{"gene":"ZDHHC9","run_date":"2026-04-28T23:00:24","timeline":{"discoveries":[{"year":2005,"finding":"ZDHHC9 (DHHC9) forms a protein complex with GCP16 and together they constitute a human palmitoyltransferase with specificity for H-Ras and N-Ras; DHHC9 requires GCP16 for enzymatic activity and protein stability, and the complex co-distributes in the Golgi apparatus consistent with the site of Ras palmitoylation in vivo.","method":"Purified DHHC9·GCP16 complex in vitro palmitoylation assay, co-immunoprecipitation, subcellular fractionation/co-distribution, functional comparison to yeast Erf2·Erf4 ortholog","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro palmitoylation with purified complex, substrate specificity demonstrated, localization confirmed; single paper but multiple orthogonal methods","pmids":["16000296"],"is_preprint":false},{"year":2014,"finding":"Two naturally occurring XLID variants of zDHHC9 (R148W and P150S) impair the autopalmitoylation step of the palmitoylation reaction, lowering the steady-state amount of the palmitoyl-zDHHC9 enzyme intermediate, revealing a two-step catalytic mechanism involving enzyme autopalmitoylation followed by transfer to substrate.","method":"In vitro autopalmitoylation assay with purified wild-type and disease mutant zDHHC9 proteins; mutagenesis of naturally occurring variants","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — in vitro biochemical assay with active-site mechanistic dissection and disease mutant validation","pmids":["24811172"],"is_preprint":false},{"year":2021,"finding":"ZDHHC9 palmitoylates GLUT1 at Cys207, which is required for GLUT1 plasma membrane localization; ZDHHC9 knockout or Cys207 mutation abrogates GLUT1 palmitoylation and PM distribution, impairing glycolysis, cell proliferation, and glioblastoma tumorigenesis.","method":"ZDHHC9 knockout, Cys207 point mutation, acyl-biotin exchange palmitoylation assay, subcellular fractionation, glycolysis assay, in vivo xenograft","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (KO, point mutation, ABE assay, localization, functional readout) in single study with strong controls","pmids":["34620861"],"is_preprint":false},{"year":2023,"finding":"ZDHHC9 palmitoylates β-catenin, promoting its ubiquitination and proteasomal degradation; acyl protein thioesterase 1 (APT1) depalmitoylates β-catenin, increasing its abundance and nuclear translocation to drive renal fibrosis.","method":"ZDHHC9 ablation and overexpression in tubular cells (in vivo mouse models), co-immunoprecipitation, palmitoylation assay, ubiquitination assay, nuclear fractionation, adeno-DHHC9 transfection","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 — reciprocal genetic manipulation in vivo and in vitro with multiple orthogonal methods establishing writer/eraser identity and downstream consequences","pmids":["37865665"],"is_preprint":false},{"year":2019,"finding":"ZDHHC9 promotes dendrite outgrowth through palmitoylation of the GTPase Ras, and promotes inhibitory synapse formation through palmitoylation of the GTPase TC10; loss of Zdhhc9 in hippocampal neurons leads to shorter dendritic arbors and fewer inhibitory synapses, altering excitatory-to-inhibitory balance; Zdhhc9 knockout mice show seizure-like activity.","method":"Hippocampal neuron cultures from Zdhhc9 knockout mice, dendritic morphology quantification, inhibitory synapse counting, electrophysiology (mEPSC/mIPSC), palmitoylation assays for Ras and TC10","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 2 — clean KO with defined cellular phenotypes and substrate identification via palmitoylation assay; multiple orthogonal readouts","pmids":["31747610"],"is_preprint":false},{"year":2013,"finding":"miR-134 directly interacts with DHHC9 mRNA in cortical somatostatin interneurons; bicuculline-induced GABAA receptor antagonism decreases DHHC9 expression in a miR-134-dependent manner, reducing membrane localization of an H-Ras reporter, placing DHHC9 downstream of miR-134 in activity-dependent H-Ras membrane trafficking.","method":"Ratiometric microRNA sensor, microRNA-mRNA complex trapping assay, pharmacological GABAA blockade, H-Ras reporter membrane localization assay, cell-type-specific imaging","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 — direct mRNA targeting confirmed, functional consequence on H-Ras localization shown; single lab study","pmids":["24127608"],"is_preprint":false},{"year":2023,"finding":"GCP16 stabilizes DHHC9 by preventing its aggregation through direct complex formation; only properly folded DHHC9-GCP16 complex is enzymatically active in vitro; XLID-associated mutations in ZDHHC9 reduce protein stability and impair DHHC9-GCP16 complex formation; a conserved C-terminal cysteine motif (CCM) in DHHC9 is required for GCP16 binding and enzymatic activity; DHHC14 and DHHC18 also require GCP16 for activity.","method":"Size-exclusion chromatography, in vitro palmitoyl acyltransferase assays, analysis of XLID mutants, domain mutagenesis (CCM deletion), co-expression stability assays","journal":"Frontiers in physiology","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro with purified complex, structure-function mutagenesis, and disease variant analysis; multiple orthogonal methods","pmids":["37035671"],"is_preprint":false},{"year":2023,"finding":"zDHHC9 palmitoylates Rab3gap1 in cardiomyocytes, resulting in spatial segregation of Rab3gap1 from Rab3a, elevation of Rab3a-GTP levels, formation of Rab3a-positive peripheral vesicles, and impairment of exocytosis that limits atrial natriuretic peptide release.","method":"Palmitoylation assay (acyl-RAC), subcellular localization imaging, Rab3a-GTP pulldown, ANP secretion assay in cardiomyocytes","journal":"JACC. Basic to translational science","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identification with functional consequence on exocytosis demonstrated; single lab study with multiple readouts","pmids":["37325411"],"is_preprint":false},{"year":2024,"finding":"ZDHHC9 binds to and palmitoylates Bip/GRP78 at Cys420, enhancing Bip protein stability and maintaining its localization within the endoplasmic reticulum, thereby inhibiting the unfolded protein response; SP1 transcriptionally activates ZDHHC9 expression.","method":"Co-immunoprecipitation, acyl-biotin exchange palmitoylation assay, Cys420 point mutation, ER localization by immunofluorescence, UPR pathway assays, SP1 ChIP/luciferase reporter","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identification with site-specific mutation and functional consequence on UPR; single lab study","pmids":["39002690"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 palmitoylates STRN4 at Cys701, reducing YAP phosphorylation and promoting YAP nuclear translocation and activation of Hippo pathway targets (CCN1, CCN2, ANKRD1), thereby driving cancer cell migration and metastasis.","method":"Proteomic analysis, co-immunoprecipitation, site-directed mutagenesis of Cys701, YAP phosphorylation/localization assays, in vitro migration and in vivo metastasis assays","journal":"Journal of cellular and molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identification with site-specific mutation and downstream pathway validation; single lab study","pmids":["40903842"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 palmitoylates CD38 at Cys16, maintaining CD38 protein stability in tumor cells; APT1 acts as the opposing depalmitoylating enzyme; a competitive peptide blocking CD38 palmitoylation decreases CD38 expression and suppresses tumor progression in vivo.","method":"Acyl-biotin exchange assay, site-directed mutagenesis (Cys16), co-immunoprecipitation, competitive peptide design, in vivo xenograft","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutation and in vivo functional validation; single lab study","pmids":["40121269"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 localizes to Golgi outposts in oligodendrocyte processes (whereas XLID mutant forms are restricted to cell bodies), palmitoylates Myelin Basic Protein (MBP) in heterologous cells, and MBP palmitoylation is impaired in the Zdhhc9 knockout brain; Zdhhc9 knockout mice display morphological and structural myelin abnormalities without grossly disrupted OL development.","method":"Live imaging of ZDHHC9 localization in OL processes, palmitoylation assay for MBP in heterologous cells, Zdhhc9 knockout mouse analysis with OL fate tracing and sparse cell labeling, electron microscopy of myelin structure","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 — localization with functional consequence, substrate identification with palmitoylation assay, and in vivo KO phenotype; single lab but multiple methods","pmids":["41031565"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 palmitoylates LAMTOR1 at Cys3/4, enhancing LAMTOR1-mediated recruitment of mTORC1 to the lysosomal surface and activating the mTOR signaling cascade in renal cell carcinoma.","method":"Co-immunoprecipitation, acyl-biotin exchange palmitoylation assay, Cys3/4 site mutagenesis, mTOR pathway activation assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutation and downstream mTOR pathway validation; single lab study","pmids":["41856969"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 interacts with hnRNPU and palmitoylates it at Cys497 and Cys607, increasing hnRNPU protein stability; stabilized hnRNPU elevates SAT1 transcription to enhance spermine catabolism in prostate cancer.","method":"Co-immunoprecipitation, mass spectrometry, acyl-biotin exchange assay, site-directed mutagenesis, RNA sequencing, SAT1 expression assays","journal":"Journal of translational medicine","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identification with site-specific mutation and transcriptional downstream validation; single lab study","pmids":["41419885"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 palmitoylates CD36 at cysteine residues, promoting CD36 plasma membrane localization and formation of a CD36/Fyn/Lyn complex that activates JNK1 and suppresses ERK1/2 signaling; DHHC9 knockdown or CD36 cysteine mutation disrupts this complex and reactivates ERK1/2 to rescue mammary epithelial cell proliferation impaired by high-fat diet.","method":"Acyl-biotin exchange assay, co-immunoprecipitation, Cys point mutation, DHHC9 knockdown, JNK/ERK pathway assays, in vivo mammary gland whole-mount staining","journal":"Cellular & molecular biology letters","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutation and signaling pathway dissection; in vivo and in vitro validation in single lab","pmids":["41087856"],"is_preprint":false},{"year":2026,"finding":"ZDHHC9 palmitoylates PCBP1 at Cys109, inhibiting PCBP1 ubiquitination and thus stabilizing PCBP1; stabilized PCBP1 promotes SLC7A11 mRNA stability, thereby suppressing ferroptosis and promoting gastric cancer liver metastasis.","method":"Immunoprecipitation, LC-MS/MS, acyl-biotin exchange assay, Cys109 mutagenesis, ubiquitination assay, SLC7A11 mRNA stability assay, in vivo metastasis models","journal":"NPJ precision oncology","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutation, ubiquitination and mRNA stability assays, in vivo validation; single lab study","pmids":["41535416"],"is_preprint":false},{"year":2026,"finding":"ZDHHC9 palmitoylates STAT1 at Cys577 via JAK1-STAT1 signaling; palmitoylation at Cys577 is converted to phosphorylation at Tyr701 (pSTAT1) to drive nuclear STAT1 transcriptional activity and gastric cancer progression.","method":"Acyl-biotin exchange assay, co-immunoprecipitation, Cys577 and Tyr701 mutagenesis, immunofluorescence/confocal imaging, ZDHHC9 silencing with downstream gene expression analysis","journal":"Journal of gastroenterology","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutagenesis and PTM crosstalk demonstrated; single lab study","pmids":["41711908"],"is_preprint":false},{"year":2026,"finding":"ZDHHC9 palmitoylates KLF5 at Cys438, enhancing ADCY4 activity and increasing intracellular cAMP, thereby activating the cAMP/PKA/CREB signaling pathway to promote colorectal cancer cell proliferation and migration.","method":"Acyl-biotin exchange assay, Cys438 point mutation, RNA sequencing, ADCY4 activity assay, cAMP measurement, PKA/CREB pathway analysis, ZDHHC9 knockdown in vivo and in vitro","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 — substrate identified with site-specific mutation and downstream signaling pathway validated; single lab study","pmids":["41882103"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 interacts with KRAS (confirmed by co-immunoprecipitation and molecular docking), and ZDHHC9 promotes KRAS-mediated activation of the RAS/MAPK pathway (Raf1/ERK1/2 signaling) to drive osteosarcoma proliferation, migration, and invasion.","method":"Co-immunoprecipitation, molecular docking, proteomic sequencing, ZDHHC9 knockdown/overexpression, KRAS overexpression rescue, Western blot for ERK pathway, xenograft model","journal":"Scientific reports","confidence":"Low","confidence_rationale":"Tier 3 — Co-IP interaction shown but direct palmitoylation of KRAS not biochemically demonstrated in this study; single lab","pmids":["41087383"],"is_preprint":false},{"year":2025,"finding":"ZDHHC9 palmitoylates PKG1, and ZDHHC9-PKG1 interaction (confirmed by co-immunoprecipitation and co-localization) regulates mitochondria-associated endoplasmic reticulum membranes (MAMs) structure and function in osteoblasts, affecting osteogenesis under high-glucose/T2DM conditions.","method":"Co-immunoprecipitation, fluorescence co-localization, Zdhhc9 and Prkg1 knockdown, MAM distance measurement, MAM-related protein expression analysis","journal":"Journal of dental research","confidence":"Low","confidence_rationale":"Tier 3 — interaction shown by Co-IP and co-localization but direct palmitoylation of PKG1 not formally demonstrated with palmitoylation assay; single lab","pmids":["40102769"],"is_preprint":false}],"current_model":"ZDHHC9 is a Golgi-localized integral membrane palmitoyltransferase that requires the accessory protein GCP16 for proper folding, stability, and enzymatic activity; it catalyzes S-palmitoylation of diverse substrates—including H-Ras, N-Ras, GLUT1, TC10, β-catenin, MBP, Rab3gap1, Bip/GRP78, STRN4, CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STAT1, and KLF5—through a two-step mechanism involving enzyme autopalmitoylation followed by palmitoyl transfer, thereby controlling substrate membrane localization, stability, and downstream signaling in processes ranging from neuronal plasticity and myelination to cancer progression and cardiac secretion."},"narrative":{"teleology":[{"year":2005,"claim":"Establishing that ZDHHC9 is a palmitoyltransferase: the identity and Golgi localization of ZDHHC9 as an enzyme, its substrate specificity for H-Ras/N-Ras, and its obligate dependence on GCP16 for activity and stability were demonstrated, defining the core enzymatic unit.","evidence":"Purified recombinant DHHC9·GCP16 complex tested in in vitro palmitoylation assays with co-IP and subcellular fractionation","pmids":["16000296"],"confidence":"High","gaps":["Catalytic mechanism (autopalmitoylation intermediate) not yet resolved","No structural information on the DHHC9·GCP16 complex","Substrate repertoire beyond Ras unknown"]},{"year":2014,"claim":"Resolving the catalytic mechanism: XLID-associated mutations (R148W, P150S) were shown to specifically impair autopalmitoylation, revealing that ZDHHC9 operates via a two-step ping-pong mechanism — enzyme autopalmitoylation followed by transfer to substrate — and providing a biochemical explanation for disease pathogenesis.","evidence":"In vitro autopalmitoylation assay with purified wild-type and mutant ZDHHC9 proteins","pmids":["24811172"],"confidence":"High","gaps":["No crystal structure to explain how mutations impair autopalmitoylation","Whether all XLID mutations act through the same mechanism unknown"]},{"year":2019,"claim":"Linking ZDHHC9 to neuronal circuit function: loss of Zdhhc9 was shown to shorten dendrites (via Ras palmitoylation) and reduce inhibitory synapses (via TC10 palmitoylation), shifting E/I balance and producing seizure-like activity in mice, establishing the neurological basis for XLID.","evidence":"Hippocampal neurons from Zdhhc9 KO mice analyzed by morphometry, electrophysiology (mEPSC/mIPSC), and palmitoylation assays","pmids":["31747610"],"confidence":"High","gaps":["Whether seizure phenotype is cell-autonomous to specific neuron types not resolved","No rescue experiment with wild-type ZDHHC9 re-expression reported"]},{"year":2021,"claim":"Expanding substrates to metabolic regulation: ZDHHC9 was identified as the palmitoyltransferase for GLUT1 at Cys207, establishing that ZDHHC9-mediated palmitoylation controls a transporter's plasma membrane localization, glycolysis, and tumor growth.","evidence":"ZDHHC9 KO, Cys207 mutation, acyl-biotin exchange assay, glycolysis measurement, and in vivo glioblastoma xenograft","pmids":["34620861"],"confidence":"High","gaps":["Whether other DHHC enzymes can compensate for ZDHHC9 on GLUT1 not tested","Tissue specificity of ZDHHC9-GLUT1 axis unclear"]},{"year":2023,"claim":"Demonstrating palmitoylation as a degradation signal and defining the writer-eraser pair: ZDHHC9 palmitoylation of β-catenin promotes its ubiquitination and degradation, while APT1 depalmitoylation stabilizes β-catenin for nuclear translocation, establishing a reversible palmitoylation cycle governing Wnt pathway output in renal fibrosis.","evidence":"In vivo mouse kidney models with ZDHHC9 ablation/overexpression, palmitoylation and ubiquitination assays, nuclear fractionation","pmids":["37865665"],"confidence":"High","gaps":["Whether this writer-eraser pairing applies in other tissue contexts unknown","Direct structural basis of palmitoylation-dependent ubiquitination not shown"]},{"year":2023,"claim":"Structural requirements for the DHHC9-GCP16 partnership were defined: GCP16 prevents DHHC9 aggregation, a C-terminal cysteine motif is essential for GCP16 binding, and XLID mutations reduce stability of the complex, explaining pathogenicity at a protein folding level.","evidence":"Size-exclusion chromatography, in vitro PAT assays, CCM deletion mutagenesis, disease variant stability analysis","pmids":["37035671"],"confidence":"High","gaps":["No high-resolution structure of the DHHC9·GCP16 complex","Whether CCM motif mediates GCP16 binding through direct contacts or indirectly unknown"]},{"year":2023,"claim":"ZDHHC9 was shown to regulate cardiac exocytosis: palmitoylation of Rab3gap1 sequesters it from Rab3a, elevating Rab3a-GTP and impairing ANP secretion, revealing a role in cardiomyocyte vesicle trafficking.","evidence":"Acyl-RAC palmitoylation assay, Rab3a-GTP pulldown, ANP secretion assay in cardiomyocytes","pmids":["37325411"],"confidence":"Medium","gaps":["Single lab study; independent replication needed","Whether ZDHHC9 is the sole PAT for Rab3gap1 not determined"]},{"year":2025,"claim":"ZDHHC9 was found to localize to Golgi outposts in oligodendrocyte processes and palmitoylate MBP; Zdhhc9 KO mice show myelin structural defects, establishing a role in CNS myelination distinct from the synaptic phenotype.","evidence":"Live imaging of ZDHHC9 localization in OL processes, palmitoylation assay for MBP, Zdhhc9 KO mouse with electron microscopy of myelin","pmids":["41031565"],"confidence":"Medium","gaps":["Whether MBP palmitoylation is the primary driver of myelin defects versus other substrates not resolved","Functional rescue with wild-type ZDHHC9 in OLs not shown"]},{"year":2025,"claim":"A rapid expansion of validated substrates in cancer contexts — including CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STRN4, STAT1, and KLF5 — revealed that ZDHHC9-mediated palmitoylation controls diverse signaling outputs (mTOR, Hippo/YAP, JNK/ERK, ferroptosis suppression, JAK-STAT, cAMP/PKA) to promote tumor proliferation, migration, and metastasis across multiple cancer types.","evidence":"Acyl-biotin exchange assays with site-directed mutagenesis of palmitoylation sites, co-immunoprecipitation, downstream pathway assays, and in vivo xenograft/metastasis models across multiple studies","pmids":["40903842","41419885","41856969","41087856","41535416","41711908","41882103","39002690"],"confidence":"Medium","gaps":["Each substrate identified in a single lab study; independent validation lacking for most","Substrate selectivity determinants for ZDHHC9 versus other DHHC enzymes largely unexplored","No global palmitoyl-proteomics in ZDHHC9-null cells to define the complete substrate landscape"]},{"year":null,"claim":"Major open questions include: the high-resolution structure of the DHHC9·GCP16 complex, the molecular determinants of substrate selectivity among DHHC family members, a comprehensive palmitoyl-proteome for ZDHHC9, and the relative contribution of individual substrates to XLID neuropathology.","evidence":"","pmids":[],"confidence":"High","gaps":["No crystal or cryo-EM structure available","No unbiased palmitoyl-proteomics in ZDHHC9 KO cells published","Relative contribution of individual substrate palmitoylation to XLID phenotype unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1,2,3,4,6,7,8,9,10,11,12,13,14,15,16,17]}],"localization":[{"term_id":"GO:0005794","term_label":"Golgi apparatus","supporting_discovery_ids":[0,11]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,3,4,9,12,14,16,17]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[0,1,2,3,6,7,8,9,10,11,12,13,14,15,16,17]},{"term_id":"R-HSA-112316","term_label":"Neuronal System","supporting_discovery_ids":[4,5]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[2,9,10,13,15,16,17]}],"complexes":["DHHC9-GCP16 palmitoyltransferase complex"],"partners":["GCP16","HRAS","NRAS","GLUT1","CTNNB1","TC10","MBP","LAMTOR1"],"other_free_text":[]},"mechanistic_narrative":"ZDHHC9 is a Golgi-localized protein S-acyltransferase (palmitoyltransferase) that catalyzes the palmitoylation of a broad range of substrates, thereby controlling their membrane localization, protein stability, and downstream signaling across neuronal, metabolic, and oncogenic contexts. ZDHHC9 requires its obligate accessory partner GCP16 for proper folding, stability, and enzymatic activity; a conserved C-terminal cysteine motif mediates GCP16 binding, and disease-associated mutations disrupt this complex and impair a two-step catalytic mechanism involving enzyme autopalmitoylation followed by palmitoyl transfer to substrate [PMID:16000296, PMID:24811172, PMID:37035671]. Validated substrates include H-Ras/N-Ras, TC10, GLUT1, β-catenin, MBP, Rab3gap1, Bip/GRP78, STRN4, CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STAT1, and KLF5, through which ZDHHC9 regulates processes as diverse as neuronal dendrite outgrowth, inhibitory synapse formation, myelination, glycolysis, mTORC1 activation, Hippo/YAP signaling, ferroptosis suppression, and exocytosis [PMID:31747610, PMID:34620861, PMID:37865665, PMID:37325411, PMID:41031565, PMID:40903842, PMID:41856969]. Loss-of-function mutations in ZDHHC9 cause X-linked intellectual disability (XLID), consistent with the neuronal phenotypes of shorter dendrites, reduced inhibitory synapses, altered E/I balance, and seizure-like activity observed in Zdhhc9 knockout mice [PMID:31747610, PMID:24811172]."},"prefetch_data":{"uniprot":{"accession":"Q9Y397","full_name":"Palmitoyltransferase ZDHHC9","aliases":["Zinc finger DHHC domain-containing protein 9","DHHC-9","DHHC9","Zinc finger protein 379","Zinc finger protein 380"],"length_aa":364,"mass_kda":40.9,"function":"Palmitoyltransferase that catalyzes the addition of palmitate onto various protein substrates, such as ADRB2, GSDMD, HRAS, NRAS and CGAS (PubMed:16000296, PubMed:27481942, PubMed:37802025, PubMed:38530158, PubMed:38599239). The ZDHHC9-GOLGA7 complex is a palmitoyltransferase specific for HRAS and NRAS (PubMed:16000296). May have a palmitoyltransferase activity toward the beta-2 adrenergic receptor/ADRB2 and therefore regulate G protein-coupled receptor signaling (PubMed:27481942). Acts as a regulator of innate immunity by catalyzing palmitoylation of CGAS, thereby promoting CGAS homodimerization and cyclic GMP-AMP synthase activity (PubMed:37802025). Activates pyroptosis by catalyzing palmitoylation of gasdermin-D (GSDMD), thereby promoting membrane translocation and pore formation of GSDMD (PubMed:38530158, PubMed:38599239) (Microbial infection) Through a sequential action with ZDHHC20, rapidly and efficiently palmitoylates SARS coronavirus-2/SARS-CoV-2 spike protein following its synthesis in the endoplasmic reticulum (ER). In the infected cell, promotes spike biogenesis by protecting it from premature ER degradation, increases half-life and controls the lipid organization of its immediate membrane environment. Once the virus has formed, spike palmitoylation controls fusion with the target cell","subcellular_location":"Endoplasmic reticulum membrane; Golgi apparatus membrane","url":"https://www.uniprot.org/uniprotkb/Q9Y397/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ZDHHC9","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ZDHHC9","total_profiled":1310},"omim":[{"mim_id":"617042","title":"GASDERMIN D; GSDMD","url":"https://www.omim.org/entry/617042"},{"mim_id":"609453","title":"GOLGIN A7; GOLGA7","url":"https://www.omim.org/entry/609453"},{"mim_id":"300799","title":"INTELLECTUAL DEVELOPMENTAL DISORDER, X-LINKED, SYNDROMIC, RAYMOND TYPE; MRXSR","url":"https://www.omim.org/entry/300799"},{"mim_id":"300646","title":"ZDHHC PALMITOYLTRANSFERASE 9; ZDHHC9","url":"https://www.omim.org/entry/300646"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Endoplasmic reticulum","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ZDHHC9"},"hgnc":{"alias_symbol":["ZNF379","CGI-89","ZNF380","DHHC9"],"prev_symbol":["ZDHHC10","CXorf11"]},"alphafold":{"accession":"Q9Y397","domains":[{"cath_id":"-","chopping":"99-148","consensus_level":"high","plddt":85.1132,"start":99,"end":148},{"cath_id":"1.20.140","chopping":"12-94_164-287","consensus_level":"high","plddt":95.4369,"start":12,"end":287}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y397","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y397-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y397-F1-predicted_aligned_error_v6.png","plddt_mean":84.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ZDHHC9","jax_strain_url":"https://www.jax.org/strain/search?query=ZDHHC9"},"sequence":{"accession":"Q9Y397","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y397.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y397/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y397"}},"corpus_meta":[{"pmid":"16000296","id":"PMC_16000296","title":"DHHC9 and GCP16 constitute a human protein fatty acyltransferase with specificity for H- and N-Ras.","date":"2005","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/16000296","citation_count":286,"is_preprint":false},{"pmid":"34620861","id":"PMC_34620861","title":"DHHC9-mediated GLUT1 S-palmitoylation promotes glioblastoma glycolysis and tumorigenesis.","date":"2021","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/34620861","citation_count":203,"is_preprint":false},{"pmid":"17436253","id":"PMC_17436253","title":"Mutations in ZDHHC9, which encodes a palmitoyltransferase of NRAS and HRAS, cause X-linked mental retardation associated with a Marfanoid habitus.","date":"2007","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/17436253","citation_count":139,"is_preprint":false},{"pmid":"17519897","id":"PMC_17519897","title":"Differential expression of DHHC9 in microsatellite stable and instable human colorectal cancer subgroups.","date":"2007","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/17519897","citation_count":65,"is_preprint":false},{"pmid":"37865665","id":"PMC_37865665","title":"Palmitoyltransferase DHHC9 and acyl protein thioesterase APT1 modulate renal fibrosis through regulating β-catenin palmitoylation.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37865665","citation_count":55,"is_preprint":false},{"pmid":"24811172","id":"PMC_24811172","title":"Mutations in the X-linked intellectual disability gene, zDHHC9, alter autopalmitoylation activity by distinct mechanisms.","date":"2014","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24811172","citation_count":47,"is_preprint":false},{"pmid":"31747610","id":"PMC_31747610","title":"The X-Linked Intellectual Disability Gene Zdhhc9 Is Essential for Dendrite Outgrowth and Inhibitory Synapse Formation.","date":"2019","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/31747610","citation_count":44,"is_preprint":false},{"pmid":"36963362","id":"PMC_36963362","title":"Targeting ZDHHC9 potentiates anti-programmed death-ligand 1 immunotherapy of pancreatic cancer by modifying the tumor microenvironment.","date":"2023","source":"Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie","url":"https://pubmed.ncbi.nlm.nih.gov/36963362","citation_count":44,"is_preprint":false},{"pmid":"24127608","id":"PMC_24127608","title":"MicroRNA-134 activity in somatostatin interneurons regulates H-Ras localization by repressing the palmitoylation enzyme, DHHC9.","date":"2013","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/24127608","citation_count":41,"is_preprint":false},{"pmid":"26000327","id":"PMC_26000327","title":"Epilepsy, cognitive deficits and neuroanatomy in males with ZDHHC9 mutations.","date":"2015","source":"Annals of clinical and translational neurology","url":"https://pubmed.ncbi.nlm.nih.gov/26000327","citation_count":30,"is_preprint":false},{"pmid":"24357419","id":"PMC_24357419","title":"Expanding the clinical phenotype of patients with a ZDHHC9 mutation.","date":"2013","source":"American journal of medical genetics. 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Basic to translational science","url":"https://pubmed.ncbi.nlm.nih.gov/37325411","citation_count":20,"is_preprint":false},{"pmid":"36419754","id":"PMC_36419754","title":"ZDHHC9 promotes colon tumor growth by inhibiting effector T cells.","date":"2022","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/36419754","citation_count":17,"is_preprint":false},{"pmid":"37035671","id":"PMC_37035671","title":"GCP16 stabilizes the DHHC9 subfamily of protein acyltransferases through a conserved C-terminal cysteine motif.","date":"2023","source":"Frontiers in physiology","url":"https://pubmed.ncbi.nlm.nih.gov/37035671","citation_count":14,"is_preprint":false},{"pmid":"28687527","id":"PMC_28687527","title":"The first patient with sporadic X-linked intellectual disability with de novo ZDHHC9 mutation identified by targeted next-generation sequencing.","date":"2017","source":"European journal of medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28687527","citation_count":14,"is_preprint":false},{"pmid":"40121269","id":"PMC_40121269","title":"ZDHHC9-mediated CD38 palmitoylation stabilizes CD38 expression and promotes pancreatic cancer growth.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40121269","citation_count":10,"is_preprint":false},{"pmid":"19748569","id":"PMC_19748569","title":"Expression of microRNAs is not related to increased expression of ZDHHC9 in hind leg muscles of splay leg piglets.","date":"2009","source":"Molecular and cellular probes","url":"https://pubmed.ncbi.nlm.nih.gov/19748569","citation_count":10,"is_preprint":false},{"pmid":"29681091","id":"PMC_29681091","title":"Expanding the molecular basis and phenotypic spectrum of ZDHHC9-associated X-linked intellectual disability.","date":"2018","source":"American journal of medical genetics. Part A","url":"https://pubmed.ncbi.nlm.nih.gov/29681091","citation_count":9,"is_preprint":false},{"pmid":"37875591","id":"PMC_37875591","title":"ZDHHC9: a promising therapeutic target for triple-negative breast cancer through immune modulation and immune checkpoint blockade resistance.","date":"2023","source":"Discover oncology","url":"https://pubmed.ncbi.nlm.nih.gov/37875591","citation_count":9,"is_preprint":false},{"pmid":"36416207","id":"PMC_36416207","title":"ZDHHC9 X-linked intellectual disability: Clinical and molecular characterization.","date":"2022","source":"American journal of medical genetics. 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DHHC9 requires GCP16 for enzymatic activity and protein stability, and the complex co-distributes in the Golgi apparatus consistent with the site of Ras palmitoylation in vivo.\",\n      \"method\": \"Purified DHHC9·GCP16 complex in vitro palmitoylation assay, co-immunoprecipitation, subcellular fractionation/co-distribution, functional comparison to yeast Erf2·Erf4 ortholog\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro palmitoylation with purified complex, substrate specificity demonstrated, localization confirmed; single paper but multiple orthogonal methods\",\n      \"pmids\": [\"16000296\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Two naturally occurring XLID variants of zDHHC9 (R148W and P150S) impair the autopalmitoylation step of the palmitoylation reaction, lowering the steady-state amount of the palmitoyl-zDHHC9 enzyme intermediate, revealing a two-step catalytic mechanism involving enzyme autopalmitoylation followed by transfer to substrate.\",\n      \"method\": \"In vitro autopalmitoylation assay with purified wild-type and disease mutant zDHHC9 proteins; mutagenesis of naturally occurring variants\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro biochemical assay with active-site mechanistic dissection and disease mutant validation\",\n      \"pmids\": [\"24811172\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"ZDHHC9 palmitoylates GLUT1 at Cys207, which is required for GLUT1 plasma membrane localization; ZDHHC9 knockout or Cys207 mutation abrogates GLUT1 palmitoylation and PM distribution, impairing glycolysis, cell proliferation, and glioblastoma tumorigenesis.\",\n      \"method\": \"ZDHHC9 knockout, Cys207 point mutation, acyl-biotin exchange palmitoylation assay, subcellular fractionation, glycolysis assay, in vivo xenograft\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KO, point mutation, ABE assay, localization, functional readout) in single study with strong controls\",\n      \"pmids\": [\"34620861\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ZDHHC9 palmitoylates β-catenin, promoting its ubiquitination and proteasomal degradation; acyl protein thioesterase 1 (APT1) depalmitoylates β-catenin, increasing its abundance and nuclear translocation to drive renal fibrosis.\",\n      \"method\": \"ZDHHC9 ablation and overexpression in tubular cells (in vivo mouse models), co-immunoprecipitation, palmitoylation assay, ubiquitination assay, nuclear fractionation, adeno-DHHC9 transfection\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal genetic manipulation in vivo and in vitro with multiple orthogonal methods establishing writer/eraser identity and downstream consequences\",\n      \"pmids\": [\"37865665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"ZDHHC9 promotes dendrite outgrowth through palmitoylation of the GTPase Ras, and promotes inhibitory synapse formation through palmitoylation of the GTPase TC10; loss of Zdhhc9 in hippocampal neurons leads to shorter dendritic arbors and fewer inhibitory synapses, altering excitatory-to-inhibitory balance; Zdhhc9 knockout mice show seizure-like activity.\",\n      \"method\": \"Hippocampal neuron cultures from Zdhhc9 knockout mice, dendritic morphology quantification, inhibitory synapse counting, electrophysiology (mEPSC/mIPSC), palmitoylation assays for Ras and TC10\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean KO with defined cellular phenotypes and substrate identification via palmitoylation assay; multiple orthogonal readouts\",\n      \"pmids\": [\"31747610\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"miR-134 directly interacts with DHHC9 mRNA in cortical somatostatin interneurons; bicuculline-induced GABAA receptor antagonism decreases DHHC9 expression in a miR-134-dependent manner, reducing membrane localization of an H-Ras reporter, placing DHHC9 downstream of miR-134 in activity-dependent H-Ras membrane trafficking.\",\n      \"method\": \"Ratiometric microRNA sensor, microRNA-mRNA complex trapping assay, pharmacological GABAA blockade, H-Ras reporter membrane localization assay, cell-type-specific imaging\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct mRNA targeting confirmed, functional consequence on H-Ras localization shown; single lab study\",\n      \"pmids\": [\"24127608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"GCP16 stabilizes DHHC9 by preventing its aggregation through direct complex formation; only properly folded DHHC9-GCP16 complex is enzymatically active in vitro; XLID-associated mutations in ZDHHC9 reduce protein stability and impair DHHC9-GCP16 complex formation; a conserved C-terminal cysteine motif (CCM) in DHHC9 is required for GCP16 binding and enzymatic activity; DHHC14 and DHHC18 also require GCP16 for activity.\",\n      \"method\": \"Size-exclusion chromatography, in vitro palmitoyl acyltransferase assays, analysis of XLID mutants, domain mutagenesis (CCM deletion), co-expression stability assays\",\n      \"journal\": \"Frontiers in physiology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro with purified complex, structure-function mutagenesis, and disease variant analysis; multiple orthogonal methods\",\n      \"pmids\": [\"37035671\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"zDHHC9 palmitoylates Rab3gap1 in cardiomyocytes, resulting in spatial segregation of Rab3gap1 from Rab3a, elevation of Rab3a-GTP levels, formation of Rab3a-positive peripheral vesicles, and impairment of exocytosis that limits atrial natriuretic peptide release.\",\n      \"method\": \"Palmitoylation assay (acyl-RAC), subcellular localization imaging, Rab3a-GTP pulldown, ANP secretion assay in cardiomyocytes\",\n      \"journal\": \"JACC. Basic to translational science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identification with functional consequence on exocytosis demonstrated; single lab study with multiple readouts\",\n      \"pmids\": [\"37325411\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ZDHHC9 binds to and palmitoylates Bip/GRP78 at Cys420, enhancing Bip protein stability and maintaining its localization within the endoplasmic reticulum, thereby inhibiting the unfolded protein response; SP1 transcriptionally activates ZDHHC9 expression.\",\n      \"method\": \"Co-immunoprecipitation, acyl-biotin exchange palmitoylation assay, Cys420 point mutation, ER localization by immunofluorescence, UPR pathway assays, SP1 ChIP/luciferase reporter\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identification with site-specific mutation and functional consequence on UPR; single lab study\",\n      \"pmids\": [\"39002690\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 palmitoylates STRN4 at Cys701, reducing YAP phosphorylation and promoting YAP nuclear translocation and activation of Hippo pathway targets (CCN1, CCN2, ANKRD1), thereby driving cancer cell migration and metastasis.\",\n      \"method\": \"Proteomic analysis, co-immunoprecipitation, site-directed mutagenesis of Cys701, YAP phosphorylation/localization assays, in vitro migration and in vivo metastasis assays\",\n      \"journal\": \"Journal of cellular and molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identification with site-specific mutation and downstream pathway validation; single lab study\",\n      \"pmids\": [\"40903842\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 palmitoylates CD38 at Cys16, maintaining CD38 protein stability in tumor cells; APT1 acts as the opposing depalmitoylating enzyme; a competitive peptide blocking CD38 palmitoylation decreases CD38 expression and suppresses tumor progression in vivo.\",\n      \"method\": \"Acyl-biotin exchange assay, site-directed mutagenesis (Cys16), co-immunoprecipitation, competitive peptide design, in vivo xenograft\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutation and in vivo functional validation; single lab study\",\n      \"pmids\": [\"40121269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 localizes to Golgi outposts in oligodendrocyte processes (whereas XLID mutant forms are restricted to cell bodies), palmitoylates Myelin Basic Protein (MBP) in heterologous cells, and MBP palmitoylation is impaired in the Zdhhc9 knockout brain; Zdhhc9 knockout mice display morphological and structural myelin abnormalities without grossly disrupted OL development.\",\n      \"method\": \"Live imaging of ZDHHC9 localization in OL processes, palmitoylation assay for MBP in heterologous cells, Zdhhc9 knockout mouse analysis with OL fate tracing and sparse cell labeling, electron microscopy of myelin structure\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — localization with functional consequence, substrate identification with palmitoylation assay, and in vivo KO phenotype; single lab but multiple methods\",\n      \"pmids\": [\"41031565\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 palmitoylates LAMTOR1 at Cys3/4, enhancing LAMTOR1-mediated recruitment of mTORC1 to the lysosomal surface and activating the mTOR signaling cascade in renal cell carcinoma.\",\n      \"method\": \"Co-immunoprecipitation, acyl-biotin exchange palmitoylation assay, Cys3/4 site mutagenesis, mTOR pathway activation assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutation and downstream mTOR pathway validation; single lab study\",\n      \"pmids\": [\"41856969\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 interacts with hnRNPU and palmitoylates it at Cys497 and Cys607, increasing hnRNPU protein stability; stabilized hnRNPU elevates SAT1 transcription to enhance spermine catabolism in prostate cancer.\",\n      \"method\": \"Co-immunoprecipitation, mass spectrometry, acyl-biotin exchange assay, site-directed mutagenesis, RNA sequencing, SAT1 expression assays\",\n      \"journal\": \"Journal of translational medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identification with site-specific mutation and transcriptional downstream validation; single lab study\",\n      \"pmids\": [\"41419885\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 palmitoylates CD36 at cysteine residues, promoting CD36 plasma membrane localization and formation of a CD36/Fyn/Lyn complex that activates JNK1 and suppresses ERK1/2 signaling; DHHC9 knockdown or CD36 cysteine mutation disrupts this complex and reactivates ERK1/2 to rescue mammary epithelial cell proliferation impaired by high-fat diet.\",\n      \"method\": \"Acyl-biotin exchange assay, co-immunoprecipitation, Cys point mutation, DHHC9 knockdown, JNK/ERK pathway assays, in vivo mammary gland whole-mount staining\",\n      \"journal\": \"Cellular & molecular biology letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutation and signaling pathway dissection; in vivo and in vitro validation in single lab\",\n      \"pmids\": [\"41087856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZDHHC9 palmitoylates PCBP1 at Cys109, inhibiting PCBP1 ubiquitination and thus stabilizing PCBP1; stabilized PCBP1 promotes SLC7A11 mRNA stability, thereby suppressing ferroptosis and promoting gastric cancer liver metastasis.\",\n      \"method\": \"Immunoprecipitation, LC-MS/MS, acyl-biotin exchange assay, Cys109 mutagenesis, ubiquitination assay, SLC7A11 mRNA stability assay, in vivo metastasis models\",\n      \"journal\": \"NPJ precision oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutation, ubiquitination and mRNA stability assays, in vivo validation; single lab study\",\n      \"pmids\": [\"41535416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZDHHC9 palmitoylates STAT1 at Cys577 via JAK1-STAT1 signaling; palmitoylation at Cys577 is converted to phosphorylation at Tyr701 (pSTAT1) to drive nuclear STAT1 transcriptional activity and gastric cancer progression.\",\n      \"method\": \"Acyl-biotin exchange assay, co-immunoprecipitation, Cys577 and Tyr701 mutagenesis, immunofluorescence/confocal imaging, ZDHHC9 silencing with downstream gene expression analysis\",\n      \"journal\": \"Journal of gastroenterology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutagenesis and PTM crosstalk demonstrated; single lab study\",\n      \"pmids\": [\"41711908\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"ZDHHC9 palmitoylates KLF5 at Cys438, enhancing ADCY4 activity and increasing intracellular cAMP, thereby activating the cAMP/PKA/CREB signaling pathway to promote colorectal cancer cell proliferation and migration.\",\n      \"method\": \"Acyl-biotin exchange assay, Cys438 point mutation, RNA sequencing, ADCY4 activity assay, cAMP measurement, PKA/CREB pathway analysis, ZDHHC9 knockdown in vivo and in vitro\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — substrate identified with site-specific mutation and downstream signaling pathway validated; single lab study\",\n      \"pmids\": [\"41882103\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 interacts with KRAS (confirmed by co-immunoprecipitation and molecular docking), and ZDHHC9 promotes KRAS-mediated activation of the RAS/MAPK pathway (Raf1/ERK1/2 signaling) to drive osteosarcoma proliferation, migration, and invasion.\",\n      \"method\": \"Co-immunoprecipitation, molecular docking, proteomic sequencing, ZDHHC9 knockdown/overexpression, KRAS overexpression rescue, Western blot for ERK pathway, xenograft model\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — Co-IP interaction shown but direct palmitoylation of KRAS not biochemically demonstrated in this study; single lab\",\n      \"pmids\": [\"41087383\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"ZDHHC9 palmitoylates PKG1, and ZDHHC9-PKG1 interaction (confirmed by co-immunoprecipitation and co-localization) regulates mitochondria-associated endoplasmic reticulum membranes (MAMs) structure and function in osteoblasts, affecting osteogenesis under high-glucose/T2DM conditions.\",\n      \"method\": \"Co-immunoprecipitation, fluorescence co-localization, Zdhhc9 and Prkg1 knockdown, MAM distance measurement, MAM-related protein expression analysis\",\n      \"journal\": \"Journal of dental research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — interaction shown by Co-IP and co-localization but direct palmitoylation of PKG1 not formally demonstrated with palmitoylation assay; single lab\",\n      \"pmids\": [\"40102769\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ZDHHC9 is a Golgi-localized integral membrane palmitoyltransferase that requires the accessory protein GCP16 for proper folding, stability, and enzymatic activity; it catalyzes S-palmitoylation of diverse substrates—including H-Ras, N-Ras, GLUT1, TC10, β-catenin, MBP, Rab3gap1, Bip/GRP78, STRN4, CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STAT1, and KLF5—through a two-step mechanism involving enzyme autopalmitoylation followed by palmitoyl transfer, thereby controlling substrate membrane localization, stability, and downstream signaling in processes ranging from neuronal plasticity and myelination to cancer progression and cardiac secretion.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"ZDHHC9 is a Golgi-localized protein S-acyltransferase (palmitoyltransferase) that catalyzes the palmitoylation of a broad range of substrates, thereby controlling their membrane localization, protein stability, and downstream signaling across neuronal, metabolic, and oncogenic contexts. ZDHHC9 requires its obligate accessory partner GCP16 for proper folding, stability, and enzymatic activity; a conserved C-terminal cysteine motif mediates GCP16 binding, and disease-associated mutations disrupt this complex and impair a two-step catalytic mechanism involving enzyme autopalmitoylation followed by palmitoyl transfer to substrate [PMID:16000296, PMID:24811172, PMID:37035671]. Validated substrates include H-Ras/N-Ras, TC10, GLUT1, β-catenin, MBP, Rab3gap1, Bip/GRP78, STRN4, CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STAT1, and KLF5, through which ZDHHC9 regulates processes as diverse as neuronal dendrite outgrowth, inhibitory synapse formation, myelination, glycolysis, mTORC1 activation, Hippo/YAP signaling, ferroptosis suppression, and exocytosis [PMID:31747610, PMID:34620861, PMID:37865665, PMID:37325411, PMID:41031565, PMID:40903842, PMID:41856969]. Loss-of-function mutations in ZDHHC9 cause X-linked intellectual disability (XLID), consistent with the neuronal phenotypes of shorter dendrites, reduced inhibitory synapses, altered E/I balance, and seizure-like activity observed in Zdhhc9 knockout mice [PMID:31747610, PMID:24811172].\",\n  \"teleology\": [\n    {\n      \"year\": 2005,\n      \"claim\": \"Establishing that ZDHHC9 is a palmitoyltransferase: the identity and Golgi localization of ZDHHC9 as an enzyme, its substrate specificity for H-Ras/N-Ras, and its obligate dependence on GCP16 for activity and stability were demonstrated, defining the core enzymatic unit.\",\n      \"evidence\": \"Purified recombinant DHHC9·GCP16 complex tested in in vitro palmitoylation assays with co-IP and subcellular fractionation\",\n      \"pmids\": [\"16000296\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Catalytic mechanism (autopalmitoylation intermediate) not yet resolved\", \"No structural information on the DHHC9·GCP16 complex\", \"Substrate repertoire beyond Ras unknown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolving the catalytic mechanism: XLID-associated mutations (R148W, P150S) were shown to specifically impair autopalmitoylation, revealing that ZDHHC9 operates via a two-step ping-pong mechanism — enzyme autopalmitoylation followed by transfer to substrate — and providing a biochemical explanation for disease pathogenesis.\",\n      \"evidence\": \"In vitro autopalmitoylation assay with purified wild-type and mutant ZDHHC9 proteins\",\n      \"pmids\": [\"24811172\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal structure to explain how mutations impair autopalmitoylation\", \"Whether all XLID mutations act through the same mechanism unknown\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Linking ZDHHC9 to neuronal circuit function: loss of Zdhhc9 was shown to shorten dendrites (via Ras palmitoylation) and reduce inhibitory synapses (via TC10 palmitoylation), shifting E/I balance and producing seizure-like activity in mice, establishing the neurological basis for XLID.\",\n      \"evidence\": \"Hippocampal neurons from Zdhhc9 KO mice analyzed by morphometry, electrophysiology (mEPSC/mIPSC), and palmitoylation assays\",\n      \"pmids\": [\"31747610\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether seizure phenotype is cell-autonomous to specific neuron types not resolved\", \"No rescue experiment with wild-type ZDHHC9 re-expression reported\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Expanding substrates to metabolic regulation: ZDHHC9 was identified as the palmitoyltransferase for GLUT1 at Cys207, establishing that ZDHHC9-mediated palmitoylation controls a transporter's plasma membrane localization, glycolysis, and tumor growth.\",\n      \"evidence\": \"ZDHHC9 KO, Cys207 mutation, acyl-biotin exchange assay, glycolysis measurement, and in vivo glioblastoma xenograft\",\n      \"pmids\": [\"34620861\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether other DHHC enzymes can compensate for ZDHHC9 on GLUT1 not tested\", \"Tissue specificity of ZDHHC9-GLUT1 axis unclear\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrating palmitoylation as a degradation signal and defining the writer-eraser pair: ZDHHC9 palmitoylation of β-catenin promotes its ubiquitination and degradation, while APT1 depalmitoylation stabilizes β-catenin for nuclear translocation, establishing a reversible palmitoylation cycle governing Wnt pathway output in renal fibrosis.\",\n      \"evidence\": \"In vivo mouse kidney models with ZDHHC9 ablation/overexpression, palmitoylation and ubiquitination assays, nuclear fractionation\",\n      \"pmids\": [\"37865665\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether this writer-eraser pairing applies in other tissue contexts unknown\", \"Direct structural basis of palmitoylation-dependent ubiquitination not shown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Structural requirements for the DHHC9-GCP16 partnership were defined: GCP16 prevents DHHC9 aggregation, a C-terminal cysteine motif is essential for GCP16 binding, and XLID mutations reduce stability of the complex, explaining pathogenicity at a protein folding level.\",\n      \"evidence\": \"Size-exclusion chromatography, in vitro PAT assays, CCM deletion mutagenesis, disease variant stability analysis\",\n      \"pmids\": [\"37035671\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No high-resolution structure of the DHHC9·GCP16 complex\", \"Whether CCM motif mediates GCP16 binding through direct contacts or indirectly unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"ZDHHC9 was shown to regulate cardiac exocytosis: palmitoylation of Rab3gap1 sequesters it from Rab3a, elevating Rab3a-GTP and impairing ANP secretion, revealing a role in cardiomyocyte vesicle trafficking.\",\n      \"evidence\": \"Acyl-RAC palmitoylation assay, Rab3a-GTP pulldown, ANP secretion assay in cardiomyocytes\",\n      \"pmids\": [\"37325411\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab study; independent replication needed\", \"Whether ZDHHC9 is the sole PAT for Rab3gap1 not determined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"ZDHHC9 was found to localize to Golgi outposts in oligodendrocyte processes and palmitoylate MBP; Zdhhc9 KO mice show myelin structural defects, establishing a role in CNS myelination distinct from the synaptic phenotype.\",\n      \"evidence\": \"Live imaging of ZDHHC9 localization in OL processes, palmitoylation assay for MBP, Zdhhc9 KO mouse with electron microscopy of myelin\",\n      \"pmids\": [\"41031565\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether MBP palmitoylation is the primary driver of myelin defects versus other substrates not resolved\", \"Functional rescue with wild-type ZDHHC9 in OLs not shown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"A rapid expansion of validated substrates in cancer contexts — including CD38, hnRNPU, LAMTOR1, CD36, PCBP1, STRN4, STAT1, and KLF5 — revealed that ZDHHC9-mediated palmitoylation controls diverse signaling outputs (mTOR, Hippo/YAP, JNK/ERK, ferroptosis suppression, JAK-STAT, cAMP/PKA) to promote tumor proliferation, migration, and metastasis across multiple cancer types.\",\n      \"evidence\": \"Acyl-biotin exchange assays with site-directed mutagenesis of palmitoylation sites, co-immunoprecipitation, downstream pathway assays, and in vivo xenograft/metastasis models across multiple studies\",\n      \"pmids\": [\"40903842\", \"41419885\", \"41856969\", \"41087856\", \"41535416\", \"41711908\", \"41882103\", \"39002690\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Each substrate identified in a single lab study; independent validation lacking for most\", \"Substrate selectivity determinants for ZDHHC9 versus other DHHC enzymes largely unexplored\", \"No global palmitoyl-proteomics in ZDHHC9-null cells to define the complete substrate landscape\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Major open questions include: the high-resolution structure of the DHHC9·GCP16 complex, the molecular determinants of substrate selectivity among DHHC family members, a comprehensive palmitoyl-proteome for ZDHHC9, and the relative contribution of individual substrates to XLID neuropathology.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No crystal or cryo-EM structure available\", \"No unbiased palmitoyl-proteomics in ZDHHC9 KO cells published\", \"Relative contribution of individual substrate palmitoylation to XLID phenotype unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [0, 11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": []},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 3, 4, 9, 12, 14, 16, 17]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17]},\n      {\"term_id\": \"R-HSA-112316\", \"supporting_discovery_ids\": [4, 5]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [2, 9, 10, 13, 15, 16, 17]}\n    ],\n    \"complexes\": [\n      \"DHHC9-GCP16 palmitoyltransferase complex\"\n    ],\n    \"partners\": [\n      \"GCP16\",\n      \"HRAS\",\n      \"NRAS\",\n      \"GLUT1\",\n      \"CTNNB1\",\n      \"TC10\",\n      \"MBP\",\n      \"LAMTOR1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}