Identification of key genes and signaling pathways involved in bovine tuberculosis challenged with Mycobacterium bovis: Comparison of RNA-Seq and microarray expression profiling data

In recent years, advances in high-throughput RNA-Seq technologies have made it possible identifying di↵erentially expressed genes between healthy and diseased tissues, better understanding of host–pathogen interaction, increased precision and sensitivity for the quantification of lowly expressed transcripts, detection of expressed coding and regulatory DNA sequence variants, and the evolution of gene regulation in different species (Ozsolak and Milos, ۲۰۱۱; McGettigan, ۲۰۱۳). Bovine tuberculosis (BTB), caused by infection with Mycobacterium bovis, is an intracellular pathogen belonging to the Mycobacterium tuberculosis complex, which is classified as the fourth most important disease of livestock in terms of zoonotic and economic impact worldwide (Wirth et al., ۲۰۰۸). Hence, characterization of the host response to M. bovis infection is essential for understanding the immunopathogenesis of the disease and for developing better control strategies. In this study, we analyzed and compared gene expression profiles generated using RNA-Seq and microarray data to examine transcriptional differences between healthy cows and M. bovis-infected cows. The results of the comparative analysis demonstrated that microarray detected a larger number of di↵erentially expressed genes (۱۳۳۶) relative to the RNA-Seq (۳۲۷) based on fold change > ± ۲ and false discovery rate < ۰.۰۵, of which ۶۸ genes were common to both technologies and demonstrated the same direction of expression. KEGG pathway analysis and Gene Ontology revealed that many di↵erentially expressed genes were enriched in several biological processes and pathways relevant to inflammatory response, defense response, regulation of T cell activation, immune response, regulation of leukocyte activation, cytokine-mediated, TNF, IL-۱۷, and Toll-like receptor signaling pathways as being well-known. These findings demonstrate that RNASeq is more accurate compared to microarray analysis in identifying di↵erential gene expression and provides new insight into the molecular mechanisms related to immune or inflammatory responses to M. bovis infection.

کلیدواژه ها:

Mycobacterium bovis ، Microarray ، RNA-Sequencing ، Pathway analysis