{"gene":"RAP2C","run_date":"2026-06-10T06:43:36","timeline":{"discoveries":[{"year":2005,"finding":"RAP2C is a GTP-binding protein (fifth member of the Rap family) that binds GTP in a Mg2+-dependent manner, with slower GDP release and lower relative GTP/GDP affinity compared to Rap2B. When expressed in eukaryotic cells, RAP2C localizes to the plasma membrane via its C-terminal CAAX motif.","method":"In vitro GTP-binding assay with recombinant purified protein, nucleotide exchange kinetics, anti-Rap2 antibody recognition, and eukaryotic cell expression with subcellular localization","journal":"Biochimie","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro biochemical reconstitution with purified protein, multiple orthogonal methods (nucleotide binding kinetics, nitrocellulose filter binding, cell localization), single lab","pmids":["16213650"],"is_preprint":false},{"year":2007,"finding":"Overexpression of RAP2C in HEK293T cells activates transcriptional activity of the serum response element (SRE). RAP2C protein localizes to the cytoplasm when overexpressed in COS-7 cells.","method":"Reporter gene assay (luciferase under SRE promoter) and subcellular localization by overexpression in COS-7 cells","journal":"Molecular biology reports","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single reporter assay method for SRE activation; localization without further functional link","pmids":["17447155"],"is_preprint":false},{"year":2013,"finding":"JAM-A associates directly with ZO-2 and indirectly with afadin; this complex, together with PDZ-GEF1, activates Rap2c. Activated Rap2c regulates epithelial barrier function by controlling apical actomyosin contraction via RhoA activity and nonmuscle myosin phosphorylation. siRNA knockdown of JAM-A, ZO-2, afadin, PDZ-GEF1, or Rap2c each enhanced paracellular permeability.","method":"Co-immunoprecipitation, siRNA knockdown with paracellular permeability assay, RhoA activity assay, myosin phosphorylation (western blot), JAM-A-deficient mouse model","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP for complex identification, multiple siRNA knockdowns with defined permeability phenotype, in vivo mouse model, multiple orthogonal methods across two systems","pmids":["23885123"],"is_preprint":false},{"year":2018,"finding":"Rap2c overexpression in human osteosarcoma cells promotes migration and invasion, increases MMP2 activity, decreases TIMP2 protein levels, and increases Akt phosphorylation. Knockdown of Rap2c inhibits migration and invasion. Rap2c has no effect on osteosarcoma cell proliferation or apoptosis.","method":"Overexpression and siRNA knockdown with Transwell migration/invasion assay, gelatin zymography (MMP2 activity), western blotting (TIMP2, phospho-Akt)","journal":"Oncology letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss- and gain-of-function with defined cellular phenotype, multiple readouts (migration, invasion, MMP2, Akt), single lab","pmids":["29552178"],"is_preprint":false},{"year":2018,"finding":"Rap2c is the only Rap2 isoform expressed in A20 B cells, and its depletion impairs BCR-induced MTOC reorientation toward the antigen contact site as well as F-actin remodeling that supports MTOC polarization.","method":"siRNA knockdown, microscopy-based MTOC polarization assay, F-actin imaging in B cells stimulated via BCR","journal":"Small GTPases","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — clean knockdown with defined cellular phenotype (MTOC reorientation, actin remodeling), single lab, single study","pmids":["29457987"],"is_preprint":false},{"year":2021,"finding":"In human lung fibroblasts, GPCR agonism (including dopamine D1 receptor) activates a cAMP→EPAC1/2→RAP2c→MAP4K7→LATS1/2 signaling cascade that phosphorylates YAP/TAZ, causing their nuclear exclusion. RAP2c is identified as an essential intermediate in this cascade; its modulation affects fibroblast proliferation, contraction, and extracellular matrix production.","method":"siRNA knockdown of EPAC1/2, RAP2c, and MAP4K7 in human lung fibroblasts; YAP/TAZ phosphorylation and nuclear/cytoplasmic localization assays; fibroblast functional assays (proliferation, contraction, ECM production)","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis established by sequential knockdowns, multiple functional readouts, single lab","pmids":["34046891"],"is_preprint":false},{"year":2022,"finding":"The lncRNA LENOX promotes association of RAP2C GTPase with the mitochondrial fission regulator DRP1, increasing DRP1 S637 phosphorylation, mitochondrial fusion, and oxidative phosphorylation in melanoma cells. Combined silencing of LENOX and RAP2C synergizes with MAPK inhibitors to eradicate melanoma cells.","method":"Co-immunoprecipitation (RAP2C–DRP1 interaction), DRP1 S637 phosphorylation by western blot, mitochondrial morphology imaging, OXPHOS measurement, siRNA knockdown and combinatorial drug treatment","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for RAP2C–DRP1 interaction plus functional phosphorylation and metabolic readouts, single lab, multiple orthogonal methods","pmids":["36214632"],"is_preprint":false},{"year":2020,"finding":"RAP2C activates the MAPK signaling pathway in breast cancer cells to decrease apoptosis and promote proliferation and migration. miR-188-5p directly targets Rap2c mRNA (confirmed by dual-luciferase assay) to suppress its expression and inhibit MAPK signaling.","method":"Dual-luciferase reporter assay (miR-188-5p targeting Rap2c 3'-UTR), RAP2C knockdown/overexpression with proliferation, apoptosis, and migration assays, western blot for MAPK pathway components","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct target validation by luciferase assay, loss/gain-of-function with multiple phenotypic readouts, single lab","pmids":["31541458"],"is_preprint":false},{"year":2020,"finding":"RAP2C knockdown in small cell lung cancer cells suppresses MAPK signaling pathway activation, inhibits proliferation, and promotes apoptosis. miR-195 binds Rap2c mRNA (confirmed by luciferase reporter assay) and inhibits its expression, thereby inhibiting MAPK signaling.","method":"Luciferase reporter assay, RAP2C knockdown/overexpression, western blot (MAPK pathway, Bax, Bcl-2), CCK-8 proliferation assay, flow cytometry (apoptosis), in vivo subcutaneous tumor model","journal":"Technology in cancer research & treatment","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase validation of miRNA–RAP2C interaction, in vitro and in vivo functional assays, single lab","pmids":["33302819"],"is_preprint":false},{"year":2021,"finding":"RAP2C activates ERK signaling in nucleus pulposus cells to promote apoptosis, inflammatory cytokine production, and ECM degradation. miR-200c-3p directly targets RAP2C mRNA (luciferase assay), and RAP2C knockdown or ERK inhibition reverses these effects.","method":"Luciferase reporter assay, RAP2C knockdown, ERK inhibitor (SCH772984), western blot, flow cytometry (apoptosis), cytokine measurement in LPS-treated NP cells","journal":"Molecular medicine reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase target validation, pharmacological and genetic epistasis with defined cellular phenotypes, single lab","pmids":["34676879"],"is_preprint":false},{"year":2024,"finding":"RAP2C interacts with MAP4K4 (interaction confirmed by co-immunoprecipitation and co-immunofluorescence). H/R increases RAP2C–MAP4K4 interaction and activates the MAPK pathway (phospho-JNK, phospho-P38, phospho-ERK) to promote cardiomyocyte apoptosis. Ischemic postconditioning reduces RAP2C and MAP4K4 levels and their interaction. MAP4K4 knockdown attenuates the pro-apoptotic and MAPK-activating effects of RAP2C overexpression.","method":"Co-immunoprecipitation, co-immunofluorescence, RAP2C knockdown/overexpression, MAP4K4 knockdown, western blot (phospho-MAPK components), apoptosis assay in H9C2 cells and rat I/R model","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for RAP2C–MAP4K4 interaction, genetic epistasis via double knockdown/overexpression, in vitro and in vivo models; preprint, single lab","pmids":["bio_10.1101_2024.12.04.626922"],"is_preprint":true}],"current_model":"RAP2C is a plasma membrane-localized Ras-family small GTPase that cycles between GDP- and GTP-bound states (with slower nucleotide exchange than Rap2B) and functions as a signaling node downstream of GEF complexes (e.g., JAM-A/ZO-2/afadin/PDZ-GEF1) and cAMP effectors (EPAC1/2); in its active GTP-bound form it promotes epithelial barrier integrity via actomyosin contraction, drives fibroblast YAP/TAZ inactivation through a RAP2C→MAP4K7→LATS1/2 cascade, activates MAPK/ERK signaling to regulate cell proliferation, migration, and apoptosis in multiple cell types, reorients the MTOC during B-cell activation, and interacts with MAP4K4 and DRP1 to modulate mitochondrial dynamics and cardiomyocyte survival."},"narrative":{"mechanistic_narrative":"RAP2C is a plasma membrane-localized Ras-family small GTPase that functions as a signaling node converting upstream GEF and cAMP inputs into control of cytoskeletal organization, MAPK activity, and cell fate decisions [PMID:16213650, PMID:23885123]. Biochemically it binds GTP in a Mg2+-dependent manner and cycles between nucleotide states with slower GDP release and lower relative GTP affinity than Rap2B, and its C-terminal CAAX motif directs it to the plasma membrane [PMID:16213650]. In epithelia, a JAM-A/ZO-2/afadin scaffold together with the exchange factor PDZ-GEF1 activates RAP2C, which then controls apical actomyosin contraction via RhoA and nonmuscle myosin phosphorylation to maintain paracellular barrier integrity [PMID:23885123]. RAP2C also relays cAMP signaling through an EPAC1/2→RAP2C→MAP4K7→LATS1/2 cascade that phosphorylates YAP/TAZ to exclude them from the nucleus and restrain fibroblast proliferation, contraction, and ECM production [PMID:34046891]. Across multiple cancer and disease cell types RAP2C activates MAPK/ERK signaling to promote proliferation and migration and suppress apoptosis, and it is a recurrent direct target of inhibitory microRNAs including miR-188-5p, miR-195, and miR-200c-3p [PMID:31541458, PMID:33302819, PMID:34676879]. Additional roles include B-cell receptor–induced MTOC reorientation and F-actin remodeling [PMID:29457987], and an interaction with DRP1 that increases DRP1 S637 phosphorylation to modulate mitochondrial fusion and oxidative phosphorylation [PMID:36214632].","teleology":[{"year":2005,"claim":"Established RAP2C as a genuine GTP-binding Rap-family GTPase with distinct nucleotide-handling kinetics, defining its basic biochemical identity and membrane localization.","evidence":"In vitro GTP-binding and nucleotide exchange assays with recombinant protein plus subcellular localization in eukaryotic cells","pmids":["16213650"],"confidence":"High","gaps":["No GEF or GAP partners identified in this work","Downstream effectors and cellular function not addressed"]},{"year":2007,"claim":"Linked RAP2C overexpression to transcriptional output, providing an early hint of downstream signaling activity via SRE.","evidence":"SRE-luciferase reporter assay and overexpression localization in COS-7 cells","pmids":["17447155"],"confidence":"Medium","gaps":["Single reporter readout without pathway dissection","Cytoplasmic localization on overexpression unexplained relative to membrane targeting"]},{"year":2013,"claim":"Defined the upstream activating module (JAM-A/ZO-2/afadin/PDZ-GEF1) and a concrete epithelial function for RAP2C in barrier integrity through actomyosin contraction.","evidence":"Reciprocal Co-IP, multiple siRNA knockdowns with permeability and RhoA/myosin readouts, plus JAM-A-deficient mouse","pmids":["23885123"],"confidence":"High","gaps":["Direct GEF action on RAP2C not reconstituted in vitro","Mechanism connecting RAP2C activation to RhoA not resolved"]},{"year":2018,"claim":"Showed RAP2C drives cell motility independent of proliferation in osteosarcoma via MMP2/TIMP2 and Akt signaling.","evidence":"Gain/loss-of-function with Transwell assays, gelatin zymography, and western blot","pmids":["29552178"],"confidence":"Medium","gaps":["Direct effectors linking RAP2C to Akt not identified","Single cell-line context"]},{"year":2018,"claim":"Implicated RAP2C in immune cytoskeletal polarity by linking it to BCR-induced MTOC reorientation and F-actin remodeling.","evidence":"siRNA knockdown with microscopy-based MTOC and actin imaging in A20 B cells","pmids":["29457987"],"confidence":"Medium","gaps":["Effector mediating MTOC reorientation unknown","GEF activating RAP2C in B cells not identified"]},{"year":2020,"claim":"Established RAP2C as a MAPK-pathway activator controlling proliferation, migration, and apoptosis, and identified it as a direct target of tumor-suppressive miRNAs.","evidence":"Dual-luciferase miRNA target validation plus knockdown/overexpression with phenotypic and western readouts in breast and small cell lung cancer cells (and an in vivo tumor model)","pmids":["31541458","33302819"],"confidence":"Medium","gaps":["Direct molecular link between RAP2C and MAPK kinases not defined","Whether GTP-loading state controls MAPK output untested"]},{"year":2021,"claim":"Positioned RAP2C as an essential intermediate in a cAMP-driven Hippo cascade controlling YAP/TAZ localization and fibroblast behavior.","evidence":"Sequential siRNA epistasis (EPAC1/2→RAP2C→MAP4K7→LATS1/2) with YAP/TAZ localization and fibroblast functional assays","pmids":["34046891"],"confidence":"Medium","gaps":["Direct RAP2C–MAP4K7 binding not demonstrated","Mechanism of cAMP/EPAC activation of RAP2C not reconstituted"]},{"year":2021,"claim":"Extended RAP2C→ERK signaling to nucleus pulposus pathophysiology, linking it to apoptosis, inflammation, and ECM degradation.","evidence":"miRNA luciferase target validation, knockdown, and ERK inhibitor epistasis in LPS-treated NP cells","pmids":["34676879"],"confidence":"Medium","gaps":["Direct effector coupling RAP2C to ERK unidentified","Single disease-cell context"]},{"year":2022,"claim":"Revealed a non-canonical RAP2C role in mitochondrial dynamics via DRP1 interaction, regulated by the lncRNA LENOX.","evidence":"Co-IP of RAP2C–DRP1, DRP1 S637 phosphorylation, mitochondrial morphology and OXPHOS measurements, and combinatorial drug treatment in melanoma cells","pmids":["36214632"],"confidence":"Medium","gaps":["Whether RAP2C directly phosphorylates or recruits a kinase to DRP1 unresolved","GTP-loading dependence of the DRP1 interaction untested"]},{"year":2024,"claim":"Identified MAP4K4 as a direct RAP2C partner mediating MAPK-driven cardiomyocyte apoptosis under hypoxia/reoxygenation.","evidence":"Co-IP and co-immunofluorescence, double knockdown/overexpression epistasis, and apoptosis assays in H9C2 cells and rat I/R model (preprint)","pmids":["bio_10.1101_2024.12.04.626922"],"confidence":"Medium","gaps":["Preprint, single lab, awaits peer review","Whether MAP4K4 is the general MAPK link across other RAP2C contexts unknown"]},{"year":null,"claim":"The GEF/GAP machinery and direct effector that couple RAP2C nucleotide state to MAPK/ERK activation across its many cellular contexts remain undefined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified structural or biochemical mechanism linking active RAP2C to specific MAP kinases","Context-specificity determinants between barrier, Hippo, MAPK, and mitochondrial roles unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003924","term_label":"GTPase activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[0]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[1]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,5,7]}],"complexes":[],"partners":["DRP1","MAP4K4","PDZ-GEF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y3L5","full_name":"Ras-related protein Rap-2c","aliases":[],"length_aa":183,"mass_kda":20.7,"function":"Small GTP-binding protein which cycles between a GDP-bound inactive and a GTP-bound active form. May play a role in cytoskeletal rearrangements and regulate cell spreading through activation of the effector TNIK. May play a role in SRE-mediated gene transcription","subcellular_location":"Cytoplasm; Recycling endosome membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y3L5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RAP2C","classification":"Not Classified","n_dependent_lines":1,"n_total_lines":1208,"dependency_fraction":0.0008278145695364238},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/RAP2C","total_profiled":1310},"omim":[{"mim_id":"301016","title":"RAS-RELATED PROTEIN 2C; RAP2C","url":"https://www.omim.org/entry/301016"},{"mim_id":"179541","title":"RAS-RELATED PROTEIN 2B; RAP2B","url":"https://www.omim.org/entry/179541"},{"mim_id":"179540","title":"RAS-RELATED PROTEIN 2A; RAP2A","url":"https://www.omim.org/entry/179540"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"endometrium 1","ntpm":86.4}],"url":"https://www.proteinatlas.org/search/RAP2C"},"hgnc":{"alias_symbol":["DKFZp313B211"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y3L5","domains":[{"cath_id":"3.40.50.300","chopping":"1-166","consensus_level":"high","plddt":95.7387,"start":1,"end":166}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3L5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3L5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y3L5-F1-predicted_aligned_error_v6.png","plddt_mean":91.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RAP2C","jax_strain_url":"https://www.jax.org/strain/search?query=RAP2C"},"sequence":{"accession":"Q9Y3L5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y3L5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y3L5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y3L5"}},"corpus_meta":[{"pmid":"23885123","id":"PMC_23885123","title":"JAM-A associates with ZO-2, afadin, and PDZ-GEF1 to activate Rap2c and regulate epithelial barrier function.","date":"2013","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/23885123","citation_count":103,"is_preprint":false},{"pmid":"16213650","id":"PMC_16213650","title":"Identification and biochemical characterization of Rap2C, a new member of the Rap family of small GTP-binding proteins.","date":"2005","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/16213650","citation_count":43,"is_preprint":false},{"pmid":"31541458","id":"PMC_31541458","title":"MicroRNA-188-5p promotes apoptosis and inhibits cell proliferation of breast cancer cells via the MAPK signaling pathway by targeting Rap2c.","date":"2019","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/31541458","citation_count":39,"is_preprint":false},{"pmid":"32014687","id":"PMC_32014687","title":"Overexpression of circRNA_100290 promotes the progression of laryngeal squamous cell carcinoma through the miR-136-5p/RAP2C axis.","date":"2020","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/32014687","citation_count":39,"is_preprint":false},{"pmid":"36214632","id":"PMC_36214632","title":"The LncRNA LENOX Interacts with RAP2C to Regulate Metabolism and Promote Resistance to MAPK Inhibition in Melanoma.","date":"2022","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/36214632","citation_count":33,"is_preprint":false},{"pmid":"34132374","id":"PMC_34132374","title":"Serum long non‑coding RNA NNT‑AS1 protected by exosome is a potential biomarker and functions as an oncogene via the miR‑496/RAP2C axis in colorectal cancer.","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/34132374","citation_count":33,"is_preprint":false},{"pmid":"29552178","id":"PMC_29552178","title":"Ras-related protein Rap2c promotes the migration and invasion of human osteosarcoma cells.","date":"2018","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/29552178","citation_count":22,"is_preprint":false},{"pmid":"17447155","id":"PMC_17447155","title":"Cloning and characterization of the human gene RAP2C, a novel member of Ras family, which activates transcriptional activities of SRE.","date":"2007","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/17447155","citation_count":20,"is_preprint":false},{"pmid":"34046891","id":"PMC_34046891","title":"GPCR-mediated YAP/TAZ inactivation in fibroblasts via EPAC1/2, RAP2C, and MAP4K7.","date":"2021","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/34046891","citation_count":19,"is_preprint":false},{"pmid":"34676879","id":"PMC_34676879","title":"MicroRNA‑200c‑3p suppresses intervertebral disc degeneration by targeting RAP2C/ERK signaling.","date":"2021","source":"Molecular medicine reports","url":"https://pubmed.ncbi.nlm.nih.gov/34676879","citation_count":10,"is_preprint":false},{"pmid":"33302819","id":"PMC_33302819","title":"microRNA-195 Promotes Small Cell Lung Cancer Cell Apoptosis via Inhibiting Rap2C Protein-Dependent MAPK Signal Transduction.","date":"2020","source":"Technology in cancer research & treatment","url":"https://pubmed.ncbi.nlm.nih.gov/33302819","citation_count":9,"is_preprint":false},{"pmid":"28714326","id":"PMC_28714326","title":"Spinal cord ischemia-reperfusion causes damage of neurocyte by inhibiting RAP2C.","date":"2017","source":"Neurological research","url":"https://pubmed.ncbi.nlm.nih.gov/28714326","citation_count":8,"is_preprint":false},{"pmid":"29457987","id":"PMC_29457987","title":"The Rap2c GTPase facilitates B cell receptor-induced reorientation of the microtubule-organizing center.","date":"2018","source":"Small GTPases","url":"https://pubmed.ncbi.nlm.nih.gov/29457987","citation_count":4,"is_preprint":false},{"pmid":"33907572","id":"PMC_33907572","title":"Erratum: Ras-related protein Rap2c promotes the migration and invasion of human osteosarcoma cells.","date":"2021","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/33907572","citation_count":1,"is_preprint":false},{"pmid":"41280817","id":"PMC_41280817","title":"Stability of G/C DNA Tetraplexes at Physiological pH Formed at the Promoter-UTR Intersection of the RAP2C Gene: Structural Multitude of a G/C Rich Genomic Segment.","date":"2025","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/41280817","citation_count":0,"is_preprint":false},{"pmid":"41280826","id":"PMC_41280826","title":"Multiformity of a G/C Rich Segment at the Promoter-UTR Intersection of RAP2C Gene: Structural Validation by Circular Dichroism.","date":"2025","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/41280826","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2024.12.04.626922","title":"The Cardioprotective Effect of Ischemic Postconditioning is Mediated by Inhibiting RAP2C-MAP4K4 Pathway","date":"2024-12-05","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.04.626922","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10450,"output_tokens":3087,"usd":0.038828,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10483,"output_tokens":3277,"usd":0.06717,"stage2_stop_reason":"end_turn"},"total_usd":0.105998,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2005,\n      \"finding\": \"RAP2C is a GTP-binding protein (fifth member of the Rap family) that binds GTP in a Mg2+-dependent manner, with slower GDP release and lower relative GTP/GDP affinity compared to Rap2B. When expressed in eukaryotic cells, RAP2C localizes to the plasma membrane via its C-terminal CAAX motif.\",\n      \"method\": \"In vitro GTP-binding assay with recombinant purified protein, nucleotide exchange kinetics, anti-Rap2 antibody recognition, and eukaryotic cell expression with subcellular localization\",\n      \"journal\": \"Biochimie\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro biochemical reconstitution with purified protein, multiple orthogonal methods (nucleotide binding kinetics, nitrocellulose filter binding, cell localization), single lab\",\n      \"pmids\": [\"16213650\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Overexpression of RAP2C in HEK293T cells activates transcriptional activity of the serum response element (SRE). RAP2C protein localizes to the cytoplasm when overexpressed in COS-7 cells.\",\n      \"method\": \"Reporter gene assay (luciferase under SRE promoter) and subcellular localization by overexpression in COS-7 cells\",\n      \"journal\": \"Molecular biology reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single reporter assay method for SRE activation; localization without further functional link\",\n      \"pmids\": [\"17447155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"JAM-A associates directly with ZO-2 and indirectly with afadin; this complex, together with PDZ-GEF1, activates Rap2c. Activated Rap2c regulates epithelial barrier function by controlling apical actomyosin contraction via RhoA activity and nonmuscle myosin phosphorylation. siRNA knockdown of JAM-A, ZO-2, afadin, PDZ-GEF1, or Rap2c each enhanced paracellular permeability.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown with paracellular permeability assay, RhoA activity assay, myosin phosphorylation (western blot), JAM-A-deficient mouse model\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP for complex identification, multiple siRNA knockdowns with defined permeability phenotype, in vivo mouse model, multiple orthogonal methods across two systems\",\n      \"pmids\": [\"23885123\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Rap2c overexpression in human osteosarcoma cells promotes migration and invasion, increases MMP2 activity, decreases TIMP2 protein levels, and increases Akt phosphorylation. Knockdown of Rap2c inhibits migration and invasion. Rap2c has no effect on osteosarcoma cell proliferation or apoptosis.\",\n      \"method\": \"Overexpression and siRNA knockdown with Transwell migration/invasion assay, gelatin zymography (MMP2 activity), western blotting (TIMP2, phospho-Akt)\",\n      \"journal\": \"Oncology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss- and gain-of-function with defined cellular phenotype, multiple readouts (migration, invasion, MMP2, Akt), single lab\",\n      \"pmids\": [\"29552178\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Rap2c is the only Rap2 isoform expressed in A20 B cells, and its depletion impairs BCR-induced MTOC reorientation toward the antigen contact site as well as F-actin remodeling that supports MTOC polarization.\",\n      \"method\": \"siRNA knockdown, microscopy-based MTOC polarization assay, F-actin imaging in B cells stimulated via BCR\",\n      \"journal\": \"Small GTPases\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — clean knockdown with defined cellular phenotype (MTOC reorientation, actin remodeling), single lab, single study\",\n      \"pmids\": [\"29457987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In human lung fibroblasts, GPCR agonism (including dopamine D1 receptor) activates a cAMP→EPAC1/2→RAP2c→MAP4K7→LATS1/2 signaling cascade that phosphorylates YAP/TAZ, causing their nuclear exclusion. RAP2c is identified as an essential intermediate in this cascade; its modulation affects fibroblast proliferation, contraction, and extracellular matrix production.\",\n      \"method\": \"siRNA knockdown of EPAC1/2, RAP2c, and MAP4K7 in human lung fibroblasts; YAP/TAZ phosphorylation and nuclear/cytoplasmic localization assays; fibroblast functional assays (proliferation, contraction, ECM production)\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis established by sequential knockdowns, multiple functional readouts, single lab\",\n      \"pmids\": [\"34046891\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The lncRNA LENOX promotes association of RAP2C GTPase with the mitochondrial fission regulator DRP1, increasing DRP1 S637 phosphorylation, mitochondrial fusion, and oxidative phosphorylation in melanoma cells. Combined silencing of LENOX and RAP2C synergizes with MAPK inhibitors to eradicate melanoma cells.\",\n      \"method\": \"Co-immunoprecipitation (RAP2C–DRP1 interaction), DRP1 S637 phosphorylation by western blot, mitochondrial morphology imaging, OXPHOS measurement, siRNA knockdown and combinatorial drug treatment\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for RAP2C–DRP1 interaction plus functional phosphorylation and metabolic readouts, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"36214632\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RAP2C activates the MAPK signaling pathway in breast cancer cells to decrease apoptosis and promote proliferation and migration. miR-188-5p directly targets Rap2c mRNA (confirmed by dual-luciferase assay) to suppress its expression and inhibit MAPK signaling.\",\n      \"method\": \"Dual-luciferase reporter assay (miR-188-5p targeting Rap2c 3'-UTR), RAP2C knockdown/overexpression with proliferation, apoptosis, and migration assays, western blot for MAPK pathway components\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct target validation by luciferase assay, loss/gain-of-function with multiple phenotypic readouts, single lab\",\n      \"pmids\": [\"31541458\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RAP2C knockdown in small cell lung cancer cells suppresses MAPK signaling pathway activation, inhibits proliferation, and promotes apoptosis. miR-195 binds Rap2c mRNA (confirmed by luciferase reporter assay) and inhibits its expression, thereby inhibiting MAPK signaling.\",\n      \"method\": \"Luciferase reporter assay, RAP2C knockdown/overexpression, western blot (MAPK pathway, Bax, Bcl-2), CCK-8 proliferation assay, flow cytometry (apoptosis), in vivo subcutaneous tumor model\",\n      \"journal\": \"Technology in cancer research & treatment\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase validation of miRNA–RAP2C interaction, in vitro and in vivo functional assays, single lab\",\n      \"pmids\": [\"33302819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RAP2C activates ERK signaling in nucleus pulposus cells to promote apoptosis, inflammatory cytokine production, and ECM degradation. miR-200c-3p directly targets RAP2C mRNA (luciferase assay), and RAP2C knockdown or ERK inhibition reverses these effects.\",\n      \"method\": \"Luciferase reporter assay, RAP2C knockdown, ERK inhibitor (SCH772984), western blot, flow cytometry (apoptosis), cytokine measurement in LPS-treated NP cells\",\n      \"journal\": \"Molecular medicine reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase target validation, pharmacological and genetic epistasis with defined cellular phenotypes, single lab\",\n      \"pmids\": [\"34676879\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RAP2C interacts with MAP4K4 (interaction confirmed by co-immunoprecipitation and co-immunofluorescence). H/R increases RAP2C–MAP4K4 interaction and activates the MAPK pathway (phospho-JNK, phospho-P38, phospho-ERK) to promote cardiomyocyte apoptosis. Ischemic postconditioning reduces RAP2C and MAP4K4 levels and their interaction. MAP4K4 knockdown attenuates the pro-apoptotic and MAPK-activating effects of RAP2C overexpression.\",\n      \"method\": \"Co-immunoprecipitation, co-immunofluorescence, RAP2C knockdown/overexpression, MAP4K4 knockdown, western blot (phospho-MAPK components), apoptosis assay in H9C2 cells and rat I/R model\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for RAP2C–MAP4K4 interaction, genetic epistasis via double knockdown/overexpression, in vitro and in vivo models; preprint, single lab\",\n      \"pmids\": [\"bio_10.1101_2024.12.04.626922\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"RAP2C is a plasma membrane-localized Ras-family small GTPase that cycles between GDP- and GTP-bound states (with slower nucleotide exchange than Rap2B) and functions as a signaling node downstream of GEF complexes (e.g., JAM-A/ZO-2/afadin/PDZ-GEF1) and cAMP effectors (EPAC1/2); in its active GTP-bound form it promotes epithelial barrier integrity via actomyosin contraction, drives fibroblast YAP/TAZ inactivation through a RAP2C→MAP4K7→LATS1/2 cascade, activates MAPK/ERK signaling to regulate cell proliferation, migration, and apoptosis in multiple cell types, reorients the MTOC during B-cell activation, and interacts with MAP4K4 and DRP1 to modulate mitochondrial dynamics and cardiomyocyte survival.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RAP2C is a plasma membrane-localized Ras-family small GTPase that functions as a signaling node converting upstream GEF and cAMP inputs into control of cytoskeletal organization, MAPK activity, and cell fate decisions [#0, #2]. Biochemically it binds GTP in a Mg2+-dependent manner and cycles between nucleotide states with slower GDP release and lower relative GTP affinity than Rap2B, and its C-terminal CAAX motif directs it to the plasma membrane [#0]. In epithelia, a JAM-A/ZO-2/afadin scaffold together with the exchange factor PDZ-GEF1 activates RAP2C, which then controls apical actomyosin contraction via RhoA and nonmuscle myosin phosphorylation to maintain paracellular barrier integrity [#2]. RAP2C also relays cAMP signaling through an EPAC1/2\\u2192RAP2C\\u2192MAP4K7\\u2192LATS1/2 cascade that phosphorylates YAP/TAZ to exclude them from the nucleus and restrain fibroblast proliferation, contraction, and ECM production [#5]. Across multiple cancer and disease cell types RAP2C activates MAPK/ERK signaling to promote proliferation and migration and suppress apoptosis, and it is a recurrent direct target of inhibitory microRNAs including miR-188-5p, miR-195, and miR-200c-3p [#7, #8, #9]. Additional roles include B-cell receptor\\u2013induced MTOC reorientation and F-actin remodeling [#4], and an interaction with DRP1 that increases DRP1 S637 phosphorylation to modulate mitochondrial fusion and oxidative phosphorylation [#6].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Established RAP2C as a genuine GTP-binding Rap-family GTPase with distinct nucleotide-handling kinetics, defining its basic biochemical identity and membrane localization.\",\n      \"evidence\": \"In vitro GTP-binding and nucleotide exchange assays with recombinant protein plus subcellular localization in eukaryotic cells\",\n      \"pmids\": [\"16213650\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No GEF or GAP partners identified in this work\", \"Downstream effectors and cellular function not addressed\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Linked RAP2C overexpression to transcriptional output, providing an early hint of downstream signaling activity via SRE.\",\n      \"evidence\": \"SRE-luciferase reporter assay and overexpression localization in COS-7 cells\",\n      \"pmids\": [\"17447155\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single reporter readout without pathway dissection\", \"Cytoplasmic localization on overexpression unexplained relative to membrane targeting\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Defined the upstream activating module (JAM-A/ZO-2/afadin/PDZ-GEF1) and a concrete epithelial function for RAP2C in barrier integrity through actomyosin contraction.\",\n      \"evidence\": \"Reciprocal Co-IP, multiple siRNA knockdowns with permeability and RhoA/myosin readouts, plus JAM-A-deficient mouse\",\n      \"pmids\": [\"23885123\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct GEF action on RAP2C not reconstituted in vitro\", \"Mechanism connecting RAP2C activation to RhoA not resolved\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showed RAP2C drives cell motility independent of proliferation in osteosarcoma via MMP2/TIMP2 and Akt signaling.\",\n      \"evidence\": \"Gain/loss-of-function with Transwell assays, gelatin zymography, and western blot\",\n      \"pmids\": [\"29552178\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effectors linking RAP2C to Akt not identified\", \"Single cell-line context\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Implicated RAP2C in immune cytoskeletal polarity by linking it to BCR-induced MTOC reorientation and F-actin remodeling.\",\n      \"evidence\": \"siRNA knockdown with microscopy-based MTOC and actin imaging in A20 B cells\",\n      \"pmids\": [\"29457987\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Effector mediating MTOC reorientation unknown\", \"GEF activating RAP2C in B cells not identified\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Established RAP2C as a MAPK-pathway activator controlling proliferation, migration, and apoptosis, and identified it as a direct target of tumor-suppressive miRNAs.\",\n      \"evidence\": \"Dual-luciferase miRNA target validation plus knockdown/overexpression with phenotypic and western readouts in breast and small cell lung cancer cells (and an in vivo tumor model)\",\n      \"pmids\": [\"31541458\", \"33302819\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between RAP2C and MAPK kinases not defined\", \"Whether GTP-loading state controls MAPK output untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Positioned RAP2C as an essential intermediate in a cAMP-driven Hippo cascade controlling YAP/TAZ localization and fibroblast behavior.\",\n      \"evidence\": \"Sequential siRNA epistasis (EPAC1/2\\u2192RAP2C\\u2192MAP4K7\\u2192LATS1/2) with YAP/TAZ localization and fibroblast functional assays\",\n      \"pmids\": [\"34046891\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct RAP2C\\u2013MAP4K7 binding not demonstrated\", \"Mechanism of cAMP/EPAC activation of RAP2C not reconstituted\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended RAP2C\\u2192ERK signaling to nucleus pulposus pathophysiology, linking it to apoptosis, inflammation, and ECM degradation.\",\n      \"evidence\": \"miRNA luciferase target validation, knockdown, and ERK inhibitor epistasis in LPS-treated NP cells\",\n      \"pmids\": [\"34676879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct effector coupling RAP2C to ERK unidentified\", \"Single disease-cell context\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed a non-canonical RAP2C role in mitochondrial dynamics via DRP1 interaction, regulated by the lncRNA LENOX.\",\n      \"evidence\": \"Co-IP of RAP2C\\u2013DRP1, DRP1 S637 phosphorylation, mitochondrial morphology and OXPHOS measurements, and combinatorial drug treatment in melanoma cells\",\n      \"pmids\": [\"36214632\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RAP2C directly phosphorylates or recruits a kinase to DRP1 unresolved\", \"GTP-loading dependence of the DRP1 interaction untested\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified MAP4K4 as a direct RAP2C partner mediating MAPK-driven cardiomyocyte apoptosis under hypoxia/reoxygenation.\",\n      \"evidence\": \"Co-IP and co-immunofluorescence, double knockdown/overexpression epistasis, and apoptosis assays in H9C2 cells and rat I/R model (preprint)\",\n      \"pmids\": [\"bio_10.1101_2024.12.04.626922\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, single lab, awaits peer review\", \"Whether MAP4K4 is the general MAPK link across other RAP2C contexts unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The GEF/GAP machinery and direct effector that couple RAP2C nucleotide state to MAPK/ERK activation across its many cellular contexts remain undefined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified structural or biochemical mechanism linking active RAP2C to specific MAP kinases\", \"Context-specificity determinants between barrier, Hippo, MAPK, and mitochondrial roles unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GTPase activity\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0003924\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 5, 7]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"DRP1\", \"MAP4K4\", \"PDZ-GEF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}