{"gene":"MVD","run_date":"2026-06-10T05:19:51","timeline":{"discoveries":[{"year":2003,"finding":"Mevalonate pyrophosphate decarboxylase (MVD/MPD) was identified as a binding partner of mortalin (mot-2/GRP75) via yeast two-hybrid screen, confirmed by mammalian two-hybrid assay and in vivo co-immunoprecipitation. Overexpression of mortalin reduced the level of Ras and phosphorylated ERK2, effects rescued by co-expression of MVD, establishing a functional link between mortalin, MVD, and Ras-ERK signaling in control of cell proliferation.","method":"Yeast two-hybrid screen, mammalian two-hybrid assay, co-immunoprecipitation, overexpression rescue experiment","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2/3 / Moderate — reciprocal two-hybrid + Co-IP in mammalian cells + functional rescue, single lab, multiple orthogonal methods","pmids":["12646231"],"is_preprint":false},{"year":2009,"finding":"Molecular docking and MD simulation of S. cerevisiae MVD identified Ala15, Lys18, Ser121, and Ser155 as residues within hydrogen-bond distance of the substrate mevalonate diphosphate (MDP); Lys22, Ser153, and Ser155 for ATP; and Tyr19, Ser121, Ser153, Gly154, and Thr209 for the inhibitor trifluoromevalonate (TFMDP). A water molecule was found between Asp302 (a known catalytic residue) and C3 of MDP, suggesting deprotonation of the C3 hydroxyl occurs via a water bridge, and Ser121 was proposed to orient MDP for phosphorylation/decarboxylation.","method":"Molecular docking (Hex 4.2) and 1.5 ns molecular dynamics simulation (GROMACS)","journal":"Journal of molecular modeling","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental mutagenesis or structural validation in this paper","pmids":["19653015"],"is_preprint":false},{"year":2002,"finding":"The MVD gene of Candida albicans encodes a 362-aa mevalonate diphosphate decarboxylase (39.5 kDa) that functionally complements a temperature-sensitive S. cerevisiae erg19(ts) mutant lacking MVD activity, demonstrating conservation of enzymatic function. Northern analysis showed MVD expression is regulated by carbon source, growth phase, and yeast-to-hypha transition.","method":"Heterologous complementation in yeast (erg19 ts mutant), Western blot (epitope-tagged protein), Northern blot","journal":"Molecular genetics and genomics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional complementation assay with protein expression confirmation, single lab, two orthogonal methods","pmids":["12073030"],"is_preprint":false},{"year":2019,"finding":"In Aspergillus oryzae, the MVD ortholog AoErg19 localizes to the vacuole (by subcellular localization analysis) and is required for ergosterol biosynthesis; both overexpression and RNAi knockdown of Aoerg19 decreased ergosterol content and increased sensitivity to ergosterol biosynthesis inhibitors, temperature stress, salt, and ethanol. Overexpression of Aoerg19 also led to feedback-mediated downregulation of Aoerg8 (mevalonate kinase).","method":"Subcellular localization (fluorescence), qRT-PCR, RNAi knockdown, overexpression, yeast complementation assay, sterol quantification","journal":"Frontiers in microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (localization, KD, OE, sterol assay) in single lab fungal ortholog study","pmids":["31156588"],"is_preprint":false},{"year":2019,"finding":"In patients with linear porokeratosis, whole-exome sequencing of paired lesional skin and blood identified a two-hit mechanism: a germline heterozygous MVD splice-site mutation (c.70+5G>A) plus a somatic frameshift deletion (c.811_815del, p.F271Afs*33) confined to lesional skin, establishing that biallelic loss of MVD function in keratinocytes is sufficient to produce porokeratosis lesions.","method":"Whole-exome sequencing of paired lesional skin and blood/saliva samples","journal":"JAMA dermatology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — paired WES with somatic/germline discrimination, single study, multiple patients with orthogonal confirmation","pmids":["30942823"],"is_preprint":false},{"year":2019,"finding":"In disseminated superficial actinic porokeratosis (DSAP) and linear porokeratosis, each individual skin lesion harbored a distinct second-hit mutation (somatic homologous recombination rendering the germline MVD mutation biallelic, or a new C>T transition in the wild-type allele) exclusively in the epidermis, demonstrating that postnatal biallelic deficiency of MVD in a single keratinocyte precursor drives clonal expansion to form each lesion (Knudson two-hit mechanism).","method":"Targeted sequencing of individual DSAP lesions and matched normal tissue; somatic recombination and mutation analysis","journal":"The Journal of investigative dermatology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple lesions from multiple patients with paired normal tissue sequencing, independently replicates the two-hit finding from PMID:30942823 using orthogonal molecular methods","pmids":["31207227"],"is_preprint":false},{"year":2021,"finding":"Three families with porokeratosis plantaris, palmaris et disseminata all carried the germline heterozygous MVD variant c.70+5G>A, and loss of heterozygosity due to a somatic second-hit mutation was found in affected skin of 2 of 3 such patients, indicating this subtype shares the same two-hit pathogenetic mechanism (biallelic MVD inactivation in keratinocytes) as other porokeratosis subtypes.","method":"Mutation analysis of blood and skin biopsy DNA; loss-of-heterozygosity analysis","journal":"Acta dermato-venereologica","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct sequencing of paired tissue samples in multiple patients, single study replicating two-hit mechanism","pmids":["33491095"],"is_preprint":false},{"year":2021,"finding":"Flow cytometry of PBMCs from porokeratosis patients with MVD variants revealed significantly decreased frequencies of CD8+ and Vγ9Vδ2 T cells compared to normal controls, and dysregulated secretion of pro-inflammatory cytokines (IFN-γ, TNF-α) by T cells, implicating MVD-dependent mevalonate pathway activity in the regulation of peripheral T-cell subsets.","method":"Flow cytometry; targeted exome sequencing for variant confirmation","journal":"Skin health and disease","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single method (flow cytometry), single small cohort, no direct enzymatic or pathway rescue experiment","pmids":["35665211"],"is_preprint":false},{"year":2023,"finding":"A CRISPR/Cas9 knock-in mouse model carrying the MvdF250S/+ mutation (equivalent to human MVDF249S, the most common pathogenic variant in Chinese porokeratosis patients) showed reduced cutaneous Mvd protein expression. Upon imiquimod challenge, MvdF250S/+ mice exhibited decreased skin inflammation (reduced IL-17a, IL-1β, and cutaneous proliferation) compared to wild-type, and also showed downregulated collagen generation, upregulated Fabp3 expression, and activated autophagy, with no significant changes in key cholesterol-regulation genes.","method":"CRISPR/Cas9 knock-in mouse model; imiquimod-induced inflammation model; Western blot; immunofluorescence; qPCR","journal":"Inflammation","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo knock-in model with multiple phenotypic readouts, single lab, orthogonal methods (protein, mRNA, histology)","pmids":["37227548"],"is_preprint":false},{"year":2021,"finding":"Immunohistochemistry of mouse cochlear tissue showed MVD protein expression is prominent in spiral ganglion cells (rather than sensory hair cells), and a homozygous missense variant in MVD co-segregated with autosomal recessive nonsyndromic profound prelingual sensorineural hearing impairment in a consanguineous Pakistani family, supported by linkage analysis and in silico structural analysis predicting conformational changes.","method":"Exome sequencing, Sanger sequencing, linkage analysis, immunohistochemistry of mouse cochlear tissue, RNAseq expression profiling, in silico protein modeling","journal":"European journal of human genetics","confidence":"Low","confidence_rationale":"Tier 3 / Weak — genetic association with IHC localization, no functional rescue or enzymatic assay; single family","pmids":["34135477"],"is_preprint":false}],"current_model":"MVD (mevalonate diphosphate decarboxylase) catalyzes the ATP-dependent decarboxylation of mevalonate 5-diphosphate to isopentenyl diphosphate in the mevalonate pathway; it physically interacts with mortalin (GRP75) to modulate Ras-ERK signaling and cell proliferation, and biallelic loss of MVD function in keratinocytes—via germline plus somatic second-hit mutations—drives clonal expansion and porokeratosis lesion formation through a Knudson two-hit mechanism, while a heterozygous knock-in mouse model demonstrates that partial MVD loss attenuates skin inflammation and activates autophagy without major effects on cholesterol gene regulation."},"narrative":{"mechanistic_narrative":"MVD encodes mevalonate diphosphate decarboxylase, a conserved enzyme of the mevalonate/sterol biosynthesis pathway whose fungal orthologs functionally complement yeast MVD-deficient mutants and are required for ergosterol production [PMID:12073030, PMID:31156588]. Beyond its metabolic role, MVD physically interacts with mortalin (GRP75); mortalin overexpression lowers Ras and phosphorylated ERK2, an effect rescued by co-expressed MVD, linking MVD to Ras-ERK signaling control of proliferation [PMID:12646231]. In human skin, biallelic loss of MVD function in keratinocytes is sufficient to cause porokeratosis: affected individuals carry a germline heterozygous MVD mutation and acquire a distinct somatic second-hit (frameshift, transition, or loss of heterozygosity) in each lesion, so that clonal expansion of an MVD-deficient keratinocyte precursor generates each lesion through a Knudson two-hit mechanism across multiple porokeratosis subtypes [PMID:30942823, PMID:31207227, PMID:33491095]. A knock-in mouse carrying a porokeratosis-equivalent Mvd variant shows reduced cutaneous Mvd protein and, upon inflammatory challenge, attenuated skin inflammation with activated autophagy and no significant change in cholesterol-regulatory genes [PMID:37227548]. A homozygous missense MVD variant co-segregates with autosomal recessive nonsyndromic sensorineural hearing impairment, with MVD protein localized to cochlear spiral ganglion cells [PMID:34135477].","teleology":[{"year":2002,"claim":"Establishing that the MVD gene product is a bona fide mevalonate diphosphate decarboxylase required showing its enzymatic function is conserved and physiologically regulated.","evidence":"Heterologous complementation of a yeast erg19(ts) mutant by Candida albicans MVD, with protein expression and Northern analysis of regulation","pmids":["12073030"],"confidence":"Medium","gaps":["Does not characterize the human MVD enzyme directly","Catalytic residues and kinetics not defined here"]},{"year":2003,"claim":"Whether MVD has roles beyond metabolism was addressed by identifying a protein partner that connects it to growth-control signaling.","evidence":"Yeast and mammalian two-hybrid plus Co-IP identifying mortalin/GRP75 binding, with overexpression rescue of mortalin-induced Ras/pERK2 suppression","pmids":["12646231"],"confidence":"Medium","gaps":["Mechanism linking the enzyme to Ras-ERK is not defined","Single lab; physiological relevance in vivo untested"]},{"year":2009,"claim":"The structural basis for substrate, ATP, and inhibitor binding was probed to rationalize the catalytic mechanism of decarboxylation.","evidence":"Molecular docking and short MD simulation of S. cerevisiae MVD predicting substrate/ATP/inhibitor-contacting residues and a water-bridge deprotonation model","pmids":["19653015"],"confidence":"Low","gaps":["Purely computational; no experimental mutagenesis or crystal structure validation","Predictions are for the yeast enzyme, not human MVD"]},{"year":2019,"claim":"The disease relevance of MVD was established by showing biallelic keratinocyte inactivation causes porokeratosis via combined germline and somatic mutations.","evidence":"Paired whole-exome sequencing of lesional skin versus blood in linear porokeratosis identifying germline splice plus somatic frameshift hits; targeted per-lesion sequencing in DSAP showing distinct second hits per lesion","pmids":["30942823","31207227"],"confidence":"High","gaps":["Downstream metabolic consequence of MVD loss in keratinocytes not mechanistically traced","How biallelic loss drives clonal expansion at the pathway level unresolved"]},{"year":2019,"claim":"Whether the vacuolar/sterol-pathway role of MVD is conserved and feedback-regulated was tested in a filamentous fungus.","evidence":"Subcellular localization, RNAi, overexpression, and sterol quantification of the Aspergillus oryzae ortholog AoErg19","pmids":["31156588"],"confidence":"Medium","gaps":["Fungal ortholog; mammalian localization not addressed","Feedback regulation of human MVD pathway not established"]},{"year":2021,"claim":"The two-hit model was extended across porokeratosis subtypes and connected to immune dysregulation in patients.","evidence":"Mutation and loss-of-heterozygosity analysis in porokeratosis plantaris/palmaris families; flow cytometry of patient PBMCs showing altered CD8+/Vd9Vd2 T-cell frequencies and cytokines","pmids":["33491095","35665211"],"confidence":"Medium","gaps":["Causal link between MVD loss and T-cell changes not demonstrated","Immune findings rest on a single small cohort with one method"]},{"year":2021,"claim":"A second disease association was proposed, linking MVD to hearing through spiral ganglion expression.","evidence":"Exome and linkage analysis in a consanguineous family with recessive hearing impairment plus mouse cochlear immunohistochemistry","pmids":["34135477"],"confidence":"Low","gaps":["No functional or enzymatic rescue; single family","Causal mechanism in auditory neurons untested"]},{"year":2023,"claim":"An in vivo model defined the cellular consequences of partial MVD loss, separating inflammatory and autophagy effects from cholesterol regulation.","evidence":"CRISPR/Cas9 MvdF250S/+ knock-in mouse with imiquimod challenge, assessed by Western blot, immunofluorescence, and qPCR","pmids":["37227548"],"confidence":"Medium","gaps":["Mechanism linking MVD loss to autophagy activation not defined","Heterozygous model does not reproduce biallelic keratinocyte loss seen in lesions"]},{"year":null,"claim":"How biallelic MVD enzymatic deficiency mechanistically drives keratinocyte clonal expansion, autophagy, and inflammation — and whether the mortalin/Ras-ERK interaction operates in these contexts — remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No defined metabolic intermediate linking MVD loss to lesion phenotype","Mortalin-MVD signaling not tested in skin or hearing models","No structural validation of human enzyme catalytic mechanism"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016829","term_label":"lyase activity","supporting_discovery_ids":[2,3]},{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[1]}],"localization":[{"term_id":"GO:0005773","term_label":"vacuole","supporting_discovery_ids":[3]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[2,3]}],"complexes":[],"partners":["HSPA9"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P53602","full_name":"Diphosphomevalonate decarboxylase","aliases":["Mevalonate (diphospho)decarboxylase","MDDase","Mevalonate pyrophosphate decarboxylase"],"length_aa":400,"mass_kda":43.4,"function":"Catalyzes the ATP dependent decarboxylation of (R)-5-diphosphomevalonate to form isopentenyl diphosphate (IPP). Functions in the mevalonate (MVA) pathway leading to isopentenyl diphosphate (IPP), a key precursor for the biosynthesis of isoprenoids and sterol synthesis","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/P53602/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/MVD","classification":"Common Essential","n_dependent_lines":886,"n_total_lines":1208,"dependency_fraction":0.7334437086092715},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000167508","cell_line_id":"CID000276","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":2},{"compartment":"big_aggregates","grade":1}],"interactors":[{"gene":"GLT8D1","stoichiometry":0.2},{"gene":"NSDHL","stoichiometry":0.2},{"gene":"ZNF554","stoichiometry":0.2},{"gene":"ACVR2B","stoichiometry":0.2},{"gene":"TTLL5","stoichiometry":0.2},{"gene":"FASN","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000276","total_profiled":1310},"omim":[{"mim_id":"614714","title":"POROKERATOSIS 7, MULTIPLE TYPES; POROK7","url":"https://www.omim.org/entry/614714"},{"mim_id":"613457","title":"CHROMOSOME 14q11-q22 DELETION SYNDROME","url":"https://www.omim.org/entry/613457"},{"mim_id":"603236","title":"MEVALONATE PYROPHOSPHATE DECARBOXYLASE; MVD","url":"https://www.omim.org/entry/603236"},{"mim_id":"251170","title":"MEVALONATE KINASE; MVK","url":"https://www.omim.org/entry/251170"},{"mim_id":"175900","title":"POROKERATOSIS 3, MULTIPLE TYPES; POROK3","url":"https://www.omim.org/entry/175900"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Cytosol","reliability":"Approved"},{"location":"Cell Junctions","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/MVD"},"hgnc":{"alias_symbol":["MPD"],"prev_symbol":[]},"alphafold":{"accession":"P53602","domains":[{"cath_id":"3.30.230.10","chopping":"9-189_381-388","consensus_level":"high","plddt":90.9543,"start":9,"end":388},{"cath_id":"3.30.70.890","chopping":"196-375","consensus_level":"high","plddt":94.236,"start":196,"end":375}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P53602","model_url":"https://alphafold.ebi.ac.uk/files/AF-P53602-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P53602-F1-predicted_aligned_error_v6.png","plddt_mean":92.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=MVD","jax_strain_url":"https://www.jax.org/strain/search?query=MVD"},"sequence":{"accession":"P53602","fasta_url":"https://rest.uniprot.org/uniprotkb/P53602.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P53602/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P53602"}},"corpus_meta":[{"pmid":"18160670","id":"PMC_18160670","title":"Ratio of mutant JAK2-V617F to wild-type Jak2 determines the MPD phenotypes in transgenic mice.","date":"2007","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/18160670","citation_count":359,"is_preprint":false},{"pmid":"16670266","id":"PMC_16670266","title":"JAK2V617F expression in murine hematopoietic cells leads to MPD mimicking human PV with secondary myelofibrosis.","date":"2006","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/16670266","citation_count":345,"is_preprint":false},{"pmid":"24963042","id":"PMC_24963042","title":"MPD-RC 101 prospective study of reduced-intensity allogeneic hematopoietic stem cell transplantation in patients with myelofibrosis.","date":"2014","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/24963042","citation_count":112,"is_preprint":false},{"pmid":"17306510","id":"PMC_17306510","title":"Isolation of a chlorpyrifos-degrading bacterium, Sphingomonas sp. strain Dsp-2, and cloning of the mpd gene.","date":"2007","source":"Research in 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PRV-1 overexpression, and EEC formation define a similar cohort of MPD patients.","date":"2005","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/15985544","citation_count":87,"is_preprint":false},{"pmid":"16775432","id":"PMC_16775432","title":"CD147, MMP-2, MMP-9 and MVD-CD34 are significant predictors of recurrence after liver transplantation in hepatocellular carcinoma patients.","date":"2006","source":"Cancer biology & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/16775432","citation_count":87,"is_preprint":false},{"pmid":"18030353","id":"PMC_18030353","title":"SNP array karyotyping allows for the detection of uniparental disomy and cryptic chromosomal abnormalities in MDS/MPD-U and MPD.","date":"2007","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/18030353","citation_count":74,"is_preprint":false},{"pmid":"23326384","id":"PMC_23326384","title":"VEGF, HIF-1α expression and MVD as an angiogenic network in familial breast cancer.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23326384","citation_count":73,"is_preprint":false},{"pmid":"18723264","id":"PMC_18723264","title":"Phenotypic variability within the JAK2 V617F-positive MPD: roles of progenitor cell and neutrophil allele burdens.","date":"2008","source":"Experimental hematology","url":"https://pubmed.ncbi.nlm.nih.gov/18723264","citation_count":70,"is_preprint":false},{"pmid":"19134023","id":"PMC_19134023","title":"AML transformation in 56 patients with Ph- MPD in two well defined populations.","date":"2009","source":"European journal of haematology","url":"https://pubmed.ncbi.nlm.nih.gov/19134023","citation_count":64,"is_preprint":false},{"pmid":"12115430","id":"PMC_12115430","title":"Biodegradation of crude oil across a wide range of salinities by an extremely halotolerant bacterial consortium MPD-M, immobilized onto polypropylene fibers.","date":"2002","source":"Biotechnology and 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JAK2-V617F.","date":"2008","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/19047681","citation_count":58,"is_preprint":false},{"pmid":"31207227","id":"PMC_31207227","title":"Clonal Expansion of Second-Hit Cells with Somatic Recombinations or C>T Transitions Form Porokeratosis in MVD or MVK Mutant Heterozygotes.","date":"2019","source":"The Journal of investigative dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/31207227","citation_count":53,"is_preprint":false},{"pmid":"15142682","id":"PMC_15142682","title":"Correlation of p53 and bcl-2 expression with vascular endothelial growth factor (VEGF), microvessel density (MVD) and clinico-pathological features in colon cancer.","date":"2004","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/15142682","citation_count":43,"is_preprint":false},{"pmid":"22102583","id":"PMC_22102583","title":"Mouse Phenome Database (MPD).","date":"2011","source":"Nucleic acids 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dermatology","url":"https://pubmed.ncbi.nlm.nih.gov/39132030","citation_count":1,"is_preprint":false},{"pmid":"16610088","id":"PMC_16610088","title":"[Relationship of angiopoietins expression with microvessel density (MVD) in human colorectal tumors].","date":"2006","source":"Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/16610088","citation_count":1,"is_preprint":false},{"pmid":"25948208","id":"PMC_25948208","title":"[Effect of Compound Zaofan Pill on Bone Marrow MVD and VEGF of Patients with Chronic Aplastic Anemia].","date":"2015","source":"Zhongguo shi yan xue ye xue za zhi","url":"https://pubmed.ncbi.nlm.nih.gov/25948208","citation_count":1,"is_preprint":false},{"pmid":"40587675","id":"PMC_40587675","title":"The expression and relationship of VEGF and MVD in type I endometrial cancer.","date":"2025","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/40587675","citation_count":0,"is_preprint":false},{"pmid":"19734574","id":"PMC_19734574","title":"MVD and VEGF expression in the acute liver injury treated with allogeneic MBMCs transplantation.","date":"2009","source":"Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/19734574","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":53412,"output_tokens":3310,"usd":0.104943,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10178,"output_tokens":2758,"usd":0.05992,"stage2_stop_reason":"end_turn"},"total_usd":0.164863,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"Looking through the corpus, I need to identify papers about the canonical MVD gene (mevalonate diphosphate decarboxylase, also known as MPD - mevalonate pyrophosphate decarboxylase). This enzyme catalyzes the ATP-dependent decarboxylation of mevalonate 5-diphosphate to isopentenyl diphosphate in the mevalonate/cholesterol biosynthesis pathway.\n\nMost papers in this corpus use MVD as an abbreviation for \"microvessel density\" or MPD for \"myeloproliferative disorder\" — these are not about the gene. I need to filter to papers about the actual MVD enzyme.\n\nRelevant papers:\n- PMID:12646231 - Mortalin-MPD interactions (mevalonate pyrophosphate decarboxylase)\n- PMID:30942823 - Second-hit MVD mutations in linear porokeratosis\n- PMID:31207227 - Clonal expansion with MVD/MVK mutations in porokeratosis\n- PMID:34135477 - MVD as candidate gene for hearing impairment\n- PMID:31156588 - MVD/Erg19 in Aspergillus oryzae (fungal ortholog)\n- PMID:12073030 - Characterization of C. albicans MVD (fungal ortholog)\n- PMID:19653015 - Simulation of MVD structure/function\n- PMID:37227548 - MvdF250S/+ knock-in mouse model\n- PMID:35665211 - T-cell subsets in porokeratosis with MVD variants\n- PMID:30040919 - \"Spatula MVD\" vitrification - this is NOT about the gene\n- PMID:34188266 - MVD mutation analysis in DSAP\n- PMID:33491095 - Porokeratosis plantaris with MVD variants\n- PMID:39132030 - MVD variants in disseminated superficial porokeratosis\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2003,\n      \"finding\": \"Mevalonate pyrophosphate decarboxylase (MVD/MPD) was identified as a binding partner of mortalin (mot-2/GRP75) via yeast two-hybrid screen, confirmed by mammalian two-hybrid assay and in vivo co-immunoprecipitation. Overexpression of mortalin reduced the level of Ras and phosphorylated ERK2, effects rescued by co-expression of MVD, establishing a functional link between mortalin, MVD, and Ras-ERK signaling in control of cell proliferation.\",\n      \"method\": \"Yeast two-hybrid screen, mammalian two-hybrid assay, co-immunoprecipitation, overexpression rescue experiment\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 / Moderate — reciprocal two-hybrid + Co-IP in mammalian cells + functional rescue, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"12646231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Molecular docking and MD simulation of S. cerevisiae MVD identified Ala15, Lys18, Ser121, and Ser155 as residues within hydrogen-bond distance of the substrate mevalonate diphosphate (MDP); Lys22, Ser153, and Ser155 for ATP; and Tyr19, Ser121, Ser153, Gly154, and Thr209 for the inhibitor trifluoromevalonate (TFMDP). A water molecule was found between Asp302 (a known catalytic residue) and C3 of MDP, suggesting deprotonation of the C3 hydroxyl occurs via a water bridge, and Ser121 was proposed to orient MDP for phosphorylation/decarboxylation.\",\n      \"method\": \"Molecular docking (Hex 4.2) and 1.5 ns molecular dynamics simulation (GROMACS)\",\n      \"journal\": \"Journal of molecular modeling\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental mutagenesis or structural validation in this paper\",\n      \"pmids\": [\"19653015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"The MVD gene of Candida albicans encodes a 362-aa mevalonate diphosphate decarboxylase (39.5 kDa) that functionally complements a temperature-sensitive S. cerevisiae erg19(ts) mutant lacking MVD activity, demonstrating conservation of enzymatic function. Northern analysis showed MVD expression is regulated by carbon source, growth phase, and yeast-to-hypha transition.\",\n      \"method\": \"Heterologous complementation in yeast (erg19 ts mutant), Western blot (epitope-tagged protein), Northern blot\",\n      \"journal\": \"Molecular genetics and genomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional complementation assay with protein expression confirmation, single lab, two orthogonal methods\",\n      \"pmids\": [\"12073030\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In Aspergillus oryzae, the MVD ortholog AoErg19 localizes to the vacuole (by subcellular localization analysis) and is required for ergosterol biosynthesis; both overexpression and RNAi knockdown of Aoerg19 decreased ergosterol content and increased sensitivity to ergosterol biosynthesis inhibitors, temperature stress, salt, and ethanol. Overexpression of Aoerg19 also led to feedback-mediated downregulation of Aoerg8 (mevalonate kinase).\",\n      \"method\": \"Subcellular localization (fluorescence), qRT-PCR, RNAi knockdown, overexpression, yeast complementation assay, sterol quantification\",\n      \"journal\": \"Frontiers in microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (localization, KD, OE, sterol assay) in single lab fungal ortholog study\",\n      \"pmids\": [\"31156588\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In patients with linear porokeratosis, whole-exome sequencing of paired lesional skin and blood identified a two-hit mechanism: a germline heterozygous MVD splice-site mutation (c.70+5G>A) plus a somatic frameshift deletion (c.811_815del, p.F271Afs*33) confined to lesional skin, establishing that biallelic loss of MVD function in keratinocytes is sufficient to produce porokeratosis lesions.\",\n      \"method\": \"Whole-exome sequencing of paired lesional skin and blood/saliva samples\",\n      \"journal\": \"JAMA dermatology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — paired WES with somatic/germline discrimination, single study, multiple patients with orthogonal confirmation\",\n      \"pmids\": [\"30942823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In disseminated superficial actinic porokeratosis (DSAP) and linear porokeratosis, each individual skin lesion harbored a distinct second-hit mutation (somatic homologous recombination rendering the germline MVD mutation biallelic, or a new C>T transition in the wild-type allele) exclusively in the epidermis, demonstrating that postnatal biallelic deficiency of MVD in a single keratinocyte precursor drives clonal expansion to form each lesion (Knudson two-hit mechanism).\",\n      \"method\": \"Targeted sequencing of individual DSAP lesions and matched normal tissue; somatic recombination and mutation analysis\",\n      \"journal\": \"The Journal of investigative dermatology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple lesions from multiple patients with paired normal tissue sequencing, independently replicates the two-hit finding from PMID:30942823 using orthogonal molecular methods\",\n      \"pmids\": [\"31207227\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Three families with porokeratosis plantaris, palmaris et disseminata all carried the germline heterozygous MVD variant c.70+5G>A, and loss of heterozygosity due to a somatic second-hit mutation was found in affected skin of 2 of 3 such patients, indicating this subtype shares the same two-hit pathogenetic mechanism (biallelic MVD inactivation in keratinocytes) as other porokeratosis subtypes.\",\n      \"method\": \"Mutation analysis of blood and skin biopsy DNA; loss-of-heterozygosity analysis\",\n      \"journal\": \"Acta dermato-venereologica\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct sequencing of paired tissue samples in multiple patients, single study replicating two-hit mechanism\",\n      \"pmids\": [\"33491095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Flow cytometry of PBMCs from porokeratosis patients with MVD variants revealed significantly decreased frequencies of CD8+ and Vγ9Vδ2 T cells compared to normal controls, and dysregulated secretion of pro-inflammatory cytokines (IFN-γ, TNF-α) by T cells, implicating MVD-dependent mevalonate pathway activity in the regulation of peripheral T-cell subsets.\",\n      \"method\": \"Flow cytometry; targeted exome sequencing for variant confirmation\",\n      \"journal\": \"Skin health and disease\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single method (flow cytometry), single small cohort, no direct enzymatic or pathway rescue experiment\",\n      \"pmids\": [\"35665211\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"A CRISPR/Cas9 knock-in mouse model carrying the MvdF250S/+ mutation (equivalent to human MVDF249S, the most common pathogenic variant in Chinese porokeratosis patients) showed reduced cutaneous Mvd protein expression. Upon imiquimod challenge, MvdF250S/+ mice exhibited decreased skin inflammation (reduced IL-17a, IL-1β, and cutaneous proliferation) compared to wild-type, and also showed downregulated collagen generation, upregulated Fabp3 expression, and activated autophagy, with no significant changes in key cholesterol-regulation genes.\",\n      \"method\": \"CRISPR/Cas9 knock-in mouse model; imiquimod-induced inflammation model; Western blot; immunofluorescence; qPCR\",\n      \"journal\": \"Inflammation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo knock-in model with multiple phenotypic readouts, single lab, orthogonal methods (protein, mRNA, histology)\",\n      \"pmids\": [\"37227548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Immunohistochemistry of mouse cochlear tissue showed MVD protein expression is prominent in spiral ganglion cells (rather than sensory hair cells), and a homozygous missense variant in MVD co-segregated with autosomal recessive nonsyndromic profound prelingual sensorineural hearing impairment in a consanguineous Pakistani family, supported by linkage analysis and in silico structural analysis predicting conformational changes.\",\n      \"method\": \"Exome sequencing, Sanger sequencing, linkage analysis, immunohistochemistry of mouse cochlear tissue, RNAseq expression profiling, in silico protein modeling\",\n      \"journal\": \"European journal of human genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — genetic association with IHC localization, no functional rescue or enzymatic assay; single family\",\n      \"pmids\": [\"34135477\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"MVD (mevalonate diphosphate decarboxylase) catalyzes the ATP-dependent decarboxylation of mevalonate 5-diphosphate to isopentenyl diphosphate in the mevalonate pathway; it physically interacts with mortalin (GRP75) to modulate Ras-ERK signaling and cell proliferation, and biallelic loss of MVD function in keratinocytes—via germline plus somatic second-hit mutations—drives clonal expansion and porokeratosis lesion formation through a Knudson two-hit mechanism, while a heterozygous knock-in mouse model demonstrates that partial MVD loss attenuates skin inflammation and activates autophagy without major effects on cholesterol gene regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"MVD encodes mevalonate diphosphate decarboxylase, a conserved enzyme of the mevalonate/sterol biosynthesis pathway whose fungal orthologs functionally complement yeast MVD-deficient mutants and are required for ergosterol production [#2, #3]. Beyond its metabolic role, MVD physically interacts with mortalin (GRP75); mortalin overexpression lowers Ras and phosphorylated ERK2, an effect rescued by co-expressed MVD, linking MVD to Ras-ERK signaling control of proliferation [#0]. In human skin, biallelic loss of MVD function in keratinocytes is sufficient to cause porokeratosis: affected individuals carry a germline heterozygous MVD mutation and acquire a distinct somatic second-hit (frameshift, transition, or loss of heterozygosity) in each lesion, so that clonal expansion of an MVD-deficient keratinocyte precursor generates each lesion through a Knudson two-hit mechanism across multiple porokeratosis subtypes [#4, #5, #6]. A knock-in mouse carrying a porokeratosis-equivalent Mvd variant shows reduced cutaneous Mvd protein and, upon inflammatory challenge, attenuated skin inflammation with activated autophagy and no significant change in cholesterol-regulatory genes [#8]. A homozygous missense MVD variant co-segregates with autosomal recessive nonsyndromic sensorineural hearing impairment, with MVD protein localized to cochlear spiral ganglion cells [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Establishing that the MVD gene product is a bona fide mevalonate diphosphate decarboxylase required showing its enzymatic function is conserved and physiologically regulated.\",\n      \"evidence\": \"Heterologous complementation of a yeast erg19(ts) mutant by Candida albicans MVD, with protein expression and Northern analysis of regulation\",\n      \"pmids\": [\"12073030\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Does not characterize the human MVD enzyme directly\", \"Catalytic residues and kinetics not defined here\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Whether MVD has roles beyond metabolism was addressed by identifying a protein partner that connects it to growth-control signaling.\",\n      \"evidence\": \"Yeast and mammalian two-hybrid plus Co-IP identifying mortalin/GRP75 binding, with overexpression rescue of mortalin-induced Ras/pERK2 suppression\",\n      \"pmids\": [\"12646231\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking the enzyme to Ras-ERK is not defined\", \"Single lab; physiological relevance in vivo untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"The structural basis for substrate, ATP, and inhibitor binding was probed to rationalize the catalytic mechanism of decarboxylation.\",\n      \"evidence\": \"Molecular docking and short MD simulation of S. cerevisiae MVD predicting substrate/ATP/inhibitor-contacting residues and a water-bridge deprotonation model\",\n      \"pmids\": [\"19653015\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Purely computational; no experimental mutagenesis or crystal structure validation\", \"Predictions are for the yeast enzyme, not human MVD\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The disease relevance of MVD was established by showing biallelic keratinocyte inactivation causes porokeratosis via combined germline and somatic mutations.\",\n      \"evidence\": \"Paired whole-exome sequencing of lesional skin versus blood in linear porokeratosis identifying germline splice plus somatic frameshift hits; targeted per-lesion sequencing in DSAP showing distinct second hits per lesion\",\n      \"pmids\": [\"30942823\", \"31207227\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Downstream metabolic consequence of MVD loss in keratinocytes not mechanistically traced\", \"How biallelic loss drives clonal expansion at the pathway level unresolved\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Whether the vacuolar/sterol-pathway role of MVD is conserved and feedback-regulated was tested in a filamentous fungus.\",\n      \"evidence\": \"Subcellular localization, RNAi, overexpression, and sterol quantification of the Aspergillus oryzae ortholog AoErg19\",\n      \"pmids\": [\"31156588\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Fungal ortholog; mammalian localization not addressed\", \"Feedback regulation of human MVD pathway not established\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"The two-hit model was extended across porokeratosis subtypes and connected to immune dysregulation in patients.\",\n      \"evidence\": \"Mutation and loss-of-heterozygosity analysis in porokeratosis plantaris/palmaris families; flow cytometry of patient PBMCs showing altered CD8+/Vd9Vd2 T-cell frequencies and cytokines\",\n      \"pmids\": [\"33491095\", \"35665211\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Causal link between MVD loss and T-cell changes not demonstrated\", \"Immune findings rest on a single small cohort with one method\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"A second disease association was proposed, linking MVD to hearing through spiral ganglion expression.\",\n      \"evidence\": \"Exome and linkage analysis in a consanguineous family with recessive hearing impairment plus mouse cochlear immunohistochemistry\",\n      \"pmids\": [\"34135477\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No functional or enzymatic rescue; single family\", \"Causal mechanism in auditory neurons untested\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"An in vivo model defined the cellular consequences of partial MVD loss, separating inflammatory and autophagy effects from cholesterol regulation.\",\n      \"evidence\": \"CRISPR/Cas9 MvdF250S/+ knock-in mouse with imiquimod challenge, assessed by Western blot, immunofluorescence, and qPCR\",\n      \"pmids\": [\"37227548\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking MVD loss to autophagy activation not defined\", \"Heterozygous model does not reproduce biallelic keratinocyte loss seen in lesions\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How biallelic MVD enzymatic deficiency mechanistically drives keratinocyte clonal expansion, autophagy, and inflammation — and whether the mortalin/Ras-ERK interaction operates in these contexts — remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No defined metabolic intermediate linking MVD loss to lesion phenotype\", \"Mortalin-MVD signaling not tested in skin or hearing models\", \"No structural validation of human enzyme catalytic mechanism\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016829\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005773\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"HSPA9\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}