Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco
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ORIGINAL PAPER
Differential expression of nuclear genes encoding mitochondrial proteins from urban and rural populations in Morocco Stephen W. Bickler 1,2,3 & James M. Prieto 4 & David M. Cauvi 2,3 & Victor De Cos 1 & Chanond Nasamran 5 & Emmanuel Ameh 6 & Said Amin 7 & Sneha Nicholson 1 & Hena Din 1 & Ana Olga Mocumbi 8,9 & Emilia Virginia Noormahomed 9 & Guillermo Tellez-Isaias 10 & Kathleen M. Fisch 5 & Antonio De Maio 2,3,11 Received: 13 January 2020 / Revised: 26 March 2020 / Accepted: 30 March 2020 # Cell Stress Society International 2020
Abstract Urbanization in low-income countries represents an important inflection point in the epidemiology of disease, with rural populations experiencing high rates of chronic and recurrent infections and urban populations displaying a profile of noncommunicable diseases. To investigate if urbanization alters the expression of genes encoding mitochondrial proteins, we queried gene microarray data from rural and urban populations living in Morocco (GSE17065). The R Bioconductor packages edgeR and limma were used to identify genes with different expression. The experimental design was modeled upon location and sex. Nuclear genes encoding mitochondrial proteins were identified from the MitoCarta2.0 database. Of the 1158 genes listed in the MitoCarta2.0 database, 847 genes (73%) were available for analysis in the Moroccan dataset. The urban-rural comparison with the greatest environmental differences showed that 76.5% of the MitoCarta2.0 genes were differentially expressed, with 97% of the genes having an increased expression in the urban area. Enrichment analysis revealed 367 significantly enriched pathways (adjusted p value < 0.05), with oxidative phosphorylation, insulin secretion and glucose regulations (adj.p values = 6.93E-16) being the top three. Four significantly perturbed KEGG disease pathways were associated with urbanization—three degenerative neurological diseases (Huntington’s, Alzheimer’s, and Parkinson’s diseases) and herpes simplex infection (false discover rate corrected p value (PGFdr) < 0.2). Mitochondrial RNA metabolic processing and translational elongation were the biological processes that had the greatest enrichment (enrichment ratios 14.0 and 14.8, respectively, FDR < 0.5). Our study links urbanization in Morocco with changes in the expression of the nuclear genes encoding mitochondrial proteins.
Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12192-020-01108-x) contains supplementary material, which is available to authorized users. * Stephen W. Bickler [email protected] James M. Prieto [email protected] David M. Cauvi [email protected] Victor De Cos [email protected] Chanond Nasamran [email protected] Emmanuel Ameh [email protected] Said Amin [email protected]
Sneha Nicholson [email protected] Hena Din [email protected] Ana Olga Mocumbi [email protected] Emilia Virginia Noormahomed [email protected] Guillermo Tellez-Isaias [email protected] Kathleen M. Fisch [email protected]
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