2024
Quantifying constraint in the human mitochondrial genome
Lake N, Ma K, Liu W, Battle S, Laricchia K, Tiao G, Puiu D, Ng K, Cohen J, Compton A, Cowie S, Christodoulou J, Thorburn D, Zhao H, Arking D, Sunyaev S, Lek M. Quantifying constraint in the human mitochondrial genome. Nature 2024, 635: 390-397. PMID: 39415008, DOI: 10.1038/s41586-024-08048-x.Peer-Reviewed Original ResearchMitochondrial genomeDeleterious variationMtDNA mutator modelHuman mitochondrial genomeGenome Aggregation DatabaseMtDNA variationMtDNA variantsMitochondrial DNANoncoding regionsMitochondrial proteinsRRNA geneGenetic variationMtDNAThree-dimensional structureMutation modelPathogenic variationDisease relevanceAggregation DatabaseGenomeLarge-scale population datasetRRNAConstrained sitesGenesTRNAPopulation datasets
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 cancersVariantsDNAMutationsCopiesCells
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 tool
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