{"gene":"ICMT","run_date":"2026-06-10T01:55:22","timeline":{"discoveries":[{"year":2011,"finding":"Crystal structure of a prokaryotic ICMT ortholog revealed a markedly different architecture from conventional methyltransferases: a core of five transmembrane α-helices with a cofactor-binding pocket in a conserved C-terminal catalytic subdomain, and a tunnel linking the reactive methyl group of SAM to the inner membrane providing access for the prenyl lipid substrate, explaining how the enzyme accommodates both a hydrophilic cofactor (SAM) and a lipophilic prenyl substrate.","method":"X-ray crystallography of prokaryotic ICMT ortholog","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional interpretation, first structural determination of ICMT fold, later confirmed by eukaryotic structure","pmids":["22195972"],"is_preprint":false},{"year":2018,"finding":"X-ray structure of eukaryotic ICMT at 2.3 Å (in complex with SAM cofactor, an ordered lipid molecule, and a monobody inhibitor) revealed that the active site spans cytosolic and membrane-exposed regions, indicating distinct entry routes for the cytosolic methyl donor SAM and for prenylcysteine substrates associated with the ER membrane.","method":"X-ray crystallography at 2.3 Å resolution with monobody-assisted crystallization","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure with cofactor and lipid bound, published in Nature with rigorous validation","pmids":["29342140"],"is_preprint":false},{"year":2004,"finding":"Human ICMT catalysis proceeds through an ordered sequential kinetic mechanism in which SAM binds first and S-adenosylhomocysteine (AdoHcy) is the final product released; the prenylcysteine substrate (BFC) and its methylated product bind different enzyme forms, established using dead-end inhibitor (FTA) and product inhibition studies.","method":"In vitro enzyme kinetics with synthetic substrate BFC, dead-end inhibitor analysis, and product inhibition studies","journal":"BMC biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — rigorous in vitro kinetic analysis with multiple inhibitor approaches and ordered mechanism determination, single lab","pmids":["15625008"],"is_preprint":false},{"year":2014,"finding":"Scanning mutagenesis of nearly half the residues of the Anopheles gambiae ICMT ortholog combined with methyltransferase assays identified 62 mutations causing reduced or undetectable catalytic activity; residues in transmembrane regions contribute to the isoprenylcysteine binding site (certain substitutions caused substrate inhibition by isoprenylcysteine), while the AdoMet-binding site resembles a distantly related prokaryotic methyltransferase, establishing that the active site spans cytosolic and membrane-embedded regions.","method":"Scanning mutagenesis combined with in vitro methyltransferase assays; structural comparison with Ma MTase crystal structure","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — systematic mutagenesis of ~half of all residues with direct activity readout, multiple orthogonal analyses, later confirmed by crystal structure","pmids":["25059662"],"is_preprint":false},{"year":2004,"finding":"Genetic inactivation of Icmt in mouse fibroblasts expressing oncogenic K-Ras inhibited K-Ras-induced oncogenic transformation (soft agar and nude mice); the mechanism involved accelerated RhoA protein turnover leading to reduced RhoA levels and a large Ras/Erk1/2-dependent increase in p21(Cip1); deletion of p21(Cip1) restored growth in soft agar of Icmt-null K-Ras cells. Icmt inactivation also blocked transformation by oncogenic B-Raf(V599E).","method":"Conditional Cre-lox knockout of Icmt in mouse embryonic fibroblasts; soft agar assay; nude mouse xenograft; p21(Cip1) double knockout rescue experiment; Western blot for Erk1/2, Akt1, RhoA","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis via double-knockout rescue, multiple in vitro and in vivo assays, clearly defined molecular pathway","pmids":["14966563"],"is_preprint":false},{"year":2006,"finding":"ICMT is the only enzyme in mouse cells capable of methylating isoprenylated CAAX proteins including all Ras proteins; in the absence of carboxyl methylation, Ras proteins are mislocalized away from the plasma membrane and exhibit a shift in electrophoretic mobility. Additionally, ICMT methylates the CXC class of isoprenylated Rab proteins.","method":"Genetic knockout (conditional Icmt deletion), subcellular fractionation, electrophoretic mobility shift assays","journal":"Methods in enzymology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic and biochemical data compiled in methods review, single lab, multiple orthogonal approaches","pmids":["16757321"],"is_preprint":false},{"year":2021,"finding":"Among the four RAS proteins, NRAS uniquely requires ICMT for delivery to the plasma membrane; this is because NRAS has only a single palmitoylation site as its secondary membrane-affinity module. ICMT-dependent carboxyl methylation of NRAS promotes efficient palmitoylation, binding to the prenyl-protein chaperone PDE6δ, and anterograde trafficking from the Golgi to the plasma membrane. FRAP of GFP-NRAS revealed increased Golgi flux in the absence of ICMT, independent of palmitoylation.","method":"ICMT knockout cells; photoactivation and FRAP of GFP-NRAS; Co-IP/binding assay with PDE6δ; palmitoylation assays; subcellular fractionation","journal":"Life science alliance","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (FRAP, co-IP, palmitoylation assay, fractionation) in single rigorous study establishing mechanism","pmids":["33579760"],"is_preprint":false},{"year":2016,"finding":"Retina-specific knockout of Icmt in mice caused progressive loss of rod and cone light-mediated responses, accompanied by defective association of isoprenylated transducin and cone phosphodiesterase 6 (PDE6α') with photoreceptor membranes, and decreased protein levels of transducin, PDE6α', and cone GRK1. Unlike Rce1 deficiency, rod PDE6 trafficked normally to the outer segment in Icmt-deficient mice, indicating that the -AAX (not methylation) blocks PDE6 transport.","method":"Retina-specific conditional Icmt knockout mice; electroretinography; subcellular fractionation; protein level quantification by Western blot","journal":"The Journal of neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean tissue-specific KO with defined electrophysiological and biochemical phenotypes, epistatic comparison with Rce1 KO","pmids":["27147662"],"is_preprint":false},{"year":2021,"finding":"Genetic knockout of Icmt improves survival of HGPS mice and restores vascular smooth muscle cell numbers in the aorta; a pharmacologic ICMT inhibitor (C75) delays senescence and stimulates proliferation of late-passage HGPS cells and Zmpste24-deficient fibroblasts, but does not influence proliferation of wild-type human cells or Zmpste24-deficient cells lacking Icmt, confirming drug specificity for the ICMT pathway.","method":"HGPS mouse model with Icmt knockout; synthetic ICMT inhibitor C75; cell proliferation and senescence assays; genetic controls (Zmpste24/Icmt double KO cells)","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic and pharmacologic evidence combined with rigorous specificity controls using Icmt-null cells, multiple cellular and in vivo readouts","pmids":["33526168"],"is_preprint":false},{"year":2019,"finding":"A potent ICMT inhibitor (UCM-1336, compound 3, IC50 = 2 μM) selectively impairs membrane association of all four RAS isoforms, decreases Ras-GTP activity, and inhibits downstream RAS signaling pathways, leading to cell death in Ras-mutated tumor cell lines and improved survival in an in vivo acute myeloid leukemia model.","method":"In vitro ICMT enzymatic assay; subcellular fractionation for RAS membrane association; Ras-GTP pull-down; cell viability assays; in vivo AML mouse model","journal":"Journal of medicinal chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — pharmacologic inhibition with mechanistic readouts (membrane fractionation, Ras-GTP), in vivo validation, single lab","pmids":["31181882"],"is_preprint":false},{"year":2007,"finding":"ICMT inhibition (using AGGC) in pulmonary artery endothelial cells caused redistribution and aggregation of the ER chaperone GRP94, followed by GRP94 protein degradation; these effects were dependent on RhoA activity and caspase activation, indicating that ICMT-dependent RhoA carboxyl methylation is required to maintain GRP94 localization and prevent unfolded protein response-associated apoptosis.","method":"ICMT chemical inhibition (AGGC); 2D-PAGE proteomics; immunofluorescence; constitutively active RhoA overexpression rescue; caspase inhibitor","journal":"American journal of respiratory cell and molecular biology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — pharmacologic inhibition with multiple readouts (proteomics, immunofluorescence, genetic rescue), but no direct carboxyl methylation assay for GRP94","pmids":["17347446"],"is_preprint":false},{"year":2022,"finding":"PFKFB4 physically interacts with ICMT, promotes ICMT/RAS interaction, controls RAS localization at the plasma membrane, and activates AKT signaling to enhance melanoma cell migration, revealing a glycolysis-independent function of PFKFB4 through ICMT.","method":"Co-immunoprecipitation (PFKFB4-ICMT interaction); subcellular localization of RAS; AKT phosphorylation assays; cell migration assays; PFKFB4 knockdown/overexpression","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP for interaction, multiple downstream readouts, but single lab and no reciprocal validation of direct binding","pmids":["35914811"],"is_preprint":false},{"year":2019,"finding":"ICMT inhibition in hepatocellular carcinoma cells suppressed the Ras/Raf/Mek/Erk signaling pathway and inhibited epithelial-mesenchymal transition (EMT), establishing ICMT as mechanistically required for oncogenic Ras signaling and EMT in HCC.","method":"ICMT siRNA knockdown and overexpression in HCC cell lines; Western blot for Ras/Raf/Mek/Erk phosphorylation; EMT marker analysis; cell growth and migration assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — multiple orthogonal functional assays with loss- and gain-of-function, but no direct biochemical measurement of methylation activity","pmids":["31451223"],"is_preprint":false},{"year":2019,"finding":"Wild-type p53 represses ICMT transcription by binding the -209 to -14 region of the ICMT promoter (shown by ChIP assay and promoter truncation/luciferase reporter analysis), while cancer-associated p53 mutants positively regulate ICMT expression through a different promoter region.","method":"ChIP assay; ICMT promoter-luciferase reporter constructs; promoter truncation analysis; p53 overexpression/knockdown in cancer cell lines","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and reporter assays directly establishing p53 binding and transcriptional repression, single lab","pmids":["30655292"],"is_preprint":false},{"year":2011,"finding":"Prenylcysteine-based ICMT inhibitors (analogs 1a and 1b) exhibit mixed-mode inhibition of human ICMT with the competitive component predominating; cellular treatment with analog 1b alters subcellular localization of GFP-KRas and inhibits both Ras activation and Erk phosphorylation in Jurkat cells.","method":"In vitro kinetic inhibition analysis (Ki determination); GFP-KRas subcellular localization by fluorescence microscopy; Ras activation assay; Erk phosphorylation Western blot","journal":"Bioorganic & medicinal chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vitro kinetics plus cellular mechanistic readouts, single lab","pmids":["22142613"],"is_preprint":false},{"year":2024,"finding":"ICMT overexpression enhances invadopodia formation and promotes in vivo lung metastasis; ICMT overexpression also promotes migration and invasion in vitro, suggesting that ICMT acts on substrates regulating the actin cytoskeleton to drive invasive structures.","method":"ICMT overexpression in cancer cell lines; invadopodia formation assay; in vivo metastasis mouse model; in vitro migration and invasion assays","journal":"Biochimie","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean gain-of-function with defined cellular phenotype (invadopodia) and in vivo metastasis, single lab","pmids":["38301884"],"is_preprint":false},{"year":2026,"finding":"ICMT inhibition (genetic and pharmacologic with UCM-1336) reduced INPP5E methylation, displaced INPP5E from membranes, and increased PI(4,5)P2 levels; forced INPP5E membrane targeting partially rescued growth defects caused by ICMT inhibition in BRAFV600E-mutant melanoma cells, identifying INPP5E as an ICMT-dependent substrate mediating BRAFV600E-driven tumor growth.","method":"Genetic ICMT knockdown; pharmacologic ICMT inhibition (UCM-1336); INPP5E methylation assay; membrane fractionation; PI(4,5)P2 measurement; forced membrane targeting rescue experiment; xenograft tumor growth assays","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic and pharmacologic approaches combined with direct substrate methylation assay, rescue experiment, and in vivo validation","pmids":["42127111"],"is_preprint":false},{"year":2025,"finding":"RAC1(P29S/C189S), which lacks the C-terminal prenylation site required for ICMT methylation, lost the ability to drive resistance to BRAFV600E inhibitors (vemurafenib/trametinib); combined ICMT inhibition (cysmethynil) with MAPK inhibitors suppressed RAC1(P29S)-driven resistance in vitro and in vivo; mechanistically, combined treatment impaired nuclear translocation of TAZ, whose transcriptional activity accounts for MAPKi resistance downstream of RAC1(P29S).","method":"RAC1 prenylation-site mutant (C189S); pharmacologic ICMT inhibition (cysmethynil) combined with MAPK inhibitors; in vitro and in vivo tumor growth assays; TAZ nuclear localization assay; constitutively-active TAZ rescue experiment","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic prenylation-site mutant plus pharmacologic inhibition with mechanistic rescue (TAZ), preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.08.10.669587"],"is_preprint":true}],"current_model":"ICMT is an integral membrane methyltransferase localized to the endoplasmic reticulum that catalyzes the final step of CAAX protein processing—SAM-dependent carboxyl methylation of isoprenylcysteine—using an ordered sequential mechanism (SAM binds first, AdoHcy released last) within an active site that spans cytosolic and membrane-embedded regions, thereby promoting plasma membrane targeting and signaling of substrates including all four RAS isoforms (with NRAS being uniquely dependent on ICMT for palmitoylation and PDE6δ-mediated anterograde Golgi trafficking), Rho GTPases, transducin, cone PDE6, prelamin A, and INPP5E; loss of ICMT mislocalizes these substrates, accelerates RhoA turnover, elevates p21(Cip1) via Ras/Erk signaling, disrupts phototransduction, and blocks oncogenic transformation by K-Ras and B-Raf, while its expression is transcriptionally repressed by wild-type p53 and upregulated by mutant p53."},"narrative":{"mechanistic_narrative":"ICMT is the terminal enzyme of CAAX protein processing, an integral endoplasmic reticulum membrane methyltransferase that catalyzes SAM-dependent carboxyl methylation of the C-terminal isoprenylcysteine of prenylated proteins, thereby controlling their membrane association and downstream signaling [PMID:16757321]. Structural and kinetic work defines the catalytic logic: an unusual fold built from transmembrane helices with a C-terminal cofactor pocket and a lipid tunnel that connects the reactive SAM methyl group to the membrane-embedded prenyl substrate [PMID:22195972], with an active site spanning cytosolic and membrane-exposed regions that provides separate entry routes for the cytosolic methyl donor and the ER-associated prenylcysteine [PMID:29342140, PMID:25059662]; catalysis follows an ordered sequential mechanism in which SAM binds first and AdoHcy is released last [PMID:15625008]. ICMT is the sole enzyme methylating isoprenylated CAAX proteins including all four RAS isoforms, and loss of methylation mislocalizes RAS away from the plasma membrane [PMID:16757321]; NRAS is uniquely ICMT-dependent because methylation promotes its palmitoylation, PDE6δ binding, and anterograde Golgi-to-membrane trafficking [PMID:33579760]. Through these substrates ICMT supports oncogenic signaling—its inactivation blocks K-Ras and B-Raf transformation by accelerating RhoA turnover and elevating p21(Cip1) via Ras/Erk [PMID:14966563], and it is required for Ras/Raf/Mek/Erk-driven signaling and substrate membrane targeting in multiple cancer contexts including the BRAFV600E-driven, INPP5E-dependent program [PMID:31451223, PMID:42127111]. ICMT also methylates substrates in specialized tissues, including transducin and cone PDE6 in photoreceptors where its retinal loss disrupts phototransduction [PMID:27147662], and its expression is transcriptionally repressed by wild-type p53 and elevated by cancer-associated p53 mutants [PMID:30655292].","teleology":[{"year":2004,"claim":"Established the catalytic mechanism of ICMT, defining how a single enzyme coordinates a hydrophilic cofactor and a lipophilic prenyl substrate.","evidence":"In vitro enzyme kinetics with synthetic substrate BFC, dead-end and product inhibition studies","pmids":["15625008"],"confidence":"High","gaps":["Kinetics performed on a synthetic small-molecule substrate, not full-length prenylated proteins","Does not localize the substrate-binding residues structurally"]},{"year":2004,"claim":"Demonstrated that ICMT is functionally required for oncogenic transformation, connecting CAAX methylation to a defined RhoA/p21(Cip1) growth-control pathway.","evidence":"Conditional Icmt knockout in mouse fibroblasts; soft agar, xenograft, and p21(Cip1) double-knockout rescue","pmids":["14966563"],"confidence":"High","gaps":["Mechanism by which methylation loss accelerates RhoA turnover not resolved","Did not identify all relevant methylated substrates contributing to transformation block"]},{"year":2006,"claim":"Established ICMT as the unique enzyme methylating isoprenylated CAAX proteins and showed methylation controls RAS membrane localization.","evidence":"Conditional Icmt knockout, subcellular fractionation, and electrophoretic mobility shift assays","pmids":["16757321"],"confidence":"Medium","gaps":["Data compiled in a methods review from a single lab","Quantitative contribution of methylation versus prenylation to localization not separated"]},{"year":2011,"claim":"Provided the first structural framework for the ICMT fold, explaining how transmembrane helices and a lipid tunnel accommodate both SAM and a prenyl substrate.","evidence":"X-ray crystallography of a prokaryotic ICMT ortholog","pmids":["22195972"],"confidence":"High","gaps":["Prokaryotic ortholog may differ from the human enzyme in detail","No bound prenylcysteine substrate captured"]},{"year":2014,"claim":"Mapped catalytic and substrate-binding residues across the enzyme, confirming the active site spans cytosolic and membrane-embedded regions.","evidence":"Scanning mutagenesis of ~half of all residues in the Anopheles gambiae ortholog with methyltransferase assays","pmids":["25059662"],"confidence":"High","gaps":["Performed on an insect ortholog rather than the human enzyme","Functional effects inferred from activity loss without structural confirmation at the time"]},{"year":2016,"claim":"Showed ICMT is required for photoreceptor function via methylation of phototransduction substrates, distinguishing methylation-dependent from -AAX-dependent trafficking.","evidence":"Retina-specific conditional Icmt knockout mice; electroretinography; subcellular fractionation; epistatic comparison with Rce1","pmids":["27147662"],"confidence":"High","gaps":["Mechanism linking methylation loss to reduced substrate protein levels unclear","Does not establish direct methylation of each affected substrate in vivo"]},{"year":2018,"claim":"Delivered a high-resolution eukaryotic ICMT structure with cofactor and lipid bound, defining distinct entry routes for SAM and prenylcysteine substrates.","evidence":"X-ray crystallography at 2.3 Å with monobody-assisted crystallization, SAM and ordered lipid bound","pmids":["29342140"],"confidence":"High","gaps":["No bound CAAX peptide substrate to define the prenylcysteine-binding mode directly","Conformational dynamics of catalysis not captured by a static structure"]},{"year":2019,"claim":"Identified p53-dependent transcriptional control of ICMT, with opposite regulation by wild-type versus mutant p53.","evidence":"ChIP assay, promoter-luciferase reporters, truncation analysis, p53 overexpression/knockdown","pmids":["30655292"],"confidence":"Medium","gaps":["Single lab; mutant-p53 activating mechanism on a distinct promoter region not fully defined","Physiological consequences of p53-driven ICMT changes not established"]},{"year":2019,"claim":"Validated ICMT pharmacologically as a target whose inhibition impairs RAS membrane association and signaling and kills Ras-mutant tumors.","evidence":"ICMT inhibitor UCM-1336; enzymatic assay, fractionation, Ras-GTP pull-down, viability assays, in vivo AML model; plus HCC siRNA/overexpression studies of Ras/Raf/Mek/Erk and EMT","pmids":["31181882","31451223"],"confidence":"Medium","gaps":["Off-target effects of inhibitors on other methylated substrates not excluded","HCC studies lack direct methylation readout"]},{"year":2021,"claim":"Explained why NRAS is uniquely ICMT-dependent—methylation enables its palmitoylation, PDE6δ binding, and Golgi-to-membrane trafficking.","evidence":"ICMT knockout cells; FRAP/photoactivation of GFP-NRAS; PDE6δ Co-IP; palmitoylation assays; fractionation","pmids":["33579760"],"confidence":"High","gaps":["Quantitative coupling between methylation and palmitoylation enzymes not defined","Generality to other single-palmitoylation CAAX proteins untested"]},{"year":2021,"claim":"Demonstrated therapeutic potential of targeting ICMT in progeria, with rigorous specificity controls.","evidence":"HGPS mice with Icmt knockout; ICMT inhibitor C75; proliferation/senescence assays; Zmpste24/Icmt double-knockout controls","pmids":["33526168"],"confidence":"High","gaps":["Direct measurement of prelamin A methylation status not reported here","Long-term consequences of systemic ICMT inhibition unaddressed"]},{"year":2022,"claim":"Identified PFKFB4 as a physical partner that enhances ICMT/RAS interaction and RAS localization, revealing a non-glycolytic input to ICMT function.","evidence":"Co-IP of PFKFB4-ICMT; RAS localization; AKT phosphorylation; migration assays; PFKFB4 knockdown/overexpression","pmids":["35914811"],"confidence":"Medium","gaps":["Single Co-IP without reciprocal validation of direct binding","Whether PFKFB4 modulates ICMT catalytic activity directly is unknown"]},{"year":2024,"claim":"Linked ICMT overexpression to invasive cell behavior, implicating its substrates in actin-based invadopodia and metastasis.","evidence":"ICMT overexpression in cancer cells; invadopodia assay; in vivo lung metastasis model; migration/invasion assays","pmids":["38301884"],"confidence":"Medium","gaps":["Specific methylated substrate driving invadopodia not identified","Single-lab gain-of-function without loss-of-function corroboration in the same model"]},{"year":2026,"claim":"Identified INPP5E as an ICMT-dependent substrate mediating BRAFV600E-driven tumor growth through membrane targeting and PI(4,5)P2 control.","evidence":"Genetic and pharmacologic ICMT inhibition; INPP5E methylation assay; fractionation; PI(4,5)P2 measurement; forced membrane targeting rescue; xenografts","pmids":["42127111"],"confidence":"High","gaps":["Rescue was only partial, implying additional substrates contribute","Precise lipid-signaling node downstream of PI(4,5)P2 not delineated"]},{"year":2025,"claim":"Connected ICMT-dependent RAC1 methylation to BRAF-inhibitor resistance via TAZ nuclear translocation, defining a combination-therapy rationale.","evidence":"RAC1 prenylation-site mutant; cysmethynil plus MAPK inhibitors; in vitro/in vivo tumor assays; TAZ localization and rescue (preprint)","pmids":["bio_10.1101_2025.08.10.669587"],"confidence":"Medium","gaps":["Preprint not yet peer-reviewed","Direct methylation of RAC1 by ICMT not biochemically demonstrated here","Generality beyond RAC1(P29S) resistance unclear"]},{"year":null,"claim":"How methylation status is dynamically read by downstream trafficking machinery and chaperones to dictate substrate fate across tissues remains incompletely defined.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structure with a bound full-length CAAX substrate","Mechanism coupling methylation to palmitoylation and PDE6δ handoff not resolved at molecular detail","Complete substrate repertoire and tissue-specific dependencies not catalogued"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,5]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[5,6,16]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[1,10]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[2,5]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,6,12,16]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[8,9,15,17]}],"complexes":[],"partners":["NRAS","KRAS","RHOA","PDE6D","INPP5E","PFKFB4","RAC1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O60725","full_name":"Protein-S-isoprenylcysteine O-methyltransferase","aliases":["Isoprenylcysteine carboxylmethyltransferase","Prenylated protein carboxyl methyltransferase","PPMT","Prenylcysteine carboxyl methyltransferase","pcCMT"],"length_aa":284,"mass_kda":31.9,"function":"Catalyzes the post-translational methylation of isoprenylated C-terminal cysteine residues","subcellular_location":"Endoplasmic reticulum membrane","url":"https://www.uniprot.org/uniprotkb/O60725/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ICMT","classification":"Not Classified","n_dependent_lines":162,"n_total_lines":1208,"dependency_fraction":0.13410596026490065},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CCDC47","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/ICMT","total_profiled":1310},"omim":[{"mim_id":"606480","title":"ZINC METALLOPROTEINASE STE24; ZMPSTE24","url":"https://www.omim.org/entry/606480"},{"mim_id":"605851","title":"ISOPRENYLCYSTEINE CARBOXYLMETHYLTRANSFERASE; ICMT","url":"https://www.omim.org/entry/605851"},{"mim_id":"150330","title":"LAMIN A/C; LMNA","url":"https://www.omim.org/entry/150330"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ICMT"},"hgnc":{"alias_symbol":["PCCMT","HSTE14","PPMT"],"prev_symbol":[]},"alphafold":{"accession":"O60725","domains":[{"cath_id":"-","chopping":"12-128","consensus_level":"medium","plddt":93.1671,"start":12,"end":128},{"cath_id":"1.20.120.1630","chopping":"129-284","consensus_level":"medium","plddt":95.7662,"start":129,"end":284}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O60725","model_url":"https://alphafold.ebi.ac.uk/files/AF-O60725-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O60725-F1-predicted_aligned_error_v6.png","plddt_mean":93.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ICMT","jax_strain_url":"https://www.jax.org/strain/search?query=ICMT"},"sequence":{"accession":"O60725","fasta_url":"https://rest.uniprot.org/uniprotkb/O60725.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O60725/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O60725"}},"corpus_meta":[{"pmid":"14966563","id":"PMC_14966563","title":"Inactivation of Icmt inhibits transformation by oncogenic K-Ras and B-Raf.","date":"2004","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/14966563","citation_count":134,"is_preprint":false},{"pmid":"23949910","id":"PMC_23949910","title":"18F-ICMT-11, a caspase-3-specific PET tracer for apoptosis: biodistribution and radiation dosimetry.","date":"2013","source":"Journal of nuclear medicine : official publication, Society of Nuclear Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/23949910","citation_count":74,"is_preprint":false},{"pmid":"11748165","id":"PMC_11748165","title":"icmT is essential for pore formation-mediated egress of Legionella pneumophila from mammalian and protozoan cells.","date":"2002","source":"Infection and immunity","url":"https://pubmed.ncbi.nlm.nih.gov/11748165","citation_count":70,"is_preprint":false},{"pmid":"22195972","id":"PMC_22195972","title":"Mechanism of isoprenylcysteine carboxyl methylation from the crystal structure of the integral membrane methyltransferase ICMT.","date":"2011","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/22195972","citation_count":46,"is_preprint":false},{"pmid":"21661760","id":"PMC_21661760","title":"Discovery and SAR of methylated tetrahydropyranyl derivatives as inhibitors of isoprenylcysteine carboxyl methyltransferase (ICMT).","date":"2011","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21661760","citation_count":41,"is_preprint":false},{"pmid":"25361001","id":"PMC_25361001","title":"Downregulation of microRNA-100 enhances the ICMT-Rac1 signaling and promotes metastasis of hepatocellular carcinoma cells.","date":"2014","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25361001","citation_count":39,"is_preprint":false},{"pmid":"31181882","id":"PMC_31181882","title":"A Potent Isoprenylcysteine Carboxylmethyltransferase (ICMT) Inhibitor Improves Survival in Ras-Driven Acute Myeloid Leukemia.","date":"2019","source":"Journal of medicinal chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31181882","citation_count":38,"is_preprint":false},{"pmid":"29342140","id":"PMC_29342140","title":"Atomic structure of the eukaryotic intramembrane RAS methyltransferase ICMT.","date":"2018","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/29342140","citation_count":36,"is_preprint":false},{"pmid":"30259091","id":"PMC_30259091","title":"Clinical translation of [18F]ICMT-11 for measuring chemotherapy-induced caspase 3/7 activation in breast and lung cancer.","date":"2018","source":"European journal of nuclear medicine and molecular imaging","url":"https://pubmed.ncbi.nlm.nih.gov/30259091","citation_count":32,"is_preprint":false},{"pmid":"11918802","id":"PMC_11918802","title":"The C-terminus of IcmT is essential for pore formation and for intracellular trafficking of Legionella pneumophila within Acanthamoeba polyphaga.","date":"2002","source":"Molecular 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suppressor.","date":"2019","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30655292","citation_count":16,"is_preprint":false},{"pmid":"36339587","id":"PMC_36339587","title":"Licoricidin combats gastric cancer by targeting the ICMT/Ras pathway in vitro and in vivo.","date":"2022","source":"Frontiers in pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/36339587","citation_count":15,"is_preprint":false},{"pmid":"17347446","id":"PMC_17347446","title":"Inhibition of ICMT induces endothelial cell apoptosis through GRP94.","date":"2007","source":"American journal of respiratory cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17347446","citation_count":15,"is_preprint":false},{"pmid":"22142613","id":"PMC_22142613","title":"Amide-modified prenylcysteine based Icmt inhibitors: Structure-activity relationships, kinetic analysis and cellular characterization.","date":"2011","source":"Bioorganic & medicinal 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effusion.","date":"2016","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/26959120","citation_count":11,"is_preprint":false},{"pmid":"25059662","id":"PMC_25059662","title":"Mutational analysis of the integral membrane methyltransferase isoprenylcysteine carboxyl methyltransferase (ICMT) reveals potential substrate binding sites.","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/25059662","citation_count":11,"is_preprint":false},{"pmid":"16757321","id":"PMC_16757321","title":"Genetic and pharmacologic analyses of the role of Icmt in Ras membrane association and function.","date":"2006","source":"Methods in enzymology","url":"https://pubmed.ncbi.nlm.nih.gov/16757321","citation_count":10,"is_preprint":false},{"pmid":"35312113","id":"PMC_35312113","title":"CircRNA hsa_circ_0018289 exerts an oncogenic role in cervical cancer progression through miR-1294/ICMT axis.","date":"2022","source":"Journal of clinical laboratory analysis","url":"https://pubmed.ncbi.nlm.nih.gov/35312113","citation_count":10,"is_preprint":false},{"pmid":"33579760","id":"PMC_33579760","title":"NRAS is unique among RAS proteins in requiring ICMT for trafficking to the plasma membrane.","date":"2021","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/33579760","citation_count":9,"is_preprint":false},{"pmid":"27147662","id":"PMC_27147662","title":"Deficiency of Isoprenylcysteine Carboxyl Methyltransferase (ICMT) Leads to Progressive Loss of Photoreceptor Function.","date":"2016","source":"The Journal of neuroscience : the official journal of the Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/27147662","citation_count":8,"is_preprint":false},{"pmid":"34984187","id":"PMC_34984187","title":"Lidocaine exerts anticancer activity in bladder cancer by targeting isoprenylcysteine carboxylmethyltransferase (ICMT).","date":"2021","source":"Translational andrology and urology","url":"https://pubmed.ncbi.nlm.nih.gov/34984187","citation_count":8,"is_preprint":false},{"pmid":"32781531","id":"PMC_32781531","title":"Development of [18F]ICMT-11 for Imaging Caspase-3/7 Activity during Therapy-Induced Apoptosis.","date":"2020","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/32781531","citation_count":7,"is_preprint":false},{"pmid":"26718043","id":"PMC_26718043","title":"9 Structure and function of isoprenylcysteine carboxylmethyltransferase (Icmt): A key enzyme in CaaX processing.","date":"2007","source":"The Enzymes","url":"https://pubmed.ncbi.nlm.nih.gov/26718043","citation_count":6,"is_preprint":false},{"pmid":"29794225","id":"PMC_29794225","title":"Depicting Changes in Tumor Biology in Response to Cetuximab Monotherapy or Combination Therapy by Apoptosis and Proliferation Imaging Using 18F-ICMT-11 and 18F-FLT PET.","date":"2018","source":"Journal of nuclear medicine : official publication, Society of Nuclear Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/29794225","citation_count":6,"is_preprint":false},{"pmid":"23725486","id":"PMC_23725486","title":"Mapping peptide thiol accessibility in membranes using a quaternary ammonium isotope-coded mass tag (ICMT).","date":"2013","source":"Bioconjugate chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/23725486","citation_count":5,"is_preprint":false},{"pmid":"38301884","id":"PMC_38301884","title":"Isoprenylcysteine carboxyl methyltransferase (ICMT) promotes invadopodia formation and metastasis in cancer cells.","date":"2024","source":"Biochimie","url":"https://pubmed.ncbi.nlm.nih.gov/38301884","citation_count":3,"is_preprint":false},{"pmid":"30125103","id":"PMC_30125103","title":"Use of an Isotope-Coded Mass Tag (ICMT) Method To Determine the Orientation of Cholesterol Oxidase on Model Membranes.","date":"2018","source":"Biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/30125103","citation_count":3,"is_preprint":false},{"pmid":"38835128","id":"PMC_38835128","title":"In silico Exploration of a Novel ICMT Inhibitor with More Solubility than Cysmethynil against Membrane Localization of KRAS Mutant in Colorectal Cancer.","date":"2024","source":"Current computer-aided drug design","url":"https://pubmed.ncbi.nlm.nih.gov/38835128","citation_count":1,"is_preprint":false},{"pmid":"41877819","id":"PMC_41877819","title":"Targeting ICMT: A promising strategy in cancer treatment (Review).","date":"2026","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/41877819","citation_count":0,"is_preprint":false},{"pmid":"42127111","id":"PMC_42127111","title":"ICMT supports BRAFV600E-driven tumor growth by membrane targeting of the CAAX protein INPP5E.","date":"2026","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/42127111","citation_count":0,"is_preprint":false},{"pmid":"41808116","id":"PMC_41808116","title":"ICMT deficiency ameliorates weight loss and mortality, but not tumor formation in a mouse model of liver cancer.","date":"2026","source":"Cell communication and signaling : CCS","url":"https://pubmed.ncbi.nlm.nih.gov/41808116","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.10.669587","title":"Concurrent inhibition of ICMT and RAF/MEK suppresses RAC1  <sup>P29S</sup>  -driven MAPKi resistance in BRAF  <sup>V600E</sup>  melanoma by regulating TAZ activity","date":"2025-08-12","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.10.669587","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":22378,"output_tokens":4892,"usd":0.070257,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13258,"output_tokens":4656,"usd":0.091345,"stage2_stop_reason":"end_turn"},"total_usd":0.161602,"stage1_batch_id":"msgbatch_01DUPACZi7AAWwuZiUjseQF4","stage2_batch_id":"msgbatch_018yt7chE3f48PEFtDwtj6AE","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2011,\n      \"finding\": \"Crystal structure of a prokaryotic ICMT ortholog revealed a markedly different architecture from conventional methyltransferases: a core of five transmembrane α-helices with a cofactor-binding pocket in a conserved C-terminal catalytic subdomain, and a tunnel linking the reactive methyl group of SAM to the inner membrane providing access for the prenyl lipid substrate, explaining how the enzyme accommodates both a hydrophilic cofactor (SAM) and a lipophilic prenyl substrate.\",\n      \"method\": \"X-ray crystallography of prokaryotic ICMT ortholog\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional interpretation, first structural determination of ICMT fold, later confirmed by eukaryotic structure\",\n      \"pmids\": [\"22195972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"X-ray structure of eukaryotic ICMT at 2.3 Å (in complex with SAM cofactor, an ordered lipid molecule, and a monobody inhibitor) revealed that the active site spans cytosolic and membrane-exposed regions, indicating distinct entry routes for the cytosolic methyl donor SAM and for prenylcysteine substrates associated with the ER membrane.\",\n      \"method\": \"X-ray crystallography at 2.3 Å resolution with monobody-assisted crystallization\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure with cofactor and lipid bound, published in Nature with rigorous validation\",\n      \"pmids\": [\"29342140\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Human ICMT catalysis proceeds through an ordered sequential kinetic mechanism in which SAM binds first and S-adenosylhomocysteine (AdoHcy) is the final product released; the prenylcysteine substrate (BFC) and its methylated product bind different enzyme forms, established using dead-end inhibitor (FTA) and product inhibition studies.\",\n      \"method\": \"In vitro enzyme kinetics with synthetic substrate BFC, dead-end inhibitor analysis, and product inhibition studies\",\n      \"journal\": \"BMC biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — rigorous in vitro kinetic analysis with multiple inhibitor approaches and ordered mechanism determination, single lab\",\n      \"pmids\": [\"15625008\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Scanning mutagenesis of nearly half the residues of the Anopheles gambiae ICMT ortholog combined with methyltransferase assays identified 62 mutations causing reduced or undetectable catalytic activity; residues in transmembrane regions contribute to the isoprenylcysteine binding site (certain substitutions caused substrate inhibition by isoprenylcysteine), while the AdoMet-binding site resembles a distantly related prokaryotic methyltransferase, establishing that the active site spans cytosolic and membrane-embedded regions.\",\n      \"method\": \"Scanning mutagenesis combined with in vitro methyltransferase assays; structural comparison with Ma MTase crystal structure\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — systematic mutagenesis of ~half of all residues with direct activity readout, multiple orthogonal analyses, later confirmed by crystal structure\",\n      \"pmids\": [\"25059662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Genetic inactivation of Icmt in mouse fibroblasts expressing oncogenic K-Ras inhibited K-Ras-induced oncogenic transformation (soft agar and nude mice); the mechanism involved accelerated RhoA protein turnover leading to reduced RhoA levels and a large Ras/Erk1/2-dependent increase in p21(Cip1); deletion of p21(Cip1) restored growth in soft agar of Icmt-null K-Ras cells. Icmt inactivation also blocked transformation by oncogenic B-Raf(V599E).\",\n      \"method\": \"Conditional Cre-lox knockout of Icmt in mouse embryonic fibroblasts; soft agar assay; nude mouse xenograft; p21(Cip1) double knockout rescue experiment; Western blot for Erk1/2, Akt1, RhoA\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis via double-knockout rescue, multiple in vitro and in vivo assays, clearly defined molecular pathway\",\n      \"pmids\": [\"14966563\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"ICMT is the only enzyme in mouse cells capable of methylating isoprenylated CAAX proteins including all Ras proteins; in the absence of carboxyl methylation, Ras proteins are mislocalized away from the plasma membrane and exhibit a shift in electrophoretic mobility. Additionally, ICMT methylates the CXC class of isoprenylated Rab proteins.\",\n      \"method\": \"Genetic knockout (conditional Icmt deletion), subcellular fractionation, electrophoretic mobility shift assays\",\n      \"journal\": \"Methods in enzymology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic and biochemical data compiled in methods review, single lab, multiple orthogonal approaches\",\n      \"pmids\": [\"16757321\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Among the four RAS proteins, NRAS uniquely requires ICMT for delivery to the plasma membrane; this is because NRAS has only a single palmitoylation site as its secondary membrane-affinity module. ICMT-dependent carboxyl methylation of NRAS promotes efficient palmitoylation, binding to the prenyl-protein chaperone PDE6δ, and anterograde trafficking from the Golgi to the plasma membrane. FRAP of GFP-NRAS revealed increased Golgi flux in the absence of ICMT, independent of palmitoylation.\",\n      \"method\": \"ICMT knockout cells; photoactivation and FRAP of GFP-NRAS; Co-IP/binding assay with PDE6δ; palmitoylation assays; subcellular fractionation\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (FRAP, co-IP, palmitoylation assay, fractionation) in single rigorous study establishing mechanism\",\n      \"pmids\": [\"33579760\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Retina-specific knockout of Icmt in mice caused progressive loss of rod and cone light-mediated responses, accompanied by defective association of isoprenylated transducin and cone phosphodiesterase 6 (PDE6α') with photoreceptor membranes, and decreased protein levels of transducin, PDE6α', and cone GRK1. Unlike Rce1 deficiency, rod PDE6 trafficked normally to the outer segment in Icmt-deficient mice, indicating that the -AAX (not methylation) blocks PDE6 transport.\",\n      \"method\": \"Retina-specific conditional Icmt knockout mice; electroretinography; subcellular fractionation; protein level quantification by Western blot\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean tissue-specific KO with defined electrophysiological and biochemical phenotypes, epistatic comparison with Rce1 KO\",\n      \"pmids\": [\"27147662\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Genetic knockout of Icmt improves survival of HGPS mice and restores vascular smooth muscle cell numbers in the aorta; a pharmacologic ICMT inhibitor (C75) delays senescence and stimulates proliferation of late-passage HGPS cells and Zmpste24-deficient fibroblasts, but does not influence proliferation of wild-type human cells or Zmpste24-deficient cells lacking Icmt, confirming drug specificity for the ICMT pathway.\",\n      \"method\": \"HGPS mouse model with Icmt knockout; synthetic ICMT inhibitor C75; cell proliferation and senescence assays; genetic controls (Zmpste24/Icmt double KO cells)\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic and pharmacologic evidence combined with rigorous specificity controls using Icmt-null cells, multiple cellular and in vivo readouts\",\n      \"pmids\": [\"33526168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A potent ICMT inhibitor (UCM-1336, compound 3, IC50 = 2 μM) selectively impairs membrane association of all four RAS isoforms, decreases Ras-GTP activity, and inhibits downstream RAS signaling pathways, leading to cell death in Ras-mutated tumor cell lines and improved survival in an in vivo acute myeloid leukemia model.\",\n      \"method\": \"In vitro ICMT enzymatic assay; subcellular fractionation for RAS membrane association; Ras-GTP pull-down; cell viability assays; in vivo AML mouse model\",\n      \"journal\": \"Journal of medicinal chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — pharmacologic inhibition with mechanistic readouts (membrane fractionation, Ras-GTP), in vivo validation, single lab\",\n      \"pmids\": [\"31181882\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"ICMT inhibition (using AGGC) in pulmonary artery endothelial cells caused redistribution and aggregation of the ER chaperone GRP94, followed by GRP94 protein degradation; these effects were dependent on RhoA activity and caspase activation, indicating that ICMT-dependent RhoA carboxyl methylation is required to maintain GRP94 localization and prevent unfolded protein response-associated apoptosis.\",\n      \"method\": \"ICMT chemical inhibition (AGGC); 2D-PAGE proteomics; immunofluorescence; constitutively active RhoA overexpression rescue; caspase inhibitor\",\n      \"journal\": \"American journal of respiratory cell and molecular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — pharmacologic inhibition with multiple readouts (proteomics, immunofluorescence, genetic rescue), but no direct carboxyl methylation assay for GRP94\",\n      \"pmids\": [\"17347446\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PFKFB4 physically interacts with ICMT, promotes ICMT/RAS interaction, controls RAS localization at the plasma membrane, and activates AKT signaling to enhance melanoma cell migration, revealing a glycolysis-independent function of PFKFB4 through ICMT.\",\n      \"method\": \"Co-immunoprecipitation (PFKFB4-ICMT interaction); subcellular localization of RAS; AKT phosphorylation assays; cell migration assays; PFKFB4 knockdown/overexpression\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP for interaction, multiple downstream readouts, but single lab and no reciprocal validation of direct binding\",\n      \"pmids\": [\"35914811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ICMT inhibition in hepatocellular carcinoma cells suppressed the Ras/Raf/Mek/Erk signaling pathway and inhibited epithelial-mesenchymal transition (EMT), establishing ICMT as mechanistically required for oncogenic Ras signaling and EMT in HCC.\",\n      \"method\": \"ICMT siRNA knockdown and overexpression in HCC cell lines; Western blot for Ras/Raf/Mek/Erk phosphorylation; EMT marker analysis; cell growth and migration assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — multiple orthogonal functional assays with loss- and gain-of-function, but no direct biochemical measurement of methylation activity\",\n      \"pmids\": [\"31451223\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Wild-type p53 represses ICMT transcription by binding the -209 to -14 region of the ICMT promoter (shown by ChIP assay and promoter truncation/luciferase reporter analysis), while cancer-associated p53 mutants positively regulate ICMT expression through a different promoter region.\",\n      \"method\": \"ChIP assay; ICMT promoter-luciferase reporter constructs; promoter truncation analysis; p53 overexpression/knockdown in cancer cell lines\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and reporter assays directly establishing p53 binding and transcriptional repression, single lab\",\n      \"pmids\": [\"30655292\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Prenylcysteine-based ICMT inhibitors (analogs 1a and 1b) exhibit mixed-mode inhibition of human ICMT with the competitive component predominating; cellular treatment with analog 1b alters subcellular localization of GFP-KRas and inhibits both Ras activation and Erk phosphorylation in Jurkat cells.\",\n      \"method\": \"In vitro kinetic inhibition analysis (Ki determination); GFP-KRas subcellular localization by fluorescence microscopy; Ras activation assay; Erk phosphorylation Western blot\",\n      \"journal\": \"Bioorganic & medicinal chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vitro kinetics plus cellular mechanistic readouts, single lab\",\n      \"pmids\": [\"22142613\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ICMT overexpression enhances invadopodia formation and promotes in vivo lung metastasis; ICMT overexpression also promotes migration and invasion in vitro, suggesting that ICMT acts on substrates regulating the actin cytoskeleton to drive invasive structures.\",\n      \"method\": \"ICMT overexpression in cancer cell lines; invadopodia formation assay; in vivo metastasis mouse model; in vitro migration and invasion assays\",\n      \"journal\": \"Biochimie\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean gain-of-function with defined cellular phenotype (invadopodia) and in vivo metastasis, single lab\",\n      \"pmids\": [\"38301884\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ICMT inhibition (genetic and pharmacologic with UCM-1336) reduced INPP5E methylation, displaced INPP5E from membranes, and increased PI(4,5)P2 levels; forced INPP5E membrane targeting partially rescued growth defects caused by ICMT inhibition in BRAFV600E-mutant melanoma cells, identifying INPP5E as an ICMT-dependent substrate mediating BRAFV600E-driven tumor growth.\",\n      \"method\": \"Genetic ICMT knockdown; pharmacologic ICMT inhibition (UCM-1336); INPP5E methylation assay; membrane fractionation; PI(4,5)P2 measurement; forced membrane targeting rescue experiment; xenograft tumor growth assays\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic and pharmacologic approaches combined with direct substrate methylation assay, rescue experiment, and in vivo validation\",\n      \"pmids\": [\"42127111\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RAC1(P29S/C189S), which lacks the C-terminal prenylation site required for ICMT methylation, lost the ability to drive resistance to BRAFV600E inhibitors (vemurafenib/trametinib); combined ICMT inhibition (cysmethynil) with MAPK inhibitors suppressed RAC1(P29S)-driven resistance in vitro and in vivo; mechanistically, combined treatment impaired nuclear translocation of TAZ, whose transcriptional activity accounts for MAPKi resistance downstream of RAC1(P29S).\",\n      \"method\": \"RAC1 prenylation-site mutant (C189S); pharmacologic ICMT inhibition (cysmethynil) combined with MAPK inhibitors; in vitro and in vivo tumor growth assays; TAZ nuclear localization assay; constitutively-active TAZ rescue experiment\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic prenylation-site mutant plus pharmacologic inhibition with mechanistic rescue (TAZ), preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.08.10.669587\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"ICMT is an integral membrane methyltransferase localized to the endoplasmic reticulum that catalyzes the final step of CAAX protein processing—SAM-dependent carboxyl methylation of isoprenylcysteine—using an ordered sequential mechanism (SAM binds first, AdoHcy released last) within an active site that spans cytosolic and membrane-embedded regions, thereby promoting plasma membrane targeting and signaling of substrates including all four RAS isoforms (with NRAS being uniquely dependent on ICMT for palmitoylation and PDE6δ-mediated anterograde Golgi trafficking), Rho GTPases, transducin, cone PDE6, prelamin A, and INPP5E; loss of ICMT mislocalizes these substrates, accelerates RhoA turnover, elevates p21(Cip1) via Ras/Erk signaling, disrupts phototransduction, and blocks oncogenic transformation by K-Ras and B-Raf, while its expression is transcriptionally repressed by wild-type p53 and upregulated by mutant p53.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ICMT is the terminal enzyme of CAAX protein processing, an integral endoplasmic reticulum membrane methyltransferase that catalyzes SAM-dependent carboxyl methylation of the C-terminal isoprenylcysteine of prenylated proteins, thereby controlling their membrane association and downstream signaling [#5]. Structural and kinetic work defines the catalytic logic: an unusual fold built from transmembrane helices with a C-terminal cofactor pocket and a lipid tunnel that connects the reactive SAM methyl group to the membrane-embedded prenyl substrate [#0], with an active site spanning cytosolic and membrane-exposed regions that provides separate entry routes for the cytosolic methyl donor and the ER-associated prenylcysteine [#1, #3]; catalysis follows an ordered sequential mechanism in which SAM binds first and AdoHcy is released last [#2]. ICMT is the sole enzyme methylating isoprenylated CAAX proteins including all four RAS isoforms, and loss of methylation mislocalizes RAS away from the plasma membrane [#5]; NRAS is uniquely ICMT-dependent because methylation promotes its palmitoylation, PDE6\\u03b4 binding, and anterograde Golgi-to-membrane trafficking [#6]. Through these substrates ICMT supports oncogenic signaling—its inactivation blocks K-Ras and B-Raf transformation by accelerating RhoA turnover and elevating p21(Cip1) via Ras/Erk [#4], and it is required for Ras/Raf/Mek/Erk-driven signaling and substrate membrane targeting in multiple cancer contexts including the BRAFV600E-driven, INPP5E-dependent program [#12, #16]. ICMT also methylates substrates in specialized tissues, including transducin and cone PDE6 in photoreceptors where its retinal loss disrupts phototransduction [#7], and its expression is transcriptionally repressed by wild-type p53 and elevated by cancer-associated p53 mutants [#13].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Established the catalytic mechanism of ICMT, defining how a single enzyme coordinates a hydrophilic cofactor and a lipophilic prenyl substrate.\",\n      \"evidence\": \"In vitro enzyme kinetics with synthetic substrate BFC, dead-end and product inhibition studies\",\n      \"pmids\": [\"15625008\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Kinetics performed on a synthetic small-molecule substrate, not full-length prenylated proteins\", \"Does not localize the substrate-binding residues structurally\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Demonstrated that ICMT is functionally required for oncogenic transformation, connecting CAAX methylation to a defined RhoA/p21(Cip1) growth-control pathway.\",\n      \"evidence\": \"Conditional Icmt knockout in mouse fibroblasts; soft agar, xenograft, and p21(Cip1) double-knockout rescue\",\n      \"pmids\": [\"14966563\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which methylation loss accelerates RhoA turnover not resolved\", \"Did not identify all relevant methylated substrates contributing to transformation block\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Established ICMT as the unique enzyme methylating isoprenylated CAAX proteins and showed methylation controls RAS membrane localization.\",\n      \"evidence\": \"Conditional Icmt knockout, subcellular fractionation, and electrophoretic mobility shift assays\",\n      \"pmids\": [\"16757321\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Data compiled in a methods review from a single lab\", \"Quantitative contribution of methylation versus prenylation to localization not separated\"]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Provided the first structural framework for the ICMT fold, explaining how transmembrane helices and a lipid tunnel accommodate both SAM and a prenyl substrate.\",\n      \"evidence\": \"X-ray crystallography of a prokaryotic ICMT ortholog\",\n      \"pmids\": [\"22195972\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Prokaryotic ortholog may differ from the human enzyme in detail\", \"No bound prenylcysteine substrate captured\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Mapped catalytic and substrate-binding residues across the enzyme, confirming the active site spans cytosolic and membrane-embedded regions.\",\n      \"evidence\": \"Scanning mutagenesis of ~half of all residues in the Anopheles gambiae ortholog with methyltransferase assays\",\n      \"pmids\": [\"25059662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Performed on an insect ortholog rather than the human enzyme\", \"Functional effects inferred from activity loss without structural confirmation at the time\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed ICMT is required for photoreceptor function via methylation of phototransduction substrates, distinguishing methylation-dependent from -AAX-dependent trafficking.\",\n      \"evidence\": \"Retina-specific conditional Icmt knockout mice; electroretinography; subcellular fractionation; epistatic comparison with Rce1\",\n      \"pmids\": [\"27147662\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism linking methylation loss to reduced substrate protein levels unclear\", \"Does not establish direct methylation of each affected substrate in vivo\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Delivered a high-resolution eukaryotic ICMT structure with cofactor and lipid bound, defining distinct entry routes for SAM and prenylcysteine substrates.\",\n      \"evidence\": \"X-ray crystallography at 2.3 \\u00c5 with monobody-assisted crystallization, SAM and ordered lipid bound\",\n      \"pmids\": [\"29342140\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No bound CAAX peptide substrate to define the prenylcysteine-binding mode directly\", \"Conformational dynamics of catalysis not captured by a static structure\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified p53-dependent transcriptional control of ICMT, with opposite regulation by wild-type versus mutant p53.\",\n      \"evidence\": \"ChIP assay, promoter-luciferase reporters, truncation analysis, p53 overexpression/knockdown\",\n      \"pmids\": [\"30655292\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab; mutant-p53 activating mechanism on a distinct promoter region not fully defined\", \"Physiological consequences of p53-driven ICMT changes not established\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Validated ICMT pharmacologically as a target whose inhibition impairs RAS membrane association and signaling and kills Ras-mutant tumors.\",\n      \"evidence\": \"ICMT inhibitor UCM-1336; enzymatic assay, fractionation, Ras-GTP pull-down, viability assays, in vivo AML model; plus HCC siRNA/overexpression studies of Ras/Raf/Mek/Erk and EMT\",\n      \"pmids\": [\"31181882\", \"31451223\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Off-target effects of inhibitors on other methylated substrates not excluded\", \"HCC studies lack direct methylation readout\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Explained why NRAS is uniquely ICMT-dependent—methylation enables its palmitoylation, PDE6\\u03b4 binding, and Golgi-to-membrane trafficking.\",\n      \"evidence\": \"ICMT knockout cells; FRAP/photoactivation of GFP-NRAS; PDE6\\u03b4 Co-IP; palmitoylation assays; fractionation\",\n      \"pmids\": [\"33579760\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative coupling between methylation and palmitoylation enzymes not defined\", \"Generality to other single-palmitoylation CAAX proteins untested\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Demonstrated therapeutic potential of targeting ICMT in progeria, with rigorous specificity controls.\",\n      \"evidence\": \"HGPS mice with Icmt knockout; ICMT inhibitor C75; proliferation/senescence assays; Zmpste24/Icmt double-knockout controls\",\n      \"pmids\": [\"33526168\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct measurement of prelamin A methylation status not reported here\", \"Long-term consequences of systemic ICMT inhibition unaddressed\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identified PFKFB4 as a physical partner that enhances ICMT/RAS interaction and RAS localization, revealing a non-glycolytic input to ICMT function.\",\n      \"evidence\": \"Co-IP of PFKFB4-ICMT; RAS localization; AKT phosphorylation; migration assays; PFKFB4 knockdown/overexpression\",\n      \"pmids\": [\"35914811\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single Co-IP without reciprocal validation of direct binding\", \"Whether PFKFB4 modulates ICMT catalytic activity directly is unknown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Linked ICMT overexpression to invasive cell behavior, implicating its substrates in actin-based invadopodia and metastasis.\",\n      \"evidence\": \"ICMT overexpression in cancer cells; invadopodia assay; in vivo lung metastasis model; migration/invasion assays\",\n      \"pmids\": [\"38301884\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Specific methylated substrate driving invadopodia not identified\", \"Single-lab gain-of-function without loss-of-function corroboration in the same model\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Identified INPP5E as an ICMT-dependent substrate mediating BRAFV600E-driven tumor growth through membrane targeting and PI(4,5)P2 control.\",\n      \"evidence\": \"Genetic and pharmacologic ICMT inhibition; INPP5E methylation assay; fractionation; PI(4,5)P2 measurement; forced membrane targeting rescue; xenografts\",\n      \"pmids\": [\"42127111\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Rescue was only partial, implying additional substrates contribute\", \"Precise lipid-signaling node downstream of PI(4,5)P2 not delineated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Connected ICMT-dependent RAC1 methylation to BRAF-inhibitor resistance via TAZ nuclear translocation, defining a combination-therapy rationale.\",\n      \"evidence\": \"RAC1 prenylation-site mutant; cysmethynil plus MAPK inhibitors; in vitro/in vivo tumor assays; TAZ localization and rescue (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.08.10.669587\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint not yet peer-reviewed\", \"Direct methylation of RAC1 by ICMT not biochemically demonstrated here\", \"Generality beyond RAC1(P29S) resistance unclear\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How methylation status is dynamically read by downstream trafficking machinery and chaperones to dictate substrate fate across tissues remains incompletely defined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structure with a bound full-length CAAX substrate\", \"Mechanism coupling methylation to palmitoylation and PDE6\\u03b4 handoff not resolved at molecular detail\", \"Complete substrate repertoire and tissue-specific dependencies not catalogued\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 5]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [5, 6, 16]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [1, 10]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [2, 5]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 6, 12, 16]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [8, 9, 15, 17]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NRAS\", \"KRAS\", \"RhoA\", \"PDE6D\", \"INPP5E\", \"PFKFB4\", \"RAC1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}