{"gene":"ST7","run_date":"2026-06-10T07:46:41","timeline":{"discoveries":[{"year":2001,"finding":"Introduction of ST7 cDNA into the prostate-cancer-derived cell line PC3 abrogated in vivo tumorigenicity in nude mice without affecting in vitro proliferation, establishing ST7 as a functional tumor suppressor gene on chromosome 7q31.","method":"cDNA re-expression in PC3 cells, subcutaneous tumor formation assay in nude mice","journal":"Nature genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean gain-of-function with defined in vivo phenotype, single lab, replicated in part by independent study (PMID:16474848)","pmids":["11279520"],"is_preprint":false},{"year":2003,"finding":"ST7 is a member of the low-density lipoprotein receptor (LDLR) superfamily (an LRP, now called LRP12); its cytoplasmic domain contains endocytosis and signal transduction motifs and directly interacts with RACK1, MIBP, and SARA as identified by yeast two-hybrid analysis, suggesting roles in endocytosis and signal transduction.","method":"Bioinformatic domain analysis, yeast two-hybrid system","journal":"Biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — yeast two-hybrid only, no in-cell validation of interactions, single lab","pmids":["12809483"],"is_preprint":false},{"year":2004,"finding":"PRMT5, associated with endogenous hSWI/SNF (BRG1 and hBRM) chromatin-remodeling complexes, methylates histone H3 at arginine 8 (H3R8) at the ST7 promoter, leading to H3K9 deacetylation and transcriptional repression of ST7.","method":"PRMT5 antisense knockdown cell line, microarray, ChIP, in vitro histone methylation assay with recombinant PRMT5, overexpression cell line","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro methylation assay with recombinant enzyme, ChIP demonstrating H3R8 methylation at ST7 promoter, loss-of-function and gain-of-function both tested, multiple orthogonal methods in single study","pmids":["15485929"],"is_preprint":false},{"year":2006,"finding":"Re-expression of ST7 in PC3 prostate cancer cells suppressed subcutaneous tumor growth in SCID mice and suppressed anchorage-independent colony formation in MDA-MB-231 breast cancer cells; expression profiling revealed ST7 predominantly induces changes in extracellular matrix remodeling genes including SPARC, IGFBP5, and several matrix metalloproteinases, suggesting ST7 mediates tumor suppression through modification of the tumor microenvironment.","method":"ST7 cDNA re-expression, SCID mouse xenograft assay, soft-agar colony formation assay, expression profiling/microarray","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — two orthogonal functional assays (in vivo and in vitro) plus gene expression profiling, single lab","pmids":["16474848"],"is_preprint":false},{"year":2010,"finding":"ST7 protein localizes to the cytoplasm (not the nucleus) in HCT-116, MCF-7, and PC-3 cancer cell lines, and no translocation to the nucleus was observed under any assayed conditions; endogenous ST7 and SERPINE1 are overexpressed when cells are arrested in the cell cycle and diminish upon re-entry into cell division.","method":"GFP/YFP/V5-tagged ST7 expression vectors, fluorescence microscopy, cell cycle synchronization, RT-PCR","journal":"Journal of cancer research and clinical oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct live-cell fluorescence localization with multiple tags plus cell-cycle synchronization experiment, single lab","pmids":["20238225"],"is_preprint":false},{"year":2019,"finding":"The CRL4DCAF4 E3 ubiquitin ligase complex (comprising CUL4A or CUL4B, DDB1, and DCAF4) specifically directs proteasomal degradation of ST7; c-Myc transcriptionally activates CUL4A and CUL4B by binding a conserved CACGTG site in their promoters, thereby increasing CRL4DCAF4 activity and reducing ST7 protein levels in colitis-associated cancer.","method":"In vitro and in vivo ubiquitination assays, co-immunoprecipitation, promoter binding/ChIP, siRNA knockdown, overexpression, xenograft mouse model","journal":"The Journal of pathology","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro and in vivo ubiquitination assays plus co-IP, promoter ChIP, multiple loss- and gain-of-function experiments with defined phenotypic readouts, multiple orthogonal methods","pmids":["30945288"],"is_preprint":false},{"year":2021,"finding":"MIB1 (mind bomb 1) E3 ubiquitin ligase targets ST7 for proteasomal degradation; loss of ST7 results in upregulation of IQGAP1, promoting pancreatic cancer cell proliferation and invasion, defining a MIB1/ST7/IQGAP1 signaling axis.","method":"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, overexpression, in vitro proliferation/invasion assays, xenograft mouse model","journal":"Molecular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional in vivo and in vitro readouts, single lab","pmids":["33793053"],"is_preprint":false},{"year":2026,"finding":"ST7 suppresses metastasis in non-small cell lung cancer by binding Y-box binding protein 1 (YBX1) and blocking its nuclear translocation, thereby suppressing MMP14 expression and inhibiting EMT; ST7 silencing enhanced EMT and metastatic progression in vitro and in a tail-vein lung metastasis mouse model.","method":"Co-immunoprecipitation (ST7–YBX1 interaction), nuclear translocation assays, siRNA knockdown, overexpression, in vitro EMT assays, in vivo tail-vein metastasis model","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP demonstrating direct ST7–YBX1 interaction, nuclear translocation assay, in vivo metastasis model, multiple orthogonal methods, single lab","pmids":["42025890"],"is_preprint":false}],"current_model":"ST7 (LRP12) is a cytoplasmic transmembrane protein of the LDLR superfamily whose expression is epigenetically silenced by PRMT5-mediated H3R8 methylation within hSWI/SNF complexes; its protein levels are regulated by ubiquitin-proteasomal degradation via at least two E3 ligase complexes (CRL4DCAF4 and MIB1); when present, ST7 suppresses tumorigenicity by remodeling the extracellular matrix, suppressing IQGAP1, and binding YBX1 to block its nuclear translocation and thereby repress MMP14 expression and EMT."},"narrative":{"mechanistic_narrative":"ST7 (LRP12) is a tumor suppressor on chromosome 7q31 whose re-expression abrogates in vivo tumorigenicity of prostate and breast cancer cells without altering in vitro proliferation [PMID:11279520, PMID:16474848]. It is a cytoplasmic transmembrane member of the LDLR superfamily; its cytoplasmic domain carries endocytosis and signaling motifs and interacts with RACK1, MIBP, and SARA in yeast two-hybrid assays [PMID:12809483], and the protein localizes to the cytoplasm rather than the nucleus across multiple cancer cell lines [PMID:20238225]. ST7 exerts tumor suppression largely by reshaping the tumor microenvironment, predominantly inducing changes in extracellular matrix remodeling genes including SPARC, IGFBP5, and matrix metalloproteinases [PMID:16474848]. Mechanistically, ST7 binds YBX1 and blocks its nuclear translocation, repressing MMP14 expression and inhibiting EMT and metastasis [PMID:42025890], and its loss upregulates IQGAP1 to drive proliferation and invasion [PMID:33793053]. ST7 expression is controlled at two levels: transcriptionally, PRMT5 associated with hSWI/SNF (BRG1/hBRM) chromatin-remodeling complexes methylates histone H3 at arginine 8 at the ST7 promoter, triggering H3K9 deacetylation and repression [PMID:15485929]; and post-translationally, the CRL4DCAF4 ligase complex (driven by c-Myc-induced CUL4A/CUL4B) and the MIB1 E3 ligase target ST7 for proteasomal degradation [PMID:30945288, PMID:33793053].","teleology":[{"year":2001,"claim":"Establishing whether the 7q31 candidate ST7 had genuine tumor-suppressor activity required functional testing; re-expression demonstrated it suppresses tumorigenicity in vivo without affecting cell-intrinsic proliferation, defining a microenvironment-dependent suppressor.","evidence":"ST7 cDNA re-expression in PC3 prostate cancer cells with subcutaneous tumor formation assay in nude mice","pmids":["11279520"],"confidence":"Medium","gaps":["Molecular mechanism of suppression undefined","No identified binding partners or pathway","Single tumor model"]},{"year":2003,"claim":"The molecular identity and interaction potential of ST7 were unknown; domain analysis placed it in the LDLR superfamily (LRP12) with a cytoplasmic domain bearing endocytosis and signaling motifs that bind RACK1, MIBP, and SARA, implicating it in endocytosis and signal transduction.","evidence":"Bioinformatic domain analysis and yeast two-hybrid screening","pmids":["12809483"],"confidence":"Low","gaps":["Yeast two-hybrid interactions not validated in cells","Functional consequence of RACK1/MIBP/SARA binding untested","No link to tumor-suppressor phenotype"]},{"year":2004,"claim":"How ST7 is silenced in cancer was unresolved; PRMT5 within hSWI/SNF complexes was shown to methylate H3R8 at the ST7 promoter and trigger H3K9 deacetylation, defining an epigenetic repression mechanism.","evidence":"PRMT5 antisense knockdown, microarray, ChIP at the ST7 promoter, and in vitro histone methylation with recombinant PRMT5","pmids":["15485929"],"confidence":"High","gaps":["Upstream signals controlling PRMT5 recruitment to ST7 promoter unknown","Whether silencing is reversible in vivo not addressed"]},{"year":2006,"claim":"The downstream effector program of ST7 suppression was unknown; expression profiling tied suppression to extracellular matrix remodeling, indicating ST7 acts through modification of the tumor microenvironment.","evidence":"ST7 re-expression with SCID xenograft and soft-agar assays plus expression profiling identifying SPARC, IGFBP5, and MMP changes","pmids":["16474848"],"confidence":"Medium","gaps":["Direct vs indirect regulation of ECM genes unresolved","No molecular partner linking ST7 to transcriptional output"]},{"year":2010,"claim":"The subcellular site of ST7 action and its cell-cycle behavior were uncharacterized; live-cell imaging confirmed cytoplasmic localization with no nuclear translocation, and synchronization linked ST7 (with SERPINE1) to cell-cycle arrest.","evidence":"GFP/YFP/V5-tagged ST7 fluorescence microscopy with cell-cycle synchronization and RT-PCR","pmids":["20238225"],"confidence":"Medium","gaps":["Mechanism coupling ST7 to cell-cycle arrest unknown","Functional significance of SERPINE1 co-regulation unclear"]},{"year":2019,"claim":"Post-translational control of ST7 abundance was undefined; the CRL4DCAF4 complex was shown to ubiquitinate ST7 for degradation, with c-Myc activating CUL4A/CUL4B to lower ST7 in colitis-associated cancer.","evidence":"In vitro and in vivo ubiquitination assays, co-IP, promoter ChIP, knockdown/overexpression, and xenograft model","pmids":["30945288"],"confidence":"High","gaps":["Degron on ST7 recognized by DCAF4 not mapped","Generality beyond colitis-associated cancer untested"]},{"year":2021,"claim":"A second degradation route and a proliferation/invasion effector were unknown; MIB1 was shown to degrade ST7, and ST7 loss derepressed IQGAP1, defining a MIB1/ST7/IQGAP1 axis in pancreatic cancer.","evidence":"Co-IP, ubiquitination assay, knockdown/overexpression, proliferation/invasion assays, and xenograft model","pmids":["33793053"],"confidence":"Medium","gaps":["Mechanism of ST7-mediated IQGAP1 suppression not resolved","Relative contribution of MIB1 vs CRL4DCAF4 across tissues unknown"]},{"year":2026,"claim":"How cytoplasmic ST7 controls a transcriptional metastatic program was unresolved; ST7 was shown to bind YBX1 and block its nuclear entry, repressing MMP14 and EMT, providing a direct molecular link between ST7 and ECM/EMT output.","evidence":"Co-IP of ST7–YBX1, nuclear translocation assays, EMT assays, and tail-vein lung metastasis mouse model","pmids":["42025890"],"confidence":"Medium","gaps":["Structural basis of ST7–YBX1 binding unknown","Whether YBX1 sequestration explains the broader ECM program of [#3] untested"]},{"year":null,"claim":"How ST7's LDLR-superfamily receptor architecture and putative endocytic/signaling partners (RACK1, MIBP, SARA) integrate with its cytoplasmic YBX1/IQGAP1 effector functions remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unifying mechanism linking receptor domain to tumor-suppressor signaling","Endocytic role suggested by domain analysis never functionally tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[6,7]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]},{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-1474244","term_label":"Extracellular matrix organization","supporting_discovery_ids":[3]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[0,3]}],"complexes":[],"partners":["YBX1","RACK1","SARA","MIB1","DCAF4"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NRC1","full_name":"Suppressor of tumorigenicity 7 protein","aliases":["Protein FAM4A1","Protein HELG"],"length_aa":585,"mass_kda":67.2,"function":"May act as a tumor suppressor","subcellular_location":"Membrane","url":"https://www.uniprot.org/uniprotkb/Q9NRC1/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ST7","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CERS6","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ST7","total_profiled":1310},"omim":[{"mim_id":"618299","title":"LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 12; LRP12","url":"https://www.omim.org/entry/618299"},{"mim_id":"617640","title":"SUPPRESSOR OF TUMORIGENICITY 7-LIKE PROTEIN; ST7L","url":"https://www.omim.org/entry/617640"},{"mim_id":"611015","title":"AUTISM, SUSCEPTIBILITY TO, 9; AUTS9","url":"https://www.omim.org/entry/611015"},{"mim_id":"605797","title":"ANKYRIN REPEAT, SAM, AND BASIC LEUCINE ZIPPER DOMAIN-CONTAINING 1; ASZ1","url":"https://www.omim.org/entry/605797"},{"mim_id":"600833","title":"SUPPRESSOR OF TUMORIGENICITY 7; ST7","url":"https://www.omim.org/entry/600833"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ST7"},"hgnc":{"alias_symbol":["TSG7","SEN4","ETS7q","HELG","RAY1","FAM4A"],"prev_symbol":["FAM4A1"]},"alphafold":{"accession":"Q9NRC1","domains":[{"cath_id":"-","chopping":"512-552","consensus_level":"medium","plddt":76.6466,"start":512,"end":552},{"cath_id":"-","chopping":"346-509","consensus_level":"medium","plddt":88.0108,"start":346,"end":509},{"cath_id":"1.20.5","chopping":"14-51","consensus_level":"medium","plddt":75.4489,"start":14,"end":51},{"cath_id":"1.10.3450","chopping":"152-332","consensus_level":"medium","plddt":91.3561,"start":152,"end":332}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NRC1","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NRC1-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NRC1-F1-predicted_aligned_error_v6.png","plddt_mean":80.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ST7","jax_strain_url":"https://www.jax.org/strain/search?query=ST7"},"sequence":{"accession":"Q9NRC1","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NRC1.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NRC1/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NRC1"}},"corpus_meta":[{"pmid":"15485929","id":"PMC_15485929","title":"Human 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anus","date":"2024-07-16","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.15.24310455","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":26422,"output_tokens":2129,"usd":0.0556,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9119,"output_tokens":3091,"usd":0.061435,"stage2_stop_reason":"end_turn"},"total_usd":0.117035,"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\": 2001,\n      \"finding\": \"Introduction of ST7 cDNA into the prostate-cancer-derived cell line PC3 abrogated in vivo tumorigenicity in nude mice without affecting in vitro proliferation, establishing ST7 as a functional tumor suppressor gene on chromosome 7q31.\",\n      \"method\": \"cDNA re-expression in PC3 cells, subcutaneous tumor formation assay in nude mice\",\n      \"journal\": \"Nature genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean gain-of-function with defined in vivo phenotype, single lab, replicated in part by independent study (PMID:16474848)\",\n      \"pmids\": [\"11279520\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"ST7 is a member of the low-density lipoprotein receptor (LDLR) superfamily (an LRP, now called LRP12); its cytoplasmic domain contains endocytosis and signal transduction motifs and directly interacts with RACK1, MIBP, and SARA as identified by yeast two-hybrid analysis, suggesting roles in endocytosis and signal transduction.\",\n      \"method\": \"Bioinformatic domain analysis, yeast two-hybrid system\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — yeast two-hybrid only, no in-cell validation of interactions, single lab\",\n      \"pmids\": [\"12809483\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PRMT5, associated with endogenous hSWI/SNF (BRG1 and hBRM) chromatin-remodeling complexes, methylates histone H3 at arginine 8 (H3R8) at the ST7 promoter, leading to H3K9 deacetylation and transcriptional repression of ST7.\",\n      \"method\": \"PRMT5 antisense knockdown cell line, microarray, ChIP, in vitro histone methylation assay with recombinant PRMT5, overexpression cell line\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro methylation assay with recombinant enzyme, ChIP demonstrating H3R8 methylation at ST7 promoter, loss-of-function and gain-of-function both tested, multiple orthogonal methods in single study\",\n      \"pmids\": [\"15485929\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Re-expression of ST7 in PC3 prostate cancer cells suppressed subcutaneous tumor growth in SCID mice and suppressed anchorage-independent colony formation in MDA-MB-231 breast cancer cells; expression profiling revealed ST7 predominantly induces changes in extracellular matrix remodeling genes including SPARC, IGFBP5, and several matrix metalloproteinases, suggesting ST7 mediates tumor suppression through modification of the tumor microenvironment.\",\n      \"method\": \"ST7 cDNA re-expression, SCID mouse xenograft assay, soft-agar colony formation assay, expression profiling/microarray\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — two orthogonal functional assays (in vivo and in vitro) plus gene expression profiling, single lab\",\n      \"pmids\": [\"16474848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"ST7 protein localizes to the cytoplasm (not the nucleus) in HCT-116, MCF-7, and PC-3 cancer cell lines, and no translocation to the nucleus was observed under any assayed conditions; endogenous ST7 and SERPINE1 are overexpressed when cells are arrested in the cell cycle and diminish upon re-entry into cell division.\",\n      \"method\": \"GFP/YFP/V5-tagged ST7 expression vectors, fluorescence microscopy, cell cycle synchronization, RT-PCR\",\n      \"journal\": \"Journal of cancer research and clinical oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct live-cell fluorescence localization with multiple tags plus cell-cycle synchronization experiment, single lab\",\n      \"pmids\": [\"20238225\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The CRL4DCAF4 E3 ubiquitin ligase complex (comprising CUL4A or CUL4B, DDB1, and DCAF4) specifically directs proteasomal degradation of ST7; c-Myc transcriptionally activates CUL4A and CUL4B by binding a conserved CACGTG site in their promoters, thereby increasing CRL4DCAF4 activity and reducing ST7 protein levels in colitis-associated cancer.\",\n      \"method\": \"In vitro and in vivo ubiquitination assays, co-immunoprecipitation, promoter binding/ChIP, siRNA knockdown, overexpression, xenograft mouse model\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro and in vivo ubiquitination assays plus co-IP, promoter ChIP, multiple loss- and gain-of-function experiments with defined phenotypic readouts, multiple orthogonal methods\",\n      \"pmids\": [\"30945288\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"MIB1 (mind bomb 1) E3 ubiquitin ligase targets ST7 for proteasomal degradation; loss of ST7 results in upregulation of IQGAP1, promoting pancreatic cancer cell proliferation and invasion, defining a MIB1/ST7/IQGAP1 signaling axis.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, siRNA knockdown, overexpression, in vitro proliferation/invasion assays, xenograft mouse model\",\n      \"journal\": \"Molecular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, ubiquitination assay, and functional in vivo and in vitro readouts, single lab\",\n      \"pmids\": [\"33793053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ST7 suppresses metastasis in non-small cell lung cancer by binding Y-box binding protein 1 (YBX1) and blocking its nuclear translocation, thereby suppressing MMP14 expression and inhibiting EMT; ST7 silencing enhanced EMT and metastatic progression in vitro and in a tail-vein lung metastasis mouse model.\",\n      \"method\": \"Co-immunoprecipitation (ST7–YBX1 interaction), nuclear translocation assays, siRNA knockdown, overexpression, in vitro EMT assays, in vivo tail-vein metastasis model\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP demonstrating direct ST7–YBX1 interaction, nuclear translocation assay, in vivo metastasis model, multiple orthogonal methods, single lab\",\n      \"pmids\": [\"42025890\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ST7 (LRP12) is a cytoplasmic transmembrane protein of the LDLR superfamily whose expression is epigenetically silenced by PRMT5-mediated H3R8 methylation within hSWI/SNF complexes; its protein levels are regulated by ubiquitin-proteasomal degradation via at least two E3 ligase complexes (CRL4DCAF4 and MIB1); when present, ST7 suppresses tumorigenicity by remodeling the extracellular matrix, suppressing IQGAP1, and binding YBX1 to block its nuclear translocation and thereby repress MMP14 expression and EMT.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ST7 (LRP12) is a tumor suppressor on chromosome 7q31 whose re-expression abrogates in vivo tumorigenicity of prostate and breast cancer cells without altering in vitro proliferation [#0, #3]. It is a cytoplasmic transmembrane member of the LDLR superfamily; its cytoplasmic domain carries endocytosis and signaling motifs and interacts with RACK1, MIBP, and SARA in yeast two-hybrid assays [#1], and the protein localizes to the cytoplasm rather than the nucleus across multiple cancer cell lines [#4]. ST7 exerts tumor suppression largely by reshaping the tumor microenvironment, predominantly inducing changes in extracellular matrix remodeling genes including SPARC, IGFBP5, and matrix metalloproteinases [#3]. Mechanistically, ST7 binds YBX1 and blocks its nuclear translocation, repressing MMP14 expression and inhibiting EMT and metastasis [#7], and its loss upregulates IQGAP1 to drive proliferation and invasion [#6]. ST7 expression is controlled at two levels: transcriptionally, PRMT5 associated with hSWI/SNF (BRG1/hBRM) chromatin-remodeling complexes methylates histone H3 at arginine 8 at the ST7 promoter, triggering H3K9 deacetylation and repression [#2]; and post-translationally, the CRL4DCAF4 ligase complex (driven by c-Myc-induced CUL4A/CUL4B) and the MIB1 E3 ligase target ST7 for proteasomal degradation [#5, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing whether the 7q31 candidate ST7 had genuine tumor-suppressor activity required functional testing; re-expression demonstrated it suppresses tumorigenicity in vivo without affecting cell-intrinsic proliferation, defining a microenvironment-dependent suppressor.\",\n      \"evidence\": \"ST7 cDNA re-expression in PC3 prostate cancer cells with subcutaneous tumor formation assay in nude mice\",\n      \"pmids\": [\"11279520\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of suppression undefined\", \"No identified binding partners or pathway\", \"Single tumor model\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"The molecular identity and interaction potential of ST7 were unknown; domain analysis placed it in the LDLR superfamily (LRP12) with a cytoplasmic domain bearing endocytosis and signaling motifs that bind RACK1, MIBP, and SARA, implicating it in endocytosis and signal transduction.\",\n      \"evidence\": \"Bioinformatic domain analysis and yeast two-hybrid screening\",\n      \"pmids\": [\"12809483\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Yeast two-hybrid interactions not validated in cells\", \"Functional consequence of RACK1/MIBP/SARA binding untested\", \"No link to tumor-suppressor phenotype\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"How ST7 is silenced in cancer was unresolved; PRMT5 within hSWI/SNF complexes was shown to methylate H3R8 at the ST7 promoter and trigger H3K9 deacetylation, defining an epigenetic repression mechanism.\",\n      \"evidence\": \"PRMT5 antisense knockdown, microarray, ChIP at the ST7 promoter, and in vitro histone methylation with recombinant PRMT5\",\n      \"pmids\": [\"15485929\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Upstream signals controlling PRMT5 recruitment to ST7 promoter unknown\", \"Whether silencing is reversible in vivo not addressed\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"The downstream effector program of ST7 suppression was unknown; expression profiling tied suppression to extracellular matrix remodeling, indicating ST7 acts through modification of the tumor microenvironment.\",\n      \"evidence\": \"ST7 re-expression with SCID xenograft and soft-agar assays plus expression profiling identifying SPARC, IGFBP5, and MMP changes\",\n      \"pmids\": [\"16474848\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect regulation of ECM genes unresolved\", \"No molecular partner linking ST7 to transcriptional output\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"The subcellular site of ST7 action and its cell-cycle behavior were uncharacterized; live-cell imaging confirmed cytoplasmic localization with no nuclear translocation, and synchronization linked ST7 (with SERPINE1) to cell-cycle arrest.\",\n      \"evidence\": \"GFP/YFP/V5-tagged ST7 fluorescence microscopy with cell-cycle synchronization and RT-PCR\",\n      \"pmids\": [\"20238225\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism coupling ST7 to cell-cycle arrest unknown\", \"Functional significance of SERPINE1 co-regulation unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Post-translational control of ST7 abundance was undefined; the CRL4DCAF4 complex was shown to ubiquitinate ST7 for degradation, with c-Myc activating CUL4A/CUL4B to lower ST7 in colitis-associated cancer.\",\n      \"evidence\": \"In vitro and in vivo ubiquitination assays, co-IP, promoter ChIP, knockdown/overexpression, and xenograft model\",\n      \"pmids\": [\"30945288\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Degron on ST7 recognized by DCAF4 not mapped\", \"Generality beyond colitis-associated cancer untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"A second degradation route and a proliferation/invasion effector were unknown; MIB1 was shown to degrade ST7, and ST7 loss derepressed IQGAP1, defining a MIB1/ST7/IQGAP1 axis in pancreatic cancer.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, knockdown/overexpression, proliferation/invasion assays, and xenograft model\",\n      \"pmids\": [\"33793053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of ST7-mediated IQGAP1 suppression not resolved\", \"Relative contribution of MIB1 vs CRL4DCAF4 across tissues unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"How cytoplasmic ST7 controls a transcriptional metastatic program was unresolved; ST7 was shown to bind YBX1 and block its nuclear entry, repressing MMP14 and EMT, providing a direct molecular link between ST7 and ECM/EMT output.\",\n      \"evidence\": \"Co-IP of ST7\\u2013YBX1, nuclear translocation assays, EMT assays, and tail-vein lung metastasis mouse model\",\n      \"pmids\": [\"42025890\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of ST7\\u2013YBX1 binding unknown\", \"Whether YBX1 sequestration explains the broader ECM program of [#3] untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ST7's LDLR-superfamily receptor architecture and putative endocytic/signaling partners (RACK1, MIBP, SARA) integrate with its cytoplasmic YBX1/IQGAP1 effector functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unifying mechanism linking receptor domain to tumor-suppressor signaling\", \"Endocytic role suggested by domain analysis never functionally tested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [6, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1474244\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"YBX1\", \"RACK1\", \"SARA\", \"MIB1\", \"DCAF4\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":{"gene":"ST7","tier":"IDENTITY","verdict":"Identity concern","subtype":"paralog","uniprot_band":"sparse","rules_fired":"R3","issue":"R3: opener equates ST7 to different HGNC gene LRP12"},"evaluation":{"faith_supported":5,"faith_total":5,"faith_pct":100.0}}