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A Focused Microarray to Study Human Mitochondrial and Nuclear Gene Expression

Neuromuscular Diseases Section, National Institute of Neurological Diseases and Stroke, vossj{at}u.washington.edu

Raghavan Raju, PhD

Neuromuscular Diseases Section, National Institute of Neurological Diseases and Stroke

Carolea Logun, MS

Functional Genomics and Proteomics Facility, Critical Care Medicine Department, Clinical Center

Robert L. Danner, MD

Functional Genomics and Proteomics Facility, Critical Care Medicine Department, Clinical Center

Peter J. Munson, PhD

Mathematical & Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland

Zoila Rangel, MS

Mathematical & Statistical Computing Laboratory, Center for Information Technology, National Institutes of Health, Bethesda, Maryland

Marinos C. Dalakas, MD

Neuromuscular Diseases Section, National Institute of Neurological Diseases and Stroke

A focused microarray (huMITOchip) was developed to study alterations of human mitochondrial and nuclear gene expression in health and disease. The huMITOchip contains 4,774 probe sets identical to the Affymetrix U 133 plus 2.0 chip covering genes affecting mitochondrial, lipid, cytokine, apoptosis, and muscle function transcripts. Unlike other gene chips, the huMITOchip has 51 probe sets that interrogate 37 genes of the mitochondrial genome. The human mitochondrial gene chip was validated against the Affymetrix U133 plus 2.0 array using an in vitro system of CCL136 muscle cell line stimulated with or without interferon gamma (IFN-). The 37 genes from the mtDNA demonstrated absolute gene expression levels ranging from 0.1 to 3,182. The comparison of the two gene chips yielded an excellent Pearson's correlation coefficient (r = 0.98). At least 17 probe sets were differentially expressed in response to IFN- on both chips, with a high degree of concordance. This is the first report on the development of a focused oligonucleotide microarray containing genes of the mitochondrial genome.

Key Words: mitochondria • microarray • gene expression • interferon gamma

Biological Research For Nursing, Vol. 9, No. 4, 272-279 (2008)
DOI: 10.1177/1099800408315160


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