Identification of key transcription factors and their functional role involved in Salmonella typhimurium infection in chicken using integrated transcriptome analysis and bioinformatics approach

• Published in: BMC genomics Vol. 24; no. 1; p. 214
• Main Authors: Ahmad, Syed Mudasir, Bhat, Sahar Saleem, Shafi, Shaista, Dar, Mashooq Ahmad, Saleem, Afnan, Haq, Zulfqarul, Farooq, Nida, Nazir, Junaid, Bhat, Basharat
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 25.04.2023; BioMed Central; BMC
• Subjects: Adenosine monophosphate; Analysis; Animal husbandry; Animal protein; Animals; Bioinformatics; Cell differentiation; Chicken; Chickens; Chickens - genetics; Computational biology; Control; Cyclic AMP; Disease Resistance; Economic impact; Ethics; Feeds; Food contamination & poisoning; Food poisoning; Food sources; Forkhead protein; FOXO3 protein; Gene expression; Gene Expression Profiling; Genes; Genomics; Humans; Identification and classification; Immune response; Immune system; Infections; Innate immunity; Interferon regulatory factor; Interferon regulatory factor 4; Liver; Lymphocytes B; Morbidity; Pathogens; Pathology; Pax5 protein; Poultry; Prevention; Protein sources; Protein-protein interactions; Proteins; Risk factors; RNA seq; Salmonella; Salmonella Infections, Animal - genetics; Salmonella typhimurium; Salmonella typhimurium - genetics; Spleen; Transcription factors; Transcription Factors - genetics; Transcriptomes; Tropical diseases; India; United States > US; RNA seq; Transcription factors; Chicken; Bioinformatics; Salmonella typhimurium
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-023-09315-3

Salmonella enterica serovar typhimurium is the cause of significant morbidity and mortality worldwide that causes economic losses to poultry and is able to cause infection in humans. Indigenous chicken breeds are a potential source of animal protein and have the added advantage of being disease resistant. An indigenous chicken, Kashmir favorella and commercial broiler were selected for understanding the mechanism of disease resistance. Following infection in Kashmir favorella, three differentially expressed genes Nuclear Factor Kappa B (NF-κB1), Forkhead Box Protein O3 (FOXO3) and Paired box 5 (Pax5) were identified. FOXO3, a transcriptional activator, is the potential marker of host resistance in Salmonella infection. NF-κB1 is an inducible transcription factor which lays the foundation for studying gene network of the innate immune response of Salmonella infection in chicken. Pax5 is essential for differentiation of pre-B cells into mature B cell. The real time PCR analysis showed that in response to Salmonella Typhimurium infection a remarkable increase of NF-κB1 (P˂0.01) FOXO3 (P˂0.01) gene expression in liver and Pax5 (P˂0.01) gene expression in spleen of Kashmir favorella was observed. The protein-protein interaction (PPI) and protein-TF interaction network by STRINGDB analysis suggests that FOXO3 is a hub gene in the network and is closely related to Salmonella infection along with NF-κB1. All the three differentially expressed genes (NF-κB1, FOXO3 and PaX5) showed their influence on 12 interacting proteins and 16 TFs, where cyclic adenosine monophosphate Response Element Binding protein (CREBBP), erythroblast transformation-specific (ETSI), Tumour-protein 53(TP53I), IKKBK, lymphoid enhancer-binding factor-1 (LEF1), and interferon regulatory factor-4 (IRF4) play role in immune responses. This study shall pave the way for newer strategies for treatment and prevention of Salmonella infection and may help in increasing the innate disease resistance.