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Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
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Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
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Bruni F. Human mtDNA-Encoded Long ncRNAs: Knotty Molecules and Complex Functions. Int J Mol Sci 2024; 25:1502. [PMID: 38338781 PMCID: PMC10855489 DOI: 10.3390/ijms25031502] [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: 12/20/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Until a few decades ago, most of our knowledge of RNA transcription products was focused on protein-coding sequences, which were later determined to make up the smallest portion of the mammalian genome. Since 2002, we have learnt a great deal about the intriguing world of non-coding RNAs (ncRNAs), mainly due to the rapid development of bioinformatic tools and next-generation sequencing (NGS) platforms. Moreover, interest in non-human ncRNAs and their functions has increased as a result of these technologies and the accessibility of complete genome sequences of species ranging from Archaea to primates. Despite not producing proteins, ncRNAs constitute a vast family of RNA molecules that serve a number of regulatory roles and are essential for cellular physiology and pathology. This review focuses on a subgroup of human ncRNAs, namely mtDNA-encoded long non-coding RNAs (mt-lncRNAs), which are transcribed from the mitochondrial genome and whose disparate localisations and functions are linked as much to mitochondrial metabolism as to cellular physiology and pathology.
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Affiliation(s)
- Francesco Bruni
- Department of Biosciences, Biotechnologies and Environment, University of Bari Aldo Moro, 70125 Bari, Italy
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Huang S, Wu Z, Wang T, Yu R, Song Z, Wang H. MmisAT and MmisP: an efficient and accurate suite of variant analysis toolkit for primary mitochondrial diseases. Hum Genomics 2023; 17:108. [PMID: 38012712 PMCID: PMC10683248 DOI: 10.1186/s40246-023-00557-6] [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: 02/26/2023] [Accepted: 11/22/2023] [Indexed: 11/29/2023] Open
Abstract
Recent advances in next-generation sequencing (NGS) technology have greatly accelerated the need for efficient annotation to accurately interpret clinically relevant genetic variants in human diseases. Therefore, it is crucial to develop appropriate analytical tools to improve the interpretation of disease variants. Given the unique genetic characteristics of mitochondria, including haplogroup, heteroplasmy, and maternal inheritance, we developed a suite of variant analysis toolkits specifically designed for primary mitochondrial diseases: the Mitochondrial Missense Variant Annotation Tool (MmisAT) and the Mitochondrial Missense Variant Pathogenicity Predictor (MmisP). MmisAT can handle protein-coding variants from both nuclear DNA and mtDNA and generate 349 annotation types across six categories. It processes 4.78 million variant data in 76 min, making it a valuable resource for clinical and research applications. Additionally, MmisP provides pathogenicity scores to predict the pathogenicity of genetic variations in mitochondrial disease. It has been validated using cross-validation and external datasets and demonstrated higher overall discriminant accuracy with a receiver operating characteristic (ROC) curve area under the curve (AUC) of 0.94, outperforming existing pathogenicity predictors. In conclusion, the MmisAT is an efficient tool that greatly facilitates the process of variant annotation, expanding the scope of variant annotation information. Furthermore, the development of MmisP provides valuable insights into the creation of disease-specific, phenotype-specific, and even gene-specific predictors of pathogenicity, further advancing our understanding of specific fields.
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Affiliation(s)
- Shuangshuang Huang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhaoyu Wu
- Department of Clinical Laboratory, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tong Wang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Rui Yu
- Department of Ophthalmology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Zhijian Song
- OrigiMed, 5th Floor, Building 3, No.115 Xin Jun Huan Road, Minhang District, Shanghai, China.
| | - Hao Wang
- Department of Clinical Laboratory, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China.
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Vila-Sanjurjo A, Mallo N, Atkins JF, Elson JL, Smith PM. Our current understanding of the toxicity of altered mito-ribosomal fidelity during mitochondrial protein synthesis: What can it tell us about human disease? Front Physiol 2023; 14:1082953. [PMID: 37457031 PMCID: PMC10349377 DOI: 10.3389/fphys.2023.1082953] [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: 11/04/2022] [Accepted: 02/28/2023] [Indexed: 07/18/2023] Open
Abstract
Altered mito-ribosomal fidelity is an important and insufficiently understood causative agent of mitochondrial dysfunction. Its pathogenic effects are particularly well-known in the case of mitochondrially induced deafness, due to the existence of the, so called, ototoxic variants at positions 847C (m.1494C) and 908A (m.1555A) of 12S mitochondrial (mt-) rRNA. It was shown long ago that the deleterious effects of these variants could remain dormant until an external stimulus triggered their pathogenicity. Yet, the link from the fidelity defect at the mito-ribosomal level to its phenotypic manifestation remained obscure. Recent work with fidelity-impaired mito-ribosomes, carrying error-prone and hyper-accurate mutations in mito-ribosomal proteins, have started to reveal the complexities of the phenotypic manifestation of mito-ribosomal fidelity defects, leading to a new understanding of mtDNA disease. While much needs to be done to arrive to a clear picture of how defects at the level of mito-ribosomal translation eventually result in the complex patterns of disease observed in patients, the current evidence indicates that altered mito-ribosome function, even at very low levels, may become highly pathogenic. The aims of this review are three-fold. First, we compare the molecular details associated with mito-ribosomal fidelity to those of general ribosomal fidelity. Second, we gather information on the cellular and organismal phenotypes associated with defective translational fidelity in order to provide the necessary grounds for an understanding of the phenotypic manifestation of defective mito-ribosomal fidelity. Finally, the results of recent experiments directly tackling mito-ribosomal fidelity are reviewed and future paths of investigation are discussed.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE, Departamento de Bioloxía e Centro de Investigacións Científicas Avanzadas (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - John F Atkins
- Schools of Biochemistry and Microbiology, University College Cork, Cork, Ireland
| | - Joanna L Elson
- The Bioscience Institute, Newcastle University, Newcastle uponTyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, Scotland, United Kingdom
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Vila-Sanjurjo A, Mallo N, Elson JL, Smith PM, Blakely EL, Taylor RW. Structural analysis of mitochondrial rRNA gene variants identified in patients with deafness. Front Physiol 2023; 14:1163496. [PMID: 37362424 PMCID: PMC10285412 DOI: 10.3389/fphys.2023.1163496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 04/18/2023] [Indexed: 06/28/2023] Open
Abstract
The last few years have witnessed dramatic advances in our understanding of the structure and function of the mammalian mito-ribosome. At the same time, the first attempts to elucidate the effects of mito-ribosomal fidelity (decoding accuracy) in disease have been made. Hence, the time is right to push an important frontier in our understanding of mitochondrial genetics, that is, the elucidation of the phenotypic effects of mtDNA variants affecting the functioning of the mito-ribosome. Here, we have assessed the structural and functional role of 93 mitochondrial (mt-) rRNA variants thought to be associated with deafness, including those located at non-conserved positions. Our analysis has used the structural description of the human mito-ribosome of the highest quality currently available, together with a new understanding of the phenotypic manifestation of mito-ribosomal-associated variants. Basically, any base change capable of inducing a fidelity phenotype may be considered non-silent. Under this light, out of 92 previously reported mt-rRNA variants thought to be associated with deafness, we found that 49 were potentially non-silent. We also dismissed a large number of reportedly pathogenic mtDNA variants, 41, as polymorphisms. These results drastically update our view on the implication of the primary sequence of mt-rRNA in the etiology of deafness and mitochondrial disease in general. Our data sheds much-needed light on the question of how mt-rRNA variants located at non-conserved positions may lead to mitochondrial disease and, most notably, provide evidence of the effect of haplotype context in the manifestation of some mt-rRNA variants.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Natalia Mallo
- Grupo GIBE. Departamento de Bioloxía e Centro Interdisciplinar de Química e Bioloxía (CICA), Universidade da Coruña (UDC), A Coruña, Spain
| | - Joanna L. Elson
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Paul M. Smith
- Department of Paediatrics, Raigmore Hospital, Inverness, United Kingdom
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
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Soto I, Couvillion M, Stirling Churchman L. Human Mitoribosome Profiling: A Re-engineered Approach Tailored to Study Mitochondrial Translation. Methods Mol Biol 2023; 2661:257-280. [PMID: 37166642 DOI: 10.1007/978-1-0716-3171-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
To understand the human mitochondrial translation process, tools are required to dissect this system at a global scale. The mechanisms and regulation of translation in mitochondria are different from those in the cytosol, and mitochondrial ribosomes have distinct biochemical properties. In this chapter, we describe in detail the modifications we have made to the ribosome profiling approach to adapt it to the unique characteristics of the human mitochondrial ribosome. This approach maximizes the fraction of mitochondrial ribosomes recovered, providing a snapshot of the mitochondrial translation landscape with minimal bias. We also describe the use of mouse lysate as an internal spike-in control for normalization, allowing quantification of global changes in translation across samples. Finally, we outline the bioinformatic pipelines to process the raw reads and identify mitoribosome A sites in the absence of untranslated regions flanking open reading frames. This method offers a subcodon-resolution time-sensitive global approach to explore the mitochondrial translation process in human cells.
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Affiliation(s)
- Iliana Soto
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Mary Couvillion
- Department of Genetics, Harvard Medical School, Boston, MA, USA
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Sabharwal A, Campbell JM, Schwab TL, WareJoncas Z, Wishman MD, Ata H, Liu W, Ichino N, Hunter DE, Bergren JD, Urban MD, Urban RM, Holmberg SR, Kar B, Cook A, Ding Y, Xu X, Clark KJ, Ekker SC. A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Genes (Basel) 2022; 13:1317. [PMID: 35893052 PMCID: PMC9331066 DOI: 10.3390/genes13081317] [Citation(s) in RCA: 2] [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: 06/25/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are a dynamic eukaryotic innovation that play diverse roles in biology and disease. The mitochondrial genome is remarkably conserved in all vertebrates, encoding the same 37-gene set and overall genomic structure, ranging from 16,596 base pairs (bp) in the teleost zebrafish (Danio rerio) to 16,569 bp in humans. Mitochondrial disorders are amongst the most prevalent inherited diseases, affecting roughly 1 in every 5000 individuals. Currently, few effective treatments exist for those with mitochondrial ailments, representing a major unmet patient need. Mitochondrial dysfunction is also a common component of a wide variety of other human illnesses, ranging from neurodegenerative disorders such as Huntington's disease and Parkinson's disease to autoimmune illnesses such as multiple sclerosis and rheumatoid arthritis. The electron transport chain (ETC) component of mitochondria is critical for mitochondrial biology and defects can lead to many mitochondrial disease symptoms. Here, we present a publicly available collection of genetic mutants created in highly conserved, nuclear-encoded mitochondrial genes in Danio rerio. The zebrafish system represents a potentially powerful new opportunity for the study of mitochondrial biology and disease due to the large number of orthologous genes shared with humans and the many advanced features of this model system, from genetics to imaging. This collection includes 15 mutant lines in 13 different genes created through locus-specific gene editing to induce frameshift or splice acceptor mutations, leading to predicted protein truncation during translation. Additionally, included are 11 lines created by the random insertion of the gene-breaking transposon (GBT) protein trap cassette. All these targeted mutant alleles truncate conserved domains of genes critical to the proper function of the ETC or genes that have been implicated in human mitochondrial disease. This collection is designed to accelerate the use of zebrafish to study many different aspects of mitochondrial function to widen our understanding of their role in biology and human disease.
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Affiliation(s)
- Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jarryd M. Campbell
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Hirotaka Ata
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Wiebin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Danielle E. Hunter
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jake D. Bergren
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Rhianna M. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Shannon R. Holmberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Alex Cook
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, 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; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
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Exposure to a Pathological Condition May Be Required for the Cells to Secrete Exosomes Containing mtDNA Aberration. J Nucleic Acids 2022; 2022:7960198. [PMID: 35465178 PMCID: PMC9020996 DOI: 10.1155/2022/7960198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/21/2022] [Accepted: 03/07/2022] [Indexed: 11/17/2022] Open
Abstract
Exosomes, nanovesicles secreted by all cells, carry out intercellular communication by transmitting biologically active cargo comprising DNA, RNA, and proteins. These biomolecules reflect the status of their parent cells and can be altered by pathological conditions. Therefore, the researchers have been investigating differential sequences and quantities of DNA associated with exosomes as valuable biomarkers of diseases. Exosomes carry different types of DNA molecules, including genomic, cytoplasmic, and mitochondrial (mtDNA). The mtDNA aberrations are reported to be a hallmark of diseases involving oxidative stress, such as cancer and neurodegenerative diseases. Establishing robust in vitro models comprising appropriate cell lineages is the first step towards investigating disease-specific anomalies and testing therapeutics. Induced pluripotent stem (iPS) cells from patients with diseases have been used for this purpose since they can differentiate into various cells. The current study investigated mtDNA aberrations in exosomes secreted by primary cancer cells and neural stem cells (NSCs) differentiated from iPS cells. The primary cancer cells were isolated from surgically removed glioblastoma multiforme (GBM) tissue, and the iPS cells were produced from control and Alzheimer's disease (AD) subjects' B lymphocytes. We detected aberrations in mtDNA associated with exosomes secreted from GBM cells but not from the NSCs. This result indicates that the cells may not secrete exosomes carrying mtDNA aberration without exposure to a pathological condition. Thus, we may need to consider this fact when we use iPS cell-derived cells as an in vitro disease model.
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Genetic Alterations in Mitochondrial DNA Are Complementary to Nuclear DNA Mutations in Pheochromocytomas. Cancers (Basel) 2022; 14:cancers14020269. [PMID: 35053433 PMCID: PMC8773562 DOI: 10.3390/cancers14020269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Mitochondrial DNA (mtDNA) alterations have been reported to play important roles in cancer development and metastasis. However, there is scarce information about pheochromocytomas and paragangliomas (PCCs/PGLs) formation. To determine the potential roles of mtDNA alterations in PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of 77 human tumors, using NGS. We also performed an analysis of copy-number alterations, large mtDNA deletion, and gene/protein expression. Our results revealed that 53.2% of the tumors harbor a mutation in the susceptibility genes and 16.9% harbor complementary mitochondrial mutations. Large deletions and depletion of mtDNA were found in 26% and 87% of tumors, respectively, accompanied by a reduced expression of the mitochondrial biogenesis markers (PCG1α, NRF1, and TFAM). Furthermore, P62 and LC3a gene expression suggested increased mitophagy, which is linked to mitochondrial dysfunction. These finding suggest a complementarity and a potential contributing role in PCCs/PGLs tumorigenesis. Abstract Background: Somatic mutations, copy-number variations, and genome instability of mitochondrial DNA (mtDNA) have been reported in different types of cancers and are suggested to play important roles in cancer development and metastasis. However, there is scarce information about pheochromocytomas and paragangliomas (PCCs/PGLs) formation. Material: To determine the potential roles of mtDNA alterations in sporadic PCCs/PGLs, we analyzed a panel of 26 nuclear susceptibility genes and the entire mtDNA sequence of seventy-seven human tumors, using next-generation sequencing, and compared the results with normal adrenal medulla tissues. We also performed an analysis of copy-number alterations, large mtDNA deletion, and gene and protein expression. Results: Our results revealed that 53.2% of the tumors harbor a mutation in at least one of the targeted susceptibility genes, and 16.9% harbor complementary mitochondrial mutations. More than 50% of the mitochondrial mutations were novel and predicted pathogenic, affecting mitochondrial oxidative phosphorylation. Large deletions were found in 26% of tumors, and depletion of mtDNA occurred in more than 87% of PCCs/PGLs. The reduction of the mitochondrial number was accompanied by a reduced expression of the regulators that promote mitochondrial biogenesis (PCG1α, NRF1, and TFAM). Further, P62 and LC3a gene expression suggested increased mitophagy, which is linked to mitochondrial dysfunction. Conclusion: The pathogenic role of these finding remains to be shown, but we suggest a complementarity and a potential contributing role in PCCs/PGLs tumorigenesis.
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Pham VH, Nguyen VL, Jung HE, Cho YS, Shin JG. The frequency of the known mitochondrial variants associated with drug-induced toxicity in a Korean population. BMC Med Genomics 2022; 15:3. [PMID: 34980117 PMCID: PMC8722126 DOI: 10.1186/s12920-021-01153-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 12/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Few studies have annotated the whole mitochondrial DNA (mtDNA) genome associated with drug responses in Asian populations. This study aimed to characterize mtDNA genetic profiles, especially the distribution and frequency of well-known genetic biomarkers associated with diseases and drug-induced toxicity in a Korean population. METHOD Whole mitochondrial genome was sequenced for 118 Korean subjects by using a next-generation sequencing approach. The bioinformatic pipeline was constructed for variant calling, haplogroup classification and annotation of mitochondrial mutation. RESULTS A total of 681 variants was identified among all subjects. The MT-TRNP gene and displacement loop showed the highest numbers of variants (113 and 74 variants, respectively). The m.16189T > C allele, which is known to reduce the mtDNA copy number in human cells was detected in 25.4% of subjects. The variants (m.2706A > G, m.3010A > G, and m.1095T > C), which are associated with drug-induced toxicity, were observed with the frequency of 99.15%, 30.51%, and 0.08%, respectively. The m.2150T > A, a genotype associated with highly disruptive effects on mitochondrial ribosomes, was identified in five subjects. The D and M groups were the most dominant groups with the frequency of 34.74% and 16.1%, respectively. CONCLUSIONS Our finding was consistent with Korean Genome Project and well reflected the unique profile of mitochondrial haplogroup distribution. It was the first study to annotate the whole mitochondrial genome with drug-induced toxicity to predict the ADRs event in clinical implementation for Korean subjects. This approach could be extended for further study for validation of the potential ethnic-specific mitochondrial genetic biomarkers in the Korean population.
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Affiliation(s)
- Vinh Hoa Pham
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Van Lam Nguyen
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea
| | - Hye-Eun Jung
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Precision Medicine, SPMED Co., Ltd., Busan, 46508, Republic of Korea
| | - Yong-Soon Cho
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea.,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea.,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea
| | - Jae-Gook Shin
- Department of Pharmacology and Pharmacogenomics Research Center, Inje University, College of Medicine, 633-165 Gaegum-Dong, Jin-Gu, Busan, Republic of Korea. .,Department of Pharmacology and Clinical Pharmacology, PharmacoGenomics Research Center, Inje University College of Medicine, Busan, 47392, Republic of Korea. .,Center for Personalized Precision Medicine of Tuberculosis, Inje University College of Medicine, Busan, Republic of Korea.
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11
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Karim L, Kosmider B, Bahmed K. Mitochondrial ribosomal stress in lung diseases. Am J Physiol Lung Cell Mol Physiol 2021; 322:L507-L517. [PMID: 34873929 DOI: 10.1152/ajplung.00078.2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Mitochondria are involved in a variety of critical cellular functions, and their impairment drives cell injury. The mitochondrial ribosome (mitoribosome) is responsible for the protein synthesis of mitochondrial DNA encoded genes. These proteins are involved in oxidative phosphorylation, respiration, and ATP production required in the cell. Mitoribosome components originate from both mitochondrial and nuclear genomes. Their dysfunction can be caused by impaired mitochondrial protein synthesis or mitoribosome misassembly, leading to a decline in mitochondrial translation. This decrease can trigger mitochondrial ribosomal stress and contribute to pulmonary cell injury, death, and diseases. This review focuses on the contribution of the impaired mitoribosome structural components and function to respiratory disease pathophysiology. We present recent findings in the fields of lung cancer, chronic obstructive pulmonary disease, interstitial lung disease, and asthma. We also include reports on the mitoribosome dysfunction in pulmonary hypertension, high altitude pulmonary edema, bacterial and viral infections. Studies of the mitoribosome alterations in respiratory diseases can lead to novel therapeutic targets.
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Affiliation(s)
- Loukmane Karim
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States
| | - Beata Kosmider
- Department of Microbiology, Immunology, and Inflammation, Temple University, Philadelphia, PA, United States.,Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Biomedical Education and Data Science, Temple University, Philadelphia, PA, United States
| | - Karim Bahmed
- Center for Inflammation and Lung Research, Temple University, Philadelphia, PA, United States.,Department of Thoracic Medicine and Surgery, Temple University, Philadelphia, PA, United States
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12
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De Luise M, Iommarini L, Marchio L, Tedesco G, Coadă CA, Repaci A, Turchetti D, Tardio ML, Salfi N, Pagotto U, Kurelac I, Porcelli AM, Gasparre G. Pathogenic Mitochondrial DNA Mutation Load Inversely Correlates with Malignant Features in Familial Oncocytic Parathyroid Tumors Associated with Hyperparathyroidism-Jaw Tumor Syndrome. Cells 2021; 10:2920. [PMID: 34831144 PMCID: PMC8616364 DOI: 10.3390/cells10112920] [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: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
While somatic disruptive mitochondrial DNA (mtDNA) mutations that severely affect the respiratory chain are counter-selected in most human neoplasms, they are the genetic hallmark of indolent oncocytomas, where they appear to contribute to reduce tumorigenic potential. A correlation between mtDNA mutation type and load, and the clinical outcome of a tumor, corroborated by functional studies, is currently lacking. Recurrent familial oncocytomas are extremely rare entities, and they offer the chance to investigate the determinants of oncocytic transformation and the role of both germline and somatic mtDNA mutations in cancer. We here report the first family with Hyperparathyroidism-Jaw Tumor (HPT-JT) syndrome showing the inherited predisposition of four individuals to develop parathyroid oncocytic tumors. MtDNA sequencing revealed a rare ribosomal RNA mutation in the germline of all HPT-JT affected individuals whose pathogenicity was functionally evaluated via cybridization technique, and which was counter-selected in the most aggressive infiltrating carcinoma, but positively selected in adenomas. In all tumors different somatic mutations accumulated on this genetic background, with an inverse clear-cut correlation between the load of pathogenic mtDNA mutations and the indolent behavior of neoplasms, highlighting the importance of the former both as modifiers of cancer fate and as prognostic markers.
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Affiliation(s)
- Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Luisa Iommarini
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Lorena Marchio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Greta Tedesco
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Camelia Alexandra Coadă
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Andrea Repaci
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Medical Genetics, IRCSS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Maria Lucia Tardio
- Unit of Pathology, IRCCS S.Orsola University Hospital, 40138 Bologna, Italy;
| | - Nunzio Salfi
- Pathology Unit, IRCCS Giannina Gaslini Children’s Research Hospital, 16147 Genova, Italy;
| | - Uberto Pagotto
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Anna Maria Porcelli
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
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13
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Shen L, McCormick EM, Muraresku CC, Falk MJ, Gai X. Clinical Bioinformatics in Precise Diagnosis of Mitochondrial Disease. Clin Lab Med 2021; 40:149-161. [PMID: 32439066 DOI: 10.1016/j.cll.2020.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Clinical bioinformatics system is well-established for diagnosing genetic disease based on next-generation sequencing, but requires special considerations when being adapted for the next-generation sequencing-based genetic diagnosis of mitochondrial diseases. Challenges are caused by the involvement of mitochondrial DNA genome in disease etiology. Heteroplasmy and haplogroup are key factors in interpreting mitochondrial DNA variant effects. Data resources and tools for analyzing variant and sequencing data are available at MSeqDR, MitoMap, and HmtDB. Revised specifications of the American College of Medical Genetics/Association of Molecular Pathology standards and guidelines for mitochondrial DNA variant interpretation are proposed by the MSeqDr Consortium and community experts.
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Affiliation(s)
- Lishuang Shen
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Colleen Clarke Muraresku
- Mitochondrial Medicine Frontier Program, Children's Hospital of Philadelphia, 3401 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Marni J Falk
- CHOP Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, The Children's Hospital of Philadelphia, ARC 1002c, 3615 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Xiaowu Gai
- Keck School of Medicine of USC, Center for Personalized Medicine, Children's Hospital Los Angeles, Suite 300, 2100 West 3rd Street, Los Angeles, CA 90057, USA.
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14
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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.
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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.
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15
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Haumann S, Boix J, Knuever J, Bieling A, Vila Sanjurjo A, Elson JL, Blakely EL, Taylor RW, Riet N, Abken H, Kashkar H, Hornig-Do HT, Wiesner RJ. Mitochondrial DNA mutations induce mitochondrial biogenesis and increase the tumorigenic potential of Hodgkin and Reed-Sternberg cells. Carcinogenesis 2021; 41:1735-1745. [PMID: 32255484 DOI: 10.1093/carcin/bgaa032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 03/17/2020] [Accepted: 04/06/2020] [Indexed: 11/14/2022] Open
Abstract
Functioning mitochondria are crucial for cancer metabolism, but aerobic glycolysis is still considered to be an important pathway for energy production in many tumor cells. Here we show that two well established, classic Hodgkin lymphoma (cHL) cell lines harbor deleterious variants within mitochondrial DNA (mtDNA) and thus exhibit reduced steady-state levels of respiratory chain complexes. However, instead of resulting in the expected bioenergetic defect, these mtDNA variants evoke a retrograde signaling response that induces mitochondrial biogenesis and ultimately results in increased mitochondrial mass as well as function and enhances proliferation in vitro as well as tumor growth in mice in vivo. When complex I assembly was impaired by knockdown of one of its subunits, this led to further increased mitochondrial mass and function and, consequently, further accelerated tumor growth in vivo. In contrast, inhibition of mitochondrial respiration in vivo by the mitochondrial complex I inhibitor metformin efficiently slowed down growth. We conclude that, as a new mechanism, mildly deleterious mtDNA variants in cHL cancer cells cause an increase of mitochondrial mass and enhanced function as a compensatory effect using a retrograde signaling pathway, which provides an obvious advantage for tumor growth.
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Affiliation(s)
- Sophie Haumann
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Pediatrics, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Julia Boix
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Jana Knuever
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Dermatology, Medical Faculty and University Hospital of Cologne, Cologne, Germany
| | - Angela Bieling
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Anton Vila Sanjurjo
- Grupo GIBE, Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, Universidade de A Coruña (UDC), A Coruña, Spain
| | - Joanna L Elson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK.,Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, Newcastle University, Newcastle upon Tyne UK
| | - Nicole Riet
- Department I for Internal Medicine, Medical Faculty and University of Cologne, 50931 Cologne, Germany
| | - Hinrich Abken
- Department I for Internal Medicine, Medical Faculty and University of Cologne, 50931 Cologne, Germany.,Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,RCI, Regensburg Center for Interventional Immunology, Chair Gene-Immunotherapy, University Hospital Regensburg, Regensburg, Germany
| | - Hamid Kashkar
- Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Institute of Medical Microbiology, Immunology and Hygiene, Medical Faculty and University Hospital of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Hue-Tran Hornig-Do
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany
| | - Rudolf J Wiesner
- Center for Physiology and Pathophysiology, Institute of Vegetative Physiology, Medical Faculty, University of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, 50931 Cologne (CMMC), University of Cologne, 50931 Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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16
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Human Mitoribosome Biogenesis and Its Emerging Links to Disease. Int J Mol Sci 2021; 22:ijms22083827. [PMID: 33917098 PMCID: PMC8067846 DOI: 10.3390/ijms22083827] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 12/20/2022] Open
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) synthesize a small subset of proteins, which are essential components of the oxidative phosphorylation machinery. Therefore, their function is of fundamental importance to cellular metabolism. The assembly of mitoribosomes is a complex process that progresses through numerous maturation and protein-binding events coordinated by the actions of several assembly factors. Dysregulation of mitoribosome production is increasingly recognized as a contributor to metabolic and neurodegenerative diseases. In recent years, mutations in multiple components of the mitoribosome assembly machinery have been associated with a range of human pathologies, highlighting their importance to cell function and health. Here, we provide a review of our current understanding of mitoribosome biogenesis, highlighting the key factors involved in this process and the growing number of mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors that lead to human disease.
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17
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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18
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Vila-Sanjurjo A, Smith PM, Elson JL. Heterologous Inferential Analysis (HIA) and Other Emerging Concepts: In Understanding Mitochondrial Variation In Pathogenesis: There is no More Low-Hanging Fruit. Methods Mol Biol 2021; 2277:203-245. [PMID: 34080154 DOI: 10.1007/978-1-0716-1270-5_14] [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] [Indexed: 06/12/2023]
Abstract
Here we summarize our latest efforts to elucidate the role of mtDNA variants affecting the mitochondrial translation machinery, namely variants mapping to the mt-rRNA and mt-tRNA genes. Evidence is accumulating to suggest that the cellular response to interference with mitochondrial translation is different from that occurring as a result of mutations in genes encoding OXPHOS proteins. As a result, it appears safe to state that a complete view of mitochondrial disease will not be obtained until we understand the effect of mt-rRNA and mt-tRNA variants on mitochondrial protein synthesis. Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis (HIA ) that can be used to make predictions concerning the disruptive potential of a large subset of mt-rRNA variants. We have used HIA to explore the mutational landscape of 12S and 16S mt-rRNA genes. Our HIA studies include a thorough classification of all rare variants reported in the literature as well as others obtained from studies performed in collaboration with physicians. HIA has also been used with non-mammalian mt-rRNA genes to elucidate how mitotypes influence the interaction of the individual and the environment. Regarding mt-tRNA variations, rapidly growing evidence shows that the spectrum of mutations causing mitochondrial disease might differ between the different mitochondrial haplogroups seen in human populations.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Departamento de Bioloxía, Facultade de Ciencias, Centro de Investigacións en Ciencias Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain.
| | - Paul M Smith
- Department of Paediatrics, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Joanna L Elson
- Biosciences Institute Newcastle, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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19
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Ferrari A, Del'Olio S, Barrientos A. The Diseased Mitoribosome. FEBS Lett 2020; 595:1025-1061. [PMID: 33314036 DOI: 10.1002/1873-3468.14024] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/17/2022]
Abstract
Mitochondria control life and death in eukaryotic cells. Harboring a unique circular genome, a by-product of an ancient endosymbiotic event, mitochondria maintains a specialized and evolutionary divergent protein synthesis machinery, the mitoribosome. Mitoribosome biogenesis depends on elements encoded in both the mitochondrial genome (the RNA components) and the nuclear genome (all ribosomal proteins and assembly factors). Recent cryo-EM structures of mammalian mitoribosomes have illuminated their composition and provided hints regarding their assembly and elusive mitochondrial translation mechanisms. A growing body of literature involves the mitoribosome in inherited primary mitochondrial disorders. Mutations in genes encoding mitoribosomal RNAs, proteins, and assembly factors impede mitoribosome biogenesis, causing protein synthesis defects that lead to respiratory chain failure and mitochondrial disorders such as encephalo- and cardiomyopathy, deafness, neuropathy, and developmental delays. In this article, we review the current fundamental understanding of mitoribosome assembly and function, and the clinical landscape of mitochondrial disorders driven by mutations in mitoribosome components and assembly factors, to portray how basic and clinical studies combined help us better understand both mitochondrial biology and medicine.
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Affiliation(s)
- Alberto Ferrari
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA
| | - Samuel Del'Olio
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, FL, USA
| | - Antoni Barrientos
- Department of Neurology, University of Miami Miller School of Medicine, FL, USA.,Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, FL, USA
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20
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Jaiswal KS, Khanna S, Ghosh A, Padhan P, Raghav SK, Gupta B. Differential mitochondrial genome in patients with Rheumatoid Arthritis. Autoimmunity 2020; 54:1-12. [PMID: 33191792 DOI: 10.1080/08916934.2020.1846182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Mitochondria play an important role in cell survival, function and lineage differentiation. Changes in mitochondrial DNA (mtDNA) may control mitochondrial functions and thus may impart an alternative cellular state thereby leading to a disease condition in the body. Rheumatoid arthritis (RA) is a chronic inflammatory autoimmune disease wherein immune cells become self-reactive causing joint inflammation, swelling and pain in patients. The changes in mtDNA may alter cellular functions thereby directing the immune cells towards an inflammatory phenotype in RA. Therefore, it becomes pertinent to identify changes in mtDNA sequence in immune cells of RA patients to understand the pathogenesis and progression of RA. METHODS mtDNA from peripheral blood mono-nuclear cells (PBMCs) of 23 RA patients and 17 healthy controls (HCs) were sequenced using next-generation sequencing (NGS). Further, single nucleotide polymorphisms (SNPs) and other variable changes in mtDNA hypervariable and coding regions, amino acid changes with a putative impact on disease, levels of heteroplasmy, copy number variations and haplogroup analysis in RA patients and HCs were analysed and compared to identify any association of mtDNA changes and RA disease. RESULTS A total of 382 single nucleotide mtDNA variants were observed, 91 (23.82%) were present in hypervariable region and 291 (76.18%) in coding region of patients and HC. The variant 513 GCA > ACA, with G present in HVR-III, known to control the mitochondrial translation function, was significantly present in RA patients. The CYTB gene had larger number of SNPs in HC samples while RNR2 was more variable in RA patients. A non-synonymous heteroplasmy in ND1 gene was found at a single nucleotide position 3533 in an increased number of RA patients as compared to the controls. A significant increase in mtDNA duplication and a higher frequency of the haplogroup U was also characteristic of RA. Also, the presence of SNPs in mitochondrial tRNA genes at two positions 12308 A > G and 15924 A > G were found to be pathogenic. CONCLUSION We herein observed an altered mtDNA sequence in immune cells of RA patients and thus a possible role of mitochondrial genome in the development of RA. The observed nucleotide changes in mtDNA control region, RNR2 gene, increased heteroplasmy and mtDNA duplication in RA patients may alter sites for transcription factor binding thereby influencing mtDNA gene expression, as well as copy numbers thereby affecting the mitochondrial proteins and their functions. These changes in mtDNA could be one of the probable reasons among many leading to the progression of RA.
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Affiliation(s)
- Kumar Sagar Jaiswal
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Shweta Khanna
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
| | - Arup Ghosh
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Prasanta Padhan
- Department of Rheumatology, Kalinga Institute of Medical Sciences, Bhubaneswar, India
| | - Sunil Kumar Raghav
- Laboratory of Immuno-Genomics and Systems Biology, Institute of Life Sciences, Bhubaneswar, India
| | - Bhawna Gupta
- Disease Biology Laboratory, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to be University, Bhubaneswar, India
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21
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Webb M, Sideris DP. Intimate Relations-Mitochondria and Ageing. Int J Mol Sci 2020; 21:ijms21207580. [PMID: 33066461 PMCID: PMC7589147 DOI: 10.3390/ijms21207580] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial dysfunction is associated with ageing, but the detailed causal relationship between the two is still unclear. We review the major phenomenological manifestations of mitochondrial age-related dysfunction including biochemical, regulatory and energetic features. We conclude that the complexity of these processes and their inter-relationships are still not fully understood and at this point it seems unlikely that a single linear cause and effect relationship between any specific aspect of mitochondrial biology and ageing can be established in either direction.
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Affiliation(s)
- Michael Webb
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
| | - Dionisia P Sideris
- Mitobridge Inc., an Astellas Company, 1030 Massachusetts Ave, Cambridge, MA 02138, USA
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22
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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.
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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
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23
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Piotrowska-Nowak A, Kosior-Jarecka E, Schab A, Wrobel-Dudzinska D, Bartnik E, Zarnowski T, Tonska K. Investigation of whole mitochondrial genome variation in normal tension glaucoma. Exp Eye Res 2018; 178:186-197. [PMID: 30312593 DOI: 10.1016/j.exer.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023]
Abstract
Glaucoma is one of the leading causes of visual impairment and blindness worldwide. However, the cause of retinal ganglion cell loss and damage of the optic nerve in its pathogenesis is largely unknown. The high energy demands of these cells may reflect their strong dependence on mitochondrial function and thus sensitivity to mitochondrial defects. To address this issue, we studied whole mitochondrial genome variation in normal tension glaucoma patients and control individuals from the Polish population using next generation sequencing. Our findings indicate that few features of mitochondrial DNA variation are different for glaucoma patients and control subjects. New insights into normal tension glaucoma development are discussed. We provide also a comprehensive approach for mitochondrial DNA analysis and variant evaluation.
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Affiliation(s)
- Agnieszka Piotrowska-Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Aleksandra Schab
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Dominika Wrobel-Dudzinska
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland; Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Tomasz Zarnowski
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Katarzyna Tonska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
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24
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Zhang QL, Yang XZ, Zhang L, Feng RQ, Zhu QH, Chen JY, Yuan ML. Adaptive evidence of mitochondrial genomes in Dolycoris baccarum (Hemiptera: Pentatomidae) to divergent altitude environments. Mitochondrial DNA A DNA Mapp Seq Anal 2018. [PMID: 29521177 DOI: 10.1080/24701394.2018.1446951] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Given mitochondrion is the 'energy and oxygen usage factories', adaptive signatures of mitochondrial genes have been extensively investigated in vertebrates from different altitudes, but few studies focus on insects. Here, we sequenced the complete mitochondrial genome (mitogenome) of Dolycoris. baccarum living in the Tibetan Plateau (DBHC, ∼3200 m above sea level (asl)) and conducted a detailed comparative analysis with another D. baccarum mitogenome (DBQY) from relatively low altitude (∼1300 m asl). All the 37 mitochondrial genes were highly conserved and under purifying selection, except for two mitochondrial protein-coding genes (MPCGs) (atp6 and nad5) that showed positively selected signatures. We therefore further examined non-synonymous substitutions in atp6 and nad5, by sequencing more individuals from three populations with different altitudes. We found that these non-synonymous substitutions were polymorphic in these populations, likely due to relaxed selection constraints in different altitudes. Purifying selection in all mitochondrial genes may be due to their functional importance for the precision of ATP production usually. Length difference in mitochondrial control regions between DBHC and DBQY was also conversed at the population level, indicating that sequence size adjustments in control region may be associated with adaptation to divergent altitudes. Quantitatively real-time PCR analysis for 12 MPCGs showed that gene expression patterns had a significant change between the two populations, suggesting that expression levels of MPCGs could be modulated by divergent environmental pressures (e.g. oxygen content and ambient temperature). These results provided an important guide for further uncovering genetic mechanisms of ecological adaptation in insects.
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Affiliation(s)
- Qi-Lin Zhang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China.,b State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science , Nanjing University , Nanjing , China
| | - Xing-Zhuo Yang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | - Li Zhang
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | - Run-Qiu Feng
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China
| | | | - Jun-Yuan Chen
- b State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science , Nanjing University , Nanjing , China
| | - Ming-Long Yuan
- a State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agricultural Science and Technology , Lanzhou University , Lanzhou , China.,d Key Laboratory of Grassland Livestock Industry Innovation , Ministry of Agriculture , Lanzhou , China
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25
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Towarnicki SG, Ballard JWO. Drosophila mitotypes determine developmental time in a diet and temperature dependent manner. JOURNAL OF INSECT PHYSIOLOGY 2017; 100:133-139. [PMID: 28619466 DOI: 10.1016/j.jinsphys.2017.06.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 06/07/2023]
Abstract
It is well known that specific mitochondrial (mt) DNA mutations can reduce organismal fitness and influence mitochondrial-nuclear interactions. However, determining specific mtDNA mutations that are beneficial has been elusive. In this study, we vary the diet and environmental temperature to study larval development time of two Drosophila melanogaster mitotypes (Alstonville and Dahomey), in two nuclear genetic backgrounds, and investigate developmental differences through weight, feeding rate, and movement. To manipulate the diet, we utilize the nutritional geometric framework to manipulate isocaloric diets of differing macronutrient ratios (1:2 and 1:16 protein: carbohydrate (P:C) ratios) and raise flies at three temperatures (19°C, 23°C and 27°C). Larvae with Dahomey mtDNA develop more slowly than Alstonville when fed the 1:2 P:C diet at all temperatures and developed more quickly when fed the 1:16 P:C diet at 23°C and 27°C. We determined that Dahomey larvae eat more, move less, and weigh more than Alstonville larvae when raised on the 1:16 P:C diet and that these physiological responses are modified by temperature. We suggest that 1 (or more) of 4 mtDNA changes is likely responsible for the observed effects and posit the mtDNA changes moderate a physiological trade-off between consumption and foraging.
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Affiliation(s)
- Samuel G Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
| | - J William O Ballard
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia.
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26
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MutPred mutational load analysis shows mildly deleterious mitochondrial DNA variants are not more prevalent in Alzheimer's patients, but may be under-represented in healthy older individuals. Mitochondrion 2017; 34:141-146. [DOI: 10.1016/j.mito.2017.04.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 02/09/2017] [Accepted: 04/06/2017] [Indexed: 12/24/2022]
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27
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Abstract
Macroautophagy/autophagy is a key catabolic process, essential for maintaining cellular homeostasis and survival through the removal and recycling of unwanted cellular material. Emerging evidence has revealed intricate connections between the RNA and autophagy research fields. While a majority of studies have focused on protein, lipid and carbohydrate catabolism via autophagy, accumulating data supports the view that several types of RNA and associated ribonucleoprotein complexes are specifically recruited to phagophores (precursors to autophagosomes) and subsequently degraded in the lysosome/vacuole. Moreover, recent studies have revealed a substantial number of novel autophagy regulators with RNA-related functions, indicating roles for RNA and associated proteins not only as cargo, but also as regulators of this process. In this review, we discuss widespread evidence of RNA catabolism via autophagy in yeast, plants and animals, reviewing the molecular mechanisms and biological importance in normal physiology, stress and disease. In addition, we explore emerging evidence of core autophagy regulation mediated by RNA-binding proteins and noncoding RNAs, and point to gaps in our current knowledge of the connection between RNA and autophagy. Finally, we discuss the pathological implications of RNA-protein aggregation, primarily in the context of neurodegenerative disease.
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Affiliation(s)
- Lisa B Frankel
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
| | - Michal Lubas
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
| | - Anders H Lund
- a Biotech Research and Innovation Centre , University of Copenhagen , Copenhagen , Denmark
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