Journal des biomarqueurs moléculaires et du diagnostic

Identification and Validation of Differentially Expressed Genes Via-s-vis Exploration of the Modular Pathways in Diseased Versus Healthy Nili Ravi Water Buffalo

Abstract

Priyabrata Behera, Simarjeet Kaur, Shiva R Sethi and Chandra Sekhar Mukhopadhyay

Peripheral blood mononuclear cells (PBMCs) were isolated from 3 groups of she-buffaloes (Tuberculosis, Metritis, and Healthy control) was sequenced by RNA-Seq (using Illumina Hiseq 2500 platform). The pre-processed reads, obtained from transcriptome sequencing, were aligned to the Bostaurus genome using the Hisat-2 program. Gene expression was studied using the String Tie program. A total of 31982 transcripts were identified. Comparisons of the entire 3 groups’ revealed 176 differentially expressed genes (DEGs) in TB vs. healthy groups and 162 DEGs in metritis vs. healthy groups. Analysis of gene ontology and pathways (molecular function and biological processes) identified certain pathways like cytokine activity, Wnt signaling, PI3K-Akt signaling, MAPK signalling (between TB and healthy groups) and cAMP signaling, Wnt signaling, TGFbeta signaling, MAPK signaling, PI3K-Akt signaling, etc. between metritis-positive and healthy buffaloes. Network analysis identified the immunerelated genes contributing to the system biology related to the disease-resistance in Nili Ravi buffalo. Besides, five differentially expressed genes have been validated using SYBR-green chemistry of qPCR. In the future, these key genes could be studied in detail to explore their potential to be promising biomarkers for selecting breeding animals with higher tolerance against these economically devastating diseases.