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Bury A, Pyle A, Vincent AE, Actis P, Hudson G. Nanobiopsy investigation of the subcellular mtDNA heteroplasmy in human tissues. Sci Rep 2024; 14:13789. [PMID: 38877095 PMCID: PMC11178779 DOI: 10.1038/s41598-024-64455-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 06/10/2024] [Indexed: 06/16/2024] Open
Abstract
Mitochondrial function is critical to continued cellular vitality and is an important contributor to a growing number of human diseases. Mitochondrial dysfunction is typically heterogeneous, mediated through the clonal expansion of mitochondrial DNA (mtDNA) variants in a subset of cells in a given tissue. To date, our understanding of the dynamics of clonal expansion of mtDNA variants has been technically limited to the single cell-level. Here, we report the use of nanobiopsy for subcellular sampling from human tissues, combined with next-generation sequencing to assess subcellular mtDNA mutation load in human tissue from mitochondrial disease patients. The ability to map mitochondrial mutation loads within individual cells of diseased tissue samples will further our understanding of mitochondrial genetic diseases.
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Affiliation(s)
- Alexander Bury
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK
- Bragg Centre for Materials Research, Leeds, UK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
| | - Paolo Actis
- School of Electronic and Electrical Engineering and Pollard Institute, University of Leeds, Leeds, UK.
- Bragg Centre for Materials Research, Leeds, UK.
| | - Gavin Hudson
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle, UK.
- NIHR Biomedical Research Centre, Faculty of Medical Science, Newcastle University, Newcastle, UK.
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Cañadas-Garre M, Baños-Jaime B, Maqueda JJ, Smyth LJ, Cappa R, Skelly R, Hill C, Brennan EP, Doyle R, Godson C, Maxwell AP, McKnight AJ. Genetic variants affecting mitochondrial function provide further insights for kidney disease. BMC Genomics 2024; 25:576. [PMID: 38858654 PMCID: PMC11163707 DOI: 10.1186/s12864-024-10449-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 05/24/2024] [Indexed: 06/12/2024] Open
Abstract
BACKGROUND Chronic kidney disease (CKD) is a complex disorder that has become a high prevalence global health problem, with diabetes being its predominant pathophysiologic driver. Autosomal genetic variation only explains some of the predisposition to kidney disease. Variations in the mitochondrial genome (mtDNA) and nuclear-encoded mitochondrial genes (NEMG) are implicated in susceptibility to kidney disease and CKD progression, but they have not been thoroughly explored. Our aim was to investigate the association of variation in both mtDNA and NEMG with CKD (and related traits), with a particular focus on diabetes. METHODS We used the UK Biobank (UKB) and UK-ROI, an independent collection of individuals with type 1 diabetes mellitus (T1DM) patients. RESULTS Fourteen mitochondrial variants were associated with estimated glomerular filtration rate (eGFR) in UKB. Mitochondrial variants and haplogroups U, H and J were associated with eGFR and serum variables. Mitochondrial haplogroup H was associated with all the serum variables regardless of the presence of diabetes. Mitochondrial haplogroup X was associated with end-stage kidney disease (ESKD) in UKB. We confirmed the influence of several known NEMG on kidney disease and function and found novel associations for SLC39A13, CFL1, ACP2 or ATP5G1 with serum variables and kidney damage, and for SLC4A1, NUP210 and MYH14 with ESKD. The G allele of TBC1D32-rs113987180 was associated with higher risk of ESKD in patients with diabetes (OR:9.879; CI95%:4.440-21.980; P = 2.0E-08). In UK-ROI, AGXT2-rs71615838 and SURF1-rs183853102 were associated with diabetic nephropathies, and TFB1M-rs869120 with eGFR. CONCLUSIONS We identified novel variants both in mtDNA and NEMG which may explain some of the missing heritability for CKD and kidney phenotypes. We confirmed the role of MT-ND5 and mitochondrial haplogroup H on renal disease (serum variables), and identified the MT-ND5-rs41535848G variant, along with mitochondrial haplogroup X, associated with higher risk of ESKD. Despite most of the associations were independent of diabetes, we also showed potential roles for NEMG in T1DM.
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Affiliation(s)
- Marisa Cañadas-Garre
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK.
- Genomic Oncology Area, Centre for Genomics and Oncological Research: Pfizer, GENYO, University of Granada-Andalusian Regional Government, PTS Granada. Avenida de La Ilustración 114, 18016, Granada, Spain.
- Hematology Department, Hospital Universitario Virgen de Las Nieves, Avenida de Las Fuerzas Armadas 2, 18014, Granada, Spain.
- Instituto de Investigación Biosanitaria de Granada (Ibs.GRANADA), Avda. de Madrid, 15, 18012, Granada, Spain.
| | - Blanca Baños-Jaime
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Instituto de Investigaciones Químicas (IIQ), Centro de Investigaciones Científicas Isla de La Cartuja (cicCartuja), Consejo Superior de Investigaciones Científicas (CSIC), Universidad de Sevilla, Avda. Américo Vespucio 49, 41092, Seville, Spain
| | - Joaquín J Maqueda
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Experimental Oncology Laboratory, IRCCS Rizzoli Orthopaedic Institute, 40136, Bologna, Italy
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126, Bologna, Italy
| | - Laura J Smyth
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ruaidhri Cappa
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Ryan Skelly
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Claire Hill
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
| | - Eoin P Brennan
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ross Doyle
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
- Mater Misericordiae University Hospital, Eccles St, Dublin, D07 R2WY, Ireland
| | - Catherine Godson
- UCD Diabetes Complications Research Centre, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- School of Medicine, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Alexander P Maxwell
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
- Regional Nephrology Unit, Belfast City Hospital, Level 11Lisburn Road, Belfast, BT9 7AB, UK
| | - Amy Jayne McKnight
- Molecular Epidemiology and Public Health Research Group, Centre for Public Health,, Queen's University Belfast, Institute for Clinical Sciences A, Royal Victoria Hospital, Belfast, BT12 6BA, UK
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Olbrich M, Hartmann AM, Künzel S, Aherrahrou Z, Schilf P, Baines JF, Ibrahim SM, Hirose M. Mitochondrial DNA variants and microbiota: An experimental strategy to identify novel therapeutic potential in chronic inflammatory diseases. Pharmacol Res 2024; 205:107231. [PMID: 38815878 DOI: 10.1016/j.phrs.2024.107231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/06/2024] [Accepted: 05/21/2024] [Indexed: 06/01/2024]
Abstract
We previously demonstrated that mice carrying natural mtDNA variants of the FVB/NJ strain (m.7778 G>T in the mt-Atp8 gene in mitochondrial complex V), namely C57BL/6 J-mtFVB/NJ (B6-mtFVB), exhibited (i) partial protection from experimental skin inflammatory diseases in an anti-murine type VII collagen antibody-induced skin inflammation model and psoriasiform dermatitis model; (ii) significantly altered metabolites, including short-chain fatty acids, according to targeted metabolomics of liver, skin and lymph node samples; and (iii) a differential composition of the gut microbiota according to bacterial 16 S rRNA gene sequencing of stool samples compared to wild-type C57BL/6 J (B6) mice. To further dissect these disease-contributing factors, we induced an experimental antibody-induced skin inflammatory disease in gnotobiotic mice. We performed shotgun metagenomic sequencing of caecum contents and untargeted metabolomics of liver, CD4+ T cell, and caecum content samples from conventional B6-mtFVB and B6 mice. We identified D-glucosamine as a candidate mediator that ameliorated disease severity in experimental antibody-induced skin inflammation by modulating immune cell function in T cells, neutrophils and macrophages. Because mice carrying mtDNA variants of the FVB/NJ strain show differential disease susceptibility to a wide range of experimental diseases, including diet-induced atherosclerosis in low-density lipoprotein receptor knockout mice and collagen antibody-induced arthritis in DBA/1 J mice, this experimental approach is valuable for identifying novel therapeutic options for skin inflammatory conditions and other chronic inflammatory diseases to which mice carrying specific mtDNA variants show differential susceptibility.
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Affiliation(s)
- Michael Olbrich
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; University Heart Centre Lübeck, Lübeck, Germany
| | | | - Sven Künzel
- Max Plank Institute of Evolutionary Biology, Plön, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - Zouhair Aherrahrou
- Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany; DZHK (German Centre for Cardiovascular Research), Partner Site Hamburg / Kiel / Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - Paul Schilf
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany
| | - John F Baines
- Max Plank Institute of Evolutionary Biology, Plön, Germany; University Heart Centre Lübeck, Lübeck, Germany; Institute of Experimental Medicine, Christian-Albrecht University of Kiel, Kiel, Germany
| | - Saleh M Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates; University Heart Centre Lübeck, Lübeck, Germany; College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, United Arab Emirates.
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany; University Heart Centre Lübeck, Lübeck, Germany; Lübeck Institute of Neurobiology, University of Lübeck, Germany.
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Shi P, Wang B, Shi S, Chu X, Liu C, Kang M, Hui J, Gou Y, Zhou R, Liu Y, Jia Y, Zhang F, Wen Y. Assessing the joint effects of mitochondrial genes and physical activity on the psychiatric phenotype of subjective well-being based on the UK Biobank data. Eur Arch Psychiatry Clin Neurosci 2024:10.1007/s00406-024-01822-y. [PMID: 38767715 DOI: 10.1007/s00406-024-01822-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/19/2024] [Indexed: 05/22/2024]
Abstract
Subjective well-being (SWB) is an important measure for mental health status. Previous research has shown that physical activity can affect an individual's well-being, yet the underlying molecular mechanism remains to be clarified. In this study, we aim to evaluate the potential interactions between mitochondrial genes and physical activity (PA) as well as their combined effects on individual well-being. SWB phenotype data in UK Biobank were enrolled for this study including nine aspects such as work/job satisfaction, health satisfaction, family relationship satisfaction, friendships satisfaction, financial situation satisfaction, ever depressed for a whole week, general happiness, general happiness with own health and belief that own life is meaningful. We made analysis for each aspects separately. Firstly, mitochondria-wide association studies (MiWAS) was conducted to assess the association of mitochondrial Single Nucleotide Polymorphisms SNP with each aspect of SWB. Then an interaction analysis of mitochondrial DNA (mtDNA) mutation and PA was performed to evaluate their joint effect on SWB status. Meanwhile, these two analysis were made for female and male group separately as well as the total samples, all under the control of possible confounding factors including gender, age, Townsend Deprivation Index (TDI), education, alcohol consumption, smoking habits, and 10 principal components. MiWAS analysis identified 45 mtSNPs associated with 9 phenotypes of SWB. For example, m.15218A > G on MT-CYB in the health satisfaction phenotype of the total subjects. Gender-specific analyses found 30 mtSNPs in females and 58 in males, involving 13 mtGenes. In mtDNA-PA interaction analysis, we also identified 10 significant mtDNA-PA interaction sets for SWB. For instance, m.13020 T > C (MT-ND5) was associated with the SWB financial situation satisfaction phenotype in all subjects (P = 0.00577). In addition, MiWAS analysis identified 12 mtGene variants associated with SWB, as MT-ND1 and MT-ND2. However, in mtDNA-PA interactions we detected 7 mtDNA affecting psychiatric disorders occurring, as in the friendships satisfaction phenotype (m.3394 T > C on MT-ND1). Our study results suggest an implication of the interaction between mitochondrial function and physical activity in the risk of psychiatric disorder development.
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Affiliation(s)
- Panxing Shi
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Bingyi Wang
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Sirong Shi
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Xiaoge Chu
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Chen Liu
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Meijuan Kang
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Jingni Hui
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yifan Gou
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ruixue Zhou
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Ye Liu
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yumeng Jia
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Feng Zhang
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Yan Wen
- NHC Key Laboratory of Environment and Endemic Diseases, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, China.
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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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Cortes-Figueiredo F, Asseyer S, Chien C, Zimmermann HG, Ruprecht K, Schmitz-Hübsch T, Bellmann-Strobl J, Paul F, Morais VA. CD4 + T cell mitochondrial genotype in Multiple Sclerosis: a cross-sectional and longitudinal analysis. Sci Rep 2024; 14:7507. [PMID: 38553515 PMCID: PMC10980703 DOI: 10.1038/s41598-024-57592-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 03/20/2024] [Indexed: 04/02/2024] Open
Abstract
Multiple Sclerosis (MS) is a chronic autoimmune demyelinating disease of the central nervous system (CNS), with a largely unknown etiology, where mitochondrial dysfunction likely contributes to neuroaxonal loss and brain atrophy. Mirroring the CNS, peripheral immune cells from patients with MS, particularly CD4+ T cells, show inappropriate mitochondrial phenotypes and/or oxidative phosphorylation (OxPhos) insufficiency, with a still unknown contribution of mitochondrial DNA (mtDNA). We hypothesized that mitochondrial genotype in CD4+ T cells might influence MS disease activity and progression. Thus, we performed a retrospective cross-sectional and longitudinal study on patients with a recent diagnosis of either Clinically Isolated Syndrome (CIS) or Relapsing-Remitting MS (RRMS) at two timepoints: 6 months (VIS1) and 36 months (VIS2) after disease onset. Our primary outcomes were the differences in mtDNA extracted from CD4+ T cells between: (I) patients with CIS/RRMS (PwMS) at VIS1 and age- and sex-matched healthy controls (HC), in the cross-sectional analysis, and (II) different diagnostic evolutions in PwMS from VIS1 to VIS2, in the longitudinal analysis. We successfully performed mtDNA whole genome sequencing (mean coverage: 2055.77 reads/base pair) in 183 samples (61 triplets). Nonetheless, mitochondrial genotype was not associated with a diagnosis of CIS/RRMS, nor with longitudinal diagnostic evolution.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Susanna Asseyer
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Claudia Chien
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Hanna G Zimmermann
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Einstein Center Digital Future, Berlin, Germany
| | - Klemens Ruprecht
- Department of Neurology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Tanja Schmitz-Hübsch
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Judith Bellmann-Strobl
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Friedemann Paul
- Experimental and Clinical Research Center, a Cooperation Between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité - Universitätsmedizin Berlin, Berlin, Germany.
- NeuroCure Clinical Research Center, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Vanessa A Morais
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal.
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Cao S, Zhang H, Liu Y, Sun Y, Chen ZJ. Cytoplasmic genome contributions to domestication and improvement of modern maize. BMC Biol 2024; 22:64. [PMID: 38481288 PMCID: PMC10938767 DOI: 10.1186/s12915-024-01859-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Studies on maize evolution and domestication are largely limited to the nuclear genomes, and the contribution of cytoplasmic genomes to selection and domestication of modern maize remains elusive. Maize cytoplasmic genomes have been classified into fertile (NA and NB) and cytoplasmic-nuclear male-sterility (CMS-S, CMS-C, and CMS-T) groups, but their contributions to modern maize breeding have not been systematically investigated. RESULTS Here we report co-selection and convergent evolution between nuclear and cytoplasmic genomes by analyzing whole genome sequencing data of 630 maize accessions modern maize and its relatives, including 24 fully assembled mitochondrial and chloroplast genomes. We show that the NB cytotype is associated with the expansion of modern maize to North America, gradually replaces the fertile NA cytotype probably through unequal division, and predominates in over 90% of modern elite inbred lines. The mode of cytoplasmic evolution is increased nucleotypic diversity among the genes involved in photosynthesis and energy metabolism, which are driven by selection and domestication. Furthermore, genome-wide association study reveals correlation of cytoplasmic nucleotypic variation with key agronomic and reproductive traits accompanied with the diversification of the nuclear genomes. CONCLUSIONS Our results indicate convergent evolution between cytoplasmic and nuclear genomes during maize domestication and breeding. These new insights into the important roles of mitochondrial and chloroplast genomes in maize domestication and improvement should help select elite inbred lines to improve yield stability and crop resilience of maize hybrids.
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Affiliation(s)
- Shuai Cao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Huanhuan Zhang
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Yang Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing, 210095, China
| | - Yi Sun
- Shanxi Key Laboratory of Minor Crops Germplasm Innovation and Molecular Breeding, Shanxi Agricultural University, Shanxi, Taiyuan, 030031, China
| | - Z Jeffrey Chen
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Cannon SJ, Hall T, Hawkes G, Colclough K, Boggan RM, Wright CF, Pickett SJ, Hattersley AT, Weedon MN, Patel KA. Penetrance and expressivity of mitochondrial variants in a large clinically unselected population. Hum Mol Genet 2024; 33:465-474. [PMID: 37988592 PMCID: PMC10877468 DOI: 10.1093/hmg/ddad194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/23/2023] Open
Abstract
Whole genome sequencing (WGS) from large clinically unselected cohorts provides a unique opportunity to assess the penetrance and expressivity of rare and/or known pathogenic mitochondrial variants in population. Using WGS from 179 862 clinically unselected individuals from the UK Biobank, we performed extensive single and rare variant aggregation association analyses of 15 881 mtDNA variants and 73 known pathogenic variants with 15 mitochondrial disease-relevant phenotypes. We identified 12 homoplasmic and one heteroplasmic variant (m.3243A>G) with genome-wide significant associations in our clinically unselected cohort. Heteroplasmic m.3243A>G (MAF = 0.0002, a known pathogenic variant) was associated with diabetes, deafness and heart failure and 12 homoplasmic variants increased aspartate aminotransferase levels including three low-frequency variants (MAF ~0.002 and beta~0.3 SD). Most pathogenic mitochondrial disease variants (n = 66/74) were rare in the population (<1:9000). Aggregated or single variant analysis of pathogenic variants showed low penetrance in unselected settings for the relevant phenotypes, except m.3243A>G. Multi-system disease risk and penetrance of diabetes, deafness and heart failure greatly increased with m.3243A>G level ≥ 10%. The odds ratio of these traits increased from 5.61, 12.3 and 10.1 to 25.1, 55.0 and 39.5, respectively. Diabetes risk with m.3243A>G was further influenced by type 2 diabetes genetic risk. Our study of mitochondrial variation in a large-unselected population identified novel associations and demonstrated that pathogenic mitochondrial variants have lower penetrance in clinically unselected settings. m.3243A>G was an exception at higher heteroplasmy showing a significant impact on health making it a good candidate for incidental reporting.
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Affiliation(s)
- Stuart J Cannon
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Timothy Hall
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Gareth Hawkes
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Kevin Colclough
- Exeter Genomics Laboratory, RILD Building, Royal Devon University Healthcare NHS Foundation Trust, Barrack Road, Exeter, EX2 5DW, United Kingdom
| | - Roisin M Boggan
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Caroline F Wright
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, United Kingdom
| | - Andrew T Hattersley
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Michael N Weedon
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
| | - Kashyap A Patel
- Department of Clinical and Biomedical Sciences, University of Exeter, 79 Heavitree Road, Exeter, EX2 4TH, United Kingdom
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9
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Jotwani V, Yang SY, Thiessen-Philbrook H, Parikh CR, Katz R, Tranah GJ, Ix JH, Cummings S, Waikar SS, Shlipak MG, Sarnak MJ, Parikh SM, Arking DE. Mitochondrial genetic variation and risk of chronic kidney disease and acute kidney injury in UK Biobank participants. Hum Genet 2024; 143:151-157. [PMID: 38349571 PMCID: PMC10881785 DOI: 10.1007/s00439-023-02615-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/28/2023] [Indexed: 02/22/2024]
Abstract
Experimental models suggest an important role for mitochondrial dysfunction in the pathogenesis of chronic kidney disease (CKD) and acute kidney injury (AKI), but little is known regarding the impact of common mitochondrial genetic variation on kidney health. We sought to evaluate associations of inherited mitochondrial DNA (mtDNA) variation with risk of CKD and AKI in a large population-based cohort. We categorized UK Biobank participants who self-identified as white into eight distinct mtDNA haplotypes, which were previously identified based on their associations with phenotypes associated with mitochondrial DNA copy number, a measure of mitochondrial function. We used linear and logistic regression models to evaluate associations of these mtDNA haplotypes with estimated glomerular filtration rate by serum creatinine and cystatin C (eGFRCr-CysC, N = 362,802), prevalent (N = 416 cases) and incident (N = 405 cases) end-stage kidney disease (ESKD), AKI defined by diagnostic codes (N = 14,170 cases), and urine albumin/creatinine ratio (ACR, N = 114,662). The mean age was 57 ± 8 years and the mean eGFR was 90 ± 14 ml/min/1.73 m2. MtDNA haplotype was significantly associated with eGFR (p = 2.8E-12), but not with prevalent ESKD (p = 5.9E-2), incident ESKD (p = 0.93), AKI (p = 0.26), or urine ACR (p = 0.54). The association of mtDNA haplotype with eGFR remained significant after adjustment for diabetes mellitus and hypertension (p = 1.2E-10). When compared to the reference haplotype, mtDNA haplotypes I (β = 0.402, standard error (SE) = 0.111; p = 2.7E-4), IV (β = 0.430, SE = 0.073; p = 4.2E-9), and V (β = 0.233, SE = 0.050; p = 2.7E-6) were each associated with higher eGFR. Among self-identified white UK Biobank participants, mtDNA haplotype was associated with eGFR, but not with ESKD, AKI or albuminuria.
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Affiliation(s)
- Vasantha Jotwani
- Department of Medicine, Kidney Health Research Collaborative, San Francisco Veterans Affairs Health Care System and University of California San Francisco, 4150 Clement Street, Bldg 2, Rm 145, San Francisco, CA, 94121, USA.
| | - Stephanie Y Yang
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Chirag R Parikh
- Division of Nephrology, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Ronit Katz
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Joachim H Ix
- Division of Nephrology-Hypertension, University of California San Diego, and Veterans Affairs San Diego Healthcare System, San Diego, CA, USA
| | - Steve Cummings
- Department of Medicine, Kidney Health Research Collaborative, San Francisco Veterans Affairs Health Care System and University of California San Francisco, 4150 Clement Street, Bldg 2, Rm 145, San Francisco, CA, 94121, USA
| | - Sushrut S Waikar
- Section of Nephrology, Department of Medicine, Boston University School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Michael G Shlipak
- Department of Medicine, Kidney Health Research Collaborative, San Francisco Veterans Affairs Health Care System and University of California San Francisco, 4150 Clement Street, Bldg 2, Rm 145, San Francisco, CA, 94121, USA
| | - Mark J Sarnak
- Division of Nephrology, Tufts Medical Center, Boston, MA, USA
| | - Samir M Parikh
- Division of Nephrology, Department of Medicine, and Department of Pharmacology, University of Texas Southwestern Medical School, Dallas, TX, USA
| | - Dan E Arking
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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10
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Silva M, Booth T, Moore J, Anastasiadou K, Walker D, Gilardet A, Barrington C, Kelly M, Williams M, Henderson M, Smith A, Bowsher D, Montgomery J, Skoglund P. An individual with Sarmatian-related ancestry in Roman Britain. Curr Biol 2024; 34:204-212.e6. [PMID: 38118448 DOI: 10.1016/j.cub.2023.11.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/22/2023]
Abstract
In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.1,2,3 In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.4,5 Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.
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Affiliation(s)
- Marina Silva
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Thomas Booth
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Joanna Moore
- Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom
| | - Kyriaki Anastasiadou
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Don Walker
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Alexandre Gilardet
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher Barrington
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Monica Kelly
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mia Williams
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Henderson
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Alex Smith
- Headland Archaeology, 13 Jane Street, Edinburgh EH6 5HE, UK
| | - David Bowsher
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Janet Montgomery
- Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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Vacchiano V, Palombo F, Ormanbekova D, Fiorini C, Fiorentino A, Caporali L, Mastrangelo A, Valentino ML, Capellari S, Liguori R, Carelli V. The genetic puzzle of a SOD1-patient with ocular ptosis and a motor neuron disease: a case report. Front Genet 2023; 14:1322067. [PMID: 38152653 PMCID: PMC10751346 DOI: 10.3389/fgene.2023.1322067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease with a complex genetic architecture, showing monogenic, oligogenic, and polygenic inheritance. In this study, we describe the case of a 71 years-old man diagnosed with ALS with atypical clinical features consisting in progressive ocular ptosis and sensorineural deafness. Genetic analyses revealed two heterozygous variants, in the SOD1 (OMIM*147450) and the TBK1 (OMIM*604834) genes respectively, and furthermore mitochondrial DNA (mtDNA) sequencing identified the homoplasmic m.14484T>C variant usually associated with Leber's Hereditary Optic Neuropathy (LHON). We discuss how all these variants may synergically impinge on mitochondrial function, possibly contributing to the pathogenic mechanisms which might ultimately lead to the neurodegenerative process, shaping the clinical ALS phenotype enriched by adjunctive clinical features.
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Affiliation(s)
- Veria Vacchiano
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Alessia Fiorentino
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Leonardo Caporali
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Andrea Mastrangelo
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Maria Lucia Valentino
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Sabina Capellari
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Rocco Liguori
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
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12
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Fähnrich A, Stephan I, Hirose M, Haarich F, Awadelkareem MA, Ibrahim S, Busch H, Wohlers I. North and East African mitochondrial genetic variation needs further characterization towards precision medicine. J Adv Res 2023; 54:59-76. [PMID: 36736695 DOI: 10.1016/j.jare.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
INTRODUCTION Mitochondria are maternally inherited cell organelles with their own genome, and perform various functions in eukaryotic cells such as energy production and cellular homeostasis. Due to their inheritance and manifold biological roles in health and disease, mitochondrial genetics serves a dual purpose of tracing the history as well as disease susceptibility of human populations across the globe. This work requires a comprehensive catalogue of commonly observed genetic variations in the mitochondrial DNAs for all regions throughout the world. So far, however, certain regions, such as North and East Africa have been understudied. OBJECTIVES To address this shortcoming, we have created the most comprehensive quality-controlled North and East African mitochondrial data set to date and use it for characterizing mitochondrial genetic variation in this region. METHODS We compiled 11 published cohorts with novel data for mitochondrial genomes from 159 Sudanese individuals. We combined these 641 mitochondrial sequences with sequences from the 1000 Genomes (n = 2504) and the Human Genome Diversity Project (n = 828) and used the tool haplocheck for extensive quality control and detection of in-sample contamination, as well as Nanopore long read sequencing for haplogroup validation of 18 samples. RESULTS Using a subset of high-coverage mitochondrial sequences, we predict 15 potentially novel haplogroups in North and East African subjects and observe likely phylogenetic deviations from the established PhyloTree reference for haplogroups L0a1 and L2a1. CONCLUSION Our findings demonstrate common hitherto unexplored variants in mitochondrial genomes of North and East Africa that lead to novel phylogenetic relationships between haplogroups present in these regions. These observations call for further in-depth population genetic studies in that region to enable the prospective use of mitochondrial genetic variation for precision medicine.
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Affiliation(s)
- Anke Fähnrich
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Isabel Stephan
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Misa Hirose
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany
| | - Franziska Haarich
- Institute for Cardiogenetics, University of Lübeck, DZHK (German Research Centre for Cardiovascular Research), Partner Site Hamburg/Lübeck/Kiel, and University Heart Center, Lübeck, Lübeck, Germany
| | - Mosab Ali Awadelkareem
- Faculty of Medical Laboratory Sciences, Al-Neelain University, Khartoum, Sudan; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford OX3 9DU, United Kingdom
| | - Saleh Ibrahim
- Genetics Division, Lübeck Institute of Experimental Dermatology, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Khalifa University, Abu Dhabi, United Arab Emirates
| | - Hauke Busch
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Inken Wohlers
- Medical Systems Biology Division, Lübeck Institute of Experimental Dermatology and Institute for Cardiogenetics, University of Lübeck, Ratzeburger Allee 160, 23562 Lübeck, Germany; Biomedical Data Science, Research Center Borstel, 23845 Borstel, Germany.
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13
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Liu L, Cheng S, Qi X, Meng P, Yang X, Pan C, Chen Y, Zhang H, Zhang Z, Zhang J, Li C, Wen Y, Jia Y, Cheng B, Zhang F. Mitochondria-wide association study observed significant interactions of mitochondrial respiratory and the inflammatory in the development of anxiety and depression. Transl Psychiatry 2023; 13:216. [PMID: 37344456 DOI: 10.1038/s41398-023-02518-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/23/2023] Open
Abstract
The aim of this study was to investigate the possible interaction of mitochondrial dysfunction and inflammatory cytokines in the risk of anxiety and depression. We utilized the UK Biobank for the sample of this study. A mitochondria-wide association(MiWAS) and interaction analysis was performed to investigate the interaction effects of mitochondrial DNA (mtDNA)×C-reactive protein (CRP) on the risks of self-reported anxiety (N = 72,476), general anxiety disorder (GAD-7) scores (N = 80,853), self-reported depression (N = 80,778), Patient Health Questionnaire (PHQ-9) scores (N = 80,520) in total samples, females and males, respectively, adjusting for sex, age, Townsend deprivation index (TDI), education score, alcohol intake, smoking and 10 principal components. In all, 25 mtSNPs and 10 mtSNPs showed significant level of association with self-reported anxiety and GAD-7 score respectively. A total of seven significant mtDNA × CRP interactions were found for anxiety, such as m.3915G>A(MT-ND1) for self-reported anxiety in total subjects (P = 6.59 × 10-3), m.4561T>C(MT-ND2) (P = 3.04 × 10-3) for GAD-7 score in total subjects. For depression, MiWAS identified 17 significant mtSNPs for self-reported depression and 14 significant mtSNPs for PHQ-9 scores. 17 significant mtDNA associations (2 for self-reported depression and 15 for PHQ-9 score) was identified, such as m.14869G>A(MT-CYB; P = 2.22 × 10-3) associated with self-reported depression and m.4561T>C (MT-ND2; P value = 3.02 × 10-8) associated with PHQ-9 score in all subjects. In addition, 5 common mtDNA shared with anxiety and depression were found in MiWAS, and 4 common mtDNA variants were detected to interact with CRP for anxiety and depression, such as m.9899T>C(MT-CO3). Our study suggests the important interaction effects of mitochondrial function and CRP on the risks of anxiety and depression.
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Affiliation(s)
- Li Liu
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Shiqiang Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xin Qi
- Precision Medicine Center, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, P. R. China
| | - Peilin Meng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Xuena Yang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chuyu Pan
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yujing Chen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Huijie Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Zhen Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Jingxi Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Chune Li
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yan Wen
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Yumeng Jia
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Bolun Cheng
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China
| | - Feng Zhang
- Key Laboratory of Trace Elements and Endemic Diseases, Collaborative Innovation Center of Endemic Disease and Health Promotion for Silk Road Region, School of Public Health, Health Science Center, Xi'an Jiaotong University, Xi'an, 710061, P. R. China.
- Department of Psychiatry, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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14
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Xing S, Jiang S, Wang S, Lin P, Sun H, Peng H, Yang J, Kong H, Wang S, Bai Q, Qiu R, Dai W, Yuan J, Ma Y, Yu X, Yao Y, Su J. Association of mitochondrial DNA variation with high myopia in a Han Chinese population. Mol Genet Genomics 2023:10.1007/s00438-023-02036-y. [PMID: 37277661 PMCID: PMC10363046 DOI: 10.1007/s00438-023-02036-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
High myopia (HM), which is characterized by oxidative stress, is one of the leading causes of visual impairment and blindness across the world. Family and population genetic studies have uncovered nuclear-genome variants in proteins functioned in the mitochondria. However, whether mitochondrial DNA mutations are involved in HM remains unexplored. Here, we performed the first large-scale whole-mitochondrial genome study in 9613 HM cases and 9606 control subjects of Han Chinese ancestry for identifying HM-associated mitochondrial variants. The single-variant association analysis identified nine novel genetic variants associated with HM reaching the entire mitochondrial wide significance level, including rs370378529 in ND2 with an odds ratio (OR) of 5.25. Interestingly, eight out of nine variants were predominantly located in related sub-haplogroups, i.e. m.5261G > A in B4b1c, m.12280A > G in G2a4, m.7912G > A in D4a3b, m.94G > A in D4e1, m.14857 T > C in D4e3, m.14280A > G in D5a2, m.16272A > G in G2a4, m.8718A > G in M71 and F1a3, indicating that the sub-haplogroup background can increase the susceptible risk for high myopia. The polygenic risk score analysis of the target and validation cohorts indicated a high accuracy for predicting HM with mtDNA variants (AUC = 0.641). Cumulatively, our findings highlight the critical roles of mitochondrial variants in untangling the genetic etiology of HM.
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Affiliation(s)
- Shilai Xing
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyi Jiang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Siyu Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Peng Lin
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Haojun Sun
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hui Peng
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Jiaying Yang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Hengte Kong
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Sheng Wang
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Qingshi Bai
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Ruowen Qiu
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
| | - Wei Dai
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China
| | - Jian Yuan
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Yunlong Ma
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China
| | - Xiaoguang Yu
- Institute of PSI Genomics, Wenzhou, 325024, China
| | - Yinghao Yao
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
| | - Jianzhong Su
- School of Ophthalmology and Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou, 325027, China.
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, 325011, China.
- National Clinical Research Center for Ocular Disease, Wenzhou, 325027, China.
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, 325101, Zhejiang, China.
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15
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Shamanskiy V, Mikhailova AA, Tretiakov EO, Ushakova K, Mikhailova AG, Oreshkov S, Knorre DA, Ree N, Overdevest JB, Lukowski SW, Gostimskaya I, Yurov V, Liou CW, Lin TK, Kunz WS, Reymond A, Mazunin I, Bazykin GA, Fellay J, Tanaka M, Khrapko K, Gunbin K, Popadin K. Secondary structure of the human mitochondrial genome affects formation of deletions. BMC Biol 2023; 21:103. [PMID: 37158879 PMCID: PMC10166460 DOI: 10.1186/s12915-023-01606-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Aging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain their distribution. Here, we hypothesized that the close proximity of direct repeats on single-stranded mitochondrial DNA (mtDNA) might play a role in the formation of deletions. RESULTS By analyzing human mtDNA deletions in the major arc of mtDNA, which is single-stranded during replication and is characterized by a high number of deletions, we found a non-uniform distribution with a "hot spot" where one deletion breakpoint occurred within the region of 6-9 kb and another within 13-16 kb of the mtDNA. This distribution was not explained by the presence of direct repeats, suggesting that other factors, such as the spatial proximity of these two regions, can be the cause. In silico analyses revealed that the single-stranded major arc may be organized as a large-scale hairpin-like loop with a center close to 11 kb and contacting regions between 6-9 kb and 13-16 kb, which would explain the high deletion activity in this contact zone. The direct repeats located within the contact zone, such as the well-known common repeat with a first arm at 8470-8482 bp (base pair) and a second arm at 13,447-13,459 bp, are three times more likely to cause deletions compared to direct repeats located outside of the contact zone. A comparison of age- and disease-associated deletions demonstrated that the contact zone plays a crucial role in explaining the age-associated deletions, emphasizing its importance in the rate of healthy aging. CONCLUSIONS Overall, we provide topological insights into the mechanism of age-associated deletion formation in human mtDNA, which could be used to predict somatic deletion burden and maximum lifespan in different human haplogroups and mammalian species.
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Affiliation(s)
- Victor Shamanskiy
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina A Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Evgenii O Tretiakov
- Department of Molecular Neurosciences, Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Kristina Ushakova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alina G Mikhailova
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Sergei Oreshkov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Dmitry A Knorre
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia Ree
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Jonathan B Overdevest
- Department of Otolaryngology, Columbia University Irving Medical Center, New York, USA
| | - Samuel W Lukowski
- Institute for Molecular Bioscience, University of Queensland, St Lucia, Brisbane, Australia
| | - Irina Gostimskaya
- Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Valerian Yurov
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Chia-Wei Liou
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Department of Neurology, Kaohsiung Chang-Gung Memorial Hospital and Chang-Gung University, Kaohsiung, Taiwan
| | - Wolfram S Kunz
- Division of Neurochemistry, Department of Experimental Epileptology and Cognition Research, University Bonn, Bonn, Germany
- Department of Epileptology, University Hospital of Bonn, Bonn, Germany
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Georgii A Bazykin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Laboratory of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russia
| | - Jacques Fellay
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Masashi Tanaka
- Department for Health and Longevity Research, National Institutes of Biomedical Innovation, Health and Nutrition, 1-23-1 Toyama, Shinjuku-Ku, Tokyo, 162-8636, Japan
- Department of Neurology, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-Ku, Tokyo, 113-8421, Japan
- Department of Clinical Laboratory, IMS Miyoshi General Hospital, Fujikubo, Miyoshi-Machi, Iruma, Saitama Prefecture, 974-3354-0041, Japan
| | | | - Konstantin Gunbin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Konstantin Popadin
- Center for Mitochondrial Functional Genomics, Immanuel Kant Baltic Federal University, Kaliningrad, Russia.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland.
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16
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Miller B, Kim SJ, Mehta HH, Cao K, Kumagai H, Thumaty N, Leelaprachakul N, Braniff RG, Jiao H, Vaughan J, Diedrich J, Saghatelian A, Arpawong TE, Crimmins EM, Ertekin-Taner N, Tubi MA, Hare ET, Braskie MN, Décarie-Spain L, Kanoski SE, Grodstein F, Bennett DA, Zhao L, Toga AW, Wan J, Yen K, Cohen P. Mitochondrial DNA variation in Alzheimer's disease reveals a unique microprotein called SHMOOSE. Mol Psychiatry 2023; 28:1813-1826. [PMID: 36127429 PMCID: PMC10027624 DOI: 10.1038/s41380-022-01769-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 08/15/2022] [Accepted: 08/26/2022] [Indexed: 01/22/2023]
Abstract
Mitochondrial DNA variants have previously associated with disease, but the underlying mechanisms have been largely elusive. Here, we report that mitochondrial SNP rs2853499 associated with Alzheimer's disease (AD), neuroimaging, and transcriptomics. We mapped rs2853499 to a novel mitochondrial small open reading frame called SHMOOSE with microprotein encoding potential. Indeed, we detected two unique SHMOOSE-derived peptide fragments in mitochondria by using mass spectrometry-the first unique mass spectrometry-based detection of a mitochondrial-encoded microprotein to date. Furthermore, cerebrospinal fluid (CSF) SHMOOSE levels in humans correlated with age, CSF tau, and brain white matter volume. We followed up on these genetic and biochemical findings by carrying out a series of functional experiments. SHMOOSE acted on the brain following intracerebroventricular administration, differentiated mitochondrial gene expression in multiple models, localized to mitochondria, bound the inner mitochondrial membrane protein mitofilin, and boosted mitochondrial oxygen consumption. Altogether, SHMOOSE has vast implications for the fields of neurobiology, Alzheimer's disease, and microproteins.
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Affiliation(s)
- Brendan Miller
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
| | - Su-Jeong Kim
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hemal H Mehta
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kevin Cao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Hiroshi Kumagai
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Neehar Thumaty
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Naphada Leelaprachakul
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Regina Gonzalez Braniff
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Henry Jiao
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Joan Vaughan
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Jolene Diedrich
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Alan Saghatelian
- Clayton Foundation Laboratories for Peptide Biology, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Thalida E Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | | | - Meral A Tubi
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Evan T Hare
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Meredith N Braskie
- Imaging Genetics Center, Institute for Neuroimaging and Informatics, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, University of Southern California, Los Angeles, CA, USA
| | - Léa Décarie-Spain
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Scott E Kanoski
- Neuroscience Graduate Program, University of Southern California, Los Angeles, CA, USA
- Human and Evolutionary Biology Section, Department of Biological Sciences, Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, CA, USA
| | - Francine Grodstein
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Lu Zhao
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Arthur W Toga
- Laboratory of Neuro Imaging, USC Stevens Neuroimaging and Informatics Institute, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - Junxiang Wan
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Kelvin Yen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Pinchas Cohen
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA.
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17
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:ijms24065798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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18
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Oxidized mitochondrial DNA induces gasdermin D oligomerization in systemic lupus erythematosus. Nat Commun 2023; 14:872. [PMID: 36797275 PMCID: PMC9935630 DOI: 10.1038/s41467-023-36522-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 02/01/2023] [Indexed: 02/18/2023] Open
Abstract
Although extracellular DNA is known to form immune complexes (ICs) with autoantibodies in systemic lupus erythematosus (SLE), the mechanisms leading to the release of DNA from cells remain poorly characterized. Here, we show that the pore-forming protein, gasdermin D (GSDMD), is required for nuclear DNA and mitochondrial DNA (mtDNA) release from neutrophils and lytic cell death following ex vivo stimulation with serum from patients with SLE and IFN-γ. Mechanistically, the activation of FcγR downregulated Serpinb1 following ex vivo stimulation with serum from patients with SLE, leading to spontaneous activation of both caspase-1/caspase-11 and cleavage of GSDMD into GSDMD-N. Furthermore, mtDNA oxidization promoted GSDMD-N oligomerization and cell death. In addition, GSDMD, but not peptidyl arginine deiminase 4 is necessary for extracellular mtDNA release from low-density granulocytes from SLE patients or healthy human neutrophils following incubation with ICs. Using the pristane-induced lupus model, we show that disease severity is significantly reduced in mice with neutrophil-specific Gsdmd deficiency or following treatment with the GSDMD inhibitor, disulfiram. Altogether, our study highlights an important role for oxidized mtDNA in inducing GSDMD oligomerization and pore formation. These findings also suggest that GSDMD might represent a possible therapeutic target in SLE.
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19
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Insulin Resistance in Mitochondrial Diabetes. Biomolecules 2023; 13:biom13010126. [PMID: 36671511 PMCID: PMC9855690 DOI: 10.3390/biom13010126] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 12/14/2022] [Accepted: 12/27/2022] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial diabetes (MD) is generally classified as a genetic defect of β-cells. The main pathophysiology is insulin secretion failure in pancreatic β-cells due to impaired mitochondrial ATP production. However, several reports have mentioned the presence of insulin resistance (IR) as a clinical feature of MD. As mitochondrial dysfunction is one of the important factors causing IR, we need to focus on IR as another pathophysiology of MD. In this special issue, we first briefly summarized the insulin signaling and molecular mechanisms of IR. Second, we overviewed currently confirmed pathogenic mitochondrial DNA (mtDNA) mutations from the MITOMAP database. The variants causing diabetes were mostly point mutations in the transfer RNA (tRNA) of the mitochondrial genome. Third, we focused on these variants leading to the recently described "tRNA modopathies" and reviewed the clinical features of patients with diabetes. Finally, we discussed the pathophysiology of MD caused by mtDNA mutations and explored the possible mechanism underlying the development of IR. This review should be beneficial to all clinicians involved in diagnostics and therapeutics related to diabetes and mitochondrial diseases.
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20
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Liu G, Ni C, Zhan J, Li W, Luo J, Liao Z, Locascio JJ, Xian W, Chen L, Pei Z, Corvol JC, Maple-Grødem J, Campbell MC, Elbaz A, Lesage S, Brice A, Hung AY, Schwarzschild MA, Hayes MT, Wills AM, Ravina B, Shoulson I, Taba P, Kõks S, Beach TG, Cormier-Dequaire F, Alves G, Tysnes OB, Perlmutter JS, Heutink P, van Hilten JJ, Barker RA, Williams-Gray CH, Scherzer CR. Mitochondrial haplogroups and cognitive progression in Parkinson's disease. Brain 2023; 146:42-49. [PMID: 36343661 PMCID: PMC10202390 DOI: 10.1093/brain/awac327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/08/2022] [Accepted: 08/22/2022] [Indexed: 11/09/2022] Open
Abstract
Mitochondria are a culprit in the onset of Parkinson's disease, but their role during disease progression is unclear. Here we used Cox proportional hazards models to exam the effect of variation in the mitochondrial genome on longitudinal cognitive and motor progression over time in 4064 patients with Parkinson's disease. Mitochondrial macro-haplogroup was associated with reduced risk of cognitive disease progression in the discovery and replication population. In the combined analysis, patients with the super macro-haplogroup J, T, U# had a 41% lower risk of cognitive progression with P = 2.42 × 10-6 compared to those with macro-haplogroup H. Exploratory analysis indicated that the common mitochondrial DNA variant, m.2706A>G, was associated with slower cognitive decline with a hazard ratio of 0.68 (95% confidence interval 0.56-0.81) and P = 2.46 × 10-5. Mitochondrial haplogroups were not appreciably linked to motor progression. This initial genetic survival study of the mitochondrial genome suggests that mitochondrial haplogroups may be associated with the pace of cognitive progression in Parkinson's disease over time.
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Affiliation(s)
- Ganqiang Liu
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Chunming Ni
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiamin Zhan
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Weimin Li
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Junfeng Luo
- Neurobiology Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhixiang Liao
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Joseph J Locascio
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Wenbiao Xian
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Ling Chen
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Zhong Pei
- Department of Neurology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Jean-Christophe Corvol
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, 4068 Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
| | - Meghan C Campbell
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alexis Elbaz
- Paris-Saclay University, UVSQ, Inserm, Gustave Roussy, ‘Exposome and Heredity’ Team, CESP, F94805 Villejuif, France
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Albert Y Hung
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael A Schwarzschild
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Michael T Hayes
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Anne-Marie Wills
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Ira Shoulson
- Department of Neurology, Center for Health and Technology, University of Rochester, Rochester, NY 14642, USA
| | - Pille Taba
- Department of Neurology and Neurosurgery, Institute of Clinical Medicine, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Sulev Kõks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, WA 6009, Australia
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Florence Cormier-Dequaire
- Sorbonne Université, Institut du Cerveau – Paris Brain Institute - ICM, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Assistance Publique Hôpitaux de Paris, Département de Neurologie et de Génétique, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Guido Alves
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, 4068 Stavanger, Norway
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
- Department of Neurology, Stavanger University Hospital, 4068 Stavanger, Norway
| | - Ole-Bjørn Tysnes
- Department of Neurology, Haukeland University Hospital, 5020 Bergen, Norway
- Department of Clinical Medicine, University of Bergen, 5020 Bergen, Norway
| | - Joel S Perlmutter
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Departments of Radiology and Neuroscience, Washington University School of Medicine, St. Louis, MO 63110, USA
- Program of Physical Therapy and Program of Occupational Therapy, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Peter Heutink
- German Center for Neurodegenerative diseases (DZNE), 72076 Tübingen, Germany
| | - Jacobus J van Hilten
- Department of Neurology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Roger A Barker
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
- Wellcome—MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0AW, UK
| | - Caroline H Williams-Gray
- John Van Geest Centre for Brain Repair, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0PY, UK
| | - Clemens R Scherzer
- APDA Center for Advanced Parkinson Research, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA
- Neurogenomics Lab, Harvard Medical School, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115, USA
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21
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Mackey DA, Ong JS, MacGregor S, Whiteman DC, Craig JE, Lopez Sanchez MIG, Kearns LS, Staffieri SE, Clarke L, McGuinness MB, Meteoukki W, Samuel S, Ruddle JB, Chen C, Fraser CL, Harrison J, Howell N, Hewitt AW. Is the disease risk and penetrance in Leber hereditary optic neuropathy actually low? Am J Hum Genet 2023; 110:170-176. [PMID: 36565701 PMCID: PMC9892764 DOI: 10.1016/j.ajhg.2022.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Pedigree analysis showed that a large proportion of Leber hereditary optic neuropathy (LHON) family members who carry a mitochondrial risk variant never lose vision. Mitochondrial haplotype appears to be a major factor influencing the risk of vision loss from LHON. Mitochondrial variants, including m.14484T>C and m.11778G>A, have been added to gene arrays, and thus many patients and research participants are tested for LHON mutations. Analysis of the UK Biobank and Australian cohort studies found more than 1 in 1,000 people in the general population carry either the m.14484T>C or the m.11778G>A LHON variant. None of the subset of carriers examined had visual acuity at 20/200 or worse, suggesting a very low penetrance of LHON. Haplogroup analysis of m.14484T>C carriers showed a high rate of haplogroup U subclades, previously shown to have low penetrance in pedigrees. Penetrance calculations of the general population are lower than pedigree calculations, most likely because of modifier genetic factors. This Matters Arising Response paper addresses the Watson et al. (2022) Matters Arising paper, published concurrently in The American Journal of Human Genetics.
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Affiliation(s)
- David A Mackey
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, 7000 TAS, Australia; The University of Western Australia, Centre for Ophthalmology and Visual Science, Lions Eye Institute, Nedlands, 6009 WA, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia.
| | - Jue-Sheng Ong
- Statistical Genetics Laboratory, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, 4006 QLD, Australia
| | - Stuart MacGregor
- Statistical Genetics Laboratory, Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, 4006 QLD, Australia
| | - David C Whiteman
- Cancer Control Group, QIMR Berghofer Medical Research Institute, Brisbane, 4006 QLD, Australia
| | - Jamie E Craig
- Flinders Medical Centre, Flinders University, Bedford Park, SA 5042, Australia
| | - M Isabel G Lopez Sanchez
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia; Ophthalmology, University of Melbourne, Department of Surgery, Parkville, 3010 VIC, Australia
| | - Lisa S Kearns
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
| | - Sandra E Staffieri
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia; Ophthalmology, University of Melbourne, Department of Surgery, Parkville, 3010 VIC, Australia
| | - Linda Clarke
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
| | - Myra B McGuinness
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
| | - Wafaa Meteoukki
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
| | - Sona Samuel
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
| | - Jonathan B Ruddle
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia; Ophthalmology, University of Melbourne, Department of Surgery, Parkville, 3010 VIC, Australia
| | - Celia Chen
- Flinders Medical Centre, Flinders University, Bedford Park, SA 5042, Australia
| | - Clare L Fraser
- Save Sight Institute, Discipline of Ophthalmology, Faculty of Health and Medicine, The University of Sydney, Sydney, 2000 NSW, Australia
| | - John Harrison
- Department of Ophthalmology, Royal Brisbane and Women's Hospital, Herston, 4006 QLD Australia
| | | | - Alex W Hewitt
- Menzies Institute for Medical Research, School of Medicine, University of Tasmania, Hobart, 7000 TAS, Australia; Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, East Melbourne, 3002 VIC, Australia
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22
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Korchivaia E, Silaeva Y, Mazunin I, Volodyaev I. The mitochondrial challenge: Disorders and prevention strategies. Biosystems 2023; 223:104819. [PMID: 36450320 DOI: 10.1016/j.biosystems.2022.104819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022]
Abstract
This short review provides basic knowledge on mitochondrial inheritance, its disorders, and potential ways to overcome them in human reproductive medicine. The latter are currently mostly associated with the so-called mitochondrial replacement (nuclear transfer) procedures, performed at different stages and with slight technical differences. Being promising but obviously highly invasive, these procedures require detailed investigation of their delayed effects on embryogenesis, pregnancy and future health. A special attention is paid to the newest available data on these issues, as well as to their limitations and possible further research directions.
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Affiliation(s)
- Elena Korchivaia
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia.
| | - Yulia Silaeva
- Ministry of Science and Higher Education of the Russian Federation Institute of Gene Biology Russian Academy of Sciences, Moscow, Russia
| | - Ilya Mazunin
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology (Skoltech), Skolkovo, Russia; Fomin Clinics, Russia; Medical Genomics LLC, Moscow, Russia
| | - Ilya Volodyaev
- Department of Embryology, Biological Faculty, Lomonosov Moscow State University, Moscow, Russia; European Medical Center, Moscow, Russia; ICARM (Interdisciplinary Clinical Association for Reproductive Medicine), Moscow, Russia
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23
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Mitochondrial Unfolded Protein Response and Integrated Stress Response as Promising Therapeutic Targets for Mitochondrial Diseases. Cells 2022; 12:cells12010020. [PMID: 36611815 PMCID: PMC9818186 DOI: 10.3390/cells12010020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/10/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
The development and application of high-throughput omics technologies have enabled a more in-depth understanding of mitochondrial biosynthesis metabolism and the pathogenesis of mitochondrial diseases. In accordance with this, a host of new treatments for mitochondrial disease are emerging. As an essential pathway in maintaining mitochondrial proteostasis, the mitochondrial unfolded protein response (UPRmt) is not only of considerable significance for mitochondrial substance metabolism but also plays a fundamental role in the development of mitochondrial diseases. Furthermore, in mammals, the integrated stress response (ISR) and UPRmt are strongly coupled, functioning together to maintain mitochondrial function. Therefore, ISR and UPRmt show great application prospects in the treatment of mitochondrial diseases. In this review, we provide an overview of the molecular mechanisms of ISR and UPRmt and focus on them as potential targets for mitochondrial disease therapy.
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24
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Silva-Pinheiro P, Mutti CD, Van Haute L, Powell CA, Nash PA, Turner K, Minczuk M. A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome. Nat Biomed Eng 2022; 7:692-703. [PMID: 36470976 DOI: 10.1038/s41551-022-00968-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/20/2022] [Indexed: 12/07/2022]
Abstract
The development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.
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Affiliation(s)
| | - Christian D Mutti
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Pavel A Nash
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Keira Turner
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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25
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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26
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Abstract
The analogy of mitochondria as powerhouses has expired. Mitochondria are living, dynamic, maternally inherited, energy-transforming, biosynthetic, and signaling organelles that actively transduce biological information. We argue that mitochondria are the processor of the cell, and together with the nucleus and other organelles they constitute the mitochondrial information processing system (MIPS). In a three-step process, mitochondria (1) sense and respond to both endogenous and environmental inputs through morphological and functional remodeling; (2) integrate information through dynamic, network-based physical interactions and diffusion mechanisms; and (3) produce output signals that tune the functions of other organelles and systemically regulate physiology. This input-to-output transformation allows mitochondria to transduce metabolic, biochemical, neuroendocrine, and other local or systemic signals that enhance organismal adaptation. An explicit focus on mitochondrial signal transduction emphasizes the role of communication in mitochondrial biology. This framework also opens new avenues to understand how mitochondria mediate inter-organ processes underlying human health.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY 10032, USA; New York State Psychiatric Institute, New York, NY 10032, USA.
| | - Orian S Shirihai
- Department of Medicine, Endocrinology, and Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
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27
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Vázquez-Coto D, Albaiceta GM, Amado-Rodríguez L, Clemente MG, Cuesta-Llavona E, Gómez J, Coto E. Common mitochondrial haplogroups as modifiers of the onset-age for critical COVID-19. Mitochondrion 2022; 67:1-5. [PMID: 36115538 PMCID: PMC9474411 DOI: 10.1016/j.mito.2022.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/09/2022] [Indexed: 02/08/2023]
Abstract
As a key regulator of innate immunity, mitochondrial function is essential to maintain antiviral activities. Common mitochondrial DNA variants (haplogroups) have been associated with different physiological capacities and the nrisk of developing several diseases. Haplogroup H was associated with increased survival among sepsis patients, and lower risk of progression toward AIDS in HIV infected and lower manifestation of severe manifestation of herpex virus disease. We studied 316 Spanish with critical COVID-19, and found that the 7028C (haplogroup H) was protective among patients with early-onset disease (≤65 vs > 65 years, p = 0.01), while the ancestral 16223T was a risk factor for early-onset critical COVID-19 (OR = 3.36, 95 %CI = 1.49-7.54). Our work suggested that common mitochondrial variants may serve as predictors of COVID-19 severity. Additional studies to confirm this effect from other populations are of special interest.
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Affiliation(s)
| | - Guillermo M. Albaiceta
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Marta G. Clemente
- Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Neumología, Hospital Universitario Central Asturias, Oviedo, Spain
| | - Elías Cuesta-Llavona
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain,Instituto de Investigación Sanitaria del Principado deAsturias, ISPA, Oviedo, Spain,Universidad de Oviedo, Oviedo, Spain,Corresponding author at: Genética Molecular-HUCA, Oviedo, Spain
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28
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Single-cell multiomics analyses of spindle-transferred human embryos suggest a mostly normal embryonic development. PLoS Biol 2022; 20:e3001741. [PMID: 35972936 PMCID: PMC9380953 DOI: 10.1371/journal.pbio.3001741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are often associated with incurable diseases and lead to detectable pathogenic variants in 1 out of 200 babies. Uncoupling of the inheritance of mtDNA and the nuclear genome by spindle transfer (ST) can potentially prevent the transmission of mtDNA mutations from mother to offspring. However, no well-established studies have critically assessed the safety of this technique. Here, using single-cell triple omics sequencing method, we systematically analyzed the genome (copy number variation), DNA methylome, and transcriptome of ST and control blastocysts. The results showed that, compared to that in control embryos, the percentage of aneuploid cells in ST embryos did not significantly change. The epiblast, primitive endoderm, and trophectoderm (TE) of ST blastocysts presented RNA expression profiles that were comparable to those of control blastocysts. However, the DNA demethylation process in TE cells of ST blastocysts was slightly slower than that in the control blastocysts. Collectively, our results suggest that ST seems generally safe for embryonic development, with a relatively minor delay in the DNA demethylation process at the blastocyst stage. Uncoupling of the inheritance of mtDNA and the nuclear genome by spindle transfer could prevent the transmission of mtDNA mutations. Systematic single-cell multiomic analyses of spindle transferred human embryos suggest this technique seems generally safe for human embryonic development and deserves further scientific evaluation and clinical testing.
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29
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Torres-Gonzalez E, Makova KD. Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans. Front Genet 2022; 13:797129. [PMID: 35846132 PMCID: PMC9277102 DOI: 10.3389/fgene.2022.797129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Most mitochondrial protein complexes include both nuclear and mitochondrial gene products, which coevolved to work together. This coevolution can be disrupted due to disparity in genetic ancestry between the nuclear and mitochondrial genomes in recently admixed populations. Such mitonuclear DNA discordance might result in phenotypic effects. Several nuclear-encoded proteins regulate expression of mitochondrial DNA (mtDNA) genes. We hypothesized that mitonuclear DNA discordance affects expression of genes encoded by mtDNA. To test this, we utilized the data from the GTEx project, which contains expression levels for ∼100 African Americans and >600 European Americans. The varying proportion of African and European ancestry in recently admixed African Americans provides a range of mitonuclear discordance values, which can be correlated with mtDNA gene expression levels (adjusted for age and ischemic time). In contrast, European Americans did not undergo recent admixture. We demonstrated that, for most mtDNA protein-coding genes, expression levels in energetically-demanding tissues were lower in African Americans than in European Americans. Furthermore, gene expression levels were lower in individuals with higher mitonuclear discordance, independent of population. Moreover, we found a negative correlation between mtDNA gene expression and mitonuclear discordance. In African Americans, the average value of African ancestry was higher for nuclear-encoded mitochondrial than non-mitochondrial genes, facilitating a match in ancestry with the mtDNA and more optimal interactions. These results represent an example of a phenotypic effect of mitonuclear discordance on human admixed populations, and have potential biomedical applications.
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Affiliation(s)
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
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30
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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] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 11/14/2022] Open
Abstract
SUMMARY We present MitoVisualize, a new tool for analysis of the human mitochondrial DNA (mtDNA). MitoVisualize enables visualization of: (i) the position and effect of variants in mitochondrial transfer RNA and ribosomal RNA secondary structures alongside curated variant annotations, (ii) data across RNA structures, such as to show all positions with disease-associated variants or with post-transcriptional modifications and (iii) the position of a base, gene or region in the circular mtDNA map, such as to show the location of a large deletion. All visualizations can be easily downloaded as figures for reuse. MitoVisualize can be useful for anyone interested in exploring mtDNA variation, though is designed to facilitate mtDNA variant interpretation in particular. AVAILABILITY AND IMPLEMENTATION MitoVisualize can be accessed via https://www.mitovisualize.org/. The source code is available at https://github.com/leklab/mito_visualize/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nicole J Lake
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
- Murdoch Children's Research Institute, Melbourne 3052, Australia
| | - Lily Zhou
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jenny Xu
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Monkol Lek
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
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31
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Germline mutations in mitochondrial complex I reveal genetic and targetable vulnerability in IDH1-mutant acute myeloid leukaemia. Nat Commun 2022; 13:2614. [PMID: 35551192 PMCID: PMC9098909 DOI: 10.1038/s41467-022-30223-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 04/20/2022] [Indexed: 11/13/2022] Open
Abstract
The interaction of germline variation and somatic cancer driver mutations is under-investigated. Here we describe the genomic mitochondrial landscape in adult acute myeloid leukaemia (AML) and show that rare variants affecting the nuclear- and mitochondrially-encoded complex I genes show near-mutual exclusivity with somatic driver mutations affecting isocitrate dehydrogenase 1 (IDH1), but not IDH2 suggesting a unique epistatic relationship. Whereas AML cells with rare complex I variants or mutations in IDH1 or IDH2 all display attenuated mitochondrial respiration, heightened sensitivity to complex I inhibitors including the clinical-grade inhibitor, IACS-010759, is observed only for IDH1-mutant AML. Furthermore, IDH1 mutant blasts that are resistant to the IDH1-mutant inhibitor, ivosidenib, retain sensitivity to complex I inhibition. We propose that the IDH1 mutation limits the flexibility for citrate utilization in the presence of impaired complex I activity to a degree that is not apparent in IDH2 mutant cells, exposing a mutation-specific metabolic vulnerability. This reduced metabolic plasticity explains the epistatic relationship between the germline complex I variants and oncogenic IDH1 mutation underscoring the utility of genomic data in revealing metabolic vulnerabilities with implications for therapy. Mitochondrial metabolism has been associated with tumourigenesis in acute myeloid leukaemia (AML) and currently considered as a potential therapeutic target. Here, the authors show, in patients with AML, that germline mutations in mitochondrial complex I are mutually exclusive with somatic mutations in the metabolic enzyme IDH1, and find IDH1 mutant cells have increased sensitivity to complex I inhibitors.
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32
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Abstract
The mechanisms that explain mitochondrial dysfunction in aging and healthspan continue to be studied, but one element has been unexplored: microproteins. Small open reading frames in circular mitochondria DNA can encode multiple microproteins, called mitochondria-derived peptides (MDPs). Currently, eight MDPs have been published: humanin, MOTS-c, and SHLPs 1–6. This Review describes recent advances in microprotein discovery with a focus on MDPs. It discusses what is currently known about MDPs in aging and how this new understanding could add to the way we understand age-related diseases including type 2 diabetes, cancer, and neurodegenerative diseases at the genomic, proteomic, and drug-development levels.
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33
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Li S, Gai X, Myint SS, Arroyo K, Morimoto L, Metayer C, de Smith AJ, Walsh KM, Wiemels JL. Mitochondrial 1555 G>A variant as a potential risk factor for childhood glioblastoma. Neurooncol Adv 2022; 4:vdac045. [PMID: 35571988 PMCID: PMC9092641 DOI: 10.1093/noajnl/vdac045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Background Childhood glioblastoma multiforme (GBM) is a highly aggressive disease with low survival, and its etiology, especially concerning germline genetic risk, is poorly understood. Mitochondria play a key role in putative tumorigenic processes relating to cellular oxidative metabolism, and mitochondrial DNA variants were not previously assessed for association with pediatric brain tumor risk. Methods We conducted an analysis of 675 mitochondrial DNA variants in 90 childhood GBM cases and 2789 controls to identify enrichment of mitochondrial variant associated with GBM risk. We also performed this analysis for other glioma subtypes including pilocytic astrocytoma. Nuclear-encoded mitochondrial gene variants were also analyzed. Results We identified m1555 A>G was significantly associated with GBM risk (adjusted OR 29.30, 95% CI 5.25–163.4, P-value 9.5 X 10–4). No association was detected for other subtypes. Haplotype analysis further supported the independent risk contributed by m1555 G>A, instead of a haplogroup joint effect. Nuclear-encoded mitochondrial gene variants identified significant associations in European (rs62036057 in WWOX, adjusted OR = 2.99, 95% CI 1.88–4.75, P-value = 3.42 X 10–6) and Hispanic (rs111709726 in EFHD1, adjusted OR = 3.57, 95% CI 1.99–6.40, P-value = 1.41 X 10–6) populations in ethnicity-stratified analyses. Conclusion We report for the first time a potential role played by a functional mitochondrial ribosomal RNA variant in childhood GBM risk, and a potential role for both mitochondrial and nuclear-mitochondrial DNA polymorphisms in GBM tumorigenesis. These data implicate cellular oxidative metabolic capacity as a contributor to the etiology of pediatric glioblastoma.
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Affiliation(s)
- Shaobo Li
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, California, USA
| | - Swe Swe Myint
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Katti Arroyo
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Libby Morimoto
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Catherine Metayer
- School of Public Health, University of California Berkeley, Berkeley, California, USA
| | - Adam J de Smith
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
| | - Kyle M Walsh
- Division of Neuro-epidemiology, Department of Neurosurgery, Duke University, Durham, North Carolina, USA
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, Department of Population and Public Health Sciences, University of Southern California, Los Angeles, California, USA
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34
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Silva-Pinheiro P, Minczuk M. The potential of mitochondrial genome engineering. Nat Rev Genet 2022; 23:199-214. [PMID: 34857922 DOI: 10.1038/s41576-021-00432-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
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Affiliation(s)
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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35
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Vilne B, Sawant A, Rudaka I. Examining the Association between Mitochondrial Genome Variation and Coronary Artery Disease. Genes (Basel) 2022; 13:genes13030516. [PMID: 35328073 PMCID: PMC8953999 DOI: 10.3390/genes13030516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/04/2022] Open
Abstract
Large-scale genome-wide association studies have identified hundreds of single-nucleotide variants (SNVs) significantly associated with coronary artery disease (CAD). However, collectively, these explain <20% of the heritability. Hypothesis: Here, we hypothesize that mitochondrial (MT)-SNVs might present one potential source of this “missing heritability”. Methods: We analyzed 265 MT-SNVs in ~500,000 UK Biobank individuals, exploring two different CAD definitions: a more stringent (myocardial infarction and/or revascularization; HARD = 20,405), and a more inclusive (angina and chronic ischemic heart disease; SOFT = 34,782). Results: In HARD cases, the most significant (p < 0.05) associations were for m.295C>T (control region) and m.12612A>G (ND5), found more frequently in cases (OR = 1.05), potentially related to reduced cardiorespiratory fitness in response to exercise, as well as for m.12372G>A (ND5) and m.11467A>G (ND4), present more frequently in controls (OR = 0.97), previously associated with lower ROS production rate. In SOFT cases, four MT-SNVs survived multiple testing corrections (at FDR < 5%), all potentially conferring increased CAD risk. Of those, m.11251A>G (ND4) and m.15452C>A (CYB) have previously shown significant associations with body height. In line with this, we observed that CAD cases were slightly less physically active, and their average body height was ~2.00 cm lower compared to controls; both traits are known to be related to increased CAD risk. Gene-based tests identified CO2 associated with HARD/SOFT CAD, whereas ND3 and CYB associated with SOFT cases (p < 0.05), dysfunction of which has been related to MT oxidative stress, obesity/T2D (CO2), BMI (ND3), and angina/exercise intolerance (CYB). Finally, we observed that macro-haplogroup I was significantly (p < 0.05) more frequent in HARD cases vs. controls (3.35% vs. 3.08%), potentially associated with response to exercise. Conclusions: We found only spurious associations between MT genome variation and HARD/SOFT CAD and conclude that more MT-SNV data in even larger study cohorts may be needed to conclusively determine the role of MT DNA in CAD.
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Affiliation(s)
- Baiba Vilne
- Bioinformatics Lab, Rīga Stradiņš University, LV-1007 Riga, Latvia;
- Correspondence:
| | - Aniket Sawant
- Bioinformatics Lab, Rīga Stradiņš University, LV-1007 Riga, Latvia;
| | - Irina Rudaka
- Scientific Laboratory of Molecular Genetics, Rīga Stradiņš University, LV-1007 Riga, Latvia;
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36
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Lechuga-Vieco AV, Latorre-Pellicer A, Calvo E, Torroja C, Pellico J, Acín-Pérez R, García-Gil ML, Santos A, Bagwan N, Bonzon-Kulichenko E, Magni R, Benito M, Justo-Méndez R, Simon AK, Sánchez-Cabo F, Vázquez J, Ruíz-Cabello J, Enríquez JA. Heteroplasmy of Wild Type Mitochondrial DNA Variants in Mice Causes Metabolic Heart Disease With Pulmonary Hypertension and Frailty. Circulation 2022; 145:1084-1101. [PMID: 35236094 PMCID: PMC8969846 DOI: 10.1161/circulationaha.121.056286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: In most eukaryotic cells, the mitochondrial DNA (mtDNA) is uniparentally transmitted and present in multiple copies derived from the clonal expansion of maternally inherited mtDNA. All copies are therefore near-identical, or homoplasmic. The presence of more than one mtDNA variant in the same cytoplasm can arise naturally or result from new medical technologies aimed at preventing mitochondrial genetic diseases and improving fertility. The latter is called divergent non-pathological mtDNAs heteroplasmy (DNPH). We hypothesized that DNPH is maladaptive and usually prevented by the cell. Methods: We engineered and characterized DNPH mice throughout their lifespan using transcriptomic, metabolomic, biochemical, physiological and phenotyping techniques. We focused on in vivo imaging techniques for non-invasive assessment of cardiac and pulmonary energy metabolism. Results: We show that DNPH impairs mitochondrial function, with profound consequences in critical tissues that cannot resolve heteroplasmy, particularly cardiac and skeletal muscle. Progressive metabolic stress in these tissues leads to severe pathology in adulthood, including pulmonary hypertension and heart failure, skeletal muscle wasting, frailty, and premature death. Symptom severity is strongly modulated by the nuclear context. Conclusions: Medical interventions that may generate DNPH should address potential incompatibilities between donor and recipient mtDNA.
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Affiliation(s)
- Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom; Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ana Latorre-Pellicer
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, ISS-Aragon, Zaragoza, Spain
| | - Enrique Calvo
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Carlos Torroja
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Juan Pellico
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Rebeca Acín-Pérez
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - María Luisa García-Gil
- Centro Nacional de Microscopia Electrónica (ICTS-CNME), Universidad Complutense de Madrid, Madrid, Spain
| | - Arnoldo Santos
- Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain; ITC, Ingeniería y Técnicas Clínicas, Madrid, Spain
| | - Navratan Bagwan
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Elena Bonzon-Kulichenko
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | | | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Anna Katharina Simon
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | | | - Jesús Vázquez
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesús Ruíz-Cabello
- CIC biomaGUNE, 2014, Donostia-San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Spain; Universidad Complutense de Madrid, Madrid, Spain
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Pickett SJ, Deen D, Pyle A, Santibanez-Koref M, Hudson G. Interactions between nuclear and mitochondrial SNPs and Parkinson's disease risk. Mitochondrion 2022; 63:85-88. [PMID: 35167983 DOI: 10.1016/j.mito.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/07/2022] [Accepted: 02/09/2022] [Indexed: 12/23/2022]
Abstract
Interactions between the products of the nuclear and mitochondrial genomes are critical for the function of most eukaryotic cells. Recently the introduction of mitochondrial replacement therapy has raised the question of incompatibilities between mitochondrial and nuclear variants, and their potential influence on the genetic makeup of human populations. Such interactions could also contribute to the variability of the penetrance of pathogenic DNA variants. This led us to investigate the frequencies of combinations of nuclear and mitochondrial SNP alleles (mitonuclear combinations) in healthy individuals (n = 5375) and in a cohort of patients with Parkinson's disease (PD, n = 2210). In the unaffected population, we were not able to find associations between nuclear and mitochondrial variants with a false discovery rate below 0.05 after accounting for multiple testing (i.e., the number of combinations examined). However, in the PD cohort, five combinations surpassed this threshold. Next, after combining both cohorts, we investigated whether these associations were modulated by disease status. All five combinations were significant (p < 10-3 for all tests). These combinations also showed significant evidence for an effect of the interaction between the mitochondrial and nuclear variants on disease risk. Their nuclear components mapped to TBCA, NIBAN3, and GLT25D1 and an uncharacterised intergenic region. In summary, starting from a single cohort design we identified combinations of nuclear and mitochondrial variants affecting PD disease risk.
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Affiliation(s)
- Sarah J Pickett
- Clinical and Translational Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Dasha Deen
- Clinical and Translational Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Angela Pyle
- Clinical and Translational Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK
| | - Mauro Santibanez-Koref
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK.
| | - Gavin Hudson
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne NE2 4HH, UK.
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In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue. Nat Commun 2022; 13:750. [PMID: 35136065 PMCID: PMC8825850 DOI: 10.1038/s41467-022-28358-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/21/2022] [Indexed: 01/01/2023] Open
Abstract
Mitochondria host key metabolic processes vital for cellular energy provision and are central to cell fate decisions. They are subjected to unique genetic control by both nuclear DNA and their own multi-copy genome - mitochondrial DNA (mtDNA). Mutations in mtDNA often lead to clinically heterogeneous, maternally inherited diseases that display different organ-specific presentation at any stage of life. For a long time, genetic manipulation of mammalian mtDNA has posed a major challenge, impeding our ability to understand the basic mitochondrial biology and mechanisms underpinning mitochondrial disease. However, an important new tool for mtDNA mutagenesis has emerged recently, namely double-stranded DNA deaminase (DddA)-derived cytosine base editor (DdCBE). Here, we test this emerging tool for in vivo use, by delivering DdCBEs into mouse heart using adeno-associated virus (AAV) vectors and show that it can install desired mtDNA edits in adult and neonatal mice. This work provides proof-of-concept for use of DdCBEs to mutagenize mtDNA in vivo in post-mitotic tissues and provides crucial insights into potential translation to human somatic gene correction therapies to treat primary mitochondrial disease phenotypes. Mutations in mitochondrial DNA can lead to clinically heterogeneous disease. Here the authors demonstrate in vivo base editing of mouse mitochondrial DNA in a post-mitotic tissue by AAV delivery of DddA-derived cytosine base editor (DdCBE).
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Valiente-Pallejà A, Tortajada J, Bulduk BK, Vilella E, Garrabou G, Muntané G, Martorell L. Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review. EBioMedicine 2022; 76:103815. [PMID: 35085849 PMCID: PMC8790490 DOI: 10.1016/j.ebiom.2022.103815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health and disease could be a cornerstone in disentangling the relationship between biochemical findings and clinical symptoms of brain disorders. This systematic review aimed to summarize the mtDNA alterations in human brain tissue reported to date that have implications for further research on the pathophysiological significance of mtDNA alterations in brain functioning. METHODS We searched the PubMed and Embase databases using distinct terms related to postmortem human brain and mtDNA up to June 10, 2021. Reports were eligible if they were empirical studies analysing mtDNA in postmortem human brains. FINDINGS A total of 158 of 637 studies fulfilled the inclusion criteria and were clustered into the following groups: MitD (48 entries), neurological diseases (NeuD, 55 entries), psychiatric diseases (PsyD, 15 entries), a miscellaneous group with controls and other clinical diseases (5 entries), ageing (20 entries), and technical issues (5 entries). Ten entries were ascribed to more than one group. Pathogenic single nucleotide variants (pSNVs), both homo- or heteroplasmic variants, have been widely reported in MitD, with heteroplasmy levels varying among brain regions; however, pSNVs are rarer in NeuD, PsyD and ageing. A lower mtDNA copy number (CN) in disease was described in most, but not all, of the identified studies. mtDNA deletions were identified in individuals in the four clinical categories and ageing. Notably, brain samples showed significantly more mtDNA deletions and at higher heteroplasmy percentages than blood samples, and several of the deletions present in the brain were not detected in the blood. Finally, mtDNA heteroplasmy, mtDNA CN and the deletion levels varied depending on the brain region studied. INTERPRETATION mtDNA alterations are well known to affect human tissues, including the brain. In general, we found that studies of MitD, NeuD, PsyD, and ageing were highly variable in terms of the type of disease or ageing process investigated, number of screened individuals, studied brain regions and technology used. In NeuD and PsyD, no particular type of mtDNA alteration could be unequivocally assigned to any specific disease or diagnostic group. However, the presence of mtDNA deletions and mtDNA CN variation imply a role for mtDNA in NeuD and PsyD. Heteroplasmy levels and threshold effects, affected brain regions, and mitotic segregation patterns of mtDNA alterations may be involved in the complex inheritance of NeuD and PsyD and in the ageing process. Therefore, more information is needed regarding the type of mtDNA alteration, the affected brain regions, the heteroplasmy levels, and their relationship with clinical phenotypes and the ageing process. FUNDING Hospital Universitari Institut Pere Mata; Institut d'Investigació Sanitària Pere Virgili; Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (PI18/00514).
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Affiliation(s)
- Alba Valiente-Pallejà
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Juan Tortajada
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Bengisu K Bulduk
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Elisabet Vilella
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function, Department of Internal Medicine-Hospital Clínic of Barcelona (HCB); Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), 08036 Barcelona, Catalonia, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Gerard Muntané
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain; Institute of Evolutionary Biology (IBE), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain
| | - Lourdes Martorell
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain.
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Junker A, Wang J, Gouspillou G, Ehinger JK, Elmér E, Sjövall F, Fisher-Wellman KH, Neufer PD, Molina AJA, Ferrucci L, Picard M. Human studies of mitochondrial biology demonstrate an overall lack of binary sex differences: A multivariate meta-analysis. FASEB J 2022; 36:e22146. [PMID: 35073429 PMCID: PMC9885138 DOI: 10.1096/fj.202101628r] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/18/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023]
Abstract
Mitochondria are maternally inherited organelles that play critical tissue-specific roles, including hormone synthesis and energy production, that influence human development, health, and aging. However, whether mitochondria from women and men exhibit consistent biological differences remains unclear, representing a major gap in knowledge. This meta-analysis systematically examined four domains and six subdomains of mitochondrial biology (total 39 measures), including mitochondrial content, respiratory capacity, reactive oxygen species (ROS) production, morphometry, and mitochondrial DNA copy number. Standardized effect sizes (Hedge's g) of sex differences were computed for each measure using data in 2258 participants (51.5% women) from 50 studies. Only two measures demonstrated aggregate binary sex differences: higher mitochondrial content in women's WAT and isolated leukocyte subpopulations (g = 0.20, χ2 p = .01), and higher ROS production in men's skeletal muscle (g = 0.49, χ2 p < .0001). Sex differences showed weak to no correlation with age or BMI. Studies with small sample sizes tended to overestimate effect sizes (r = -.17, p < .001), and sex differences varied by tissue examined. Our findings point to a wide variability of findings in the literature concerning possible binary sex differences in mitochondrial biology. Studies specifically designed to capture sex- and gender-related differences in mitochondrial biology are needed, including detailed considerations of physical activity and sex hormones.
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Affiliation(s)
- Alex Junker
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, New York, USA
| | - Jennifer Wang
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, New York, USA
| | - Gilles Gouspillou
- Département des Sciences de l’Activité Physique, Faculté des Sciences, Université du Québec à Montréal (UQAM), Montreal, Québec, Canada
| | - Johannes K. Ehinger
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden,Otorhinolaryngology Head and Neck Surgery, Department of Clinical Sciences, Skåne University Hospital, Lund University, Lund, Sweden
| | - Eskil Elmér
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Fredrik Sjövall
- Mitochondrial Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kelsey H. Fisher-Wellman
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA,Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - P. Darrell Neufer
- East Carolina Diabetes and Obesity Institute, East Carolina University, Greenville, North Carolina, USA,Department of Physiology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Anthony J. A. Molina
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, New York, USA,Department of Neurology, H. Houston Merritt Center, Columbia University Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, New York, USA,NewYork State Psychiatric Institute, New York, New York, USA
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Laricchia KM, Lake NJ, Watts NA, Shand M, Haessly A, Gauthier L, Benjamin D, Banks E, Soto J, Garimella K, Emery J, Rehm HL, MacArthur DG, Tiao G, Lek MV, Mootha VK, Calvo SE. Mitochondrial DNA variation across 56,434 individuals in gnomAD. Genome Res 2022; 32:569-582. [PMID: 35074858 PMCID: PMC8896463 DOI: 10.1101/gr.276013.121] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 01/19/2022] [Indexed: 11/25/2022]
Abstract
Genomic databases of allele frequency are extremely helpful for evaluating clinical variants of unknown significance; however, until now, databases such as the Genome Aggregation Database (gnomAD) have focused on nuclear DNA and have ignored the mitochondrial genome (mtDNA). Here we present a pipeline to call mtDNA variants that addresses three technical challenges: (i) detecting homoplasmic and heteroplasmic variants, present respectively in all or a fraction of mtDNA molecules, (ii) circular mtDNA genome, and (iii) misalignment of nuclear sequences of mitochondrial origin (NUMTs). We observed that mtDNA copy number per cell varied across gnomAD cohorts and influenced the fraction of NUMT-derived false-positive variant calls, which can account for the majority of putative heteroplasmies. To avoid false positives, we excluded contaminated samples, cell lines, and samples prone to NUMT misalignment due to few mtDNA copies. Furthermore, we report variants with heteroplasmy greater than 10%. We applied this pipeline to 56,434 whole genome sequences in the gnomAD v3.1 database that includes individuals of European (58%), African (25%), Latino (10%), and Asian (5%) ancestry. Our gnomAD v3.1 release contains population frequencies for 10,850 unique mtDNA variants at more than half of all mtDNA bases. We report frequencies within each nuclear ancestral population and mitochondrial haplogroup. Homoplasmic variants account for most variant calls (98%) and unique variants (85%). We observed that 1/250 individuals carry a pathogenic mtDNA variant with heteroplasmy above 10%. These mtDNA population allele frequencies are freely accessible and will aid in diagnostic interpretation and research studies.
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Künstner A, Schilf P, Busch H, Ibrahim SM, Hirose M. Changes of Gut Microbiota by Natural mtDNA Variant Differences Augment Susceptibility to Metabolic Disease and Ageing. Int J Mol Sci 2022; 23:ijms23031056. [PMID: 35162979 PMCID: PMC8835372 DOI: 10.3390/ijms23031056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/13/2022] [Accepted: 01/18/2022] [Indexed: 12/30/2022] Open
Abstract
We recently reported on two mouse strains carrying different single nucleotide variations in the mitochondrial complex I gene, i.e., B6-mtBPL mice carrying m.11902T>C and B6-mtALR carrying m.4738C>A. B6-mtBPL mice exhibited a longer lifespan and a lower metabolic disease susceptibility despite mild mitochondrial functional differences in steady-state. As natural polymorphisms in the mitochondrial DNA (mtDNA) are known to be associated with distinct patterns of gut microbial composition, we further investigated the gut microbiota composition in these mice strains. In line with mouse phenotypes, we found a significantly lower abundance of Proteobacteria, which is positively associated with pathological conditions, in B6-mtBPL compared to B6-mtALR mice. A prediction of functional profile of significantly differential bacterial genera between these strains revealed an involvement of glucose metabolism pathways. Whole transcriptome analysis of liver samples from B6-mtBPL and B6-mtALR mice confirmed these findings. Thus, both host gene expression and gut microbial changes caused by the mtDNA variant differences may contribute to the ageing and metabolic phenotypes observed in these mice strains. Since gut microbiota are easier to modulate, compared with mtDNA variants, identification of such mtDNA variants, specific gut bacterial species and bacterial metabolites may be a potential intervention to modulate common diseases, which are differentially susceptible to individuals with different mtDNA variants.
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Affiliation(s)
- Axel Künstner
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; (A.K.); (P.S.); (H.B.); (S.M.I.)
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Paul Schilf
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; (A.K.); (P.S.); (H.B.); (S.M.I.)
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; (A.K.); (P.S.); (H.B.); (S.M.I.)
- Institute for Cardiogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Saleh M. Ibrahim
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; (A.K.); (P.S.); (H.B.); (S.M.I.)
- College of Medicine and Sharjah Institute for Medical Research, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Misa Hirose
- Lübeck Institute of Experimental Dermatology, University of Lübeck, 23562 Lübeck, Germany; (A.K.); (P.S.); (H.B.); (S.M.I.)
- Correspondence:
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Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci 2021; 22:12031. [PMID: 34769461 PMCID: PMC8584537 DOI: 10.3390/ijms222112031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/06/2023] Open
Abstract
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Filipa S. Carvalho
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| | - Ana Catarina Fonseca
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - José M. Ferro
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Vanessa A. Morais
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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Picard M. Blood mitochondrial DNA copy number: What are we counting? Mitochondrion 2021; 60:1-11. [PMID: 34157430 PMCID: PMC8464495 DOI: 10.1016/j.mito.2021.06.010] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/12/2021] [Accepted: 06/17/2021] [Indexed: 02/06/2023]
Abstract
There is growing scientific interest to develop scalable biological measures that capture mitochondrial (dys)function. Mitochondria have their own genome, the mitochondrial DNA (mtDNA). It has been proposed that the number of mtDNA copies per cell (mtDNA copy number; mtDNAcn) reflects mitochondrial health. The common availability of stored DNA material or existing DNA sequencing data, especially from blood and other easy-to-collect samples, has made its quantification a popular approach in clinical and epidemiological studies. However, the interpretation of mtDNAcn is not univocal, and either a reduction or elevation in mtDNAcn can indicate dysfunction. The major determinants of blood-derived mtDNAcn are the heterogeneous cell type composition of leukocytes and platelet abundance, which can change with time of day, aging, and with disease. Hematopoiesis is a likely driver of blood mtDNAcn. Here we discuss the rationale and available methods to quantify mtDNAcn, the influence of blood cell type variations, and consider important gaps in knowledge that need to be resolved to maximize the scientific value around the investigation of blood mtDNAcn.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA; Department of Neurology, Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA.
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McInerney TW, Fulton-Howard B, Patterson C, Paliwal D, Jermiin LS, Patel HR, Pa J, Swerdlow RH, Goate A, Easteal S, Andrews SJ. A globally diverse reference alignment and panel for imputation of mitochondrial DNA variants. BMC Bioinformatics 2021; 22:417. [PMID: 34470617 PMCID: PMC8409003 DOI: 10.1186/s12859-021-04337-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/16/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Variation in mitochondrial DNA (mtDNA) identified by genotyping microarrays or by sequencing only the hypervariable regions of the genome may be insufficient to reliably assign mitochondrial genomes to phylogenetic lineages or haplogroups. This lack of resolution can limit functional and clinical interpretation of a substantial body of existing mtDNA data. To address this limitation, we developed and evaluated a large, curated reference alignment of complete mtDNA sequences as part of a pipeline for imputing missing mtDNA single nucleotide variants (mtSNVs). We call our reference alignment and pipeline MitoImpute. RESULTS We aligned the sequences of 36,960 complete human mitochondrial genomes downloaded from GenBank, filtered and controlled for quality. These sequences were reformatted for use in imputation software, IMPUTE2. We assessed the imputation accuracy of MitoImpute by measuring haplogroup and genotype concordance in data from the 1000 Genomes Project and the Alzheimer's Disease Neuroimaging Initiative (ADNI). The mean improvement of haplogroup assignment in the 1000 Genomes samples was 42.7% (Matthew's correlation coefficient = 0.64). In the ADNI cohort, we imputed missing single nucleotide variants. CONCLUSION These results show that our reference alignment and panel can be used to impute missing mtSNVs in existing data obtained from using microarrays, thereby broadening the scope of functional and clinical investigation of mtDNA. This improvement may be particularly useful in studies where participants have been recruited over time and mtDNA data obtained using different methods, enabling better integration of early data collected using less accurate methods with more recent sequence data.
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Affiliation(s)
- Tim W McInerney
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Brian Fulton-Howard
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Christopher Patterson
- Keck School of Medicine, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Devashi Paliwal
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Lars S Jermiin
- CSIRO Land and Water, Commonwealth Scientific Industrial and Research Organization, Acton, ACT, 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT, 2601, Australia
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Hardip R Patel
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Judy Pa
- Keck School of Medicine, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Los Angeles, CA, USA
- Department of Neurology, Alzheimer's Disease Research Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Russell H Swerdlow
- Department of Neurology, Alzheimer's Disease Center, University of Kansas, Fairway, KS, USA
| | - Alison Goate
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA
| | - Simon Easteal
- John Curtin School of Medical Research, Australian National University, Australian Capital Territory, Canberra, Australia
| | - Shea J Andrews
- Genetics and Genomic Sciences, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY, 10029, USA.
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