{"gene":"CHML","run_date":"2026-04-28T17:28:52","timeline":{"discoveries":[{"year":1994,"finding":"CHML encodes REP-2 (Rab escort protein 2), which binds newly synthesized Rab proteins and facilitates geranylgeranyl (GG) group attachment by the Rab GG transferase catalytic component; GG transfer is absolutely dependent on REP participation. REP-2 was approximately equal to REP-1 in supporting GG attachment to Rab1A, Rab5A, and Rab6, but only 25% as active toward Rab3A and Rab3D. Replacing the C-terminal 12 amino acids of Rab3A with those of Rab1A restored REP-2 activity to normal, demonstrating substrate specificity is determined by Rab C-terminal sequence.","method":"Recombinant protein production, in vitro GG transferase assay, domain-swap mutagenesis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro reconstitution with mutagenesis, foundational paper with 159 citations","pmids":["8294464"],"is_preprint":false},{"year":2019,"finding":"CHML promotes HCC cell migration, invasion, and metastasis by escorting Rab14 to the membrane, facilitating constant Rab14 recycling. Rab14-positive vesicles carry metastasis regulators Mucin13 and CD44 as cargo, contributing to the pro-metastatic effect.","method":"siRNA knockdown, overexpression, in vitro migration/invasion assays, in vivo metastasis model, co-immunoprecipitation, vesicle cargo identification","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (KD/OE, in vivo, Co-IP, cargo identification) in a single study, 43 citations","pmids":["31175290"],"is_preprint":false},{"year":2022,"finding":"CHML/Rep2 is a transcriptional target of NRF2 via an antioxidant response element (ARE) in its promoter (-1622 to -1612). Loss of Rep2 inhibits mTOR translocation and activation at the lysosome, while overexpression enhances it, establishing Rep2 as a mediator of mTOR lysosomal function downstream of NRF2.","method":"siRNA knockdown, overexpression, ARE reporter/promoter analysis, mTOR localization imaging at lysosome, cell proliferation assay","journal":"Molecular oncology","confidence":"Medium","confidence_rationale":"Tier 2 — multiple methods (promoter analysis, KD/OE, localization) but single lab with limited replication","pmids":["35184380"],"is_preprint":false},{"year":2021,"finding":"CHML promotes proliferation and inhibits apoptosis of non-small cell lung cancer cells via direct binding to Rab5A, as demonstrated by co-immunoprecipitation. CHML is regulated upstream by miR-199a-3p, which targets CHML mRNA.","method":"siRNA knockdown, xenograft mouse model, co-immunoprecipitation, miRNA overexpression/inhibition","journal":"Pathology, research and practice","confidence":"Medium","confidence_rationale":"Tier 3 — single Co-IP for binding, functional phenotype confirmed in vivo, single lab","pmids":["34649053"],"is_preprint":false},{"year":2025,"finding":"CHML promotes HCC cell migration and invasion by upregulating SLC44A3 (a choline transporter), increasing choline uptake and phosphatidic acid (PA) production, which in turn activates MAPK and PI3K-AKT signaling cascades. This mechanism was identified through integration of transcriptomics and untargeted metabolomics after CHML knockout or overexpression.","method":"CHML knockout/overexpression, transcriptome sequencing, untargeted metabolomics, wound healing, Transwell assay, xenograft model","journal":"Frontiers in oncology","confidence":"Low","confidence_rationale":"Tier 3 — mechanistic pathway inferred from omics integration, limited direct biochemical validation of SLC44A3-PA-MAPK/PI3K axis, single lab, 0 citations","pmids":["40842592"],"is_preprint":false}],"current_model":"CHML encodes REP-2, a Rab escort protein that binds newly synthesized Rab GTPases (including Rab1A, Rab5A, Rab6, and Rab14) and escorts them to the membrane while facilitating geranylgeranylation by the Rab GG transferase; it shows substrate specificity differences from REP-1 particularly toward Rab3A/3D, and in cancer contexts it promotes metastasis by recycling Rab14 to the membrane (carrying Mucin13/CD44 cargo), regulates mTOR lysosomal activation downstream of NRF2, and interacts with Rab5A to promote cell proliferation."},"narrative":{"teleology":[{"year":1994,"claim":"Establishing that REP-2 is an essential cofactor for Rab geranylgeranylation resolved how newly synthesized Rab GTPases acquire their lipid anchors and revealed that REP-2 and REP-1 differ in substrate specificity, particularly toward Rab3A/3D, dictated by Rab C-terminal sequences.","evidence":"In vitro geranylgeranyl transferase assay with recombinant REP-2 and domain-swap mutagenesis of Rab C-termini","pmids":["8294464"],"confidence":"High","gaps":["Structural basis of the REP-2/Rab interaction and how C-terminal residues determine selectivity was not resolved","Whether REP-2 has escort functions beyond prenylation (e.g., membrane delivery) was not directly tested","In vivo phenotype of REP-2 loss in mammalian systems was not assessed"]},{"year":2019,"claim":"Demonstrating that CHML escorts Rab14 to membranes in HCC cells, enabling vesicular transport of Mucin13 and CD44, established a specific post-prenylation escort function driving cancer metastasis.","evidence":"siRNA knockdown, overexpression, in vivo metastasis model, co-immunoprecipitation, and vesicle cargo identification in HCC cells","pmids":["31175290"],"confidence":"High","gaps":["Whether CHML-dependent Rab14 recycling operates in normal hepatocytes or is specific to transformed cells","Mechanism by which Mucin13/CD44 are selectively loaded onto Rab14-positive vesicles is unknown","Whether other Rab substrates contribute to the metastatic phenotype was not dissected"]},{"year":2021,"claim":"Showing that CHML binds Rab5A and promotes NSCLC proliferation while being regulated by miR-199a-3p extended CHML's cancer-relevant Rab partnerships beyond Rab14 and identified a post-transcriptional regulatory axis.","evidence":"Co-immunoprecipitation of CHML–Rab5A, siRNA knockdown, xenograft model, and miRNA overexpression/inhibition in NSCLC cells","pmids":["34649053"],"confidence":"Medium","gaps":["CHML–Rab5A interaction rests on a single co-IP without reciprocal validation or domain mapping","Whether the proliferative effect depends on Rab5A prenylation or an escort-independent mechanism is unclear","miR-199a-3p regulation not confirmed with endogenous miRNA knockout"]},{"year":2022,"claim":"Identifying CHML as an NRF2 transcriptional target that mediates mTOR lysosomal recruitment linked Rab escort function to nutrient-sensing signaling and antioxidant response pathways.","evidence":"ARE promoter analysis, siRNA knockdown, overexpression, and mTOR lysosomal localization imaging","pmids":["35184380"],"confidence":"Medium","gaps":["Which specific Rab substrate(s) mediate mTOR lysosomal translocation downstream of CHML is not identified","ChIP-seq confirmation of direct NRF2 occupancy at the CHML promoter in multiple cell types is lacking","Whether NRF2–CHML–mTOR axis operates in non-cancer contexts is untested"]},{"year":2025,"claim":"Proposing that CHML upregulates SLC44A3-mediated choline uptake to increase phosphatidic acid production and activate MAPK/PI3K-AKT signaling introduced a metabolic mechanism for CHML-driven HCC invasion, though the pathway lacks direct biochemical validation.","evidence":"CHML knockout/overexpression with integrated transcriptomics and untargeted metabolomics, Transwell and xenograft assays in HCC cells","pmids":["40842592"],"confidence":"Low","gaps":["SLC44A3–PA–MAPK/PI3K axis is inferred from omics correlation without direct biochemical validation of causality","Whether SLC44A3 upregulation depends on a specific Rab substrate escorted by CHML is unknown","Single-lab study with no independent replication or citations"]},{"year":null,"claim":"It remains unknown which specific Rab substrates mediate CHML's effects on mTOR lysosomal activation and choline metabolism, and no structural model of REP-2 in complex with any human Rab has been determined.","evidence":"","pmids":[],"confidence":"High","gaps":["No structural model of REP-2 bound to a Rab substrate or the geranylgeranyltransferase complex","Complete inventory of Rab substrates preferentially dependent on REP-2 vs REP-1 in vivo is missing","In vivo phenotype of CHML loss in a mammalian genetic model has not been reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0031410","term_label":"cytoplasmic vesicle","supporting_discovery_ids":[1]},{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[1]}],"complexes":[],"partners":["RAB1A","RAB5A","RAB6A","RAB14","RAB3A"],"other_free_text":[]},"mechanistic_narrative":"CHML encodes Rab escort protein 2 (REP-2), which binds newly synthesized Rab GTPases and is absolutely required for their geranylgeranylation by the Rab geranylgeranyltransferase complex; REP-2 shows activity comparable to REP-1 toward Rab1A, Rab5A, and Rab6 but reduced activity toward Rab3A/3D, with substrate specificity governed by the Rab C-terminal sequence [PMID:8294464]. In hepatocellular carcinoma, CHML promotes metastasis by escorting Rab14 to membranes, enabling Rab14-positive vesicles carrying Mucin13 and CD44 to drive migration and invasion [PMID:31175290]. CHML is transcriptionally activated by NRF2 through an antioxidant response element in its promoter and mediates mTOR translocation and activation at the lysosome [PMID:35184380]."},"prefetch_data":{"uniprot":{"accession":"P26374","full_name":"Rab proteins geranylgeranyltransferase component A 2","aliases":["Choroideremia-like protein","Rab escort protein 2","REP-2"],"length_aa":656,"mass_kda":74.1,"function":"Substrate-binding subunit (component A) of the Rab geranylgeranyltransferase (GGTase) complex. Binds unprenylated Rab proteins and presents the substrate peptide to the catalytic component B. The component A is thought to be regenerated by transferring its prenylated Rab back to the donor membrane. Less effective than CHM in supporting prenylation of Rab3 family","subcellular_location":"Cytoplasm, cytosol","url":"https://www.uniprot.org/uniprotkb/P26374/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/CHML","classification":"Not Classified","n_dependent_lines":5,"n_total_lines":1208,"dependency_fraction":0.0041390728476821195},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"RAB14","stoichiometry":0.2},{"gene":"RAB35","stoichiometry":0.2},{"gene":"RAB4A","stoichiometry":0.2},{"gene":"RAB7A","stoichiometry":0.2},{"gene":"RABGGTA","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/CHML","total_profiled":1310},"omim":[{"mim_id":"612433","title":"DEAFNESS, AUTOSOMAL RECESSIVE 45; DFNB45","url":"https://www.omim.org/entry/612433"},{"mim_id":"606695","title":"OPSIN 3; OPN3","url":"https://www.omim.org/entry/606695"},{"mim_id":"118825","title":"CHM-LIKE; CHML","url":"https://www.omim.org/entry/118825"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/CHML"},"hgnc":{"alias_symbol":["REP-2"],"prev_symbol":[]},"alphafold":{"accession":"P26374","domains":[{"cath_id":"3.50.50.60","chopping":"9-94_381-450_562-601","consensus_level":"medium","plddt":93.8992,"start":9,"end":601}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P26374","model_url":"https://alphafold.ebi.ac.uk/files/AF-P26374-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P26374-F1-predicted_aligned_error_v6.png","plddt_mean":79.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CHML","jax_strain_url":"https://www.jax.org/strain/search?query=CHML"},"sequence":{"accession":"P26374","fasta_url":"https://rest.uniprot.org/uniprotkb/P26374.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P26374/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P26374"}},"corpus_meta":[{"pmid":"8294464","id":"PMC_8294464","title":"REP-2, a Rab escort protein encoded by the choroideremia-like gene.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/8294464","citation_count":159,"is_preprint":false},{"pmid":"31175290","id":"PMC_31175290","title":"CHML promotes liver cancer metastasis by facilitating Rab14 recycle.","date":"2019","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/31175290","citation_count":43,"is_preprint":false},{"pmid":"12684786","id":"PMC_12684786","title":"Identification, cDNA cloning and possible roles of seed-specific rice asparaginyl endopeptidase, REP-2.","date":"2003","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/12684786","citation_count":20,"is_preprint":false},{"pmid":"8188272","id":"PMC_8188272","title":"Mapping of the choroideremia-like (CHML) gene at 1q42-qter and mutation analysis in patients with Usher syndrome type II.","date":"1994","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/8188272","citation_count":15,"is_preprint":false},{"pmid":"35184380","id":"PMC_35184380","title":"CHML is an NRF2 target gene that regulates mTOR function.","date":"2022","source":"Molecular oncology","url":"https://pubmed.ncbi.nlm.nih.gov/35184380","citation_count":5,"is_preprint":false},{"pmid":"34649053","id":"PMC_34649053","title":"CHML targeted by miR-199a-3p promotes non-small cell lung cancer cell growth via binding to Rab5A.","date":"2021","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/34649053","citation_count":5,"is_preprint":false},{"pmid":"11724310","id":"PMC_11724310","title":"Antitumor activity of cytotropic heterogeneous molecular lipids (CHML) on human breast cancer xenograft in nude mice.","date":"2001","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/11724310","citation_count":4,"is_preprint":false},{"pmid":"37895215","id":"PMC_37895215","title":"Bioengineered Hybrid Rep 2/6 Gene Improves Encapsulation of a Single-Stranded Expression Cassette into AAV6 Vectors.","date":"2023","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/37895215","citation_count":4,"is_preprint":false},{"pmid":"10652570","id":"PMC_10652570","title":"CHML suppresses cell growth and induces apoptosis in multiple human tumor lines.","date":"1999","source":"Anticancer research","url":"https://pubmed.ncbi.nlm.nih.gov/10652570","citation_count":3,"is_preprint":false},{"pmid":"40842592","id":"PMC_40842592","title":"CHML regulates migration and invasion in hepatocellular carcinoma via transcriptional and metabolic reprogramming.","date":"2025","source":"Frontiers in oncology","url":"https://pubmed.ncbi.nlm.nih.gov/40842592","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6362,"output_tokens":1408,"usd":0.020103},"stage2":{"model":"claude-opus-4-6","input_tokens":4624,"output_tokens":1970,"usd":0.108555},"total_usd":0.128658,"stage1_batch_id":"msgbatch_011kfMfE81o6CTcyhVUqumuW","stage2_batch_id":"msgbatch_01DTputS6WNkH745x1nVSoBo","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"CHML encodes REP-2 (Rab escort protein 2), which binds newly synthesized Rab proteins and facilitates geranylgeranyl (GG) group attachment by the Rab GG transferase catalytic component; GG transfer is absolutely dependent on REP participation. REP-2 was approximately equal to REP-1 in supporting GG attachment to Rab1A, Rab5A, and Rab6, but only 25% as active toward Rab3A and Rab3D. Replacing the C-terminal 12 amino acids of Rab3A with those of Rab1A restored REP-2 activity to normal, demonstrating substrate specificity is determined by Rab C-terminal sequence.\",\n      \"method\": \"Recombinant protein production, in vitro GG transferase assay, domain-swap mutagenesis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with mutagenesis, foundational paper with 159 citations\",\n      \"pmids\": [\"8294464\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CHML promotes HCC cell migration, invasion, and metastasis by escorting Rab14 to the membrane, facilitating constant Rab14 recycling. Rab14-positive vesicles carry metastasis regulators Mucin13 and CD44 as cargo, contributing to the pro-metastatic effect.\",\n      \"method\": \"siRNA knockdown, overexpression, in vitro migration/invasion assays, in vivo metastasis model, co-immunoprecipitation, vesicle cargo identification\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KD/OE, in vivo, Co-IP, cargo identification) in a single study, 43 citations\",\n      \"pmids\": [\"31175290\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"CHML/Rep2 is a transcriptional target of NRF2 via an antioxidant response element (ARE) in its promoter (-1622 to -1612). Loss of Rep2 inhibits mTOR translocation and activation at the lysosome, while overexpression enhances it, establishing Rep2 as a mediator of mTOR lysosomal function downstream of NRF2.\",\n      \"method\": \"siRNA knockdown, overexpression, ARE reporter/promoter analysis, mTOR localization imaging at lysosome, cell proliferation assay\",\n      \"journal\": \"Molecular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple methods (promoter analysis, KD/OE, localization) but single lab with limited replication\",\n      \"pmids\": [\"35184380\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"CHML promotes proliferation and inhibits apoptosis of non-small cell lung cancer cells via direct binding to Rab5A, as demonstrated by co-immunoprecipitation. CHML is regulated upstream by miR-199a-3p, which targets CHML mRNA.\",\n      \"method\": \"siRNA knockdown, xenograft mouse model, co-immunoprecipitation, miRNA overexpression/inhibition\",\n      \"journal\": \"Pathology, research and practice\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single Co-IP for binding, functional phenotype confirmed in vivo, single lab\",\n      \"pmids\": [\"34649053\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"CHML promotes HCC cell migration and invasion by upregulating SLC44A3 (a choline transporter), increasing choline uptake and phosphatidic acid (PA) production, which in turn activates MAPK and PI3K-AKT signaling cascades. This mechanism was identified through integration of transcriptomics and untargeted metabolomics after CHML knockout or overexpression.\",\n      \"method\": \"CHML knockout/overexpression, transcriptome sequencing, untargeted metabolomics, wound healing, Transwell assay, xenograft model\",\n      \"journal\": \"Frontiers in oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — mechanistic pathway inferred from omics integration, limited direct biochemical validation of SLC44A3-PA-MAPK/PI3K axis, single lab, 0 citations\",\n      \"pmids\": [\"40842592\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"CHML encodes REP-2, a Rab escort protein that binds newly synthesized Rab GTPases (including Rab1A, Rab5A, Rab6, and Rab14) and escorts them to the membrane while facilitating geranylgeranylation by the Rab GG transferase; it shows substrate specificity differences from REP-1 particularly toward Rab3A/3D, and in cancer contexts it promotes metastasis by recycling Rab14 to the membrane (carrying Mucin13/CD44 cargo), regulates mTOR lysosomal activation downstream of NRF2, and interacts with Rab5A to promote cell proliferation.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"CHML encodes Rab escort protein 2 (REP-2), which binds newly synthesized Rab GTPases and is absolutely required for their geranylgeranylation by the Rab geranylgeranyltransferase complex; REP-2 shows activity comparable to REP-1 toward Rab1A, Rab5A, and Rab6 but reduced activity toward Rab3A/3D, with substrate specificity governed by the Rab C-terminal sequence [PMID:8294464]. In hepatocellular carcinoma, CHML promotes metastasis by escorting Rab14 to membranes, enabling Rab14-positive vesicles carrying Mucin13 and CD44 to drive migration and invasion [PMID:31175290]. CHML is transcriptionally activated by NRF2 through an antioxidant response element in its promoter and mediates mTOR translocation and activation at the lysosome [PMID:35184380].\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Establishing that REP-2 is an essential cofactor for Rab geranylgeranylation resolved how newly synthesized Rab GTPases acquire their lipid anchors and revealed that REP-2 and REP-1 differ in substrate specificity, particularly toward Rab3A/3D, dictated by Rab C-terminal sequences.\",\n      \"evidence\": \"In vitro geranylgeranyl transferase assay with recombinant REP-2 and domain-swap mutagenesis of Rab C-termini\",\n      \"pmids\": [\"8294464\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural basis of the REP-2/Rab interaction and how C-terminal residues determine selectivity was not resolved\",\n        \"Whether REP-2 has escort functions beyond prenylation (e.g., membrane delivery) was not directly tested\",\n        \"In vivo phenotype of REP-2 loss in mammalian systems was not assessed\"\n      ]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrating that CHML escorts Rab14 to membranes in HCC cells, enabling vesicular transport of Mucin13 and CD44, established a specific post-prenylation escort function driving cancer metastasis.\",\n      \"evidence\": \"siRNA knockdown, overexpression, in vivo metastasis model, co-immunoprecipitation, and vesicle cargo identification in HCC cells\",\n      \"pmids\": [\"31175290\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether CHML-dependent Rab14 recycling operates in normal hepatocytes or is specific to transformed cells\",\n        \"Mechanism by which Mucin13/CD44 are selectively loaded onto Rab14-positive vesicles is unknown\",\n        \"Whether other Rab substrates contribute to the metastatic phenotype was not dissected\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Showing that CHML binds Rab5A and promotes NSCLC proliferation while being regulated by miR-199a-3p extended CHML's cancer-relevant Rab partnerships beyond Rab14 and identified a post-transcriptional regulatory axis.\",\n      \"evidence\": \"Co-immunoprecipitation of CHML–Rab5A, siRNA knockdown, xenograft model, and miRNA overexpression/inhibition in NSCLC cells\",\n      \"pmids\": [\"34649053\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"CHML–Rab5A interaction rests on a single co-IP without reciprocal validation or domain mapping\",\n        \"Whether the proliferative effect depends on Rab5A prenylation or an escort-independent mechanism is unclear\",\n        \"miR-199a-3p regulation not confirmed with endogenous miRNA knockout\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Identifying CHML as an NRF2 transcriptional target that mediates mTOR lysosomal recruitment linked Rab escort function to nutrient-sensing signaling and antioxidant response pathways.\",\n      \"evidence\": \"ARE promoter analysis, siRNA knockdown, overexpression, and mTOR lysosomal localization imaging\",\n      \"pmids\": [\"35184380\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Which specific Rab substrate(s) mediate mTOR lysosomal translocation downstream of CHML is not identified\",\n        \"ChIP-seq confirmation of direct NRF2 occupancy at the CHML promoter in multiple cell types is lacking\",\n        \"Whether NRF2–CHML–mTOR axis operates in non-cancer contexts is untested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proposing that CHML upregulates SLC44A3-mediated choline uptake to increase phosphatidic acid production and activate MAPK/PI3K-AKT signaling introduced a metabolic mechanism for CHML-driven HCC invasion, though the pathway lacks direct biochemical validation.\",\n      \"evidence\": \"CHML knockout/overexpression with integrated transcriptomics and untargeted metabolomics, Transwell and xenograft assays in HCC cells\",\n      \"pmids\": [\"40842592\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"SLC44A3–PA–MAPK/PI3K axis is inferred from omics correlation without direct biochemical validation of causality\",\n        \"Whether SLC44A3 upregulation depends on a specific Rab substrate escorted by CHML is unknown\",\n        \"Single-lab study with no independent replication or citations\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown which specific Rab substrates mediate CHML's effects on mTOR lysosomal activation and choline metabolism, and no structural model of REP-2 in complex with any human Rab has been determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural model of REP-2 bound to a Rab substrate or the geranylgeranyltransferase complex\",\n        \"Complete inventory of Rab substrates preferentially dependent on REP-2 vs REP-1 in vivo is missing\",\n        \"In vivo phenotype of CHML loss in a mammalian genetic model has not been reported\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0031410\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"RAB1A\",\n      \"RAB5A\",\n      \"RAB6A\",\n      \"RAB14\",\n      \"RAB3A\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}