phage display phenotypic antibody screen, in vitro filopodia-like structure assay, immunolocalization in Xenopus and during Chlamydia infection\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — phage display functional screen combined with in vivo localization and pathogen entry model, single lab\",\n      \"pmids\": [\"32328641\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Upon CD28 triggering, SNX9 is recruited to CD28 clusters at the immunological synapse and generates membrane tubulation from CD28 clusters (shown by 3D correlative light and electron microscopy). SNX9 regulates the stability of CD28 clusters, CD28 phosphorylation, and IL-2 cytokine production.\",\n      \"method\": \"3D correlative light and electron microscopy (CLEM), super-resolution microscopy, CD28 phosphorylation assay, IL-2 production assay\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — CLEM showing tubulation from CD28 clusters with functional signaling readouts, single lab\",\n      \"pmids\": [\"35050850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The crystal structure of SNX9 SH3 in complex with an eastern equine encephalitis virus (EEEV) nsP3 peptide reveals that the length and composition of the n-Src loop determines specificity for an unusual RxAPxxP class I SH3 binding motif (with Ala instead of Pro/Leu at the hydrophobic position). The HTLV-1 Gag polyprotein also contains this motif, and it is required for efficient HTLV-1 infection.\",\n      \"method\": \"X-ray crystal structure of SH3–peptide complex, mutagenesis of binding interface residues, affinity measurements, viral infection assay\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with mutagenesis and functional viral infection readout, single lab but Tier 1 method\",\n      \"pmids\": [\"35390274\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SNX9 deletion in CD8 T cells decreases PLCγ1, Ca2+, and NFATc2-mediated TCR signaling downstream of TCR/CD28 stimulation and reduces expression of exhaustion transcription factors NR4A1/3 and TOX, resulting in enhanced memory differentiation, IFNγ secretion, and improved CAR-T anti-tumor efficacy in vivo.\",\n      \"method\": \"Pooled CRISPR-Cas9 screen, individual gene knockout validation, calcium flux assay, NFATc2 signaling readout, adoptive transfer in vivo tumor model\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — CRISPR screen validated individually with multiple signaling readouts plus in vivo functional assay, replicated across multiple T cell contexts\",\n      \"pmids\": [\"36732507\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Drosophila, Sh3px1 (SNX9 ortholog) facilitates selective autophagy of the TAK1/TAB2 (Tak1/Tab2) kinase complex by interacting with Tab2 and the autophagy protein Atg8a, thereby targeting the complex to the autophagy platform and preventing constitutive activation of the IMD innate immune pathway.\",\n      \"method\": \"Co-immunoprecipitation, genetic epistasis in Drosophila IMD pathway, autophagy flux assays\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP and genetic epistasis with defined pathway readout in Drosophila, single lab\",\n      \"pmids\": [\"35081354\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Drosophila Nedd4-long (dNedd4Lo) directly binds SH3PX1 (SNX9 ortholog) via the SH3PX1 SH3 domain interacting with a proline-rich sequence in the dNedd4Lo Middle region. Postsynaptic overexpression of dNedd4Lo reduces SH3PX1 levels at the subsynaptic reticulum and impairs presynaptic neurotransmitter release at the neuromuscular junction.\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation in S2 cells, in vivo overexpression with immunofluorescence and electrophysiology\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding validated in vitro and in cells with functional synaptic readout, single lab\",\n      \"pmids\": [\"30518551\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"SNX9 interacts directly with YAP and increases LATS1-mediated phosphorylation of YAP, resulting in cytoplasmic retention of YAP, decreased YAP/TEAD4 transcriptional activity, and suppression of Hippo target gene expression and cyst development in polycystic kidney disease cells.\",\n      \"method\": \"Co-immunoprecipitation, YAP phosphorylation assay, transcriptional reporter assay, gain- and loss-of-function in ADPKD cell lines and Pkd1-/- mice\",\n      \"journal\": \"Frontiers in cell and developmental biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-IP with functional readouts but single lab, single paper with no independent validation of the direct interaction mechanism\",\n      \"pmids\": [\"32974348\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SNX9 (and SNX18) act as cargo adaptors for β-arrestin-independent GPCR endocytosis. SNX9 is recruited to CXCR4 at the plasma membrane and interacts directly with the receptor's carboxyl-terminal tail in a phosphorylation-dependent manner to promote agonist-stimulated CXCR4 endocytosis.\",\n      \"method\": \"siRNA knockdown of SNX9/SNX18 and β-arrestins with CXCR4 internalization assay, co-immunoprecipitation of SNX9 with CXCR4 C-tail\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — receptor internalization assay with KD and direct binding assay, single lab with two methods\",\n      \"pmids\": [\"39511325\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNX9 forms a complex with NUMB (Ex3-containing isoform) at the plasma membrane and recruits p53 in a SNX9-dependent manner. This complex is internalized and trafficked to multivesicular bodies for exosomal secretion of p53, requiring both SNX9 and NUMB.\",\n      \"method\": \"Co-immunoprecipitation, live-cell imaging, exosome isolation and p53 tracking, SNX9 knockdown with functional p53 trafficking readout\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint, single lab, co-IP and imaging without independent replication\",\n      \"pmids\": [\"bio_10.1101_2025.08.16.670648\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The SNX9 PX domain uses a non-canonical interface to selectively bind and sequester PI(3,4)P2 over PI(4,5)P2 during macropinocytic membrane ruffling. Mutational disruption of this non-canonical interface abolishes PI(3,4)P2 protection, demonstrating that SNX9 protects PI(3,4)P2 from hydrolysis. Actin assembly by SNX9 requires the combined PX-BAR and SH3 domain network; SNX9 can build both branched and bundled actin networks.\",\n      \"method\": \"Biolayer interferometry, cell-free reconstitution, live-cell imaging, molecular dynamics simulations, cryo-electron tomography, mutagenesis of PX domain residues\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple orthogonal methods including in vitro reconstitution, cryo-ET, and mutagenesis in a single preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.03.26.645564\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"In B cells, SNX9 promotes the association of PI3K with CD19 in an AIM2-dependent manner, facilitating downstream PI3K-AKT signaling, and is involved in BCR/CD19 endocytosis and antigen uptake via SNX9-WASP interaction.\",\n      \"method\": \"IP-MS to identify SNX9 as AIM2 interactor, co-immunoprecipitation, BCR endocytosis assay, AIM2 knockout mice\",\n      \"journal\": \"Cell death and differentiation\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — IP-MS hit with co-IP and functional assay, single lab, mechanism not fully dissected for SNX9 specifically\",\n      \"pmids\": [\"41437148\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZG16 physically interacts with SNX9 and recruits the E3 ubiquitin ligase ITCH to promote ubiquitin-proteasome-dependent degradation of SNX9.\",\n      \"method\": \"IP-LC/MS, co-immunoprecipitation, GST pulldown, ubiquitination assay\",\n      \"journal\": \"Hepatology international\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-IP and pulldown identifying ubiquitination machinery, single lab, mechanism partially characterized\",\n      \"pmids\": [\"41781795\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"RAB40C promotes SNX9 degradation via the ubiquitin-proteasome pathway; silencing RAB40C increases SNX9 expression and influences Hippo signaling pathway target proteins.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown with proliferation/invasion readouts\",\n      \"journal\": \"Central-European journal of immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — co-IP and functional knockdown, single lab, limited mechanistic detail in abstract\",\n      \"pmids\": [\"42245125\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"SNX9 PX-BAR domain binds more PI(4,5)P2 and PI(3)P-containing liposomes than PI(3,4)P2 liposomes in terms of total binding capacity despite similar affinities. Actin assembly by SNX9 on membranes requires both PX-BAR and SH3 domain interactions.\",\n      \"method\": \"Biolayer interferometry, cell-free actin reconstitution, superresolution microscopy (3D-dSTORM)\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution and biophysical binding assays with superresolution imaging, single lab\",\n      \"pmids\": [\"40105919\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SNX9 is a multidomain scaffold protein (SH3-PX-BAR) that is transiently recruited to clathrin-coated pits during late-stage vesicle formation, where it directly binds and stimulates dynamin GTPase activity to drive membrane scission; simultaneously, its SH3 domain recruits N-WASP and synaptojanin to coordinate actin polymerization via the Arp2/3 complex, while its PX-BAR domain senses and deforms phosphoinositide-rich membranes (PI(4,5)P2, PI(3)P, and PI(3,4)P2) into tubules; beyond clathrin-mediated endocytosis, SNX9 regulates RhoGTPase-dependent clathrin-independent endocytosis, acts as a cargo adaptor for β-arrestin-independent GPCR internalization, promotes filopodium biogenesis, coordinates membrane remodeling at the immunological synapse to regulate CD28 signaling, mediates T cell exhaustion downstream of TCR/CD28 stimulation by modulating PLCγ1-Ca2+-NFATc2 signaling, and is subject to tyrosine phosphorylation by ACK2 and ubiquitin-proteasome degradation mediated by ITCH and RAB40C.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SNX9 is a multidomain SH3-PX-BAR scaffold that couples membrane deformation to actin dynamics during the late stages of clathrin-mediated endocytosis [#0, #2]. Through its PX and BAR domains it senses and tubulates phosphoinositide-rich membranes, while its SH3 domain recruits the actin machinery: SNX9 binds and stimulates dynamin GTPase activity to drive vesicle scission [#0], recruits N-WASP and dynamin to membrane tubules, engages the Arp2/3 complex via its low-complexity domain, and binds and stimulates PtdIns(4)P-5-kinases to reinforce local phosphoinositide synthesis [#2]. On membranes bearing both PI(3)P and PI(4,5)P2, SNX9 acts as an adaptor that mobilizes N-WASP/Arp2/3 actin polymerization in a Cdc42-dependent manner [#7], and its PX domain uses a non-canonical interface to selectively bind PI(3,4)P2 during macropinocytic ruffling [#22]. C-terminal BAR/coiled-coil-mediated dimerization is required for its proper localization and regulation [#5]. SNX9 functions partially redundantly with its paralog SNX18, which also heterodimerizes with it and shares dynamin, N-WASP, and synaptojanin interactions [#6, #11]. Beyond canonical endocytosis, SNX9 supports RhoA/Cdc42-dependent clathrin-independent endocytosis and cell motility [#10], filopodium biogenesis [#13], cytokinesis and mitotic progression [#8], and acts as a cargo adaptor for beta-arrestin-independent GPCR internalization by binding the phosphorylated CXCR4 C-tail [#20]. In immune cells, SNX9 is recruited to CD28 clusters at the immunological synapse to generate membrane tubulation and regulate CD28 signaling and IL-2 production [#14], and it modulates TCR/CD28-driven PLCγ1-Ca2+-NFATc2 signaling to promote CD8 T cell exhaustion, such that its deletion enhances memory differentiation and CAR-T anti-tumor efficacy [#16]. SNX9 also serves as a host factor exploited by pathogens and viruses, including the EPEC effector EspF and an unusual RxAPxxP SH3-binding motif present in EEEV nsP3 and HTLV-1 Gag [#9, #15].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"The first identified SNX9 partners established it as an SH3-domain adaptor engaging the cytoplasmic tails of ADAM-family metalloprotease disintegrins, hinting at a role in membrane-protein trafficking.\",\n      \"evidence\": \"Yeast two-hybrid, GST pulldown, and co-IP from COS-7 cells showing SH3-mediated binding to MDC9/ADAM9 and MDC15 precursors\",\n      \"pmids\": [\"10531379\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the interaction was not defined\", \"Did not address endocytic or membrane-remodeling activity\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Linking SNX9 to ACK2 and clathrin revealed it as a tyrosine-phosphorylated component of receptor downregulation, connecting it to growth-factor receptor degradation.\",\n      \"evidence\": \"Co-IP, kinase-dead ACK2(K158R) mutant, and EGF receptor degradation assay\",\n      \"pmids\": [\"11799118\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of SNX9 phosphorylation not resolved\", \"Did not establish mechanism of EGFR degradation\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Biochemical and live-cell work established the core endocytic function: SNX9 directly stimulates dynamin GTPase activity and is recruited to clathrin-coated pits at the scission stage, with knockdown blocking transferrin uptake.\",\n      \"evidence\": \"In vitro dynamin binding and GTPase assays on liposomes, TIRF microscopy, siRNA knockdown with transferrin readout; parallel SH3-domain mapping of synaptojanin-1 and ACK1 binding\",\n      \"pmids\": [\"15703209\", \"16137687\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define how multiple SH3 ligands are coordinated\", \"Structural basis of dynamin stimulation not resolved\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Mapping the dimerization determinant explained how SNX9 architecture controls its regulation, showing C-terminal BAR/coiled-coil dimerization is required for ACK2 binding, phosphorylation, and localization.\",\n      \"evidence\": \"Truncation mutagenesis, co-IP, and localization assays\",\n      \"pmids\": [\"16316319\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not connect dimerization to membrane tubulation directly\", \"No structural model of the dimer\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Reconstitution defined SNX9 as a membrane-deforming hub: its PX-BAR-LC module tubulates membranes and recruits N-WASP, dynamin, and Arp2/3, while PX-domain stimulation of PI(4)P-5-kinases creates a phosphoinositide feedback loop at endocytic sites.\",\n      \"evidence\": \"In vitro liposome tubulation, domain mutants, co-IP, and kinase activity assays\",\n      \"pmids\": [\"18388313\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"In vivo significance of the kinase feedback loop not tested\", \"Coupling of tubulation to scission timing not defined\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Two studies broadened SNX9's roles: a redundant partnership with SNX18 in clathrin-mediated endocytosis, and exploitation of its membrane-deforming activity by the bacterial effector EspF for pathogen invasion.\",\n      \"evidence\": \"Co-IP, GTPase assays, TIRF, and transferrin uptake for SNX18 redundancy; SNX9/EspF mutagenesis and bacterial invasion assays with CCP/dynamin inhibitors\",\n      \"pmids\": [\"20427313\", \"20088948\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Degree of SNX9/SNX18 functional overlap in vivo unclear\", \"EspF-driven invasion shown to be dynamin-independent but scission mechanism unresolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identifying a mitotic requirement distinguished a non-endocytic SNX9 function, as depletion caused cytokinesis failure and chromosome segregation defects without blocking transferrin uptake.\",\n      \"evidence\": \"siRNA, time-lapse microscopy, localization of MRLC, Rab11 endosomes, and Golgi, with transferrin uptake control\",\n      \"pmids\": [\"22718350\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular partners at the cytokinetic bridge not identified\", \"Whether mitotic role uses the same membrane-remodeling machinery unknown\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Cell-free reconstitution showed SNX9 acts as a curvature- and lipid-specific actin adaptor, replacing toca-1 to drive Cdc42-dependent N-WASP/Arp2/3 polymerization on PI(3)P/PI(4,5)P2 membranes.\",\n      \"evidence\": \"Cell-free actin polymerization on defined-lipid liposomes with systematic component omission\",\n      \"pmids\": [\"23589871\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological context where SNX9 substitutes for toca-1 not defined\", \"Did not address branched vs bundled network outcomes\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"SNX9 was established as a multifunctional scaffold for RhoGTPase-dependent clathrin-independent endocytosis and motility, capable of substituting for the RhoGAP GRAF1.\",\n      \"evidence\": \"Knockdown with RhoA/Cdc42 activation assays, invasion and CIE assays, GRAF1 rescue\",\n      \"pmids\": [\"26960793\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical effect of SNX9 on RhoA/Cdc42 nucleotide state not shown\", \"Mechanism of GRAF1 substitution unresolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"SNX9 was shown to non-redundantly control surface ADAM9 levels and substrate shedding, refining the redundancy boundary with SNX18, and an SH3-mediated interaction with a Nedd4-family ligase implicated it in synaptic regulation.\",\n      \"evidence\": \"Co-IP, single and double SNX9/SNX18 knockdown, surface ADAM9 quantification and EphB4 shedding; in vitro binding, co-IP, and NMJ electrophysiology in Drosophila\",\n      \"pmids\": [\"29622675\", \"30518551\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether ADAM9 regulation uses canonical endocytic machinery unclear\", \"Functional consequence of Nedd4-mediated SNX9 turnover at synapses not fully defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Drosophila genetics placed the SNX9 ortholog in an endocytosis-autophagy network controlling EGFR degradation versus recycling, with loss hyperactivating ERK/Ca2+/ER-stress signaling to drive stem cell proliferation.\",\n      \"evidence\": \"Genetic screen and epistasis with Dynamin, Rab5/7, Atg, and Rab11 pathway genes in intestinal stem cells\",\n      \"pmids\": [\"31006650\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct biochemical role of SNX9 in autophagosome formation not isolated\", \"Conservation of the recycling-versus-degradation switch in mammals untested here\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"SNX9 was found at endogenous filopodia and reported to modulate Hippo signaling, extending its functions to filopodium biogenesis and YAP regulation.\",\n      \"evidence\": \"Phage-display antibody screen, in vitro filopodia assay, and immunolocalization in Xenopus/Chlamydia; co-IP, YAP phosphorylation and reporter assays in ADPKD models\",\n      \"pmids\": [\"32328641\", \"32974348\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking SNX9 membrane/actin activity to filopodial elongation not defined\", \"The direct SNX9-YAP interaction (Low confidence) lacks independent validation\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Structural and immunological studies defined SNX9's SH3 specificity for an unusual RxAPxxP motif exploited by viruses and revealed a CD28-synapse function generating membrane tubulation that tunes T cell activation.\",\n      \"evidence\": \"Crystal structure of SH3-EEEV nsP3 peptide with mutagenesis and HTLV-1 infection assay; 3D-CLEM, super-resolution, CD28 phosphorylation and IL-2 assays\",\n      \"pmids\": [\"35390274\", \"35050850\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous host ligands of the RxAPxxP-binding mode not catalogued\", \"How CD28-cluster tubulation mechanistically alters signaling unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"A CRISPR screen identified SNX9 as a driver of CD8 T cell exhaustion through PLCγ1-Ca2+-NFATc2 signaling, making its deletion a strategy to enhance CAR-T efficacy.\",\n      \"evidence\": \"Pooled CRISPR-Cas9 screen, individual knockout, calcium flux and NFATc2 readouts, and in vivo adoptive transfer tumor model\",\n      \"pmids\": [\"36732507\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct molecular link between SNX9 and PLCγ1 not biochemically defined\", \"Whether membrane-remodeling activity underlies the signaling effect unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"SNX9 was established as a cargo adaptor for beta-arrestin-independent GPCR endocytosis, binding the phosphorylated CXCR4 C-tail to drive agonist-stimulated internalization.\",\n      \"evidence\": \"siRNA of SNX9/SNX18 and beta-arrestins with CXCR4 internalization assay and co-IP with the receptor C-tail\",\n      \"pmids\": [\"39511325\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Generality across other GPCRs not established\", \"Phosphosite dependence of binding not mapped\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Biophysical and structural studies refined SNX9 lipid selectivity, defining a non-canonical PX interface that selectively binds and protects PI(3,4)P2 during macropinocytosis and showing actin assembly requires the integrated PX-BAR/SH3 network.\",\n      \"evidence\": \"Biolayer interferometry, cell-free reconstitution, cryo-ET, MD simulations, and 3D-dSTORM (one peer-reviewed, one preprint)\",\n      \"pmids\": [\"40105919\", \"bio_10.1101_2025.03.26.645564\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo role of PI(3,4)P2 protection in macropinocytosis not fully established\", \"Preprint findings not yet peer-reviewed\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Multiple reports placed SNX9 under ubiquitin-proteasome control, identifying ITCH (via ZG16) and RAB40C as drivers of its degradation, implicating turnover in disease-relevant signaling.\",\n      \"evidence\": \"IP-MS/co-IP, GST pulldown, and ubiquitination assays for ITCH/ZG16 and RAB40C-mediated degradation with knockdown functional readouts\",\n      \"pmids\": [\"41781795\", \"42245125\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single-lab co-IP findings without independent validation\", \"Physiological contexts triggering SNX9 degradation not defined\", \"Direct ubiquitination sites on SNX9 not mapped\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How SNX9's conserved membrane-deforming and actin-nucleating biochemistry is selectively deployed across its many cellular roles — endocytosis, cytokinesis, filopodia, immune synapse signaling, and GPCR adaptation — and how its abundance is regulated to set these outcomes remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking domain activities to context-specific functions\", \"Regulatory inputs (phosphorylation, degradation) not integrated into a quantitative model\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 7, 20]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [2, 22, 26]},\n      {\"term_id\": \"GO:0008092\", \"supporting_discovery_ids\": [2, 7, 26]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 10]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 2, 14, 20]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005856\", \"supporting_discovery_ids\": [2, 7, 13, 26]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [0, 2, 6, 20]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [14, 16, 23]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [10, 16, 20]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DNM2\", \"WASL\", \"SYNJ1\", \"SNX18\", \"ADAM9\", \"TNK2\", \"CXCR4\", \"CD28\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}