Human Mitochondrial Complex I Deficiency: Investigating Transcriptional Responses by Microarray

Abstract

NADH:ubiquinone oxidoreductase (complex I) deficiency is one of the most frequently encountered defects of the mitochondrial energy generating system. A deficiency of this enzyme complex leads to a wide variety in clinical disease expression. The cell biological consequences of such mutations, however, are poorly understood. We investigated transcriptional responses in fibroblast cell lines harboring mutations in the five different nuclear DNA encoded subunits using a mitochondria-targeting microarray. Expression profiles of cell lines cultured under conditions that favor glycolytic metabolism were compared to profiles when cultured under conditions favoring oxidative metabolism. Approximately 60 genes displayed differential expression under these conditions in either all mutated cell lines or selected cell lines only. A marked induction of metallothioneins as well as ATP1G1 transcripts was detected in all patient cell lines. Transcriptional responses such as the induction of heat shock protein transcripts, decreased PDK1, BNIP3 and mitochondrial genome encoding gene transcripts occurred in selected patient cell lines. The observed transcript profile points to a common, putative defensive, response relating to oxidative stress. Although further investigations of other human OXPHOS system diseases is warranted, these results clearly underline that functional genomics holds for the study of inherited metabolic disease.

Microarray - complex I deficiency - transcriptional responses - metallothionein - mitochondria - inherited diseases - genomics

References

• 1 Abel J, de Ruiter N. Inhibition of hydroxyl-radical-generated DNA degradation by metallothionein.  Toxicol Lett. 1989;  47 191-196
• 2 Allen R G, Tresini M. Oxidative stress and gene regulation.  Free Radic Biol Med. 2000;  28 463-499
• 3 Barrientos A, Moraes C T. Titrating the effects of mitochondrial complex I impairment in the cell physiology.  J Biol Chem. 1999;  23 16188-16197
• 4 Benit P, Chretien D, Kadhom N, de Lonlay-Debeney P, Cormier-Daire V, Cabral A. et al . Large-scale deletion and point mutations of the nuclear NDUFV1 and NDUFS1 genes in mitochondrial complex I deficiency.  Am J Hum Genet. 2001;  68 1344-1352
• 5 Brons P P, Pennings A H, Haanen C, Wessels H M, Boezeman J B. Simultaneous measurement of DNA content and cell-surface immunofluorescence of human bone marrow cells using a single laser flow cytometer.  Cytometry. 1990;  11 837-844
• 6 Chen G, Ray R, Dubik D, Shi L, Cizeau J, Bleackley R C. et al . The E1 B 19 K/Bcl-2-binding protein Nip3 is a dimeric mitochondrial protein that activates apoptosis.  J Exp Med. 1997;  15 1975-1983
• 7 Collombet J M, Faure-Vigny H, Mandon G, Dumoulin R, Boissier S, Bernard A. et al . Expression of oxidative phosphorylation genes in muscle cell cultures from patients with mitochondrial myopathies.  Mol Cell Biochem. 1997;  168 73-85
• 8 Cooperstein S J, Lazarow A. A microspectrophotometric method for the determination of cytochrome c oxidase.  J Biol Chem. 1951;  189 665-670
• 9 Dalton T P, Shertzer H G, Puga A. Regulation of gene expression by reactive oxygen.  Annu Rev Pharmacol Toxicol. 1999;  39 67-101
• 10 DiMauro S, Schon E. Mitochondrial DNA mutations in human disease.  Am J Hum Genet. 2001;  106 4-17
• 11 Duda R O, Hart P E, Stork P G. Pattern Classification. New York; Wiley-Interscience 2000
• 12 Eickhoff B, Korn B, Schick M, Poutska A, van der Bosch J. Normalization of array hybridization experiments in differential gene expression analysis.  Nucleic Acids Res. 1999;  27 e33
• 13 Elliot R M, Southon S, Archer D B. Oxidative insult specifically decreases levels of a mitochondrial transcript.  Free Radic Biol Med. 1999;  26 646-655
• 14 Goshal K, Jacob S T. Regulation of metallothionein gene expression.  Prog Nucleic Acid Res Mol Biol. 2001;  66 357-384
• 15 Halgren R G, Fielden M R, Fong C J, Zacharewski T R. Assessment of clone identity and sequence fidelity for 1189 IMAGE cDNA clones.  Nucleic Acids Res. 2001;  29 582-588
• 16 Heddi A, Stepien G, Benke P J, Wallace D C. Coordinate induction of gene expression in tissues of mitochondrial disease.  J Biol Chem. 1999;  274 22968-22976
• 17 Hegde P, Qi R, Abernathy K, Gay C, Dharap S, Gaspard R. et al . A concise guide to cDNA microarray analysis.  Biotechniques. 2000;  29 548-562
• 18 Ide T, Tsutsui H, Kinugawa S, Utsumi H, Kang D, Hattori N. et al . Mitochondrial electron transport complex I is a potential source of oxygen free radicals in the failing myocardium.  Circ Res. 1999;  85 357-363
• 19 Jacob S T, Ghoshal K, Sheridan J F. Induction of metallothionein by stress and its molecular mechanisms.  Gene Expr. 1999;  7 301-310
• 20 Kawai K, Liu S X, Tyurin V A, Tyurina Y Y, Borisenko G G, Jiang J F. et al . Antioxidant and antiapoptotic function of metallothioneins in HL-60 cells challenged with copper nitrilotriacetate.  Chem Res Toxicol. 2000;  13 1275-1286
• 21 Lenaz G. Role of mitochondria in oxidative stress and ageing.  Biochim Biophys Acta. 1998;  1366 53-67
• 22 Loeffen J, Elpeleg O, Smeitink J, Smeets R, Stockler-Ipsiroglu S, Mandel H. et al . Mutations in the complex I NDUFS2 gene of patients with cardiomyopathy and encephalomyopathy.  Ann Neurol. 2001;  49 195-201
• 23 Loeffen J, Smeitink J, Triepels R, Smeets R, Schuelke M, Sengers R. et al . The first nuclear-encoded complex I mutation in a patient with Leigh syndrome.  Am J Hum Genet. 1998;  63 1598-1608
• 24 Loeffen J L, Smeitink J A, Trijbels J M, Janssen A J, Triepels R H, Sengers R C. et al . Isolated complex I deficiency in children: clinical, biochemical and genetic aspects.  Hum Mutat. 2000;  15 123-134
• 25 Madamanchi N R, Li S, Patterson C, Runge M S. Reactive oxygen species regulate heat-shock protein 70 via the JAK/STAT pathway.  Arterioscler Thromb Vasc Biol. 2001;  21 321-326
• 26 Melov S, Coskun P E, Wallace D C. Mouse models of mitochondrial disease, oxidative stress and senescence.  Mutat Res. 1999;  434 233-242
• 27 Munnich A, Rustin P. Clinical spectrum and diagnosis of mitochondrial disorders.  Am J Med Genet. 2001;  106 4-17
• 28 Raha S, Robinson B H. Mitochondria, oxygen free radicals, disease and ageing.  Trends Biochem Sci. 2000;  25 502-508
• 29 Robinson B H. Use of fiboblast and lymphoblast cultures for detection of respiratory chain defects. Attardi GM, Chomyn A Mitochondrial Biogenesis and Genetics, Part B. Methods in Enzymology 264. New York; Academic Press 1996: 454-465
• 30 Robinson B H, Petrovna-Benedict R, Buncic J R, Wallace D C. Nonviability of cells with oxidative defects in galactose medium: a screening tests for affected patient fibroblasts.  Biochem Med Metab Biol. 1992;  48 122-126
• 31 Rötig A, Valnot I, Mugnier C, Rustin P, Munnich A. Screening human ETS database for identification of candidate genes in respiratory chain deficiency.  Mol Genet Metab. 2000;  69 223-232
• 32 Smeitink J, van den Heuvel L, DiMauro S. The genetics and pathology of oxidative phosphorylation.  Nat Rev Genet. 2001;  2 342-352
• 33 Smeitink J, Sengers R, Trijbels F, van den Heuvel L. Human NADH:ubiquinone oxidoreductase.  J Bioenerg Biomembr. 2001;  33 259-266
• 34 Smeitink J, van den Heuvel L. Human mitochondrial complex I in health and disease.  Am J Hum Genet. 1999;  64 1505-1510
• 35 Srere P A. Citrate synthase, EC 4137 citrate oxaloacetate lyase (Co-A-acetylating). Lowenstein JM Citric Acid Cycle. Methods in Enzymology 13. New York; Academic Press 1969: 3-11
• 36 Thornalley P J, Vasak M. Possible role for metallothionein in protection against radiation-induced oxidative stress. Kinetics and mechanism of its reaction with superoxide and hydroxyl radicals.  Biochim Biophys Acta. 1985;  827 36-44
• 37 Traven A, Wong J M, Xu D, Sopta M, Ingles C J. Interorganellar communication. Altered nuclear gene expression profiles in a yeast mitochondrial DNA mutant.  J Biol Chem. 2001;  276 4020-4027
• 38 Triepels R H, van den Heuvel L P, Trijbels J M, Smeitink J A. Respiratory complex I deficiency.  Am J Med Genet. 2001;  106 37-45
• 39 Wang G W, Zhou Z, Klein J B, Kang Y J. Inhibition of hypoxia/reoxygenation-induced apoptosis in metallothionein-overexpressing cardiomyocytes.  Am J Physiol Heart Circ Physiol. 2001;  280 H2292-H2299
• 40 Wei Y H, Ma Y S, Lee H C, Lee C F, Lu C Y. Mitochondrial theory of aging matures - roles of mtDNA mutation and oxidative stress in human aging.  Zhonghua Yi Xue Za Zhi (Taipei). 2001;  64 259-270
• 41 Wendt C H, Gick G, Sharma R, Zhuang Y, Deng W, Ingbar D H. Upregulation of Na, K-ATPase beta 1 transcription by hyperoxia is mediated by SP1/SP3 binding.  J Biol Chem. 2000;  275 41396-41404
• 42 Yakes F M, van Houten B. Mitochondrial DNA damage is more extensive and persists longer than nuclear DNA damage in human cells following oxidative stress.  Proc Natl Acad Sci USA. 1997;  94 514-519