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Frye RE, Rincon N, McCarty PJ, Brister D, Scheck AC, Rossignol DA. Biomarkers of mitochondrial dysfunction in autism spectrum disorder: A systematic review and meta-analysis. Neurobiol Dis 2024; 197:106520. [PMID: 38703861 DOI: 10.1016/j.nbd.2024.106520] [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: 03/17/2024] [Revised: 04/27/2024] [Accepted: 04/29/2024] [Indexed: 05/06/2024] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder affecting 1 in 36 children and is associated with physiological abnormalities, most notably mitochondrial dysfunction, at least in a subset of individuals. This systematic review and meta-analysis discovered 204 relevant articles which evaluated biomarkers of mitochondrial dysfunction in ASD individuals. Significant elevations (all p < 0.01) in the prevalence of lactate (17%), pyruvate (41%), alanine (15%) and creatine kinase (9%) were found in ASD. Individuals with ASD had significant differences (all p < 0.01) with moderate to large effect sizes (Cohen's d' ≥ 0.6) compared to controls in mean pyruvate, lactate-to-pyruvate ratio, ATP, and creatine kinase. Some studies found abnormal TCA cycle metabolites associated with ASD. Thirteen controlled studies reported mitochondrial DNA (mtDNA) deletions or variations in the ASD group in blood, peripheral blood mononuclear cells, lymphocytes, leucocytes, granulocytes, and brain. Meta-analyses discovered significant differences (p < 0.01) in copy number of mtDNA overall and in ND1, ND4 and CytB genes. Four studies linked specific mtDNA haplogroups to ASD. A series of studies found a subgroup of ASD with elevated mitochondrial respiration which was associated with increased sensitivity of the mitochondria to physiological stressors and neurodevelopmental regression. Lactate, pyruvate, lactate-to-pyruvate ratio, carnitine, and acyl-carnitines were associated with clinical features such as delays in language, social interaction, cognition, motor skills, and with repetitive behaviors and gastrointestinal symptoms, although not all studies found an association. Lactate, carnitine, acyl-carnitines, ATP, CoQ10, as well as mtDNA variants, heteroplasmy, haplogroups and copy number were associated with ASD severity. Variability was found across biomarker studies primarily due to differences in collection and processing techniques as well as the intrinsic heterogeneity of the ASD population. Several studies reported alterations in mitochondrial metabolism in mothers of children with ASD and in neonates who develop ASD. Treatments targeting mitochondria, particularly carnitine and ubiquinol, appear beneficial in ASD. The link between mitochondrial dysfunction in ASD and common physiological abnormalities in individuals with ASD including gastrointestinal disorders, oxidative stress, and immune dysfunction is outlined. Several subtypes of mitochondrial dysfunction in ASD are discussed, including one related to neurodevelopmental regression, another related to alterations in microbiome metabolites, and another related to elevations in acyl-carnitines. Mechanisms linking abnormal mitochondrial function with alterations in prenatal brain development and postnatal brain function are outlined. Given the multisystem complexity of some individuals with ASD, this review presents evidence for the mitochondria being central to ASD by contributing to abnormalities in brain development, cognition, and comorbidities such as immune and gastrointestinal dysfunction as well as neurodevelopmental regression. A diagnostic approach to identify mitochondrial dysfunction in ASD is outlined. From this evidence, it is clear that many individuals with ASD have alterations in mitochondrial function which may need to be addressed in order to achieve optimal clinical outcomes. The fact that alterations in mitochondrial metabolism may be found during pregnancy and early in the life of individuals who eventually develop ASD provides promise for early life predictive biomarkers of ASD. Further studies may improve the understanding of the role of the mitochondria in ASD by better defining subgroups and understanding the molecular mechanisms driving some of the unique changes found in mitochondrial function in those with ASD.
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Affiliation(s)
- Richard E Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ, USA; Southwest Autism Research and Resource Center, Phoenix, AZ, USA; Rossignol Medical Center, Phoenix, AZ, USA.
| | | | - Patrick J McCarty
- Tulane University School of Medicine, New Orleans, LA 70113, United States of America.
| | | | - Adrienne C Scheck
- Autism Discovery and Treatment Foundation, Phoenix, AZ, USA; Department of Child Health, University of Arizona College of Medicine - Phoenix, Phoenix, AZ 85004, United States of America.
| | - Daniel A Rossignol
- Autism Discovery and Treatment Foundation, Phoenix, AZ, USA; Rossignol Medical Center, Aliso Viejo, CA, USA
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Wei R, Yehia L, Ni Y, Eng C. The mitochondrial genome as a modifier of autism versus cancer phenotypes in PTEN hamartoma tumor syndrome. HGG ADVANCES 2023; 4:100199. [PMID: 37216009 PMCID: PMC10193119 DOI: 10.1016/j.xhgg.2023.100199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/13/2023] [Indexed: 05/24/2023] Open
Abstract
Cancer and autism spectrum disorder/developmental delay (ASD/DD) are two common clinical phenotypes in individuals with germline PTEN variants (PTEN hamartoma tumor syndrome, PHTS). Burgeoning studies have shown that genomic and metabolomic factors may act as modifiers of ASD/DD versus cancer in PHTS. Recently, we showed copy number variations to be associated with ASD/DD versus cancer in these PHTS individuals. We also found that mitochondrial complex II variants occurring in 10% of PHTS individuals modify breast cancer risk and thyroid cancer histology. These studies suggest that mitochondrial pathways could act as important factors in PHTS phenotype development. However, the mitochondrial genome (mtDNA) has never been systematically studied in PHTS. We therefore investigated the mtDNA landscape extracted from whole-genome sequencing data from 498 PHTS individuals, including 164 with ASD/DD (PHTS-onlyASD/DD), 184 with cancer (PHTS-onlyCancer), 132 with neither ASD/DD nor cancer (PHTS-neither), and 18 with both ASD/DD and cancer (PHTS-ASDCancer). We demonstrate that PHTS-onlyASD/DD has significantly higher mtDNA copy number than PHTS-onlyCancer group (p = 9.2 × 10-3 in all samples; p = 4.2 × 10-3 in the H haplogroup). PHTS-neither group has significantly higher mtDNA variant burden than PHTS-ASDCancer group (p = 4.6 × 10-2); the PHTS-noCancer group (PHTS-onlyASD/DD and PHTS-neither groups) also shows higher variant burden than the PHTS-Cancer group (PHTS-onlyCancer and PHTS-ASD/Cancer groups; p = 3.3 × 10-2). Our study implicates the mtDNA as a modifier of ASD/DD versus cancer phenotype development in PHTS.
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Affiliation(s)
- Ruipeng Wei
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Nutrition, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Lamis Yehia
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Ying Ni
- Center for Immunotherapy & Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH 44195, USA
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
- Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
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3
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Anitha A, Thanseem I, Iype M, Thomas SV. Mitochondrial dysfunction in cognitive neurodevelopmental disorders: Cause or effect? Mitochondrion 2023; 69:18-32. [PMID: 36621534 DOI: 10.1016/j.mito.2023.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/21/2022] [Accepted: 01/04/2023] [Indexed: 01/07/2023]
Abstract
Mitochondria have a crucial role in brain development and neurogenesis, both in embryonic and adult brains. Since the brain is the highest energy consuming organ, it is highly vulnerable to mitochondrial dysfunction. This has been implicated in a range of brain disorders including, neurodevelopmental conditions, psychiatric illnesses, and neurodegenerative diseases. Genetic variations in mitochondrial DNA (mtDNA), and nuclear DNA encoding mitochondrial proteins, have been associated with several cognitive disorders. However, it is not yet clear whether mitochondrial dysfunction is a primary cause of these conditions or a secondary effect. Our review article deals with this topic, and brings out recent advances in mitochondria-oriented therapies. Mitochondrial dysfunction could be involved in the pathogenesis of a subset of disorders involving cognitive impairment. In these patients, mitochondrial dysfunction could be the cause of the condition, rather than the consequence. There are vast areas in this topic that remains to be explored and elucidated.
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Affiliation(s)
- Ayyappan Anitha
- Dept. of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Shoranur, Palakkad 679 523, Kerala, India.
| | - Ismail Thanseem
- Dept. of Neurogenetics, Institute for Communicative and Cognitive Neurosciences (ICCONS), Shoranur, Palakkad 679 523, Kerala, India
| | - Mary Iype
- Dept. of Pediatric Neurology, Government Medical College, Thiruvananthapuram 695 011, Kerala, India; Dept. of Neurology, ICCONS, Thiruvananthapuram 695 033, Kerala, India
| | - Sanjeev V Thomas
- Dept. of Neurology, ICCONS, Thiruvananthapuram 695 033, Kerala, India
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Ryan NM, Heron EA. Evidence for parent-of-origin effects in autism spectrum disorder: a narrative review. J Appl Genet 2023; 64:303-317. [PMID: 36710277 PMCID: PMC10076404 DOI: 10.1007/s13353-022-00742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 01/31/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of early-onset neurodevelopmental disorders known to be highly heritable with a complex genetic architecture. Abnormal brain developmental trajectories that impact synaptic functioning, excitation-inhibition balance and brain connectivity are now understood to play a central role in ASD. Ongoing efforts to identify the genetic underpinnings still prove challenging, in part due to phenotypic and genetic heterogeneity.This review focuses on parent-of-origin effects (POEs), where the phenotypic effect of an allele depends on its parental origin. POEs include genomic imprinting, transgenerational effects, mitochondrial DNA, sex chromosomes and mutational transmission bias. The motivation for investigating these mechanisms in ASD has been driven by their known impacts on early brain development and brain functioning, in particular for the most well-documented POE, genomic imprinting. Moreover, imprinting is implicated in syndromes such as Angelman and Prader-Willi, which frequently share comorbid symptoms with ASD. In addition to other regions in the genome, this comprehensive review highlights the 15q11-q13 and 7q chromosomal regions as well as the mitochondrial DNA as harbouring the majority of currently identified POEs in ASD.
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Affiliation(s)
- Niamh M Ryan
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland
| | - Elizabeth A Heron
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Dublin, Ireland.
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Caporali L, Fiorini C, Palombo F, Romagnoli M, Baccari F, Zenesini C, Visconti P, Posar A, Scaduto MC, Ormanbekova D, Battaglia A, Tancredi R, Cameli C, Viggiano M, Olivieri A, Torroni A, Maestrini E, Rochat MJ, Bacchelli E, Carelli V, Maresca A. Dissecting the multifaceted contribution of the mitochondrial genome to autism spectrum disorder. Front Genet 2022; 13:953762. [PMID: 36419830 PMCID: PMC9676943 DOI: 10.3389/fgene.2022.953762] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2023] Open
Abstract
Autism spectrum disorder (ASD) is a clinically heterogeneous class of neurodevelopmental conditions with a strong, albeit complex, genetic basis. The genetic architecture of ASD includes different genetic models, from monogenic transmission at one end, to polygenic risk given by thousands of common variants with small effects at the other end. The mitochondrial DNA (mtDNA) was also proposed as a genetic modifier for ASD, mostly focusing on maternal mtDNA, since the paternal mitogenome is not transmitted to offspring. We extensively studied the potential contribution of mtDNA in ASD pathogenesis and risk through deep next generation sequencing and quantitative PCR in a cohort of 98 families. While the maternally-inherited mtDNA did not seem to predispose to ASD, neither for haplogroups nor for the presence of pathogenic mutations, an unexpected influence of paternal mtDNA, apparently centered on haplogroup U, came from the Italian families extrapolated from the test cohort (n = 74) when compared to the control population. However, this result was not replicated in an independent Italian cohort of 127 families and it is likely due to the elevated paternal age at time of conception. In addition, ASD probands showed a reduced mtDNA content when compared to their unaffected siblings. Multivariable regression analyses indicated that variants with 15%-5% heteroplasmy in probands are associated to a greater severity of ASD based on ADOS-2 criteria, whereas paternal super-haplogroups H and JT were associated with milder phenotypes. In conclusion, our results suggest that the mtDNA impacts on ASD, significantly modifying the phenotypic expression in the Italian population. The unexpected finding of protection induced by paternal mitogenome in term of severity may derive from a role of mtDNA in influencing the accumulation of nuclear de novo mutations or epigenetic alterations in fathers' germinal cells, affecting the neurodevelopment in the offspring. This result remains preliminary and needs further confirmation in independent cohorts of larger size. If confirmed, it potentially opens a different perspective on how paternal non-inherited mtDNA may predispose or modulate other complex diseases.
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Affiliation(s)
- Leonardo Caporali
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Claudio Fiorini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Palombo
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Flavia Baccari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Corrado Zenesini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Epidemiologia e Statistica, Bologna, Italy
| | - Paola Visconti
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Annio Posar
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Maria Cristina Scaduto
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOSI Disturbi dello Spettro Autistico, Bologna, Italy
| | - Danara Ormanbekova
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Agatino Battaglia
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Raffaella Tancredi
- IRCCS Stella Maris Foundation, Department of Developmental Neuroscience, Pisa, Italy
| | - Cinzia Cameli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Marta Viggiano
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Magali Jane Rochat
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma Diagnostica Funzionale Neuroradiologica, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Valerio Carelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
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Yang Z, Slone J, Huang T. Next-Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy. Curr Protoc 2022; 2:e412. [PMID: 35532282 DOI: 10.1002/cpz1.412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a very important role in many crucial cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondrial genomes. Mutant and wild-type mitochondrial DNA (mtDNA) may co-exist as heteroplasmy and cause human disease. The purpose of the protocols in this article is to simultaneously determine the mtDNA sequence and quantify the heteroplasmy level using parallel sequencing. The protocols include mitochondrial genomic DNA PCR amplification of two full-length products using two distinct sets of PCR primers. The PCR products are mixed at an equimolar ratio, and the samples are then barcoded and sequenced with high-throughput next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree/level of heteroplasmy. © 2022 Wiley Periodicals LLC. Basic Protocol 1: PCR amplification of mitochondrial DNA Basic Protocol 2: Analysis of next-generation sequencing of mitochondrial DNA Basic Protocol 3: Mutect2 pipeline for automated sample processing and large-scale data analysis.
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Affiliation(s)
- Zeyu Yang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jesse Slone
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Taosheng Huang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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7
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Gyllenhammer LE, Rasmussen JM, Bertele N, Halbing A, Entringer S, Wadhwa PD, Buss C. Maternal Inflammation During Pregnancy and Offspring Brain Development: The Role of Mitochondria. BIOLOGICAL PSYCHIATRY. COGNITIVE NEUROSCIENCE AND NEUROIMAGING 2022; 7:498-509. [PMID: 34800727 PMCID: PMC9086015 DOI: 10.1016/j.bpsc.2021.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/20/2021] [Accepted: 11/04/2021] [Indexed: 01/06/2023]
Abstract
The association between maternal immune activation (MIA) during pregnancy and risk for offspring neuropsychiatric disorders has been increasingly recognized over the past several years. Among the mechanistic pathways that have been described through which maternal inflammation during pregnancy may affect fetal brain development, the role of mitochondria has received little attention. In this review, the role of mitochondria as a potential mediator of the association between MIA during pregnancy and offspring brain development and risk for psychiatric disorders will be proposed. As a basis for this postulation, convergent evidence is presented supporting the obligatory role of mitochondria in brain development, the role of mitochondria as mediators and initiators of inflammatory processes, and evidence of mitochondrial dysfunction in preclinical MIA exposure models and human neurodevelopmental disorders. Elucidating the role of mitochondria as a potential mediator of MIA-induced alterations in brain development and neurodevelopmental disease risk may not only provide new insight into the pathophysiology of mental health disorders that have their origins in exposure to infection/immune activation during pregnancy but also offer new therapeutic targets.
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Affiliation(s)
- Lauren E Gyllenhammer
- Development, Health and Disease Research Program, University of California, Irvine, School of Medicine, Irvine, California; Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, California
| | - Jerod M Rasmussen
- Development, Health and Disease Research Program, University of California, Irvine, School of Medicine, Irvine, California; Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, California
| | - Nina Bertele
- Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Amy Halbing
- Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany; Einstein Center for Neurosciences Berlin, Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sonja Entringer
- Development, Health and Disease Research Program, University of California, Irvine, School of Medicine, Irvine, California; Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, California; Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Pathik D Wadhwa
- Development, Health and Disease Research Program, University of California, Irvine, School of Medicine, Irvine, California; Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, California; Department of Psychiatry and Human Behavior, University of California, Irvine, School of Medicine, Irvine, California; Department of Obstetrics and Gynecology, University of California, Irvine, School of Medicine, Irvine, California; Department of Epidemiology, University of California, Irvine, School of Medicine, Irvine, California
| | - Claudia Buss
- Development, Health and Disease Research Program, University of California, Irvine, School of Medicine, Irvine, California; Department of Pediatrics, University of California, Irvine, School of Medicine, Irvine, California; Department of Medical Psychology, Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany.
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8
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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.
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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.
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9
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Mahalaxmi I, Subramaniam MD, Gopalakrishnan AV, Vellingiri B. Dysfunction in Mitochondrial Electron Transport Chain Complex I, Pyruvate Dehydrogenase Activity, and Mutations in ND1 and ND4 Gene in Autism Spectrum Disorder Subjects from Tamil Nadu Population, India. Mol Neurobiol 2021; 58:5303-5311. [PMID: 34279772 DOI: 10.1007/s12035-021-02492-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/11/2021] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterised by impaired social interaction and behavioural abnormalities. Growing evidence proved that impairment in mitochondrial functions could inhibit energy production and may contribute to the onset of ASD. Genetic variants in the genes of mitochondrial DNA (mtDNA) could interrupt the normal energy metabolism and production in the brain which lead to a wide range of structural and functional changes in the brain resulting in ASD. The present study aims to compare the activities of mitochondrial electron transport chain (ETC) complex I, pyruvate dehydrogenase (PDH) and specific mitochondrial DNA gene (MT-ND1 and MT-ND4) variants associated with ASD subjects in the Tamil Nadu population. Mutational analysis revealed that most mutations in ASD subjects showed synonymous type followed by missense in both the ND1 and ND4 genes. Interestingly, we found that the complex I and PDH dysfunctions may have a role in ASD compared to the controls (p ≤ 0.0001). Hence, the results of the present study suggest that mitochondrial dysfunction, specifically the complex I genes, may play a major role in the onset of ASD, concluding that further research on mitochondrial genes are mandatory to unravel the mechanism behind ASD pathogenesis.
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Affiliation(s)
- Iyer Mahalaxmi
- Livestock Farming and Bioresource Technology, Tamil Nadu, India
| | - Mohana Devi Subramaniam
- SN ONGC, Department of Genetics and Molecular Biology, Vision Research Foundation, Chennai, 600-006, India
| | - Abilash Valsala Gopalakrishnan
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Tamil Nadu, Vellore, 632 014, India
| | - Balachandar Vellingiri
- Human Molecular Cytogenetics and Stem Cell Laboratory, Department of Human Genetics and Molecular Biology, Bharathiar University, Coimbatore, 641-046, Tamil Nadu, India.
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10
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Brunst KJ, Zhang L, Zhang X, Baccarelli AA, Bloomquist T, Wright RJ. Associations Between Maternal Lifetime Stress and Placental Mitochondrial DNA Mutations in an Urban Multiethnic Cohort. Biol Psychiatry 2021; 89:570-578. [PMID: 33229036 PMCID: PMC7889635 DOI: 10.1016/j.biopsych.2020.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Disrupted placental functioning due to stress can have lifelong implications. Cumulative stress and trauma are likely to have lasting impacts on maternal physiological functioning and offspring development, resulting in increased risk for later-life complex disorders for which racial disparities exist. METHODS This study examined the association between maternal lifetime stress and placental mitochondrial DNA mutational load in an urban multiethnic cohort. Maternal lifetime exposure to stressful events was assessed using the validated Life Stressor Checklist-Revised. Whole mitochondrial DNA sequencing was performed and mutations were determined for 365 placenta samples with complete exposure and covariate data. Multivariable regression was used to model maternal lifetime stress in relation to placental mitochondrial DNA mutational load. Racial/ethnic differences were examined by cross-product terms and contrast statements. Gene-wise analyses were conducted. RESULTS We identified 13,189 heteroplasmies (Phred score > 10,000, minor allele frequency < 0.5, number of mutant reads > 1). Women experiencing increased psychosocial stress over their lifetime exhibited a higher number of total placental mitochondrial mutations (β = .23, 95% confidence interval = .03 to .42) and heteroplasmic mutations (β = .18, 95% confidence interval = .05 to .31) but not homoplasmic mutations (β = -.008, 95% confidence interval = -.03 to .01); the strongest associations were observed among Black women and genes coding for NADH dehydrogenase and cytochrome c oxidase subunits. CONCLUSIONS Cumulative maternal lifetime stress is associated with a greater mitochondrial mutational load, particularly among Black women. The impact of racial/ethnic differences in mutational load on placental function directly affecting offspring development and/or leading to chronic disease disparities warrants further investigation.
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Affiliation(s)
- Kelly J. Brunst
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, 160 Panzeca Way, Cincinnati, OH 45267
| | - Li Zhang
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, 160 Panzeca Way, Cincinnati, OH 45267
| | - Xiang Zhang
- University of Cincinnati, College of Medicine, Department of Environmental and Public Health Sciences, 160 Panzeca Way, Cincinnati, OH 45267
| | - Andrea A. Baccarelli
- Columbia University, Mailman School of Public Health, Department of Environmental Health Sciences, 722 West 168 Street, New York, NY 10032
| | - Tessa Bloomquist
- Columbia University, Mailman School of Public Health, Department of Environmental Health Sciences, 722 West 168 Street, New York, NY 10032
| | - Rosalind J. Wright
- Icahn School of Medicine at Mount Sinai, Department of Pediatrics and Department of Environmental Medicine & Public Health, 1 Gustave L. Levy Place, New York, NY 10029
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11
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Dashti M, Alsaleh H, Eaaswarkhanth M, John SE, Nizam R, Melhem M, Hebbar P, Sharma P, Al-Mulla F, Thanaraj TA. Delineation of Mitochondrial DNA Variants From Exome Sequencing Data and Association of Haplogroups With Obesity in Kuwait. Front Genet 2021; 12:626260. [PMID: 33659027 PMCID: PMC7920096 DOI: 10.3389/fgene.2021.626260] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/13/2021] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND/OBJECTIVES Whole-exome sequencing is a valuable tool to determine genetic variations that are associated with rare and common health conditions. A limited number of studies demonstrated that mitochondrial DNA can be captured using whole-exome sequencing. Previous studies have suggested that mitochondrial DNA variants and haplogroup lineages are associated with obesity. Therefore, we investigated the role of mitochondrial variants and haplogroups contributing to the risk of obesity in Arabs in Kuwait using exome sequencing data. SUBJECTS/METHODS Indirect mitochondrial genomes were extracted from exome sequencing data from 288 unrelated native Arab individuals from Kuwait. The cohort was divided into obese [body mass index (BMI) ≥ 30 kg/m2] and non-obese (BMI < 30 kg/m2) groups. Mitochondrial variants were identified, and haplogroups were classified and compared with other sequencing technologies. Statistical analysis was performed to determine associations and identify mitochondrial variants and haplogroups affecting obesity. RESULTS Haplogroup R showed a protective effect on obesity [odds ratio (OR) = 0.311; P = 0.006], whereas haplogroup L individuals were at high risk of obesity (OR = 2.285; P = 0.046). Significant differences in mitochondrial variants between the obese and non-obese groups were mainly haplogroup-defining mutations and were involved in processes in energy generation. The majority of mitochondrial variants and haplogroups extracted from exome were in agreement with technical replica from Sanger and whole-genome sequencing. CONCLUSIONS This is the first to utilize whole-exome data to extract entire mitochondrial haplogroups to study its association with obesity in an Arab population.
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Affiliation(s)
- Mohammed Dashti
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Hussain Alsaleh
- Kuwait Identification DNA Laboratory, General Department of Criminal Evidence, Ministry of Interior, Kuwait City, Kuwait
| | | | - Sumi Elsa John
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Rasheeba Nizam
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Motasem Melhem
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prashantha Hebbar
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Prem Sharma
- Department Special Services Facilities, Dasman Diabetes Institute, Kuwait City, Kuwait
| | - Fahd Al-Mulla
- Genetics and Bioinformatics Department, Dasman Diabetes Institute, Kuwait City, Kuwait
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12
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FINSTERER J. Autism spectrum disorder: A mitochondrial disorder. IRANIAN JOURNAL OF CHILD NEUROLOGY 2021; 15:115-117. [PMID: 34782849 PMCID: PMC8570633 DOI: 10.22037/ijcn.v16i2.33066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 04/28/2021] [Indexed: 11/23/2022]
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13
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Citrigno L, Muglia M, Qualtieri A, Spadafora P, Cavalcanti F, Pioggia G, Cerasa A. The Mitochondrial Dysfunction Hypothesis in Autism Spectrum Disorders: Current Status and Future Perspectives. Int J Mol Sci 2020; 21:ijms21165785. [PMID: 32806635 PMCID: PMC7461038 DOI: 10.3390/ijms21165785] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/28/2020] [Accepted: 08/04/2020] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorders (ASDs) constitute a set of heterogeneous neurodevelopmental conditions, characterized by a wide genetic variability that has led to hypothesize a polygenic origin. The metabolic profiles of patients with ASD suggest a possible implication of mitochondrial pathways. Although different physiological and biochemical studies reported deficits in mitochondrial oxidative phosphorylation in subjects with ASD, the role of mitochondrial DNA variations has remained relatively unexplored. In this review, we report and discuss very recent evidence to demonstrate the key role of mitochondrial disorders in the development of ASD.
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Affiliation(s)
- Luigi Citrigno
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
| | - Maria Muglia
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
| | - Antonio Qualtieri
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
| | - Patrizia Spadafora
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
| | - Francesca Cavalcanti
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 98164 Messina, Italy;
| | - Antonio Cerasa
- Institute for Biomedical Research and Innovation, National Research Council, IRIB-CNR, 87050 Mangone CS, Italy; (L.C.); (M.M.); (A.Q.); (P.S.); (F.C.)
- S’Anna Institute and Research in Advanced Neurorehabilitation (RAN), 88100 Crotone, Italy
- Correspondence: ; Tel.: +39-333-9633511
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14
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Kreiman BL, Boles RG. State of the Art of Genetic Testing for Patients With Autism: A Practical Guide for Clinicians. Semin Pediatr Neurol 2020; 34:100804. [PMID: 32446438 DOI: 10.1016/j.spen.2020.100804] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The explosion in knowledge, technology, and clinical capabilities regarding genetics and genetic testing has expanded greatly in recent years, and these gains have rapidly been applied to individuals with autism spectrum disorder (ASD). However, most clinicians are unaware or confused in regards to whom to test, what tests to order, and how testing might alter management and improve outcomes. This review will address these issues. Research shows that ASD is highly genetic, and while monogenic cases are common, most patients have multiple genes interacting in disease pathogenesis. However, as genetics dictates disease risk, not outcomes, this does not exclude environmental factors. Clinically actionable genetics test results can be found across the phenotypically-heterogeneous ASD spectrum; thus recommendations are to test everyone. As ASD is also highly genetically heterogeneous, testing should address a wide range of variant types, including both large (historically detected by microarray) and small (detected by sequencing), at least across all genes (exome). Additional specialized testing important in ASD diagnostics includes fragile X, mitochondrial DNA, and pharmacogenetics; the latter often informative for which drug to order, at which dose. Recently, whole genome sequencing has emerged as a favorite since all of the above testing, and more, can be performed at a lower total cost than individual test orders. Trio (child plus parents) sequencing is often indicated, especially in more "severe" cases in order to find new (de novo) variants not present in either parent. Additionally, Angelman syndrome testing should be considered in appropriate cases. Current testing provides a precise diagnosis in many cases with ASD. Beyond diagnosis, genetic testing can oftentimes help elucidate potentially treatable risk factors that predispose the individual patient to develop disease. In this clinician's experience (RGB), this information leads to improved outcomes in as many as one-half of cases. Clinical improvement can occur in common associated ASD symptoms (attention, behavior, and anxiety) and/or in general systemtic symptoms (nausea, fatigue, pain), as demonstrated in brief case reports. Practical guidance is provided regarding assisting clinicians to choose the appropriate test(s) and laboratory, as well as how to get testing paid for. Recent cost reductions now allow for most families to benefit from genetic testing.
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Affiliation(s)
- Bracha L Kreiman
- The Center for Neurological and Neurodevelopmental Health, Voorhees, NJ; Molecular and Mitochondrial Medicine, Pasadena, CA
| | - Richard G Boles
- The Center for Neurological and Neurodevelopmental Health, Voorhees, NJ; Molecular and Mitochondrial Medicine, Pasadena, CA.
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15
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Cappa R, de Campos C, Maxwell AP, McKnight AJ. "Mitochondrial Toolbox" - A Review of Online Resources to Explore Mitochondrial Genomics. Front Genet 2020; 11:439. [PMID: 32457801 PMCID: PMC7225359 DOI: 10.3389/fgene.2020.00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This 'mitochondrial toolbox' summary resource will enable researchers to rapidly identify the resource(s) most suitable for their needs. These resources fulfil a variety of functions, with some being highly specialised. No single tool will provide all users with the resources they require; therefore, the most suitable tool will vary between users depending on the nature of the work they aim to carry out. Genetics resources are well established for phylogeny and DNA sequence changes, but further epigenetic and gene expression resources need to be developed for mitochondrial genomics.
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Affiliation(s)
- Ruaidhri Cappa
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Cassio de Campos
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Amy J McKnight
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
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16
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Clinical utility of whole genome sequencing for the detection of mitochondrial genome mutations. J Genet Genomics 2020; 47:167-169. [PMID: 32317151 DOI: 10.1016/j.jgg.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 03/12/2020] [Indexed: 01/25/2023]
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17
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Kanellopoulos AK, Mariano V, Spinazzi M, Woo YJ, McLean C, Pech U, Li KW, Armstrong JD, Giangrande A, Callaerts P, Smit AB, Abrahams BS, Fiala A, Achsel T, Bagni C. Aralar Sequesters GABA into Hyperactive Mitochondria, Causing Social Behavior Deficits. Cell 2020; 180:1178-1197.e20. [DOI: 10.1016/j.cell.2020.02.044] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 01/01/2020] [Accepted: 02/18/2020] [Indexed: 12/21/2022]
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18
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Hirsch MM, Deckmann I, Santos-Terra J, Staevie GZ, Fontes-Dutra M, Carello-Collar G, Körbes-Rockenbach M, Brum Schwingel G, Bauer-Negrini G, Rabelo B, Gonçalves MCB, Corrêa-Velloso J, Naaldijk Y, Castillo ARG, Schneider T, Bambini-Junior V, Ulrich H, Gottfried C. Effects of single-dose antipurinergic therapy on behavioral and molecular alterations in the valproic acid-induced animal model of autism. Neuropharmacology 2020; 167:107930. [PMID: 31904357 DOI: 10.1016/j.neuropharm.2019.107930] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/23/2019] [Accepted: 12/26/2019] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) is characterized by deficits in communication and social interaction, restricted interests, and stereotyped behavior. Environmental factors, such as prenatal exposure to valproic acid (VPA), may contribute to the increased risk of ASD. Since disturbed functioning of the purinergic signaling system has been associated with the onset of ASD and used as a potential therapeutic target for ASD in both clinical and preclinical studies, we analyzed the effects of suramin, a non-selective purinergic antagonist, on behavioral, molecular and immunological in an animal model of autism induced by prenatal exposure to VPA. Treatment with suramin (20 mg/kg, intraperitoneal) restored sociability in the three-chamber apparatus and decreased anxiety measured by elevated plus maze apparatus, but had no impact on decreased reciprocal social interactions or higher nociceptive threshold in VPA rats. Suramin treatment did not affect VPA-induced upregulation of P2X4 and P2Y2 receptor expression in the hippocampus, and P2X4 receptor expression in the medial prefrontal cortex, but normalized an increased level of interleukin 6 (IL-6). Our results suggest an important role of purinergic signaling modulation in behavioral, molecular, and immunological aberrations described in VPA model, and indicate that the purinergic signaling system might be a potential target for pharmacotherapy in preclinical studies of ASD.
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Affiliation(s)
- Mauro Mozael Hirsch
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil.
| | - Iohanna Deckmann
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Júlio Santos-Terra
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Gabriela Zanotto Staevie
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Mellanie Fontes-Dutra
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Giovanna Carello-Collar
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Marília Körbes-Rockenbach
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Gustavo Brum Schwingel
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Guilherme Bauer-Negrini
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Bruna Rabelo
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil
| | - Maria Carolina Bittencourt Gonçalves
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes , 748, 05508-000, Vila Universitãria, São Paulo, SP, Brazil
| | - Juliana Corrêa-Velloso
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes , 748, 05508-000, Vila Universitãria, São Paulo, SP, Brazil
| | - Yahaira Naaldijk
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes , 748, 05508-000, Vila Universitãria, São Paulo, SP, Brazil
| | - Ana Regina Geciauskas Castillo
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes , 748, 05508-000, Vila Universitãria, São Paulo, SP, Brazil
| | - Tomasz Schneider
- School of Medicine, Pharmacy and Health, Durham University, Durham, DH1, UK
| | - Victorio Bambini-Junior
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil; School of Pharmacy and Biomedical Sciences, University of Central Lancashire, PR1 2HE, Lancashire, Preston, England, UK; Autism Wellbeing And Research Development (AWARD) Institute, University of Central Lancashire, PR1 2HE, Lancashire, Preston, England, UK
| | - Henning Ulrich
- Department of Biochemistry, Institute of Chemistry, Universidade de São Paulo (USP), Avenida Professor Lineu Prestes , 748, 05508-000, Vila Universitãria, São Paulo, SP, Brazil; Autism Wellbeing And Research Development (AWARD) Institute, University of Central Lancashire, PR1 2HE, Lancashire, Preston, England, UK
| | - Carmem Gottfried
- Translational Research Group in Autism Spectrum Disorders-GETTEA, Universidade Federal do Rio Grande do Sul (UFRGS), Rua Ramiro Barcelos, 2600, 90035-003, Porto Alegre, RS, Brazil; Department of Biochemistry, Universidade Federal do Rio Grande do Sul (UFRGS), Ramiro Barcelos Street, 2600, 90035-003, Porto Alegre, RS, Brazil; National Institute of Science and Technology on Neuroimmunomodulation (INCT-NIM), Avenida Brasil, 4365, Manguinhos, 21045-900, Rio de Janeiro, RJ, Brazil; Autism Wellbeing And Research Development (AWARD) Institute, University of Central Lancashire, PR1 2HE, Lancashire, Preston, England, UK.
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19
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Garret P, Bris C, Procaccio V, Amati-Bonneau P, Vabres P, Houcinat N, Tisserant E, Feillet F, Bruel AL, Quéré V, Philippe C, Sorlin A, Tran Mau-Them F, Vitobello A, Costa JM, Boughalem A, Trost D, Faivre L, Thauvin-Robinet C, Duffourd Y. Deciphering exome sequencing data: Bringing mitochondrial DNA variants to light. Hum Mutat 2019; 40:2430-2443. [PMID: 31379041 DOI: 10.1002/humu.23885] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 06/27/2019] [Accepted: 07/30/2019] [Indexed: 12/13/2022]
Abstract
The expanding use of exome sequencing (ES) in diagnosis generates a huge amount of data, including untargeted mitochondrial DNA (mtDNA) sequences. We developed a strategy to deeply study ES data, focusing on the mtDNA genome on a large unspecific cohort to increase diagnostic yield. A targeted bioinformatics pipeline assembled mitochondrial genome from ES data to detect pathogenic mtDNA variants in parallel with the "in-house" nuclear exome pipeline. mtDNA data coming from off-target sequences (indirect sequencing) were extracted from the BAM files in 928 individuals with developmental and/or neurological anomalies. The mtDNA variants were filtered out based on database information, cohort frequencies, haplogroups and protein consequences. Two homoplasmic pathogenic variants (m.9035T>C and m.11778G>A) were identified in 2 out of 928 unrelated individuals (0.2%): the m.9035T>C (MT-ATP6) variant in a female with ataxia and the m.11778G>A (MT-ND4) variant in a male with a complex mosaic disorder and a severe ophthalmological phenotype, uncovering undiagnosed Leber's hereditary optic neuropathy (LHON). Seven secondary findings were also found, predisposing to deafness or LHON, in 7 out of 928 individuals (0.75%). This study demonstrates the usefulness of including a targeted strategy in ES pipeline to detect mtDNA variants, improving results in diagnosis and research, without resampling patients and performing targeted mtDNA strategies.
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Affiliation(s)
- Philippine Garret
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Laboratoire CERBA, Saint-Ouen-l'Aumône, France
| | - Céline Bris
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Vincent Procaccio
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Patrizia Amati-Bonneau
- Institut MITOVASC, UMR CNRS 6015-INSERM1083, University of Angers, Angers, France.,Centre de Référence maladies mitochondriales, CHU Angers, Angers, France
| | - Pierre Vabres
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Service Dermatologie, CHU Dijon Bourgogne, Dijon, France
| | - Nada Houcinat
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Emilie Tisserant
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - François Feillet
- Service de Pédiatrie, Hôpital d'Enfants Brabois, CHRU Nancy, Vandoeuvre les Nancy, France.,INSERM-University of Lorraine-CHRU Nancy, UMRS 1256 NGERE, Nancy, France.,Centre de Références des maladies héréditaires du métabolisme, CHRU de Nancy, Nancy, France
| | - Ange-Line Bruel
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Virginie Quéré
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Christophe Philippe
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Arthur Sorlin
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Maladies Dermatologiques en Mosaïque », Service de dermatologie, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Frédéric Tran Mau-Them
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Antonio Vitobello
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | | | | | | | - Laurence Faivre
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Centre de Référence Maladies Rares « Anomalies du développement et syndromes malformatifs », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de compétences des maladies mitochondriales, Dijon University Hospital, Dijon, France
| | - Christel Thauvin-Robinet
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France.,Centre de Référence Maladies Rares « déficience intellectuelle », Centre de Génétique, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
| | - Yannis Duffourd
- INSERM-University of Burgundy-Franche Comté, UMR1231 GAD, Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU-TRANSLAD, Dijon University Hospital, Dijon, France
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20
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Castora FJ. Mitochondrial function and abnormalities implicated in the pathogenesis of ASD. Prog Neuropsychopharmacol Biol Psychiatry 2019; 92:83-108. [PMID: 30599156 DOI: 10.1016/j.pnpbp.2018.12.015] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria are the powerhouse that generate over 90% of the ATP produced in cells. In addition to its role in energy production, the mitochondrion also plays a major role in carbohydrate, fatty acid, amino acid and nucleotide metabolism, programmed cell death (apoptosis), generation of and protection against reactive oxygen species (ROS), immune response, regulation of intracellular calcium ion levels and even maintenance of gut microbiota. With its essential role in bio-energetic as well as non-energetic biological processes, it is not surprising that proper cellular, tissue and organ function is dependent upon proper mitochondrial function. Accordingly, mitochondrial dysfunction has been shown to be directly linked to a variety of medical disorders, particularly neuromuscular disorders and increasing evidence has linked mitochondrial dysfunction to neurodegenerative and neurodevelopmental disorders such as Alzheimer's Disease (AD), Parkinson's Disease (PD), Rett Syndrome (RS) and Autism Spectrum Disorders (ASD). Over the last 40 years there has been a dramatic increase in the diagnosis of ASD and, more recently, an increasing body of evidence indicates that mitochondrial dysfunction plays an important role in ASD development. In this review, the latest evidence linking mitochondrial dysfunction and abnormalities in mitochondrial DNA (mtDNA) to the pathogenesis of autism will be presented. This review will also summarize the results of several recent `approaches used for improving mitochondrial function that may lead to new therapeutic approaches to managing and/or treating ASD.
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Affiliation(s)
- Frank J Castora
- Department of Physiological Sciences, Eastern Virginia Medical School, Norfolk, VA, USA; Department of Neurology, Eastern Virginia Medical School, Norfolk, VA, USA.
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21
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Bris C, Goudenege D, Desquiret-Dumas V, Charif M, Colin E, Bonneau D, Amati-Bonneau P, Lenaers G, Reynier P, Procaccio V. Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing. Front Genet 2018; 9:632. [PMID: 30619459 PMCID: PMC6297213 DOI: 10.3389/fgene.2018.00632] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/27/2018] [Indexed: 11/13/2022] Open
Abstract
The development of next generation sequencing (NGS) has greatly enhanced the diagnosis of mitochondrial disorders, with a systematic analysis of the whole mitochondrial DNA (mtDNA) sequence and better detection sensitivity. However, the exponential growth of sequencing data renders complex the interpretation of the identified variants, thereby posing new challenges for the molecular diagnosis of mitochondrial diseases. Indeed, mtDNA sequencing by NGS requires specific bioinformatics tools and the adaptation of those developed for nuclear DNA, for the detection and quantification of mtDNA variants from sequence alignment to the calling steps, in order to manage the specific features of the mitochondrial genome including heteroplasmy, i.e., coexistence of mutant and wildtype mtDNA copies. The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity. An evaluation of the most prominent bioinformatics tools showed that their ability to predict the pathogenicity was highly variable indicating that special efforts should be directed at developing new bioinformatics tools dedicated to the mitochondrial genome. In addition, massive parallel sequencing raised several issues related to the interpretation of very low mtDNA mutational loads, discovery of variants of unknown significance, and mutations unrelated to patient phenotype or the co-occurrence of mtDNA variants. This review provides an overview of the current strategies and bioinformatics tools for accurate annotation, prioritization and reporting of mtDNA variations from NGS data, in order to carry out accurate genetic counseling in individuals with primary mitochondrial diseases.
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Affiliation(s)
- Céline Bris
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - David Goudenege
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Valérie Desquiret-Dumas
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Majida Charif
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Estelle Colin
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Pascal Reynier
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
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22
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Diagnostic and Severity-Tracking Biomarkers for Autism Spectrum Disorder. J Mol Neurosci 2018; 66:492-511. [DOI: 10.1007/s12031-018-1192-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 09/25/2018] [Indexed: 01/06/2023]
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23
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Rose S, Niyazov DM, Rossignol DA, Goldenthal M, Kahler SG, Frye RE. Clinical and Molecular Characteristics of Mitochondrial Dysfunction in Autism Spectrum Disorder. Mol Diagn Ther 2018; 22:571-593. [PMID: 30039193 PMCID: PMC6132446 DOI: 10.1007/s40291-018-0352-x] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Autism spectrum disorder (ASD) affects ~ 2% of children in the United States. The etiology of ASD likely involves environmental factors triggering physiological abnormalities in genetically sensitive individuals. One of these major physiological abnormalities is mitochondrial dysfunction, which may affect a significant subset of children with ASD. Here we systematically review the literature on human studies of mitochondrial dysfunction related to ASD. Clinical aspects of mitochondrial dysfunction in ASD include unusual neurodevelopmental regression, especially if triggered by an inflammatory event, gastrointestinal symptoms, seizures, motor delays, fatigue and lethargy. Traditional biomarkers of mitochondrial disease are widely reported to be abnormal in ASD, but appear non-specific. Newer biomarkers include buccal cell enzymology, biomarkers of fatty acid metabolism, non-mitochondrial enzyme function, apoptosis markers and mitochondrial antibodies. Many genetic abnormalities are associated with mitochondrial dysfunction in ASD, including chromosomal abnormalities, mitochondrial DNA mutations and large-scale deletions, and mutations in both mitochondrial and non-mitochondrial nuclear genes. Mitochondrial dysfunction has been described in immune and buccal cells, fibroblasts, muscle and gastrointestinal tissue and the brains of individuals with ASD. Several environmental factors, including toxicants, microbiome metabolites and an oxidized microenvironment are shown to modulate mitochondrial function in ASD tissues. Investigations of treatments for mitochondrial dysfunction in ASD are promising but preliminary. The etiology of mitochondrial dysfunction and how to define it in ASD is currently unclear. However, preliminary evidence suggests that the mitochondria may be a fruitful target for treatment and prevention of ASD. Further research is needed to better understand the role of mitochondrial dysfunction in the pathophysiology of ASD.
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Affiliation(s)
- Shannon Rose
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Dmitriy M Niyazov
- Section of Medical Genetics, Ochsner Health System, New Orleans, LA, USA
| | | | - Michael Goldenthal
- Department of Pediatrics, Neurology Section, St. Christopher's Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Stephen G Kahler
- Department of Pediatrics, University of Arkansas for Medical Sciences and Arkansas Children's Research Institute, Little Rock, AR, USA
| | - Richard E Frye
- Division of Neurodevelopmental Disorders, Department of Neurology, Barrow Neurological Institute, Phoenix Children's Hospital, 1919 E Thomas St, Phoenix, AZ, USA.
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.
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24
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Cruz ACP, Ferrasa A, Muotri AR, Herai RH. Frequency and association of mitochondrial genetic variants with neurological disorders. Mitochondrion 2018; 46:345-360. [PMID: 30218715 DOI: 10.1016/j.mito.2018.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/24/2018] [Accepted: 09/11/2018] [Indexed: 12/17/2022]
Abstract
Mitochondria are small cytosolic organelles and the main source of energy production for the cells, especially in the brain. This organelle has its own genome, the mitochondrial DNA (mtDNA), and genetic variants in this molecule can alter the normal energy metabolism in the brain, contributing to the development of a wide assortment of Neurological Disorders (ND), including neurodevelopmental syndromes, neurodegenerative diseases and neuropsychiatric disorders. These ND are comprised by a heterogeneous group of syndromes and diseases that encompass different cognitive phenotypes and behavioral disorders, such as autism, Asperger's syndrome, pervasive developmental disorder, attention deficit hyperactivity disorder, Huntington disease, Leigh Syndrome and bipolar disorder. In this work we carried out a Systematic Literature Review (SLR) to identify and describe the mitochondrial genetic variants associated with the occurrence of ND. Most of genetic variants found in mtDNA were associated with Single Nucleotide Polimorphisms (SNPs), ~79%, with ~15% corresponding to deletions, ~3% to Copy Number Variations (CNVs), ~2% to insertions and another 1% included mtDNA replication problems and genetic rearrangements. We also found that most of the variants were associated with coding regions of mitochondrial proteins but were also found in regulatory transcripts (tRNA and rRNA) and in the D-Loop replication region of the mtDNA. After analysis of mtDNA deletions and CNV, none of them occur in the D-Loop region. This SLR shows that all transcribed mtDNA molecules have mutations correlated with ND. Finally, we describe that all mtDNA variants found were associated with deterioration of cognitive (dementia) and intellectual functions, learning disabilities, developmental delays, and personality and behavior problems.
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Affiliation(s)
- Ana Carolina P Cruz
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences (PPGCS), School of Medicine (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná 80215-901, Brazil
| | - Adriano Ferrasa
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences (PPGCS), School of Medicine (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná 80215-901, Brazil; Department of Informatics (DEINFO), Universidade Estadual de Ponta Grossa (UEPG), Ponta Grossa, Paraná 84030-900, Brazil
| | - Alysson R Muotri
- University of California San Diego, School of Medicine, Department of Pediatrics/Rady Children's Hospital San Diego, Department of Cellular & Molecular Medicine, Stem Cell Program, La Jolla, CA 92037-0695, USA
| | - Roberto H Herai
- Experimental Multiuser Laboratory (LEM), Graduate Program in Health Sciences (PPGCS), School of Medicine (PPGCS), Pontifícia Universidade Católica do Paraná (PUCPR), Curitiba, Paraná 80215-901, Brazil; Lico Kaesemodel Institute (ILK), Curitiba, Paraná 80240-000, Brazil.
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25
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Brockhage R, Slone J, Ma Z, Hegde MR, Valencia CA, Huang T. Validation of the diagnostic potential of mtDNA copy number derived from whole genome sequencing. J Genet Genomics 2018; 45:S1673-8527(18)30098-5. [PMID: 29910094 DOI: 10.1016/j.jgg.2018.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 06/03/2018] [Accepted: 06/04/2018] [Indexed: 02/05/2023]
Affiliation(s)
- Rachel Brockhage
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Jesse Slone
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Zeqiang Ma
- PerkinElmer Genomics, Branford, CT 06405, USA
| | - Madhuri R Hegde
- PerkinElmer Genomics, Branford, CT 06405, USA; Department of Human Genetics, Emory University, Atlanta, GA 30322, USA; School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - C Alexander Valencia
- PerkinElmer Genomics, Branford, CT 06405, USA; West China Hospital, Sichuan University, Chengdu 610041, China
| | - Taosheng Huang
- Division of Human Genetics, Children's Hospital Medical Center, Cincinnati, OH 45229, USA; Human Aging Research Institute, Nanchang University, Nanchang 330031, China.
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26
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Valiente-Pallejà A, Torrell H, Muntané G, Cortés MJ, Martínez-Leal R, Abasolo N, Alonso Y, Vilella E, Martorell L. Genetic and clinical evidence of mitochondrial dysfunction in autism spectrum disorder and intellectual disability. Hum Mol Genet 2018; 27:891-900. [DOI: 10.1093/hmg/ddy009] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 12/30/2017] [Indexed: 02/06/2023] Open
Affiliation(s)
- Alba Valiente-Pallejà
- Research Department, Hospital Universitari Institut Pere Mata, E43206 Reus, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
| | | | - Gerard Muntané
- Research Department, Hospital Universitari Institut Pere Mata, E43206 Reus, Spain
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC), Universitat Pompeu Fabra, E08003 Barcelona, Catalonia, Spain
| | - Maria J Cortés
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
- Intellectual Disability-Developmental Disorders Research Unit (UNIVIDD), Fundació Villablanca, E43204 Reus, Catalonia, Spain
- Facultat de Medicina i CIències de la Salut, Universitat Rovira i Virgili (URV), E43201 Reus, Catalonia, Spain
| | - Rafael Martínez-Leal
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
- Intellectual Disability-Developmental Disorders Research Unit (UNIVIDD), Fundació Villablanca, E43204 Reus, Catalonia, Spain
- Facultat de Medicina i CIències de la Salut, Universitat Rovira i Virgili (URV), E43201 Reus, Catalonia, Spain
| | - Nerea Abasolo
- Center for Omic Sciences, 43204 Reus, Catalonia, Spain
| | - Yolanda Alonso
- Research Department, Hospital Universitari Institut Pere Mata, E43206 Reus, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
- Facultat de Medicina i CIències de la Salut, Universitat Rovira i Virgili (URV), E43201 Reus, Catalonia, Spain
| | - Elisabet Vilella
- Research Department, Hospital Universitari Institut Pere Mata, E43206 Reus, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
- Facultat de Medicina i CIències de la Salut, Universitat Rovira i Virgili (URV), E43201 Reus, Catalonia, Spain
| | - Lourdes Martorell
- Research Department, Hospital Universitari Institut Pere Mata, E43206 Reus, Spain
- Institut d’Investigació Sanitària Pere Virgili (IISPV), E43204 Reus, Catalonia, Spain
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), E43204 Reus, Catalonia, Spain
- Facultat de Medicina i CIències de la Salut, Universitat Rovira i Virgili (URV), E43201 Reus, Catalonia, Spain
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27
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Valenti D, Braidy N, De Rasmo D, Signorile A, Rossi L, Atanasov AG, Volpicella M, Henrion-Caude A, Nabavi SM, Vacca RA. Mitochondria as pharmacological targets in Down syndrome. Free Radic Biol Med 2018; 114:69-83. [PMID: 28838841 DOI: 10.1016/j.freeradbiomed.2017.08.014] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/16/2017] [Accepted: 08/18/2017] [Indexed: 12/17/2022]
Abstract
Mitochondria play a pivotal role in cellular energy-generating processes and are considered master regulators of cell life and death fate. Mitochondrial function integrates signalling networks in several metabolic pathways controlling neurogenesis and neuroplasticity. Indeed, dysfunctional mitochondria and mitochondrial-dependent activation of intracellular stress cascades are critical initiating events in many human neurodegenerative or neurodevelopmental diseases including Down syndrome (DS). It is well established that trisomy of human chromosome 21 can cause DS. DS is associated with neurodevelopmental delay, intellectual disability and early neurodegeneration. Recently, molecular mechanisms responsible for mitochondrial damage and energy deficits have been identified and characterized in several DS-derived human cells and animal models of DS. Therefore, therapeutic strategies targeting mitochondria could have great potential for new treatment regimens in DS. The purpose of this review is to highlight recent studies concerning mitochondrial impairment in DS, focusing on alterations of the molecular pathways controlling mitochondrial function. We will also discuss the effects and molecular mechanisms of naturally occurring and chemically synthetized drugs that exert neuroprotective effects through modulation of mitochondrial function and attenuation of oxidative stress. These compounds might represent novel therapeutic tools for the modulation of energy deficits in DS.
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Affiliation(s)
- Daniela Valenti
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Council of Research, Bari, Italy
| | - Nady Braidy
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Australia
| | - Domenico De Rasmo
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Council of Research, Bari, Italy
| | - Anna Signorile
- Department of Basic Medical Sciences, Neuroscience and Sense Organs, University of Bari, Italy
| | - Leonardo Rossi
- Department of Clinical and Experimental Medicine, University of Pisa, Italy
| | - A G Atanasov
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, 05-552 Jastrzebiec, Poland; Department of Pharmacognosy, University of Vienna, 1090 Vienna, Austria; Department of Vascular Biology and Thrombosis Research, Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Mariateresa Volpicella
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Alexandra Henrion-Caude
- INSERM U1163, Université Paris Descartes, Sorbonne Paris Cité, Institut Imagine, GenAtlas Platform, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - S M Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - R A Vacca
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Council of Research, Bari, Italy.
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