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Cellular and Molecular Biology 13: Expression Profiling in Tumors and Model Systems

The third generation human mitochondria-focused cDNA microarray (hMitChip3) and its software for analysis of gene expression in cells derived from healthy and diseased individuals

Xueyan Bai, Jun Wu, Salvatore Alesci, Irini Manoli, Qiuyang Zhang, Phili W. Gold, Marc R. Blackman, George P. Chrousos, Allan L. Goldstein, Owen M. Rennert and Yan A. Su
Xueyan Bai
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Jun Wu
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Salvatore Alesci
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Irini Manoli
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Qiuyang Zhang
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Phili W. Gold
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Marc R. Blackman
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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George P. Chrousos
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Allan L. Goldstein
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Owen M. Rennert
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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Yan A. Su
Department of Biochemistry and Molecular Biology, George Washington University School of Medicine, Washington, DC, Reproductive Biology and Medicine Branch, National Institute of Child Health and Human Development, NIH, Bethesda, MD, Clinical Neuroendocrinology, National Institute of Mental Health, NIH, Bethesda, MD, Laboratory of Clinical Investigation, National Center for Complementary and Alternative Medicine, NIH, Bethesda, MD, First Department of Pediatrics, UOA, Athens, Greece, Laboratory of Clinical Genomics, National Institute of Child Health and Human Development, NIH, Bethesda, MD
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DOI:  Published April 2006
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Proc Amer Assoc Cancer Res, Volume 47, 2006

Abstract

839

Mitochondria play a central role in the life cycle of the cell in health and disease. These intracellular organelles are in essence “energy factories” providing the ATP for the cell and are involved in calcium signaling, steroid hormone and heme biosynthesis, generation of radical oxygen species, apoptosis and a significant number of other metabolic activities. Human mitochondrial DNA (mtDNA) codes for 37 genes; yet, most proteins needed for mitochondrial structure and function are encoded by nuclear DNA (nDNA). While defects in mtDNA or nDNA result in rare genetic syndromes such as childhood mitochondrial encephalomyopathies, primary or secondary mitochondrial dysfunction has been associated with the pathogenesis of a wide range of common abnormalities, such as obesity, diabetes, cancer, neurodegeneration, cardiomyopathy, coronary artery disease, depression and aging. To facilitate the systematic study of the role of mitochondria in health and disease, we developed a third generation human mitochondria-focused cDNA microarray (hMitChip3) and software for analysis of the gene expression profile. hMitChip3 consists of mtDNA-encoded 37 genes, nDNA-encoded 1,053 genes and hundreds of control-elements for filtering data and calculating expression ratios, all in triplicate. Functional categories of the hMitChip3 genes include mitochondrial structure and biogenesis, metabolism, energy production, signal transduction, survival, apoptosis, and stress response. Analysis of Cy3- and Cy5-labeled melanocyte and melanoma cDNA samples hybridized to hMitChip3 to study the Warburg effect (i.e. tumor cells produce ATP by metabolizing glucose at a significantly higher rate than normal cells) demonstrated consistency (R2 = 1.0) of informative gene expression among triplicate signals within hMitChip3 and reproducibility (R2 > 0.80) of hMitChip3 in triplicate experiments. We shall present both statistical data showing the high quality of hMitChip3, and the accompanying software, as a novel integral tool for mitochondria-oriented research.

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Cancer Research: 66 (8 Supplement)
April 2006
Volume 66, Issue 8 Supplement
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The third generation human mitochondria-focused cDNA microarray (hMitChip3) and its software for analysis of gene expression in cells derived from healthy and diseased individuals
Xueyan Bai, Jun Wu, Salvatore Alesci, Irini Manoli, Qiuyang Zhang, Phili W. Gold, Marc R. Blackman, George P. Chrousos, Allan L. Goldstein, Owen M. Rennert and Yan A. Su
Cancer Res April 15 2006 (66) (8 Supplement) 198;

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The third generation human mitochondria-focused cDNA microarray (hMitChip3) and its software for analysis of gene expression in cells derived from healthy and diseased individuals
Xueyan Bai, Jun Wu, Salvatore Alesci, Irini Manoli, Qiuyang Zhang, Phili W. Gold, Marc R. Blackman, George P. Chrousos, Allan L. Goldstein, Owen M. Rennert and Yan A. Su
Cancer Res April 15 2006 (66) (8 Supplement) 198;
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Cancer Research Online ISSN: 1538-7445
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