2024
Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms
Hong Y, Pasca S, Shi W, Puiu D, Lake N, Lek M, Ru M, Grove M, Prizment A, Joshu C, Platz E, Guallar E, Arking D, Gondek L. Mitochondrial heteroplasmy improves risk prediction for myeloid neoplasms. Nature Communications 2024, 15: 10133. PMID: 39578475, PMCID: PMC11584845, DOI: 10.1038/s41467-024-54443-3.Peer-Reviewed Original ResearchConceptsClonal hematopoiesis of indeterminate potentialClonal hematopoiesisVariant allele fractionHeteroplasmic variantsIndeterminate potentialMyeloid neoplasmsHeteroplasmyMultiple mutationsAllele fractionMutationsHigh-risk groupPathogenic risk factorsMarkersRisk score modelDeleteriousnessSpliceosomeHematologic malignanciesRisk stratificationNeoplasm developmentNeoplasmsNeoplasm incidenceRisk factorsVariants
2023
Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality
Hong Y, Battle S, Shi W, Puiu D, Pillalamarri V, Xie J, Pankratz N, Lake N, Lek M, Rotter J, Rich S, Kooperberg C, Reiner A, Auer P, Heard-Costa N, Liu C, Lai M, Murabito J, Levy D, Grove M, Alonso A, Gibbs R, Dugan-Perez S, Gondek L, Guallar E, Arking D. Deleterious heteroplasmic mitochondrial mutations are associated with an increased risk of overall and cancer-specific mortality. Nature Communications 2023, 14: 6113. PMID: 37777527, PMCID: PMC10542802, DOI: 10.1038/s41467-023-41785-7.Peer-Reviewed Original ResearchConceptsSingle nucleotide variantsOwn circular genomeState of heteroplasmyAging-related diseasesNuclear genomeMitochondrial genomeCircular genomeMtDNA single nucleotide variantsMitochondrial DNASomatic cellsMitochondrial mutationsMtDNA heteroplasmyGenomeNucleotide variantsHeteroplasmyDNA moleculesFunctional roleMitochondriaUK BiobankCertain cancersVariantsDNAMutationsCopiesCellsMulti-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease
Amarasekera S, Hock D, Lake N, Calvo S, Grønborg S, Krzesinski E, Amor D, Fahey M, Simons C, Wibrand F, Mootha V, Lek M, Lunke S, Stark Z, Østergaard E, Christodoulou J, Thorburn D, Stroud D, Compton A. Multi-omics identifies large mitoribosomal subunit instability caused by pathogenic MRPL39 variants as a cause of pediatric onset mitochondrial disease. Human Molecular Genetics 2023, 32: 2441-2454. PMID: 37133451, PMCID: PMC10360397, DOI: 10.1093/hmg/ddad069.Peer-Reviewed Original ResearchMeSH KeywordsDNA, MitochondrialHumansLeigh DiseaseMitochondriaMitochondrial DiseasesMitochondrial ProteinsMultiomicsMutationRibosomal ProteinsConceptsQuantitative proteomicsMitochondrial oxidative phosphorylation systemProtein complex assemblySmall mitoribosomal subunitExome sequencingOxidative phosphorylation systemMitochondrial deoxyribonucleic acidMitochondrial ribosomesMitoribosomal subunitDeoxyribonucleic acidGene-disease associationsLarge subunitOXPHOS disordersSmall subunitComplex assemblyPhosphorylation systemProteomic dataComplex abundanceFunctional validationDisease genesGenome sequencingMitochondrial diseaseCryptic exonGene matchingProtein signatures
2022
MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA
Lake NJ, Zhou L, Xu J, Lek M. MitoVisualize: a resource for analysis of variants in human mitochondrial RNAs and DNA. Bioinformatics 2022, 38: 2967-2969. PMID: 35561159, DOI: 10.1093/bioinformatics/btac216.Peer-Reviewed Original ResearchConceptsRibosomal RNA secondary structuresHuman mitochondrial RNAMitochondrial transfer RNAsPost-transcriptional modificationsHuman mitochondrial DNADisease-associated variantsRNA secondary structureEffects of variantsMtDNA mapMitochondrial RNAMtDNA variationMitochondrial DNATransfer RNAAnalysis of variantsRNA structureSecondary structureVariant annotationLarge deletionsSupplementary dataVariant interpretationRNADNAVariantsGenesNew toolMitochondrial DNA variation across 56,434 individuals in gnomAD
Laricchia KM, Lake NJ, Watts NA, Shand M, Haessly A, Gauthier L, Benjamin D, Banks E, Soto J, Garimella K, Emery J, Consortium G, Rehm HL, MacArthur DG, Tiao G, Lek M, Mootha VK, Calvo SE. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Research 2022, 32: gr.276013.121. PMID: 35074858, PMCID: PMC8896463, DOI: 10.1101/gr.276013.121.Peer-Reviewed Original ResearchMeSH KeywordsCell NucleusDNA, MitochondrialGene FrequencyGenomeGenome, MitochondrialHumansMitochondriaSequence Analysis, DNAConceptsMtDNA variantsMitochondrial DNA variationPathogenic mtDNA variantsWhole genome sequencesUnique mtDNA variantsGenome Aggregation DatabasePopulation allele frequenciesAllele frequenciesMtDNA copy numberMitochondrial genomeNuclear sequencesVariant callsDNA variationIndividuals of EuropeanMtDNA genomeAncestral populationsMtDNA moleculesGenomic databasesHeteroplasmic variantsNuclear DNAHomoplasmic variantsMitochondrial originFalse positive variant callsMtDNA copiesMitochondrial haplogroups
2017
Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome
Lake N, Webb B, Stroud D, Richman T, Ruzzenente B, Compton A, Mountford H, Pulman J, Zangarelli C, Rio M, Boddaert N, Assouline Z, Sherpa M, Schadt E, Houten S, Byrnes J, McCormick E, Zolkipli-Cunningham Z, Haude K, Zhang Z, Retterer K, Bai R, Calvo S, Mootha V, Christodoulou J, Rötig A, Filipovska A, Cristian I, Falk M, Metodiev M, Thorburn D. Biallelic Mutations in MRPS34 Lead to Instability of the Small Mitoribosomal Subunit and Leigh Syndrome. American Journal Of Human Genetics 2017, 101: 239-254. PMID: 28777931, PMCID: PMC5544391, DOI: 10.1016/j.ajhg.2017.07.005.Peer-Reviewed Original ResearchConceptsSmall mitoribosomal subunitMitoribosomal subunitHuman oxidative phosphorylation (OXPHOS) systemMitochondrial protein translationOxidative phosphorylation systemMitochondrial translation defectQuantitative proteomic analysisSpecific cellular pathwaysLeigh syndromeLentiviral-mediated expressionMitoribosomal proteinsMitochondrial ribosomesOXPHOS subunitsMitochondrial translationOXPHOS defectsProtein translationMitochondrial DNATranslation defectsUnrelated familiesProteomic analysisPhosphorylation systemQuantitative proteomicsCellular pathwaysProtein subunitsSubunit proteinsATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism
Desai R, Frazier A, Durigon R, Patel H, Jones A, Rosa I, Lake N, Compton A, Mountford H, Tucker E, Mitchell A, Jackson D, Sesay A, Di Re M, van den Heuvel L, Burke D, Francis D, Lunke S, McGillivray G, Mandelstam S, Mochel F, Keren B, Jardel C, Turner A, Andrews P, Smeitink J, Spelbrink J, Heales S, Kohda M, Ohtake A, Murayama K, Okazaki Y, Lombès A, Holt I, Thorburn D, Spinazzola A. ATAD3 gene cluster deletions cause cerebellar dysfunction associated with altered mitochondrial DNA and cholesterol metabolism. Brain 2017, 140: 1595-1610. PMID: 28549128, PMCID: PMC5445257, DOI: 10.1093/brain/awx094.Peer-Reviewed Original ResearchConceptsATAD3A geneHigh-throughput sequencing technologyIntegration of mitochondriaMitochondrial DNA organizationCholesterol homeostasisCellular cholesterol homeostasisSingle nucleotide polymorphism arrayMitochondrial DNA abnormalitiesNiemann-Pick type C diseaseNucleotide polymorphism arrayWhole-exome sequencing dataDNA organizationExome sequencing dataMitochondrial DNACausal genesCholesterol metabolismGenomic analysisGenomic rearrangementsSequencing technologiesHigh homologySequencing dataType C diseaseDrug-induced perturbationsGene cluster deletionsGenes