{"gene":"RASAL3","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2015,"finding":"RASAL3 possesses RasGAP activity (but not Rap1GAP activity) and represses TCR-stimulated ERK phosphorylation in T cells; systemic RASAL3-deficient mice show reduced peripheral naive CD4 and CD8 T cells due to increased apoptosis, establishing RASAL3 as required for naive T cell survival in vivo.","method":"In vitro RasGAP/Rap1GAP activity assays, ERK phosphorylation assays in T cell lines, systemic knockout mice with flow cytometry and adoptive transfer experiments","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 1-2 — enzymatic activity confirmed in vitro, combined with clean KO mouse phenotype and adoptive transfer rescue experiment","pmids":["25793935"],"is_preprint":false},{"year":2015,"finding":"RASAL3 is predominantly expressed in hematopoietic cells (NKT, B, T cells) and negatively regulates Ras/ERK signaling in NKT cells; RASAL3-deficient mice show severe decrease of NKT cells in liver and reduced IL-4/IFN-γ production, with augmented ERK phosphorylation in RASAL3-deficient NKT cells upon α-GalCer stimulation.","method":"Systemic RASAL3-knockout mice, α-GalCer stimulation, flow cytometry, ERK phosphorylation assays, cytokine measurement","journal":"European journal of immunology","confidence":"High","confidence_rationale":"Tier 2 — clean KO mouse with multiple orthogonal readouts (cell numbers, cytokine production, ERK phosphorylation)","pmids":["25652366"],"is_preprint":false},{"year":2017,"finding":"Rasal3-deficient mice show ameliorated Th1- and Th2-dependent contact hypersensitivity reactions due to increased death of activated T cells with reduced Bcl2 expression, demonstrating that Rasal3 controls inflammatory response magnitude by supporting survival of both naive and activated T cells.","method":"Rasal3-knockout mice, contact hypersensitivity model, flow cytometry, Bcl2 expression analysis","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 — clean KO with defined in vivo phenotype, single lab","pmids":["29291408"],"is_preprint":false},{"year":2018,"finding":"RASAL3 is epigenetically silenced (promoter hypermethylation) in cancer-associated fibroblasts (CAF), leading to oncogenic Ras activity that drives macropinocytosis-mediated glutamine synthesis; stromal glutamine fuels prostate cancer anaplerosis and neuroendocrine differentiation.","method":"Epigenetic analysis of CAF, orthotopic xenograft models, macropinocytosis inhibition, glutamine transport inhibition, androgen deprivation therapy models","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal in vitro and in vivo experiments, functional rescue with inhibitors, replicated in clinical samples","pmids":["30047926"],"is_preprint":false},{"year":2018,"finding":"The catalytic (GAP) domain of RASAL3 interacts with Rac2 and stimulates Rac2 GTPase activity in vitro, whereas p50 rhoGAP did not markedly affect Rac2 activity, indicating RASAL3 has RasGAP family activity toward the hematopoietic Rho GTPase Rac2.","method":"In vitro GTPase activity assay with purified RASAL3 catalytic domain and Rac2","journal":"Biomedical reports","confidence":"Medium","confidence_rationale":"Tier 1 — direct in vitro enzymatic assay, but single lab and single method","pmids":["30271600"],"is_preprint":false},{"year":2021,"finding":"RASAL3 is highly expressed in neutrophils, its expression is upregulated by exogenous stimuli, and RASAL3 deficiency triggers augmented neutrophil responses and hyperinflammation; RASAL3-KO mice show accelerated mortality in a septic shock model via severe organ damage and hyperinflammatory neutrophil response.","method":"RASAL3-knockout mice, LPS septic shock model, sickle cell disease mouse model, neutrophil activation assays","journal":"Frontiers in immunology","confidence":"High","confidence_rationale":"Tier 2 — clean KO with two independent in vivo disease models and defined cellular phenotype","pmids":["34777356"],"is_preprint":false},{"year":2022,"finding":"CD229 (SLAMF3) interacts with RASAL3 as identified by co-immunoprecipitation coupled with mass spectrometry; intercellular tyrosine phosphorylation-mediated self-activation of CD229 activates the RAS/ERK signaling pathway via interaction with RASAL3 to promote multiple myeloma cell proliferation.","method":"Co-immunoprecipitation coupled with mass spectrometry, co-culture with immunofluorescence assay, in vitro proliferation assays, xenograft mouse model","journal":"Aging","confidence":"Medium","confidence_rationale":"Tier 2-3 — Co-IP/MS identification of interaction combined with functional in vitro and in vivo readouts, single lab","pmids":["36445333"],"is_preprint":false},{"year":2023,"finding":"Optogenetic recruitment of RASAL3 to the cell front of HL-60 neutrophils extinguished protrusions and changed migration direction; global membrane recruitment caused cells to polarize and move more rapidly in an mTORC2-dependent but largely PI3K-independent manner, establishing RASAL3 as a direct regulator of actin assembly, cell polarity, and migration via Ras suppression.","method":"Optogenetic targeting (light-inducible recruitment) in differentiated HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, pharmacological inhibition of mTORC2 and PI3K","journal":"Developmental cell","confidence":"High","confidence_rationale":"Tier 1-2 — acute optogenetic perturbation with spatial precision, multiple cell types, pharmacological validation of downstream pathway","pmids":["37220748"],"is_preprint":false},{"year":2023,"finding":"ALKBH5 (m6A demethylase) regulates Rasal3 mRNA stability in an m6A-dependent posttranscriptional manner; ALKBH5 deficiency reduces Rasal3 expression, thereby activating RAS/RAF/ERK signaling and increasing cardiomyocyte apoptosis in doxorubicin-induced cardiotoxicity.","method":"Alkbh5-knockout, knockin, and myocardial-specific knockout mice; cardiac function assessment; m6A modification analysis; signal transduction studies","journal":"iScience","confidence":"Medium","confidence_rationale":"Tier 2 — multiple genetic mouse models with defined molecular mechanism, single lab","pmids":["36876119"],"is_preprint":false},{"year":2024,"finding":"RASAL3 physically and functionally interacts with CCDC88B and ARHGEF2 as part of a complex; Rasal3-mutant dendritic cells show enhanced migratory properties in vitro, and RASAL3 and ARHGEF2 act in opposing fashions to regulate RHOA activation, establishing a CCDC88B/RASAL3/ARHGEF2 complex that controls DC migration.","method":"Co-immunoprecipitation, proximity-ligation assay, Rasal3-mutant mouse DC migration assays, RHOA activation assays, neuroinflammation and colitis mouse models","journal":"Communications biology","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP for complex identification, clean mutant mice, multiple in vitro and in vivo functional readouts","pmids":["38200184"],"is_preprint":false},{"year":2024,"finding":"Optogenetic global or rear-targeted recruitment of RASAL3 in HL-60 neutrophils and macrophages causes cell polarization and accelerated migration through increased rear actomyosin contractility followed by sustained mTORC2-dependent actin polymerization at the front; this RasGAP-mediated polarization depends critically on myosin II activity.","method":"Optogenetic membrane recruitment in HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, myosin II inhibition, mTORC2 inhibition, computational simulations","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 1-2 — acute optogenetic perturbation with spatial control, pharmacological dissection of mechanism, replicated in two cell types and supported by computational model","pmids":["38951708"],"is_preprint":false}],"current_model":"RASAL3 is a hematopoietic RasGAP (and Rac2GAP) that negatively regulates Ras/ERK signaling in immune cells (T cells, NKT cells, neutrophils, dendritic cells) to control their survival, activation, and migration; in the context of cell polarity, optogenetic studies show that local RASAL3-mediated Ras suppression extinguishes protrusions while global Ras suppression paradoxically drives mTORC2/myosin II-dependent polarization and faster migration, and in stromal fibroblasts its epigenetic silencing activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer progression."},"narrative":{"teleology":[{"year":2015,"claim":"Establishing that RASAL3 is a bona fide RasGAP required for T and NKT cell homeostasis resolved the identity of the RasGAP governing Ras/ERK signaling downstream of TCR engagement in lymphocytes.","evidence":"In vitro RasGAP/Rap1GAP assays, ERK phosphorylation in T cell lines, systemic RASAL3-KO mice with flow cytometry and adoptive transfer; parallel KO analysis of NKT cells with α-GalCer stimulation and cytokine measurement","pmids":["25793935","25652366"],"confidence":"High","gaps":["Structural basis for Ras selectivity over Rap1 unknown","Mechanism linking excess ERK activity to apoptosis rather than proliferation in naive T cells not defined"]},{"year":2017,"claim":"Demonstrating that RASAL3-deficient activated T cells die with reduced Bcl2 in a contact hypersensitivity model established that RASAL3 controls inflammatory magnitude by supporting survival of both naive and effector T cells.","evidence":"RASAL3-KO mice in Th1/Th2 contact hypersensitivity models with Bcl2 expression analysis","pmids":["29291408"],"confidence":"Medium","gaps":["Whether RASAL3 directly regulates Bcl2 transcription or acts indirectly through ERK not resolved","Single-lab observation without independent replication"]},{"year":2018,"claim":"Showing that RASAL3 epigenetic silencing in cancer-associated fibroblasts activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer revealed a tumor-extrinsic, stromal function for RASAL3 loss beyond immune cells.","evidence":"CAF epigenetic profiling, orthotopic xenograft models, macropinocytosis and glutamine transport inhibition, clinical sample validation","pmids":["30047926"],"confidence":"High","gaps":["Whether RASAL3 silencing occurs in fibroblasts of other tumor types not explored","Direct link between specific Ras isoform activation and macropinocytosis induction not defined"]},{"year":2018,"claim":"Discovering that the RASAL3 catalytic domain stimulates Rac2 GTPase activity in vitro expanded RASAL3's substrate repertoire beyond Ras to the hematopoietic Rho-family GTPase Rac2.","evidence":"In vitro GTPase activity assay with purified RASAL3 GAP domain and Rac2","pmids":["30271600"],"confidence":"Medium","gaps":["Rac2GAP activity not confirmed in cellular context","Structural basis for dual Ras/Rac2 specificity not characterized","Single-method, single-lab result"]},{"year":2021,"claim":"Extending RASAL3's immune role to neutrophils, where its loss triggers hyperinflammation and accelerated septic mortality, showed that RASAL3 is a broad negative regulator across innate and adaptive immune lineages.","evidence":"RASAL3-KO mice in LPS septic shock and sickle cell disease models, neutrophil activation assays","pmids":["34777356"],"confidence":"High","gaps":["Specific Ras isoform(s) hyperactivated in neutrophils not identified","Whether Rac2GAP activity contributes to neutrophil phenotype untested"]},{"year":2022,"claim":"Identification of CD229 (SLAMF3) as a RASAL3-interacting partner in myeloma cells suggested a receptor-proximal mechanism by which RASAL3 is recruited to regulate Ras/ERK at the plasma membrane.","evidence":"Co-immunoprecipitation coupled with mass spectrometry, co-culture immunofluorescence, proliferation assays, xenograft model","pmids":["36445333"],"confidence":"Medium","gaps":["Reciprocal Co-IP not described","Whether SLAMF3-RASAL3 interaction is direct or scaffolded not resolved","Unclear if this interaction is generalizable beyond myeloma"]},{"year":2023,"claim":"Optogenetic studies revealed that RASAL3-mediated local Ras suppression directly controls protrusion and migration direction, while global Ras suppression paradoxically drives mTORC2-dependent polarization, uncovering a spatial logic for RasGAP function in cell motility.","evidence":"Light-inducible membrane recruitment of RASAL3 in HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, PI3K and mTORC2 pharmacological inhibition","pmids":["37220748"],"confidence":"High","gaps":["Molecular link from global Ras suppression to mTORC2 activation unclear","Role of Rac2GAP activity versus RasGAP activity in migration phenotype not dissected"]},{"year":2023,"claim":"Demonstrating that ALKBH5-dependent m6A demethylation stabilizes Rasal3 mRNA revealed an epitranscriptomic layer of RASAL3 regulation, linking its expression to cardiomyocyte survival under doxorubicin stress.","evidence":"Alkbh5-KO, knock-in, and cardiac-specific KO mice; m6A modification analysis; RAS/RAF/ERK signaling and apoptosis readouts","pmids":["36876119"],"confidence":"Medium","gaps":["Whether m6A regulation of RASAL3 operates in hematopoietic cells unknown","Specific m6A sites on Rasal3 mRNA not mapped","Single-lab observation"]},{"year":2024,"claim":"Identification of a CCDC88B/RASAL3/ARHGEF2 complex that oppositely regulates RHOA in dendritic cells established a multiprotein signaling module through which RASAL3 restrains DC migration and neuroinflammation.","evidence":"Reciprocal Co-IP, proximity-ligation assay, Rasal3-mutant DC migration assays, RHOA activation assays, EAE and colitis mouse models","pmids":["38200184"],"confidence":"High","gaps":["How RASAL3's RasGAP activity integrates with RHOA regulation through ARHGEF2 is mechanistically unresolved","Stoichiometry and structure of the ternary complex unknown"]},{"year":2024,"claim":"A refined optogenetic and computational analysis established that RASAL3-induced polarization depends on myosin II–mediated rear contractility preceding sustained mTORC2-driven front protrusion, defining the temporal sequence of the RasGAP-driven polarization circuit.","evidence":"Optogenetic rear-targeted and global RASAL3 recruitment in HL-60 and RAW cells, myosin II and mTORC2 inhibition, computational simulation","pmids":["38951708"],"confidence":"High","gaps":["Identity of the upstream sensor that couples Ras suppression to myosin II activation unknown","Whether this polarization circuit operates in vivo during chemotaxis not tested"]},{"year":null,"claim":"How RASAL3's dual RasGAP and Rac2GAP activities are coordinated in vivo, and whether the CCDC88B/RASAL3/ARHGEF2 complex operates in cell types beyond dendritic cells, remain open questions.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of RASAL3 exists","Relative contribution of RasGAP vs Rac2GAP activity to each physiological phenotype not dissected","Whether myosin II–mTORC2 polarization axis downstream of RASAL3 functions during in vivo immune surveillance untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,1,4,7,10]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,4]}],"localization":[{"term_id":"GO:0005886","term_label":"plasma membrane","supporting_discovery_ids":[7,10]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,9]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,3,6,7,8,10]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[1,2,5,9]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[3,6]}],"complexes":["CCDC88B/RASAL3/ARHGEF2 complex"],"partners":["CCDC88B","ARHGEF2","RAC2","SLAMF3","ALKBH5"],"other_free_text":[]},"mechanistic_narrative":"RASAL3 is a hematopoietic RasGAP that negatively regulates Ras/ERK signaling to control immune cell survival, activation, and migration. RASAL3 possesses RasGAP activity (but not Rap1GAP activity) and additionally stimulates Rac2 GTPase activity in vitro; in T cells and NKT cells, it represses TCR-stimulated ERK phosphorylation, and its genetic ablation causes increased apoptosis of naive and activated T cells (with reduced Bcl2 expression), depletion of NKT cells, and neutrophil hyperinflammation [PMID:25793935, PMID:25652366, PMID:29291408, PMID:34777356]. Optogenetic studies in neutrophils and macrophages demonstrate that local RASAL3-mediated Ras suppression extinguishes protrusions and redirects migration, while global Ras suppression drives myosin II–dependent rear contractility and mTORC2-dependent front actin polymerization, producing cell polarization and accelerated movement [PMID:37220748, PMID:38951708]. RASAL3 forms a complex with CCDC88B and ARHGEF2 that opposes RHOA activation to regulate dendritic cell migration, and epigenetic silencing of RASAL3 in cancer-associated fibroblasts activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer progression [PMID:38200184, PMID:30047926]."},"prefetch_data":{"uniprot":{"accession":"Q86YV0","full_name":"RAS protein activator like-3","aliases":[],"length_aa":1011,"mass_kda":111.9,"function":"Functions as a Ras GTPase-activating protein. Plays an important role in the expansion and functions of natural killer T (NKT) cells in the liver by negatively regulating RAS activity and the down-stream ERK signaling pathway","subcellular_location":"Cytoplasm; Cytoplasm, cell cortex","url":"https://www.uniprot.org/uniprotkb/Q86YV0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/RASAL3","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/RASAL3","total_profiled":1310},"omim":[{"mim_id":"616561","title":"RAS PROTEIN ACTIVATOR-LIKE 3; RASAL3","url":"https://www.omim.org/entry/616561"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Plasma membrane","reliability":"Approved"}],"tissue_specificity":"Group enriched","tissue_distribution":"Detected in many","driving_tissues":[{"tissue":"bone marrow","ntpm":22.2},{"tissue":"intestine","ntpm":19.0},{"tissue":"lung","ntpm":10.6},{"tissue":"lymphoid tissue","ntpm":39.2}],"url":"https://www.proteinatlas.org/search/RASAL3"},"hgnc":{"alias_symbol":["FLJ21438"],"prev_symbol":[]},"alphafold":{"accession":"Q86YV0","domains":[{"cath_id":"-","chopping":"129-146_236-295","consensus_level":"medium","plddt":84.2477,"start":129,"end":295},{"cath_id":"2.60.40.150","chopping":"297-427","consensus_level":"medium","plddt":85.5055,"start":297,"end":427},{"cath_id":"1.10.506.10","chopping":"476-480_509-695","consensus_level":"medium","plddt":89.8848,"start":476,"end":695}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YV0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YV0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q86YV0-F1-predicted_aligned_error_v6.png","plddt_mean":66.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RASAL3","jax_strain_url":"https://www.jax.org/strain/search?query=RASAL3"},"sequence":{"accession":"Q86YV0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q86YV0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q86YV0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q86YV0"}},"corpus_meta":[{"pmid":"30047926","id":"PMC_30047926","title":"Stromal epigenetic alterations drive metabolic and neuroendocrine prostate cancer reprogramming.","date":"2018","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/30047926","citation_count":140,"is_preprint":false},{"pmid":"31627186","id":"PMC_31627186","title":"Epigenetic changes in fibroblasts drive cancer metabolism and differentiation.","date":"2019","source":"Endocrine-related cancer","url":"https://pubmed.ncbi.nlm.nih.gov/31627186","citation_count":37,"is_preprint":false},{"pmid":"29967623","id":"PMC_29967623","title":"Transcriptome Analysis of Bronchoalveolar Lavage Fluid From Children With Mycoplasma pneumoniae Pneumonia Reveals Natural Killer and T Cell-Proliferation Responses.","date":"2018","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/29967623","citation_count":35,"is_preprint":false},{"pmid":"25652366","id":"PMC_25652366","title":"RASAL3, a novel hematopoietic RasGAP protein, regulates the number and functions of NKT cells.","date":"2015","source":"European journal of immunology","url":"https://pubmed.ncbi.nlm.nih.gov/25652366","citation_count":32,"is_preprint":false},{"pmid":"37220748","id":"PMC_37220748","title":"Actuation of single downstream nodes in growth factor network steers immune cell migration.","date":"2023","source":"Developmental cell","url":"https://pubmed.ncbi.nlm.nih.gov/37220748","citation_count":29,"is_preprint":false},{"pmid":"25793935","id":"PMC_25793935","title":"The Ras GTPase-activating protein Rasal3 supports survival of naive T cells.","date":"2015","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/25793935","citation_count":21,"is_preprint":false},{"pmid":"26503545","id":"PMC_26503545","title":"Identification of potential mutations and genomic alterations in the epithelial and spindle cell components of biphasic synovial sarcomas using a human exome SNP chip.","date":"2015","source":"BMC medical genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26503545","citation_count":19,"is_preprint":false},{"pmid":"28619727","id":"PMC_28619727","title":"RNA-seq implicates deregulation of the immune system in the pathogenesis of diverticulitis.","date":"2017","source":"American journal of physiology. Gastrointestinal and liver physiology","url":"https://pubmed.ncbi.nlm.nih.gov/28619727","citation_count":19,"is_preprint":false},{"pmid":"33403589","id":"PMC_33403589","title":"Differential DNA Methylation Profiles in Patients with Temporal Lobe Epilepsy and Hippocampal Sclerosis ILAE Type I.","date":"2021","source":"Journal of molecular neuroscience : MN","url":"https://pubmed.ncbi.nlm.nih.gov/33403589","citation_count":18,"is_preprint":false},{"pmid":"32514133","id":"PMC_32514133","title":"Digenic inheritance of subclinical variants in Noonan Syndrome patients: an alternative pathogenic model?","date":"2020","source":"European journal of human genetics : EJHG","url":"https://pubmed.ncbi.nlm.nih.gov/32514133","citation_count":17,"is_preprint":false},{"pmid":"34777356","id":"PMC_34777356","title":"RASAL3 Is a Putative RasGAP Modulating Inflammatory Response by Neutrophils.","date":"2021","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/34777356","citation_count":16,"is_preprint":false},{"pmid":"38951708","id":"PMC_38951708","title":"Ras suppression potentiates rear actomyosin contractility-driven cell polarization and migration.","date":"2024","source":"Nature cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/38951708","citation_count":15,"is_preprint":false},{"pmid":"29291408","id":"PMC_29291408","title":"Rasal3-mediated T cell survival is essential for inflammatory responses.","date":"2017","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/29291408","citation_count":13,"is_preprint":false},{"pmid":"34225643","id":"PMC_34225643","title":"Transcriptomics unravels molecular players shaping dorsal lip hypertrophy in the vacuum cleaner cichlid, Gnathochromis permaxillaris.","date":"2021","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/34225643","citation_count":13,"is_preprint":false},{"pmid":"36876119","id":"PMC_36876119","title":"m6A demethylase ALKBH5 attenuates doxorubicin-induced cardiotoxicity via posttranscriptional stabilization of Rasal3.","date":"2023","source":"iScience","url":"https://pubmed.ncbi.nlm.nih.gov/36876119","citation_count":8,"is_preprint":false},{"pmid":"33301959","id":"PMC_33301959","title":"The impact of blood-processing time on the proteome of human peripheral blood mononuclear cells.","date":"2020","source":"Biochimica et biophysica acta. Proteins and proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/33301959","citation_count":8,"is_preprint":false},{"pmid":"34846677","id":"PMC_34846677","title":"DNA Methylome Mapping Identifies Epigenetic Abnormalities in Intestinal Lymphocyte Regulation in Human Necrotizing Enterocolitis.","date":"2021","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34846677","citation_count":6,"is_preprint":false},{"pmid":"38200184","id":"PMC_38200184","title":"CCDC88B interacts with RASAL3 and ARHGEF2 and regulates dendritic cell function in neuroinflammation and colitis.","date":"2024","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/38200184","citation_count":5,"is_preprint":false},{"pmid":"34157800","id":"PMC_34157800","title":"[Expression of RASGRP2 in Lung Adenocarcinoma and Its Effect 
on Immune Microenvironment].","date":"2021","source":"Zhongguo fei ai za zhi = Chinese journal of lung cancer","url":"https://pubmed.ncbi.nlm.nih.gov/34157800","citation_count":5,"is_preprint":false},{"pmid":"36445333","id":"PMC_36445333","title":"CD229 interacts with RASAL3 to activate RAS/ERK pathway in multiple myeloma proliferation.","date":"2022","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/36445333","citation_count":4,"is_preprint":false},{"pmid":"31887652","id":"PMC_31887652","title":"Change of Ras and its guanosine triphosphatases (GTPases) during development and regression in bovine corpus luteum.","date":"2019","source":"Theriogenology","url":"https://pubmed.ncbi.nlm.nih.gov/31887652","citation_count":3,"is_preprint":false},{"pmid":"30271600","id":"PMC_30271600","title":"RASAL3 preferentially stimulates GTP hydrolysis of the Rho family small GTPase Rac2.","date":"2018","source":"Biomedical reports","url":"https://pubmed.ncbi.nlm.nih.gov/30271600","citation_count":1,"is_preprint":false},{"pmid":"37693515","id":"PMC_37693515","title":"Ras-mediated homeostatic control of front-back signaling dictates cell polarity.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37693515","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.12.25335624","title":"Multi-Omics Molecular Profiling Enables Rapid Diagnosis of Erythrodermic Skin Diseases","date":"2025-09-14","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.12.25335624","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13417,"output_tokens":2751,"usd":0.040758},"stage2":{"model":"claude-opus-4-6","input_tokens":6088,"output_tokens":2917,"usd":0.155048},"total_usd":0.195806,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2015,\n      \"finding\": \"RASAL3 possesses RasGAP activity (but not Rap1GAP activity) and represses TCR-stimulated ERK phosphorylation in T cells; systemic RASAL3-deficient mice show reduced peripheral naive CD4 and CD8 T cells due to increased apoptosis, establishing RASAL3 as required for naive T cell survival in vivo.\",\n      \"method\": \"In vitro RasGAP/Rap1GAP activity assays, ERK phosphorylation assays in T cell lines, systemic knockout mice with flow cytometry and adoptive transfer experiments\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — enzymatic activity confirmed in vitro, combined with clean KO mouse phenotype and adoptive transfer rescue experiment\",\n      \"pmids\": [\"25793935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"RASAL3 is predominantly expressed in hematopoietic cells (NKT, B, T cells) and negatively regulates Ras/ERK signaling in NKT cells; RASAL3-deficient mice show severe decrease of NKT cells in liver and reduced IL-4/IFN-γ production, with augmented ERK phosphorylation in RASAL3-deficient NKT cells upon α-GalCer stimulation.\",\n      \"method\": \"Systemic RASAL3-knockout mice, α-GalCer stimulation, flow cytometry, ERK phosphorylation assays, cytokine measurement\",\n      \"journal\": \"European journal of immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO mouse with multiple orthogonal readouts (cell numbers, cytokine production, ERK phosphorylation)\",\n      \"pmids\": [\"25652366\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Rasal3-deficient mice show ameliorated Th1- and Th2-dependent contact hypersensitivity reactions due to increased death of activated T cells with reduced Bcl2 expression, demonstrating that Rasal3 controls inflammatory response magnitude by supporting survival of both naive and activated T cells.\",\n      \"method\": \"Rasal3-knockout mice, contact hypersensitivity model, flow cytometry, Bcl2 expression analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined in vivo phenotype, single lab\",\n      \"pmids\": [\"29291408\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RASAL3 is epigenetically silenced (promoter hypermethylation) in cancer-associated fibroblasts (CAF), leading to oncogenic Ras activity that drives macropinocytosis-mediated glutamine synthesis; stromal glutamine fuels prostate cancer anaplerosis and neuroendocrine differentiation.\",\n      \"method\": \"Epigenetic analysis of CAF, orthotopic xenograft models, macropinocytosis inhibition, glutamine transport inhibition, androgen deprivation therapy models\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal in vitro and in vivo experiments, functional rescue with inhibitors, replicated in clinical samples\",\n      \"pmids\": [\"30047926\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The catalytic (GAP) domain of RASAL3 interacts with Rac2 and stimulates Rac2 GTPase activity in vitro, whereas p50 rhoGAP did not markedly affect Rac2 activity, indicating RASAL3 has RasGAP family activity toward the hematopoietic Rho GTPase Rac2.\",\n      \"method\": \"In vitro GTPase activity assay with purified RASAL3 catalytic domain and Rac2\",\n      \"journal\": \"Biomedical reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — direct in vitro enzymatic assay, but single lab and single method\",\n      \"pmids\": [\"30271600\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"RASAL3 is highly expressed in neutrophils, its expression is upregulated by exogenous stimuli, and RASAL3 deficiency triggers augmented neutrophil responses and hyperinflammation; RASAL3-KO mice show accelerated mortality in a septic shock model via severe organ damage and hyperinflammatory neutrophil response.\",\n      \"method\": \"RASAL3-knockout mice, LPS septic shock model, sickle cell disease mouse model, neutrophil activation assays\",\n      \"journal\": \"Frontiers in immunology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with two independent in vivo disease models and defined cellular phenotype\",\n      \"pmids\": [\"34777356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CD229 (SLAMF3) interacts with RASAL3 as identified by co-immunoprecipitation coupled with mass spectrometry; intercellular tyrosine phosphorylation-mediated self-activation of CD229 activates the RAS/ERK signaling pathway via interaction with RASAL3 to promote multiple myeloma cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation coupled with mass spectrometry, co-culture with immunofluorescence assay, in vitro proliferation assays, xenograft mouse model\",\n      \"journal\": \"Aging\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2-3 — Co-IP/MS identification of interaction combined with functional in vitro and in vivo readouts, single lab\",\n      \"pmids\": [\"36445333\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Optogenetic recruitment of RASAL3 to the cell front of HL-60 neutrophils extinguished protrusions and changed migration direction; global membrane recruitment caused cells to polarize and move more rapidly in an mTORC2-dependent but largely PI3K-independent manner, establishing RASAL3 as a direct regulator of actin assembly, cell polarity, and migration via Ras suppression.\",\n      \"method\": \"Optogenetic targeting (light-inducible recruitment) in differentiated HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, pharmacological inhibition of mTORC2 and PI3K\",\n      \"journal\": \"Developmental cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — acute optogenetic perturbation with spatial precision, multiple cell types, pharmacological validation of downstream pathway\",\n      \"pmids\": [\"37220748\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ALKBH5 (m6A demethylase) regulates Rasal3 mRNA stability in an m6A-dependent posttranscriptional manner; ALKBH5 deficiency reduces Rasal3 expression, thereby activating RAS/RAF/ERK signaling and increasing cardiomyocyte apoptosis in doxorubicin-induced cardiotoxicity.\",\n      \"method\": \"Alkbh5-knockout, knockin, and myocardial-specific knockout mice; cardiac function assessment; m6A modification analysis; signal transduction studies\",\n      \"journal\": \"iScience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple genetic mouse models with defined molecular mechanism, single lab\",\n      \"pmids\": [\"36876119\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"RASAL3 physically and functionally interacts with CCDC88B and ARHGEF2 as part of a complex; Rasal3-mutant dendritic cells show enhanced migratory properties in vitro, and RASAL3 and ARHGEF2 act in opposing fashions to regulate RHOA activation, establishing a CCDC88B/RASAL3/ARHGEF2 complex that controls DC migration.\",\n      \"method\": \"Co-immunoprecipitation, proximity-ligation assay, Rasal3-mutant mouse DC migration assays, RHOA activation assays, neuroinflammation and colitis mouse models\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP for complex identification, clean mutant mice, multiple in vitro and in vivo functional readouts\",\n      \"pmids\": [\"38200184\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Optogenetic global or rear-targeted recruitment of RASAL3 in HL-60 neutrophils and macrophages causes cell polarization and accelerated migration through increased rear actomyosin contractility followed by sustained mTORC2-dependent actin polymerization at the front; this RasGAP-mediated polarization depends critically on myosin II activity.\",\n      \"method\": \"Optogenetic membrane recruitment in HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, myosin II inhibition, mTORC2 inhibition, computational simulations\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 — acute optogenetic perturbation with spatial control, pharmacological dissection of mechanism, replicated in two cell types and supported by computational model\",\n      \"pmids\": [\"38951708\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RASAL3 is a hematopoietic RasGAP (and Rac2GAP) that negatively regulates Ras/ERK signaling in immune cells (T cells, NKT cells, neutrophils, dendritic cells) to control their survival, activation, and migration; in the context of cell polarity, optogenetic studies show that local RASAL3-mediated Ras suppression extinguishes protrusions while global Ras suppression paradoxically drives mTORC2/myosin II-dependent polarization and faster migration, and in stromal fibroblasts its epigenetic silencing activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer progression.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"RASAL3 is a hematopoietic RasGAP that negatively regulates Ras/ERK signaling to control immune cell survival, activation, and migration. RASAL3 possesses RasGAP activity (but not Rap1GAP activity) and additionally stimulates Rac2 GTPase activity in vitro; in T cells and NKT cells, it represses TCR-stimulated ERK phosphorylation, and its genetic ablation causes increased apoptosis of naive and activated T cells (with reduced Bcl2 expression), depletion of NKT cells, and neutrophil hyperinflammation [PMID:25793935, PMID:25652366, PMID:29291408, PMID:34777356]. Optogenetic studies in neutrophils and macrophages demonstrate that local RASAL3-mediated Ras suppression extinguishes protrusions and redirects migration, while global Ras suppression drives myosin II–dependent rear contractility and mTORC2-dependent front actin polymerization, producing cell polarization and accelerated movement [PMID:37220748, PMID:38951708]. RASAL3 forms a complex with CCDC88B and ARHGEF2 that opposes RHOA activation to regulate dendritic cell migration, and epigenetic silencing of RASAL3 in cancer-associated fibroblasts activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer progression [PMID:38200184, PMID:30047926].\",\n  \"teleology\": [\n    {\n      \"year\": 2015,\n      \"claim\": \"Establishing that RASAL3 is a bona fide RasGAP required for T and NKT cell homeostasis resolved the identity of the RasGAP governing Ras/ERK signaling downstream of TCR engagement in lymphocytes.\",\n      \"evidence\": \"In vitro RasGAP/Rap1GAP assays, ERK phosphorylation in T cell lines, systemic RASAL3-KO mice with flow cytometry and adoptive transfer; parallel KO analysis of NKT cells with α-GalCer stimulation and cytokine measurement\",\n      \"pmids\": [\"25793935\", \"25652366\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis for Ras selectivity over Rap1 unknown\", \"Mechanism linking excess ERK activity to apoptosis rather than proliferation in naive T cells not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Demonstrating that RASAL3-deficient activated T cells die with reduced Bcl2 in a contact hypersensitivity model established that RASAL3 controls inflammatory magnitude by supporting survival of both naive and effector T cells.\",\n      \"evidence\": \"RASAL3-KO mice in Th1/Th2 contact hypersensitivity models with Bcl2 expression analysis\",\n      \"pmids\": [\"29291408\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether RASAL3 directly regulates Bcl2 transcription or acts indirectly through ERK not resolved\", \"Single-lab observation without independent replication\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Showing that RASAL3 epigenetic silencing in cancer-associated fibroblasts activates Ras-driven macropinocytosis and glutamine secretion that fuels prostate cancer revealed a tumor-extrinsic, stromal function for RASAL3 loss beyond immune cells.\",\n      \"evidence\": \"CAF epigenetic profiling, orthotopic xenograft models, macropinocytosis and glutamine transport inhibition, clinical sample validation\",\n      \"pmids\": [\"30047926\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether RASAL3 silencing occurs in fibroblasts of other tumor types not explored\", \"Direct link between specific Ras isoform activation and macropinocytosis induction not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Discovering that the RASAL3 catalytic domain stimulates Rac2 GTPase activity in vitro expanded RASAL3's substrate repertoire beyond Ras to the hematopoietic Rho-family GTPase Rac2.\",\n      \"evidence\": \"In vitro GTPase activity assay with purified RASAL3 GAP domain and Rac2\",\n      \"pmids\": [\"30271600\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Rac2GAP activity not confirmed in cellular context\", \"Structural basis for dual Ras/Rac2 specificity not characterized\", \"Single-method, single-lab result\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extending RASAL3's immune role to neutrophils, where its loss triggers hyperinflammation and accelerated septic mortality, showed that RASAL3 is a broad negative regulator across innate and adaptive immune lineages.\",\n      \"evidence\": \"RASAL3-KO mice in LPS septic shock and sickle cell disease models, neutrophil activation assays\",\n      \"pmids\": [\"34777356\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Specific Ras isoform(s) hyperactivated in neutrophils not identified\", \"Whether Rac2GAP activity contributes to neutrophil phenotype untested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identification of CD229 (SLAMF3) as a RASAL3-interacting partner in myeloma cells suggested a receptor-proximal mechanism by which RASAL3 is recruited to regulate Ras/ERK at the plasma membrane.\",\n      \"evidence\": \"Co-immunoprecipitation coupled with mass spectrometry, co-culture immunofluorescence, proliferation assays, xenograft model\",\n      \"pmids\": [\"36445333\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reciprocal Co-IP not described\", \"Whether SLAMF3-RASAL3 interaction is direct or scaffolded not resolved\", \"Unclear if this interaction is generalizable beyond myeloma\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Optogenetic studies revealed that RASAL3-mediated local Ras suppression directly controls protrusion and migration direction, while global Ras suppression paradoxically drives mTORC2-dependent polarization, uncovering a spatial logic for RasGAP function in cell motility.\",\n      \"evidence\": \"Light-inducible membrane recruitment of RASAL3 in HL-60 neutrophils and RAW 264.7 macrophages, live-cell imaging, PI3K and mTORC2 pharmacological inhibition\",\n      \"pmids\": [\"37220748\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link from global Ras suppression to mTORC2 activation unclear\", \"Role of Rac2GAP activity versus RasGAP activity in migration phenotype not dissected\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating that ALKBH5-dependent m6A demethylation stabilizes Rasal3 mRNA revealed an epitranscriptomic layer of RASAL3 regulation, linking its expression to cardiomyocyte survival under doxorubicin stress.\",\n      \"evidence\": \"Alkbh5-KO, knock-in, and cardiac-specific KO mice; m6A modification analysis; RAS/RAF/ERK signaling and apoptosis readouts\",\n      \"pmids\": [\"36876119\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether m6A regulation of RASAL3 operates in hematopoietic cells unknown\", \"Specific m6A sites on Rasal3 mRNA not mapped\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identification of a CCDC88B/RASAL3/ARHGEF2 complex that oppositely regulates RHOA in dendritic cells established a multiprotein signaling module through which RASAL3 restrains DC migration and neuroinflammation.\",\n      \"evidence\": \"Reciprocal Co-IP, proximity-ligation assay, Rasal3-mutant DC migration assays, RHOA activation assays, EAE and colitis mouse models\",\n      \"pmids\": [\"38200184\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How RASAL3's RasGAP activity integrates with RHOA regulation through ARHGEF2 is mechanistically unresolved\", \"Stoichiometry and structure of the ternary complex unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"A refined optogenetic and computational analysis established that RASAL3-induced polarization depends on myosin II–mediated rear contractility preceding sustained mTORC2-driven front protrusion, defining the temporal sequence of the RasGAP-driven polarization circuit.\",\n      \"evidence\": \"Optogenetic rear-targeted and global RASAL3 recruitment in HL-60 and RAW cells, myosin II and mTORC2 inhibition, computational simulation\",\n      \"pmids\": [\"38951708\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the upstream sensor that couples Ras suppression to myosin II activation unknown\", \"Whether this polarization circuit operates in vivo during chemotaxis not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How RASAL3's dual RasGAP and Rac2GAP activities are coordinated in vivo, and whether the CCDC88B/RASAL3/ARHGEF2 complex operates in cell types beyond dendritic cells, remain open questions.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of RASAL3 exists\", \"Relative contribution of RasGAP vs Rac2GAP activity to each physiological phenotype not dissected\", \"Whether myosin II–mTORC2 polarization axis downstream of RASAL3 functions during in vivo immune surveillance untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 1, 4, 7, 10]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [7, 10]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 3, 6, 7, 8, 10]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [1, 2, 5, 9]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [3, 6]}\n    ],\n    \"complexes\": [\n      \"CCDC88B/RASAL3/ARHGEF2 complex\"\n    ],\n    \"partners\": [\n      \"CCDC88B\",\n      \"ARHGEF2\",\n      \"RAC2\",\n      \"SLAMF3\",\n      \"ALKBH5\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}