{"gene":"ZDHHC18","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2022,"finding":"ZDHHC18 is a palmitoyltransferase that catalyzes palmitoylation of cGAS at cysteine C474. This modification reduces cGAS interaction with double-stranded DNA and inhibits cGAS dimerization, thereby restricting cGAS enzymatic activity. ZDHHC18 negatively regulates cGAS-mediated innate immune signaling; Zdhhc18-deficient mice show enhanced resistance to DNA virus infection.","method":"Biochemical palmitoylation assays, site-directed mutagenesis (C474 cGAS mutant), co-immunoprecipitation, cell-based innate immune reporter assays, Zdhhc18 knockout mouse model","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of substrate site, in vivo KO model with defined phenotype, multiple orthogonal methods in a single rigorous study","pmids":["35438208"],"is_preprint":false},{"year":2022,"finding":"ZDHHC18 palmitoylates MDH2 (malate dehydrogenase 2) at cysteine C138, increasing MDH2 enzymatic activity and sustaining mitochondrial respiration. Glutamine deprivation enhances the ZDHHC18–MDH2 interaction. Re-expression of palmitoylation-deficient MDH2 (C138S) fails to restore mitochondrial respiration or ovarian cancer cell growth, confirming the functional requirement of this modification.","method":"Palmitoylation assay, co-immunoprecipitation, site-directed mutagenesis (C138S MDH2 mutant), siRNA knockdown, in vitro and in vivo proliferation/respiration assays","journal":"Science China. Life sciences","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, palmitoylation assay, mutagenesis of substrate site, in vitro and in vivo rescue experiments with multiple orthogonal methods","pmids":["35366151"],"is_preprint":false},{"year":2025,"finding":"ZDHHC18 catalyzes palmitoylation of HRAS, which is required for HRAS translocation to the plasma membrane and its subsequent activation. HRAS palmitoylation drives downstream MEK/ERK phosphorylation, activates RREB1, and enhances SMAD binding to Snai1 cis-regulatory regions, promoting partial epithelial-mesenchymal transition (EMT) and profibrotic cytokine production in tubular epithelial cells. Tubule-specific Zdhhc18 deletion attenuates renal fibrosis in UUO and folic acid mouse models.","method":"Palmitoylation assay, subcellular fractionation/membrane localization imaging, tubule-specific conditional KO mouse models (UUO, folic acid), ZDHHC18 overexpression, Western blot for MEK/ERK/RREB1/SMAD signaling","journal":"The Journal of clinical investigation","confidence":"High","confidence_rationale":"Tier 2 / Strong — conditional KO in vivo models, palmitoylation assay, localization experiments, downstream signaling pathway defined with multiple orthogonal methods","pmids":["39913299"],"is_preprint":false},{"year":2019,"finding":"ZDHHC18 (and ZDHHC23) competitively interact with the BMI1 E3 ubiquitin ligase RNF144A, regulating BMI1 polyubiquitination and protein accumulation. This mechanism controls glioma stem cell plasticity and survival in different GBM subset niches.","method":"Co-immunoprecipitation, LC-MS/MS protein complex identification, Western blot, xenograft model, colony formation and flow cytometry assays","journal":"Journal of experimental & clinical cancer research : CR","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and MS complex identification, in vivo xenograft, single lab with multiple methods but mechanistic detail limited in abstract","pmids":["30658672"],"is_preprint":false},{"year":2024,"finding":"ZDHHC18 palmitoylates SARS-CoV-2 ORF3a at evolutionarily conserved Cys130/Cys133 residues, stabilizing ORF3a by masking a proteasomal degradation signal. This palmitoylation competitively inhibits TRIM16-dependent K27-linked polyubiquitination of ORF3a, preventing its degradation and enhancing viral replication and inflammatory responses. A designed ORF3a-mimicking palmitoylation-inhibitory peptide (OPIP) blocked this palmitoylation and reduced SARS-CoV-2 pathogenicity.","method":"Palmitoylation assay, site-directed mutagenesis (Cys130/133 mutants), ubiquitination assay, co-immunoprecipitation, OPIP peptide inhibition, viral replication and inflammation assays","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 2 / Strong — palmitoylation assay with site mutagenesis, ubiquitination assay, Co-IP of competing modifications, peptide inhibitor validation, multiple orthogonal methods","pmids":["42107085"],"is_preprint":false},{"year":2024,"finding":"ZDHHC18 palmitoylates MDH2, and this modification prevents MDH2 ubiquitination, increasing MDH2 protein stability and contributing to ripretinib resistance in gastrointestinal stromal tumors.","method":"Proteome-ubiquitinome mass spectrometry sequencing, palmitoylation assay, co-immunoprecipitation, Western blot","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — MS-based ubiquitinomics plus palmitoylation assay, single lab, corroborates earlier MDH2 palmitoylation finding by independent group","pmids":["38973363"],"is_preprint":false},{"year":2025,"finding":"ZDHHC18 facilitates cGAS localization to the Golgi apparatus via its intrinsically disordered region (IDR), which undergoes phase separation to recruit cGAS and dsDNA into biomolecular condensates, suppressing cGAS activity and downstream innate immune signaling.","method":"Subcellular localization imaging (ER, Golgi, endosome markers), phase separation assay, IDR domain analysis, dsDNA challenge experiments, downstream signaling readout","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — localization imaging and phase separation assay, multiple methods but preprint, single lab, not yet peer-reviewed","pmids":["bio_10.1101_2025.08.01.668185"],"is_preprint":true},{"year":2025,"finding":"Knockdown of ZDHHC18 in Burkitt lymphoma cell lines decreased cell viability, establishing a functional role for ZDHHC18 in supporting B-cell lymphoma growth.","method":"shRNA/siRNA knockdown of ZDHHC18 in four Burkitt lymphoma cell lines, cell viability assay","journal":"International journal of biological macromolecules","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — knockdown with viability phenotype across four cell lines, single lab, no direct substrate or pathway mechanism identified in this paper","pmids":["40645243"],"is_preprint":false},{"year":2025,"finding":"ZDHHC18 was identified as a palmitoyltransferase for LYPLA2 in ccRCC. ZDHHC18 knockdown inhibited ccRCC cell proliferation, migration, and invasion in vitro.","method":"Bioinformatics, molecular docking, Co-IP/palmitoylation assay (implied by 'laboratory assays'), knockdown in ccRCC cell lines (786-O and Caki-1)","journal":"BMC genomic data","confidence":"Low","confidence_rationale":"Tier 3 / Weak — substrate identification via bioinformatics and molecular docking with limited experimental validation described in the abstract, single lab","pmids":["42218414"],"is_preprint":false}],"current_model":"ZDHHC18 is a DHHC-family palmitoyltransferase that palmitoylates multiple substrates—including cGAS (at C474), MDH2 (at C138), HRAS, and SARS-CoV-2 ORF3a—to regulate innate immune signaling (suppressing cGAS-mediated DNA sensing and stabilizing viral proteins), mitochondrial metabolism, and pro-fibrotic RAS-MEK/ERK-SMAD signaling; it also interacts with the E3 ligase RNF144A to control BMI1 ubiquitination in glioma stem cells, and its palmitoylation of substrates can antagonize their ubiquitin-dependent degradation."},"narrative":{"mechanistic_narrative":"ZDHHC18 is a DHHC-family protein palmitoyltransferase that controls innate immune signaling, mitochondrial metabolism, and pro-fibrotic signal transduction by S-palmitoylating distinct substrate cysteines [PMID:35438208, PMID:35366151, PMID:39913299]. In the cGAS DNA-sensing pathway it palmitoylates cGAS at C474, weakening cGAS binding to double-stranded DNA and blocking its dimerization, so that ZDHHC18 acts as a negative regulator of antiviral signaling—an activity reflected in enhanced resistance to DNA virus infection in Zdhhc18-deficient mice [PMID:35438208]. In metabolism, it palmitoylates MDH2 at C138 to raise malate dehydrogenase activity and sustain mitochondrial respiration, a modification engaged under glutamine deprivation and required for ovarian cancer cell growth [PMID:35366151]. In epithelial cells it palmitoylates HRAS to drive its plasma-membrane translocation and activation, feeding MEK/ERK and RREB1/SMAD signaling that promotes partial EMT and renal fibrosis, with tubule-specific deletion attenuating fibrosis in vivo [PMID:39913299]. A recurring theme is that ZDHHC18-mediated palmitoylation antagonizes ubiquitin-dependent turnover of its targets: it stabilizes MDH2 by preventing its ubiquitination [PMID:38973363] and stabilizes SARS-CoV-2 ORF3a at Cys130/Cys133 by competitively blocking TRIM16-dependent K27-linked polyubiquitination, thereby enhancing viral replication [PMID:42107085]. Independently of its enzymatic activity, ZDHHC18 competes with the E3 ligase RNF144A to regulate BMI1 polyubiquitination and accumulation in glioma stem cells [PMID:30658672]. Loss-of-function reduces viability across Burkitt lymphoma and ccRCC tumor cells, indicating a broad pro-tumorigenic role [PMID:40645243].","teleology":[{"year":2022,"claim":"Established ZDHHC18 as a negative regulator of cytosolic DNA sensing by defining cGAS as a direct palmitoylation substrate, answering how an enzymatic modification restrains cGAS activity.","evidence":"Palmitoylation assays, C474 substrate mutagenesis, reciprocal Co-IP, immune reporter assays, and a Zdhhc18 knockout mouse with antiviral phenotype","pmids":["35438208"],"confidence":"High","gaps":["Does not define how ZDHHC18 itself is regulated to time cGAS suppression","Structural basis of how C474 palmitoylation blocks DNA binding/dimerization not resolved"]},{"year":2022,"claim":"Extended ZDHHC18 function to metabolism by showing it palmitoylates MDH2 at C138 to boost enzyme activity and respiration, linking the enzyme to nutrient-responsive cancer growth.","evidence":"Palmitoylation assay, C138S rescue experiments, siRNA knockdown, and in vitro/in vivo respiration and proliferation assays in ovarian cancer","pmids":["35366151"],"confidence":"High","gaps":["Mechanism by which glutamine deprivation enhances the ZDHHC18-MDH2 interaction unknown","Whether MDH2 palmitoylation is reversed by a specific thioesterase not addressed"]},{"year":2019,"claim":"Revealed a non-catalytic role: ZDHHC18 (with ZDHHC23) competes with the E3 ligase RNF144A to control BMI1 ubiquitination, governing glioma stem cell plasticity.","evidence":"Reciprocal Co-IP, LC-MS/MS complex identification, xenograft, colony formation and flow cytometry","pmids":["30658672"],"confidence":"Medium","gaps":["Whether palmitoyltransferase activity contributes to RNF144A competition not determined","BMI1 itself not shown to be a palmitoylation substrate"]},{"year":2024,"claim":"Showed palmitoylation can directly antagonize ubiquitin-dependent degradation, with ZDHHC18 stabilizing SARS-CoV-2 ORF3a by masking a degron and blocking TRIM16-dependent ubiquitination.","evidence":"Palmitoylation and ubiquitination assays, Cys130/133 mutagenesis, Co-IP of competing modifications, OPIP peptide inhibition, viral replication assays","pmids":["42107085"],"confidence":"High","gaps":["Whether host substrates are similarly protected from degradation via the same mechanism not generalized here","In vivo therapeutic window of OPIP not defined"]},{"year":2024,"claim":"Connected ZDHHC18-MDH2 palmitoylation to protein stability and drug resistance, showing the modification prevents MDH2 ubiquitination in GIST.","evidence":"Proteome-ubiquitinome mass spectrometry, palmitoylation assay, Co-IP, Western blot","pmids":["38973363"],"confidence":"Medium","gaps":["Ubiquitin ligase acting on MDH2 not identified","Whether the stability effect is separable from the earlier activity-enhancing effect unclear"]},{"year":2025,"claim":"Defined a pro-fibrotic signaling axis in which ZDHHC18 palmitoylates HRAS to enable membrane localization and MEK/ERK-RREB1/SMAD-driven EMT.","evidence":"Palmitoylation and membrane-localization assays, tubule-specific conditional KO (UUO, folic acid), signaling Western blots","pmids":["39913299"],"confidence":"High","gaps":["Whether ZDHHC18 selectively targets HRAS over other RAS isoforms not resolved","Upstream signals controlling ZDHHC18 in tubular epithelium unknown"]},{"year":2025,"claim":"Proposed a phase-separation mechanism whereby ZDHHC18's intrinsically disordered region recruits cGAS and dsDNA to Golgi-associated condensates to suppress immune signaling, complementing the earlier palmitoylation model.","evidence":"Subcellular localization imaging, phase-separation and IDR analysis, dsDNA challenge (preprint)","pmids":["bio_10.1101_2025.08.01.668185"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Relationship between condensate formation and C474 palmitoylation of cGAS not integrated"]},{"year":2025,"claim":"Demonstrated a broad tumor-supportive dependency on ZDHHC18 in B-cell lymphoma without defining the responsible substrate.","evidence":"shRNA/siRNA knockdown across four Burkitt lymphoma cell lines with viability readout","pmids":["40645243"],"confidence":"Medium","gaps":["No substrate or pathway mechanism identified in lymphoma","No in vivo validation"]},{"year":2025,"claim":"Nominated LYPLA2 as an additional ZDHHC18 substrate in ccRCC linked to proliferation and invasion.","evidence":"Bioinformatics, molecular docking, implied palmitoylation/Co-IP assays, knockdown in 786-O and Caki-1 cells","pmids":["42218414"],"confidence":"Low","gaps":["Substrate assignment rests largely on bioinformatics/docking with limited experimental validation","Palmitoylation site on LYPLA2 not defined"]},{"year":null,"claim":"How ZDHHC18 substrate selectivity is achieved and how its own activity, localization, and IDR-driven condensation are regulated across immune, metabolic, and fibrotic contexts remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of the enzyme or its substrate-recognition determinants","Regulators and depalmitoylases counteracting ZDHHC18 not identified","Mechanism coupling palmitoylation to blockade of ubiquitination not generalized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,4]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,2,4]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,5]}],"complexes":[],"partners":["CGAS","MDH2","HRAS","RNF144A","LYPLA2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NUE0","full_name":"Palmitoyltransferase ZDHHC18","aliases":["DHHC domain-containing cysteine-rich protein 18","DHHC-18","Zinc finger DHHC domain-containing protein 18"],"length_aa":388,"mass_kda":42.0,"function":"Palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates, such as CGAS, HRAS and LCK (PubMed:23034182, PubMed:27481942, PubMed:35438208). Acts as a negative regulator of the cGAS-STING pathway be mediating palmitoylation and inactivation of CGAS (PubMed:35438208). May also have a palmitoyltransferase activity toward the beta-2 adrenergic receptor/ADRB2 and therefore regulate G protein-coupled receptor signaling (PubMed:27481942)","subcellular_location":"Golgi apparatus membrane","url":"https://www.uniprot.org/uniprotkb/Q9NUE0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZDHHC18","classification":"Not Classified","n_dependent_lines":19,"n_total_lines":1208,"dependency_fraction":0.015728476821192054},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZDHHC18","total_profiled":1310},"omim":[{"mim_id":"620963","title":"ZDHHC PALMITOYLTRANSFERASE 18; ZDHHC18","url":"https://www.omim.org/entry/620963"},{"mim_id":"613973","title":"CYCLIC GMP-AMP SYNTHASE; CGAS","url":"https://www.omim.org/entry/613973"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"bone marrow","ntpm":107.7}],"url":"https://www.proteinatlas.org/search/ZDHHC18"},"hgnc":{"alias_symbol":["DKFZp667O2416"],"prev_symbol":[]},"alphafold":{"accession":"Q9NUE0","domains":[{"cath_id":"-","chopping":"73-151_235-345","consensus_level":"high","plddt":93.9089,"start":73,"end":345}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NUE0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NUE0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NUE0-F1-predicted_aligned_error_v6.png","plddt_mean":80.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZDHHC18","jax_strain_url":"https://www.jax.org/strain/search?query=ZDHHC18"},"sequence":{"accession":"Q9NUE0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NUE0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NUE0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NUE0"}},"corpus_meta":[{"pmid":"35438208","id":"PMC_35438208","title":"ZDHHC18 negatively regulates cGAS-mediated innate immunity through palmitoylation.","date":"2022","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/35438208","citation_count":86,"is_preprint":false},{"pmid":"35366151","id":"PMC_35366151","title":"Palmitoylation of MDH2 by ZDHHC18 activates mitochondrial respiration and accelerates ovarian cancer growth.","date":"2022","source":"Science China. Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35366151","citation_count":72,"is_preprint":false},{"pmid":"30658672","id":"PMC_30658672","title":"DHHC protein family targets different subsets of glioma stem cells in specific niches.","date":"2019","source":"Journal of experimental & clinical cancer research : CR","url":"https://pubmed.ncbi.nlm.nih.gov/30658672","citation_count":51,"is_preprint":false},{"pmid":"29024729","id":"PMC_29024729","title":"Integrating genome-wide association study and expression quantitative trait locus study identifies multiple genes and gene sets associated with schizophrenia.","date":"2017","source":"Progress in neuro-psychopharmacology & biological psychiatry","url":"https://pubmed.ncbi.nlm.nih.gov/29024729","citation_count":25,"is_preprint":false},{"pmid":"38973363","id":"PMC_38973363","title":"USP5 Promotes Ripretinib Resistance in Gastrointestinal Stromal Tumors by MDH2 Deubiquition.","date":"2024","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/38973363","citation_count":18,"is_preprint":false},{"pmid":"39913299","id":"PMC_39913299","title":"ZDHHC18 promotes renal fibrosis development by regulating HRAS palmitoylation.","date":"2025","source":"The Journal of clinical investigation","url":"https://pubmed.ncbi.nlm.nih.gov/39913299","citation_count":14,"is_preprint":false},{"pmid":"38472042","id":"PMC_38472042","title":"When pyro(ptosis) meets palm(itoylation).","date":"2024","source":"Cytokine & growth factor reviews","url":"https://pubmed.ncbi.nlm.nih.gov/38472042","citation_count":14,"is_preprint":false},{"pmid":"36386830","id":"PMC_36386830","title":"Novel peripheral blood diagnostic biomarkers screened by machine learning algorithms in ankylosing spondylitis.","date":"2022","source":"Frontiers in genetics","url":"https://pubmed.ncbi.nlm.nih.gov/36386830","citation_count":8,"is_preprint":false},{"pmid":"40551107","id":"PMC_40551107","title":"Palmitoylation regulators drive the progression of clear cell renal cell carcinoma through Inhibition of cuproptosis: insights into the role of ZDHHC18.","date":"2025","source":"Cancer cell international","url":"https://pubmed.ncbi.nlm.nih.gov/40551107","citation_count":4,"is_preprint":false},{"pmid":"40867242","id":"PMC_40867242","title":"Explainable Machine Learning Models for Glioma Subtype Classification and Survival Prediction.","date":"2025","source":"Cancers","url":"https://pubmed.ncbi.nlm.nih.gov/40867242","citation_count":4,"is_preprint":false},{"pmid":"35941161","id":"PMC_35941161","title":"Analysis of genomic alterations in cancer associated human pancreatic stellate cells.","date":"2022","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/35941161","citation_count":4,"is_preprint":false},{"pmid":"40645243","id":"PMC_40645243","title":"Palmitoylation by ZDHHC family members regulate B-cell lymphoma growth.","date":"2025","source":"International journal of biological macromolecules","url":"https://pubmed.ncbi.nlm.nih.gov/40645243","citation_count":2,"is_preprint":false},{"pmid":"41790354","id":"PMC_41790354","title":"Multi-omics analysis suggests ZDHHC18 as a potential risk factor for clear cell renal cell carcinoma linked to myeloid DC morphology.","date":"2026","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41790354","citation_count":0,"is_preprint":false},{"pmid":"42107085","id":"PMC_42107085","title":"ZDHHC18-Mediated Palmitoylation of ORF3a Promotes SARS-CoV-2 Pathogenesis by Antagonizing TRIM16-Mediated Ubiquitination and Proteasomal Degradation.","date":"2026","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/42107085","citation_count":0,"is_preprint":false},{"pmid":"42023227","id":"PMC_42023227","title":"Acylation modification mediated post-translational modifications learning signature reveals ZDHHC18 promotes progression of lung adenocarcinoma by attenuating immunocyte activation.","date":"2026","source":"Frontiers in immunology","url":"https://pubmed.ncbi.nlm.nih.gov/42023227","citation_count":0,"is_preprint":false},{"pmid":"41357761","id":"PMC_41357761","title":"Integrated Genomic and Functional Characterization of Palmitoylation in Clear Cell Renal Cell Carcinoma.","date":"2025","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/41357761","citation_count":0,"is_preprint":false},{"pmid":"41099891","id":"PMC_41099891","title":"An Investigation of the Causal Link Between Palmoylation Genes and Epilepsy Utilising Multi-omics Mendelian Randomisation Analysis and Validation Through Single-Cell Evidence.","date":"2025","source":"Journal of molecular neuroscience : MN","url":"https://pubmed.ncbi.nlm.nih.gov/41099891","citation_count":0,"is_preprint":false},{"pmid":"42218414","id":"PMC_42218414","title":"Exploring the functional role of palmitoylation genes in clear cell renal cell carcinoma and their impact on tumor 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This modification reduces cGAS interaction with double-stranded DNA and inhibits cGAS dimerization, thereby restricting cGAS enzymatic activity. ZDHHC18 negatively regulates cGAS-mediated innate immune signaling; Zdhhc18-deficient mice show enhanced resistance to DNA virus infection.\",\n      \"method\": \"Biochemical palmitoylation assays, site-directed mutagenesis (C474 cGAS mutant), co-immunoprecipitation, cell-based innate immune reporter assays, Zdhhc18 knockout mouse model\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of substrate site, in vivo KO model with defined phenotype, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"35438208\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"ZDHHC18 palmitoylates MDH2 (malate dehydrogenase 2) at cysteine C138, increasing MDH2 enzymatic activity and sustaining mitochondrial respiration. Glutamine deprivation enhances the ZDHHC18–MDH2 interaction. Re-expression of palmitoylation-deficient MDH2 (C138S) fails to restore mitochondrial respiration or ovarian cancer cell growth, confirming the functional requirement of this modification.\",\n      \"method\": \"Palmitoylation assay, co-immunoprecipitation, site-directed mutagenesis (C138S MDH2 mutant), siRNA knockdown, in vitro and in vivo proliferation/respiration assays\",\n      \"journal\": \"Science China. Life sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, palmitoylation assay, mutagenesis of substrate site, in vitro and in vivo rescue experiments with multiple orthogonal methods\",\n      \"pmids\": [\"35366151\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC18 catalyzes palmitoylation of HRAS, which is required for HRAS translocation to the plasma membrane and its subsequent activation. HRAS palmitoylation drives downstream MEK/ERK phosphorylation, activates RREB1, and enhances SMAD binding to Snai1 cis-regulatory regions, promoting partial epithelial-mesenchymal transition (EMT) and profibrotic cytokine production in tubular epithelial cells. Tubule-specific Zdhhc18 deletion attenuates renal fibrosis in UUO and folic acid mouse models.\",\n      \"method\": \"Palmitoylation assay, subcellular fractionation/membrane localization imaging, tubule-specific conditional KO mouse models (UUO, folic acid), ZDHHC18 overexpression, Western blot for MEK/ERK/RREB1/SMAD signaling\",\n      \"journal\": \"The Journal of clinical investigation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — conditional KO in vivo models, palmitoylation assay, localization experiments, downstream signaling pathway defined with multiple orthogonal methods\",\n      \"pmids\": [\"39913299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ZDHHC18 (and ZDHHC23) competitively interact with the BMI1 E3 ubiquitin ligase RNF144A, regulating BMI1 polyubiquitination and protein accumulation. This mechanism controls glioma stem cell plasticity and survival in different GBM subset niches.\",\n      \"method\": \"Co-immunoprecipitation, LC-MS/MS protein complex identification, Western blot, xenograft model, colony formation and flow cytometry assays\",\n      \"journal\": \"Journal of experimental & clinical cancer research : CR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and MS complex identification, in vivo xenograft, single lab with multiple methods but mechanistic detail limited in abstract\",\n      \"pmids\": [\"30658672\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZDHHC18 palmitoylates SARS-CoV-2 ORF3a at evolutionarily conserved Cys130/Cys133 residues, stabilizing ORF3a by masking a proteasomal degradation signal. This palmitoylation competitively inhibits TRIM16-dependent K27-linked polyubiquitination of ORF3a, preventing its degradation and enhancing viral replication and inflammatory responses. A designed ORF3a-mimicking palmitoylation-inhibitory peptide (OPIP) blocked this palmitoylation and reduced SARS-CoV-2 pathogenicity.\",\n      \"method\": \"Palmitoylation assay, site-directed mutagenesis (Cys130/133 mutants), ubiquitination assay, co-immunoprecipitation, OPIP peptide inhibition, viral replication and inflammation assays\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — palmitoylation assay with site mutagenesis, ubiquitination assay, Co-IP of competing modifications, peptide inhibitor validation, multiple orthogonal methods\",\n      \"pmids\": [\"42107085\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZDHHC18 palmitoylates MDH2, and this modification prevents MDH2 ubiquitination, increasing MDH2 protein stability and contributing to ripretinib resistance in gastrointestinal stromal tumors.\",\n      \"method\": \"Proteome-ubiquitinome mass spectrometry sequencing, palmitoylation assay, co-immunoprecipitation, Western blot\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — MS-based ubiquitinomics plus palmitoylation assay, single lab, corroborates earlier MDH2 palmitoylation finding by independent group\",\n      \"pmids\": [\"38973363\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC18 facilitates cGAS localization to the Golgi apparatus via its intrinsically disordered region (IDR), which undergoes phase separation to recruit cGAS and dsDNA into biomolecular condensates, suppressing cGAS activity and downstream innate immune signaling.\",\n      \"method\": \"Subcellular localization imaging (ER, Golgi, endosome markers), phase separation assay, IDR domain analysis, dsDNA challenge experiments, downstream signaling readout\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — localization imaging and phase separation assay, multiple methods but preprint, single lab, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.08.01.668185\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Knockdown of ZDHHC18 in Burkitt lymphoma cell lines decreased cell viability, establishing a functional role for ZDHHC18 in supporting B-cell lymphoma growth.\",\n      \"method\": \"shRNA/siRNA knockdown of ZDHHC18 in four Burkitt lymphoma cell lines, cell viability assay\",\n      \"journal\": \"International journal of biological macromolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — knockdown with viability phenotype across four cell lines, single lab, no direct substrate or pathway mechanism identified in this paper\",\n      \"pmids\": [\"40645243\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC18 was identified as a palmitoyltransferase for LYPLA2 in ccRCC. ZDHHC18 knockdown inhibited ccRCC cell proliferation, migration, and invasion in vitro.\",\n      \"method\": \"Bioinformatics, molecular docking, Co-IP/palmitoylation assay (implied by 'laboratory assays'), knockdown in ccRCC cell lines (786-O and Caki-1)\",\n      \"journal\": \"BMC genomic data\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — substrate identification via bioinformatics and molecular docking with limited experimental validation described in the abstract, single lab\",\n      \"pmids\": [\"42218414\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZDHHC18 is a DHHC-family palmitoyltransferase that palmitoylates multiple substrates—including cGAS (at C474), MDH2 (at C138), HRAS, and SARS-CoV-2 ORF3a—to regulate innate immune signaling (suppressing cGAS-mediated DNA sensing and stabilizing viral proteins), mitochondrial metabolism, and pro-fibrotic RAS-MEK/ERK-SMAD signaling; it also interacts with the E3 ligase RNF144A to control BMI1 ubiquitination in glioma stem cells, and its palmitoylation of substrates can antagonize their ubiquitin-dependent degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ZDHHC18 is a DHHC-family protein palmitoyltransferase that controls innate immune signaling, mitochondrial metabolism, and pro-fibrotic signal transduction by S-palmitoylating distinct substrate cysteines [#0, #1, #2]. In the cGAS DNA-sensing pathway it palmitoylates cGAS at C474, weakening cGAS binding to double-stranded DNA and blocking its dimerization, so that ZDHHC18 acts as a negative regulator of antiviral signaling—an activity reflected in enhanced resistance to DNA virus infection in Zdhhc18-deficient mice [#0]. In metabolism, it palmitoylates MDH2 at C138 to raise malate dehydrogenase activity and sustain mitochondrial respiration, a modification engaged under glutamine deprivation and required for ovarian cancer cell growth [#1]. In epithelial cells it palmitoylates HRAS to drive its plasma-membrane translocation and activation, feeding MEK/ERK and RREB1/SMAD signaling that promotes partial EMT and renal fibrosis, with tubule-specific deletion attenuating fibrosis in vivo [#2]. A recurring theme is that ZDHHC18-mediated palmitoylation antagonizes ubiquitin-dependent turnover of its targets: it stabilizes MDH2 by preventing its ubiquitination [#5] and stabilizes SARS-CoV-2 ORF3a at Cys130/Cys133 by competitively blocking TRIM16-dependent K27-linked polyubiquitination, thereby enhancing viral replication [#4]. Independently of its enzymatic activity, ZDHHC18 competes with the E3 ligase RNF144A to regulate BMI1 polyubiquitination and accumulation in glioma stem cells [#3]. Loss-of-function reduces viability across Burkitt lymphoma and ccRCC tumor cells, indicating a broad pro-tumorigenic role [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Established ZDHHC18 as a negative regulator of cytosolic DNA sensing by defining cGAS as a direct palmitoylation substrate, answering how an enzymatic modification restrains cGAS activity.\",\n      \"evidence\": \"Palmitoylation assays, C474 substrate mutagenesis, reciprocal Co-IP, immune reporter assays, and a Zdhhc18 knockout mouse with antiviral phenotype\",\n      \"pmids\": [\"35438208\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define how ZDHHC18 itself is regulated to time cGAS suppression\", \"Structural basis of how C474 palmitoylation blocks DNA binding/dimerization not resolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Extended ZDHHC18 function to metabolism by showing it palmitoylates MDH2 at C138 to boost enzyme activity and respiration, linking the enzyme to nutrient-responsive cancer growth.\",\n      \"evidence\": \"Palmitoylation assay, C138S rescue experiments, siRNA knockdown, and in vitro/in vivo respiration and proliferation assays in ovarian cancer\",\n      \"pmids\": [\"35366151\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which glutamine deprivation enhances the ZDHHC18-MDH2 interaction unknown\", \"Whether MDH2 palmitoylation is reversed by a specific thioesterase not addressed\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed a non-catalytic role: ZDHHC18 (with ZDHHC23) competes with the E3 ligase RNF144A to control BMI1 ubiquitination, governing glioma stem cell plasticity.\",\n      \"evidence\": \"Reciprocal Co-IP, LC-MS/MS complex identification, xenograft, colony formation and flow cytometry\",\n      \"pmids\": [\"30658672\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether palmitoyltransferase activity contributes to RNF144A competition not determined\", \"BMI1 itself not shown to be a palmitoylation substrate\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Showed palmitoylation can directly antagonize ubiquitin-dependent degradation, with ZDHHC18 stabilizing SARS-CoV-2 ORF3a by masking a degron and blocking TRIM16-dependent ubiquitination.\",\n      \"evidence\": \"Palmitoylation and ubiquitination assays, Cys130/133 mutagenesis, Co-IP of competing modifications, OPIP peptide inhibition, viral replication assays\",\n      \"pmids\": [\"42107085\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether host substrates are similarly protected from degradation via the same mechanism not generalized here\", \"In vivo therapeutic window of OPIP not defined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected ZDHHC18-MDH2 palmitoylation to protein stability and drug resistance, showing the modification prevents MDH2 ubiquitination in GIST.\",\n      \"evidence\": \"Proteome-ubiquitinome mass spectrometry, palmitoylation assay, Co-IP, Western blot\",\n      \"pmids\": [\"38973363\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Ubiquitin ligase acting on MDH2 not identified\", \"Whether the stability effect is separable from the earlier activity-enhancing effect unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Defined a pro-fibrotic signaling axis in which ZDHHC18 palmitoylates HRAS to enable membrane localization and MEK/ERK-RREB1/SMAD-driven EMT.\",\n      \"evidence\": \"Palmitoylation and membrane-localization assays, tubule-specific conditional KO (UUO, folic acid), signaling Western blots\",\n      \"pmids\": [\"39913299\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether ZDHHC18 selectively targets HRAS over other RAS isoforms not resolved\", \"Upstream signals controlling ZDHHC18 in tubular epithelium unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Proposed a phase-separation mechanism whereby ZDHHC18's intrinsically disordered region recruits cGAS and dsDNA to Golgi-associated condensates to suppress immune signaling, complementing the earlier palmitoylation model.\",\n      \"evidence\": \"Subcellular localization imaging, phase-separation and IDR analysis, dsDNA challenge (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.08.01.668185\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Relationship between condensate formation and C474 palmitoylation of cGAS not integrated\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Demonstrated a broad tumor-supportive dependency on ZDHHC18 in B-cell lymphoma without defining the responsible substrate.\",\n      \"evidence\": \"shRNA/siRNA knockdown across four Burkitt lymphoma cell lines with viability readout\",\n      \"pmids\": [\"40645243\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No substrate or pathway mechanism identified in lymphoma\", \"No in vivo validation\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Nominated LYPLA2 as an additional ZDHHC18 substrate in ccRCC linked to proliferation and invasion.\",\n      \"evidence\": \"Bioinformatics, molecular docking, implied palmitoylation/Co-IP assays, knockdown in 786-O and Caki-1 cells\",\n      \"pmids\": [\"42218414\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Substrate assignment rests largely on bioinformatics/docking with limited experimental validation\", \"Palmitoylation site on LYPLA2 not defined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ZDHHC18 substrate selectivity is achieved and how its own activity, localization, and IDR-driven condensation are regulated across immune, metabolic, and fibrotic contexts remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of the enzyme or its substrate-recognition determinants\", \"Regulators and depalmitoylases counteracting ZDHHC18 not identified\", \"Mechanism coupling palmitoylation to blockade of ubiquitination not generalized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 5]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"cGAS\", \"MDH2\", \"HRAS\", \"RNF144A\", \"LYPLA2\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}