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Brockmann SJ, Buck E, Casoli T, Meirelles JL, Ruf WP, Fabbietti P, Holzmann K, Weishaupt JH, Ludolph AC, Conti F, Danzer KM. Mitochondrial genome study in blood of maternally inherited ALS cases. Hum Genomics 2023; 17:70. [PMID: 37507754 PMCID: PMC10375681 DOI: 10.1186/s40246-023-00516-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND ALS is a heterogeneous disease in which different factors such as mitochondrial phenotypes act in combination with a genetic predisposition. This study addresses the question of whether homoplasmic (total mitochondrial genome of a sample is affected) and/or heteroplasmic mutations (wildtype and mutant mitochondrial DNA molecules coexist) might play a role in familial ALS. Blood was drawn from familial ALS patients with a possible maternal pattern of inheritance according to their pedigrees, which was compared to blood of ALS patients without maternal association as well as age-matched controls. In two cohorts, we analyzed the mitochondrial genome from whole blood or isolated white blood cells and platelets using a resequencing microarray (Affymetrix MitoChip v2.0) that is able to detect homoplasmic and heteroplasmic mitochondrial DNA mutations and allows the assessment of low-level heteroplasmy. RESULTS We identified an increase in homoplasmic ND5 mutations, a subunit of respiratory chain complex I, in whole blood of ALS patients that allowed maternal inheritance. This effect was more pronounced in patients with bulbar onset. Heteroplasmic mutations were significantly increased in different mitochondrial genes in platelets of patients with possible maternal inheritance. No increase of low-level heteroplasmy was found in maternal ALS patients. CONCLUSION Our results indicate a contribution of homoplasmic ND5 mutations to maternally associated ALS with bulbar onset. Therefore, it might be conceivable that specific maternally transmitted rather than randomly acquired mitochondrial DNA mutations might contribute to the disease process. This stands in contrast with observations from Alzheimer's and Parkinson's diseases showing an age-dependent accumulation of unspecific mutations in mitochondrial DNA.
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Affiliation(s)
- Sarah J Brockmann
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
| | - Eva Buck
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Tiziana Casoli
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - João L Meirelles
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Wolfgang P Ruf
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
| | - Paolo Fabbietti
- Unit of Geriatric Pharmacoepidemiology, IRCCS INRCA, Ancona, Italy
| | | | - Jochen H Weishaupt
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
- Division for Neurodegenerative Diseases, Neurology Department, University Medicine Mannheim, Heidelberg University, Mannheim, Germany
| | - Albert C Ludolph
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany
| | - Fiorenzo Conti
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
- Section of Neuroscience and Cell Biology, Department of Experimental and Clinical Medicine, Università Politecnica delle Marche, Ancona, Italy
| | - Karin M Danzer
- Department of Neurology, University Clinic, University of Ulm, Ulm, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Ulm, Germany.
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Gonzalez‐Freire M, Moore AZ, Peterson CA, Kosmac K, McDermott MM, Sufit RL, Guralnik JM, Polonsky T, Tian L, Kibbe MR, Criqui MH, Li L, Leeuwenburgh C, Ferrucci L. Associations of Peripheral Artery Disease With Calf Skeletal Muscle Mitochondrial DNA Heteroplasmy. J Am Heart Assoc 2020; 9:e015197. [PMID: 32200714 PMCID: PMC7428597 DOI: 10.1161/jaha.119.015197] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/24/2020] [Indexed: 12/13/2022]
Abstract
Background Patients with peripheral artery disease (PAD) undergo frequent episodes of ischemia-reperfusion in lower extremity muscles that may negatively affect mitochondrial health and are associated with impaired mobility. We hypothesized that skeletal muscle from PAD patients will show high mitochondrial DNA heteroplasmy, especially in regions more susceptible to oxidative damage, such as the displacement loop, and that the degree of heteroplasmy will be correlated with the severity of ischemia and mobility impairment. Methods and Results Mitochondrial mutations and deletions and their relative abundance were identified by targeted mitochondrial DNA sequencing in biopsy specimens of gastrocnemius muscle from 33 PAD (ankle brachial index <0.9) and 9 non-PAD (ankle brachial index >0.9) subjects aged ≥60 years. The probability of heteroplasmy per DNA base was significantly higher for PAD subjects than non-PAD within each region. In adjusted models, PAD was associated with higher heteroplasmy than non-PAD (P=0.003), but the association was limited to microheteroplasmy, that is heteroplasmy found in 1% to 5% of all mitochondrial genomes (P=0.004). Heteroplasmy in the displacement loop and coding regions were significantly higher for PAD than non-PAD subjects after adjustment for age, sex, race, and diabetes mellitus (P=0.037 and 0.004, respectively). Low mitochondrial damage, defined by both low mitochondrial DNA copy number and low microheteroplasmy, was associated with better walking performance. Conclusions People with PAD have higher "low frequency" heteroplasmy in gastrocnemius muscle compared with people without PAD. Among people with PAD, those who had evidence of least mitochondrial damage, had better walking performance than those with more mitochondrial damage. Registration URL: http://www.clinicaltrials.gov. Unique identifier: NCT02246660.
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Affiliation(s)
- Marta Gonzalez‐Freire
- National Institutes on HealthNational Institute on AgingBaltimoreMD
- Health Research Institute of the Balearic Islands (IdISBa)Palma de MallorcaIlles BalearsSpain
| | - A. Zenobia Moore
- National Institutes on HealthNational Institute on AgingBaltimoreMD
| | - Charlotte A. Peterson
- College of Health Sciences and Center for Muscle BiologyUniversity of KentuckyLexingtonKY
| | - Kate Kosmac
- College of Health Sciences and Center for Muscle BiologyUniversity of KentuckyLexingtonKY
| | - Mary M. McDermott
- Department of MedicineNorthwestern University Feinberg School of MedicineChicagoIL
- Department of Preventive MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Robert L. Sufit
- Department of NeurologyNorthwestern University Feinberg School of MedicineChicagoIL
| | | | | | - Lu Tian
- Department of Health Research & PolicyStanford UniversityStanfordCA
| | | | - Michael H. Criqui
- Department of Family Medicine and Public HealthUniversity of California at San DiegoLa JollaCA
| | - Lingyu Li
- Department of MedicineNorthwestern University Feinberg School of MedicineChicagoIL
| | - Christian Leeuwenburgh
- Department of Aging and Geriatric ResearchUniversity of Florida Institute on AgingGainesvilleFL
| | - Luigi Ferrucci
- National Institutes on HealthNational Institute on AgingBaltimoreMD
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Elamir A, ElRefai SM, Ghazy SE. Molecular alterations of mitochondrial D-loop in oral leukoplakia. J Cell Biochem 2019; 120:13944-13951. [PMID: 30945332 DOI: 10.1002/jcb.28668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 02/01/2019] [Accepted: 02/14/2019] [Indexed: 11/07/2022]
Abstract
BACKGROUND Over the years, numerous studies proposed a crucial role of mutations of nuclear DNA in the carcinogenesis process. Of late, many researchers suppose that alterations of mitochondrial DNA should not be excepted from this analysis. Mutational analysis of mitochondrial DNA displayed that mitochondrial D-loop is assessed as a hotspot for molecular alterations in various types of malignant tumors encompassing oral squamous cell carcinoma. Squamous cell carcinoma is believed to emerge through precancerous stages, which might be merely morphologic aspects of cumulative genetic variations. METHODS In keeping with this model of molecular tumor progression, this study aimed to investigate the qualitative and quantitative alterations that might occur in mitochondrial D-loop in oral leukoplakia whether dysplastic or not by semiquantitation of a product of the polymerase chain reaction and sequence analyses of mitochondrial D-loop gene. RESULTS Statistically significant increases in the mean values of D-loop concentrations were observed across the dysplasia gradient of oral leukoplakia. Sequence analyses revealed the presence of point mutations in both dysplastic and nondysplastic oral leukoplakia but not in normal mucosa. CONCLUSION The results of this study suggested that quantitative and qualitative alterations in mitochondrial D-loop could be a promising molecular marker for early detection and progression of the malignancy.
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Affiliation(s)
- Azza Elamir
- Department of Medical Biochemistry, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Sahar M ElRefai
- Department of Oral Pathology, Faculty of Dentistry, Princess Nourah University, Riyadh, Kingdom of Saudi Arabia
| | - Shaimaa E Ghazy
- Department of Oral Pathology, Faculty of Dentistry, Ain Shams University, Cairo, Egypt
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Soon BH, Abdul Murad NA, Then SM, Abu Bakar A, Fadzil F, Thanabalan J, Mohd Haspani MS, Toh CJ, Mohd Tamil A, Harun R, Wan Ngah WZ, Jamal R. Mitochondrial DNA Mutations in Grade II and III Glioma Cell Lines Are Associated with Significant Mitochondrial Dysfunction and Higher Oxidative Stress. Front Physiol 2017; 8:231. [PMID: 28484394 PMCID: PMC5399085 DOI: 10.3389/fphys.2017.00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/31/2017] [Indexed: 01/13/2023] Open
Abstract
The role of mitochondria in tumorigenesis has regained much attention as it could dysregulate cellular energetics, oxidative stress and apoptosis. However, the role of mitochondria in different grade gliomasis still unknown. This study aimed to identify mitochondrial DNA (mtDNA) sequence variations that could possibly affect the mitochondrial functions and also the oxidative stress status. Three different grades of human glioma cell lines and a normal human astrocyte cell line were cultured in-vitro and tested for oxidative stress biomarkers. Relative oxidative stress level, mitochondria activity, and mitochondrial mass were determined by live cell imaging with confocal laser scanning microscope using CM-H2DCFDA, MitoTracker Green, and MitoTracker Orange stains. The entire mitochondrial genome was sequenced using the AffymetrixGeneChip Human Mitochondrial Resequencing Array 2.0. The mitochondrial sequence variations were subjected to phylogenetic haplogroup assessment and pathogenicity of the mutations were predicted using pMUT and PolyPhen2. The Grade II astrocytoma cells showed increased oxidative stress wherea high level of 8-OHdG and oxidative stress indicator were observed. Simultaneously, Grade II and III glioma cells showed relatively poor mitochondria functions and increased number of mutations in the coding region of the mtDNA which could be due to high levels of oxidative stress in these cells. These non-synonymous mtDNA sequence variations were predicted to be pathogenic and could possibly lead to protein dysfunction, leading to oxidative phosphorylation (OXPHOS) impairment, mitochondria dysfunction and could create a vicious cycle of oxidative stress. The Grade IV cells had no missense mutation but preserved intact mitochondria and excellent antioxidant defense mechanisms thus ensuring better survival. In conclusion, Grade II and III glioma cells demonstrated coding region mtDNA mutations, leading to mitochondrial dysfunction and higher oxidative stress.
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Affiliation(s)
- Bee Hong Soon
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia.,Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Sue-Mian Then
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia.,The University of Nottingham Malaysia CampusSemenyih, Malaysia
| | - Azizi Abu Bakar
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Farizal Fadzil
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Jegan Thanabalan
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | | | - Charng Jeng Toh
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Azmi Mohd Tamil
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Roslan Harun
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Wan Z Wan Ngah
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
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Identification and characterization of the novel point mutation m.3634A>G in the mitochondrial MT-ND1 gene associated with LHON syndrome. Biochim Biophys Acta Mol Basis Dis 2016; 1863:182-187. [PMID: 27613247 DOI: 10.1016/j.bbadis.2016.09.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 09/01/2016] [Accepted: 09/05/2016] [Indexed: 11/20/2022]
Abstract
Leber's hereditary optic neuropathy (LHON) is a mitochondrial genetic disease characterized by bilateral acute or subacute progressive central visual loss. Most cases of LHON syndrome are caused by point mutations in the MT-ND1, MT-ND4, and MT-ND6 genes. Here, we report a novel homoplasmic mutation in the MT-ND1 gene (m.3634A>G, p.Ser110Gly) in a patient with the classical clinical features of LHON syndrome. Several observations support the idea that the mutation is pathogenic and involved in the clinical phenotype of the patient: 1) The mutation affected a highly conserved amino acid, 2) A pathogenic mutation in the same amino acid (m.3635G>A, p.Ser110Asn) was previously reported in a patient with LHON syndrome, 3) The mutation is not recorded in the Mitomap or Human Mitochondrial Genome Database, 4) In silico predictors classified the mutation as "probably damaging", and 5) Cybrids carrying the mutation showed decreased Complex I enzyme activity, lower cell proliferation, and decreased mitochondrial membrane potential relative to control cybrids.
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6
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Parikh S, Goldstein A, Koenig MK, Scaglia F, Enns GM, Saneto R, Anselm I, Cohen BH, Falk MJ, Greene C, Gropman AL, Haas R, Hirano M, Morgan P, Sims K, Tarnopolsky M, Van Hove JLK, Wolfe L, DiMauro S. Diagnosis and management of mitochondrial disease: a consensus statement from the Mitochondrial Medicine Society. Genet Med 2014; 17:689-701. [PMID: 25503498 DOI: 10.1038/gim.2014.177] [Citation(s) in RCA: 333] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 11/06/2014] [Indexed: 12/13/2022] Open
Abstract
PURPOSE The purpose of this statement is to review the literature regarding mitochondrial disease and to provide recommendations for optimal diagnosis and treatment. This statement is intended for physicians who are engaged in diagnosing and treating these patients. METHODS The Writing Group members were appointed by the Mitochondrial Medicine Society. The panel included members with expertise in several different areas. The panel members utilized a comprehensive review of the literature, surveys, and the Delphi method to reach consensus. We anticipate that this statement will need to be updated as the field continues to evolve. RESULTS Consensus-based recommendations are provided for the diagnosis and treatment of mitochondrial disease. CONCLUSION The Delphi process enabled the formation of consensus-based recommendations. We hope that these recommendations will help standardize the evaluation, diagnosis, and care of patients with suspected or demonstrated mitochondrial disease.
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Affiliation(s)
- Sumit Parikh
- Department of Neurology, Center for Child Neurology, Cleveland Clinic Children's Hospital, Cleveland, Ohio, USA
| | - Amy Goldstein
- Department of Pediatrics, Division of Child Neurology, Children's Hospital of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mary Kay Koenig
- Department of Pediatrics, Division of Child and Adolescent Neurology, University of Texas Medical School at Houston, Houston, Texas, USA
| | - Fernando Scaglia
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas, USA
| | - Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University Lucile Packard Children's Hospital, Palo Alto, California, USA
| | - Russell Saneto
- Department of Neurology, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA.,Department of Pediatrics, Seattle Children's Hospital, University of Washington, Seattle, Washington, USA
| | - Irina Anselm
- Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Bruce H Cohen
- Department of Pediatrics, NeuroDevelopmental Science Center, Children's Hospital Medical Center of Akron, Akron, Ohio, USA
| | - Marni J Falk
- Division of Human Genetics, Department of Pediatrics, The Children's Hospital of Philadelphia and University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Carol Greene
- Department of Pediatrics, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Andrea L Gropman
- Department of Neurology, Children's National Medical Center and the George Washington University of the Health Sciences, Washington, DC, USA
| | - Richard Haas
- Department of Neurosciences and Pediatrics, UCSD Medical Center and Rady Children's Hospital San Diego, La Jolla, California, USA
| | - Michio Hirano
- Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Phil Morgan
- Department of Anesthesiology, Seattle Children's Hospital, Seattle, Washington, USA
| | - Katherine Sims
- Department of Neurology, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Mark Tarnopolsky
- Department of Pediatrics and Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Johan L K Van Hove
- Department of Pediatrics, Clinical Genetics and Metabolism, Children's Hospital Colorado, Denver, Colorado, USA
| | - Lynne Wolfe
- National Institutes of Health, Bethesda, Maryland, USA
| | - Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, New York, USA
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7
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Epidermal nerve fiber density, oxidative stress, and mitochondrial haplogroups in HIV-infected Thais initiating therapy. AIDS 2014; 28:1625-33. [PMID: 24785954 DOI: 10.1097/qad.0000000000000297] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
OBJECTIVE We explored associations between mitochondrial DNA (mtDNA) haplogroups, epidermal nerve fiber density (ENFD), and HIV-associated sensory neuropathy (HIV-SN) in a randomized trial of Thai patients initiating antiretroviral therapy (ART). DESIGN The South East Asia Research Collaboration with Hawaii 003 study evaluated toxicity of nucleoside reverse transcriptase inhibitors (stavudine vs. zidovudine vs. tenofovir). We present secondary analyses of mtDNA haplogroups and ENFD changes. METHODS ENFD, peripheral blood mononuclear cell mitochondrial complex I and IV, and 8-oxo-deoxyguanine (8-oxo-dG) were quantified. Peripheral blood mononuclear cell mtDNA sequences were obtained for haplogroup determination. Multivariate regression of ENFD change was performed. RESULTS Paired ENFD was available from 118 patients. Median age, CD4 cell count, and height at entry were 34 years, 172 cells/μl, and 162 cm, respectively. Major haplogroups included M (42%), F (21%), and B (16%). Baseline ENFD, CD4 cell count, randomized ART, and biomarkers did not differ by haplogroup. Haplogroup B patients were older (P=0.02) at baseline, and had an increase in median ENFD (+1.5 vs. -2.9 fibers/mm; P=0.03) and 8-oxo-dG break frequency (+0.05 vs. 0.00; P=0.05) compared to other haplogroups. In a multivariate model, haplogroup B was associated with increased ENFD (β=3.5, P=0.009) at week 24, whereas older age (P=0.02), higher baseline CD4 cell count, (P=0.03), higher complex I level (P=0.03), and higher ENFD (P<0.001) at baseline were all associated with decreased ENFD. Three of the six HIV-SN cases were haplogroup B (P=0.05). CONCLUSIONS Thai persons belonging to mtDNA haplogroup B had increased ENFD and 8-oxo-dG on ART, and were more likely to develop HIV-SN. These results suggest that mtDNA variation influences early oxidative damage and ENFD changes.
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Blanco-Grau A, Bonaventura-Ibars I, Coll-Cantí J, Melià MJ, Martinez R, Martínez-Gallo M, Andreu AL, Pinós T, García-Arumí E. Identification and biochemical characterization of the novel mutation m.8839G>C in the mitochondrial ATP6 gene associated with NARP syndrome. GENES BRAIN AND BEHAVIOR 2013; 12:812-20. [PMID: 24118886 DOI: 10.1111/gbb.12089] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/25/2013] [Accepted: 09/30/2013] [Indexed: 12/21/2022]
Abstract
Mutations in the ATP6 gene are reported to be associated with Leber hereditary optic neuropathy, bilateral striatal necrosis, coronary atherosclerosis risk and neuropathy, ataxia and retinitis pigmentosa (NARP)/maternally inherited Leigh syndromes. Here, we present a patient with NARP syndrome, in whom a previously undescribed mutation was detected in the ATP6 gene: m.8839G>C. Several observations support the concept that m.8839G>C is pathogenically involved in the clinical phenotype of this patient: (1) the mutation was heteroplasmic in muscle; (2) mutation load was higher in the symptomatic patient than in the asymptomatic carriers; (3) cybrids carrying this mutation presented lower cell proliferation, increased mitochondrial DNA (mtDNA) copy number, increased steady-state OxPhos protein levels and decreased mitochondrial membrane potential with respect to isogenic wild-type cybrids; (4) this change was not observed in 2959 human mtDNAs from different mitochondrial haplogroups; (5) the affected amino acid was conserved in all the ATP6 sequences analyzed; and (6) using in silico prediction, the mutation was classified as 'probably damaging'. However, measurement of ATP synthesis showed no differences between wild-type and mutated cybrids. Thus, we suggest that m.8839G>C may lower the efficiency between proton translocation within F0 and F1 rotation, required for ATP synthesis. Further experiments are needed to fully characterize the molecular mechanisms involved in m.8839G>C pathogenicity.
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Affiliation(s)
- A Blanco-Grau
- Departament de Patología Mitocondrial i Neuromuscular, Universitari Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona
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Yuan JH, Sakiyama Y, Higuchi I, Inamori Y, Higuchi Y, Hashiguchi A, Higashi K, Yoshimura A, Takashima H. Mitochondrial myopathy with autophagic vacuoles in patients with the m.8344A>G mutation. J Clin Pathol 2013; 66:659-64. [PMID: 23559353 DOI: 10.1136/jclinpath-2012-201431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND AND AIMS In mitochondrial myopathy, autophagy is presumed to play an important role in mitochondrial dysfunction. Rimmed vacuoles (RVs), a sign of autophagy, can be seen as a secondary phenomenon in muscle ragged-red fibres (RRFs), whereas the uncommon presentation is that some fibres contain RVs, but without any mitochondrial abnormalities. To investigate the pathogenesis beneath this pathological phenomenon. METHODS We reviewed 783 skeletal muscle specimens and selected five obtained from patients with suspected mitochondrial myopathy, characterised by clearly visible autophagic vacuoles in non-RRFs, besides the coexistence of RRFs and cytochrome oxidase-negative fibres. Immunohistochemical staining with LC-3, and electron microscopy studies were performed. Using resequencing microarray and a next-generation sequencing system, the mitochondrial DNA was screened for mutations and the heteroplasmic level was measured in skeletal muscle and blood. RESULTS Muscle fibres with RVs and RRFs, as well as some morphologically normal fibres, stained strongly for LC-3. Electron microscopy disclosed significant abnormal mitochondrial proliferation and existence of autophagic vacuoles. After mutation screening, m.8344A>G in the tRNA(Lys) gene was detected in two patients. The heteroplasmy of mutated G was 45.1% in skeletal muscle and 17.8% in blood in patient 1; patient 2 exhibited 80.3% mutated G in skeletal muscle and 25.2% in blood. CONCLUSIONS These findings demonstrate a new pathological phenotype for the m.8344A>G mutation- related disease and also provide pathological evidence of a correlation between mitochondrial abnormalities and autophagy.
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Affiliation(s)
- Jun-Hui Yuan
- Department of Neurology and Geriatrics, Kagoshima University, Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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Zamzami MA, Duley JA, Price GR, Venter DJ, Yarham JW, Taylor RW, Catley LP, Florin THJ, Marinaki AM, Bowling F. Inosine triphosphate pyrophosphohydrolase (ITPA) polymorphic sequence variants in adult hematological malignancy patients and possible association with mitochondrial DNA defects. J Hematol Oncol 2013; 6:24. [PMID: 23547827 PMCID: PMC3765497 DOI: 10.1186/1756-8722-6-24] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Accepted: 03/13/2013] [Indexed: 01/27/2023] Open
Abstract
Background Inosine triphosphate pyrophosphohydrolase (ITPase) is a ‘house-cleaning’ enzyme that degrades non-canonical (‘rogue’) nucleotides. Complete deficiency is fatal in knockout mice, but a mutant polymorphism resulting in low enzyme activity with an accumulation of ITP and other non-canonical nucleotides, appears benign in humans. We hypothesised that reduced ITPase activity may cause acquired mitochondrial DNA (mtDNA) defects. Furthermore, we investigated whether accumulating mtDNA defects may then be a risk factor for cell transformation, in adult haematological malignancy (AHM). Methods DNA was extracted from peripheral blood and bone marrow samples. Microarray-based sequencing of mtDNA was performed on 13 AHM patients confirmed as carrying the ITPA 94C>A mutation causing low ITPase activity, and 4 AHM patients with wildtype ITPA. The frequencies of ITPA 94C>A and IVS2+21A>C polymorphisms were studied from 85 available AHM patients. Results ITPA 94C>A was associated with a significant increase in total heteroplasmic/homoplasmic mtDNA mutations (p<0.009) compared with wildtype ITPA, following exclusion of haplogroup variants. This suggested that low ITPase activity may induce mitochondrial abnormalities. Compared to the normal population, frequencies for the 94C>A and IVS2+21A>C mutant alleles among the AHM patients were higher for myelodyplastic syndrome (MDS) - but below significance; were approximately equivalent for chronic lymphoblastic leukemia; and were lower for acute myeloid leukemia. Conclusions This study invokes a new paradigm for the evolution of MDS, where nucleotide imbalances produced by defects in ‘house-cleaning’ genes may induce mitochondrial dysfunction, compromising cell integrity. It supports recent studies which point towards an important role for ITPase in cellular surveillance of rogue nucleotides.
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Dakubo GD. Mitochondrial genome analysis in biofluids for early cancer detection and monitoring. ACTA ACUST UNITED AC 2013; 2:263-75. [PMID: 23495657 DOI: 10.1517/17530059.2.3.263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
BACKGROUND Biofluids collected in a non-invasive fashion are potentially valuable samples for assaying genomic alterations for early detection and monitoring of cancer. The low cellularity and nucleic acid content in biofluids, the high copy number of the mitochondrial genome (mtgenome) and its noted early imprints in cancer make this molecule theoretically more sensitive than nuclear targets to measure for early cancer detection. OBJECTIVE This review explores mtgenome analysis in biofluids and addresses the question of whether targeting the mtgenome in biofluids is superior or equivalent to analysis of nuclear genomic alterations. METHODS The literature was retrieved from PubMed using a combination of the following keywords: mtDNA, mutation, deletion, content, copy number, cancer, biofluids, bodily fluids and the specific cancers described here. Studies that analyzed mtgenome alterations in biofluids were included. Analytical methods available for assaying mtgenome changes in biofluids are discussed. RESULTS Despite the limited data available, mtgenome changes in biofluids have been demonstrated in a wide variety of cancer patients. CONCLUSION Mtgenome analysis in biofluids is feasible and relatively easy. Despite the paucity of data, tumor-specific mtgenome changes are observed in biofluids of cancer patients. Given the multiple copies per cell of the mtgenome, future cancer detection efforts should consider complementary analysis of mtgenome changes in biofluids.
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Affiliation(s)
- Gabriel D Dakubo
- Senior Scientist Genesis Genomics, Inc., 290 Munro Street, Ste 1000, Thunder Bay, Ontario, P7A 7T1, Canada +1 807 768 4516 ; +1 807 346 8105 ;
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Pinós T, Melià MJ, Ortiz N, Martinez-Vea A, Raventós-Estellé A, Gallardo E, Hernández-Losa J, Cámara Y, Andreu AL, García-Arumí E. Identification of the novel mutation m.5658T>C in the mitochondrial tRNA(Asn) gene in a patient with myopathy, bilateral ptosis and ophthalmoparesis. Neuromuscul Disord 2013; 23:330-6. [PMID: 23375258 DOI: 10.1016/j.nmd.2013.01.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/25/2012] [Accepted: 01/02/2013] [Indexed: 12/13/2022]
Abstract
We report a heteroplasmic novel mutation m.5658T>C in the mt-tRNA(Asn) gene in a patient who initially presented myopathy, bilateral ptosis and ophthalmoparesis and several years later developed a non-nephrotic proteinuria. The muscle biopsy showed cytochrome c oxidase (COX) negative and ragged red fibers and in the kidney biopsy that was taken in order to identify the causes of non-nephrotic proteinuria, a focal segmental glomerulosclerosis was observed. Using laser capture microdissection we isolated COX negative fibers and COX positive fibers from the muscle of the patient and determined that there was a clear increase in the mutation load in the COX negative muscle fibers. However, the low degree of mutation load found in the renal biopsy of the patient does not allow us to conclude that the m.5658T>C mutation is responsible for focal glomerulosclerosis. Additionally, we hypothesize that the mutated m.5658T nucleotide might be structurally relevant, as it is one of the fifteen nucleotides conserved in all the species analyzed and is situated contiguously to the discriminator base in the 3'end of the mt-tRNA, where the tRNase Z cleaves the 3' trailer sequence during mt-tRNA maturation.
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Affiliation(s)
- Tomàs Pinós
- Departament de Patología Mitocondrial i Neuromuscular, Hospital Universitari Vall d'Hebron Institut de Recerca, Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Hammoudi N, Ahmed KBR, Garcia-Prieto C, Huang P. Metabolic alterations in cancer cells and therapeutic implications. CHINESE JOURNAL OF CANCER 2012; 30:508-25. [PMID: 21801600 PMCID: PMC4013402 DOI: 10.5732/cjc.011.10267] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cancer metabolism has emerged as an important area of research in recent years. Elucidation of the metabolic differences between cancer and normal cells and the underlying mechanisms will not only advance our understanding of fundamental cancer cell biology but also provide an important basis for the development of new therapeutic strategies and novel compounds to selectively eliminate cancer cells by targeting their unique metabolism. This article reviews several important metabolic alterations in cancer cells, with an emphasis on increased aerobic glycolysis (the Warburg effect) and glutamine addiction, and discusses the mechanisms that may contribute to such metabolic changes. In addition, metabolic alterations in cancer stem cells, mitochondrial metabolism and its influence on drug sensitivity, and potential therapeutic strategies and agents that target cancer metabolism are also discussed.
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Affiliation(s)
- Naima Hammoudi
- Department of Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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14
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Kassauei K, Habbe N, Mullendore ME, Karikari CA, Maitra A, Feldmann G. Mitochondrial DNA mutations in pancreatic cancer. ACTA ACUST UNITED AC 2012; 37:57-64. [PMID: 17827523 DOI: 10.1007/s12029-007-0008-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 01/19/2023]
Abstract
BACKGROUND Somatic mutations of mitochondrial DNA (mtDNA) are increasingly being recognized in many human cancers, but automated sequencing of 16.5 kb of DNA poses an onerous task. We have recently described an oligonucleotide microarray (MitoChip) for rapid and accurate sequencing of the entire mitochondrial genome (Zhou et al., J Mol Diagnostics, 8: 9_14, 2006), greatly facilitating the analysis of mtDNA mutations in cancer. In this report, we perform a comprehensive cataloging of somatic mutations in the mitochondrial genome of human pancreatic cancers using our novel array-based approach. MATERIALS AND METHODS MitoChip analysis was performed on DNA isolated from 15 histologically confirmed resection specimens of pancreatic ductal adenocarcinomas. In all cases, matched nonneoplastic pancreatic tissue was obtained as germline control for mtDNA sequence. DNA was extracted from snap-frozen cryostat-embedded specimens and hybridized to the sequencing microarray after appropriate polymerase chain reaction amplification and labeling steps. The vast majority of somatic mutational analyses of mtDNA in human cancers utilize lymphocyte DNA as germline control, without excluding the potential for organ-specific polymorphisms. Therefore, we also examined a series of 15 paired samples of DNA obtained from nonneoplastic pancreata and corresponding EBV-immortalized lymphoblastoid cell lines to determine whether lymphocyte DNA provides an accurate surrogate for the mtDNA sequence of pancreatic tissue. RESULTS We sequenced 497,070 base pairs of mtDNA in the 15 matched samples of pancreatic cancer and nonneoplastic pancreatic tissue, and 467,269 base pairs (94.0%) were assigned by the automated genotyping software. All 15 pancreatic cancers demonstrated at least one somatic mtDNA mutation compared to the control germline DNA with a range of 1-14 alterations. Of the 71 somatic mutations observed in our series, 18 were nonsynonymous coding region alterations (i.e., resulting in an amino acid change), 22 were synonymous coding region alterations, and 31 involved noncoding mtDNA segments (including ribosomal and transfer RNAs). Overall, somatic mutations in the coding region most commonly involved the ND4, COI, and CYTB genes; of note, an A-G transition at nucleotide position 841 in the 12sRNA was observed in three independent samples. In the paired analysis of nonneoplastic pancreata and lymphoblastoid cell line DNA, 14 nucleotide discrepancies were observed out of 226,876 nucleotide sequences (a concordance rate of 99.99%), with 9 samples demonstrating a perfect match across all bases assigned. CONCLUSIONS Our findings confirm that somatic mtDNA mutations are common in pancreatic cancers, and therefore, have the potential to be a clinically useful biomarker for early detection. Further, our studies confirm that lymphocyte DNA is an excellent, albeit not perfect, surrogate for nonneoplastic pancreatic tissues in terms of being utilized as a germline control. Finally, our report confirms the utility of a high-throughput array-based platform for mtDNA mutational analyses of human cancers.
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Affiliation(s)
- Keyanoosh Kassauei
- Department of Pathology, Johns Hopkins University School of Medicine, 1550 Orleans Street, Baltimore, MD 21231, USA
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15
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Dasgupta S, Soudry E, Mukhopadhyay N, Shao C, Yee J, Lam S, Lam W, Zhang W, Gazdar AF, Fisher PB, Sidransky D. Mitochondrial DNA mutations in respiratory complex-I in never-smoker lung cancer patients contribute to lung cancer progression and associated with EGFR gene mutation. J Cell Physiol 2012; 227:2451-60. [PMID: 21830212 DOI: 10.1002/jcp.22980] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations were reported in different cancers. However, the nature and role of mtDNA mutation in never-smoker lung cancer patients including patients with epidermal growth factor receptor (EGFR) and KRAS gene mutation are unknown. In the present study, we sequenced entire mitochondrial genome (16.5 kb) in matched normal and tumors obtained from 30 never-smoker and 30 current-smoker lung cancer patients, and determined the mtDNA content. All the patients' samples were sequenced for KRAS (exon 2) and EGFR (exon 19 and 21) gene mutation. The impact of forced overexpression of a respiratory complex-I gene mutation was evaluated in a lung cancer cell line. We observed significantly higher (P = 0.006) mtDNA mutation in the never-smokers compared to the current-smoker lung cancer patients. MtDNA mutation was significantly higher (P = 0.026) in the never-smoker Asian compared to the current-smoker Caucasian patients' population. MtDNA mutation was significantly (P = 0.007) associated with EGFR gene mutation in the never-smoker patients. We also observed a significant increase (P = 0.037) in mtDNA content among the never-smoker lung cancer patients. The majority of the coding mtDNA mutations targeted respiratory complex-I and forced overexpression of one of these mutations resulted in increased in vitro proliferation, invasion, and superoxide production in lung cancer cells. We observed a higher prevalence and new relationship between mtDNA alterations among never-smoker lung cancer patients and EGFR gene mutation. Moreover, a representative mutation produced strong growth effects after forced overexpression in lung cancer cells. Signature mtDNA mutations provide a basis to develop novel biomarkers and therapeutic strategies for never-smoker lung cancer patients.
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Affiliation(s)
- Santanu Dasgupta
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, USA.
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16
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Abstract
Mitochondria are ubiquitous organelles in eukaryotic cells principally responsible for regulating cellular energy metabolism, free radical production, and the execution of apoptotic pathways. Abnormal oxidative phosphorylation (OXPHOS) and aerobic metabolism as a result of mitochondrial dysfunction have long been hypothesized to be involved in tumorigenesis. In the past decades, numerous somatic mutations in both the coding and control regions of mitochondrial DNA (mtDNA) have been extensively examined in a broad range of primary human cancers, underscoring that accumulation of mtDNA alterations may be a critical factor in eliciting persistent mitochondrial defects and consequently contributing to cancer initiation and progression. However, the roles of these mtDNA mutations in the carcinogenic process remain largely unknown. This review outlines a wide variety of somatic mtDNA mutations identified in common human malignancies and highlights recent advances in understanding the causal roles of mtDNA variations in neoplastic transformation and tumor progression. In addition, it briefly illustrates how mtDNA alterations activate mitochondria-to-nucleus retrograde signaling so as to modulate the expression of relevant nuclear genes or induce epigenetic changes and promote malignant phenotypes in cancer cells. The present state of our knowledge regarding how mutational changes in the mitochondrial genome could be used as a diagnostic biomarker for early detection of cancer and as a potential target in the development of new therapeutic approaches is also discussed. These findings strongly indicate that mtDNA mutations exert a crucial role in the pathogenic mechanisms of tumor development, but continued investigations are definitely required to further elucidate the functional significance of specific mtDNA mutations in the etiology of human cancers.
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Zamzami MA, Price GR, Taylor RW, Blakely EL, Oancea I, Bowling F, Duley JA. Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0. BMC Res Notes 2011; 4:426. [PMID: 22011414 PMCID: PMC3208482 DOI: 10.1186/1756-0500-4-426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 10/20/2011] [Indexed: 01/07/2023] Open
Abstract
Background Developments in DNA resequencing microarrays include mitochondrial DNA (mtDNA) sequencing and mutation detection. Failure by the microarray to identify a base, compared to the reference sequence, is designated an 'N-call.' This study re-examined the N-call distribution of mtDNA samples sequenced by the Affymetrix MitoChip v.2.0, based on the hypothesis that N-calls may represent insertions or deletions (indels) in mtDNA. Findings We analysed 16 patient mtDNA samples using MitoChip. N-calls by the proprietary GSEQ software were significantly reduced when either of the freeware on-line algorithms ResqMi or sPROFILER was utilized. With sPROFILER, this decrease in N-calls had no effect on the homoplasmic or heteroplasmic mutation levels compared to GSEQ software, but ResqMi produced a significant change in mutation load, as well as producing longer N-cell stretches. For these reasons, further analysis using ResqMi was not attempted. Conventional DNA sequencing of the longer N-calls stretches from sPROFILER revealed 7 insertions and 12 point mutations. Moreover, analysis of single-base N-calls of one mtDNA sample found 3 other point mutations. Conclusions Our study is the first to analyse N-calls produced from GSEQ software for the MitoChipv2.0. By narrowing the focus to longer stretches of N-calls revealed by sPROFILER, conventional sequencing was able to identify unique insertions and point mutations. Shorter N-calls also harboured point mutations, but the absence of deletions among N-calls suggests that probe confirmation affects binding and thus N-calling. This study supports the contention that the GSEQ is more capable of assigning bases when used in conjunction with sPROFILER.
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18
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Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy. BMC Bioinformatics 2011; 12:402. [PMID: 22011106 PMCID: PMC3234255 DOI: 10.1186/1471-2105-12-402] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Accepted: 10/19/2011] [Indexed: 01/09/2023] Open
Abstract
Background Mitochondrial genome sequence analysis is critical to the diagnostic evaluation of mitochondrial disease. Existing methodologies differ widely in throughput, complexity, cost efficiency, and sensitivity of heteroplasmy detection. Affymetrix MitoChip v2.0, which uses a sequencing-by-genotyping technology, allows potentially accurate and high-throughput sequencing of the entire human mitochondrial genome to be completed in a cost-effective fashion. However, the relatively low call rate achieved using existing software tools has limited the wide adoption of this platform for either clinical or research applications. Here, we report the design and development of a custom bioinformatics software pipeline that achieves a much improved call rate and accuracy for the Affymetrix MitoChip v2.0 platform. We used this custom pipeline to analyze MitoChip v2.0 data from 24 DNA samples representing a broad range of tissue types (18 whole blood, 3 skeletal muscle, 3 cell lines), mutations (a 5.8 kilobase pair deletion and 6 known heteroplasmic mutations), and haplogroup origins. All results were compared to those obtained by at least one other mitochondrial DNA sequence analysis method, including Sanger sequencing, denaturing HPLC-based heteroduplex analysis, and/or the Illumina Genome Analyzer II next generation sequencing platform. Results An average call rate of 99.75% was achieved across all samples with our custom pipeline. Comparison of calls for 15 samples characterized previously by Sanger sequencing revealed a total of 29 discordant calls, which translates to an estimated 0.012% for the base call error rate. We successfully identified 4 known heteroplasmic mutations and 24 other potential heteroplasmic mutations across 20 samples that passed quality control. Conclusions Affymetrix MitoChip v2.0 analysis using our optimized MitoChip Filtering Protocol (MFP) bioinformatics pipeline now offers the high sensitivity and accuracy needed for reliable, high-throughput and cost-efficient whole mitochondrial genome sequencing. This approach provides a viable alternative of potential utility for both clinical diagnostic and research applications to traditional Sanger and other emerging sequencing technologies for whole mitochondrial genome analysis.
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Okamoto Y, Higuchi I, Sakiyama Y, Tokunaga S, Watanabe O, Arimura K, Nakagawa M, Takashima H. A new mitochondria-related disease showing myopathy with episodic hyper-creatine kinase-emia. Ann Neurol 2011; 70:486-92. [PMID: 21905081 DOI: 10.1002/ana.22498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
OBJECTIVE To elucidate the relationship between mitochondrial DNA (mtDNA) alterations and a mitochondrial disease with a distinct combination of characteristic symptoms, namely episodic hyper-creatine kinase (CK)-emia and mild myopathy. METHODS We selected 9 patients with mtDNA np8291 alteration from 586 patients suspected to have a mitochondrial disease, and assessed them clinically, pathologically, and genetically. These 9 patients had undiagnosed mitochondrial myopathy with episodic hyper-CK-emia, all showing similar symptoms and progression. RESULTS Patients had mild muscle weakness and episodic hyper-CK-emia triggered by infections or drugs. Five of 9 patients were initially diagnosed with other conditions, such as myasthenia gravis, polymyositis, viral myositis, and drug-induced myopathy, because these conditions were acute or subacute, and 9 patients showed the same 16 mtDNA alterations, which have been reported to be nonpathological polymorphisms. Muscle biopsy revealed ragged-red fibers, highly expressed succinate dehydrogenase staining fibers, and cytochrome c oxidase-deficient fibers. Because their mitochondrial sequence data was almost the same, and 9 patients live in widely separated cities in Japan, the alterations may have arisen from a single source. INTERPRETATION These findings suggest that mild myopathy with episodic hyper-CK-emia associated with some of the 16 mtDNA alterations or at least with their mitochondria, could be a novel mitochondrial disease. Therefore, we propose that this disease be named as "mitochondrial myopathy with episodic hyper-CK-emia (MIMECK)." These alterations could work concomitantly and probably modify the impact of medications or other environmental factors. We believe these findings provide an insight into a novel aspect of mitochondrial disease pathogenesis.
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Affiliation(s)
- Yuji Okamoto
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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20
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Inherited mitochondrial variants are not a major cause of age-related hearing impairment in the European population. Mitochondrion 2011; 11:729-34. [DOI: 10.1016/j.mito.2011.05.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2010] [Revised: 05/13/2011] [Accepted: 05/25/2011] [Indexed: 11/20/2022]
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21
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Dasgupta S, Shao C, Keane TE, Duberow DP, Mathies RA, Fisher PB, Kiemeney LA, Sidransky D. Detection of mitochondrial deoxyribonucleic acid alterations in urine from urothelial cell carcinoma patients. Int J Cancer 2011; 131:158-64. [PMID: 21826645 DOI: 10.1002/ijc.26357] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Accepted: 07/29/2011] [Indexed: 11/09/2022]
Abstract
Our study aims at understanding the timing and nature of mitochondrial deoxyribonucleic acid (mtDNA) alterations in urothelial cell carcinoma (UCC) and their detection in urine sediments. The entire 16.5 kb mitochondrial genome was sequenced in matched normal lymphocytes, tumor and urine sediments from 31 UCC patients and compared to different clinical stages and histological grades. The mtDNA content index was examined in all the specimens. Sixty-five percent (20/31) of the patients harbored at least 1 somatic mtDNA mutation. A total of 25 somatic mtDNA mutations were detected, which were more frequent in the respiratory complex coding regions (Complex I, III, IV and V) of the mtDNA and significantly affected respiratory Complex III compared to the other complexes (p = 0.021-0.039). Compared to Stage Ta, mtDNA mutation was higher in Stage T1 and significantly higher in Stage T2 (p = 0.01) patients. MtDNA mutation was also significantly higher (p = 0.04) in Stage T2 compared to Stage T1 patients. Ninety percent (18/20) of the patients harboring mtDNA mutation in the tumor also had mutation in their urine sediments. Eighty percent (20/25) of the tumor-associated mtDNA mutations was detectable in the urine sediments. Compared to the normal lymphocytes, the mtDNA content increased significantly in the tumor (p = 0.0013) and corresponding urine sediments (p = 0.0025) in 19/25 (76%) patients analyzed. Our results indicate that mtDNA alterations occur frequently in progressive stages of UCC patients and are readily detectable in the urine sediments. MtDNA mutations appear to provide a promising tool for developing early detection and monitoring strategies for UCC patients.
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Affiliation(s)
- Santanu Dasgupta
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, USA.
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22
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Kirches E. Mitochondrial and nuclear genes of mitochondrial components in cancer. Curr Genomics 2011; 10:281-93. [PMID: 19949549 PMCID: PMC2709939 DOI: 10.2174/138920209788488517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 04/29/2009] [Accepted: 04/30/2009] [Indexed: 11/22/2022] Open
Abstract
Although the observation of aerobic glycolysis of tumor cells by Otto v. Warburg had demonstrated abnormalities of mitochondrial energy metabolism in cancer decades ago, there was no clear evidence for a functional role of mutant mitochondrial proteins in cancer development until the early years of the 21(st) century. In the year 2000, a major breakthrough was achieved by the observation, that several genes coding for subunits of the respiratory chain (ETC) complex II, succinate dehydrogenase (SDH) are tumor suppressor genes in heritable paragangliomas, fulfilling Knudson's classical two-hit hypothesis. A functional inactivation of both alleles by germline mutations and chromosomal losses in the tumor tissue was found in the patients. Later, SDH mutations were also identified in sporadic paragangliomas and pheochromocytomas. Genes of the mitochondrial ATP-synthase and of mitochondrial iron homeostasis have been implicated in cancer development at the level of cell culture and mouse experiments. In contrast to the well established role of some nuclear SDH genes, a functional impact of the mitochondrial genome itself (mtDNA) in cancer development remains unclear. Nevertheless, the extremely high frequency of mtDNA mutations in solid tumors raises the question, whether this small circular genome might be applicable to early cancer detection. This is a meaningful approach, especially in cancers, which tend to spread tumor cells early into bodily fluids or faeces, which can be screened by non-invasive methods.
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Affiliation(s)
- E Kirches
- Department of Neuropathology, Otto-von-Guericke University, Magdeburg, Germany
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23
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Sakiyama Y, Okamoto Y, Higuchi I, Inamori Y, Sangatsuda Y, Michizono K, Watanabe O, Hatakeyama H, Goto YI, Arimura K, Takashima H. A new phenotype of mitochondrial disease characterized by familial late-onset predominant axial myopathy and encephalopathy. Acta Neuropathol 2011; 121:775-83. [PMID: 21424749 PMCID: PMC3098999 DOI: 10.1007/s00401-011-0818-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/11/2011] [Accepted: 03/11/2011] [Indexed: 01/08/2023]
Abstract
Axial myopathy is a rare neuromuscular disease that is characterized by paraspinal muscle atrophy and abnormal posture, most notably camptocormia (also known as bent spine). The genetic cause of familial axial myopathy is unknown. Described here are the clinical features and cause of late-onset predominant axial myopathy and encephalopathy. A 73-year-old woman presented with a 10-year history of severe paraspinal muscle atrophy and cerebellar ataxia. Her 84-year-old sister also developed late-onset paraspinal muscle atrophy and generalized seizures with encephalopathy. Computed tomography showed severe atrophy and fatty degeneration of their paraspinal muscles. Their mother and maternal aunt also developed bent spines. The existence of many ragged-red fibers and cytochrome c oxidase-negative fibers in the biceps brachii muscle of the proband indicated a mitochondrial abnormality. No significant abnormalities were observed in the respiratory chain enzyme activities; however, the activities of complexes I and IV were relatively low compared with the activities of other complexes. Sequence analysis of the mitochondrial DNA from the muscle revealed a novel heteroplasmic mutation (m.602C>T) in the mitochondrial tRNAPhe gene. This familial case of late-onset predominant axial myopathy and encephalopathy may represent a new clinical phenotype of a mitochondrial disease.
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Affiliation(s)
- Yusuke Sakiyama
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Yuji Okamoto
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Itsuro Higuchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Yukie Inamori
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Yoko Sangatsuda
- Department of Psychiatry, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kumiko Michizono
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Osamu Watanabe
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
| | - Hideyuki Hatakeyama
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Yu-ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, Japan
| | | | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima City, Kagoshima 890-8520 Japan
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Abstract
Mitochondria control essential cellular activities including generation of ATP via oxidative phosphorylation. Mitochondrial DNA (mtDNA) mutations in the regulatory D-loop region and somatic mtDNA mutations are common in primary human cancers. The biological impact of a given mutation may vary, depending on the nature of the mutation and the proportion of mutant mtDNAs carried by the cell. Identification of mtDNA mutations in precancerous lesions supports their early contribution to cell transformation and cancer progression. Introduction of mtDNA mutations in transformed cells has been associated with increased ROS production and tumor growth. Studies reveal that increased and altered mtDNA plays a role in the development of cancer but further work is required to establish the functional significance of specific mitochondrial mutations in cancer and disease progression. This review offers some insight into the extent of mtDNA mutations, their functional consequences in tumorigenesis, mitochondrial therapeutics, and future clinical application.
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Affiliation(s)
- Aditi Chatterjee
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA
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25
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Tranah GJ. Mitochondrial-nuclear epistasis: implications for human aging and longevity. Ageing Res Rev 2011; 10:238-52. [PMID: 20601194 DOI: 10.1016/j.arr.2010.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2010] [Revised: 06/17/2010] [Accepted: 06/17/2010] [Indexed: 12/22/2022]
Abstract
There is substantial evidence that mitochondria are involved in the aging process. Mitochondrial function requires the coordinated expression of hundreds of nuclear genes and a few dozen mitochondrial genes, many of which have been associated with either extended or shortened life span. Impaired mitochondrial function resulting from mtDNA and nuclear DNA variation is likely to contribute to an imbalance in cellular energy homeostasis, increased vulnerability to oxidative stress, and an increased rate of cellular senescence and aging. The complex genetic architecture of mitochondria suggests that there may be an equally complex set of gene interactions (epistases) involving genetic variation in the nuclear and mitochondrial genomes. Results from Drosophila suggest that the effects of mtDNA haplotypes on longevity vary among different nuclear allelic backgrounds, which could account for the inconsistent associations that have been observed between mitochondrial DNA (mtDNA) haplogroups and survival in humans. A diversity of pathways may influence the way mitochondria and nuclear-mitochondrial interactions modulate longevity, including: oxidative phosphorylation; mitochondrial uncoupling; antioxidant defenses; mitochondrial fission and fusion; and sirtuin regulation of mitochondrial genes. We hypothesize that aging and longevity, as complex traits having a significant genetic component, are likely to be controlled by nuclear gene variants interacting with both inherited and somatic mtDNA variability.
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26
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Challen C, Brown H, Cai C, Betts G, Paterson I, Sloan P, West C, Birch-Machin M, Robinson M. Mitochondrial DNA mutations in head and neck cancer are infrequent and lack prognostic utility. Br J Cancer 2011; 104:1319-24. [PMID: 21427725 PMCID: PMC3078603 DOI: 10.1038/bjc.2011.96] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Mitochondrial DNA (mtDNA) mutations occur in head and neck squamous cell carcinoma (HNSCC) and are most frequently detected in the displacement-loop (D-loop) region. The D-loop is considered to be important because it controls mitochondrial gene expression and mtDNA replication. There is currently no evidence that mtDNA mutations can be used as prognostic or predictive biomarkers in HNSCC. Methods: We used denaturing high performance liquid chromatography to screen the entire mitochondrial genome of six oral squamous cell carcinoma-derived cell lines and then focused on detecting D-loop abnormalities in 34 HNSCC tissue samples. Results: Mitochondrial DNA mutations are not ubiquitous in HNSCC because only half of the cell lines had detectable mtDNA abnormalities following screening of the entire mitochondrial genome and only 18% (6 of 34) of tissue samples had D-loop mutations. There was no correlation between D-loop mutations and determinates of clinical outcome; specifically, tumour stage and the expression of hypoxia-inducible genes included in a highly prognostic hypoxia metagene. Conclusions: Taken together, these data suggest that mtDNA D-loop mutations are stochastic events that may not significantly influence the biology of HNSCC and supports the hypothesis that mtDNA mutations in cancer represent bystander genotoxic damage as a consequence of tumour development and progression.
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Affiliation(s)
- C Challen
- Centre for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle-upon-Tyne NE2 4BW, UK
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27
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Jarchow-Choy SK, Krueger AT, Liu H, Gao J, Kool ET. Fluorescent xDNA nucleotides as efficient substrates for a template-independent polymerase. Nucleic Acids Res 2010; 39:1586-94. [PMID: 20947563 PMCID: PMC3045586 DOI: 10.1093/nar/gkq853] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Template independent polymerases, and terminal deoxynucleotidyl transferase (TdT) in particular, have been widely used in enzymatic labeling of DNA 3′-ends, yielding fluorescently-labeled polymers. The majority of fluorescent nucleotides used as TdT substrates contain tethered fluorophores attached to a natural nucleotide, and can be hindered by undesired fluorescence characteristics such as self-quenching. We previously documented the inherent fluorescence of a set of four benzo-expanded deoxynucleoside analogs (xDNA) that maintain Watson–Crick base pairing and base stacking ability; however, their substrate abilities for standard template-dependent polymerases were hampered by their large size. However, it seemed possible that a template-independent enzyme, due to lowered geometric constraints, might be less restrictive of nucleobase size. Here, we report the synthesis and study of xDNA nucleoside triphosphates, and studies of their substrate abilities with TdT. We find that this polymerase can incorporate each of the four xDNA monomers with kinetic efficiencies that are nearly the same as those of natural nucleotides, as measured by steady-state methods. As many as 30 consecutive monomers could be incorporated. Fluorescence changes over time could be observed in solution during the enzymatic incorporation of expanded adenine (dxATP) and cytosine (dxCTP) analogs, and after incorporation, when attached to a glass solid support. For (dxA)n polymers, monomer emission quenching and long-wavelength excimer emission was observed. For (dxC)n, fluorescence enhancement was observed in the polymer. TdT-mediated synthesis may be a useful approach for creating xDNA labels or tags on DNA, making use of the fluorescence and strong hybridization properties of the xDNA.
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Gowrisankar S, Lerner-Ellis JP, Cox S, White ET, Manion M, LeVan K, Liu J, Farwell LM, Iartchouk O, Rehm HL, Funke BH. Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications. J Mol Diagn 2010; 12:818-27. [PMID: 20864638 DOI: 10.2353/jmoldx.2010.100014] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Medical sequencing for diseases with locus and allelic heterogeneities has been limited by the high cost and low throughput of traditional sequencing technologies. "Second-generation" sequencing (SGS) technologies allow the parallel processing of a large number of genes and, therefore, offer great promise for medical sequencing; however, their use in clinical laboratories is still in its infancy. Our laboratory offers clinical resequencing for dilated cardiomyopathy (DCM) using an array-based platform that interrogates 19 of more than 30 genes known to cause DCM. We explored both the feasibility and cost effectiveness of using PCR amplification followed by SGS technology for sequencing these 19 genes in a set of five samples enriched for known sequence alterations (109 unique substitutions and 27 insertions and deletions). While the analytical sensitivity for substitutions was comparable to that of the DCM array (98%), SGS technology performed better than the DCM array for insertions and deletions (90.6% versus 58%). Overall, SGS performed substantially better than did the current array-based testing platform; however, the operational cost and projected turnaround time do not meet our current standards. Therefore, efficient capture methods and/or sample pooling strategies that shorten the turnaround time and decrease reagent and labor costs are needed before implementing this platform into routine clinical applications.
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Affiliation(s)
- Sivakumar Gowrisankar
- Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Genetic Medicine, 65 Landsdowne St., Cambridge, MA 02139, USA
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Dasgupta S, Koch R, Westra WH, Califano JA, Ha PK, Sidransky D, Koch WM. Mitochondrial DNA mutation in normal margins and tumors of recurrent head and neck squamous cell carcinoma patients. Cancer Prev Res (Phila) 2010; 3:1205-11. [PMID: 20660573 PMCID: PMC3040952 DOI: 10.1158/1940-6207.capr-10-0018] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations were reported in primary head and neck squamous cell carcinoma (HNSCC) patients. However, very little information is available on the mtDNA mutation pattern in the histologically negative surgical margins and tumors of HNSCC patients who experienced tumor recurrence. The present study aimed at understanding the nature and timing of mtDNA mutation in histologically negative margins, and tumors in HNSCC patients who developed local recurrence during the follow-ups. The entire 16.5-kb mitochondrial genome was sequenced in matched normal lymphocytes, histologically normal margins, and tumors of 50 recurrent HNSCC patients. The mtDNA mutations were then compared with clinical parameters. Forty-eight percent (24 of 50) of patients harbored at least one somatic mtDNA mutation in the tumor, and a total of 37 somatic mtDNA mutations were detected. The mtDNA mutations were mostly heteroplasmic in nature and nucleotide transitions (A<-->G; T<-->C). Forty-six percent of the mutations (17 of 37) were detected in the tumors and were also detectable in the corresponding histologically normal margin of the patients. The mtDNA mutations involved both coding and noncoding regions of the mtDNA. The majority (9 of 17, 53%) of the noncoding mutations involved tRNAs. Seventy-five percent (15 of 20) of the coding mtDNA mutations were nonsynonymous in nature and mainly affected cytochrome c oxidase (Complex IV), frequently altered in different human mitochondrial diseases including cancer. Analysis of mtDNA mutation could be an invaluable tool for molecular assessment of histologically negative margins and as well for monitoring HNSCC patients with locoregional recurrences.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/mortality
- Carcinoma, Squamous Cell/pathology
- Case-Control Studies
- DNA Mutational Analysis
- DNA, Mitochondrial/analysis
- DNA, Mitochondrial/genetics
- Genome, Mitochondrial
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/mortality
- Head and Neck Neoplasms/pathology
- Health
- Humans
- Middle Aged
- Mutation/physiology
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/mortality
- Neoplasm Recurrence, Local/pathology
- Survival Analysis
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Affiliation(s)
- Santanu Dasgupta
- Department of Otolaryngology, Johns Hopkins University School of Medicine, 601 North Caroline Street, JHOC 6221, Baltimore, MD 21287, USA
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Abstract
PURPOSE Genetic tests for the most commonly mutated genes in dilated cardiomyopathy (DCM) can confirm a clinical diagnosis in the proband and inform family management. Presymptomatic family members can be identified, allowing for targeted clinical monitoring to minimize adverse outcomes. However, the marked locus and allelic heterogeneity associated with DCM have made clinical genetic testing challenging. Novel sequencing platforms have now opened up avenues for more comprehensive diagnostic testing while simultaneously decreasing test cost and turn around time. METHODS By using a custom design based on triplicate resequencing and separate genotyping of known disease-causing variants, we developed the DCM CardioChip for efficient analysis of 19 genes previously implicated in causing DCM. RESULTS The chip's analytical sensitivity for known and novel substitution variants is 100% and 98%, respectively. In screening 73 previously tested DCM patients who did not carry clinically significant variants in 10 genes, 7 variants of likely clinical significance were identified in the remaining 9 genes included on the chip. Compared with traditional Sanger-based sequencing, test cost and turn around time were reduced by approximately 50%. CONCLUSIONS The DCM CardioChip is a highly efficient screening test with a projected clinical sensitivity of 26-29%.
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Moore AZ, Biggs ML, Matteini A, O'Connor A, McGuire S, Beamer BA, Fallin MD, Fried LP, Walston J, Chakravarti A, Arking DE. Polymorphisms in the mitochondrial DNA control region and frailty in older adults. PLoS One 2010; 5:e11069. [PMID: 20548781 PMCID: PMC2883558 DOI: 10.1371/journal.pone.0011069] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2009] [Accepted: 05/21/2010] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Mitochondria contribute to the dynamics of cellular metabolism, the production of reactive oxygen species, and apoptotic pathways. Consequently, mitochondrial function has been hypothesized to influence functional decline and vulnerability to disease in later life. Mitochondrial genetic variation may contribute to altered susceptibility to the frailty syndrome in older adults. METHODOLOGY/PRINCIPAL FINDINGS To assess potential mitochondrial genetic contributions to the likelihood of frailty, mitochondrial DNA (mtDNA) variation was compared in frail and non-frail older adults. Associations of selected SNPs with a muscle strength phenotype were also explored. Participants were selected from the Cardiovascular Health Study (CHS), a population-based observational study (1989-1990, 1992-1993). At baseline, frailty was identified as the presence of three or more of five indicators (weakness, slowness, shrinking, low physical activity, and exhaustion). mtDNA variation was assessed in a pilot study, including 315 individuals selected as extremes of the frailty phenotype, using an oligonucleotide sequencing microarray based on the Revised Cambridge Reference Sequence. Three mtDNA SNPs were statistically significantly associated with frailty across all pilot participants or in sex-stratified comparisons: mt146, mt204, and mt228. In addition to pilot participants, 4,459 additional men and women with frailty classifications, and an overlapping subset of 4,453 individuals with grip strength measurements, were included in the study population genotyped at mt204 and mt228. In the study population, the mt204 C allele was associated with greater likelihood of frailty (adjusted odds ratio = 2.04, 95% CI = 1.07-3.60, p = 0.020) and lower grip strength (adjusted coefficient = -2.04, 95% CI = -3.33- -0.74, p = 0.002). CONCLUSIONS This study supports a role for mitochondrial genetic variation in the frailty syndrome and later life muscle strength, demonstrating the importance of the mitochondrial genome in complex geriatric phenotypes.
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Affiliation(s)
- Ann Z. Moore
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Mary L. Biggs
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Amy Matteini
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Ashley O'Connor
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah McGuire
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Brock A. Beamer
- Division of Gerontology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - M. Danielle Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Linda P. Fried
- Columbia University Mailman School of Public Health, New York, New York, United States of America
| | - Jeremy Walston
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dan E. Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
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Johnston DS, Su YA, Alesci S. Mitochondrial gene profiling: translational perspectives. Pharmacogenomics 2010; 10:1645-55. [PMID: 19842937 DOI: 10.2217/pgs.09.112] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The last decade has witnessed the development of multiple microarray platforms designed to study, in a comprehensive fashion, the expression and sequence of both mitochondrial and nuclear genes that encode mitochondrial proteins. Mitochondrial dysfunction has been implicated in a number of severe medical conditions including cancer, metabolic diseases (i.e., cardiovascular, diabetes and obesity) and neurodegenerative disorders and it is responsible for the adverse effects of numerous drugs. Profiling of the genetic and genomic status of mitochondria with focused microarrays offers the promise of rapidly and robustly identifying novel biomarkers for early disease diagnoses and prognoses, predicting of drug safety, liability, and selecting and stratifying of patients in clinical trials.
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Affiliation(s)
- Daniel S Johnston
- Discovery Translational Medicine, Wyeth Research, 500 Arcola Rd, S2323, Collegeville, PA 19426, USA
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Chang SS, Jiang WW, Smith I, Glazer C, Sun WY, Mithani S, Califano JA. Chronic cigarette smoke extract treatment selects for apoptotic dysfunction and mitochondrial mutations in minimally transformed oral keratinocytes. Int J Cancer 2010; 126:19-27. [PMID: 19634139 PMCID: PMC2818069 DOI: 10.1002/ijc.24777] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cigarette smoke demonstrates a carcinogenic effect through chronic exposure, not acute exposures. However, current cell line models study only the acute effects of cigarette smoke. Using a cell line model, we compared the effects of acute versus chronic cigarette smoke extract (CSE) on mitochondria in minimally transformed oral keratinocytes (OKF6). OKF6 cells were treated with varying concentrations of CSE for 6 months. Cells were analyzed monthly by flow cytometry for mitochondrial membrane potential (MMP), cytochrome c release, caspase 3 activation and viability after CSE exposure. At each time point, the same assays were performed after 24 hr of valinomycin (MMP-depolarizing agent) treatment. The mitochondrial DNA of chronically CSE-treated cells was sequenced. After 6 months of CSE treatment, the cells were increasingly resistant to CSE-mediated and valinomycin-induced cell death. In addition, chronic CSE treatment caused chronic depolarization of MMP, cytochrome c release and caspase activation. Cells grown in the presence of only CSE vapor also exhibited the same resistance and chronic baseline apoptotic activation. Mitochondrial DNA sequencing found that chronic CSE-treated cells had more amino acid-changing mitochondrial mutations than acutely treated cells. CSE treatment of normal cells select for apoptotic dysfunction as well as mitochondrial mutations. These findings suggest that chronic tobacco exposure induces carcinogenesis via selection of apoptosis resistance and mitochondrial mutation in addition to previously known genotoxic effects that were found by acute treatments. Chronic models of tobacco exposure on upper aerodigestive epithelia may be more insightful than models of acute exposure in studying head and neck carcinogenesis.
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Affiliation(s)
- Steven S. Chang
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
| | - Wei Wen Jiang
- Department of Oral Mucosal Diseases, Affiliated 9th People's Hospital School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ian Smith
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
| | - Chad Glazer
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
| | - Wen-Yue Sun
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
| | - Suhail Mithani
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
| | - Joseph A. Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287
- Milton J Dance Head and Neck Center, Greater Baltimore Medical Center, 6569 North Charles Street, Physicians Pavilion West, Suite 200, Baltimore, MD 21204
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Mithani SK, Shao C, Tan M, Smith IM, Califano JA, El-Naggar AK, Ha PK. Mitochondrial mutations in adenoid cystic carcinoma of the salivary glands. PLoS One 2009; 4:e8493. [PMID: 20041111 PMCID: PMC2795173 DOI: 10.1371/journal.pone.0008493] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2009] [Accepted: 12/02/2009] [Indexed: 11/29/2022] Open
Abstract
Background The MitoChip v2.0 resequencing array is an array-based technique allowing for accurate and complete sequencing of the mitochondrial genome. No studies have investigated mitochondrial mutation in salivary gland adenoid cystic carcinomas. Methodology The entire mitochondrial genome of 22 salivary gland adenoid cystic carcinomas (ACC) of salivary glands and matched leukocyte DNA was sequenced to determine the frequency and distribution of mitochondrial mutations in ACC tumors. Principal Findings Seventeen of 22 ACCs (77%) carried mitochondrial mutations, ranging in number from 1 to 37 mutations. A disproportionate number of mutations occurred in the D-loop. Twelve of 17 tumors (70.6%) carried mutations resulting in amino acid changes of translated proteins. Nine of 17 tumors (52.9%) with a mutation carried an amino acid changing mutation in the nicotinamide adenine dinucleotide dehydrogenase (NADH) complex. Conclusions/Significance Mitochondrial mutation is frequent in salivary ACCs. The high incidence of amino acid changing mutations implicates alterations in aerobic respiration in ACC carcinogenesis. D-loop mutations are of unclear significance, but may be associated with alterations in transcription or replication.
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Affiliation(s)
- Suhail K. Mithani
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Chunbo Shao
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Marietta Tan
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Ian M. Smith
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
| | - Joseph A. Califano
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Johns Hopkins Head and Neck Surgery at the Greater Baltimore Medical Center, Milton J. Dance Head and Neck Center, Baltimore, Maryland, United States of America
| | - Adel K. El-Naggar
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Patrick K. Ha
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland, United States of America
- Johns Hopkins Head and Neck Surgery at the Greater Baltimore Medical Center, Milton J. Dance Head and Neck Center, Baltimore, Maryland, United States of America
- * E-mail:
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Thieme M, Lottaz C, Niederstätter H, Parson W, Spang R, Oefner PJ. ReseqChip: automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly. BMC Bioinformatics 2009; 10:440. [PMID: 20028526 PMCID: PMC3087351 DOI: 10.1186/1471-2105-10-440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 12/22/2009] [Indexed: 12/02/2022] Open
Abstract
Background The Affymetrix MitoChip v2.0 is an oligonucleotide tiling array for the resequencing of the human mitochondrial (mt) genome. For each of 16,569 nucleotide positions of the mt genome it holds two sets of four 25-mer probes each that match the heavy and the light strand of a reference mt genome and vary only at their central position to interrogate all four possible alleles. In addition, the MitoChip v2.0 carries alternative local context probes to account for known mtDNA variants. These probes have been neglected in most studies due to the lack of software for their automated analysis. Results We provide ReseqChip, a free software that automates the process of resequencing mtDNA using multiple local context probes on the MitoChip v2.0. ReseqChip significantly improves base call rate and sequence accuracy. ReseqChip is available at http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-live/trunk/Bio/Microarray/Tools/. Conclusions ReseqChip allows for the automated consolidation of base calls from alternative local mt genome context probes. It thereby improves the accuracy of resequencing, while reducing the number of non-called bases.
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Affiliation(s)
- Marian Thieme
- Institute of Functional Genomics, University of Regensburg, Josef-Engert-Str, 9, D-93053 Regensburg, Germany.
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Barker PE, Murthy M. Biomarker Validation for Aging: Lessons from mtDNA Heteroplasmy Analyses in Early Cancer Detection. Biomark Insights 2009; 4:165-79. [PMID: 20029650 PMCID: PMC2796862 DOI: 10.4137/bmi.s2253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The anticipated biological and clinical utility of biomarkers has attracted significant interest recently. Aging and early cancer detection represent areas active in the search for predictive and prognostic biomarkers. While applications differ, overlapping biological features, analytical technologies and specific biomarker analytes bear comparison. Mitochondrial DNA (mtDNA) as a biomarker in both biological models has been evaluated. However, it remains unclear whether mtDNA changes in aging and cancer represent biological relationships that are causal, incidental, or a combination of both. This article focuses on evaluation of mtDNA-based biomarkers, emerging strategies for quantitating mtDNA admixtures, and how current understanding of mtDNA in aging and cancer evolves with introduction of new technologies. Whether for cancer or aging, lessons from mtDNA based biomarker evaluations are several. Biological systems are inherently dynamic and heterogeneous. Detection limits for mtDNA sequencing technologies differ among methods for low-level DNA sequence admixtures in healthy and diseased states. Performance metrics of analytical mtDNA technology should be validated prior to application in heterogeneous biologically-based systems. Critical in evaluating biomarker performance is the ability to distinguish measurement system variance from inherent biological variance, because it is within the latter that background healthy variability as well as high-value, disease-specific information reside.
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Affiliation(s)
- Peter E. Barker
- Bioassay Methods Group, Biochemical Sciences Division, Bldg 227/B248, NIST, 100 Bureau Drive, Gaithersburg, Maryland
| | - Mahadev Murthy
- Division of Aging Biology (DAB), National Institute on Aging, 7201 Wisconsin Ave., GW 2C231, Bethesda, MD 20892.
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Mitochondrial DNA mutations and human disease. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1797:113-28. [PMID: 19761752 DOI: 10.1016/j.bbabio.2009.09.005] [Citation(s) in RCA: 417] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 01/07/2023]
Abstract
Mitochondrial disorders are a group of clinically heterogeneous diseases, commonly defined by a lack of cellular energy due to oxidative phosphorylation (OXPHOS) defects. Since the identification of the first human pathological mitochondrial DNA (mtDNA) mutations in 1988, significant efforts have been spent in cataloguing the vast array of causative genetic defects of these disorders. Currently, more than 250 pathogenic mtDNA mutations have been identified. An ever-increasing number of nuclear DNA mutations are also being reported as the majority of proteins involved in mitochondrial metabolism and maintenance are nuclear-encoded. Understanding the phenotypic diversity and elucidating the molecular mechanisms at the basis of these diseases has however proved challenging. Progress has been hampered by the peculiar features of mitochondrial genetics, an inability to manipulate the mitochondrial genome, and difficulties in obtaining suitable models of disease. In this review, we will first outline the unique features of mitochondrial genetics before detailing the diseases and their genetic causes, focusing specifically on primary mtDNA genetic defects. The functional consequences of mtDNA mutations that have been characterised to date will also be discussed, along with current and potential future diagnostic and therapeutic advances.
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Hall TA, Sannes-Lowery KA, McCurdy LD, Fisher C, Anderson T, Henthorne A, Gioeni L, Budowle B, Hofstadler SA. Base Composition Profiling of Human Mitochondrial DNA Using Polymerase Chain Reaction and Direct Automated Electrospray Ionization Mass Spectrometry. Anal Chem 2009; 81:7515-26. [DOI: 10.1021/ac901222y] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Thomas A. Hall
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Kristin A. Sannes-Lowery
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Leslie D. McCurdy
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Constance Fisher
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Theodore Anderson
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Almira Henthorne
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Lora Gioeni
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Bruce Budowle
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
| | - Steven A. Hofstadler
- Ibis Biosciences, subsidiary of Abbott Molecular, Inc., Carlsbad, California 92008, Federal Bureau of Investigation, Quantico, Virginia 22135, Armed Forces DNA Identification Laboratory, Rockville, Maryland 20850, and Department of Forensic and Investigative Genetics, Institute of Investigative Genetics, University of North Texas Health Science Center, Fort Worth, Texas 76107
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Dasgupta S, Yung RC, Westra WH, Rini DA, Brandes J, Sidransky D. Following mitochondrial footprints through a long mucosal path to lung cancer. PLoS One 2009; 4:e6533. [PMID: 19657397 PMCID: PMC2719062 DOI: 10.1371/journal.pone.0006533] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2009] [Accepted: 07/06/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) mutations are reported in different tumors. However, there is no information on the temporal development of the mtDNA mutations/content alteration and their extent in normal and abnormal mucosa continuously exposed to tobacco smoke in lung cancer patients. METHODOLOGY We examined the pattern of mtDNA alteration (mtDNA mutation and content index) in 25 airway mucosal biopsies, corresponding tumors and normal lymph nodes obtained from three patients with primary lung cancers. In addition, we examined the pattern of mtDNA mutation in corresponding tumors and normal lymph nodes obtained from eight other patients with primary lung cancers. The entire 16.5 kb mitochondrial genome was sequenced on Affymetrix Mitochip v2.0 sequencing platform in every sample. To examine mtDNA content index, we performed real-time PCR analysis. PRINCIPAL FINDINGS The airway mucosal biopsies obtained from three lung cancer patients were histopathologically negative but exhibited multiple clonal mtDNA mutations detectable in the corresponding tumors. One of the patients was operated twice for the removal of tumor from the right upper and left lower lobe respectively within a span of two years. Both of these tumors exhibited twenty identical mtDNA mutations. MtDNA content increased significantly (P<0.001) in the lung cancer and all the histologically negative mucosal biopsies except one compared to the control lymph node. CONCLUSIONS/SIGNIFICANCE Our results document the extent of massive clonal patches that develop in lifetime smokers and ultimately give rise to clinically significant cancers. These observations shed light on the extent of disease in the airway of smokers traceable through mtDNA mutation. MtDNA mutation could be a reliable tool for molecular assessment of respiratory epithelium exposed to continuous smoke as well as disease detection and monitoring. Functional analysis of the pathogenic mtDNA mutations may be useful to understand their role in lung tumorigenesis.
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Affiliation(s)
- Santanu Dasgupta
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Rex C. Yung
- Division of Pulmonary & Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - William H. Westra
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David A. Rini
- Department of Art as Applied to Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Johann Brandes
- Division of Pulmonary & Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, Maryland, United States of America
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41
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Rollins B, Martin MV, Sequeira PA, Moon EA, Morgan LZ, Watson SJ, Schatzberg A, Akil H, Myers RM, Jones EG, Wallace DC, Bunney WE, Vawter MP. Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder. PLoS One 2009; 4:e4913. [PMID: 19290059 PMCID: PMC2654519 DOI: 10.1371/journal.pone.0004913] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2008] [Accepted: 02/15/2009] [Indexed: 02/06/2023] Open
Abstract
Background Mitochondria provide most of the energy for brain cells by the process of oxidative phosphorylation. Mitochondrial abnormalities and deficiencies in oxidative phosphorylation have been reported in individuals with schizophrenia (SZ), bipolar disorder (BD), and major depressive disorder (MDD) in transcriptomic, proteomic, and metabolomic studies. Several mutations in mitochondrial DNA (mtDNA) sequence have been reported in SZ and BD patients. Methodology/Principal Findings Dorsolateral prefrontal cortex (DLPFC) from a cohort of 77 SZ, BD, and MDD subjects and age-matched controls (C) was studied for mtDNA sequence variations and heteroplasmy levels using Affymetrix mtDNA resequencing arrays. Heteroplasmy levels by microarray were compared to levels obtained with SNaPshot and allele specific real-time PCR. This study examined the association between brain pH and mtDNA alleles. The microarray resequencing of mtDNA was 100% concordant with conventional sequencing results for 103 mtDNA variants. The rate of synonymous base pair substitutions in the coding regions of the mtDNA genome was 22% higher (p = 0.0017) in DLPFC of individuals with SZ compared to controls. The association of brain pH and super haplogroup (U, K, UK) was significant (p = 0.004) and independent of postmortem interval time. Conclusions Focusing on haplogroup and individual susceptibility factors in psychiatric disorders by considering mtDNA variants may lead to innovative treatments to improve mitochondrial health and brain function.
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Affiliation(s)
- Brandi Rollins
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Maureen V. Martin
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - P. Adolfo Sequeira
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Emily A. Moon
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Ling Z. Morgan
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Stanley J. Watson
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Alan Schatzberg
- Department of Psychiatry, Stanford University, Palo Alto, California, United States of America
| | - Huda Akil
- Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Richard M. Myers
- Hudson Alpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Edward G. Jones
- Neuroscience Center, University of California Davis, Davis, California, United States of America
| | - Douglas C. Wallace
- Molecular and Mitochondrial Medicine and Genetics, University of California Irvine, Irvine, California, United States of America
| | - William E. Bunney
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
| | - Marquis P. Vawter
- Department of Psychiatry & Human Behavior, University of California Irvine, Irvine, California, United States of America
- * E-mail:
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42
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Hartmann A, Thieme M, Nanduri LK, Stempfl T, Moehle C, Kivisild T, Oefner PJ. Validation of microarray-based resequencing of 93 worldwide mitochondrial genomes. Hum Mutat 2009; 30:115-22. [PMID: 18623076 DOI: 10.1002/humu.20816] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human mitochondrial genome consists of a multicopy, circular dsDNA molecule of 16,569 base pairs. It encodes for 13 proteins, two ribosomal genes, and 22 tRNAs that are essential in the generation of cellular ATP by oxidative phosphorylation in eukaryotic cells. Germline mutations in mitochondrial DNA (mtDNA) are an important cause of maternally inherited diseases, while somatic mtDNA mutations may play important roles in aging and cancer. mtDNA polymorphisms are also widely used in population and forensic genetics. Therefore, methods that allow the rapid, inexpensive and accurate sequencing of mtDNA are of great interest. One such method is the Affymetrix GeneChip Human Mitochondrial Resequencing Array 2.0 (MitoChip v.2.0) (Santa Clara, CA). A direct comparison of 93 worldwide mitochondrial genomes sequenced by both the MitoChip and dideoxy terminator sequencing revealed an average call rate of 99.48% and an accuracy of > or =99.98% for the MitoChip. The good performance was achieved by using in-house software for the automated analysis of additional probes on the array that cover the most common haplotypes in the hypervariable regions (HVR). Failure to call a base was associated mostly with the presence of either a run of > or =4 C bases or a sequence variant within 12 bases up- or downstream of that base. A major drawback of the MitoChip is its inability to detect insertions/deletions and its low sensitivity and specificity in the detection of heteroplasmy. However, the vast majority of haplogroup defining polymorphism in the mtDNA phylogeny could be called unambiguously and more rapidly than with conventional sequencing.
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Affiliation(s)
- Anne Hartmann
- Institute of Functional Genomics, University of Regensburg, Regensburg, Germany
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43
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Pietka G, Kukwa W, Bartnik E, Scińska A, Czarnecka AM. [Mitochondrial DNA mutations in the pathogenesis in the head and neck squamous cell carcinoma]. Otolaryngol Pol 2008; 62:158-64. [PMID: 18637439 DOI: 10.1016/s0030-6657(08)70233-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Data reported until today suggested a pivotal role of nuclear DNA mutations in the process of carcinogenesis. Recently more and more authors claim that disruption of mitochondrial DNA should not be excluded from this analysis. mtDNA have been reported in many cancers of head and neck region. Mitochondrial D-loop has been proven to be mutation hot - spot with majority of mutations in the positions 303 to 315 of poly-C tract. Data show that 37% of patients with premalignant lesions and 62% with carcinoma in situ are positive for mtDNA mutations. Moreover mutations in genes encoding ND2, ND5, COIII, CYTB, and ATP6 were observed in 17% of patients. Mutations in mitochondrial rRNA genes occured in similar number of cases. Neoplastic cells undifferentiation and disease progression is accompanied by multiplication of mtDNA number and increased mtDNA content. mtDNA content corellates with the stage of the disease. mtDNA mutations faciliate cell proliferation and inhibit apoptosis by increasing the production of ractive oxygen species (ROS). Cells harbouring mutated mtDNA have increased proliferation rate, as increased ROS concentration may act as an endogenous growth factor.
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Affiliation(s)
- Grzegorz Pietka
- Instytut Genetyki i Biotechnologii Uniwersytetu Warszawskiego
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44
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Abstract
Earlier studies of mitochondrial mutations in melanoma have focused on analysis of selected mitochondrial genes and the displacement loop (D-loop) region using conventional sequencing. In this study we use data from a whole mitochondria-sequencing array, the MitoChip v2.0, to characterize the mutations that are present throughout the mitochondrial genome. The mitochondrial genome of DNA derived from 14 fresh melanoma specimens and two melanoma cell lines, and autologous lymphocytes or immortalized B cells, respectively, were sequenced using the MitoChip v2.0. Paired comparative sequence analysis was carried out to define somatic mutations. Somatic mitochondrial DNA mutations were identified in 12/16 (75%) melanomas, compared with germline lymphocyte DNA. One hundred mutations were present among these 12 melanomas. A disproportionate number of mutations occurred in the D-loop. Furthermore, 9/16 (56.3%) melanomas carried mutations, which resulted in amino acid substitutions in functional genes. In the 10 samples carrying nicotinamide adenine dinucleotide dehydrogenase (ND) complex mutations, multiple mutations were present at a rate significantly greater than the expected frequency based on the size of ND complex genes (P=0.028, Fisher's exact test). Mitochondrial mutation is a frequent occurrence in melanoma. The high rate of missense mutations and the propensity for the ND complex implicate a role for alterations in mitochondrial respiratory function in melanoma carcinogenesis. Mutations of the noncoding D-loop are of unclear significance, but may be associated with alterations in transcription or replication. Further studies are needed to delineate the timing and functional significance of these mutations, and their role in the pathogenesis of this disease.
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45
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Haas RH, Parikh S, Falk MJ, Saneto RP, Wolf NI, Darin N, Wong LJ, Cohen BH, Naviaux RK. The in-depth evaluation of suspected mitochondrial disease. Mol Genet Metab 2008; 94:16-37. [PMID: 18243024 PMCID: PMC2810849 DOI: 10.1016/j.ymgme.2007.11.018] [Citation(s) in RCA: 252] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2007] [Revised: 11/21/2007] [Accepted: 11/21/2007] [Indexed: 12/12/2022]
Abstract
Mitochondrial disease confirmation and establishment of a specific molecular diagnosis requires extensive clinical and laboratory evaluation. Dual genome origins of mitochondrial disease, multi-organ system manifestations, and an ever increasing spectrum of recognized phenotypes represent the main diagnostic challenges. To overcome these obstacles, compiling information from a variety of diagnostic laboratory modalities can often provide sufficient evidence to establish an etiology. These include blood and tissue histochemical and analyte measurements, neuroimaging, provocative testing, enzymatic assays of tissue samples and cultured cells, as well as DNA analysis. As interpretation of results from these multifaceted investigations can become quite complex, the Diagnostic Committee of the Mitochondrial Medicine Society developed this review to provide an overview of currently available and emerging methodologies for the diagnosis of primary mitochondrial disease, with a focus on disorders characterized by impairment of oxidative phosphorylation. The aim of this work is to facilitate the diagnosis of mitochondrial disease by geneticists, neurologists, and other metabolic specialists who face the challenge of evaluating patients of all ages with suspected mitochondrial disease.
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Affiliation(s)
- Richard H. Haas
- Departments of Neurosciences & Pediatrics, University of California San Diego, La Jolla, CA and Rady Children's Hospital San Diego, San Diego, CA
- Corresponding Author: Richard H. Haas, MB, BChir, MRCP, Professor of Neurosciences and Pediatrics, University of California San Diego, T. 858-822-6700; F. 858-822-6707;
| | - Sumit Parikh
- Division of Neuroscience, The Cleveland Clinic, Cleveland, OH
| | - Marni J. Falk
- Division of Human Genetics, The Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA
| | - Russell P. Saneto
- Division of Pediatric Neurology, Children's Hospital and Regional Medical Center, University of Washington, Seattle, WA
| | - Nicole I. Wolf
- Department of Child Neurology, University Children's Hospital, Heidelberg, Germany
| | - Niklas Darin
- Division of Child Neurology, The Queen Silvia Children's Hospital, Göteborg, Sweden
| | - Lee-Jun Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bruce H. Cohen
- Division of Neuroscience, The Cleveland Clinic, Cleveland, OH
| | - Robert K. Naviaux
- Departments of Medicine and Pediatrics, Division of Medical and Biochemical Genetics, University of California San Diego, La Jolla, CA and Rady Children's Hospital San Diego, San Diego, CA
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Empirical evaluation of a new method for calculating signal-to-noise ratio for microarray data analysis. Appl Environ Microbiol 2008; 74:2957-66. [PMID: 18344333 DOI: 10.1128/aem.02536-07] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Signal-to-noise-ratio (SNR) thresholds for microarray data analysis were experimentally determined with an oligonucleotide array that contained perfect-match (PM) and mismatch (MM) probes based upon four genes from Shewanella oneidensis MR-1. A new SNR calculation, called the signal-to-both-standard-deviations ratio (SSDR), was developed and evaluated, along with other two methods, the signal-to-standard-deviation ratio (SSR) and the signal-to-background ratio (SBR). At a low stringency, the thresholds of the SSR, SBR, and SSDR were 2.5, 1.60, and 0.80 with an oligonucleotide and a PCR amplicon as target templates and 2.0, 1.60, and 0.70 with genomic DNAs as target templates. Slightly higher thresholds were obtained under high-stringency conditions. The thresholds of the SSR and SSDR decreased with an increase in the complexity of targets (e.g., target types) and the presence of background DNA and a decrease in the compositions of targets, while the SBR remained unchanged in all situations. The lowest percentage of false positives and false negatives was observed with the SSDR calculation method, suggesting that it may be a better SNR calculation for more accurate determination of SNR thresholds. Positive spots identified by SNR thresholds were verified by the Student t test, and consistent results were observed. This study provides general guidance for users to select appropriate SNR thresholds for different samples under different hybridization conditions.
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Mithani SK, Smith IM, Zhou S, Gray A, Koch WM, Maitra A, Califano JA. Mitochondrial resequencing arrays detect tumor-specific mutations in salivary rinses of patients with head and neck cancer. Clin Cancer Res 2008; 13:7335-40. [PMID: 18094415 DOI: 10.1158/1078-0432.ccr-07-0220] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Alterations of the mitochondrial genome have been identified in multiple solid tumors and in many head and neck squamous cell carcinomas (HNSCC). Identification of mitochondrial mutations in the salivary rinses of patients with HNSCC has potential application in disease detection. In this study, we used the MitoChip v2.0 mitochondrial genome resequencing array to detect minor populations of mitochondrial DNA in salivary rinses of patients with HNSCC. EXPERIMENTAL DESIGN Salivary rinses from 13 patients with HNSCC, whose tumors carried mitochondrial mutations, were collected before surgical resection. DNA isolated from salivary rinses and serial dilutions of DNA derived from HNSCC-derived cell lines with known mitochondrial mutations were sequenced using the MitoChip, and analyzed using a quantitative algorithm which we developed to detect minor populations of mitochondrial DNA from MitoChip probe intensity data. RESULTS We detected heteroplasmic populations of mitochondrial DNA up to a 1:200 dilution using MitoChip v2.0 and our analysis algorithm. A logarithmic relationship between the magnitude of assay intensity and concentration of minor mitochondrial populations was shown. This technique was able to identify tumor-specific mitochondrial mutations in salivary rinses from 10 of 13 (76.9%) patients with head and neck cancer. CONCLUSIONS Minor populations of mitochondrial DNA and disease-specific mitochondrial mutations in salivary rinses of patients with HNSCC can be successfully identified using the MitoChip resequencing array and the algorithm which we have developed. This technique has potential application in the surveillance of patients after resection and may have applicability in the surveillance of body fluids in other tumor types.
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Affiliation(s)
- Suhail K Mithani
- Department of Surgery, Division of Plastic and Reconstructive Surgery, Johns Hopkins Medical Institutions, Baltimore, MD 21287, USA
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Maragh S, Jakupciak JP, Wagner PD, Rom WN, Sidransky D, Srivastava S, O'Connell CD. Multiple strand displacement amplification of mitochondrial DNA from clinical samples. BMC MEDICAL GENETICS 2008; 9:7. [PMID: 18257929 PMCID: PMC2268916 DOI: 10.1186/1471-2350-9-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 02/07/2008] [Indexed: 01/23/2023]
Abstract
Background Whole genome amplification (WGA) methods allow diagnostic laboratories to overcome the common problem of insufficient DNA in patient specimens. Further, body fluid samples useful for cancer early detection are often difficult to amplify with traditional PCR methods. In this first application of WGA on the entire human mitochondrial genome, we compared the accuracy of mitochondrial DNA (mtDNA) sequence analysis after WGA to that performed without genome amplification. We applied the method to a small group of cancer cases and controls and demonstrated that WGA is capable of increasing the yield of starting DNA material with identical genetic sequence. Methods DNA was isolated from clinical samples and sent to NIST. Samples were amplified by PCR and those with no visible amplification were re-amplified using the Multiple Displacement Amplificaiton technique of whole genome amplification. All samples were analyzed by mitochip for mitochondrial DNA sequence to compare sequence concordance of the WGA samples with respect to native DNA. Real-Time PCR analysis was conducted to determine the level of WGA amplification for both nuclear and mtDNA. Results In total, 19 samples were compared and the concordance rate between WGA and native mtDNA sequences was 99.995%. All of the cancer associated mutations in the native mtDNA were detected in the WGA amplified material and heteroplasmies in the native mtDNA were detected with high fidelity in the WGA material. In addition to the native mtDNA sequence present in the sample, 13 new heteroplasmies were detected in the WGA material. Conclusion Genetic screening of mtDNA amplified by WGA is applicable for the detection of cancer associated mutations. Our results show the feasibility of this method for: 1) increasing the amount of DNA available for analysis, 2) recovering the identical mtDNA sequence, 3) accurately detecting mtDNA point mutations associated with cancer.
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Affiliation(s)
- Samantha Maragh
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
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Mithani SK, Taube JM, Zhou S, Smith IM, Koch WM, Westra WH, Califano JA. Mitochondrial mutations are a late event in the progression of head and neck squamous cell cancer. Clin Cancer Res 2007; 13:4331-5. [PMID: 17671113 DOI: 10.1158/1078-0432.ccr-06-2613] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To determine the timing of mitochondrial mutations in the progression of head and neck squamous cell carcinoma. EXPERIMENTAL DESIGN Twenty-three mitochondrial mutations were identified in 12 tumors using a high-throughput mitochondrial sequencing array. Areas of adjacent dysplastic and normal epithelium adjacent to tumors were sequenced using conventional methods for the presence of mutations that occurred in the corresponding tumor. RESULTS Two of 23 (8.7%) tumor mitochondrial mutations (2 of 12 tumors) were present in both the areas of adjacent dysplasia and normal epithelium. Five of 23 (21.7%) tumor mitochondrial mutations (4 of 12 tumors) were present in areas of adjacent dysplasia. Eleven of 12 tumors contained nonsynonymous mutations that resulted in protein coding alterations. A significant difference (P < 0.01, chi(2)) was found in the incidence of mitochondrial mutation that occurred after development of cancer compared with adjacent areas dysplasia and normal epithelium. CONCLUSIONS The majority of mitochondrial mutations occur during or after the transition of preneoplastic epithelium to cancer in head and neck squamous cell carcinoma, indicating that these are a late event in head and neck carcinogenesis.
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Affiliation(s)
- Suhail K Mithani
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, Maryland 21287-0910, USA
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Lévêque M, Marlin S, Jonard L, Procaccio V, Reynier P, Amati-Bonneau P, Baulande S, Pierron D, Lacombe D, Duriez F, Francannet C, Mom T, Journel H, Catros H, Drouin-Garraud V, Obstoy MF, Dollfus H, Eliot MM, Faivre L, Duvillard C, Couderc R, Garabedian EN, Petit C, Feldmann D, Denoyelle F. Whole mitochondrial genome screening in maternally inherited non-syndromic hearing impairment using a microarray resequencing mitochondrial DNA chip. Eur J Hum Genet 2007; 15:1145-55. [PMID: 17637808 DOI: 10.1038/sj.ejhg.5201891] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Mitochondrial DNA (mtDNA) mutations have been implicated in non-syndromic hearing loss either as primary or as predisposing factors. As only a part of the mitochondrial genome is usually explored in deafness, its prevalence is probably under-estimated. Among 1350 families with non-syndromic sensorineural hearing loss collected through a French collaborative network, we selected 29 large families with a clear maternal lineage and screened them for known mtDNA mutations in 12S rRNA, tRNASer(UCN) and tRNALeu(UUR) genes. When no mutation could be identified, a whole mitochondrial genome screening was performed, using a microarray resequencing chip: the MitoChip version 2.0 developed by Affymetrix Inc. Known mtDNA mutations was found in nine of the 29 families, which are described in the article: five with A1555G, two with the T7511C, one with 7472insC and one with A3243G mutation. In the remaining 20 families, the resequencing Mitochip detected 258 mitochondrial homoplasmic variants and 107 potentially heteroplasmic variants. Controls were made by direct sequencing on selected fragments and showed a high sensibility of the MitoChip but a low specificity, especially for heteroplasmic variations. An original analysis on the basis of species conservation, frequency and phylogenetic investigation was performed to select the more probably pathogenic variants. The entire genome analysis allowed us to identify five additional families with a putatively pathogenic mitochondrial variant: T669C, C1537T, G8078A, G12236A and G15077A. These results indicate that the new MitoChip platform is a rapid and valuable tool for identification of new mtDNA mutations in deafness.
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