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Luo L, Wang M, Liu Y, Li J, Bu F, Yuan H, Tang R, Liu C, He G. Sequencing and characterizing human mitochondrial genomes in the biobank-based genomic research paradigm. SCIENCE CHINA. LIFE SCIENCES 2025; 68:1610-1625. [PMID: 39843848 DOI: 10.1007/s11427-024-2736-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Accepted: 09/18/2024] [Indexed: 01/24/2025]
Abstract
Human mitochondrial DNA (mtDNA) harbors essential mutations linked to aging, neurodegenerative diseases, and complex muscle disorders. Due to its uniparental and haploid inheritance, mtDNA captures matrilineal evolutionary trajectories, playing a crucial role in population and medical genetics. However, critical questions about the genomic diversity patterns, inheritance models, and evolutionary and medical functions of mtDNA remain unresolved or underexplored, particularly in the transition from traditional genotyping to large-scale genomic analyses. This review summarizes recent advancements in data-driven genomic research and technological innovations that address these questions and clarify the biological impact of nuclear-mitochondrial segments (NUMTs) and mtDNA variants on human health, disease, and evolution. We propose a streamlined pipeline to comprehensively identify mtDNA and NUMT genomic diversity using advanced sequencing and computational technologies. Haplotype-resolved mtDNA sequencing and assembly can distinguish authentic mtDNA variants from NUMTs, reduce diagnostic inaccuracies, and provide clearer insights into heteroplasmy patterns and the authenticity of paternal inheritance. This review emphasizes the need for integrative multi-omics approaches and emerging long-read sequencing technologies to gain new insights into mutation mechanisms, the influence of heteroplasmy and paternal inheritance on mtDNA diversity and disease susceptibility, and the detailed functions of NUMTs.
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Affiliation(s)
- Lintao Luo
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Yunhui Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Jianbo Li
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Fengxiao Bu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Huijun Yuan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
| | - Chao Liu
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China.
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China.
- Anti-Drug Technology Center of Guangdong Province, Guangzhou, 510230, China.
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2
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Cheng Y, Huang CR, Cheng YH, Chang YC, Weng PL, Lan KC. The Potential Protective Role of Mitochondrial Haplogroup R in Ovarian Response: An Exploratory Study. Int J Mol Sci 2025; 26:2513. [PMID: 40141157 PMCID: PMC11941838 DOI: 10.3390/ijms26062513] [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: 01/06/2025] [Revised: 03/01/2025] [Accepted: 03/06/2025] [Indexed: 03/28/2025] Open
Abstract
An investigation of the mtDNA haplogroup in 96 Taiwanese women with diminished ovarian response (DOR) and normal ovarian response (NOR) showed that only the haplogroup R is less likely to experience DOR than other mtDNA haplogroups. When analyzing the relationship between age and mitochondria-related markers (mtDNA copy number, ROS levels, and telomere length), it was observed that ROS levels and telomere length exhibited age-dependent changes, and the number of retrieved oocytes decreased with age. However, in the R haplogroup, these mitochondria-related markers remained stable and did not show significant changes with age. Additionally, in the R haplogroup, the number of oocytes did not decline with age, suggesting a unique protective effect associated with this haplogroup. Our study supports the notion that the mtDNA haplogroup may serve as a biomarker for infertility in Taiwanese women.
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Affiliation(s)
- Yun Cheng
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
| | - Cheng-Rung Huang
- Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (C.-R.H.); (Y.-H.C.); (Y.-C.C.); (P.-L.W.)
| | - Yin-Hua Cheng
- Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (C.-R.H.); (Y.-H.C.); (Y.-C.C.); (P.-L.W.)
| | - Yung-Chiao Chang
- Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (C.-R.H.); (Y.-H.C.); (Y.-C.C.); (P.-L.W.)
| | - Pei-Ling Weng
- Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (C.-R.H.); (Y.-H.C.); (Y.-C.C.); (P.-L.W.)
| | - Kuo-Chung Lan
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
- Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; (C.-R.H.); (Y.-H.C.); (Y.-C.C.); (P.-L.W.)
- Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung 412, Taiwan
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Abood S, Oota H. Human dispersal into East Eurasia: ancient genome insights and the need for research on physiological adaptations. J Physiol Anthropol 2025; 44:5. [PMID: 39953642 PMCID: PMC11829451 DOI: 10.1186/s40101-024-00382-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Accepted: 12/25/2024] [Indexed: 02/17/2025] Open
Abstract
Humans have long pondered their genesis. The answer to the great question of where Homo sapiens come from has evolved in conjunction with biotechnologies that have allowed us to more brightly illuminate our distant past. The "Multiregional Evolution" model was once the hegemonic theory of Homo sapiens origins, but in the last 30 years, it has been supplanted by the "Out of Africa" model. Here, we review the major findings that have resulted in this paradigmatic shift. These include hominin brain expansion, classical insight from the mitochondrial genome (mtDNA) regarding the timing of the divergence point between Africans and non-Africans, and next-generation sequencing (NGS) of the Neanderthal and Denisovan genomes. These findings largely bolstered the "Out of Africa" model, although they also revealed a small degree of introgression of the Neanderthal and Denisovan genomes into those of non-African Homo sapiens. We also review paleogenomic studies for which migration route, north or south, early migrants to East Eurasia most likely traversed. Whichever route was taken, the migrants moved to higher latitudes, which necessitated adaptation for lower light conditions, colder clines, and pro-adipogenic mechanisms to counteract food scarcity. Further genetic and epigenetic investigations of these physiological adaptations constitute an integral aspect of the story of human origins and human migration to East Asia.
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Affiliation(s)
- Steven Abood
- Department of Biological Sciences, Graduate School of Science, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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Kozin MS, Kulakova OG, Kiselev IS, Semina EV, Kakotkin VV, Agapov MA, Favorova OO. Mitochondrial Genome Variants and Alzheimer's Disease. BIOCHEMISTRY. BIOKHIMIIA 2025; 90:S146-S163. [PMID: 40164157 DOI: 10.1134/s0006297924603174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/04/2024] [Accepted: 05/14/2024] [Indexed: 04/02/2025]
Abstract
Alzheimer's disease (AD), a severe neurodegenerative disease of the central nervous system, is the most common cause of cognitive impairment in people over the age of 60. The etiology and pathogenesis of Alzheimer's disease are still unclear despite decades of active research. Numerous studies have shown that neurodegenerative processes in AD are associated with the mitochondrial dysfunction. In this review, we briefly discuss the results of these studies and present the reported evidence that mitochondrial dysfunction in AD is associated with mitochondrial DNA (mtDNA) variations. The results of association analysis of mtDNA haplogroups and individual polymorphic variants, including those whose combinations define haplogroups, with AD are described in detail. These data clearly indicate the role of variations in the mitochondrial genome in the susceptibility to AD, although the problem of significance of individual mtDNA variants is far from being resolved.
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Affiliation(s)
- Maxim S Kozin
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia.
- Chazov National Medical Research Center of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117513, Russia
| | - Olga G Kulakova
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
- Chazov National Medical Research Center of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117513, Russia
| | - Ivan S Kiselev
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
- Chazov National Medical Research Center of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117513, Russia
| | | | - Viktor V Kakotkin
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
| | - Mikhail A Agapov
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
| | - Olga O Favorova
- Immanuel Kant Baltic Federal University, Kaliningrad, 236016, Russia
- Chazov National Medical Research Center of Cardiology, Ministry of Health of the Russian Federation, Moscow, 121552, Russia
- Pirogov Russian National Research Medical University, Ministry of Health of the Russian Federation, Moscow, 117513, Russia
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Arbeithuber B, Anthony K, Higgins B, Oppelt P, Shebl O, Tiemann-Boege I, Chiaromonte F, Ebner T, Makova KD. Mitochondrial DNA mutations in human oocytes undergo frequency-dependent selection but do not increase with age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.09.627454. [PMID: 39713397 PMCID: PMC11661235 DOI: 10.1101/2024.12.09.627454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
Abstract
Mitochondria, cellular powerhouses, harbor DNA (mtDNA) inherited from the mothers. MtDNA mutations can cause diseases, yet whether they increase with age in human germline cells-oocytes-remains understudied. Here, using highly accurate duplex sequencing of full-length mtDNA, we detected de novo mutations in single oocytes, blood, and saliva in women between 20 and 42 years of age. We found that, with age, mutations increased in blood and saliva but not in oocytes. In oocytes, mutations with high allele frequencies (≥1%) were less prevalent in coding than non-coding regions, whereas mutations with low allele frequencies (<1%) were more uniformly distributed along mtDNA, suggesting frequency-dependent purifying selection. In somatic tissues, mutations caused elevated amino acid changes in protein-coding regions, suggesting positive or destructive selection. Thus, mtDNA in human oocytes is protected against accumulation of mutations having functional consequences and with aging. These findings are particularly timely as humans tend to reproduce later in life.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Experimental Gynaecology and Obstetrics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Kate Anthony
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Bonnie Higgins
- Department of Biology, Penn State University, University Park, PA 16802, USA
| | - Peter Oppelt
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Omar Shebl
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Irene Tiemann-Boege
- Institute of Biophysics, Johannes Kepler University Linz, Altenberger Strasse 69, 4040 Linz, Austria
| | - Francesca Chiaromonte
- Center for Medical Genomics, Penn State University, University Park, PA 16802, USA
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802 USA
- Sant’Anna School of Advanced Studies, Pisa, 56127 Italy
| | - Thomas Ebner
- Department of Gynaecology, Obstetrics and Gynaecological Endocrinology, Johannes Kepler University Linz, Kepler University Hospital, Altenberger Strasse 69, 4040 Linz and Krankenhausstrasse 26, 4020, Linz, Austria
| | - Kateryna D. Makova
- Department of Biology, Penn State University, University Park, PA 16802, USA
- Center for Medical Genomics, Penn State University, University Park, PA 16802, USA
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Pu J, Lin X, Dong W. Phylogeny and divergence time estimation of the subfamily Amphipsyllinae based on the Frontopsylla diqingensis mitogenome. Front Vet Sci 2024; 11:1494204. [PMID: 39723187 PMCID: PMC11668791 DOI: 10.3389/fvets.2024.1494204] [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: 09/15/2024] [Accepted: 11/22/2024] [Indexed: 12/28/2024] Open
Abstract
Fleas are primarily parasites of small mammals and serve as essential vectors of the transmission of plague. The subfamily Amphipsyllinae (Siphonaptera: Leptopsyllidae) consists of 182 species across 13 genera, widely distributed worldwide. Only two species of Amphipsyllinae have been sequenced for complete mitogenomes to date. It hinders the taxonomy and evolutionary history studies of fleas. In this study, we first sequenced the Frontopsylla diqingensis mitogenome and performed comparative mitogenomic analyses with the two other species (Frontopsylla spadix and Paradoxopsyllus custodis) in Amphipsyllinae available in the NCBI database. The evolutionary process of Amphipsyllinae was comprehensively analyzed in terms of nucleotide composition, codon usage, nucleotide diversity, tRNA secondary structure, nucleotide skew, phylogeny tree, and divergence time. Nucleotide diversity and tRNAs of three species of fleas of Amphipsyllinae have differences among different species. The effective number of codon (ENC)-plot, neutrality curve, PR2, and correspondence analysis (COA) showed that the codon preference of Amphipsyllinae was influenced mainly by natural selection. For phylogenetic trees and divergence time of the order Siphonaptera, our results showed two concatenated data matrices, namely, PCG: (((Ceratophyllidae + Leptopsyllidae) + ((Vermipsyllidae + Hystrichopsyllidae) + Ctenophthalmidae)) + (Pulicidae + Pygiopsyllidae)); PCGRNA: ((((Ceratophyllidae + Leptopsyllidae) + ((Vermipsyllidae + Hystrichopsyllidae) + Ctenophthalmidae)) + Pulicidae) + Pygiopsyllidae). We concluded that P. custodis and Macrostylophora euteles from GenBank are the same species by phylogenetic trees and sequence alignment, and supported the monophyly of Amphipsyllinae. Amphipsyllinae diverged in the Cenozoic, approximately 73.37-40.32 million years ago (Mya). The majority of the species within the intraordinal divergence into extant lineages occurred after the K-Pg boundary. The common ancestor of the extant order Siphonaptera diverged during the Cretaceous. Our findings supported those of Zhu et al. (1). This study provides new insights into the evolutionary history and taxonomy of the order Siphonaptera.
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Affiliation(s)
| | | | - Wenge Dong
- Yunnan Provincial Key Laboratory for Zoonosis Control and Prevention, Institute of Pathogens and Vectors, Dali University, Dali, China
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Slapnik B, Šket R, Črepinšek K, Tesovnik T, Bizjan BJ, Kovač J. The quality and detection limits of mitochondrial heteroplasmy by long read nanopore sequencing. Sci Rep 2024; 14:26778. [PMID: 39501054 PMCID: PMC11538439 DOI: 10.1038/s41598-024-78270-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2024] [Accepted: 10/29/2024] [Indexed: 11/08/2024] Open
Abstract
This study evaluates long-read and short-read sequencing for mitochondrial DNA (mtDNA) heteroplasmy detection. 592,315 bootstrapped datasets generated from two single-nucleotide mismatched ultra-deep sequenced mtDNA samples were used to assess basecalling error and accuracy, limit of heteroplasmy detection, and heteroplasmy detection across various coverage depths. Results showed high Phred scores of data with GC-rich sequence bias for long reads. Limit of detection of 12% heteroplasmy was identified, showing strong correlation (R2 ≥ 0.955) with expected heteroplasmy but underreporting tendency of high-level variants. Nanopore sequencing shows potential for direct applicability in mitochondrial diseases diagnostics, but stringent validation processes to ensure diagnostic result quality are required.
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Affiliation(s)
- Barbara Slapnik
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Robert Šket
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Klementina Črepinšek
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Tine Tesovnik
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Barbara Jenko Bizjan
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia
| | - Jernej Kovač
- Clinical Institute for Special Laboratory Diagnostics, University Children's Hospital, University Medical Centre Ljubljana, Ljubljana, 1000, Slovenia.
- Faculty of Medicine, University of Ljubljana, Ljubljana, 1000, Slovenia.
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Haig D. Germline ecology: Managed herds, tolerated flocks, and pest control. J Hered 2024; 115:643-659. [PMID: 38447039 DOI: 10.1093/jhered/esae004] [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: 08/13/2023] [Accepted: 03/04/2024] [Indexed: 03/08/2024] Open
Abstract
Multicopy sequences evolve adaptations for increasing their copy number within nuclei. The activities of multicopy sequences under constraints imposed by cellular and organismal selection result in a rich intranuclear ecology in germline cells. Mitochondrial and ribosomal DNA are managed as domestic herds subject to selective breeding by the genes of the single-copy genome. Transposable elements lead a peripatetic existence in which they must continually move to new sites to keep ahead of inactivating mutations at old sites and undergo exponential outbreaks when the production of new copies exceeds the rate of inactivation of old copies. Centromeres become populated by repeats that do little harm. Organisms with late sequestration of germ cells tend to evolve more "junk" in their genomes than organisms with early sequestration of germ cells.
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Affiliation(s)
- David Haig
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, United States
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9
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Lallemand S, Oyhenart J, Valot B, Borne R, Bohard L, Umhang G, Karamon J, Konyaev S, Rönnberg C, Gottstein B, Weil-Verhoeven D, Richou C, Bresson-Hadni S, Millon L, Bellanger AP, Knapp J. Challenging the phylogenetic relationships among Echinococcus multilocularis isolates from main endemic areas. Int J Parasitol 2024; 54:569-582. [PMID: 38815855 DOI: 10.1016/j.ijpara.2024.05.004] [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: 01/16/2024] [Revised: 04/05/2024] [Accepted: 05/23/2024] [Indexed: 06/01/2024]
Abstract
Alveolar echinococcosis (AE) is a rare but severe disease that affects more than 18,000 people worldwide per year. The complete sequencing of the mitochondrial genome of Echinococcus multilocularis has made it possible to study the genetic diversity of the parasite and its spatial and temporal evolution. We amplified the whole mitochondrial genome by PCR, using one uniplex and two multiplex reactions to cover the 13,738 bp of the mitogenome, and then sequenced the amplicons with Illumina technology. In total, 113 samples from Europe, Asia, the Arctic and North America were analyzed. Three major haplogroups were found: HG1, which clustered samples from Alaska (including Saint-Lawrence Island), Yakutia (Russia) and Svalbard; HG2, with samples from Asia, North America and Europe; and HG3, subdivided into three micro-haplogroups. HG3a included samples from North America and Europe, whereas HG3b and HG3c only include samples from Europe. In France, HG3a included samples from patients more recently diagnosed in a region outside the historical endemic area. A fourth putative haplogroup, HG4, was represented by only one isolate from Olkhon Island (Russia). The increased discriminatory power of the complete sequencing of the E. multilocularis mitogenome has made it possible to highlight four distinct geographical clusters, one being divided into three micro-haplogroups in France.
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Affiliation(s)
- Séverine Lallemand
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France
| | - Jorge Oyhenart
- Instituto de Ciencias de la Tierra y Ambientales de La Pampa, Consejo Nacional de Investigaciones Científicas y Técnicas - Facultad de Ciencias Naturales Universidad Nacional de La Pampa, La Pampa, Argentina
| | - Benoit Valot
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France
| | - Romain Borne
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France
| | - Louis Bohard
- Department of Infectiology, University Hospital of Besançon, 25030 Besançon, France
| | - Gérald Umhang
- INTERFAS Unit, National Reference Laboratory for Echinococcus spp., Rabies and Wildlife Laboratory, ANSES, Malzéville, France
| | - Jacek Karamon
- Department of Parasitology and Invasive Diseases, National Veterinary Research Institute, Puławy, Poland
| | - Sergey Konyaev
- Institute of Systematics and Ecology of Animals, SB RAS, Novosibirsk, Russia
| | - Caroline Rönnberg
- Public Health Agency of Sweden, Department of Microbiology, Unit for Parasitology, Solna, Sweden
| | - Bruno Gottstein
- Institute of Infectious Diseases, Faculty of Medicine, University of Bern, CH-3012 Bern, Switzerland
| | - Delphine Weil-Verhoeven
- Department of Hepatology and Intensive Cares, University Hospital of Besançon, 25030 Besançon, France
| | - Carine Richou
- Department of Hepatology and Intensive Cares, University Hospital of Besançon, 25030 Besançon, France
| | - Solange Bresson-Hadni
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France; Department of Parasitology-Mycology, Reference National Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France
| | - Laurence Millon
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France; Department of Parasitology-Mycology, Reference National Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France
| | - Anne-Pauline Bellanger
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France; Department of Parasitology-Mycology, Reference National Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France
| | - Jenny Knapp
- UMR CNRS 6249 Chrono-Environnement, University of Franche-Comté, 16 Route de Gray, 25030 Besançon cedex, France; Department of Parasitology-Mycology, Reference National Centre for Echinococcoses, University Hospital of Besançon, 25030 Besançon, France.
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10
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Árnadóttir ER, Moore KHS, Guðmundsdóttir VB, Ebenesersdóttir SS, Guity K, Jónsson H, Stefánsson K, Helgason A. The rate and nature of mitochondrial DNA mutations in human pedigrees. Cell 2024; 187:3904-3918.e8. [PMID: 38851187 DOI: 10.1016/j.cell.2024.05.022] [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: 08/26/2023] [Revised: 03/06/2024] [Accepted: 05/13/2024] [Indexed: 06/10/2024]
Abstract
We examined the rate and nature of mitochondrial DNA (mtDNA) mutations in humans using sequence data from 64,806 contemporary Icelanders from 2,548 matrilines. Based on 116,663 mother-child transmissions, 8,199 mutations were detected, providing robust rate estimates by nucleotide type, functional impact, position, and different alleles at the same position. We thoroughly document the true extent of hypermutability in mtDNA, mainly affecting the control region but also some coding-region variants. The results reveal the impact of negative selection on viable deleterious mutations, including rapidly mutating disease-associated 3243A>G and 1555A>G and pre-natal selection that most likely occurs during the development of oocytes. Finally, we show that the fate of new mutations is determined by a drastic germline bottleneck, amounting to an average of 3 mtDNA units effectively transmitted from mother to child.
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Affiliation(s)
| | | | - Valdís B Guðmundsdóttir
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | - Kamran Guity
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kári Stefánsson
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
| | - Agnar Helgason
- deCODE Genetics/Amgen Inc., Reykjavik, Iceland; Department of Anthropology, University of Iceland, Reykjavik, Iceland.
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11
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Borrelli E, Bandello F, Boon CJF, Carelli V, Lenaers G, Reibaldi M, Sadda SR, Sadun AA, Sarraf D, Yu-Wai-Man P, Barboni P. Mitochondrial retinopathies and optic neuropathies: The impact of retinal imaging on modern understanding of pathogenesis, diagnosis, and management. Prog Retin Eye Res 2024; 101:101264. [PMID: 38703886 DOI: 10.1016/j.preteyeres.2024.101264] [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: 01/11/2024] [Revised: 03/18/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
Advancements in ocular imaging have significantly broadened our comprehension of mitochondrial retinopathies and optic neuropathies by examining the structural and pathological aspects of the retina and optic nerve in these conditions. This article aims to review the prominent imaging characteristics associated with mitochondrial retinopathies and optic neuropathies, aiming to deepen our insight into their pathogenesis and clinical features. Preceding this exploration, the article provides a detailed overview of the crucial genetic and clinical features, which is essential for the proper interpretation of in vivo imaging. More importantly, we will provide a critical analysis on how these imaging modalities could serve as biomarkers for characterization and monitoring, as well as in guiding treatment decisions. However, these imaging methods have limitations, which will be discussed along with potential strategies to mitigate them. Lastly, the article will emphasize the potential advantages and future integration of imaging techniques in evaluating patients with mitochondrial eye disorders, considering the prospects of emerging gene therapies.
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Affiliation(s)
- Enrico Borrelli
- Department of Surgical Sciences, University of Turin, Turin, Italy; Department of Ophthalmology, "City of Health and Science" Hospital, Turin, Italy.
| | - Francesco Bandello
- Vita-Salute San Raffaele University, Milan, Italy; IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam University Medical Centers, Amsterdam, the Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Valerio Carelli
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy; IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Guy Lenaers
- Equipe MitoLab, Unité MitoVasc, INSERM U1083, Université d'Angers, 49933, Angers, France; Service de Neurologie, CHU d'Angers, 49100, Angers, France
| | - Michele Reibaldi
- Department of Surgical Sciences, University of Turin, Turin, Italy; Department of Ophthalmology, "City of Health and Science" Hospital, Turin, Italy
| | - Srinivas R Sadda
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Doheny Eye Institute, Los Angeles, CA, USA
| | - Alfredo A Sadun
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Doheny Eye Institute, Los Angeles, CA, USA
| | - David Sarraf
- Department of Ophthalmology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA; Retinal Disorders and Ophthalmic Genetics Division, Stein Eye Institute, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Patrick Yu-Wai-Man
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; Institute of Ophthalmology, University College London, London, UK
| | - Piero Barboni
- IRCCS San Raffaele Scientific Institute, Milan, Italy; Studio Oculistico d'Azeglio, Bologna, Italy.
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12
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [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: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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13
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Hou YF, Wei JF, Zhao TY, Li CF, Wang F. First complete mitochondrial genome of the tribe Coccini (Hemiptera, Coccomorpha, Coccidae) and its phylogenetic implications. Zookeys 2023; 1180:333-354. [PMID: 38312323 PMCID: PMC10838174 DOI: 10.3897/zookeys.1180.109116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/07/2023] [Indexed: 02/06/2024] Open
Abstract
Soft scale insects (Hemiptera, Coccidae) are important pests of various agricultural and horticultural crops and ornamental plants. They have negative impacts on agriculture and forestry. The tribe Coccini represents one of the most ancient evolutionary lineages of soft scale insects. However, no complete Coccini mitochondrial genome (mitogenome) is available in public databases. Here, we described the complete mitogenome of Coccushesperidum L., 1758. The 15,566 bp mitogenome of C.hesperidum had a high A+T content (83.4%) and contained a typical set of 37 genes, with 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and two ribosomal RNA genes (rRNAs). Only seven tRNAs had the typical clover-leaf secondary structure and the remaining tRNAs lacked the DHU arm, TψC arm or both. Moreover, a comparative analysis of all reported scale insect mitogenomes from GenBank database was performed. The mitogenomes of scale insects showed high similarities in base composition and A+T content. Additionally, our phylogenetic analysis confirmed the monophyly of Coccomorpha and revealed that the archaeococcoids were the most basal lineage within Coccomorpha, while Ericeruspela and Didesmococcuskoreanus, belonging to Coccidae, were often mixed with Aclerdidae, making Coccidae a paraphyletic group. These findings expand the mitogenome database of scale insects and provide new insights on mitogenome evolution for future studies across different insect groups.
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Affiliation(s)
- Yun-Feng Hou
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
| | - Jiu-Feng Wei
- College of Plant Protection, Shanxi Agricultural University, Jinzhong, Shanxi, 030801, China Shanxi Agricultural University Jinzhong China
| | - Tian-You Zhao
- Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management, College of Plant Protection, China Agricultural University, Beijing, 100193, China China Agricultural University Beijing China
| | - Cai-Feng Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
| | - Fang Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaborative Innovation Center for Eco-Environment, Hebei Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, Hebei, 050024, China Hebei Normal University Shijiazhuang China
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14
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Hernández CL. Mitochondrial DNA in Human Diversity and Health: From the Golden Age to the Omics Era. Genes (Basel) 2023; 14:1534. [PMID: 37628587 PMCID: PMC10453943 DOI: 10.3390/genes14081534] [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: 06/19/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small fraction of our hereditary material. However, this molecule has had an overwhelming presence in scientific research for decades until the arrival of high-throughput studies. Several appealing properties justify the application of mtDNA to understand how human populations are-from a genetic perspective-and how individuals exhibit phenotypes of biomedical importance. Here, I review the basics of mitochondrial studies with a focus on the dawn of the field, analysis methods and the connection between two sides of mitochondrial genetics: anthropological and biomedical. The particularities of mtDNA, with respect to inheritance pattern, evolutionary rate and dependence on the nuclear genome, explain the challenges of associating mtDNA composition and diseases. Finally, I consider the relevance of this single locus in the context of omics research. The present work may serve as a tribute to a tool that has provided important insights into the past and present of humankind.
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Affiliation(s)
- Candela L Hernández
- Department of Biodiversity, Ecology and Evolution, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain
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15
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Vadakedath S, Kandi V, Ca J, Vijayan S, Achyut KC, Uppuluri S, Reddy PKK, Ramesh M, Kumar PP. Mitochondrial Deoxyribonucleic Acid (mtDNA), Maternal Inheritance, and Their Role in the Development of Cancers: A Scoping Review. Cureus 2023; 15:e39812. [PMID: 37397663 PMCID: PMC10314188 DOI: 10.7759/cureus.39812] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2023] [Indexed: 07/04/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is a small, circular, double-stranded DNA inherited from the mother during fertilization. Evolutionary evidence supported by the endosymbiotic theory identifies mitochondria as an organelle that could have descended from prokaryotes. This may be the reason for the independent function and inheritance pattern shown by mtDNA. The unstable nature of mtDNA due to the lack of protective histones, and effective repair systems make it more vulnerable to mutations. The mtDNA and its mutations could be maternally inherited thereby predisposing the offspring to various cancers like breast and ovarian cancers among others. Although mitochondria are considered heteroplasmic wherein variations among the multiple mtDNA genomes are noticed, mothers can have mitochondrial populations that are homoplasmic for a given mitochondrial mutation. Homoplasmic mitochondrial mutations may be transmitted to all maternal offspring. However, due to the complex interplay between the mitochondrial and nuclear genomes, it is often difficult to predict disease outcomes, even with homoplasmic mitochondrial populations. Heteroplasmic mtDNA mutations can be maternally inherited, but the proportion of mutated alleles differs markedly between offspring within one generation. This led to the genetic bottleneck hypothesis, explaining the rapid changes in allele frequency witnessed during the transmission of mtDNA from one generation to the next. Although a physical reduction in mtDNA has been demonstrated in several species, a comprehensive understanding of the molecular mechanisms is yet to be demonstrated. Despite initially thought to be limited to the germline, there is evidence that blockages exist in different cell types during development, perhaps explaining why different tissues in the same organism contain different levels of mutated mtDNA. In this review, we comprehensively discuss the potential mechanisms through which mtDNA undergoes mutations and the maternal mode of transmission that contributes to the development of tumors, especially breast and ovarian cancers.
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Affiliation(s)
| | - Venkataramana Kandi
- Clinical Microbiology, Prathima Institute of Medical Sciences, Karimnagar, IND
| | - Jayashankar Ca
- Internal Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, IND
| | - Swapna Vijayan
- Pediatrics, Sir CV Raman General Hospital, Bengaluru, IND
| | - Kushal C Achyut
- Internal Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bangalore, IND
| | - Shivani Uppuluri
- Internal Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, IND
| | - Praveen Kumar K Reddy
- General Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, IND
| | - Monish Ramesh
- Internal Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, IND
| | - P Pavan Kumar
- General Medicine, Vydehi Institute of Medical Sciences and Research Centre, Bengaluru, IND
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16
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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17
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Vanichanukulyakit J, Khacha-ananda S, Monum T, Mahawong P, Moophayak K, Penkhrue W, Khumpook T, Thongsahuan S. The Analysis of Genetic Polymorphism on Mitochondrial Hypervariable Region III in Thai Population. Genes (Basel) 2023; 14:682. [PMID: 36980954 PMCID: PMC10048634 DOI: 10.3390/genes14030682] [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: 02/19/2023] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Mitochondrial DNA (mtDNA) analysis is a genetic marker for human identification, especially matrilineal inheritance. Hypervariable regions (HVR) I and II of mtDNA have been currently performed for human identification worldwide. Further examination of HVRIII has been conducted with the aim of enhancing the power of discrimination. The aim of this research is to provide informative data on the polymorphisms of HVRIII in the Thai population in order to establish a national database for human identification. Thai people who were unrelated through the maternal lineage were recruited for blood collections. The mtDNA was extracted by Chelex extraction, amplified by polymerase chain reaction, and analyzed using Sequencing Analysis Software. The most common mutation in HVRIII was base substitution, followed by deletion and insertion. We discovered 40 unique haplotypes, with haplotype 489C being the most frequent. The haplotype diversity, power of discrimination, and random match probability were 0.8014, 0.7987, and 0.2013, respectively. Five-CA repeats were the most frequently observed in nucleotide positions 514-523. Our database can be employed as supplementary markers in addition to nuclear deoxyribonucleic acid (DNA) markers in forensic investigations. Moreover, the data could potentially enhance genetic identification and anthropological genetics research in Thailand.
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Affiliation(s)
- Jirat Vanichanukulyakit
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Supakit Khacha-ananda
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
- Research Center in Bioresources for Agriculture, Industry and Medicine, Chiang Mai University, 239, Huay Kaew Road, Muang, Chiang Mai 50200, Thailand
| | - Tawachai Monum
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | - Phatcharin Mahawong
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; (J.V.); (T.M.); (P.M.)
| | | | - Watsana Penkhrue
- School of Preclinic, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand;
| | - Taddaow Khumpook
- Faculty of Science at Sriracha, Kasetsart University, Sriracha Campus, Chonburi 20230, Thailand;
| | - Sorawat Thongsahuan
- Faculty of Veterinary Science, Prince of Songkla University, Songkhla 90110, Thailand;
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18
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Inoue Y, Igarashi T, Hasebe Y, Kawagishi-Hotta M, Okuno R, Yamada T, Hasegawa S. Identification of mitochondrial genetic variants associated with human corneocyte size in Japanese women. Exp Dermatol 2022; 31:1944-1948. [PMID: 36067013 DOI: 10.1111/exd.14673] [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: 04/07/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 12/14/2022]
Abstract
Mitochondria have their own DNA (mtDNA). Genetic variants are likely to accumulate in mtDNA, and its base substitution rate is known to be very fast, 10-20 times faster than that of nuclear DNA. For this reason, mtSNPs (mitochondrial genome single nucleotide polymorphisms) are frequently detected in mtDNA. Several thousands of copies of mtDNA are considered to be present in a cell, and variants that have occurred in mtDNA are expected to markedly affect the intracellular energy production system and ROS (reactive oxygen species) kinetics. Therefore, recently, mtSNPs have come to be considered very important as a determinant of the individual constitution such as the life-span and disease susceptibility. In this study, we searched for mtSNPs that affect the individual corneocyte size using samples from 358 Japanese women. As a result, mtSNPs 10609C and 12406A were found to be significantly related to the corneocyte size in the outermost layer of the epidermis. There have been a large number of reports concerning the association between mtSNPs and individual constitution, but little evaluation of their relationships with epidermal properties has been made. The results of the present study first suggested that mtSNPs may affect the epidermal properties in Japanese women.
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Affiliation(s)
- Yu Inoue
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshio Igarashi
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan
| | - Yuichi Hasebe
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Mika Kawagishi-Hotta
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Ryosuke Okuno
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Yamada
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan
| | - Seiji Hasegawa
- Research Laboratories, Nippon Menard Cosmetic Co., Ltd, Nagoya, Japan.,Nagoya University-MENARD Collaborative Research Chair, Nagoya University Graduate School of Medicine, Nagoya, Japan
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19
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Dahal S, Siddiqua H, Sharma S, Babu RK, Rathore D, Sharma S, Raghavan SC. Unleashing a novel function of Endonuclease G in mitochondrial genome instability. eLife 2022; 11:e69916. [PMID: 36394256 PMCID: PMC9711528 DOI: 10.7554/elife.69916] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Having its genome makes the mitochondrion a unique and semiautonomous organelle within cells. Mammalian mitochondrial DNA (mtDNA) is a double-stranded closed circular molecule of about 16 kb coding for 37 genes. Mutations, including deletions in the mitochondrial genome, can culminate in different human diseases. Mapping the deletion junctions suggests that the breakpoints are generally seen at hotspots. '9 bp deletion' (8271-8281), seen in the intergenic region of cytochrome c oxidase II/tRNALys, is the most common mitochondrial deletion. While it is associated with several diseases like myopathy, dystonia, and hepatocellular carcinoma, it has also been used as an evolutionary marker. However, the mechanism responsible for its fragility is unclear. In the current study, we show that Endonuclease G, a mitochondrial nuclease responsible for nonspecific cleavage of nuclear DNA during apoptosis, can induce breaks at sequences associated with '9 bp deletion' when it is present on a plasmid or in the mitochondrial genome. Through a series of in vitro and intracellular studies, we show that Endonuclease G binds to G-quadruplex structures formed at the hotspot and induces DNA breaks. Therefore, we uncover a new role for Endonuclease G in generating mtDNA deletions, which depends on the formation of G4 DNA within the mitochondrial genome. In summary, we identify a novel property of Endonuclease G, besides its role in apoptosis and the recently described 'elimination of paternal mitochondria during fertilisation.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Humaira Siddiqua
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Ravi K Babu
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Diksha Rathore
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
| | - Sheetal Sharma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science BangaloreBangaloreIndia
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20
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Zelada‐Mázmela E, Reyes‐Flores LE, Sánchez‐Velásquez JJ, Ingar C, Santos‐Rojas LE. Population structure and demographic history of the gastropod Thaisella chocolata (Duclos, 1832) from the Southeast Pacific inferred from mitochondrial DNA analyses. Ecol Evol 2022; 12:e9276. [PMID: 36177117 PMCID: PMC9463045 DOI: 10.1002/ece3.9276] [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: 04/17/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/25/2022] Open
Abstract
The present-day population structure of a species reflects the combination of oceanographic currents, life-history traits, and historical events. However, little is known about the mechanisms that have shaped the gene lineage distribution of marine species inhabiting the Southeast Pacific. Here, we provide a comprehensive phylogeographical study of a species distributed along the Southeast Pacific coastal region by analyzing the endemic gastropod Thaisella chocolata (Duclos, 1832). Sequencing of mitochondrial cytochrome c oxidase subunit 1 (CO1) and 16S rRNA revealed strikingly high haplotypic nucleotide and genetic diversity but a lack of significant population differentiation within the survey area. In addition, a star-shaped phylogeny and significantly negative Tajima's D and Fu's Fs tests of neutrality suggested historical occurrence of rapid demographic expansion. Mismatch distributions and Bayesian inference analyses also confirmed T. chocolata to have undergone two ancestral demographic expansions. Calculations suggested that these expansions began in the lower and middle Pleistocene epoch, likely due to continental shelf development and climatic conditions. These findings could help establish a genetic baseline for T. chocolata as the first step toward sustainable spatial management of this species, as well as understand this species' response to future climate change.
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Affiliation(s)
- Eliana Zelada‐Mázmela
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of SciencesUniversidad Nacional del SantaNuevo ChimbotePeru
| | - Lorenzo E. Reyes‐Flores
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of SciencesUniversidad Nacional del SantaNuevo ChimbotePeru
| | - Julissa J. Sánchez‐Velásquez
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of SciencesUniversidad Nacional del SantaNuevo ChimbotePeru
| | - Claudia Ingar
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of SciencesUniversidad Nacional del SantaNuevo ChimbotePeru
| | - Luis E. Santos‐Rojas
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of SciencesUniversidad Nacional del SantaNuevo ChimbotePeru
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21
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Roy A, Kandettu A, Ray S, Chakrabarty S. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148554. [PMID: 35341749 DOI: 10.1016/j.bbabio.2022.148554] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
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Affiliation(s)
- Abhipsa Roy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Swagat Ray
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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22
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Arbeithuber B, Cremona MA, Hester J, Barrett A, Higgins B, Anthony K, Chiaromonte F, Diaz FJ, Makova KD. Advanced age increases frequencies of de novo mitochondrial mutations in macaque oocytes and somatic tissues. Proc Natl Acad Sci U S A 2022; 119:e2118740119. [PMID: 35394879 PMCID: PMC9169796 DOI: 10.1073/pnas.2118740119] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/25/2022] [Indexed: 12/18/2022] Open
Abstract
Mutations in mitochondrial DNA (mtDNA) contribute to multiple diseases. However, how new mtDNA mutations arise and accumulate with age remains understudied because of the high error rates of current sequencing technologies. Duplex sequencing reduces error rates by several orders of magnitude via independently tagging and analyzing each of the two template DNA strands. Here, using duplex sequencing, we obtained high-quality mtDNA sequences for somatic tissues (liver and skeletal muscle) and single oocytes of 30 unrelated rhesus macaques, from 1 to 23 y of age. Sequencing single oocytes minimized effects of natural selection on germline mutations. In total, we identified 17,637 tissue-specific de novo mutations. Their frequency increased ∼3.5-fold in liver and ∼2.8-fold in muscle over the ∼20 y assessed. Mutation frequency in oocytes increased ∼2.5-fold until the age of 9 y, but did not increase after that, suggesting that oocytes of older animals maintain the quality of their mtDNA. We found the light-strand origin of replication (OriL) to be a hotspot for mutation accumulation with aging in liver. Indeed, the 33-nucleotide-long OriL harbored 12 variant hotspots, 10 of which likely disrupt its hairpin structure and affect replication efficiency. Moreover, in somatic tissues, protein-coding variants were subject to positive selection (potentially mitigating toxic effects of mitochondrial activity), the strength of which increased with the number of macaques harboring variants. Our work illuminates the origins and accumulation of somatic and germline mtDNA mutations with aging in primates and has implications for delayed reproduction in modern human societies.
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Affiliation(s)
- Barbara Arbeithuber
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Experimental Gynaecology, Obstetrics and Gynaecological Endocrinology, Kepler University Hospital Linz, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Marzia A. Cremona
- Department of Operations and Decision Systems, Université Laval, Québec, QC G1V0A6, Canada
- Population Health and Optimal Health Practices, CHU de Québec - Université Laval Research Center, Québec, QC G1V4G2, Canada
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
| | - James Hester
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Alison Barrett
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Bonnie Higgins
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Kate Anthony
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
| | - Francesca Chiaromonte
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
- Department of Statistics, The Pennsylvania State University, University Park, PA 16802
- Institute of Economics and EMbeDS, Sant'Anna School of Advanced Studies, Pisa 56127, Italy
| | - Francisco J. Diaz
- Department of Animal Science, The Pennsylvania State University, University Park, PA 16802
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA 16802
- Center for Medical Genomics, The Pennsylvania State University, University Park, PA 16802
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23
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Feng W, Arrey G, Zole E, lv W, Liang X, Han P, Mohiyuddin M, Pilegaard H, Regenberg B. Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9. Comput Struct Biotechnol J 2022; 20:3059-3067. [PMID: 35782732 PMCID: PMC9233219 DOI: 10.1016/j.csbj.2022.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/12/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is common in eukaryotic cells. Amplification of oncogenes on large eccDNA (ecDNA) can drive biological processes such as tumorigenesis, and identification of eccDNA by sequencing after removal of chromosomal DNA is therefore important for understanding their impact on the expressed phenotype. However, the circular mitochondrial DNA (mtDNA) might challenge the detection of eccDNA because the average somatic cell has hundreds of copies of mtDNA. Here we show that 61.2–99.5% of reads from eccDNA-enriched samples correspond to mtDNA in mouse tissues. We have developed a method to selectively remove mtDNA from total circular DNA by CRISPR/Cas9 guided cleavage of mtDNA with one single-guide RNA (sgRNA) or two sgRNAs followed by exonuclease degradation of the linearized mtDNA. Sequencing revealed that mtDNA reads were 85.9% ± 12.6% removed from eccDNA of 9 investigated mouse tissues. CRISPR/Cas9 cleavage also efficiently removed mtDNA from a human HeLa cell line and colorectal cancer samples. We identified up to 14 times more, and also larger eccDNA in CRISPR/Cas9 treated colorectal cancer samples than in untreated samples. We foresee that the method can be applied to effectively remove mtDNA from any eukaryotic species to obtain higher eccDNA yields.
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24
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Lankheet I, Vicente M, Barbieri C, Schlebusch C. The performance of common SNP arrays in assigning African mitochondrial haplogroups. BMC Genom Data 2021; 22:43. [PMID: 34674637 PMCID: PMC8532338 DOI: 10.1186/s12863-021-01000-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 10/12/2021] [Indexed: 11/20/2022] Open
Abstract
Background Mitochondrial haplogroup assignment is an important tool for forensics and evolutionary genetics. African populations are known to display a high diversity of mitochondrial haplogroups. In this research we explored mitochondrial haplogroup assignment in African populations using commonly used genome-wide SNP arrays. Results We show that, from eight commonly used SNP arrays, two SNP arrays outperform the other arrays when it comes to the correct assignment of African mitochondrial haplogroups. One array enables the recognition of 81% of the African mitochondrial haplogroups from our compiled dataset of full mitochondrial sequences. Other SNP arrays were able to assign 4–62% of the African mitochondrial haplogroups present in our dataset. We also assessed the performance of available software for assigning mitochondrial haplogroups from SNP array data. Conclusions These results provide the first cross-checked quantification of mitochondrial haplogroup assignment performance from SNP array data. Mitochondrial haplogroup frequencies inferred from most common SNP arrays used for human population analysis should be considered with caution. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01000-2.
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Affiliation(s)
- Imke Lankheet
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Mário Vicente
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.,Centre for Palaeogenetics, Svante Arrhenius vägen 20C, SE-106 91, Stockholm, Sweden
| | - Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.,Department of Linguistic and Cultural Evolution (DLCE), Max-Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany
| | - Carina Schlebusch
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden. .,Palaeo-Research Institute, University of Johannesburg, P.O. Box 524, Auckland Park, 2006, South Africa. .,SciLifeLab, Uppsala, Sweden.
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25
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Allam M, Mahrous NS. Molecular genetic diversity of some rabbit breeds based on mitochondrial 16S rRNA sequences. WORLD RABBIT SCIENCE 2021. [DOI: 10.4995/wrs.2021.15110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
<p>The present study was performed to assess the genetic variations among six rabbit breeds in Egypt based on mitochondrial 16S rRNA sequences. The length of partial mitochondrial 16S rRNA in the six rabbit breeds ranged from 546 bp to 558 bp. The sequenced regions were submitted to GenBank/NCBI under accession numbers (MW052052 - MW052057). The average content of A+T was 57% in all breeds. Among breeds, the percentages of genetic distance values were ranged from 0.000 to 0.004. The highest P-distance (0.004) was found between the New Zealand White breed and all other breeds. The results support the suitability of mitochondrial 16S rRNA for genetic diversity analysis of rabbit breeds and the applicability for future research on genetic relationships and the phylogeny of rabbit breeds.</p>
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26
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Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, Haak W. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci Rep 2021; 11:15005. [PMID: 34294811 PMCID: PMC8298398 DOI: 10.1038/s41598-021-94491-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
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Affiliation(s)
- Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey
| | - Kamen Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | | | - Miroslav Dobeš
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey
| | - Michal Ernée
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | | | | | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Emmanuel Ghesquière
- Inrap Grand Ouest, Bourguébus, France.,Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław, Poland.,Archeolodzy.org Foundation, Wrocław, Poland
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archeology, Weimar, Germany
| | - Marcello Mannino
- Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Stéphane Rottier
- Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Ludwig Maximilian University Munich, 80799, Munich, Germany
| | | | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
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27
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Dahal S, Siddiqua H, Katapadi VK, Iyer D, Raghavan SC. Characterization of G4 DNA formation in mitochondrial DNA and their potential role in mitochondrial genome instability. FEBS J 2021; 289:163-182. [PMID: 34228888 DOI: 10.1111/febs.16113] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 07/06/2021] [Indexed: 12/16/2022]
Abstract
Mitochondria possess their own genome which can be replicated independently of nuclear DNA. Mitochondria being the powerhouse of the cell produce reactive oxygen species, due to which the mitochondrial genome is frequently exposed to oxidative damage. Previous studies have demonstrated an association of mitochondrial deletions to aging and human disorders. Many of these deletions were present adjacent to non-B DNA structures. Thus, we investigate noncanonical structures associated with instability in mitochondrial genome. In silico studies revealed the presence of > 100 G-quadruplex motifs (of which 5 have the potential to form 3-plate G4 DNA), 23 inverted repeats, and 3 mirror repeats in the mitochondrial DNA (mtDNA). Further analysis revealed that among the deletion breakpoints from patients with mitochondrial disorders, majority are located at G4 DNA motifs. Interestingly, ~ 50% of the deletions were at base-pair positions 8271-8281, ~ 35% were due to deletion at 12362-12384, and ~ 12% due to deletion at 15516-15545. Formation of 3-plate G-quadruplex DNA structures at mitochondrial fragile regions was characterized using electromobility shift assay, circular dichroism (CD), and Taq polymerase stop assay. All 5 regions could fold into both intramolecular and intermolecular G-quadruplex structures in a KCl-dependent manner. G4 DNA formation was in parallel orientation, which was abolished in the presence of LiCl. The formation of G4 DNA affected both replication and transcription. Finally, immunolocalization of BG4 with MitoTracker confirmed the formation of G-quadruplex in mitochondrial genome. Thus, we characterize the formation of 5 different G-quadruplex structures in human mitochondrial region, which may contribute toward formation of mitochondrial deletions.
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Affiliation(s)
- Sumedha Dahal
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Humaira Siddiqua
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vijeth K Katapadi
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Divyaanka Iyer
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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28
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Ogoh K, Futahashi R, Ohmiya Y. Intraspecific nucleotide polymorphisms in seven complete sequences of mitochondrial DNA of the luminous ostracod, Vargula hilgendorfii (Crustacea, Ostracoda). GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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29
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Wibowo MC, Yang Z, Borry M, Hübner A, Huang KD, Tierney BT, Zimmerman S, Barajas-Olmos F, Contreras-Cubas C, García-Ortiz H, Martínez-Hernández A, Luber JM, Kirstahler P, Blohm T, Smiley FE, Arnold R, Ballal SA, Pamp SJ, Russ J, Maixner F, Rota-Stabelli O, Segata N, Reinhard K, Orozco L, Warinner C, Snow M, LeBlanc S, Kostic AD. Reconstruction of ancient microbial genomes from the human gut. Nature 2021; 594:234-239. [PMID: 33981035 PMCID: PMC8189908 DOI: 10.1038/s41586-021-03532-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 04/12/2021] [Indexed: 12/26/2022]
Abstract
Loss of gut microbial diversity1–6 in industrial populations is associated with chronic diseases7, underscoring the importance of studying our ancestral gut microbiome. However, relatively little is known about the composition of pre-industrial gut microbiomes. Here we performed a large-scale de novo assembly of microbial genomes from palaeofaeces. From eight authenticated human palaeofaeces samples (1,000–2,000 years old) with well-preserved DNA from southwestern USA and Mexico, we reconstructed 498 medium- and high-quality microbial genomes. Among the 181 genomes with the strongest evidence of being ancient and of human gut origin, 39% represent previously undescribed species-level genome bins. Tip dating suggests an approximate diversification timeline for the key human symbiont Methanobrevibacter smithii. In comparison to 789 present-day human gut microbiome samples from eight countries, the palaeofaeces samples are more similar to non-industrialized than industrialized human gut microbiomes. Functional profiling of the palaeofaeces samples reveals a markedly lower abundance of antibiotic-resistance and mucin-degrading genes, as well as enrichment of mobile genetic elements relative to industrial gut microbiomes. This study facilitates the discovery and characterization of previously undescribed gut microorganisms from ancient microbiomes and the investigation of the evolutionary history of the human gut microbiota through genome reconstruction from palaeofaeces. Ancient microbiomes from palaeofaeces are more similar to non-industrialized than industrialized human gut microbiomes regardless of geography, but 39% of their de novo reconstructed genomes represent previously undescribed microbial species.
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Affiliation(s)
- Marsha C Wibowo
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Zhen Yang
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Combinatorics and Optimization, University of Waterloo, Waterloo, Ontario, Canada
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Hübner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kun D Huang
- CIBIO Department, University of Trento, Trento, Italy.,Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy
| | - Braden T Tierney
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Samuel Zimmerman
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Francisco Barajas-Olmos
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Cecilia Contreras-Cubas
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Humberto García-Ortiz
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Jacob M Luber
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA.,Department of Microbiology, Harvard Medical School, Boston, MA, USA.,Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Philipp Kirstahler
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tre Blohm
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Francis E Smiley
- Department of Anthropology, Northern Arizona University, Flagstaff, AZ, USA
| | - Richard Arnold
- Pahrump Paiute Tribe and Consolidated Group of Tribes and Organizations, Pahrump, NV, USA
| | - Sonia A Ballal
- Department of Gastroenterology, Hepatology and Nutrition, Boston Children's Hospital, Boston, MA, USA
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Julia Russ
- Morrison Microscopy Core Research Facility, Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Omar Rota-Stabelli
- Research and Innovation Centre, Fondazione Edmund Mach, San Michele all'Adige, Italy.,Center Agriculture Food Environment (C3A), University of Trento, Trento, Italy
| | - Nicola Segata
- CIBIO Department, University of Trento, Trento, Italy
| | - Karl Reinhard
- School of Natural Resources, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Lorena Orozco
- Immunogenomics and Metabolic Diseases Laboratory, Secretaría de Salud, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Department of Anthropology, Harvard University, Cambridge, MA, USA.,Faculty of Biological Sciences, Friedrich-Schiller University, Jena, Germany
| | - Meradeth Snow
- Department of Anthropology, University of Montana, Missoula, MT, USA
| | - Steven LeBlanc
- Peabody Museum of Archaeology and Ethnology, Harvard University, Cambridge, MA, USA
| | - Aleksandar D Kostic
- Section on Pathophysiology and Molecular Pharmacology, Joslin Diabetes Center, Boston, MA, USA. .,Department of Microbiology, Harvard Medical School, Boston, MA, USA.
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30
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Schwartz JH. Evolution, systematics, and the unnatural history of mitochondrial DNA. Mitochondrial DNA A DNA Mapp Seq Anal 2021; 32:126-151. [PMID: 33818247 DOI: 10.1080/24701394.2021.1899165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The tenets underlying the use of mtDNA in phylogenetic and systematic analyses are strict maternal inheritance, clonality, homoplasmy, and difference due to mutation: that is, there are species-specific mtDNA sequences and phylogenetic reconstruction is a matter of comparing these sequences and inferring closeness of relatedness from the degree of sequence similarity. Yet, how mtDNA behavior became so defined is mysterious. Even though early studies of fertilization demonstrated for most animals that not only the head, but the sperm's tail and mitochondria-bearing midpiece penetrate the egg, the opposite - only the head enters the egg - became fact, and mtDNA conceived as maternally transmitted. When midpiece/tail penetration was realized as true, the conceptions 'strict maternal inheritance', etc., and their application to evolutionary endeavors, did not change. Yet there is mounting evidence of paternal mtDNA transmission, paternal and maternal combination, intracellular recombination, and intra- and intercellular heteroplasmy. Clearly, these phenomena impact the systematic and phylogenetic analysis of mtDNA sequences.
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Affiliation(s)
- Jeffrey H Schwartz
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
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Mitochondrial genome stability in human: understanding the role of DNA repair pathways. Biochem J 2021; 478:1179-1197. [DOI: 10.1042/bcj20200920] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 11/17/2022]
Abstract
Mitochondria are semiautonomous organelles in eukaryotic cells and possess their own genome that replicates independently. Mitochondria play a major role in oxidative phosphorylation due to which its genome is frequently exposed to oxidative stress. Factors including ionizing radiation, radiomimetic drugs and replication fork stalling can also result in different types of mutations in mitochondrial DNA (mtDNA) leading to genome fragility. Mitochondria from myopathies, dystonia, cancer patient samples show frequent mtDNA mutations such as point mutations, insertions and large-scale deletions that could account for mitochondria-associated disease pathogenesis. The mechanism by which such mutations arise following exposure to various DNA-damaging agents is not well understood. One of the well-studied repair pathways in mitochondria is base excision repair. Other repair pathways such as mismatch repair, homologous recombination and microhomology-mediated end joining have also been reported. Interestingly, nucleotide excision repair and classical nonhomologous DNA end joining are not detected in mitochondria. In this review, we summarize the potential causes of mitochondrial genome fragility, their implications as well as various DNA repair pathways that operate in mitochondria.
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Cerliani MB, Mayordomo AC, Sanchez Dova A, Soarez JN, Fuhr Etcheverry J, Piñero TA, Cajal AR, Jauk F, García-Rivello H, Vaccaro CA, Richard SM, Bravi CM, Pavicic WH. Maternal ancestry and hematological cancer risk: case-control study in an Argentinean population. Per Med 2021; 18:269-281. [PMID: 33728969 DOI: 10.2217/pme-2020-0062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: We investigated the role of maternal ancestry in neoplastic hematological malignancies (HMs) risk in a population from Central Argentina. Materials & methods: We analyzed 125 cases with HMs and 310 controls from a public hospital, and a set of 202 colorectal, breast, lung, and hematologic cancer patients from a private hospital. Results: A decreased risk for HMs was associated with the Native American haplogroup B2 (odds ratio = 0.49; 95% CI: 0.25-0.92; p = 0.02). The sub-Saharan African parahaplogroup L was associated with higher susceptibility for disease (odds ratio = 3.10; 95% CI: 1.04-9.31; p = 0.043). Although the mean ancestral proportions in the total studied population was as published (61.7% Native American, 34.6% European and 3.7% African), an unequal distribution was observed between hospitals. Conclusion: We confirmed the tri-hybrid nature of the Argentinean population, with proportions varying within the country. Our finding supports the notion that associated haplogroup is population and cancer specific.
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Affiliation(s)
- María Belén Cerliani
- Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA-CONICET-UNLP, La Plata, BsAs, Argentina.,Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina
| | - Andrea Constanza Mayordomo
- Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA-CONICET-UNLP, La Plata, BsAs, Argentina.,Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina
| | - Anaclara Sanchez Dova
- Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA-CONICET-UNLP, La Plata, BsAs, Argentina
| | - Julieta Natalia Soarez
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Josefina Fuhr Etcheverry
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Tamara Alejandra Piñero
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Andrea Romina Cajal
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Federico Jauk
- Servicio de Anatomía Patológica, Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Hernán García-Rivello
- Servicio de Anatomía Patológica, Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Carlos Alberto Vaccaro
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
| | - Silvina Mariel Richard
- Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA-CONICET-UNLP, La Plata, BsAs, Argentina
| | - Claudio Marcelo Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CICPBA-CONICET-UNLP, La Plata, BsAs, Argentina
| | - Walter Hernán Pavicic
- Programa de Cáncer Hereditario (Pro.Can.He.), Hospital Italiano de Buenos Aires, CABA, BsAs, Argentina.,Instituto de Medicina Traslacional e Ingeniería Biomédica (IMTIB), IUHI-HIBA-CONICET, CABA, BsAs, Argentina
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Yang FC, Tseng B, Lin CY, Yu YJ, Linacre A, Lee JCI. Population inference based on mitochondrial DNA control region data by the nearest neighbors algorithm. Int J Legal Med 2021; 135:1191-1199. [PMID: 33586030 DOI: 10.1007/s00414-021-02520-3] [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] [Received: 11/30/2020] [Accepted: 01/27/2021] [Indexed: 11/24/2022]
Abstract
Population and geographic assignment are frequently undertaken using DNA sequences on the mitochondrial genome. Assignment to broad continental populations is common, although finer resolution to subpopulations can be less accurate due to shared genetic ancestry at a local level and members of different ancestral subpopulations cohabiting the same geographic area. This study reports on the accuracy of population and subpopulation assignment by using the sequence data obtained from the 3070 mitochondrial genomes and applying the K-nearest neighbors (KNN) algorithm. These data also included training samples used for continental and population assignment comprised of 1105 Europeans (including Austria, France, Germany, Spain, and England and Caucasian countries), 374 Africans (including North and East Africa and non-specific area (Pan-Africa)), and 1591 Asians (including Japan, Philippines, and Taiwan). Subpopulations included in this study were 1153 mitochondrial DNA (mtDNA) control region sequences from 12 subpopulations in Taiwan (including Han, Hakka, Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiyat, Tsou, Tao, and Pingpu). Additionally, control region sequence data from a further 50 samples, obtained from the Sigma Company, were included after they were amplified and sequenced. These additional 50 samples acted as the "testing samples" to verify the accuracy of the population. In this study, based on genetic distances as genetic metric, we used the KNN algorithm and the K-weighted-nearest neighbors (KWNN) algorithm weighted by genetic distance to classify individuals into continental populations, and subpopulations within the same continent. Accuracy results of ethnic inferences at the level of continental populations and of subpopulations among KNN and KWNN algorithms were obtained. The training sample set achieved an overall accuracy of 99 to 82% for assignment to their continental populations with K values from 1 to 101. Population assignment for subpopulations with K assignments from 1 to 5 reached an accuracy of 77 to 54%. Four out of 12 Taiwanese populations returned an accuracy of assignment of over 60%, Ami (66%), Atayal (67%), Saisiyat (66%), and Tao (80%). For the testing sample set, results of ethnic prediction for continental populations with recommended K values as 5, 10, and 35, based on results of the training sample set, achieved overall an accuracy of 100 to 94%. This study provided an accurate method in population assignment for not only continental populations but also subpopulations, which can be useful in forensic and anthropological studies.
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Affiliation(s)
- Fu-Chi Yang
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Bill Tseng
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Chun-Yen Lin
- Institute of Forensic Medicine, Ministry of Justice, New Taipei City, 23016, Taiwan
| | - Yu-Jen Yu
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan
| | - Adrian Linacre
- College of Science & Engineering, Flinders University, Adelaide, 5001, Australia
| | - James Chun-I Lee
- Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan.
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34
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Rehman GU. Mitochondrial DNA analysis of Chitrali population of Pakistan from ancient human bones. Meta Gene 2021. [DOI: 10.1016/j.mgene.2020.100821] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Cost-effective straightforward method for captured whole mitogenome sequencing of ancient DNA. Forensic Sci Int 2020; 319:110638. [PMID: 33340848 DOI: 10.1016/j.forsciint.2020.110638] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 10/28/2020] [Accepted: 11/29/2020] [Indexed: 11/21/2022]
Abstract
Working with mitochondrial DNA from highly degraded samples is challenging. We present a whole mitogenome Illumina-based sequencing method suitable for highly degraded samples. The method makes use of double-stranded library preparation with hybridization-based target enrichment. The aim of the study was to implement a new user-friendly method for analysing many ancient DNA samples at low cost. The method combines the Swift 2S™ Turbo library preparation kit and xGen® panel for mitogenome enrichment. Swift allows to use low input of aDNA and own adapters and primers, handles inhibitors well, and has only two purification steps. xGen is straightforward to use and is able to leverage already pooled libraries. Given the ancient DNA is more challenging to work with, the protocol was developed with several improvements, especially multiplying DNA input in case of low concentration DNA extractions followed by AMPure® beads size selection and real-time pre-capture PCR monitoring in order to avoid cycle-optimization step. Nine out of eleven analysed samples successfully retrieved mitogenomes. Hence, our method provides an effective analysis of whole mtDNA, and has proven to be fast, cost-effective, straightforward, with utilisation in population-wide research of burial sites.
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Abstract
The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.
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Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14221, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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37
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Fu YT, Dong Y, Wang W, Nie Y, Liu GH, Shao R. Fragmented mitochondrial genomes evolved in opposite directions between closely related macaque louse Pedicinus obtusus and colobus louse Pedicinus badii. Genomics 2020; 112:4924-4933. [PMID: 32898640 DOI: 10.1016/j.ygeno.2020.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/08/2020] [Accepted: 09/03/2020] [Indexed: 02/06/2023]
Abstract
We report for the first time the fragmented mitochondrial (mt) genomes of two Pedicinus species: Pedicinus obtusus and Pedicinus badii, and compared them with the lice of humans and chimpanzees. Despite being congeneric, the two monkey lice are distinct from each other in mt karyotype. The variation in mt karyotype between the two Pedicinus lice is the most pronounced among the congeneric species of sucking lice observed to date and is attributable to the opposite directions between them in mt karyotype evolution. Two of the inferred ancestral mt minichromosomes of the higher primate lice merged as one in the macaque louse whereas one of the ancestral minichromosomes split into two in the colobus louse after these two species diverged from their most recent common ancestor. Our results showed that mt genome fragmentation was a two-way process in the higher primate lice, and minichromosome merger was more common than previously thought.
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Affiliation(s)
- Yi-Tian Fu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, PR China
| | - Yalun Dong
- GeneCology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Wei Wang
- GeneCology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia
| | - Yu Nie
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, PR China
| | - Guo-Hua Liu
- Hunan Provincial Key Laboratory of Protein Engineering in Animal Vaccines, College of Veterinary Medicine, Hunan Agricultural University, Changsha 410128, PR China.
| | - Renfu Shao
- GeneCology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland 4556, Australia.
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38
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Attimonelli M, Preste R, Vitale O, Lott MT, Procaccio V, Shiping Z, Wallace DC. Bioinformatics resources, databases, and tools for human mtDNA. THE HUMAN MITOCHONDRIAL GENOME 2020:277-304. [DOI: 10.1016/b978-0-12-819656-4.00012-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2025]
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Bücking R, Cox MP, Hudjashov G, Saag L, Sudoyo H, Stoneking M. Archaic mitochondrial DNA inserts in modern day nuclear genomes. BMC Genomics 2019; 20:1017. [PMID: 31878873 PMCID: PMC6933719 DOI: 10.1186/s12864-019-6392-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 12/12/2019] [Indexed: 12/15/2022] Open
Abstract
Background Traces of interbreeding of Neanderthals and Denisovans with modern humans in the form of archaic DNA have been detected in the genomes of present-day human populations outside sub-Saharan Africa. Up to now, only nuclear archaic DNA has been detected in modern humans; we therefore attempted to identify archaic mitochondrial DNA (mtDNA) residing in modern human nuclear genomes as nuclear inserts of mitochondrial DNA (NUMTs). Results We analysed 221 high-coverage genomes from Oceania and Indonesia using an approach which identifies reads that map both to the nuclear and mitochondrial DNA. We then classified reads according to the source of the mtDNA, and found one NUMT of Denisovan mtDNA origin, present in 15 analysed genomes; analysis of the flanking region suggests that this insertion is more likely to have happened in a Denisovan individual and introgressed into modern humans with the Denisovan nuclear DNA, rather than in a descendant of a Denisovan female and a modern human male. Conclusions Here we present our pipeline for detecting introgressed NUMTs in next generation sequencing data that can be used on genomes sequenced in the future. Further discovery of such archaic NUMTs in modern humans can be used to detect interbreeding between archaic and modern humans and can reveal new insights into the nature of such interbreeding events.
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Affiliation(s)
- Robert Bücking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany.
| | - Murray P Cox
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Georgi Hudjashov
- School of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Lauri Saag
- Institute of Genomics, University of Tartu, Tartu, 51010, Estonia
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, 10430, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, 10430, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany
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McHugo GP, Dover MJ, MacHugh DE. Unlocking the origins and biology of domestic animals using ancient DNA and paleogenomics. BMC Biol 2019; 17:98. [PMID: 31791340 PMCID: PMC6889691 DOI: 10.1186/s12915-019-0724-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 11/13/2019] [Indexed: 12/13/2022] Open
Abstract
Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed new light on the genetic origins of domesticates, and on the process of domestication itself. High-resolution paleogenomic data sets now provide unprecedented opportunities to explore the development of animal agriculture across the world. In addition, functional population genomics studies of domestic and wild animals can deliver comparative information useful for understanding recent human evolution.
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Affiliation(s)
- Gillian P McHugo
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michael J Dover
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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Bottleneck and selection in the germline and maternal age influence transmission of mitochondrial DNA in human pedigrees. Proc Natl Acad Sci U S A 2019; 116:25172-25178. [PMID: 31757848 PMCID: PMC6911200 DOI: 10.1073/pnas.1906331116] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Heteroplasmy-the presence of multiple mitochondrial DNA (mtDNA) haplotypes in an individual-can lead to numerous mitochondrial diseases. The presentation of such diseases depends on the frequency of the heteroplasmic variant in tissues, which, in turn, depends on the dynamics of mtDNA transmissions during germline and somatic development. Thus, understanding and predicting these dynamics between generations and within individuals is medically relevant. Here, we study patterns of heteroplasmy in 2 tissues from each of 345 humans in 96 multigenerational families, each with, at least, 2 siblings (a total of 249 mother-child transmissions). This experimental design has allowed us to estimate the timing of mtDNA mutations, drift, and selection with unprecedented precision. Our results are remarkably concordant between 2 complementary population-genetic approaches. We find evidence for a severe germline bottleneck (7-10 mtDNA segregating units) that occurs independently in different oocyte lineages from the same mother, while somatic bottlenecks are less severe. We demonstrate that divergence between mother and offspring increases with the mother's age at childbirth, likely due to continued drift of heteroplasmy frequencies in oocytes under meiotic arrest. We show that this period is also accompanied by mutation accumulation leading to more de novo mutations in children born to older mothers. We show that heteroplasmic variants at intermediate frequencies can segregate for many generations in the human population, despite the strong germline bottleneck. We show that selection acts during germline development to keep the frequency of putatively deleterious variants from rising. Our findings have important applications for clinical genetics and genetic counseling.
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Boyko AN, Kozin MS, Osmak GZ, Kulakova OG, Favorova OO. Mitochondrial genome and risk of multiple sclerosis. ACTA ACUST UNITED AC 2019. [DOI: 10.14412/2074-2711-2019-3-43-46] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Mitochondrial DNA (mtDNA) polymorphism makes a certain contribution to the formation of a genetic risk of multiple sclerosis (MS).Objective: to analyze the frequency of mtDNA variants in patients with MS and control individuals in the Russian population. A similar study was conducted for the first time.Patients and methods. The polymorphism of mtDNA was studied in the Russian population: in 283 unrelated patients with relapsing-remitting MS and in 290 unrelated healthy controls matched for gender and age.Results and discussion. The frequency of haplogroup J in the patients with MS was twice higher than that in the control group (p=0.0055) (odds ratio (OR) 2.00; 95% confidence interval (CI). 1.21–3.41). This association was mostly observed in women (p=0.0083) (OR 2.20; 95% CI, 1.19–4.03). There was also a significant association of the A allele of MT-ND5 (m. 13708G>A) with MS (p=0.03) (OR 1.89; 95% CI 1.11–3.32). Sex stratification showed that the association with MS was significant only in women (p=0.009; OR, 2.52; 95% CI, 1.29–5.14). Further investigations will aim to analyze mtDNA variability (at the level of individual polymorphisms, haplogroups, and whole genome) in patients with relapsing-remitting MS and in those with primary progressive MS versus healthy individuals and patients with relapsing-remitting MS according to disease severity.Conclusion. The data obtained in the Russian population suggest that mtDNA variations are involved in MS risk, to a greater extent in women.
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Affiliation(s)
- A. N. Boyko
- N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia;
Federal Center of Cerebrovascular Disease and Stroke, Ministry of Health of Russia
| | - M. S. Kozin
- N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia;
Federal Center of Cerebrovascular Disease and Stroke, Ministry of Health of Russia
| | - G. Zh. Osmak
- N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia;
Federal Center of Cerebrovascular Disease and Stroke, Ministry of Health of Russia
| | - O. G. Kulakova
- N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia
| | - O. O. Favorova
- N.I. Pirogov Russian National Research Medical University, Ministry of Health of Russia
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Sanabria DJ, Mojsiejczuk LN, Torres C, Meyer AG, Mbayed VA, Liotta DJ, Campos RH, Schurr TG, Badano I. Genetic diversity of the JC polyomavirus (JCPyV) and mitochondrial DNA ancestry in Misiones, Argentina. INFECTION GENETICS AND EVOLUTION 2019; 75:104011. [PMID: 31446138 DOI: 10.1016/j.meegid.2019.104011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 11/16/2022]
Abstract
BACKGROUND The use of human and viral genetic markers offers a novel way to study human migration in multiethnic populations of Latin America. OBJECTIVES Our goal was to characterize the genetic diversity and geographical origins of JC Polyomavirus (JCPyV) and the genetic ancestry of mitochondrial DNA (mtDNA) in inhabitants from 25 de Mayo, Misiones-Argentina, a small village of largely German ancestry located close to the border with Brazil. We also evaluated the extent of agreement between viral and mtDNA markers for the different ancestry components of this population. STUDY DESIGN 68 individuals were analyzed for JCPyV and mtDNA diversity. JCPyV detection and typing was conducted in urine samples by PCR amplification, sequencing and phylogenetic analysis of the VP1 gene. mtDNA ancestry was assessed through HVS1 sequencing, with the resulting haplotypes being classified into haplogroups of Amerindian, European and African origin. The distribution of JCPyV diversity and mtDNA ancestry in the population was statistically evaluated by Fisher exact test and the level of agreement of both markers at the individual level was evaluated by Cohen's kappa coefficient. RESULTS Our analysis showed that 57.4% of the samples were positive for JCPyV. Of these, the 47.6% were Asian-American Type 2, 33.3% European Type 1 and 19.1% African Type 3 in origin. The mtDNA ancestry of the study participants was 33.3% Amerindian and 66.7% European. There was a significant difference among the distribution of JCPyV diversity and mtDNA ancestry (p = 0.009) and at the individual level there was no correlation between the distribution of the both markers (κ = 0.154, p = 0.297). CONCLUSION The apparent incongruence between JCPyV diversity and mtDNA ancestry may reflect the original settlement process and more recent migration to 25 de Mayo, the latter involving viral spread through migrants from Brazil. Some potential limitations to our interpretations are also discussed.
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Affiliation(s)
- Daiana J Sanabria
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina.
| | - Laura N Mojsiejczuk
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Torres
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Alejandro G Meyer
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Viviana A Mbayed
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Domingo J Liotta
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina
| | - Rodolfo H Campos
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina; Cátedra de Virología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Theodore G Schurr
- Laboratory of Molecular Anthropology, Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104-6398, USA
| | - Ines Badano
- Laboratorio de Biología Molecular Aplicada, Universidad Nacional de Misiones, Posadas, Misiones, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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Amorim A, Fernandes T, Taveira N. Mitochondrial DNA in human identification: a review. PeerJ 2019; 7:e7314. [PMID: 31428537 PMCID: PMC6697116 DOI: 10.7717/peerj.7314] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 06/18/2019] [Indexed: 11/21/2022] Open
Abstract
Mitochondrial DNA (mtDNA) presents several characteristics useful for forensic studies, especially related to the lack of recombination, to a high copy number, and to matrilineal inheritance. mtDNA typing based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where the DNA content is low. Evaluation and reporting of the results requires careful consideration of biological issues as well as other issues such as nomenclature and reference population databases. In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics.
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Affiliation(s)
- António Amorim
- Instituto Nacional de Medicina Legal e Ciências Forenses, Lisboa, Portugal
- Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Teresa Fernandes
- Escola de Ciências e Tecnologias, Universidade de Évora, Évora, Portugal
- Research Center for Anthropology and Health (CIAS), Universidade de Coimbra, Coimbra, Portugal
| | - Nuno Taveira
- Instituto Universitário Egas Moniz (IUEM), Almada, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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Baptista Rosas RC, Mercado Sesma A, Hernández Ortega L, Hernandez Gonzalez L, Vega Avalos J, Arreola Cruz AA. The utility of genomic public databases to mitochondrial haplotyping in contemporary Mestizo population of Mexican origin. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:567-572. [PMID: 30897996 DOI: 10.1080/24701394.2019.1580271] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
There are different public databases and open access information that can be exploited to be reused in different research projects. With this concept in mind, we carried out a study to answer the question about the prevalence of haplogroups in human populations of modern Mexico. Since the publication of genomic and mitochondrial data in Latin American populations are very scarce and with very small samples, our work proposes to consider the availability of genomic and genetic data collections that can be reused for other purposes, different from those initially proposed in the investigations where the sequences were obtained. The objective of the present study was to explore the population structure of Mexico using available information in the public database. Through the search of information in the nucleotide database of National Center of Biotechnology Information (NCBI) of complete sequences of mitochondrial genome (16 Kb) of indigenous people, Mexican Mestizo population and Mexican-Americans living in the United States, they were classified according to the polymorphisms associated with haplogroups A, B, C and D reported in the literature as the most frequent. We obtained 283 sequences, of which 255 were selected with the criteria mentioned. The haplotyping results showed 113 different clades and subclades distributed in a general way in eight haplogroups. The most frequent groups that dominate the population were the haplogroup A with 90 individuals representing 36%, followed by haplogroup B in 65 individuals representing 26% of the sample.
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Affiliation(s)
- Raúl C Baptista Rosas
- a Department of Sciences of Health-Diseases as Individual Process, Centro Universitario de Tonalá, Universidad de Guadalajara , Tonalá , Mexico
| | - Arieh Mercado Sesma
- a Department of Sciences of Health-Diseases as Individual Process, Centro Universitario de Tonalá, Universidad de Guadalajara , Tonalá , Mexico
| | - Luis Hernández Ortega
- b Department of Biomedicine , Centro Universitario de Tonalá, Universidad de Guadalajara , Tonalá , Mexico
| | - Luis Hernandez Gonzalez
- c School of Medicine , Centro Universitario de Tonalá, Universidad de Guadalajara , Tonalá , Mexico
| | - Jorge Vega Avalos
- c School of Medicine , Centro Universitario de Tonalá, Universidad de Guadalajara , Tonalá , Mexico
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Duan M, Chen L, Ge Q, Lu N, Li J, Pan X, Qiao Y, Tu J, Lu Z. Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data. Gene 2019; 699:145-154. [PMID: 30876822 DOI: 10.1016/j.gene.2019.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Detecting heteroplasmic variations in the mitochondrial genome can help identify potential pathogenic possibilities, which is significant for disease prevention. The development of next-generation sequencing changed the quantification of mitochondrial DNA (mtDNA) heteroplasmy from scanning limited recorded points to the entire mitochondrial genome. However, due to the presence of nuclear mtDNA homologous sequences (nuMTs), maximally retaining real variations while excluding falsest heteroplasmic variations from nuMTs and sequencing errors presents a dilemma. RESULTS Herein, we used an improved method for detecting low-frequency mtDNA heteroplasmic variations from whole genome sequencing data, including point variations and short-fragment length alterations, and evaluated the effect of this method. A two-step alignment was designed and performed to accelerate data processing, to obtain and retain the true mtDNA reads and to eliminate most nuMTs reads. After analyzing whole genome sequencing data of K562 and GM12878 cells, ~90% of heteroplasmic point variations were identified in MitoMap. The results were consistent with the results of an amplification refractory mutation system qPCR. Many linkages of the detected heteroplasmy variations were also discovered. CONCLUSIONS Our improved method is a simple, efficient and accurate way to mine mitochondrial low-frequency heteroplasmic variations from whole genome sequencing data. By evaluating the highest misalignment possibility caused by the remaining nuMTs-like reads and sequencing errors, our procedure can detect mtDNA heteroplasmic variations whose heteroplasmy frequencies are as low as 0.2%.
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Affiliation(s)
- Mengqin Duan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liang Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Junji Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuan Pan
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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Bybjerg-Grauholm J, Hagen CM, Gonçalves VF, Bækvad-Hansen M, Hansen CS, Hedley PL, Kanters JK, Nielsen J, Theisen M, Mors O, Kennedy J, Als TD, Demur AB, Nordentoft M, Børglum A, Mortensen PB, Werge TM, Hougaard DM, Christiansen M. Complex spatio-temporal distribution and genomic ancestry of mitochondrial DNA haplogroups in 24,216 Danes. PLoS One 2018; 13:e0208829. [PMID: 30543675 PMCID: PMC6292624 DOI: 10.1371/journal.pone.0208829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroups (hgs) are evolutionarily conserved sets of mtDNA SNP-haplotypes with characteristic geographical distribution. Associations of hgs with disease and physiological characteristics have been reported, but have frequently not been reproducible. Using 418 mtDNA SNPs on the PsychChip (Illumina), we assessed the spatio-temporal distribution of mtDNA hgs in Denmark from DNA isolated from 24,642 geographically un-biased dried blood spots (DBS), collected from 1981 to 2005 through the Danish National Neonatal Screening program. ADMIXTURE was used to establish the genomic ancestry of all samples using a reference of 100K+ autosomal SNPs in 2,248 individuals from nine populations. Median-joining analysis determined that the hgs were highly variable, despite being typically Northern European in origin, suggesting multiple founder events. Furthermore, considerable heterogeneity and variation in nuclear genomic ancestry was observed. Thus, individuals with hg H exhibited 95%, and U hgs 38.2% - 92.5%, Danish ancestry. Significant clines between geographical regions and rural and metropolitan populations were found. Over 25 years, macro-hg L increased from 0.2% to 1.2% (p = 1.1*E-10), and M from 1% to 2.4% (p = 3.7*E-8). Hg U increased among the R macro-hg from 14.1% to 16.5% (p = 1.9*E-3). Genomic ancestry, geographical skewedness, and sub-hg distribution suggested that the L, M and U increases are due to immigration. The complex spatio-temporal dynamics and genomic ancestry of mtDNA in the Danish population reflect repeated migratory events and, in later years, net immigration. Such complexity may explain the often contradictory and population-specific reports of mito-genomic association with disease.
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Affiliation(s)
| | - Christian M. Hagen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christine S. Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Paula L. Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jimmi Nielsen
- Aalborg Psychiatric Hospital. Aalborg University Hospital, Aalborg, Denmark
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Mors
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - James Kennedy
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Thomas D. Als
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Alfonso B. Demur
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | | | - Anders Børglum
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Preben B. Mortensen
- Center for Register Research, Institute of Economics, Aarhus University, Århus, Denmark
| | - Thomas M. Werge
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - David M. Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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Svendsen AJ, Tan Q, Jakobsen MA, Thyagarajan B, Nygaard M, Christiansen L, Mengel-From J. White blood cell mitochondrial DNA copy number is decreased in rheumatoid arthritis and linked with risk factors. A twin study. J Autoimmun 2018; 96:142-146. [PMID: 30327147 DOI: 10.1016/j.jaut.2018.09.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 09/19/2018] [Accepted: 09/21/2018] [Indexed: 01/10/2023]
Abstract
Low mitochondrial DNA copy number (mtDNA CN) has been associated with e.g. cancer, cardiovascular and autoimmune diseases. We aimed to study a potential association between mtDNA CN and rheumatoid arthritis (RA). The relative quantity of mitochondrial DNA compared to nuclear DNA was measured in peripheral white blood cells from 149 RA affected twin pairs and 1321 non-affected twin pairs. Multiple regression analysis including RA discordant twin pairs was performed in order to separate specific effects of RA and familial RA predisposition using non-RA affected twin pairs as reference group. In addition, we performed a twin pair level analysis including only RA discordant twin pairs evaluating the effect of cell type, auto antibodies and RA genetic risk factors. Both the RA twins and their non-affected co-twins had significantly lower mtDNA CN than non-affected twins (-28.7 and -23.1 mtDNA CN, respectively). Adjusting for cell count attenuated these differences (-23.1 mtDNA CN and -20.1 mtDNA CN respectively). Within RA discordant twin pairs PTPN22(T) positive RA twins had a significantly lower amount than their co-twins (-16.3 mtDNA CN). PTPN22(T) had no effect among twins from non-affected twin pairs. MtDNA CN is significantly lower in persons with established RA and in predisposed non-affected RA co-twins suggesting that mitochondrial variation may be involved in the RA disease pathways. Our results also suggest that the RA associated genetic risk factor, PTPN22(T), further decreases the mtDNA CN, but only in carriers with established RA.
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Affiliation(s)
- Anders J Svendsen
- Department of Internal Medicine, Odense University Hospital, Svendborg, Denmark; Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Marianne A Jakobsen
- Department of Clinical Immunology, Odense University Hospital, Odense, Denmark
| | - Bharat Thyagarajan
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, USA
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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Kim HR, Kang MG, Lee YE, Na BR, Noh MS, Yang SH, Shin JH, Shin MG. Spectrum of mitochondrial genome instability and implication of mitochondrial haplogroups in Korean patients with acute myeloid leukemia. Blood Res 2018; 53:240-249. [PMID: 30310792 PMCID: PMC6170299 DOI: 10.5045/br.2018.53.3.240] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/01/2018] [Accepted: 08/05/2018] [Indexed: 11/17/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) mutations may regulate the progression and chemosensitivity of leukemia. Few studies regarding mitochondrial aberrations and haplogroups in acute myeloid leukemia (AML) and their clinical impacts have been reported. Therefore, we focused on the mtDNA length heteroplasmies minisatellite instability (MSI), copy number alterations, and distribution of mitochondrial haplogroups in Korean patients with AML. Methods This study investigated 74 adult patients with AML and 70 controls to evaluate mtDNA sequence alterations, MSI, mtDNA copy number, haplogroups, and their clinical implications. The hypervariable (HV) control regions (HV1 and HV2), tRNAleu1gene, and cytochrome b gene of mtDNA were analyzed. Two mtDNA minisatellite markers, 16189 poly-C (16184CCCCCTCCCC16193, 5CT4C) and 303 poly-C (303CCCCCCCTCCCCC315, 7CT5C), were used to examine the mtDNA MSI. Results In AML, most mtDNA sequence variants were single nucleotide substitutions, but there were no significant differences compared to those in controls. The number of mtMSI patterns increased in AML. The mean mtDNA copy number of AML patients increased approximately 9-fold compared to that of controls (P<0.0001). Haplogroup D4 was found in AML with a higher frequency compared to that in controls (31.0% vs. 15.7%, P=0.046). None of the aforementioned factors showed significant impacts on the outcomes. Conclusion AML cells disclosed more heterogeneous patterns with the mtMSI markers and had increased mtDNA copy numbers. These findings implicate mitochondrial genome instability in primary AML cells. Therefore, mtDNA haplogroup D4 might be associated with AML risk among Koreans.
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Affiliation(s)
- Hye Ran Kim
- College of Korean Medicine, Dongshin University, Naju, Korea
| | - Min-Gu Kang
- Department of Laboratory Medicine, Gwangyang Sarang General Hospital, Gwangyang, Korea
| | - Young Eun Lee
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Bo Ram Na
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Min Seo Noh
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Seung Hyun Yang
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea
| | - Jong-Hee Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
| | - Myun-Geun Shin
- Department of Laboratory Medicine, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea.,Brain Korea 21 Plus Project, Chonnam National University Medical School, Gwangju, Korea.,Environmental Health Center for Childhood Leukemia and Cancer, Chonnam National University Medical School and Chonnam National University Hwasun Hospital, Hwasun, Korea
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50
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Kozin MS, Kulakova OG, Favorova OO. Involvement of Mitochondria in Neurodegeneration in Multiple Sclerosis. BIOCHEMISTRY (MOSCOW) 2018; 83:813-830. [PMID: 30200866 DOI: 10.1134/s0006297918070052] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Functional disruption and neuronal loss followed by progressive dysfunction of the nervous system underlies the pathogenesis of numerous disorders defined as "neurodegenerative diseases". Multiple sclerosis, a chronic inflammatory demyelinating disease of the central nervous system resulting in serious neurological dysfunctions and disability, is one of the most common neurodegenerative diseases. Recent studies suggest that disturbances in mitochondrial functioning are key factors leading to neurodegeneration. In this review, we consider data on mitochondrial dysfunctions in multiple sclerosis, which were obtained both with patients and with animal models. The contemporary data indicate that the axonal degeneration in multiple sclerosis largely results from the activation of Ca2+-dependent proteases and from misbalance of ion homeostasis caused by energy deficiency. The genetic studies analyzing association of mitochondrial DNA polymorphic variants in multiple sclerosis suggest the participation of mitochondrial genome variability in the development of this disease, although questions of the involvement of individual genomic variants are far from being resolved.
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Affiliation(s)
- M S Kozin
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia. .,National Medical Research Center of Cardiology, Moscow, 121552, Russia
| | - O G Kulakova
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia. .,National Medical Research Center of Cardiology, Moscow, 121552, Russia
| | - O O Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia.,National Medical Research Center of Cardiology, Moscow, 121552, Russia
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