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Kaur P, Nazeer N, Gurjar V, Tiwari R, Kumar Mishra P. Nanophotonic waveguide-based sensing of circulating cell-free mitochondrial DNA: implications for personalized medicine. Drug Discov Today 2024:104086. [PMID: 38960132 DOI: 10.1016/j.drudis.2024.104086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) has emerged as a promising biomarker, with potential implications for disease diagnosis. Changes in mtDNA, such as deletions, mutations or variations in the number of copies, have been associated with mitochondrial disorders, heart diseases, cancer and age-related non-communicable diseases. Previous methods, such as polymerase chain reaction-based approaches, next-generation sequencing and imaging-based techniques, have shown improved accuracy in identifying rare mtDNA variants or mutations, but they have limitations. This article explains the basic principles and benefits of using planar optical waveguide-based detection devices, which represent an advanced approach in the field of sensing.
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Affiliation(s)
- Prasan Kaur
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nazim Nazeer
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Vikas Gurjar
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Rajnarayan Tiwari
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Pradyumna Kumar Mishra
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India.
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Ikekpeazu JE, Orji OC, Uchendu IK, Ezeanyika LU. Mitochondrial and Oxidative Impacts of Short and Long-term Administration of HAART on HIV Patients. CURRENT CLINICAL PHARMACOLOGY 2020; 15:110-124. [PMID: 31486756 PMCID: PMC7579318 DOI: 10.2174/1574884714666190905162237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 04/05/2019] [Accepted: 07/11/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND There may be a possible link between the use of HAART and oxidative stress-related mitochondrial dysfunction in HIV patients. We evaluated the mitochondrial and oxidative impacts of short and long-term administration of HAART on HIV patients attending the Enugu State University Teaching (ESUT) Hospital, Enugu, Nigeria following short and long-term therapy. METHODS 96 patients categorized into four groups of 24 individuals were recruited for the study. Group 1 comprised of age-matched, apparently healthy, sero-negative individuals (the No HIV group); group 2 consisted of HIV sero-positive individuals who had not started any form of treatment (the Treatment naïve group). Individuals in group 3 were known HIV patients on HAART for less than one year (Short-term treatment group), while group 4 comprised of HIV patients on HAART for more than one year (Long-term treatment group). All patients were aged between 18 to 60 years and attended the HIV clinic at the time of the study. Determination of total antioxidant status (TAS in nmol/l), malondialdehyde (MDA in mmol/l), CD4+ count in cells/μl, and genomic studies were all done using standard operative procedures. RESULTS We found that the long-term treatment group had significantly raised the levels of MDA, as well as significantly diminished TAS compared to the Short-term treatment and No HIV groups (P<0.05). In addition, there was significantly elevated variation in the copy number of mitochondrial genes (mtDNA: D-loop, ATPase 8, TRNALEU uur) in the long-term treatment group. CONCLUSION Long-term treatment with HAART increases oxidative stress and causes mitochondrial alterations in HIV patients.
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Affiliation(s)
| | | | - Ikenna K. Uchendu
- Address correspondence to this author at the Department of Medical Laboratory Science, Faculty of Health Science and Technology, College of Medicine, University of Nigeria Enugu Campus, Enugu State, Nigeria;, Tel: +2347068199556; E-mail:
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Voss JG, Dobra A, Morse C, Kovacs JA, Danner RL, Munson PJ, Logan C, Rangel Z, Adelsberger JW, McLaughlin M, Adams LD, Raju R, Dalakas MC. Fatigue-related gene networks identified in CD(14)+ cells isolated from HIV-infected patients: part I: research findings. Biol Res Nurs 2013; 15:137-51. [PMID: 23324479 DOI: 10.1177/1099800411421957] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PURPOSE Human immunodeficiency virus (HIV)-related fatigue (HRF) is multicausal and potentially related to mitochondrial dysfunction caused by antiretroviral therapy with nucleoside reverse transcriptase inhibitors (NRTIs). METHODOLOGY The authors compared gene expression profiles of CD14(+) cells of low versus high fatigued, NRTI-treated HIV patients to healthy controls (n = 5/group). The authors identified 32 genes predictive of low versus high fatigue and 33 genes predictive of healthy versus HIV infection. The authors constructed genetic networks to further elucidate the possible biological pathways in which these genes are involved. RELEVANCE FOR NURSING PRACTICE: Genes including the actin cytoskeletal regulatory proteins Prokineticin 2 and Cofilin 2 along with mitochondrial inner membrane proteins are involved in multiple pathways and were predictors of fatigue status. Previously identified inflammatory and signaling genes were predictive of HIV status, clearly confirming our results and suggesting a possible further connection between mitochondrial function and HIV. Isolated CD14(+) cells are easily accessible cells that could be used for further study of the connection between fatigue and mitochondrial function of HIV patients. IMPLICATION FOR PRACTICE The findings from this pilot study take us one step closer to identifying biomarker targets for fatigue status and mitochondrial dysfunction. Specific biomarkers will be pertinent to the development of methodologies to diagnosis, monitor, and treat fatigue and mitochondrial dysfunction.
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Affiliation(s)
- Joachim G Voss
- Biobehavioral Nursing & Health Systems Department, University of Washington, School of Nursing, Seattle, WA 98195, USA.
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Elstner M, Turnbull DM. Transcriptome analysis in mitochondrial disorders. Brain Res Bull 2012; 88:285-93. [DOI: 10.1016/j.brainresbull.2011.07.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Accepted: 07/24/2011] [Indexed: 12/21/2022]
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Morse CG, Voss JG, Rakocevic G, McLaughlin M, Vinton CL, Huber C, Hu X, Yang J, Huang DW, Logun C, Danner RL, Rangel ZG, Munson PJ, Orenstein JM, Rushing EJ, Lempicki RA, Dalakas MC, Kovacs JA. HIV infection and antiretroviral therapy have divergent effects on mitochondria in adipose tissue. J Infect Dis 2012; 205:1778-87. [PMID: 22476717 PMCID: PMC3357134 DOI: 10.1093/infdis/jis101] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 06/28/2011] [Accepted: 07/05/2011] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Although human immunodeficiency virus (HIV) infection and antiretroviral therapy (ART) affect mitochondrial DNA (mtDNA) content and function, comprehensive evaluations of their effects on mitochondria in muscle, adipose tissue, and blood cells are limited. METHODS Mitochondrial DNA quantification, mitochondrial genome sequencing, and gene expression analysis were performed on muscle, adipose tissue, and peripheral blood mononuclear cell (PBMC) samples from untreated HIV-positive patients, HIV-positive patients receiving nucleoside reverse transcriptase inhibitor (NRTI)-based ART, and HIV-negative controls. RESULTS The adipose tissue mtDNA/nuclear DNA (nDNA) ratio was increased in untreated HIV-infected patients (ratio, 353) and decreased in those receiving ART (ratio, 162) compared with controls (ratio, 255; P < .05 for both comparisons); the difference between the 2 HIV-infected groups was also significant (P = .002). In HIV-infected participants, mtDNA/nDNA in adipose tissue correlated with the level of activation (CD38+ /HLA-DR+) for CD4+ and CD8+ lymphocytes. No significant differences in mtDNA content were noted in muscle or PMBCs among groups. Exploratory DNA microarray analysis identified differential gene expression between patient groups, including a subset of adipose tissue genes. CONCLUSIONS HIV infection and ART have opposing effects on mtDNA content in adipose tissue; immune activation may mediate the effects of HIV, whereas NRTIs likely mediate the effects of ART.
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Affiliation(s)
- Caryn G Morse
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892-1403, USA.
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Voss JG, Dobra A, Morse C, Kovacs JA, Raju R, Danner RL, Munson PJ, Logan C, Rangel Z, Adelsberger JW, McLaughlin M, Adams LD, Dalakas MC. Fatigue-related gene networks identified in CD14+ cells isolated from HIV-infected patients: part II: statistical analysis. Biol Res Nurs 2011; 15:152-9. [PMID: 22084402 DOI: 10.1177/1099800411423307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
PURPOSE In limited samples of valuable biological tissues, univariate ranking methods of microarray analyses often fail to show significant differences among expression profiles. In order to allow for hypothesis generation, novel statistical modeling systems can be greatly beneficial. The authors applied new statistical approaches to solve the issue of limited experimental data to generate new hypotheses in CD14(+) cells of patients with HIV-related fatigue (HRF) and healthy controls. METHODOLOGY We compared gene expression profiles of CD14(+) cells of nucleoside reverse transcriptase inhibitor (NRTI)-treated HIV patients with low versus high fatigue to healthy controls (n = 5 each). With novel Bayesian modeling procedures, the authors identified 32 genes predictive of low versus high fatigue and 33 genes predictive of healthy versus HIV infection. Sparse association and liquid association networks further elucidated the possible biological pathways in which these genes are involved. RELEVANCE FOR NURSING PRACTICE: Genetic networks developed in a comprehensive Bayesian framework from small sample sizes allow nursing researchers to design future research approaches to address such issues as HRF. IMPLICATION FOR PRACTICE The findings from this pilot study may take us one step closer to the development of useful biomarker targets for fatigue status. Specific and reliable tests are needed to diagnosis, monitor and treat fatigue and mitochondrial dysfunction.
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Affiliation(s)
- Joachim G Voss
- Biobehavioral Nursing & Health Systems Department, School of Nursing, University of Washington, Seattle, WA 98195, USA.
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Raju R, Jian B, Hubbard W, Chaudry I. The Mitoscriptome in Aging and Disease. Aging Dis 2011; 2:174-180. [PMID: 21532982 PMCID: PMC3084006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 04/18/2011] [Accepted: 04/18/2011] [Indexed: 05/30/2023] Open
Abstract
Mitochondria are the major sites where energy is produced in the cell. Functions of organs such as the heart which has high energy demand are seriously affected by dysfunction of mitochondria. The functional changes in energy-dependent organs such as heart due to aging or any other cause are expected to be reflected in changes in expression of genes related to mitochondrial structure and function. Conversely, alteration of mitochondrial gene expression by any reason may also adversely affect function of organs such as heart that are energy-dependent. Molecular profiling of mitochondrial gene expression is therefore critical to understanding the mechanism of organ dysfunction. Mitochondrial structure and function are controlled by genes in the nuclear DNA and those in the mitochondrial DNA (mtDNA). The transcriptome from these two sources, together, contributing to the structure and function of mitochondria may be called mitoscriptome. This review elaborates on data gathered using a gene chip, RoMitochip, developed in our laboratory to study mitochondrial functional alteration in cardiomyocytes and left ventricular tissue following hypoxia or hemorrhagic injury. RoMitochip consists of probesets representing genes from nuclear DNA and mtDNA of both mice and rats. Our experiments using this chip in in vitro model of hypoxia and in vivo hemorrhagic injury model determined mitoscriptome signatures following hypoxia and hemorrhage, respectively. In addition, we also discuss past initiatives from other investigators that led to the development of microarray tools to profile mitoscriptome.
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Affiliation(s)
- Raghavan Raju
- Correspondence should be addressed to: Raghavan Raju PhD, Department of Surgery, VH-G094, Volker Hall, 1670 University Blvd, Birmingham, AL 35294, USA.
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Su YA, Zhang Q, Su DM, Tang MX. Rat mitochondrion-neuron focused microarray (rMNChip) and bioinformatics tools for rapid identification of differential pathways in brain tissues. Int J Biol Sci 2011; 7:308-22. [PMID: 21494430 PMCID: PMC3076503 DOI: 10.7150/ijbs.7.308] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2011] [Accepted: 03/25/2011] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial function is of particular importance in brain because of its high demand for energy (ATP) and efficient removal of reactive oxygen species (ROS). We developed rat mitochondrion-neuron focused microarray (rMNChip) and integrated bioinformatics tools for rapid identification of differential pathways in brain tissues. rMNChip contains 1,500 genes involved in mitochondrial functions, stress response, circadian rhythms and signal transduction. The bioinformatics tool includes an algorithm for computing of differentially expressed genes, and a database for straightforward and intuitive interpretation for microarray results. Our application of these tools to RNA samples derived from rat frontal cortex (FC), hippocampus (HC) and hypothalamus (HT) led to the identification of differentially-expressed signal-transduction-bioenergenesis and neurotransmitter-synthesis pathways with a dominant number of genes (FC/HC = 55/6; FC/HT = 55/4) having significantly (p<0.05, FDR<10.70%) higher (≥1.25 fold) RNA levels in the frontal cortex than the others, strongly suggesting active generation of ATP and neurotransmitters and efficient removal of ROS. Thus, these tools for rapid and efficient identification of differential pathways in brain regions will greatly facilitate our systems-biological study and understanding of molecular mechanisms underlying complex and multifactorial neurodegenerative diseases.
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Affiliation(s)
- Yan A Su
- Department of Gene and Protein Biomarkers, GenProMarkers Inc., Rockville, MD 20850, USA.
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Jian B, Yang S, Chen D, Zou L, Chatham JC, Chaudry I, Raju R. Aging influences cardiac mitochondrial gene expression and cardiovascular function following hemorrhage injury. Mol Med 2010; 17:542-9. [PMID: 21193900 DOI: 10.2119/molmed.2010.00195] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 12/21/2010] [Indexed: 01/07/2023] Open
Abstract
Cardiac dysfunction and mortality associated with trauma and sepsis increase with age. Mitochondria play a critical role in the energy demand of cardiac muscles, and thereby on the function of the heart. Specific molecular pathways responsible for mitochondrial functional alterations after injury in relation to aging are largely unknown. To further investigate this, 6- and 22-month-old rats were subjected to trauma-hemorrhage (T-H) or sham operation and euthanized following resuscitation. Left ventricular tissue was profiled using our custom rodent mitochondrial gene chip (RoMitochip). Our experiments demonstrated a declined left ventricular performance and decreased alteration in mitochondrial gene expression with age following T-H and we have identified c-Myc, a pleotropic transcription factor, to be the most upregulated gene in 6- and 22-month-old rats after T-H. Following T-H, while 142 probe sets were altered significantly (39 up and 103 down) in 6-month-old rats, only 66 were altered (30 up and 36 down) in 22-month-old rats; 36 probe sets (11 up and 25 down) showed the same trend in both groups. The expression of c-Myc and cardiac death promoting gene Bnip3 were increased, and Pgc1-α and Ppar-α a decreased following T-H. Eleven tRNA transcripts on mtDNA were upregulated following T-H in the aged animals, compared with the sham group. Our observations suggest a c-myc-regulated mitochondrial dysfunction following T-H injury and marked decrease in age-dependent changes in the transcriptional profile of mitochondrial genes following T-H, possibly indicating cellular senescence. To our knowledge, this is the first report on mitochondrial gene expression profile following T-H in relation to aging.
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Affiliation(s)
- Bixi Jian
- Center for Surgical Research, Department of Surgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
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Okuzaki D, Fukushima T, Tougan T, Ishii T, Kobayashi S, Yoshizaki K, Akita T, Nojima H. Genopal™: a novel hollow fibre array for focused microarray analysis. DNA Res 2010; 17:369-79. [PMID: 21059707 PMCID: PMC2993541 DOI: 10.1093/dnares/dsq025] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Expression profiling of target genes in patient blood is a powerful tool for RNA diagnosis. Here, we describe Genopal™, a novel platform ideal for efficient focused microarray analysis. Genopal™, which consists of gel-filled fibres, is advantageous for high-quality mass production via large-scale slicing of the Genopal™ block. We prepared two arrays, infectant and autoimmunity, that provided highly reliable data in terms of repetitive scanning of the same and/or distinct microarrays. Moreover, we demonstrated that Genopal™ had sensitivity sufficient to yield signals in short hybridization times (0.5 h). Application of the autoimmunity array to blood samples allowed us to identify an expression pattern specific to Takayasu arteritis based on the Spearman rank correlation by comparing the reference profile with those of several autoimmune diseases and healthy volunteers (HVs). The comparison of these data with those obtained by other methods revealed that they exhibited similar expression profiles of many target genes. Taken together, these data demonstrate that Genopal™ is an advantageous platform for focused microarrays with regard to its low cost, rapid results and reliable quality.
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Affiliation(s)
- Daisuke Okuzaki
- Department of Molecular Genetics, Research Institute for Microbial Diseases, Suita, Osaka, Japan
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Pandey A, Suman S, Chandna S. Predictive role of mitochondrial genome in the stress resistance of insects and nematodes. Bioinformation 2010; 5:21-7. [PMID: 21346874 PMCID: PMC3040000 DOI: 10.6026/97320630005021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2010] [Accepted: 04/09/2010] [Indexed: 02/05/2023] Open
Abstract
Certain insects (e.g., moths and butterflies; order Lepidoptera) and nematodes are considered as excellent experimental models to study the cellular stress
signaling mechanisms since these organisms are far more stress-resistant as compared to mammalian system. Multiple factors have been implicated in this
unusual response, including the oxidative stress response mechanisms. Radiation or chemical-induced mitochondrial oxidative stress occurs through
damage caused to the components of electron transport chain (ETC) leading to leakage of electrons and generation of superoxide radicals. This may be
countered through quick replacement of damaged mitochondrial proteins by upregulated expression. Since the ETC comprises of various proteins coded
by mitochondrial DNA, variation in the composition, expressivity and regulation of mitochondrial genome could greatly influence mitochondrial role
under oxidative stress conditions. Therefore, we carried out in silico analysis of mitochondrial DNA in these organisms and compared it with that of the
stress-sensitive humans/mammals. Parameters such as mitochondrial genome organization, codon bias, gene expressivity and GC3 content were studied.
Gene arrangement and Shine-Dalgarno (SD) sequence patterns indicating translational regulation were distinct in insect and nematodes as compared to
humans. A higher codon bias (ENC≫35) and lower GC3 content (≫0.20) were observed in mitochondrial genes of insect and nematodes as compared to
humans (ENC>42; GC3>0.20), coupled with low codon adaptation index among insects. These features indeed favour higher expressivity of
mitochondrial proteins and might help maintain the mitochondrial physiology under stress conditions. Therefore, our study indicates that mitochondrial
genome organization may influence stress-resistance of insects and nematodes.
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Affiliation(s)
- Akshay Pandey
- Natural Radiation Response Mechanisms Group, Division of Radiation Biosciences, Institute of Nuclear Medicine and Allied Sciences, Brig. S.K. Mazumdar Road, Delhi -110054, India
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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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