1
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Braveman P, Heck K, Dominguez TP, Marchi K, Burke W, Holm N. African immigrants' favorable preterm birth rates challenge genetic etiology of the Black-White disparity in preterm birth. Front Public Health 2024; 11:1321331. [PMID: 38239790 PMCID: PMC10794556 DOI: 10.3389/fpubh.2023.1321331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 12/07/2023] [Indexed: 01/22/2024] Open
Abstract
Background We examined over a million California birth records for 2010 through 2021 to investigate whether disparities in preterm birth (PTB) by nativity and race support the widely held but hitherto unsubstantiated belief that genetic differences explain the persistent Black-White disparity in PTB. Methods We examined PTB rates and risk ratios among African-, Caribbean-, and U.S.-born Black women compared to U.S.-born White women. Multivariate analyses adjusted for maternal age, education, number of live births, delivery payer, trimester of prenatal care initiation, pre-pregnancy BMI, smoking, and prevalence of poverty in a woman's residence census tract; and for paternal education. Results In adjusted analyses, African-born Black women's PTB rates were no different from those of U.S.-born White women. Discussion The results add to prior evidence making a genetic etiology for the racial disparity in PTB unlikely. If genetic differences tied to "race" explained the Black-White disparity in PTB among U.S.-born women, the African immigrants in this study would have had higher rates of PTB, not the lower rates observed. Multiple explanations for the observed patterns and their implications are discussed. Failure to distinguish causes of PTB from causes of the racial disparity in PTB have likely contributed to erroneous attribution of the racial disparity to genetic differences. Based on the literature, unmeasured experiences of racism, including racism-related stress and adverse environmental exposures, are plausible explanations for the PTB disparity between Black and White U.S.-born women. The favorable birth outcomes of African-born Black immigrants may reflect less exposure to racism during sensitive life periods, e.g., childhood, when they were in African countries, where Black people are in the racial majority.
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Affiliation(s)
- Paula Braveman
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Katherine Heck
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Tyan Parker Dominguez
- Suzanne Dworak-Peck School of Social Work, University of Southern California, Los Angeles, CA, United States
| | - Kristen Marchi
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Wylie Burke
- Department of Bioethics and Humanities, University of Washington, Seattle, Washington, DC, United States
| | - Nicole Holm
- Department of Family and Community Medicine, University of California, San Francisco, San Francisco, CA, United States
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2
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Zaidi AA, Verma A, Morse C, Ritchie MD, Mathieson I. The genetic and phenotypic correlates of mtDNA copy number in a multi-ancestry cohort. HGG ADVANCES 2023; 4:100202. [PMID: 37255673 PMCID: PMC10225932 DOI: 10.1016/j.xhgg.2023.100202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/25/2023] [Indexed: 06/01/2023] Open
Abstract
Mitochondrial DNA copy number (mtCN) is often treated as a proxy for mitochondrial (dys-) function and disease risk. Pathological changes in mtCN are common symptoms of rare mitochondrial disorders, but reported associations between mtCN and common diseases vary across studies. To understand the biology of mtCN, we carried out genome- and phenome-wide association studies of mtCN in 30,666 individuals from the Penn Medicine BioBank (PMBB)-a diverse cohort of largely African and European ancestry. We estimated mtCN in peripheral blood using exome sequence data, taking cell composition into account. We replicated known genetic associations of mtCN in the PMBB and found that their effects are highly correlated between individuals of European and African ancestry. However, the heritability of mtCN was much higher among individuals of largely African ancestry ( h 2 = 0.3 ) compared with European ancestry individuals( h 2 = 0.1 ) . Admixture mapping suggests that there are undiscovered variants underlying mtCN that are differentiated in frequency between individuals with African and European ancestry. We show that mtCN is associated with many health-related phenotypes. We discovered robust associations between mtDNA copy number and diseases of metabolically active tissues, such as cardiovascular disease and liver damage, that were consistent across African and European ancestry individuals. Other associations, such as epilepsy and prostate cancer, were only discovered in either individuals with European or African ancestry but not both. We show that mtCN-phenotype associations can be sensitive to blood cell composition and environmental modifiers, explaining why such associations are inconsistent across studies. Thus, mtCN-phenotype associations must be interpreted with care.
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Affiliation(s)
- Arslan A. Zaidi
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anurag Verma
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Colleen Morse
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Penn Medicine BioBank
- Center for Translational Bioinformatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Marylyn D. Ritchie
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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3
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Torres-Gonzalez E, Makova KD. Exploring the Effects of Mitonuclear Interactions on Mitochondrial DNA Gene Expression in Humans. Front Genet 2022; 13:797129. [PMID: 35846132 PMCID: PMC9277102 DOI: 10.3389/fgene.2022.797129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Most mitochondrial protein complexes include both nuclear and mitochondrial gene products, which coevolved to work together. This coevolution can be disrupted due to disparity in genetic ancestry between the nuclear and mitochondrial genomes in recently admixed populations. Such mitonuclear DNA discordance might result in phenotypic effects. Several nuclear-encoded proteins regulate expression of mitochondrial DNA (mtDNA) genes. We hypothesized that mitonuclear DNA discordance affects expression of genes encoded by mtDNA. To test this, we utilized the data from the GTEx project, which contains expression levels for ∼100 African Americans and >600 European Americans. The varying proportion of African and European ancestry in recently admixed African Americans provides a range of mitonuclear discordance values, which can be correlated with mtDNA gene expression levels (adjusted for age and ischemic time). In contrast, European Americans did not undergo recent admixture. We demonstrated that, for most mtDNA protein-coding genes, expression levels in energetically-demanding tissues were lower in African Americans than in European Americans. Furthermore, gene expression levels were lower in individuals with higher mitonuclear discordance, independent of population. Moreover, we found a negative correlation between mtDNA gene expression and mitonuclear discordance. In African Americans, the average value of African ancestry was higher for nuclear-encoded mitochondrial than non-mitochondrial genes, facilitating a match in ancestry with the mtDNA and more optimal interactions. These results represent an example of a phenotypic effect of mitonuclear discordance on human admixed populations, and have potential biomedical applications.
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Affiliation(s)
| | - Kateryna D. Makova
- Department of Biology, The Pennsylvania State University, University Park, PA, United States
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4
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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.
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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
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5
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Spontaneous preterm birth: the underpinnings in the maternal and fetal genomes. NPJ Genom Med 2021; 6:43. [PMID: 34103530 PMCID: PMC8187433 DOI: 10.1038/s41525-021-00209-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 05/20/2021] [Indexed: 12/20/2022] Open
Abstract
Preterm birth (PTB) is a major cause of neonatal mortality and health complications in infants. Elucidation of its genetic underpinnings can lead to improved understanding of the biological mechanisms and boost the development of methods to predict PTB. Although recent genome-based studies of both mother and fetus have identified several genetic loci which might be implicated in PTB, these results suffer from a lack of consistency across multiple studies and populations. Moreover, results of functional validation of most of these findings are unavailable. Since medically indicated preterm deliveries have well-known heterogeneous causes, we have reviewed only those studies which investigated spontaneous preterm birth (sPTB) and have attempted to suggest probable biological mechanisms by which the implicated genetic factors might result in sPTB. We expect our review to provide a panoramic view of the genetics of sPTB.
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6
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Sendra L, García-Mares A, Herrero MJ, Aliño SF. Mitochondrial DNA Replacement Techniques to Prevent Human Mitochondrial Diseases. Int J Mol Sci 2021; 22:ijms22020551. [PMID: 33430493 PMCID: PMC7827455 DOI: 10.3390/ijms22020551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 01/27/2023] Open
Abstract
Background: Mitochondrial DNA (mtDNA) diseases are a group of maternally inherited genetic disorders caused by a lack of energy production. Currently, mtDNA diseases have a poor prognosis and no known cure. The chance to have unaffected offspring with a genetic link is important for the affected families, and mitochondrial replacement techniques (MRTs) allow them to do so. MRTs consist of transferring the nuclear DNA from an oocyte with pathogenic mtDNA to an enucleated donor oocyte without pathogenic mtDNA. This paper aims to determine the efficacy, associated risks, and main ethical and legal issues related to MRTs. Methods: A bibliographic review was performed on the MEDLINE and Web of Science databases, along with searches for related clinical trials and news. Results: A total of 48 publications were included for review. Five MRT procedures were identified and their efficacy was compared. Three main risks associated with MRTs were discussed, and the ethical views and legal position of MRTs were reviewed. Conclusions: MRTs are an effective approach to minimizing the risk of transmitting mtDNA diseases, but they do not remove it entirely. Global legal regulation of MRTs is required.
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Affiliation(s)
- Luis Sendra
- Unidad de Farmacogenética, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (L.S.); (S.F.A.)
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain;
| | - Alfredo García-Mares
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain;
| | - María José Herrero
- Unidad de Farmacogenética, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (L.S.); (S.F.A.)
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain;
- Correspondence: ; Tel.: +34-961-246-675
| | - Salvador F. Aliño
- Unidad de Farmacogenética, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (L.S.); (S.F.A.)
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, 46010 Valencia, Spain;
- Unidad de Farmacología Clínica, Área del Medicamento, Hospital Universitario y Politécnico La Fe, 46026 Valencia, Spain
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7
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Lien YC, Zhang Z, Barila G, Green-Brown A, Elovitz MA, Simmons RA. Intrauterine Inflammation Alters the Transcriptome and Metabolome in Placenta. Front Physiol 2020; 11:592689. [PMID: 33250783 PMCID: PMC7674943 DOI: 10.3389/fphys.2020.592689] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 10/12/2020] [Indexed: 01/22/2023] Open
Abstract
Placental insufficiency is implicated in spontaneous preterm birth (SPTB) associated with intrauterine inflammation. We hypothesized that intrauterine inflammation leads to deficits in the capacity of the placenta to maintain bioenergetic and metabolic stability during pregnancy ultimately resulting in SPTB. Using a mouse model of intrauterine inflammation that leads to preterm delivery, we performed RNA-seq and metabolomics studies to assess how intrauterine inflammation alters gene expression and/or modulates metabolite production and abundance in the placenta. 1871 differentially expressed genes were identified in LPS-exposed placenta. Among them, 1,149 and 722 transcripts were increased and decreased, respectively. Ingenuity pathway analysis showed alterations in genes and canonical pathways critical for regulating oxidative stress, mitochondrial function, metabolisms of glucose and lipids, and vascular reactivity in LPS-exposed placenta. Many upstream regulators and master regulators important for nutrient-sensing and mitochondrial function were also altered in inflammation exposed placentae, including STAT1, HIF1α, mTOR, AMPK, and PPARα. Comprehensive quantification of metabolites demonstrated significant alterations in the glucose utilization, metabolisms of branched-chain amino acids, lipids, purine and pyrimidine, as well as carbon flow in TCA cycle in LPS-exposed placenta compared to control placenta. The transcriptome and metabolome were also integrated to assess the interactions of altered genes and metabolites. Collectively, significant and biologically relevant alterations in the placenta transcriptome and metabolome were identified in placentae exposed to intrauterine inflammation. Altered mitochondrial function and energy metabolism may underline the mechanisms of inflammation-induced placental dysfunction.
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Affiliation(s)
- Yu-Chin Lien
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zhe Zhang
- Center for Biomedical Informatics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Guillermo Barila
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Amy Green-Brown
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Michal A Elovitz
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Rebecca A Simmons
- Department of Obstetrics and Gynecology, Maternal and Child Health Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.,Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
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8
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Qi L, Chen X, Wang J, Lv B, Zhang J, Ni B, Xue Z. Mitochondria: the panacea to improve oocyte quality? ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:789. [PMID: 32042805 DOI: 10.21037/atm.2019.12.02] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Oocyte quality is one of the most important factors involving in female reproduction. The number of compromised oocytes will increase with maternal age, while mitochondrial dysfunction has implicated in age-related poor oocyte. Together with the successful application of ooplasmic transfer (OT) and the critical role of mitochondria in the oocyte, functional mitochondria transfer may be a feasible strategy to improve oocyte quality. However, limitation on ethics and laws are strictly and optimal condition or methods to exert transferring need to be further explored. Therefore, the role of oocyte mitochondria and the effective molecular involving in oocyte quality will be hot topics in next few years. In this review, we summarize the potential mechanism of mitochondria in oocyte and embryo development and discuss the next step for mitochondrial transfer therapy.
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Affiliation(s)
- Lingbin Qi
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200092, China
| | - Xian Chen
- Shenzhen Key Laboratory for Reproductive Immunology of Peri-implantation, Shenzhen Zhongshan Institute for Reproduction and Genetics, Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen 518045, China
| | - Jian Wang
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200092, China
| | - Bo Lv
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200092, China
| | - Junhui Zhang
- Reproductive Medical Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei 230032, China
| | - Bin Ni
- NHC Key Laboratory of Birth Defect for Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Changsha 410008, China
| | - Zhigang Xue
- Department of Regenerative Medicine, Tongji University School of Medicine, Shanghai 200092, China.,Reproductive Medicine Center, Tongji Hospital, Tongji University School of Medicine, Shanghai 200065, China
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9
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Shtolz N, Mishmar D. The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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10
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Kaufman BA, Picard M, Sondheimer N. Mitochondrial DNA, nuclear context, and the risk for carcinogenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2019; 60:455-462. [PMID: 29332303 PMCID: PMC6045969 DOI: 10.1002/em.22169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/25/2017] [Accepted: 12/20/2017] [Indexed: 05/05/2023]
Abstract
The inheritance of mitochondrial DNA (mtDNA) from mother to child is complicated by differences in the stability of the mitochondrial genome. Although the germ line mtDNA is protected through the minimization of replication between generations, sequence variation can occur either through mutation or due to changes in the ratio between distinct genomes that are present in the mother (known as heteroplasmy). Thus, the unpredictability in transgenerational inheritance of mtDNA may cause the emergence of pathogenic mitochondrial and cellular phenotypes in offspring. Studies of the role of mitochondrial metabolism in cancer have a long and rich history, but recent evidence strongly suggests that changes in mitochondrial genotype and phenotype play a significant role in the initiation, progression and treatment of cancer. At the intersection of these two fields lies the potential for emerging mtDNA mutations to drive carcinogenesis in the offspring. In this review, we suggest that this facet of transgenerational carcinogenesis remains underexplored and is a potentially important contributor to cancer. Environ. Mol. Mutagen. 60:455-462, 2019. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Brett A. Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Vascular Medicine Institute, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA (USA)
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY 10032 USA
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Medical Center, New York, NY 10032 USA
- Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY 10032 USA
| | - Neal Sondheimer
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada M5G1X8
- Department of Paediatrics, The University of Toronto School of Medicine, Toronto, ON, Canada M5G1X8
- Correspondence to: Neal Sondheimer, 555 University Avenue, Toronto ON M5G 1X8, p – 416-813-7654 x 301480, f – 416-813-5345,
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11
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Abstract
The maternally inherited mitochondrial DNA (mtDNA) is located inside every mitochondrion, in variable number of copies, and it contains 37 crucial genes for cellular bioenergetics. This chapter will discuss the unique features of this circular genome including heteroplasmy, haplogroups, among others, along with the corresponding clinical relevance for each. The discussion also covers the nuclear-encoded mitochondrial genes (N > 1000) and the epistatic interactions between mtDNA and the nuclear genome. Examples of mitochondrial diseases related to specific mtDNA mutation sites of relevance for humans are provided. This chapter aims to provide an overview of mitochondrial genetics as an emerging hot topic for the future of medicine.
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Affiliation(s)
- Vanessa F Gonçalves
- Molecular Brain Sciences Department, Centre for Addiction and Mental Health, Toronto, Canada.
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12
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Naeem MM, Sondheimer N. Heteroplasmy Shifting as Therapy for Mitochondrial Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:257-267. [PMID: 31452145 DOI: 10.1007/978-981-13-8367-0_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial disease can arise due to pathogenic sequence variants in the mitochondrial DNA (mtDNA) that prevent cells from meeting their energy demands. Mitochondrial diseases are often fatal and currently there are no treatments directed towards the underlying cause of disease. Pathogenic variants in mtDNA often exist in a state of heteroplasmy, with coexistence of pathogenic and wild type mtDNA. The load of heteroplasmy, defined as the relative amount of pathogenic mtDNA to wild type mtDNA, corresponds to timing and symptom severity. Thus, changing the heteroplasmy load may lead to a shift in disease onset and symptom severity. Here we review techniques aimed at preventing inheritance of pathogenic mtDNA via mitochondrial replacement therapy (MRT) and strategies geared toward shifting of heteroplasmy in individuals with active mitochondrial disease. MRT strategies seek to create embryos with the nuclear genetic makeup of the intended parents and wild type mtDNA from a donor in order to avoid known maternal pathogenic variants. Heteroplasmy shift approaches in patients are of two categories: nuclease dependent and nuclease independent strategies. Despite initial success in mouse models and patient cells, these techniques have not reached clinical use. Translational attempts in this area are urgently needed to improve therapies for a currently untreatable set of disorders.
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Affiliation(s)
- Mansur M Naeem
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada
| | - Neal Sondheimer
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada.
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13
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Sirota M, Thomas CG, Liu R, Zuhl M, Banerjee P, Wong RJ, Quaintance CC, Leite R, Chubiz J, Anderson R, Chappell J, Kim M, Grobman W, Zhang G, Rokas A, England SK, Parry S, Shaw GM, Simpson JL, Thomson E, Butte AJ. Enabling precision medicine in neonatology, an integrated repository for preterm birth research. Sci Data 2018; 5:180219. [PMID: 30398470 PMCID: PMC6219406 DOI: 10.1038/sdata.2018.219] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/19/2018] [Indexed: 12/14/2022] Open
Abstract
Preterm birth, or the delivery of an infant prior to 37 weeks of gestation, is a significant cause of infant morbidity and mortality. In the last decade, the advent and continued development of molecular profiling technologies has enabled researchers to generate vast amount of 'omics' data, which together with integrative computational approaches, can help refine the current knowledge about disease mechanisms, diagnostics, and therapeutics. Here we describe the March of Dimes' Database for Preterm Birth Research (http://www.immport.org/resources/mod), a unique resource that contains a variety of 'omics' datasets related to preterm birth. The database is open publicly, and as of January 2018, links 13 molecular studies with data across tens of thousands of patients from 6 measurement modalities. The data in the repository are highly diverse and include genomic, transcriptomic, immunological, and microbiome data. Relevant datasets are augmented with additional molecular characterizations of almost 25,000 biological samples from public databases. We believe our data-sharing efforts will lead to enhanced research collaborations and coordination accelerating the overall pace of discovery in preterm birth research.
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Affiliation(s)
- Marina Sirota
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA.,Department of Pediatrics, University of California, San Francisco, CA 94158, USA
| | | | - Rebecca Liu
- Enterprise Science And Computing, Inc., Rockville, MD 20850, USA
| | - Maya Zuhl
- March of Dimes, White Plains, NY 10605, USA
| | | | - Ronald J Wong
- March of Dimes Prematurity Research Center at Stanford, Department of Pediatrics, Stanford University School of Medicine Stanford, CA 94305, USA
| | - Cecele C Quaintance
- March of Dimes Prematurity Research Center at Stanford, Department of Pediatrics, Stanford University School of Medicine Stanford, CA 94305, USA
| | - Rita Leite
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jessica Chubiz
- Department of Obstetrics and Gynecology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Rebecca Anderson
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Joanne Chappell
- Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Mara Kim
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - William Grobman
- Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60637, USA
| | - Ge Zhang
- Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA.,Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN 37212, USA
| | - Sarah K England
- Department of Obstetrics and Gynecology, Washington University in St Louis, St. Louis, MO 63110, USA
| | - Samuel Parry
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gary M Shaw
- March of Dimes Prematurity Research Center at Stanford, Department of Pediatrics, Stanford University School of Medicine Stanford, CA 94305, USA
| | | | | | - Atul J Butte
- Institute for Computational Health Sciences, University of California, San Francisco, CA 94158, USA.,Department of Pediatrics, University of California, San Francisco, CA 94158, USA
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14
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Zhang G, Srivastava A, Bacelis J, Juodakis J, Jacobsson B, Muglia LJ. Genetic studies of gestational duration and preterm birth. Best Pract Res Clin Obstet Gynaecol 2018; 52:33-47. [PMID: 30007778 PMCID: PMC6290110 DOI: 10.1016/j.bpobgyn.2018.05.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 04/18/2018] [Accepted: 05/04/2018] [Indexed: 01/12/2023]
Abstract
The fine control of birth timing is important to human survival and evolution. A key challenge in studying the mechanisms underlying the regulation of human birth timing is that human parturition is a unique to human event — animal models provide only limited information. The duration of gestation or the risk of preterm birth is a complex human trait under genetic control from both maternal and fetal genomes. Genomic discoveries through genome-wide association (GWA) studies would implicate relevant genes and pathways. Similar to other complex human traits, gestational duration is likely to be influenced by numerous genetic variants of small effect size. The detection of these small-effect genetic variants requires very large sample sizes. In addition, several practical and analytical challenges, in particular the involvement of both maternal and fetal genomes, further complicate the genetic studies of gestational duration and other pregnancy phenotypes. Despite these challenges, large-scale GWA studies have already identified several genomic loci associated with gestational duration or the risk of preterm birth. These genomic discoveries have revealed novel insights about the biology of human birth timing. Expanding genomic discoveries in larger datasets by more refined analytical approaches, together with the functional analysis of the identified genomic loci, will collectively elucidate the biological processes underlying the control of human birth timing.
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Affiliation(s)
- Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, USA; The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, USA; March of Dimes Prematurity Research Center Ohio Collaborative, USA; Department of Pediatrics, University of Cincinnati College of Medicine, USA.
| | - Amit Srivastava
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, USA; The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, USA; March of Dimes Prematurity Research Center Ohio Collaborative, USA; Department of Pediatrics, University of Cincinnati College of Medicine, USA
| | - Jonas Bacelis
- Department of Obstetrics and Gynecology, Sahlgrenska University Hospital Östra (East), Gothenburg, Sweden
| | - Julius Juodakis
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bo Jacobsson
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Genetics and Bioinformatics, Area of Health Data and Digitalisation, Norwegian Institute of Public Health, Oslo, Norway
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, USA; The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, USA; March of Dimes Prematurity Research Center Ohio Collaborative, USA; Department of Pediatrics, University of Cincinnati College of Medicine, USA
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