1
|
Li X, Liu X, Chen X, Wang Y, Wu S, Li F, Su Y, Chen L, Xiao J, Ma J, Qin P. Leukocyte mitochondrial DNA copy number and cardiovascular disease: A systematic review and meta-analysis of cohort studies. iScience 2024; 27:110522. [PMID: 39220264 PMCID: PMC11363494 DOI: 10.1016/j.isci.2024.110522] [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: 01/17/2024] [Revised: 05/10/2024] [Accepted: 07/12/2024] [Indexed: 09/04/2024] Open
Abstract
Increasing cohort studies have examined the link between mitochondrial DNA copy number (mtDNA-CN) and cardiovascular disease (CVD), with inconsistent findings. We searched PubMed, EMBASE, and Web of Science up to July 11, 2023 and used a random-effects model to calculate summary hazard ratios (HRs) and 95% confidence intervals (CIs). This systematic review and meta-analysis included 8 articles encompassing 29 studies with 646,398 participants. Individuals with the lowest mtDNA-CN had a summary HR of 1.27 (95% CI 1.02-1.59) for CVD, 1.18 (95% CI 0.92-1.50) for coronary heart disease (CHD), 1.10 (95% CI 0.89-1.37) for stroke, and 1.30 (95% CI 1.07-1.56) for heart failure (HF). Decreased mtDNA-CN is linked to an increased risk of CVD and HF but not CHD and stroke. These findings suggest mtDNA-CN from leukocytes may be a potential early biomarker for CVD. However, more prospective studies with long follow-up are needed.
Collapse
Affiliation(s)
- Xinying Li
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
- School of Public Health, Shantou University, Shantou, Guangdong, China
| | - Xiaoning Liu
- Department of Respiratory and Critical Care Medicine, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaojuan Chen
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
- School of Public Health, Shantou University, Shantou, Guangdong, China
| | - Yanqi Wang
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
- School of Public Health, Shantou University, Shantou, Guangdong, China
| | - Shuning Wu
- Department of Thyroid and Breast Surgery, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Fengjuan Li
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
- School of Public Health, Shantou University, Shantou, Guangdong, China
| | - Yuhao Su
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
- School of Public Health, Shantou University, Shantou, Guangdong, China
| | - Lifang Chen
- Department of Cardiovascular Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518000, Guangdong, China
| | - Jian Xiao
- Department of Cardiovascular Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen 518000, Guangdong, China
| | - Jianping Ma
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
| | - Pei Qin
- Center for Clinical Epidemiology and Evidence-Based Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, Guangdong, China
| |
Collapse
|
2
|
Rugman-Jones PF, Dodge CE, Stouthamer R. Pervasive heteroplasmy in an invasive ambrosia beetle (Scolytinae) in southern California. Heredity (Edinb) 2024:10.1038/s41437-024-00722-0. [PMID: 39266674 DOI: 10.1038/s41437-024-00722-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 09/14/2024] Open
Abstract
Heteroplasmy, the presence of multiple mitochondrial genotypes (mitotypes) within an individual, has long been thought to be a rare aberrance that is quickly removed by selection or drift. However, heteroplasmy is being reported in natural populations of eukaryotes with increasing frequency, in part due to improved diagnostic methods. Here, we report a seemingly stable heteroplasmic state in California populations of the polyphagous shothole borer (PSHB), Euwallacea fornicatus; an invasive ambrosia beetle that is causing significant tree dieback. We develop and validate a qPCR assay utilizing locked nucleic acid probes to detect different mitotypes, and qualitatively assess heteroplasmy in individual PSHB. We prove the utility of this assay by: (1) mitotyping field-collected PSHB, documenting the prevalence of heteroplasmy across its range in California; and, (2) measuring relative titers of each mitotype across multiple generations of heteroplasmic laboratory colonies to assess the stability of transmission through the maternal germline. We show that our findings are unlikely to be explained by the existence of NUMTs by next generation sequencing of contiguous sections of mitochondrial DNA, where each of the observed heteroplasmic sites are found within fully functional coding regions of mtDNA. Subsequently, we find heteroplasmic individuals are common in Californian field populations, and that heteroplasmy persists for at least 10 generations in experimental colonies. We also looked for evidence of the common occurrence of paternal leakage, but found none. In light of our results, we discuss competing hypotheses as to how heteroplasmy may have arisen, and continues to perpetuate, in Californian PSHB populations.
Collapse
Affiliation(s)
- Paul F Rugman-Jones
- Department of Entomology, University of California, Riverside, CA, 92521, USA.
| | - Christine E Dodge
- Department of Entomology, University of California, Riverside, CA, 92521, USA
- Forest Pest Methods Laboratory, USDA-APHIS-PPQ-S&T, 1398 W. Truck Rd, Buzzards Bay, MA, 02542, USA
| | - Richard Stouthamer
- Department of Entomology, University of California, Riverside, CA, 92521, USA
| |
Collapse
|
3
|
Sequeira JJ, Panda M, Dixit S, Kumawat R, Mustak MS, Sharma AN, Chaubey G, Shrivastava P. Forensic Characterization, Genomic Variability and Ancestry Analysis of Six Populations from Odisha Using mtDNA SNPs and Autosomal STRs. Biochem Genet 2024:10.1007/s10528-024-10887-2. [PMID: 39039324 DOI: 10.1007/s10528-024-10887-2] [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: 01/04/2024] [Accepted: 07/14/2024] [Indexed: 07/24/2024]
Abstract
Located on India's eastern coast, Odisha is known for its diverse tribes and castes. In the early days of genome sequencing technology, researchers primarily studied the Austroasiatic communities inhabiting this region to reconstruct the ancient origins and dispersal of this broad linguistic group. However, current research has shifted towards identifying population and individual-specific genome variation for forensic applications. This study aims to analyze the forensic efficiency and ancestry of six populations from Odisha. We assessed the SF mtDNA-SNP60™ PCR Amplification Kit by comparing it with PowerPlex® Fusion 6C System, a widely used autosomal STR (aSTR) kit, in an Indian cohort. Although the mtDNA SNP kit showed low discriminating power for individuals of a diverse population, it could identify deep lineage divergence. Also, we utilized mitochondrial and autosomal variation information to analyze the ancestry of six endogamous ethnic groups in Odisha. We observe two extremities-populations with higher West Asian affinity and those with East Asian affinity. This observation is in congruence with the existing information of their tribal and non-tribal affiliation. When compared with neighbouring populations from Central and Eastern India, multivariate analysis showed that the Brahmins clustered separately or with the Gopala, Kaibarta appeared as an intermediate, Pana and Kandha clustered with the Gonds, and Savara with the Munda tribes. Our findings indicate significant deep lineage stratification in the ethnic populations of Odisha and a gene flow from West and East Asia. The artefacts of unique deep lineage in such a diverse population will help in improving forensic identification. In addition, we conclude that the SF mtDNA-SNP60 PCR Amplification Kit may be used only as a supplementary tool for forensic analysis.
Collapse
Affiliation(s)
- Jaison Jeevan Sequeira
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Mangalore, 574199, India
| | - Muktikanta Panda
- Department of Anthropology, Model Degree College, Malkangiri, Odisha, 764045, India
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India
| | - Shivani Dixit
- DNA Division, Central Forensic Science Laboratory, Chandigarh, 160036, India
| | - Ramkishan Kumawat
- DNA Division, State Forensic Science Laboratory, Jaipur, Rajasthan, India
| | - Mohammed S Mustak
- Department of Applied Zoology, Mangalore University, Mangalagangothri, Mangalore, 574199, India
| | - Awdhesh Narayan Sharma
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India
| | - Gyaneshwer Chaubey
- DNA Division, Central Forensic Science Laboratory, Chandigarh, 160036, India
- Department of Zoology, Banaras Hindu University (BHU), Varanasi, India
| | - Pankaj Shrivastava
- Department of Anthropology, Dr. Harisingh Gour Vishwavidyalaya (A Central University), Sagar, Madhya Pradesh, 470003, India.
- Regional Forensic Science Laboratory, Government of MP, Gwalior, Madhya Pradesh, India.
| |
Collapse
|
4
|
Vahedi Raad M, Firouzabadi AM, Tofighi Niaki M, Henkel R, Fesahat F. The impact of mitochondrial impairments on sperm function and male fertility: a systematic review. Reprod Biol Endocrinol 2024; 22:83. [PMID: 39020374 PMCID: PMC11253428 DOI: 10.1186/s12958-024-01252-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/27/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Besides adenine triphosphate (ATP) production for sustaining motility, the mitochondria of sperm also host other critical cellular functions during germ cell development and fertilization including calcium homeostasis, generation of reactive oxygen species (ROS), apoptosis, and in some cases steroid hormone biosynthesis. Normal mitochondrial membrane potential with optimal mitochondrial performance is essential for sperm motility, capacitation, acrosome reaction, and DNA integrity. RESULTS Defects in the sperm mitochondrial function can severely harm the fertility potential of males. The role of sperm mitochondria in fertilization and its final fate after fertilization is still controversial. Here, we review the current knowledge on human sperm mitochondria characteristics and their physiological and pathological conditions, paying special attention to improvements in assistant reproductive technology and available treatments to ameliorate male infertility. CONCLUSION Although mitochondrial variants associated with male infertility have potential clinical use, research is limited. Further understanding is needed to determine how these characteristics lead to adverse pregnancy outcomes and affect male fertility potential.
Collapse
Affiliation(s)
- Minoo Vahedi Raad
- Department of Biology & Anatomical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amir Masoud Firouzabadi
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
- Department of Physiology, School of Medical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Maryam Tofighi Niaki
- Health Reproductive Research Center, Sari Branch, Islamic Azad University, Sari, Iran
| | - Ralf Henkel
- LogixX Pharma, Theale, Berkshire, UK.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Medical Bioscience, University of the Western Cape, Bellville, South Africa.
| | - Farzaneh Fesahat
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
| |
Collapse
|
5
|
Goodman SJ, Carr IM. Drawing mitochondrial genomes with circularMT. Bioinformatics 2024; 40:btae450. [PMID: 39002115 PMCID: PMC11272167 DOI: 10.1093/bioinformatics/btae450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/05/2024] [Accepted: 07/11/2024] [Indexed: 07/15/2024] Open
Abstract
SUMMARY Mitochondrial DNA sequences are used extensively in phylogeographic and phylogenetic studies for a wide range of organisms. With the advent of low-cost, high throughput 'next generation' DNA sequencing, and user-friendly bioinformatics pipelines for generating and annotating whole mitochondrial genome assemblies, the analysis of whole mitochondrial genomes has become an important component of phylogenomic studies for taxa with high species diversity but limited coverage for other genomic resources. An important step in characterizing de novo mitochondrial genome assemblies is to evaluate and describe structural rearrangements relative to reference taxa. Accessible tools are needed to help visualize gene and noncoding feature complement, their order and strand orientation. However, there are few dedicated applications that generate high quality genome diagrams. Here we present circularMT and circularMT-console that allow users to create highly customizable, publication quality images, of linear and circular mitochondrial genome maps, either individually, or integrated into an analysis pipeline. AVAILABILITY AND IMPLEMENTATION Both applications are implemented in C#, with binaries, source code and user guides available on GitHub (https://github.com/msjimc/circularMT). An archive of the published version is available on Zenodo (https://zenodo.org/records/10912319). SUPPLEMENTARY INFORMATION This paper has no supplementary data.
Collapse
Affiliation(s)
- Simon J Goodman
- School of Biology, Faculty of Biological Science, University of Leeds, Leeds LS2 9JT, United Kingdom
| | - Ian M Carr
- Leeds Institute of Medical Research at St James's, School of Medicine, University of Leeds, Leeds LS9 7TF, United Kingdom
| |
Collapse
|
6
|
Amar D, Gay NR, Jimenez-Morales D, Jean Beltran PM, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul DA, Hershman SG, Ferrasse A, Xia A, Lanza I, Fernández FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector RS, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME. The mitochondrial multi-omic response to exercise training across rat tissues. Cell Metab 2024; 36:1411-1429.e10. [PMID: 38701776 PMCID: PMC11152996 DOI: 10.1016/j.cmet.2023.12.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/27/2023] [Accepted: 12/15/2023] [Indexed: 05/05/2024]
Abstract
Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.
Collapse
Affiliation(s)
- David Amar
- Stanford University, Stanford, CA, USA; Insitro, San Francisco, CA, USA
| | | | | | | | | | | | | | - Yifei Sun
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | | | - David A Gaul
- Georgia Institute of Technology, Atlanta, GA, USA
| | | | | | - Ashley Xia
- National Institutes of Health, Bethesda, MD, USA
| | | | | | | | | | | | - Martin J Walsh
- Icahn School of Medicine at Mount Sinai, New York City, NY, USA
| | - Lauren M Sparks
- Translational Research Institute AdventHealth, Orlando, FL, USA
| | | | | | - John Thyfault
- University of Kansas Medical Center, Kansas City, KS, USA
| | | | | | - Paul M Coen
- Translational Research Institute AdventHealth, Orlando, FL, USA
| | - Simon Schenk
- University of California, San Diego, La Jolla, CA, USA
| | - Sue C Bodine
- Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | |
Collapse
|
7
|
Dan ME, Portner EJ, Bowman JS, Semmens BX, Owens SM, Greenwald SM, Choy CA. Using low volume eDNA methods to sample pelagic marine animal assemblages. PLoS One 2024; 19:e0303263. [PMID: 38748719 PMCID: PMC11095688 DOI: 10.1371/journal.pone.0303263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024] Open
Abstract
Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380-1800 mL) collected at depths of 0-2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand.
Collapse
Affiliation(s)
- Michelle E. Dan
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Elan J. Portner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Jeff S. Bowman
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Brice X. Semmens
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah M. Owens
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - Stephanie M. Greenwald
- Biosciences Division, Argonne National Laboratory, Lemont, Illinois, United States of America
| | - C. Anela Choy
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
8
|
Koranteng J, Chung KF, Michaeloudes C, Bhavsar P. The role of mitochondria in eosinophil function: implications for severe asthma pathogenesis. Front Cell Dev Biol 2024; 12:1360079. [PMID: 38495619 PMCID: PMC10940389 DOI: 10.3389/fcell.2024.1360079] [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: 12/22/2023] [Accepted: 02/13/2024] [Indexed: 03/19/2024] Open
Abstract
Mitochondria are key metabolic hubs involved in cellular energy production and biosynthesis. ATP is generated primarily by glucose and fatty acid oxidation through the tricarboxylic acid (TCA) cycle and oxidative phosphorylation (OXPHOS) in the mitochondria. During OXPHOS there is also production of reactive oxygen species (ROS), which are involved in the regulation of cellular function. Mitochondria are also central in the regulating cell survival and death, particularly in the intrinsic apoptosis pathway. Severe asthma is a heterogeneous disease driven by various immune mechanisms. Severe eosinophilic asthma entails a type 2 inflammatory response and peripheral and lung eosinophilia, associated with severe airflow obstruction, frequent exacerbations and poor response to treatment. Mitochondrial dysfunction and altered metabolism have been observed in airway epithelial and smooth muscle cells from patients with asthma. However, the role of mitochondria in the development of eosinophilia and eosinophil-mediated inflammation in severe asthma is unknown. In this review, we discuss the currently limited literature on the role of mitochondria in eosinophil function and how it is regulated by asthma-relevant cytokines, including interleukin (IL)-5 and granulocyte-macrophage colony-stimulating factor (GM-CSF), as well as by corticosteroid drugs. Moreover, we summarise the evidence on the role of mitochondria in the regulation of eosinophils apoptosis and eosinophil extracellular trap formation. Finally, we discuss the possible role of altered mitochondrial function in eosinophil dysfunction in severe asthma and suggest possible research avenues in order to better understand their role in disease pathogenesis, and identify novel therapeutic targets.
Collapse
Affiliation(s)
- Janice Koranteng
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton & Harefield NHS Trust, London, United Kingdom
| | | | - Pankaj Bhavsar
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
- Royal Brompton & Harefield NHS Trust, London, United Kingdom
| |
Collapse
|
9
|
Xu W, Hong YS, Hu B, Comhair SAA, Janocha AJ, Zein JG, Chen R, Meyers DA, Mauger DT, Ortega VE, Bleecker ER, Castro M, Denlinger LC, Fahy JV, Israel E, Levy BD, Jarjour NN, Moore WC, Wenzel SE, Gaston B, Liu C, Arking DE, Erzurum SC. Mitochondrial DNA Copy Number Variation in Asthma Risk, Severity, and Exacerbations. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.05.23299392. [PMID: 38106101 PMCID: PMC10723502 DOI: 10.1101/2023.12.05.23299392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Rationale Although airway oxidative stress and inflammation are central to asthma pathogenesis, there is limited knowledge of the relationship of asthma risk, severity, or exacerbations to mitochondrial dysfunction, which is pivotal to oxidant generation and inflammation. Objectives We investigated whether mitochondrial DNA copy number (mtDNA-CN) as a measure of mitochondrial function is associated with asthma diagnosis, severity, oxidative stress, and exacerbations. Methods We measured mtDNA-CN in blood in two cohorts. In the UK Biobank (UKB), we compared mtDNA-CN in mild and moderate-severe asthmatics to non-asthmatics. In the Severe Asthma Research Program (SARP), we evaluated mtDNA-CN in relation to asthma severity, biomarkers of oxidative stress and inflammation, and exacerbations. Measures and Main Results In UK Biobank, asthmatics (n = 29,768) have lower mtDNA-CN compared to non-asthmatics (n = 239,158) (beta, -0.026 [95% CI, -0.038 to -0.014], P = 2.46×10-5). While lower mtDNA-CN is associated with asthma, mtDNA-CN did not differ by asthma severity in either UKB or SARP. Biomarkers of inflammation show that asthmatics have higher white blood cells (WBC), neutrophils, eosinophils, fraction exhaled nitric oxide (FENO), and lower superoxide dismutase (SOD) than non-asthmatics, confirming greater oxidative stress in asthma. In one year follow-up in SARP, higher mtDNA-CN is associated with reduced risk of three or more exacerbations in the subsequent year (OR 0.352 [95% CI, 0.164 to 0.753], P = 0.007). Conclusions Asthma is characterized by mitochondrial dysfunction. Higher mtDNA-CN identifies an exacerbation-resistant asthma phenotype, suggesting mitochondrial function is important in exacerbation risk.
Collapse
Affiliation(s)
- Weiling Xu
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
| | - Yun Soo Hong
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Suzy A. A. Comhair
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
| | - Allison J. Janocha
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
| | - Joe G. Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, Ohio
| | - Ruoying Chen
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | | - David T. Mauger
- Department of Public Health Sciences, Pennsylvania State University School of Medicine, Hershey, Pennsylvania
| | - Victor E. Ortega
- Department of Internal Medicine, Division of Respiratory Medicine, Mayo Clinic, Scottsdale, Arizona
| | | | - Mario Castro
- Department of Medicine, University of Kansas School of Medicine, Kansas City, Kansas
| | - Loren C. Denlinger
- Division of Allergy, Pulmonary and Critical Care Medicine, University of Wisconsin, Madison, Wisconsin
| | - John V. Fahy
- Department of Medicine, San Francisco School of Medicine, University of California, San Francisco, California
| | - Elliot Israel
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Bruce D. Levy
- Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Nizar N. Jarjour
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Wendy C. Moore
- Department of Internal Medicine, Wake Forest University School of Medicine, Winston-Salem, North Carolina
| | - Sally E. Wenzel
- Department of Environmental and Occupational Health, Graduate School of Public Health, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Benjamin Gaston
- Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, Indiana
| | - Chunyu Liu
- Department of Biostatistics, School of Public Health, Boston University, Boston, Massachusetts
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Serpil C. Erzurum
- Department of Inflammation and Immunity, Cleveland Clinic, Cleveland, Ohio
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | | |
Collapse
|
10
|
Liu X, Du W, Wang C, Wu Y, Chen W, Zheng Y, Wang M, Liu H, Yang Q, Qian S, Chen L, Liu C. A multilocus DNA mini-barcode assay to identify twenty vertebrate wildlife species. iScience 2023; 26:108275. [PMID: 38026223 PMCID: PMC10651681 DOI: 10.1016/j.isci.2023.108275] [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: 07/27/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
The world faces significant challenges in preserving the diversity of vertebrate species due to wildlife crimes. DNA barcoding, an effective molecular marker for insufficient nuclear DNA, is an authentic and quick identification technique to trace the origin of seized samples in forensic investigations. Here, we present a multiplex assay capable of identifying twenty vertebrate wildlife species utilizing twenty species-specific primers that target short fragments of the mitochondrial Cyt b, COI, 16S rRNA, and 12S rRNA genes. The assay achieved strong species specificity and sensitivity with a detection limit as low as 5 pg of DNA input. Additionally, it effectively discriminated a minor contributor (≥1%) from binary mixtures and successfully identified of noninvasive samples, inhibited DNA samples, artificially degraded DNA samples, and case samples, demonstrating a sensitive, robust, practical and easily interpretable tool in screening, and investigating forensic wildlife crimes.
Collapse
Affiliation(s)
- Xueyuan Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Weian Du
- School of Stomatology and Medicine, Foshan University, Foshan, Guangdong 528000, China
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Chen Wang
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yajiang Wu
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Wu Chen
- Guangzhou Zoo & Guangzhou Wildlife Research Center, Guangzhou, Guangdong 510070, China
| | - Yangyang Zheng
- Guangdong Homy Genetics Ltd., Foshan, Guangdong 528000, China
| | - Mengge Wang
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Hong Liu
- Guangzhou Forensic Science Institute & Guangdong Province Key Laboratory of Forensic Genetics, Guangzhou, Guangdong 510030, China
| | - Qianyong Yang
- College of Medicine of Jiujiang University, Jiujiang, Jiangxi 332000 China
| | - Shui Qian
- Foshan Public Security Bureau, Foshan, Guangdong 528000, China
| | - Ling Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, China
- National Anti-Drug Laboratory Guangdong Regional Center, Guangzhou, Guangdong 510230, China
| |
Collapse
|
11
|
Koller A, Lamina C, Brandl C, Zimmermann ME, Stark KJ, Weissensteiner H, Würzner R, Heid IM, Kronenberg F. Systemic Evidence for Mitochondrial Dysfunction in Age-Related Macular Degeneration as Revealed by mtDNA Copy Number Measurements in Peripheral Blood. Int J Mol Sci 2023; 24:16406. [PMID: 38003595 PMCID: PMC10671207 DOI: 10.3390/ijms242216406] [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: 10/13/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Mitochondrial dysfunction is a common occurrence in the aging process and is observed in diseases such as age-related macular degeneration (AMD). Increased levels of reactive oxygen species lead to damaged mitochondrial DNA (mtDNA), resulting in dysfunctional mitochondria, and, consequently, mtDNA causes further harm in the retinal tissue. However, it is unclear whether the effects are locally restricted to the high-energy-demanding retinal pigment epithelium or are also systematically present. Therefore, we measured mtDNA copy number (mtDNA-CN) in peripheral blood using a qPCR approach with plasmid normalization in elderly participants with and without AMD from the AugUR study (n = 2262). We found significantly lower mtDNA-CN in the blood of participants with early (n = 453) and late (n = 170) AMD compared to AMD-free participants (n = 1630). In regression analyses, we found lower mtDNA-CN to be associated with late AMD when compared with AMD-free participants. Each reduction of mtDNA-CN by one standard deviation increased the risk for late AMD by 24%. This association was most pronounced in geographic atrophy (OR = 1.76, 95% CI 1.19-2.60, p = 0.004), which has limited treatment options. These findings provide new insights into the relationship between mtDNA-CN in blood and AMD, suggesting that it may serve as a more accessible biomarker than mtDNA-CN in the retina.
Collapse
Affiliation(s)
- Adriana Koller
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.K.); (C.L.); (H.W.)
| | - Claudia Lamina
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.K.); (C.L.); (H.W.)
| | - Caroline Brandl
- Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany; (C.B.); (M.E.Z.); (K.J.S.); (I.M.H.)
- Department of Ophthalmology, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Martina E. Zimmermann
- Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany; (C.B.); (M.E.Z.); (K.J.S.); (I.M.H.)
| | - Klaus J. Stark
- Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany; (C.B.); (M.E.Z.); (K.J.S.); (I.M.H.)
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.K.); (C.L.); (H.W.)
| | - Reinhard Würzner
- Institute of Hygiene and Medical Microbiology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Iris M. Heid
- Department of Genetic Epidemiology, University of Regensburg, 93053 Regensburg, Germany; (C.B.); (M.E.Z.); (K.J.S.); (I.M.H.)
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Medical University of Innsbruck, 6020 Innsbruck, Austria; (A.K.); (C.L.); (H.W.)
| |
Collapse
|
12
|
Liu G, Zheng Y, Wu Q, Feng T, Xia Y, Chen D, Ren L, Bai X, Li Q, Chen D, Lv M, Liao M, Liang W, Zhang L, Qu S. Assessment of ForenSeq mtDNA Whole Genome Kit for forensic application. Int J Legal Med 2023; 137:1693-1703. [PMID: 37731065 DOI: 10.1007/s00414-023-03084-0] [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: 07/14/2023] [Accepted: 09/07/2023] [Indexed: 09/22/2023]
Abstract
Mitochondrial DNA (mtDNA) is an indispensable genetic marker in forensic genetics. The emergence and development of massively parallel sequencing (MPS) makes it possible to obtain complete mitochondrial genome sequences more quickly and accurately. The study evaluated the advantages and limitations of the ForenSeq mtDNA Whole Genome Kit in the practical application of forensic genetics by detecting human genomic DNA standards and thirty-three case samples. We used control DNA with different amount to determine sensitivity of the assay. Even when the input DNA is as low as 2.5 pg, most of the mitochondrial genome sequences could still be covered. For the detection of buccal swabs and aged case samples (bloodstains, bones, teeth), most samples could achieve complete coverage of mitochondrial genome. However, when ancient samples and hair samples without hair follicles were sequenced by the kit, it failed to obtain sequence information. In general, the ForenSeq mtDNA Whole Genome Kit has certain applicability to forensic low template and degradation samples, and these results provide the data basis for subsequent forensic applications of the assay. The overall detection process and subsequent analysis are easy to standardize, and it has certain application potential in forensic cases.
Collapse
Affiliation(s)
- Guihong Liu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Yazi Zheng
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Qiushuo Wu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Tao Feng
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Yu Xia
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dan Chen
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Li Ren
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Xiaogang Bai
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Qingqing Li
- Criminal Investigation Bureau, Chengdu Public Security Bureau, Criminal Science and Technology Division, Chengdu, 610000, Sichuan, China
| | - Dezhi Chen
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Meili Lv
- Department of Immunology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Miao Liao
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| | - Shengqiu Qu
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan, China.
| |
Collapse
|
13
|
Onieva A, Martin J, R Cuesta-Aguirre D, Planells V, Coronado-Zamora M, Beyer K, Vega T, Lozano JE, Santos C, Aluja MP. Complete mitochondrial DNA profile in stroke: A geographical matched case-control study in Spanish population. Mitochondrion 2023; 73:51-61. [PMID: 37793469 DOI: 10.1016/j.mito.2023.10.001] [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: 01/17/2023] [Revised: 08/28/2023] [Accepted: 10/01/2023] [Indexed: 10/06/2023]
Abstract
INTRODUCTION Stroke, the second leading cause of death worldwide, is a complex disease influenced by many risk factors among which we can find reactive oxygen species (ROS). Since mitochondria are the main producers of cellular ROS, nowadays studies are trying to elucidate the role of these organelles and its DNA (mtDNA) variation in stroke risk. The aim of the present study was to perform a comprehensive evaluation of the association between mtDNA mutations and mtDNA content and stroke risk. MATERIAL AND METHODS Homoplasmic and heteroplasmic mutations of the mtDNA were analysed in a case-controls study using 110 S cases and their corresponding control individuals. Mitochondrial DNA copy number (mtDNA-CN) was analysed in 73 of those case-control pairs. RESULTS Our results suggest that haplogroup V, specifically variants m.72C > T, m.4580G > A, m.15904C > T and m.16298 T > C have a protective role in relation to stroke risk. On the contrary, variants m.73A > G, m.11719G > A and m.14766C > T appear to be genetic risk factors for stroke. In this study, we found no statistically significant association between stroke risk and mitochondrial DNA copy number. CONCLUSIONS These results demonstrate the possible role of mtDNA genetics on the pathogenesis of stroke, probably through alterations in mitochondrial ROS production.
Collapse
Affiliation(s)
- Ana Onieva
- Unitat d'Antropologia Biològica, Departament BAVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| | - Joan Martin
- Department of Genetics and Microbiology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Daniel R Cuesta-Aguirre
- Unitat d'Antropologia Biològica, Departament BAVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Violeta Planells
- Unitat d'Antropologia Biològica, Departament BAVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Marta Coronado-Zamora
- Institut de Biotecnologia i Biomedicina; Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Katrin Beyer
- Department of Pathology, Germans Trias i Pujol Research Institute, Badalona 08916 Barcelona, Spain
| | - Tomás Vega
- Dirección General de Salud Pública. Consejería de Sanidad. Junta de Castilla y León, 47007 Valladolid, Spain
| | - José Eugenio Lozano
- Dirección General de Salud Pública. Consejería de Sanidad. Junta de Castilla y León, 47007 Valladolid, Spain
| | - Cristina Santos
- Unitat d'Antropologia Biològica, Departament BAVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain
| | - Maria Pilar Aluja
- Unitat d'Antropologia Biològica, Departament BAVE, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Barcelona, Spain.
| |
Collapse
|
14
|
Tessema B, Haag J, Sack U, König B. The Determination of Mitochondrial Mass Is a Prerequisite for Accurate Assessment of Peripheral Blood Mononuclear Cells' Oxidative Metabolism. Int J Mol Sci 2023; 24:14824. [PMID: 37834272 PMCID: PMC10573504 DOI: 10.3390/ijms241914824] [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: 08/30/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Mitochondria are responsible for ATP synthesis through oxidative phosphorylation in cells. However, there are limited data on the influence of mitochondrial mass (MM) in the adequate assessment of cellular stress assay (CSA) results in human peripheral blood mononuclear cells (PBMCs). Therefore, the aim of this study was to determine MM in PBMCS and assess its influence on the results of CSA measurements. Blood samples were collected and sent to the laboratory for MM and CSA measurements during different seasons of the year. The mitochondrial mass was determined based on the mtDNA:nDNA ratio in PBMCs using quantitative real-time PCR (qRT-PCR). CSA was measured using Seahorse technology. The MM was significantly lower during summer and autumn compared to winter and spring (p < 0.0001). On the contrary, we found that the maximal respiration per mitochondrion (MP) was significantly higher in summer and autumn compared to winter and spring (p < 0.0001). The estimated effect of MM on mitochondrial performance was -0.002 pmol/min/mitochondrion (p < 0.0001) and a correlation coefficient (r) of -0.612. Similarly, MM was negatively correlated with maximal respiration (r = -0.12) and spare capacity (in % r = -0.05, in pmol/min r = -0.11). In conclusion, this study reveals that MM changes significantly with seasons and is negatively correlated with CSA parameters and MP. Our findings indicate that the mitochondrial mass is a key parameter for determination of mitochondrial fitness. Therefore, we recommend the determination of MM during the measurement of CSA parameters for the correct interpretation and assessment of mitochondrial function.
Collapse
Affiliation(s)
- Belay Tessema
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
- Department of Medical Microbiology, College of Medicine and Health Sciences, University of Gondar, Gondar P.O. Box 196, Ethiopia
| | - Janine Haag
- Magdeburg Molecular Diagnostics GmbH & Co. KG, 39104 Magdeburg, Germany; (J.H.); (B.K.)
| | - Ulrich Sack
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany;
| | - Brigitte König
- Magdeburg Molecular Diagnostics GmbH & Co. KG, 39104 Magdeburg, Germany; (J.H.); (B.K.)
- Institute of Medical Microbiology and Virology, Faculty of Medicine, University of Leipzig, 04103 Leipzig, Germany
| |
Collapse
|
15
|
Lichter EZ, Trease AJ, Cooper K, Stauch KL, Fox HS. Effects of Parkin on the Mitochondrial Genome in the Heart and Brain of Mitochondrial Mutator Mice. Adv Biol (Weinh) 2023; 7:e2300154. [PMID: 37376822 DOI: 10.1002/adbi.202300154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Indexed: 06/29/2023]
Abstract
Mitochondrial dysfunction has been implicated in neurodegenerative diseases like Parkinson's disease (PD). This study investigates the role of Parkin, a protein involved in mitochondrial quality control, and strongly linked to PD, in the context of mitochondrial DNA (mtDNA) mutations. Mitochondrial mutator mice (PolgD257A/D257A ) (Polg) are used and bred with Parkin knockout (PKO) mice or mice with disinhibited Parkin (W402A). In the brain, mtDNA mutations are analyzed in synaptosomes, presynaptic neuronal terminals, which are far from neuronal soma, which likely renders mitochondria there more vulnerable compared with brain homogenate. Surprisingly, PKO results in reduced mtDNA mutations in the brain but increased control region multimer (CRM) in synaptosomes. In the heart, both PKO and W402A lead to increased mutations, with W402A showing more mutations in the heart than PKO. Computational analysis reveals many of these mutations are deleterious. These findings suggest that Parkin plays a tissue-dependent role in regulating mtDNA damage response, with differential effects in the brain and heart. Understanding the specific role of Parkin in different tissues may provide insights into the underlying mechanisms of PD and potential therapeutic strategies. Further investigation into these pathways can enhance the understanding of neurodegenerative diseases associated with mitochondrial dysfunction.
Collapse
Affiliation(s)
- Eliezer Z Lichter
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Andrew J Trease
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Kathryn Cooper
- School of Interdisciplinary Informatics, University of Nebraska Omaha, Omaha, NE, 68182, USA
| | - Kelly L Stauch
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Howard S Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| |
Collapse
|
16
|
Bevill SM, Casaní-Galdón S, El Farran CA, Cytrynbaum EG, Macias KA, Oldeman SE, Oliveira KJ, Moore MM, Hegazi E, Adriaens C, Najm FJ, Demetri GD, Cohen S, Mullen JT, Riggi N, Johnstone SE, Bernstein BE. Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma. CELL GENOMICS 2023; 3:100321. [PMID: 37492096 PMCID: PMC10363746 DOI: 10.1016/j.xgen.2023.100321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/09/2023] [Accepted: 04/14/2023] [Indexed: 07/27/2023]
Abstract
Amplification of MDM2 on supernumerary chromosomes is a common mechanism of P53 inactivation across tumors. Here, we investigated the impact of MDM2 overexpression on chromatin, gene expression, and cellular phenotypes in liposarcoma. Three independent regulatory circuits predominate in aggressive, dedifferentiated tumors. RUNX and AP-1 family transcription factors bind mesenchymal gene enhancers. P53 and MDM2 co-occupy enhancers and promoters associated with P53 signaling. When highly expressed, MDM2 also binds thousands of P53-independent growth and stress response genes, whose promoters engage in multi-way topological interactions. Overexpressed MDM2 concentrates within nuclear foci that co-localize with PML and YY1 and could also contribute to P53-independent phenotypes associated with supraphysiologic MDM2. Importantly, we observe striking cell-to-cell variability in MDM2 copy number and expression in tumors and models. Whereas liposarcoma cells are generally sensitive to MDM2 inhibitors and their combination with pro-apoptotic drugs, MDM2-high cells tolerate them and may underlie the poor clinical efficacy of these agents.
Collapse
Affiliation(s)
- Samantha M. Bevill
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Salvador Casaní-Galdón
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Chadi A. El Farran
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Eli G. Cytrynbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kevin A. Macias
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Sylvie E. Oldeman
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Kayla J. Oliveira
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Molly M. Moore
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Esmat Hegazi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Carmen Adriaens
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
| | - Fadi J. Najm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - George D. Demetri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| | - Sonia Cohen
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - John T. Mullen
- Department of Surgery, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicolò Riggi
- Department of Cell and Tissue Genomics (CTG), Genentech Inc, South San Francisco, CA 94080, USA
| | - Sarah E. Johnstone
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Bradley E. Bernstein
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Departments of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Center at Harvard, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
17
|
Bonfigli A, Cesare P, Volpe AR, Colafarina S, Forgione A, Aloisi M, Zarivi O, Poma AMG. Estimation of DNA Degradation in Archaeological Human Remains. Genes (Basel) 2023; 14:1238. [PMID: 37372418 DOI: 10.3390/genes14061238] [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: 04/19/2023] [Revised: 06/01/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
The evaluation of the integrity and quantity of DNA extracted from archaeological human remains is a fundamental step before using the latest generation sequencing techniques in the study of evolutionary processes. Ancient DNA is highly fragmented and chemically modified; therefore, the present study aims to identify indices that can allow the identification of potentially amplifiable and sequenceable DNA samples, reducing failures and research costs. Ancient DNA was extracted from five human bone remains from the archaeological site of Amiternum L'Aquila, Italy dating back to the 9th-12th century and was compared with standard DNA fragmented by sonication. Given the different degradation kinetics of mitochondrial DNA compared to nuclear DNA, the mitochondrially encoded 12s RNA and 18s ribosomal RNA genes were taken into consideration; fragments of various sizes were amplified in qPCR and the size distribution was thoroughly investigated. DNA damage degree was evaluated by calculating damage frequency (λ) and the ratio between the amount of the different fragments and that of the smallest fragment (Q). The results demonstrate that both indices were found to be suitable for identifying, among the samples tested, those less damaged and suitable for post-extraction analysis; mitochondrial DNA is more damaged than nuclear, in fact, amplicons up to 152 bp and 253 bp, respectively are obtained.
Collapse
Affiliation(s)
- Antonella Bonfigli
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Patrizia Cesare
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Anna Rita Volpe
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Sabrina Colafarina
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Alfonso Forgione
- Department of Human Studies, University of L'Aquila, 67100 L'Aquila, Italy
| | - Massimo Aloisi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | - Osvaldo Zarivi
- Department of Life, Health and Environmental Sciences, University of L'Aquila, 67100 L'Aquila, Italy
| | | |
Collapse
|
18
|
Tsyba N, Feng G, Grub LK, Held JP, Strozak AM, Burkewitz K, Patel MR. Tissue-specific heteroplasmy segregation is accompanied by a sharp mtDNA decline in Caenorhabditis elegans soma. iScience 2023; 26:106349. [PMID: 36968071 PMCID: PMC10031119 DOI: 10.1016/j.isci.2023.106349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Mutations in the mitochondrial genome (mtDNA) can be pathogenic. Owing to the multi-copy nature of mtDNA, wild-type copies can compensate for the effects of mutant mtDNA. Wild-type copies available for compensation vary depending on the mutant load and the total copy number. Here, we examine both mutant load and copy number in the tissues of Caenorhabditis elegans. We found that neurons, but not muscles, have modestly higher mutant load than rest of the soma. We also uncovered different effect of aak-2 knockout on the mutant load in the two tissues. The most surprising result was a sharp decline in somatic mtDNA content over time. The scale of the copy number decline surpasses the modest shifts in mutant load, suggesting that it may exert a substantial effect on mitochondrial function. In summary, measuring both the copy number and the mutant load provides a more comprehensive view of the mutant mtDNA dynamics.
Collapse
Affiliation(s)
- Nikita Tsyba
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Gaomin Feng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
| | - Lantana K. Grub
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - James P. Held
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Adrianna M. Strozak
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristopher Burkewitz
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
| | - Maulik R. Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
- Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN37232, USA
- Evolutionary Studies, Vanderbilt University, Nashville, TN37235, USA
| |
Collapse
|
19
|
McQuate A, Knecht S, Raible DW. Activity regulates a cell type-specific mitochondrial phenotype in zebrafish lateral line hair cells. eLife 2023; 12:e80468. [PMID: 36912880 PMCID: PMC10129330 DOI: 10.7554/elife.80468] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
Hair cells of the inner ear are particularly sensitive to changes in mitochondria, the subcellular organelles necessary for energy production in all eukaryotic cells. There are over 30 mitochondrial deafness genes, and mitochondria are implicated in hair cell death following noise exposure, aminoglycoside antibiotic exposure, as well as in age-related hearing loss. However, little is known about the basic aspects of hair cell mitochondrial biology. Using hair cells from the zebrafish lateral line as a model and serial block-face scanning electron microscopy, we have quantifiably characterized a unique hair cell mitochondrial phenotype that includes (1) a high mitochondrial volume and (2) specific mitochondrial architecture: multiple small mitochondria apically, and a reticular mitochondrial network basally. This phenotype develops gradually over the lifetime of the hair cell. Disrupting this mitochondrial phenotype with a mutation in opa1 impacts mitochondrial health and function. While hair cell activity is not required for the high mitochondrial volume, it shapes the mitochondrial architecture, with mechanotransduction necessary for all patterning, and synaptic transmission necessary for the development of mitochondrial networks. These results demonstrate the high degree to which hair cells regulate their mitochondria for optimal physiology and provide new insights into mitochondrial deafness.
Collapse
Affiliation(s)
- Andrea McQuate
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Department of Otolaryngology-HNS, University of WashingtonSeattleUnited States
| | - Sharmon Knecht
- Department of Biological Structure, University of WashingtonSeattleUnited States
| | - David W Raible
- Department of Biological Structure, University of WashingtonSeattleUnited States
- Department of Otolaryngology-HNS, University of WashingtonSeattleUnited States
| |
Collapse
|
20
|
Sex-related difference of association of mitochondrial DNA copy number with PTSD in U.S. service members. J Psychiatr Res 2023; 159:1-5. [PMID: 36652751 DOI: 10.1016/j.jpsychires.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/27/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Gender differences in the lifetime prevalence of post-traumatic stress disorder (PTSD) have been well described with rates reported as approximately 10%-12% in females and 5%-6% in males (Olff, 2017). This study examined whether the sex-related difference of mitochondrial DNA copy number (mtDNAcn), an emerging systemic index of mitochondrial biogenesis and function can serve as a potential biomarker for PTSD. Leukocyte mtDNAcn of service members with PTSD (male = 127, female = 24) or without PTSD (male = 621, female = 78) was assessed using a TaqMan assay. The results were validated by the absolute quantification of QX-200 droplet digital PCR (ddPCR). PTSD symptoms and symptom severity were assessed using the PTSD Checklist (PCL), a 17-item, DSM-based, self-report questionnaire with well-established validity and reliability. DSM-IV criteria and PTSD were determined by PCL total score. We found that mtDNAcn of female subjects with PTSD was significantly higher compared to either male or female non-PTSD controls or male subjects with PTSD (p < 0.05). There was no significant difference in mtDNAcn between males with PTSD and male/female controls without PTSD. Using in vitro cultured SH-SY5Y cells (human neuroblastoma), we demonstrated that estrogen (Estro) treatment significantly decreased mtDNAcn (P < 0.001) compared to the vehicle control. We also found that pre-treatment with either synthetic glucocorticoid dexamethasone (Dex) or Estro blocker tamoxifen (Tamox) attenuated the estrogen-induced decreases of mtDNAcn. Our data suggest that mtDNAcn may be gender-dependent in the Servicemembers with PTSD. Glucocorticoid and/or estrogen receptors may play a role in the regulation of mtDNAcn. The sex-related difference of mtDNAcn may serve as a PTSD biomarker for females.
Collapse
|
21
|
Zhang L, Ma J, Shen Z, Wang B, Jiang Q, Ma F, Ju Y, Duan G, Zhang Q, Su X. Low copy numbers for mitochondrial DNA moderates the strength of nuclear-cytoplasmic incompatibility in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:739-754. [PMID: 36308719 DOI: 10.1111/jipb.13400] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
Plant cells contain only small amounts of mitochondrial DNA (mtDNA), with the genomic information shared among multiple mitochondria. The biological relevance and molecular mechanism underlying this hallmark of plant cells has been unclear. Here, we report that Arabidopsis thaliana plants exhibited significantly reduced growth and mitochondrial dysfunction when the mtDNA copy number was increased to the degree that each mitochondrion possessed DNA. The amounts of mitochondrion-encoded transcripts increased several fold in the presence of elevated mtDNA levels. However, the efficiency of RNA editing decreased with this excess of mitochondrion-encoded transcripts, resulting in impaired assembly of mitochondrial complexes containing mtDNA-encoded subunits, such as respiratory complexes I and IV. These observations indicate the occurrence of nuclear-mitochondrial incompatibility in the cells with increased amounts of mtDNA and provide an initial answer to the fundamental question of why plant cells have much lower mtDNA levels than animal cells. We propose that keeping mtDNA levels low moderates nuclear-mitochondrial incompatibility and that this may be a crucial factor driving plant cells to restrict the copy numbers of mtDNA.
Collapse
Affiliation(s)
- Liguang Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Jin Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhaorui Shen
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Bo Wang
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
| | - Qingling Jiang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Fei Ma
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Yan Ju
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Guangxing Duan
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Quan Zhang
- Key Laboratory of Ministry of Education for Cell Proliferation and Differentiation, College of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiaodong Su
- State Key Laboratory of Protein and Plant Gene Research and Biomedical Pioneering Innovation Center (BIOPIC), College of Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
22
|
Amar D, Gay NR, Jimenez-Morales D, Beltran PMJ, Ramaker ME, Raja AN, Zhao B, Sun Y, Marwaha S, Gaul D, Hershman SG, Xia A, Lanza I, Fernandez FM, Montgomery SB, Hevener AL, Ashley EA, Walsh MJ, Sparks LM, Burant CF, Rector RS, Thyfault J, Wheeler MT, Goodpaster BH, Coen PM, Schenk S, Bodine SC, Lindholm ME. The mitochondrial multi-omic response to exercise training across tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523698. [PMID: 36711881 PMCID: PMC9882193 DOI: 10.1101/2023.01.13.523698] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yifei Sun
- Icahn School of Medicine at Mount Sinai, New York City, NY
| | | | | | | | - Ashley Xia
- National Institutes of Health, Bethesda, MD
| | | | | | | | | | | | - Martin J Walsh
- Icahn School of Medicine at Mount Sinai, New York City, NY
| | - Lauren M Sparks
- AdventHealth Translational Research Institute for Metabolism and Diabetes, Orlando, FL
| | | | | | - John Thyfault
- University of Kansas Medical Center, Kansas City, KS
| | | | - Bret H. Goodpaster
- AdventHealth Translational Research Institute for Metabolism and Diabetes, Orlando, FL
| | - Paul M. Coen
- AdventHealth Translational Research Institute for Metabolism and Diabetes, Orlando, FL
| | - Simon Schenk
- University of California, San Diego, La Jolla, CA
| | | | | | | |
Collapse
|
23
|
Willis JCW, Silva-Pinheiro P, Widdup L, Minczuk M, Liu DR. Compact zinc finger base editors that edit mitochondrial or nuclear DNA in vitro and in vivo. Nat Commun 2022; 13:7204. [PMID: 36418298 PMCID: PMC9684478 DOI: 10.1038/s41467-022-34784-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
DddA-derived cytosine base editors (DdCBEs) use programmable DNA-binding TALE repeat arrays, rather than CRISPR proteins, a split double-stranded DNA cytidine deaminase (DddA), and a uracil glycosylase inhibitor to mediate C•G-to-T•A editing in nuclear and organelle DNA. Here we report the development of zinc finger DdCBEs (ZF-DdCBEs) and the improvement of their editing performance through engineering their architectures, defining improved ZF scaffolds, and installing DddA activity-enhancing mutations. We engineer variants with improved DNA specificity by integrating four strategies to reduce off-target editing. We use optimized ZF-DdCBEs to install or correct disease-associated mutations in mitochondria and in the nucleus. Leveraging their small size, we use a single AAV9 to deliver into heart, liver, and skeletal muscle in post-natal mice ZF-DdCBEs that efficiently install disease-associated mutations. While off-target editing of ZF-DdCBEs is likely too high for therapeutic applications, these findings demonstrate a compact, all-protein base editing research tool for precise editing of organelle or nuclear DNA without double-strand DNA breaks.
Collapse
Affiliation(s)
- Julian C W Willis
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | | | - Lily Widdup
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
24
|
Campbell T, Slone J, Huang T. Mitochondrial Genome Variants as a Cause of Mitochondrial Cardiomyopathy. Cells 2022; 11:cells11182835. [PMID: 36139411 PMCID: PMC9496904 DOI: 10.3390/cells11182835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are small double-membraned organelles responsible for the generation of energy used in the body in the form of ATP. Mitochondria are unique in that they contain their own circular mitochondrial genome termed mtDNA. mtDNA codes for 37 genes, and together with the nuclear genome (nDNA), dictate mitochondrial structure and function. Not surprisingly, pathogenic variants in the mtDNA or nDNA can result in mitochondrial disease. Mitochondrial disease primarily impacts tissues with high energy demands, including the heart. Mitochondrial cardiomyopathy is characterized by the abnormal structure or function of the myocardium secondary to genetic defects in either the nDNA or mtDNA. Mitochondrial cardiomyopathy can be isolated or part of a syndromic mitochondrial disease. Common manifestations of mitochondrial cardiomyopathy are a phenocopy of hypertrophic cardiomyopathy, dilated cardiomyopathy, and cardiac conduction defects. The underlying pathophysiology of mitochondrial cardiomyopathy is complex and likely involves multiple abnormal processes in the cell, stemming from deficient oxidative phosphorylation and ATP depletion. Possible pathophysiology includes the activation of alternative metabolic pathways, the accumulation of reactive oxygen species, dysfunctional mitochondrial dynamics, abnormal calcium homeostasis, and mitochondrial iron overload. Here, we highlight the clinical assessment of mtDNA-related mitochondrial cardiomyopathy and offer a novel hypothesis of a possible integrated, multivariable pathophysiology of disease.
Collapse
|
25
|
Development and validation of a SYBR green-based mitochondrial DNA quantification method by following the MIQE and other guidelines. Leg Med (Tokyo) 2022; 58:102096. [PMID: 35689884 DOI: 10.1016/j.legalmed.2022.102096] [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: 01/30/2022] [Revised: 04/11/2022] [Accepted: 05/27/2022] [Indexed: 01/28/2023]
Abstract
In forensic mitochondrial DNA (mtDNA) analysis, quantitative PCR (qPCR) is usually performed to obtain high-quality sequence data for subsequent Sanger or massively parallel sequencing. Unlike methods for nuclear DNA quantification using qPCR, a calibrator is necessary to obtain mtDNA concentrations (i.e., copies/µL). Herein, we developed and validated a mtDNA quantification method based on a SYBR Green assay by following MIQE [Bustin et al., Clin. Chem. 55 (2009) 611-22] and other guidelines. Primers were designed to amplify nucleotide positions 16,190-16,420 in hypervariable region 1 for qPCR using PowerUp SYBR Green and QuantStudio 5. The optimized conditions were 0.3 µM each primer and an annealing temperature of 60 °C under a 2-step cycling protocol. K562 DNA at 100 pg/µL was converted into a mtDNA concentration of 16,400 copies/µL using linearized plasmid DNA. This mtDNA calibrator was obtained by cloning the synthesized DNA fragments of mtDNA (positions 16,140-16,470) containing a 100-bp inversion. The linear dynamic range of the K562 standard curve was 10,000-0.1 pg/µL (r2 ≥ 0.999). The accuracy was examined using NIST SRM 2372a, and its components A, B, and C were quantified with differences of -29.4%, -35.0%, and -22.0%, respectively, against the mtDNA concentrations calculated from published NIST data. We also examined the specificity of the primers, stability of the reaction mix, precision, tolerance against PCR inhibitors, and cross-reactivity against DNA from various animal taxa. Our newly developed mtDNA quantification method is expected to be useful for forensic mtDNA analysis.
Collapse
|
26
|
Raad MV, Fesahat F, Talebi AR, Hosseini-Sharifabad M, Horoki AZ, Afsari M, Sarcheshmeh AA. Altered methyltransferase gene expression, mitochondrial copy number and 4977-bp common deletion in subfertile men with variable sperm parameters. Andrologia 2022; 54:e14531. [PMID: 35841193 DOI: 10.1111/and.14531] [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: 05/18/2022] [Revised: 06/15/2022] [Accepted: 06/26/2022] [Indexed: 11/29/2022] Open
Abstract
Semen parameters have been found to predict reproductive success poorly and are the most prevalent diagnostic tool for male infertility. There are few conflicting reports regarding the correlation of DNMT genes expression, mitochondrial DNA copy number (mtDNAcn) and deletion (mtDNAdel) with different sperm parameters. To investigate DNMT mRNA level, mtDNAcn and deletion in infertile men, with different sperm parameters, compared with fertile men, semen samples from 30 men with unknown male infertility and normal sperm parameters (experimental group I), 30 infertile patients with at least two abnormal sperm parameters (experimental group II) and 30 fertile normozoospermic men (control group) were collected. After semen analysis, total RNA and DNA were extracted. The isolated DNA was used for assessing the respective mtDNAcn and the presence of common 4977 bp deletion in mtDNA by applying real-time quantitative PCR and multiplex PCR, respectively. Synthesized cDNA from total RNAs was used to quantify DNMT1, DNMT3A and DNMT3B transcripts in study groups by using real-time quantitative reverse-transcription PCR. Significantly higher proportions of mtDNAcn were found in experimental group II. DNMT1 was significantly downregulated in both experimental groups and 4977 bp deletion was not detected. Progressive motility and normal morphology were significantly and negatively correlated with mtDNAcn. A significant positive correlation was detected between sperm parameters and DNMT1 mRNA levels. In conclusion, infertile men with different sperm parameter qualities showed elevated mtDNA content. Abnormal sperm parameters associated with DNMT1 gene expression indicate the possibility of changes in some epigenetic aspects of spermatogenesis in subfertile men with different sperm parameters.
Collapse
Affiliation(s)
- Minoo Vahedi Raad
- Department of Biology & Anatomical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Farzaneh Fesahat
- Reproductive Immunology Research Center, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Ali Reza Talebi
- Department of Biology & Anatomical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | | - Ali Zare Horoki
- Department of Urology, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Maliheh Afsari
- Department of Biology & Anatomical Sciences, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | | |
Collapse
|
27
|
Improving Environmental DNA Sensitivity for Dreissenid Mussels by Targeting Tandem Repeat Regions of the Mitochondrial Genome. WATER 2022. [DOI: 10.3390/w14132069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The recent genetic revolution through the analysis of aquatic environmental DNA (eDNA) has become a powerful tool for improving the detection of rare and/or invasive species. For the majority of eDNA studies, genetic assays are designed to target mitochondrial genes commonly referred to as “barcode” regions. However, unlike the typical structure of an animal mitochondrial genome, those for the invasive zebra and quagga mussels are greatly expanded with large extended tandem repeat regions. These sections of repeated DNA can appear hundreds of times within the genome compared to a single copy for the mitochondrial barcode genes. This higher number of target copies per mitochondrial genome presents an opportunity to increase eDNA assay sensitivity for these species. Therefore, we designed and evaluated new eDNA assays to target the extended repeat sections for both zebra and quagga mussels. These assays lower the limit of detection of genomic DNA by 100-fold for zebra mussels and 10-fold for quagga mussels. Additionally, these newly developed assays provided longer durations of detection during degradation mesocosm experiments and greater sensitivity for eDNA detection from water samples collected across western Lake Erie compared to standard assays targeting mitochondrial genes. This work illustrates how understanding the complete genomic structure of an organism can improve eDNA analysis.
Collapse
|
28
|
Anderson L, Camus MF, Monteith KM, Salminen TS, Vale PF. Variation in mitochondrial DNA affects locomotor activity and sleep in Drosophila melanogaster. Heredity (Edinb) 2022; 129:225-232. [PMID: 35764697 PMCID: PMC9519576 DOI: 10.1038/s41437-022-00554-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 01/20/2023] Open
Abstract
Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved among many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. Our results demonstrate that Drosophila strains from different locations differ in sleep and activity, and that females are generally more active than males. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we were able to quantify the among-line variance attributable to mitochondrial DNA, and we establish that mtDNA variation affects both activity and sleep, in a sex-specific manner. Altogether our study highlights the important role that mitochondrial genome variation plays on organismal physiology and behaviour.
Collapse
Affiliation(s)
- Lucy Anderson
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - M Florencia Camus
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London, WC1E 6BT, UK
| | - Katy M Monteith
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tiina S Salminen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Pedro F Vale
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
29
|
Fujii K, Mita Y, Watahiki H, Fukagawa T, Kitayama T, Mizuno N, Nakahara H, Sekiguchi K. Poly_NumtS_430 or HSA_NumtS_587 observed in massively parallel sequencing of the mitochondrial HV1 and HV2 regions. Forensic Sci Int Genet 2022; 59:102717. [DOI: 10.1016/j.fsigen.2022.102717] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 03/12/2022] [Accepted: 05/01/2022] [Indexed: 11/04/2022]
|
30
|
CRISPR-free base editors with enhanced activity and expanded targeting scope in mitochondrial and nuclear DNA. Nat Biotechnol 2022; 40:1378-1387. [PMID: 35379961 PMCID: PMC9463067 DOI: 10.1038/s41587-022-01256-8] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/08/2022] [Indexed: 12/21/2022]
Abstract
The all-protein cytosine base editor DdCBE uses TALE proteins and a double-stranded DNA-specific cytidine deaminase (DddA) to mediate targeted C•G-to-T•A editing. To improve editing efficiency and overcome the strict TC sequence-context constraint of DddA, we used phage-assisted non-continuous and continuous evolution to evolve DddA variants with improved activity and expanded targeting scope. Compared to canonical DdCBEs, base editors with evolved DddA6 improved mitochondrial DNA (mtDNA) editing efficiencies at TC by 3.3-fold on average. DdCBEs containing evolved DddA11 offered a broadened HC (H = A, C or T) sequence compatibility for both mitochondrial and nuclear base editing, increasing average editing efficiencies at AC and CC targets from less than 10% for canonical DdCBE to 15-30% and up to 50% in cell populations sorted to express both halves of DdCBE. We used these evolved DdCBEs to efficiently install disease-associated mtDNA mutations in human cells at non-TC target sites. DddA6 and DddA11 substantially increase the effectiveness and applicability of all-protein base editing.
Collapse
|
31
|
Walker BR, Moraes CT. Nuclear-Mitochondrial Interactions. Biomolecules 2022; 12:biom12030427. [PMID: 35327619 PMCID: PMC8946195 DOI: 10.3390/biom12030427] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/21/2022] [Accepted: 02/26/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondria, the cell’s major energy producers, also act as signaling hubs, interacting with other organelles both directly and indirectly. Despite having its own circular genome, the majority of mitochondrial proteins are encoded by nuclear DNA. To respond to changes in cell physiology, the mitochondria must send signals to the nucleus, which can, in turn, upregulate gene expression to alter metabolism or initiate a stress response. This is known as retrograde signaling. A variety of stimuli and pathways fall under the retrograde signaling umbrella. Mitochondrial dysfunction has already been shown to have severe implications for human health. Disruption of retrograde signaling, whether directly associated with mitochondrial dysfunction or cellular environmental changes, may also contribute to pathological deficits. In this review, we discuss known signaling pathways between the mitochondria and the nucleus, examine the possibility of direct contacts, and identify pathological consequences of an altered relationship.
Collapse
Affiliation(s)
- Brittni R. Walker
- Neuroscience Program, University of Miami Miller School of Medicine, 1420 NW 9th Avenue, Rm. 229, Miami, FL 33136, USA;
| | - Carlos T. Moraes
- Department of Neurology, University of Miami Miller School of Medicine, 1420 NW 9th Avenue, Rm. 229, Miami, FL 33136, USA
- Correspondence: ; Tel.: +1-305-243-5858
| |
Collapse
|
32
|
Abstract
Although currently employed therapies for heart failure decrease overall mortality and improve patient quality of life temporarily, the disease is known to progress even for patients who receive all guideline-recommended therapies. This indicates that our concise understanding of heart failure and of disease progression is incomplete, and there is a need for new interventions that may augment, or even supplant, currently available options. A literature review reveals that an exciting, novel area of current research is focused on mitochondria, which are uniquely juxtaposed at the sites of both generation of high-energy molecules and initiation of programmed cell death. Elamipretide is being studied both to maintain cellular biogenetics and prevent reactive oxygen species-induced cell damage by targeting and stabilizing the cardiolipin-cytochrome c supercomplex. Thus far, elamipretide has been shown to increase left ventricular ejection fraction in dog models of heart failure with reduced ejection fraction and to prevent left ventricular remodeling in rats. In early-phase clinical trials, elamipretide administration has not resulted in any severe adverse events, and it has shown promising improvements in cardiac hemodynamics at highest doses. Nonetheless, additional studies are necessary to describe the long-term safety and efficacy of elamipretide.
Collapse
|
33
|
Palevich N, Maclean PH. Sequencing and Reconstructing Helminth Mitochondrial Genomes Directly from Genomic Next-Generation Sequencing Data. Methods Mol Biol 2022; 2369:27-40. [PMID: 34313982 DOI: 10.1007/978-1-0716-1681-9_3] [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] [Indexed: 02/09/2023]
Abstract
We present a detailed method for extraction of high-molecular weight genomic DNA suitable for numerous DNA sequencing applications, and a straightforward in silico approach for reconstructing novel mitochondrial (mt) genomes directly from total genomic DNA extracts derived from next-generation sequencing (NGS) data sets. The in silico post-sequencing pipeline described is fast, accurate, and highly efficient, with modest memory requirements that can be performed using a standard desktop computer. The approach is particularly effective for obtaining mitochondrial genomes for species with little or no mitochondrial sequence information currently available and overcomes many of the limitations of traditional strategies. The described methodologies are also applicable for metagenomics sequencing from mixed or pooled samples containing multiple species and subsequent specific assembly of specific mitochondrial genomes.
Collapse
Affiliation(s)
- Nikola Palevich
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand.
| | - Paul Haydon Maclean
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| |
Collapse
|
34
|
Varunjikar MS, Moreno-Ibarguen C, Andrade-Martinez JS, Tung HS, Belghit I, Palmblad M, Olsvik PA, Reyes A, Rasinger JD, Lie KK. Comparing novel shotgun DNA sequencing and state-of-the-art proteomics approaches for authentication of fish species in mixed samples. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108417] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
35
|
Song MH, Yan C, Li JT. MEANGS: an efficient seed-free tool for de novo assembling animal mitochondrial genome using whole genome NGS data. Brief Bioinform 2021; 23:6481918. [PMID: 34941991 DOI: 10.1093/bib/bbab538] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/23/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
Advances in next-generation sequencing (NGS) technologies have led to an exponential increase in the number of whole genome sequences (WGS) in databases. This wealth of WGS data has greatly facilitated the recovery of full mitochondrial genomes (mitogenomes), which are vital for phylogenetic, evolutionary and ecological studies. Unfortunately, most existing software cannot easily assemble mitogenome reference sequences conveniently or efficiently. Therefore, we developed a seed-free de novo assembly tool, MEANGS, which applies the trie-search method to extend contigs from self-discovery seeds and assemble a mitogenome from animal WGS data. We then used data from 16 species with different qualities to compare the performance of MEANGS with three other available programs. MEANGS exhibited the best overall performance since it was the only one that completed all tests, and it assembled full or partial mitogenomes for all of the tested samples while the others failed. Furthermore, MEANGS selects superior assembly sequences and annotates protein-coding genes. Thus, MEANGS can be one of the most efficient software for generating high-quality mitogenomes so far, the further use of it will benefit the study on mitogenome based on whole genome NGS data. MEANGS is available at https://github.com/YanCCscu/meangs.
Collapse
Affiliation(s)
- Meng-Huan Song
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| | - Jia-Tang Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610040, China
| |
Collapse
|
36
|
Holt AG, Davies AM. The Effect of Mitochondrial DNA Half-Life on Deletion Mutation Proliferation in Long Lived Cells. Acta Biotheor 2021; 69:671-695. [PMID: 34131800 DOI: 10.1007/s10441-021-09417-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/07/2021] [Indexed: 01/21/2023]
Abstract
The proliferation of mitochondrial DNA (mtDNA) with deletion mutations has been linked to aging and age related neurodegenerative conditions. In this study we model the effect of mtDNA half-life on mtDNA competition and selection. It has been proposed that mutation deletions ([Formula: see text]) have a replicative advantage over wild-type ([Formula: see text]) and that this is detrimental to the host cell, especially in post-mitotic cells. An individual cell can be viewed as forming a closed ecosystem containing a large population of independently replicating mtDNA. Within this enclosed environment a selfishly replicating [Formula: see text] would compete with the [Formula: see text] for space and resources to the detriment of the host cell. In this paper, we use a computer simulation to model cell survival in an environment where [Formula: see text] compete with [Formula: see text] such that the cell expires upon [Formula: see text] extinction. We focus on the survival time for long lived post-mitotic cells, such as neurons. We confirm previous observations that [Formula: see text] do have a replicative advantage over [Formula: see text]. As expected, cell survival times diminished with increased mutation probabilities, however, the relationship between survival time and mutation rate was non-linear, that is, a ten-fold increase in mutation probability only halved the survival time. The results of our model also showed that a modest increase in half-life had a profound affect on extending cell survival time, thereby, mitigating the replicative advantage of [Formula: see text]. Given the relevance of mitochondrial dysfunction to various neurodegenerative conditions, we propose that therapies to increase mtDNA half-life could significantly delay their onset.
Collapse
|
37
|
Hu Y, Zhang X, Wang O, Xing X, Cui M, Wang M, Song C, Liao Q. Spectrum of mitochondrial genomic variation in parathyroid neoplasms. Endocrine 2021; 74:690-697. [PMID: 34296389 DOI: 10.1007/s12020-021-02825-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/10/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE Mitochondrial DNA (mtDNA) variations have been implicated in various cancer types. Several attempts have been made in benign parathyroid adenoma (PA); however, mtDNA variants and copy number alterations have not been investigated in parathyroid carcinoma (PC). The present study aimed to explore the variations in the mitochondrial genome in parathyroid neoplasms. METHODS In this study, ultradeep targeted sequencing of mtDNA was performed in 12 cases with PC and 25 cases with PA. Germline and somatic variants in the mitochondrial genome were analysed according to clinical features. The mtDNA copy number relative to nuclear DNA was measured. RESULTS A total of 821 germline variants and 23 somatic mutations were identified. All 160 germline nonsynonymous variants in the coding sequence (CDS) were predicted to be likely benign, and germline variants frequently occurred (26.3%) in the displacement loop region. Tumour somatic mutation in a CDS with heteroplasmic factor (HF) >0.8 showed a higher mtDNA copy number (p = 0.039). Using Spearman's rank test, tumour mtDNA copy number revealed a positive correlation with serum levels of intact parathyroid hormone and calcium. CONCLUSION Our results demonstrate that null recurrent mtDNA mutational hotspots were PC specific. An increased mtDNA copy number in parathyroid neoplasms was associated with somatic CDS mutations with a high HF and major clinical features. Larger cohort investigations should be performed in future analyses.
Collapse
Affiliation(s)
- Ya Hu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiang Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ou Wang
- Department of Endocrinology, Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoping Xing
- Department of Endocrinology, Laboratory of Endocrinology, National Health Commission, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ming Cui
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Mengyi Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Chengli Song
- Novogene Bioinformatics Institute, Beijing, China
| | - Quan Liao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
| |
Collapse
|
38
|
Calarco CA, Fox ME, Van Terheyden S, Turner MD, Alipio JB, Chandra R, Lobo MK. Mitochondria-Related Nuclear Gene Expression in the Nucleus Accumbens and Blood Mitochondrial Copy Number After Developmental Fentanyl Exposure in Adolescent Male and Female C57BL/6 Mice. Front Psychiatry 2021; 12:737389. [PMID: 34867530 PMCID: PMC8637046 DOI: 10.3389/fpsyt.2021.737389] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/06/2021] [Indexed: 12/21/2022] Open
Abstract
The potency of the synthetic opioid fentanyl and its increased clinical availability has led to the rapid escalation of use in the general population, increased recreational exposure, and subsequently opioid-related overdoses. The wide-spread use of fentanyl has, consequently, increased the incidence of in utero exposure to the drug, but the long-term effects of this type of developmental exposure are not yet understood. Opioid use has also been linked to reduced mitochondrial copy number in blood in clinical populations, but the link between this peripheral biomarker and genetic or functional changes in reward-related brain circuitry is still unclear. Additionally, mitochondrial-related gene expression in reward-related brain regions has not been examined in the context of fentanyl exposure, despite the growing literature demonstrating drugs of abuse impact mitochondrial function, which subsequently impacts neuronal signaling. The current study uses exposure to fentanyl via dam access to fentanyl drinking water during gestation and lactation as a model for developmental drug exposure. This perinatal drug-exposure is sufficient to impact mitochondrial copy number in circulating blood leukocytes, as well as mitochondrial-related gene expression in the nucleus accumbens (NAc), a reward-related brain structure, in a sex-dependent manner in adolescent offspring. Specific NAc gene expression is correlated with both blood mitochondrial copy number and with anxiety related behaviors dependent on developmental exposure to fentanyl and sex. These data indicate that developmental fentanyl exposure impacts mitochondrial function in both the brain and body in ways that can impact neuronal signaling and may prime the brain for altered reward-related behavior in adolescence and later into adulthood.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Mary Kay Lobo
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States
| |
Collapse
|
39
|
Ivanov AV, Popravko DS, Safenkova IV, Zvereva EA, Dzantiev BB, Zherdev AV. Rapid Full-Cycle Technique to Control Adulteration of Meat Products: Integration of Accelerated Sample Preparation, Recombinase Polymerase Amplification, and Test-Strip Detection. Molecules 2021; 26:6804. [PMID: 34833896 PMCID: PMC8622786 DOI: 10.3390/molecules26226804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 12/01/2022] Open
Abstract
Verifying the authenticity of food products is essential due to the recent increase in counterfeit meat-containing food products. The existing methods of detection have a number of disadvantages. Therefore, simple, cheap, and sensitive methods for detecting various types of meat are required. In this study, we propose a rapid full-cycle technique to control the chicken or pig adulteration of meat products, including 3 min of crude DNA extraction, 20 min of recombinase polymerase amplification (RPA) at 39 °C, and 10 min of lateral flow assay (LFA) detection. The cytochrome B gene was used in the developed RPA-based test for chicken and pig identification. The selected primers provided specific RPA without DNA nuclease and an additional oligonucleotide probe. As a result, RPA-LFA, based on designed fluorescein- and biotin-labeled primers, detected up to 0.2 pg total DNA per μL, which provided up to 0.001% w/w identification of the target meat component in the composite meat. The RPA-LFA of the chicken and pig meat identification was successfully applied to processed meat products and to meat after heating. The results were confirmed by real-time PCR. Ultimately, the developed analysis is specific and enables the detection of pork and chicken impurities with high accuracy in raw and processed meat mixtures. The proposed rapid full-cycle technique could be adopted for the authentication of other meat products.
Collapse
Affiliation(s)
| | | | | | | | | | - Anatoly V. Zherdev
- Research Centre of Biotechnology, A.N. Bach Institute of Biochemistry, Russian Academy of Sciences, Leninsky Prospect 33, 119071 Moscow, Russia; (A.V.I.); (D.S.P.); (I.V.S.); (E.A.Z.); (B.B.D.)
| |
Collapse
|
40
|
Chella Krishnan K, Vergnes L, Acín-Pérez R, Stiles L, Shum M, Ma L, Mouisel E, Pan C, Moore TM, Péterfy M, Romanoski CE, Reue K, Björkegren JLM, Laakso M, Liesa M, Lusis AJ. Sex-specific genetic regulation of adipose mitochondria and metabolic syndrome by Ndufv2. Nat Metab 2021; 3:1552-1568. [PMID: 34697471 PMCID: PMC8909918 DOI: 10.1038/s42255-021-00481-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 09/17/2021] [Indexed: 12/28/2022]
Abstract
We have previously suggested a central role for mitochondria in the observed sex differences in metabolic traits. However, the mechanisms by which sex differences affect adipose mitochondrial function and metabolic syndrome are unclear. Here we show that in both mice and humans, adipose mitochondrial functions are elevated in females and are strongly associated with adiposity, insulin resistance and plasma lipids. Using a panel of diverse inbred strains of mice, we identify a genetic locus on mouse chromosome 17 that controls mitochondrial mass and function in adipose tissue in a sex- and tissue-specific manner. This locus contains Ndufv2 and regulates the expression of at least 89 mitochondrial genes in females, including oxidative phosphorylation genes and those related to mitochondrial DNA content. Overexpression studies indicate that Ndufv2 mediates these effects by regulating supercomplex assembly and elevating mitochondrial reactive oxygen species production, which generates a signal that increases mitochondrial biogenesis.
Collapse
Affiliation(s)
- Karthickeyan Chella Krishnan
- Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA.
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA, USA.
| | - Laurent Vergnes
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Rebeca Acín-Pérez
- Department of Medicine/Division of Endocrinology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Linsey Stiles
- Department of Medicine/Division of Endocrinology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Michael Shum
- Department of Medicine/Division of Endocrinology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular Medicine, Faculty of Medicine, Universite Laval, Quebec City, Quebec, Canada
| | - Lijiang Ma
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Etienne Mouisel
- INSERM, UMR1297, Institute of Metabolic and Cardiovascular Diseases, University of Toulouse, Paul Sabatier University, Toulouse, France
| | - Calvin Pan
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Timothy M Moore
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA, USA
| | - Miklós Péterfy
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA, USA
- College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, USA
| | - Casey E Romanoski
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, AZ, USA
| | - Karen Reue
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Johan L M Björkegren
- Department of Genetics and Genomic Sciences, The Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Integrated Cardio Metabolic Centre, Department of Medicine, Karolinska Institutet, Karolinska Universitetssjukhuset, Huddinge, Sweden
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio, Finland
| | - Marc Liesa
- Department of Medicine/Division of Endocrinology, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aldons J Lusis
- Department of Medicine/Division of Cardiology, University of California, Los Angeles, CA, USA.
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA, USA.
| |
Collapse
|
41
|
Stauffer S, Jucker M, Keggin T, Marques V, Andrello M, Bessudo S, Cheutin M, Borrero‐Pérez GH, Richards E, Dejean T, Hocdé R, Juhel J, Ladino F, Letessier TB, Loiseau N, Maire E, Mouillot D, Mutis Martinezguerra M, Manel S, Polanco Fernández A, Valentini A, Velez L, Albouy C, Pellissier L, Waldock C. How many replicates to accurately estimate fish biodiversity using environmental DNA on coral reefs? Ecol Evol 2021; 11:14630-14643. [PMID: 34765130 PMCID: PMC8571620 DOI: 10.1002/ece3.8150] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/31/2021] [Accepted: 09/08/2021] [Indexed: 01/22/2023] Open
Abstract
Quantifying fish species diversity in rich tropical marine environments remains challenging. Environmental DNA (eDNA) metabarcoding is a promising tool to face this challenge through the filtering, amplification, and sequencing of DNA traces from water samples. However, because eDNA concentration is low in marine environments, the reliability of eDNA to detect species diversity can be limited. Using an eDNA metabarcoding approach to identify fish Molecular Taxonomic Units (MOTUs) with a single 12S marker, we aimed to assess how the number of sampling replicates and filtered water volume affect biodiversity estimates. We used a paired sampling design of 30 L per replicate on 68 reef transects from 8 sites in 3 tropical regions. We quantified local and regional sampling variability by comparing MOTU richness, compositional turnover, and compositional nestedness. We found strong turnover of MOTUs between replicated pairs of samples undertaken in the same location, time, and conditions. Paired samples contained non-overlapping assemblages rather than subsets of one another. As a result, non-saturated localized diversity accumulation curves suggest that even 6 replicates (180 L) in the same location can underestimate local diversity (for an area <1 km). However, sampling regional diversity using ~25 replicates in variable locations (often covering 10 s of km) often saturated biodiversity accumulation curves. Our results demonstrate variability of diversity estimates possibly arising from heterogeneous distribution of eDNA in seawater, highly skewed frequencies of eDNA traces per MOTU, in addition to variability in eDNA processing. This high compositional variability has consequences for using eDNA to monitor temporal and spatial biodiversity changes in local assemblages. Avoiding false-negative detections in future biomonitoring efforts requires increasing replicates or sampled water volume to better inform management of marine biodiversity using eDNA.
Collapse
Affiliation(s)
- Salomé Stauffer
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Meret Jucker
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | - Thomas Keggin
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Virginie Marques
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Marco Andrello
- Institute for the Study of Anthropic Impacts and Sustainability in the Marine EnvironmentNational Research CouncilRomeItaly
| | - Sandra Bessudo
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | | | - Giomar Helena Borrero‐Pérez
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Eilísh Richards
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
| | | | - Régis Hocdé
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | | | - Felipe Ladino
- Fundación Malpelo y otros ecosistemas marinosBogotáColombia
| | - Tom B. Letessier
- Institute of ZoologyZoological Society of LondonLondonUK
- Marine Futures LabUniversity of Western AustraliaCrawleyWAAustralia
| | | | - Eva Maire
- Lancaster Environment CentreLancaster UniversityLancasterUK
| | | | - Maria Mutis Martinezguerra
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | - Stéphanie Manel
- CEFEUniv. MontpellierCNRSEPHE‐PSL UniversityIRDUniv. Paul Valéry Montpellier 3MontpellierFrance
| | - Andrea Polanco Fernández
- Instituto de Investigaciones Marinas y Costeras‐INVEMAR Museo de Historia Natural Marina de Colombia (MHNMC)Santa MartaColombia
| | | | - Laure Velez
- MARBECUniv. MontpellierCNRSIFREMERIRDMontpellierFrance
| | - Camille Albouy
- IFREMERunité Écologie et Modèles pour l’HalieutiqueNantesFrance
| | - Loïc Pellissier
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Conor Waldock
- Landscape EcologyInstitute of Terrestrial EcosystemsDepartment of Environmental Systems ScienceETH ZürichZürichSwitzerland
- Unit of Land Change ScienceSwiss Federal Research Institute WSLBirmensdorfSwitzerland
| |
Collapse
|
42
|
Abstract
Mitochondria are considered to be the powerhouse of the cell. Normal functioning of the mitochondria is not only essential for cellular energy production but also for several immunomodulatory processes. Macrophages operate in metabolic niches and rely on rapid adaptation to specific metabolic conditions such as hypoxia, nutrient limitations, or reactive oxygen species to neutralize pathogens. In this regard, the fast reprogramming of mitochondrial metabolism is indispensable to provide the cells with the necessary energy and intermediates to efficiently mount the inflammatory response. Moreover, mitochondria act as a physical scaffold for several proteins involved in immune signaling cascades and their dysfunction is immediately associated with a dampened immune response. In this review, we put special focus on mitochondrial function in macrophages and highlight how mitochondrial metabolism is involved in macrophage activation.
Collapse
Affiliation(s)
- Mohamed Zakaria Nassef
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Jasmin E Hanke
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| | - Karsten Hiller
- Department of Bioinformatics and Biochemistry, Braunschweig Integrated Center of Systems Biology (BRICS), Technische Universität Braunschweig, Brunswick, Germany
| |
Collapse
|
43
|
Fan HC, Lee HF, Yue CT, Chi CS. Clinical Characteristics of Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-Like Episodes. Life (Basel) 2021; 11:life11111111. [PMID: 34832987 PMCID: PMC8617702 DOI: 10.3390/life11111111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome, a maternally inherited mitochondrial disorder, is characterized by its genetic, biochemical and clinical complexity. The most common mutation associated with MELAS syndrome is the mtDNA A3243G mutation in the MT-TL1 gene encoding the mitochondrial tRNA-leu(UUR), which results in impaired mitochondrial translation and protein synthesis involving the mitochondrial electron transport chain complex subunits, leading to impaired mitochondrial energy production. Angiopathy, either alone or in combination with nitric oxide (NO) deficiency, further contributes to multi-organ involvement in MELAS syndrome. Management for MELAS syndrome is amostly symptomatic multidisciplinary approach. In this article, we review the clinical presentations, pathogenic mechanisms and options for management of MELAS syndrome.
Collapse
Affiliation(s)
- Hueng-Chuen Fan
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
- Department of Medical Research, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan
- Department of Rehabilitation, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiu-Fen Lee
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung 407, Taiwan;
| | - Chen-Tang Yue
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
| | - Ching-Shiang Chi
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
- Correspondence: ; Tel.: +886-4-26581919-4301
| |
Collapse
|
44
|
García-Olivares V, Muñoz-Barrera A, Lorenzo-Salazar JM, Zaragoza-Trello C, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Iñigo-Campos A, González-Montelongo R, Flores C. A benchmarking of human mitochondrial DNA haplogroup classifiers from whole-genome and whole-exome sequence data. Sci Rep 2021; 11:20510. [PMID: 34654896 PMCID: PMC8519921 DOI: 10.1038/s41598-021-99895-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 09/28/2021] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial genome (mtDNA) is of interest for a range of fields including evolutionary, forensic, and medical genetics. Human mitogenomes can be classified into evolutionary related haplogroups that provide ancestral information and pedigree relationships. Because of this and the advent of high-throughput sequencing (HTS) technology, there is a diversity of bioinformatic tools for haplogroup classification. We present a benchmarking of the 11 most salient tools for human mtDNA classification using empirical whole-genome (WGS) and whole-exome (WES) short-read sequencing data from 36 unrelated donors. We also assessed the best performing tool in third-generation long noisy read WGS data obtained with nanopore technology for a subset of the donors. We found that, for short-read WGS, most of the tools exhibit high accuracy for haplogroup classification irrespective of the input file used for the analysis. However, for short-read WES, Haplocheck and MixEmt were the most accurate tools. Based on the performance shown for WGS and WES, and the accompanying qualitative assessment, Haplocheck stands out as the most complete tool. For third-generation HTS data, we also showed that Haplocheck was able to accurately retrieve mtDNA haplogroups for all samples assessed, although only after following assembly-based approaches (either based on a referenced-based assembly or a hybrid de novo assembly). Taken together, our results provide guidance for researchers to select the most suitable tool to conduct the mtDNA analyses from HTS data.
Collapse
Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - José M Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | | | - Luis A Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico Y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain.
- Instituto de Tecnologías Biomédicas (ITB), Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.
| |
Collapse
|
45
|
Mori C, Matsumura S. Development and validation of simultaneous identification of 26 mammalian and poultry species by a multiplex assay. Int J Legal Med 2021; 136:1-12. [PMID: 34626212 DOI: 10.1007/s00414-021-02711-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022]
Abstract
A multiplex PCR assay was developed to simultaneously identify 22 mammalian species (alpaca, Asiatic black bear, Bactrian camel, brown rat, cat, cattle, common raccoon, dog, European rabbit, goat, horse, house mouse, human, Japanese badger, Japanese wild boar, masked palm civet, pig, raccoon dog, red fox, sheep, Siberian weasel, and sika deer) and four poultry species (chicken, domestic turkey, Japanese quail, and mallard), even from a biological sample containing a DNA mixture of multiple species. The assay was designed to identify species through multiplex PCR and capillary electrophoresis, with a combination of amplification of a partial region of the mitochondrial D-loop by universal primer sets and a partial region of the cytochrome b (cyt b) gene by species-specific primer sets. The assay was highly sensitive, with a detection limit of 100 copies of mitochondrial DNA. The assay's ability to identify species from complex DNA mixtures was demonstrated using an experimental sample consisting of 10 species. Efficacy, accuracy, and reliability of the assay were validated for use in forensic analysis with the guidelines of Scientific Working Group on DNA Analysis Methods (SWGDAM). The multiplex PCR assay developed in this study enables cost-effective, highly sensitive, and simultaneous species identification without massively parallel sequencing (MPS) platforms. Thus, the technique described is straightforward and suitable for routine forensic investigations.
Collapse
Affiliation(s)
- Chikahiro Mori
- The United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan. .,Forensic Science Laboratory, Gifu Prefectural Police Headquarters, 2-1-1 Yabutaminami, Gifu, 500-8501, Japan.
| | - Shuichi Matsumura
- Faculty of Applied Biological Sciences, Gifu University, 1-1 Yanagido, Gifu, 501-1193, Japan
| |
Collapse
|
46
|
Wanner N, Larsen PA, McLain A, Faulk C. The mitochondrial genome and Epigenome of the Golden lion Tamarin from fecal DNA using Nanopore adaptive sequencing. BMC Genomics 2021; 22:726. [PMID: 34620074 PMCID: PMC8499546 DOI: 10.1186/s12864-021-08046-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 09/29/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. RESULTS Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3' side of several coding regions. CONCLUSIONS Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
Collapse
Affiliation(s)
- Nicole Wanner
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN USA
| | - Adam McLain
- Department of Biology and Chemistry, College of Arts and Sciences, SUNY Polytechnic Institute, Utica, NY USA
| | - Christopher Faulk
- Department of Animal Sciences, University of Minnesota, College of Food, Agricultural, and Natural Resource Sciences, 1988 Fitch Ave., Saint Paul, MN 55108 USA
| |
Collapse
|
47
|
Garoña A, Hülter NF, Romero Picazo D, Dagan T. Segregational drift constrains the evolutionary rate of prokaryotic plasmids. Mol Biol Evol 2021; 38:5610-5624. [PMID: 34550379 PMCID: PMC8662611 DOI: 10.1093/molbev/msab283] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Plasmids are extrachromosomal genetic elements in prokaryotes that have been recognized as important drivers of microbial ecology and evolution. Plasmids are found in multiple copies inside their host cell where independent emergence of mutations may lead to intracellular genetic heterogeneity. The intracellular plasmid diversity is thus subject to changes upon cell division. However, the effect of plasmid segregation on plasmid evolution remains understudied. Here, we show that genetic drift during cell division—segregational drift—leads to the rapid extinction of novel plasmid alleles. We established a novel experimental approach to control plasmid allele frequency at the levels of a single cell and the whole population. Following the dynamics of plasmid alleles in an evolution experiment, we find that the mode of plasmid inheritance—random or clustered—is an important determinant of plasmid allele dynamics. Phylogenetic reconstruction of our model plasmid in clinical isolates furthermore reveals a slow evolutionary rate of plasmid-encoded genes in comparison to chromosomal genes. Our study provides empirical evidence that genetic drift in plasmid evolution occurs at multiple levels: the host cell and the population of hosts. Segregational drift has implications for the evolutionary rate heterogeneity of extrachromosomal genetic elements.
Collapse
Affiliation(s)
- Ana Garoña
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
| | - Nils F Hülter
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
| | | | - Tal Dagan
- Institute of General Microbiology, Kiel University, Kiel, 24118, Germany
| |
Collapse
|
48
|
Ghemrawi M, Fischinger F, Duncan G, Dukes MJ, Guilliano M, McCord B. Developmental validation of SpeID: A pyrosequencing-based assay for species identification. Forensic Sci Int Genet 2021; 55:102560. [PMID: 34507077 DOI: 10.1016/j.fsigen.2021.102560] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/16/2021] [Accepted: 06/30/2021] [Indexed: 11/19/2022]
Abstract
In crime scenes, biological exhibits are often human in origin, yet biological stains from other fauna may also be present at a crime scene, creating confusion during an investigation. Furthermore, identifying the source of a biological sample can be critical during an investigation. To identify the presence of biological material from non-human sources, it is common to use genetic markers within mitochondrial DNA such as cytochrome b, 16S rRNA, and 12S rRNA genes. This process usually requires DNA sequencing, a process that is neither quick nor easy. In general, a faster, more standardized method for species identification from tissue and body fluids is desirable.For this reason, we have developed a vertebrate specific real-time quantitation method that is followed by an automated pyrosequencing-based procedure that sequences a short fragment within the 12S rRNA gene. Using no more than 35 bases, the assay can distinguish between 32 different species commonly found in and around a household with a turnaround time of 6 h from extraction to sequencing. -Using this procedure, up to 48 samples can be run at a time without the need for expensive reagents or bioinformatic skills.
Collapse
Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States
| | | | - George Duncan
- Nova Southeastern University, Dania Beach, Fl 33004, United State
| | | | | | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, United States.
| |
Collapse
|
49
|
Alikhani M, Touati E, Karimipoor M, Vosough M, Mohammadi M. Mitochondrial DNA Copy Number Variations in Gastrointestinal Tract Cancers: Potential Players. J Gastrointest Cancer 2021; 53:770-781. [PMID: 34486088 DOI: 10.1007/s12029-021-00707-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Alterations of mitochondria have been linked to several cancers. Also, the mitochondrial DNA copy number (mtDNA-CN) is altered in various cancers, including gastrointestinal tract (GIT) cancers, and several research groups have investigated its potential as a cancer biomarker. However, the exact causes of mtDNA-CN variations are not yet revealed. This review discussed the conceivable players in this scheme, including reactive oxygen species (ROS), mtDNA genetic variations, DNA methylation, telomere length, autophagy, immune system activation, aging, and infections, and discussed their possible impact in the initiation and progression of cancer. By further exploring such mechanisms, mtDNA-CN variations may be effectively utilized as cancer biomarkers and provide grounds for developing novel cancer therapeutic agents.
Collapse
Affiliation(s)
- Mehdi Alikhani
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Eliette Touati
- Unit of Helicobacter Pathogenesis, Department of Microbiology, CNRS UMR2001, Institut Pasteur, 25-28 Rue du Dr Roux cedex 15, 75724, Paris, France
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Massoud Vosough
- Department of Regenerative Medicine, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Marjan Mohammadi
- Medical Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
50
|
Yang Z, Slone J, Wang X, Zhan J, Huang Y, Namjou B, Kaufman KM, Pauciulo M, Harley JB, Muglia LJ, Chepelev I, Huang T. Validation of low-coverage whole-genome sequencing for mitochondrial DNA variants suggests mitochondrial DNA as a genetic cause of preterm birth. Hum Mutat 2021; 42:1602-1614. [PMID: 34467602 PMCID: PMC9290920 DOI: 10.1002/humu.24279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/06/2023]
Abstract
Preterm birth (PTB), or birth that occurs earlier than 37 weeks of gestational age, is a major contributor to infant mortality and neonatal hospitalization. Mutations in the mitochondrial genome (mtDNA) have been linked to various rare mitochondrial disorders and may be a contributing factor in PTB given that maternal genetic factors have been strongly linked to PTB. However, to date, no study has found a conclusive connection between a particular mtDNA variant and PTB. Given the high mtDNA copy number per cell, an automated pipeline was developed for detecting mtDNA variants using low‐coverage whole‐genome sequencing (lcWGS) data. The pipeline was first validated against samples of known heteroplasmy, and then applied to 929 samples from a PTB cohort from diverse ethnic backgrounds with an average gestational age of 27.18 weeks (range: 21–30). Our new pipeline successfully identified haplogroups and a large number of mtDNA variants in this large PTB cohort, including 8 samples carrying known pathogenic variants and 47 samples carrying rare mtDNA variants. These results confirm that lcWGS can be utilized to reliably identify mtDNA variants. These mtDNA variants may make a contribution toward preterm birth in a small proportion of live births.
Collapse
Affiliation(s)
- Zeyu Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jack Zhan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Michael Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| |
Collapse
|