Assessment of reference genes for qRT-PCR normalization to elucidate host response to African swine fever infection

• Published in: Brazilian journal of microbiology Vol. 55; no. 3; pp. 2943 - 2952
• Main Authors: Rajkhowa, Swaraj, Sonowal, Joyshikh, Sengar, Gyanendra Singh, Pegu, Seema Rani, Deb, Rajib, Das, Pranab Jyoti, Doley, Juwar, Paul, Souvik, Gupta, Vivek Kumar
• Format: Journal Article
• Language: English
• Published: Cham Springer International Publishing 01.09.2024; Springer Nature B.V
• Subjects: African swine fever; African Swine Fever - virology; African Swine Fever Virus - genetics; Algorithms; Animals; Biomedical and Life Sciences; Fever; Food Microbiology; Gene expression; Gene Expression Profiling; Gene regulation; Genes; Genes, Essential - genetics; Heart; Hogs; Infections; Kidneys; Life Sciences; Liver; Lymph nodes; Lymphatic system; Medical Microbiology; Microbial Ecology; Microbial Genetics and Genomics; Microbiology; Mycology; Real time; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - standards; Reference Standards; rRNA; Spleen; Stability analysis; Swine; Tissues; Veterinary and Animal Production - Research Paper; Viral infections; Reference gene; ASFV; Swine; Data normalization; qRT-PCR; Endogenous control gene
• ISSN: 1517-8382; 1678-4405; 1678-4405
• DOI: 10.1007/s42770-024-01439-2

Viral infection disrupts the normal regulation of the host gene’s expression. In order to normalise the expression of dysregulated host genes upon virus infection, analysis of stable reference housekeeping genes using quantitative real-time-PCR (qRT-PCR) is necessary. In the present study, healthy and African swine fever virus (ASFV) infected porcine tissues were assessed for the expression stability of five widely used housekeeping genes (HPRT1, B2M, 18 S rRNA, PGK1 and H3F3A) as reference genes using standard algorithm. Total RNA from each tissue sample (lymph node, spleen, kidney, heart and liver) from healthy and ASFV-infected pigs was extracted and subsequently cDNA was synthesized, and subjected to qRT-PCR. Stability analysis of reference genes expression was performed using the Comparative delta CT, geNorm, BestKeeper and NormFinder algorithm available at RefFinder for the different groups. Direct Cycle threshold (CT) values of samples were used as an input for the web-based tool RefFinder. HPRT1 in spleen, 18 S rRNA in liver and kidney and H3F3A in heart and lymph nodes were found to be stable in the individual healthy tissue group (group A). The majority of the ASFV-infected organs (liver, kidney, heart, lymph node) exhibited H3F3A as stable reference gene with the exception of the ASFV-infected spleen, where HPRT1 was found to be the stable gene (group B). HPRT1 was found to be stable in all combinations of all CT values of both healthy and ASFV-infected porcine tissues (group C). Of five different reference genes investigated for their stability in qPCR analysis, the present study revealed that the 18 S rRNA, H3F3A and HPRT1 genes were optimal reference genes in healthy and ASFV-infected different porcine tissue samples. The study revealed the stable reference genes found in healthy as well as ASF-infected pigs and these reference genes identified through this study will form the baseline data which will be very useful in future investigations on gene expression in ASFV-infected pigs.