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Open Access Highly Accessed Research article

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

Alena Čížková125, Viktor Stránecký12, Robert Ivánek124, Hana Hartmannová12, Lenka Nosková2, Lenka Piherová12, Markéta Tesařová13, Hana Hansíková13, Tomáš Honzík3, Jiří Zeman13, Petr Divina4, Andrea Potocká15, Jan Paul15, Wolfgang Sperl6, Johannes A Mayr6, Sara Seneca7, Josef Houštĕk15 and Stanislav Kmoch12*

Author affiliations

1 Center for Applied Genomics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic

2 Institute of Inherited Metabolic Disorders, 1st Faculty of Medicine, Charles University, Prague, Czech Republic

3 Department of Pediatrics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic

4 Institute of Molecular Genetics, Academy of Science of the Czech Republic, Prague, Czech Republic

5 Department of Bioenergetics, Institute of Physiology, Academy of Science of the Czech Republic, Prague, Czech Republic

6 Department of Pediatrics, Paracelsus Medical University, Salzburg, Austria

7 Center of Medical Genetics, Free University Brussels, Brussels, Belgium

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Citation and License

BMC Genomics 2008, 9:38  doi:10.1186/1471-2164-9-38

Published: 25 January 2008

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 mt9205ΔTA 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.

Conclusion

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.