1
|
Yuan N, Shen L, Peng Q, Sha R, Wang Z, Xie Z, You X, Feng Y. SRSF1 Is Required for Mitochondrial Homeostasis and Thermogenic Function in Brown Adipocytes Through its Control of Ndufs3 Splicing. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2306871. [PMID: 38569495 PMCID: PMC11151030 DOI: 10.1002/advs.202306871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 02/04/2024] [Indexed: 04/05/2024]
Abstract
RNA splicing dysregulation and the involvement of specific splicing factors are emerging as common factors in both obesity and metabolic disorders. The study provides compelling evidence that the absence of the splicing factor SRSF1 in mature adipocytes results in whitening of brown adipocyte tissue (BAT) and impaired thermogenesis, along with the inhibition of white adipose tissue browning in mice. Combining single-nucleus RNA sequencing with transmission electron microscopy, it is observed that the transformation of BAT cell types is associated with dysfunctional mitochondria, and SRSF1 deficiency leads to degenerated and fragmented mitochondria within BAT. The results demonstrate that SRSF1 effectively binds to constitutive exon 6 of Ndufs3 pre-mRNA and promotes its inclusion. Conversely, the deficiency of SRSF1 results in impaired splicing of Ndufs3, leading to reduced levels of functional proteins that are essential for mitochondrial complex I assembly and activity. Consequently, this deficiency disrupts mitochondrial integrity, ultimately compromising the thermogenic capacity of BAT. These findings illuminate a novel role for SRSF1 in influencing mitochondrial function and BAT thermogenesis through its regulation of Ndufs3 splicing within BAT.
Collapse
Affiliation(s)
- Ningyang Yuan
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
| | - Lei Shen
- Department of General SurgeryZhongshan HospitalFudan UniversityShanghai200032China
| | - Qian Peng
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Rula Sha
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Zhenzhen Wang
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Zhiqi Xie
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Xue You
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
| | - Ying Feng
- CAS Key Laboratory of Nutrition, Metabolism and Food SafetyShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
- Lin He's Academician Workstation of New Medicine and Clinical Translation in Jining Medical UniversityJining Medical UniversityJining272067China
| |
Collapse
|
2
|
Jiang Y, Cheng S, Shi Y, Xu Z, Wang H, Li Y, Liu Y, Li Z, Jiang Y, Meng X, Cheng S, Li H, Wang C, Wang Y. Subtype-Specific Association of Mitochondrial DNA Copy Number With Poststroke/TIA Outcomes in 10 241 Patients in China. Stroke 2024; 55:1261-1270. [PMID: 38511332 DOI: 10.1161/strokeaha.123.045069] [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: 09/03/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Mitochondrial DNA copy number (mtDNA-CN) is associated with the severity and mortality in patients with stroke, but the associations in different stroke subtypes remain unexplored. METHODS We conducted an observational prospective cohort analysis on patients with ischemic stroke or transient ischemic attack enrolled in the Third China National Stroke Registry. We applied logistic models to assess the association of mtDNA-CN with functional outcome (modified Rankin Scale score, 3-6 versus 0-2) and Cox proportional hazard models to assess the association with stroke recurrence (treating mortality as a competing risk) and mortality during a 12-month follow-up, adjusting for sex, age, physical activity, National Institutes of Health Stroke Scale at admission, history of stroke and peripheral artery disease, small artery occlusion, and interleukin-6. Subgroup analyses stratified by age and stroke subtypes were conducted. RESULTS The Third China National Stroke Registry enrolled 15 166 patients, of which 10 241 with whole-genome sequencing data were retained (mean age, 62.2 [SD, 11.2] years; 68.8% men). The associations between mtDNA-CN and poststroke/transient ischemic attack outcomes were specific to patients aged ≤65 years, with lower mtDNA-CN significantly associated with stroke recurrence in 12 months (subdistribution hazard ratio, 1.15 per SD lower mtDNA-CN [95% CI, 1.04-1.27]; P=5.2×10-3) and higher all-cause mortality in 3 months (hazard ratio, 2.19 [95% CI, 1.41-3.39]; P=5.0×10-4). Across subtypes, the associations of mtDNA-CN with stroke recurrence were specific to stroke of undetermined cause (subdistribution hazard ratio, 1.28 [95% CI, 1.11-1.48]; P=6.6×10-4). In particular, lower mtDNA-CN was associated with poorer functional outcomes in stroke of undetermined cause patients diagnosed with embolic stroke of undetermined source (odds ratio, 1.53 [95% CI, 1.20-1.94]; P=5.4×10-4), which remained significant after excluding patients with recurrent stroke (odds ratio, 1.49 [95% CI, 1.14-1.94]; P=3.0×10-3). CONCLUSIONS Lower mtDNA-CN is associated with higher stroke recurrence rate and all-cause mortality, as well as poorer functional outcome at follow-up, among stroke of undetermined cause, embolic stroke of undetermined source, and younger patients.
Collapse
Affiliation(s)
- Yi Jiang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Yi Jiang, H.W., Shanshan Cheng, C.W.)
| | - Si Cheng
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
- Changping Laboratory, Beijing, China (Si Cheng, Yong Jiang, Y.W.)
- Clinical Center for Precision Medicine in Stroke (Si Cheng, Y.W.), Capital Medical University, Beijing, China
| | - Yanfeng Shi
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Zhe Xu
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Huihui Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Yi Jiang, H.W., Shanshan Cheng, C.W.)
| | - Yanran Li
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Yang Liu
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Zixiao Li
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Yong Jiang
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
- Changping Laboratory, Beijing, China (Si Cheng, Yong Jiang, Y.W.)
| | - Xia Meng
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Shanshan Cheng
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Yi Jiang, H.W., Shanshan Cheng, C.W.)
| | - Hao Li
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
| | - Chaolong Wang
- Department of Epidemiology and Biostatistics, Ministry of Education Key Laboratory of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China (Yi Jiang, H.W., Shanshan Cheng, C.W.)
| | - Yongjun Wang
- Department of Neurology (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- Center of Excellence for Omics Research (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, H.L., Y.W.), Beijing Tiantan Hospital, Capital Medical University, China
- China National Clinical Research Center for Neurological Diseases, Beijing (Si Cheng, Y.S., Z.X., Y. Li, Y. Liu, Z.L., Yong Jiang, X.M., H.L., Y.W.)
- Changping Laboratory, Beijing, China (Si Cheng, Yong Jiang, Y.W.)
- Clinical Center for Precision Medicine in Stroke (Si Cheng, Y.W.), Capital Medical University, Beijing, China
- Advanced Innovation Center for Human Brain Protection (Y.W.), Capital Medical University, Beijing, China
| |
Collapse
|
3
|
Di Pierro E, Perrone M, Franco M, Granata F, Duca L, Lattuada D, De Luca G, Graziadei G. Mitochondrial DNA Copy Number Drives the Penetrance of Acute Intermittent Porphyria. Life (Basel) 2023; 13:1923. [PMID: 37763326 PMCID: PMC10532762 DOI: 10.3390/life13091923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
No published study has investigated the mitochondrial count in patients suffering from acute intermittent porphyria (AIP). In order to determine whether mitochondrial content can influence the pathogenesis of porphyria, we measured the mitochondrial DNA (mtDNA) copy number in the peripheral blood cells of 34 patients and 37 healthy individuals. We found that all AIP patients had a low number of mitochondria, likely as a result of a protective mechanism against an inherited heme synthesis deficiency. Furthermore, we identified a close correlation between disease penetrance and decreases in the mitochondrial content and serum levels of PERM1, a marker of mitochondrial biogenesis. In a healthy individual, mitochondrial count is usually modulated to fit its ability to respond to various environmental stressors and bioenergetic demands. In AIP patients, coincidentally, the phenotype only manifests in response to endogenous and exogenous triggers factors. Therefore, these new findings suggest that a deficiency in mitochondrial proliferation could affect the individual responsiveness to stimuli, providing a new explanation for the variability in the clinical manifestations of porphyria. However, the metabolic and/or genetic factors responsible for this impairment remain to be identified. In conclusion, both mtDNA copy number per cell and mitochondrial biogenesis seem to play a role in either inhibiting or promoting disease expression. They could serve as two novel biomarkers for porphyria.
Collapse
Affiliation(s)
- Elena Di Pierro
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| | - Miriana Perrone
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| | - Milena Franco
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Francesca Granata
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| | - Lorena Duca
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| | - Debora Lattuada
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| | - Giacomo De Luca
- School of Internal Medicine, University of Milan, 20122 Milan, Italy;
| | - Giovanna Graziadei
- Foundation IRCCS Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy; (M.P.); (F.G.); (L.D.); (D.L.); (G.G.)
| |
Collapse
|
4
|
Bris C, Goudenège D, Desquiret-Dumas V, Gueguen N, Bannwarth S, Gaignard P, Rucheton B, Trimouille A, Allouche S, Rouzier C, Saadi S, Jardel C, Slama A, Barth M, Verny C, Spinazzi M, Cassereau J, Colin E, Armelle M, Pereon Y, Martin-Negrier ML, Paquis-Flucklinger V, Letournel F, Lenaers G, Bonneau D, Reynier P, Amati-Bonneau P, Procaccio V. Improved detection of mitochondrial DNA instability in mitochondrial genome maintenance disorders. Genet Med 2021; 23:1769-1778. [PMID: 34040194 DOI: 10.1038/s41436-021-01206-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Diseases caused by defects in mitochondrial DNA (mtDNA) maintenance machinery, leading to mtDNA deletions, form a specific group of disorders. However, mtDNA deletions also appear during aging, interfering with those resulting from mitochondrial disorders. METHODS Here, using next-generation sequencing (NGS) data processed by eKLIPse and data mining, we established criteria distinguishing age-related mtDNA rearrangements from those due to mtDNA maintenance defects. MtDNA deletion profiles from muscle and urine patient samples carrying pathogenic variants in nuclear genes involved in mtDNA maintenance (n = 40) were compared with age-matched controls (n = 90). Seventeen additional patient samples were used to validate the data mining model. RESULTS Overall, deletion number, heteroplasmy level, deletion locations, and the presence of repeats at deletion breakpoints were significantly different between patients and controls, especially in muscle samples. The deletion number was significantly relevant in adults, while breakpoint repeat lengths surrounding deletions were discriminant in young subjects. CONCLUSION Altogether, eKLIPse analysis is a powerful tool for measuring the accumulation of mtDNA deletions between patients of different ages, as well as in prioritizing novel variants in genes involved in mtDNA stability.
Collapse
Affiliation(s)
- Celine Bris
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - David Goudenège
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Naig Gueguen
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Pauline Gaignard
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Benoit Rucheton
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Aurelien Trimouille
- Service de Génétique médicale, Centre Hospitalier Universitaire de Bordeaux, Bordeaux, France
| | - Stephane Allouche
- Service de Biochimie, EA4650, Centre Hospitalier Universitaire, Caen, France
| | - Cecile Rouzier
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Samira Saadi
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | - Claude Jardel
- Département de Biochimie et Génétique, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Abdel Slama
- Service de Biochimie, CHU Bicêtre, APHP Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Magalie Barth
- Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Christophe Verny
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Marco Spinazzi
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Julien Cassereau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Magot Armelle
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | - Yann Pereon
- Centre de Référence Maladies Neuromusculaires, CHU Nantes, Nantes, France
| | | | | | - Franck Letournel
- UF de Neurobiologie-Neuropathologie, UMR INSERM 1066 - CNRS 6021, MINT, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France.,Département de Biochimie et Génétique, CHU d'Angers, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015, INSERM U1083, Institut MitoVasc, Université d'Angers, Angers, France. .,Département de Biochimie et Génétique, CHU d'Angers, Angers, France.
| |
Collapse
|
5
|
McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat 2020; 41:2028-2057. [PMID: 32906214 DOI: 10.1002/humu.24107] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
Collapse
Affiliation(s)
- Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Amel Karaa
- Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christine M Stanley
- Variantyx, Inc, Framingham, Massachusetts, USA.,QNA Diagnostics, Cambridge, Massachusetts, USA
| | | | - Anshu Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Neal Sondheimer
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| |
Collapse
|
6
|
Ciesielski GL, Nadalutti CA, Oliveira MT, Jacobs HT, Griffith JD, Kaguni LS. Structural rearrangements in the mitochondrial genome of Drosophila melanogaster induced by elevated levels of the replicative DNA helicase. Nucleic Acids Res 2019; 46:3034-3046. [PMID: 29432582 PMCID: PMC5887560 DOI: 10.1093/nar/gky094] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 02/02/2018] [Indexed: 01/10/2023] Open
Abstract
Pathological conditions impairing functions of mitochondria often lead to compensatory upregulation of the mitochondrial DNA (mtDNA) replisome machinery, and the replicative DNA helicase appears to be a key factor in regulating mtDNA copy number. Moreover, mtDNA helicase mutations have been associated with structural rearrangements of the mitochondrial genome. To evaluate the effects of elevated levels of the mtDNA helicase on the integrity and replication of the mitochondrial genome, we overexpressed the helicase in Drosophila melanogaster Schneider cells and analyzed the mtDNA by two-dimensional neutral agarose gel electrophoresis and electron microscopy. We found that elevation of mtDNA helicase levels increases the quantity of replication intermediates and alleviates pausing at the replication slow zones. Though we did not observe a concomitant alteration in mtDNA copy number, we observed deletions specific to the segment of repeated elements in the immediate vicinity of the origin of replication, and an accumulation of species characteristic of replication fork stalling. We also found elevated levels of RNA that are retained in the replication intermediates. Together, our results suggest that upregulation of mtDNA helicase promotes the process of mtDNA replication but also results in genome destabilization.
Collapse
Affiliation(s)
- Grzegorz L Ciesielski
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
| | - Cristina A Nadalutti
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marcos T Oliveira
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA
| | - Howard T Jacobs
- Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland.,Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Laurie S Kaguni
- Department of Biochemistry and Molecular Biology and Center for Mitochondrial Science and Medicine, Michigan State University, East Lansing, MI, USA.,Institute of Biosciences and Medical Technology, University of Tampere, FI-33014 Tampere, Finland
| |
Collapse
|
7
|
Grady JP, Pickett SJ, Ng YS, Alston CL, Blakely EL, Hardy SA, Feeney CL, Bright AA, Schaefer AM, Gorman GS, McNally RJ, Taylor RW, Turnbull DM, McFarland R. mtDNA heteroplasmy level and copy number indicate disease burden in m.3243A>G mitochondrial disease. EMBO Mol Med 2019; 10:emmm.201708262. [PMID: 29735722 PMCID: PMC5991564 DOI: 10.15252/emmm.201708262] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mitochondrial disease associated with the pathogenic m.3243A>G variant is a common, clinically heterogeneous, neurogenetic disorder. Using multiple linear regression and linear mixed modelling, we evaluated which commonly assayed tissue (blood N = 231, urine N = 235, skeletal muscle N = 77) represents the m.3243A>G mutation load and mitochondrial DNA (mtDNA) copy number most strongly associated with disease burden and progression. m.3243A>G levels are correlated in blood, muscle and urine (R2 = 0.61–0.73). Blood heteroplasmy declines by ~2.3%/year; we have extended previously published methodology to adjust for age. In urine, males have higher mtDNA copy number and ~20% higher m.3243A>G mutation load; we present formulas to adjust for this. Blood is the most highly correlated mutation measure for disease burden and progression in m.3243A>G‐harbouring individuals; increasing age and heteroplasmy contribute (R2 = 0.27, P < 0.001). In muscle, heteroplasmy, age and mtDNA copy number explain a higher proportion of variability in disease burden (R2 = 0.40, P < 0.001), although activity level and disease severity are likely to affect copy number. Whilst our data indicate that age‐corrected blood m.3243A>G heteroplasmy is the most convenient and reliable measure for routine clinical assessment, additional factors such as mtDNA copy number may also influence disease severity.
Collapse
Affiliation(s)
- John P Grady
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Steven A Hardy
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Catherine L Feeney
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Alexandra A Bright
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Andrew M Schaefer
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Gráinne S Gorman
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Richard Jq McNally
- Institute of Health and Society, Newcastle University, Newcastle upon Tyne, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK
| |
Collapse
|
8
|
Bris C, Goudenege D, Desquiret-Dumas V, Charif M, Colin E, Bonneau D, Amati-Bonneau P, Lenaers G, Reynier P, Procaccio V. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing. Front Genet 2018; 9:632. [PMID: 30619459 PMCID: PMC6297213 DOI: 10.3389/fgene.2018.00632] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.
Collapse
Affiliation(s)
- Céline Bris
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - David Goudenege
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Valérie Desquiret-Dumas
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Majida Charif
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Estelle Colin
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Pascal Reynier
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| |
Collapse
|
9
|
Xia CY, Liu Y, Yang HR, Yang HY, Liu JX, Ma YN, Qi Y. Reference Intervals of Mitochondrial DNA Copy Number in Peripheral Blood for Chinese Minors and Adults. Chin Med J (Engl) 2017; 130:2435-2440. [PMID: 29052564 PMCID: PMC5684636 DOI: 10.4103/0366-6999.216395] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) content measured by different techniques cannot be compared between studies, and age- and tissue-related control values are hardly available. In the present study, we aimed to establish the normal reference range of mtDNA copy number in the Chinese population. METHODS Two healthy cohorts of 200 Chinese minors (0.1-18.0 years) and 200 adults (18.0-88.0 years) were recruited. Then, they were further categorized into eight age groups. The absolute mtDNA copy number per cell was measured by a quantitative real-time polymerase chain reaction. We subsequently used this range to evaluate mtDNA content in four patients (0.5-4.0 years) with molecularly proven mitochondrial depletion syndromes (MDSs) and 83 cases of mitochondrial disease patients harboring the m.3243A>G mutation. RESULTS The reference range of mtDNA copy number in peripheral blood was 175-602 copies/cell (mean: 325 copies/cell) in minors and 164-500 copies/cell (mean: 287 copies/cell) in adults. There was a decreasing trend in mtDNA copy number in blood with increasing age, especially in 0-2-year-old and >50-year-old donors. The mean mtDNA copy number level among the mitochondrial disease patients with m.3243A>G mutation was significantly higher than that of healthy controls. The mtDNA content of POLG, DGUOK, TK2, and SUCLA2 genes in blood samples from MDS patients was reduced to 25%, 38%, 32%, and 24%, respectively. CONCLUSIONS We primarily establish the reference intervals of mtDNA copy number, which might contribute to the clinical diagnosis and monitoring of mitochondrial disease.
Collapse
Affiliation(s)
- Chang-Yu Xia
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yu Liu
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Hui-Rong Yang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Hong-Yun Yang
- Department of Clinical Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Jing-Xia Liu
- Department of Clinical Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yi-Nan Ma
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
10
|
Abdullaev SA, Minkabirova GM, Bezlepkin VG, Gaziev AI. Cell-free DNA in the urine of rats exposed to ionizing radiation. RADIATION AND ENVIRONMENTAL BIOPHYSICS 2015; 54:297-304. [PMID: 25935210 DOI: 10.1007/s00411-015-0599-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
Investigation of cell-free DNA (cf-DNA) in body fluids, as a potential biomarker for assessing the effect of ionizing radiation on the organism, is of considerable interest. We investigated changes in the contents of cell-free mitochondrial DNA (cf-mtDNA) and cell-free nuclear DNA (cf-nDNA) in the urine of X-ray-exposed rats. Assays of cf-mtDNA and cf-nDNA were performed by a real-time PCR in rat urine collected before and after irradiation of animals with doses of 3 and 5 Gy. We also determined the presence of mutations in urine cf-mtDNA, as recognized by Surveyor nuclease. A sharp increase in cf-mtDNA and cf-nDNA in the urine of irradiated rats was observed within 24 h after exposure, followed by a decrease to normal levels. In all cases, the contents of cf-mtDNA fragment copies (estimated by gene tRNA) were significantly higher than those of cf-nDNA estimated by gene GAPDH. A certain portion of mutant cf-mtDNA fragments was detected in the urine of exposed rats, whereas they were absent in the urine of the same animals before irradiation. These preliminary data also suggest that the increased levels of urine cf-mtDNA and cf-nDNA may be a potential biomarker for noninvasive assessment of how the organism responds to ionizing radiation influence.
Collapse
Affiliation(s)
- Serazhutdin A Abdullaev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Science (RAS), Pushchino, Moscow Region, 142290, Russia,
| | | | | | | |
Collapse
|
11
|
Zhang Y, Ma Y, Bu D, Liu H, Xia C, Zhang Y, Zhu S, Pan H, Pei P, Zheng X, Wang S, Xu Y, Qi Y. Deletion of a 4977-bp Fragment in the Mitochondrial Genome Is Associated with Mitochondrial Disease Severity. PLoS One 2015; 10:e0128624. [PMID: 26024530 PMCID: PMC4449107 DOI: 10.1371/journal.pone.0128624] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 04/30/2015] [Indexed: 12/22/2022] Open
Abstract
Large deletions in mitochondrial DNA (mtDNA) may be involved in the pathogenesis of mitochondrial disease. In this study, we investigated the relationship between a 4,977-bp deletion in the mitochondrial genome (ΔmtDNA4977) and the severity of clinical symptoms in patients with mitochondrial disease lacking known point mutations. A total of 160 patients with mitochondrial disease and 101 healthy controls were recruited for this study. The copy numbers of ΔmtDNA4977 and wild-type mtDNA were determined by real-time quantitative PCR and analyzed using Spearman’s bivariate correlation analysis, t-tests, or one-way ANOVA. The overall ΔmtDNA4977 copy number per cell and the proportion of mtDNA4977 relative to the total wild-type mtDNA, increased with patient age and symptom severity. Surprisingly, the total mtDNA copy number decreased with increasing symptom severity. Our analyses revealed that increases in the proportion and total copy number of ΔmtDNA4977 in the blood may be associated with disease severity in patients with mitochondrial dysfunction.
Collapse
Affiliation(s)
- Yanchun Zhang
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Yinan Ma
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
- * E-mail: (YM); (YQ)
| | - Dingfang Bu
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Hui Liu
- Department of Respiratory, Beijing Children’s Hospital, Beijing, 100045, China
| | - Changyu Xia
- Department of Clinical Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Ying Zhang
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Sainan Zhu
- Department of Biostatistics, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Hong Pan
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Pei Pei
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Xuefei Zheng
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Songtao Wang
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Yufeng Xu
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
| | - Yu Qi
- Department of Central Laboratory, Peking University First Hospital, No. 8, West District, Beijing, 100034, China
- * E-mail: (YM); (YQ)
| |
Collapse
|
12
|
D'Erchia AM, Atlante A, Gadaleta G, Pavesi G, Chiara M, De Virgilio C, Manzari C, Mastropasqua F, Prazzoli GM, Picardi E, Gissi C, Horner D, Reyes A, Sbisà E, Tullo A, Pesole G. Tissue-specific mtDNA abundance from exome data and its correlation with mitochondrial transcription, mass and respiratory activity. Mitochondrion 2014; 20:13-21. [PMID: 25446395 DOI: 10.1016/j.mito.2014.10.005] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/23/2014] [Accepted: 10/29/2014] [Indexed: 01/12/2023]
Abstract
Eukaryotic cells contain a population of mitochondria, variable in number and shape, which in turn contain multiple copies of a tiny compact genome (mtDNA) whose expression and function is strictly coordinated with the nuclear one. mtDNA copy number varies between different cell or tissues types, both in response to overall metabolic and bioenergetics demands and as a consequence or cause of specific pathological conditions. Here we present a novel and reliable methodology to assess the effective mtDNA copy number per diploid genome by investigating off-target reads obtained by whole-exome sequencing (WES) experiments. We also investigate whether and how mtDNA copy number correlates with mitochondrial mass, respiratory activity and expression levels. Analyzing six different tissues from three age- and sex-matched human individuals, we found a highly significant linear correlation between mtDNA copy number estimated by qPCR and the frequency of mtDNA off target WES reads. Furthermore, mtDNA copy number showed highly significant correlation with mitochondrial gene expression levels as measured by RNA-Seq as well as with mitochondrial mass and respiratory activity. Our methodology makes thus feasible, at a large scale, the investigation of mtDNA copy number in diverse cell-types, tissues and pathological conditions or in response to specific treatments.
Collapse
Affiliation(s)
- Anna Maria D'Erchia
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy
| | - Anna Atlante
- Istituto di Biomembrane e Bioenergetica, CNR, via Amendola 165/A, Bari 70126, Italy
| | - Gemma Gadaleta
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Caterina De Virgilio
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy
| | - Caterina Manzari
- Istituto di Biomembrane e Bioenergetica, CNR, via Amendola 165/A, Bari 70126, Italy
| | - Francesca Mastropasqua
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy
| | - Gian Marco Prazzoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Ernesto Picardi
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy
| | - Carmela Gissi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - David Horner
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, Milano 20133, Italy
| | - Aurelio Reyes
- Mitochondrial Biology Unit, Medical Research Council, Wellcome Trust/MRC Building, Hills Road, Cambridge CB2 0XY, United Kingdom
| | - Elisabetta Sbisà
- Istituto di Tecnologie Biomediche- Sede di Bari, CNR, Via Amendola 122/D, Bari 70126, Italy
| | - Apollonia Tullo
- Istituto di Tecnologie Biomediche- Sede di Bari, CNR, Via Amendola 122/D, Bari 70126, Italy
| | - Graziano Pesole
- Dipartimento di Bioscienze, Biotecnologie e Biofarmaceutica, Università degli Studi di Bari Aldo Moro, Via Orabona 4, Bari 70126, Italy; Istituto di Biomembrane e Bioenergetica, CNR, via Amendola 165/A, Bari 70126, Italy.
| |
Collapse
|