title: Development of a human mitochondrial oligonucleotide microarray (h-MitoArray) and gene expression analysis of fibroblast cell lines from 13 patients with isolated F1Fo ATP synthase deficiency.
abstract: BACKGROUND
  To strengthen research and differential diagnostics of mitochondrial disorders, we constructed and validated an oligonucleotide microarray (h-MitoArray) allowing expression analysis of 1632 human genes involved in mitochondrial biology, cell cycle regulation, signal transduction and apoptosis. Using h-MitoArray we analyzed gene expression profiles in 9 control and 13 fibroblast cell lines from patients with F1Fo ATP synthase deficiency consisting of 2 patients with mt9205deltaTA microdeletion and a genetically heterogeneous group of 11 patients with not yet characterized nuclear defects. Analysing gene expression profiles, we attempted to classify patients into expected defect specific subgroups, and subsequently reveal group specific compensatory changes, identify potential phenotype causing pathways and define candidate disease causing genes.
  
  
  RESULTS
  Molecular studies, in combination with unsupervised clustering methods, defined three subgroups of patient cell lines--M group with mtDNA mutation and N1 and N2 groups with nuclear defect. Comparison of expression profiles and functional annotation, gene enrichment and pathway analyses of differentially expressed genes revealed in the M group a transcription profile suggestive of synchronized suppression of mitochondrial biogenesis and G1/S arrest. The N1 group showed elevated expression of complex I and reduced expression of complexes III, V, and V-type ATP synthase subunit genes, reduced expression of genes involved in phosphorylation dependent signaling along MAPK, Jak-STAT, JNK, and p38 MAP kinase pathways, signs of activated apoptosis and oxidative stress resembling phenotype of premature senescent fibroblasts. No specific functionally meaningful changes, except of signs of activated apoptosis, were detected in the N2 group. Evaluation of individual gene expression profiles confirmed already known ATP6/ATP8 defect in patients from the M group and indicated several candidate disease causing genes for nuclear defects.
  
  
  CONCLUSIONS
  Our analysis showed that deficiency in the ATP synthase protein complex amount is generally accompanied by only minor changes in expression of ATP synthase related genes. It also suggested that the site (mtDNA vs nuclear DNA) and the severity (ATP synthase content) of the underlying defect have diverse effects on cellular gene expression phenotypes, which warrants further investigation of cell cycle regulatory and signal transduction pathways in other OXPHOS disorders and related pharmacological models.
authors.affiliation: Center for Applied Genomics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic. acizk@LF1.cuni.cz
authors.forename: Alena
authors.initials: A
authors.lastname: Cízková
authors.forename: Viktor
authors.initials: V
authors.lastname: Stránecký
authors.forename: Robert
authors.initials: R
authors.lastname: Ivánek
authors.forename: Hana
authors.initials: H
authors.lastname: Hartmannová
authors.forename: Lenka
authors.initials: L
authors.lastname: Nosková
authors.forename: Lenka
authors.initials: L
authors.lastname: Piherová
authors.forename: Markéta
authors.initials: M
authors.lastname: Tesarová
authors.forename: Hana
authors.initials: H
authors.lastname: Hansíková
authors.forename: Tomás
authors.initials: T
authors.lastname: Honzík
authors.forename: Jirí
authors.initials: J
authors.lastname: Zeman
authors.forename: Petr
authors.initials: P
authors.lastname: Divina
authors.forename: Andrea
authors.initials: A
authors.lastname: Potocká
authors.forename: Jan
authors.initials: J
authors.lastname: Paul
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Sperl
authors.forename: Johannes A
authors.initials: JA
authors.lastname: Mayr
authors.forename: Sara
authors.initials: S
authors.lastname: Seneca
authors.forename: Josef
authors.initials: J
authors.lastname: Houstĕk
authors.forename: Stanislav
authors.initials: S
authors.lastname: Kmoch
mesh_terms: D002460:Cell Line; D016000:Cluster Analysis; D004272:DNA, Mitochondrial / Q000235:genetics*; D005347:Fibroblasts / Q000201:enzymology; D020869:Gene Expression Profiling / Q000379:methods* / Q000706:statistics & numerical data; D054629:Genome, Mitochondrial; D006801:Humans; D028361:Mitochondrial Diseases / Q000145:classification / Q000175:diagnosis / Q000201:enzymology* / Q000235:genetics*; D025261:Mitochondrial Proton-Translocating ATPases / Q000172:deficiency* / Q000235:genetics*; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000706:statistics & numerical data; D010641:Phenotype; D025341:Principal Component Analysis; D017384:Sequence Deletion
chemical_list: D004272:DNA, Mitochondrial; C474451:F1F0-ATP synthase; D025261:Mitochondrial Proton-Translocating ATPases