Identification of differentially expressed genes and their major pathways among the patient with COVID-19, cystic fibrosis, and chronic kidney disease

Golap Babu; Fahim Alam Nobel

doi:10.1016/j.imu.2022.101038

Identification of differentially expressed genes and their major pathways among the patient with COVID-19, cystic fibrosis, and chronic kidney disease

Inform Med Unlocked. 2022:32:101038. doi: 10.1016/j.imu.2022.101038. Epub 2022 Aug 7.

Authors

Golap Babu¹, Fahim Alam Nobel²

Affiliations

¹ Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, 1342, Bangladesh.
² Department of Biochemistry and Molecular Biology, Mawlana Bhashani Science and Technology University, Santosh, Tangail, 1902, Bangladesh.

Abstract

The SARS-CoV-2 virus causes Coronavirus disease, an infectious disease. The majority of people who are infected with this virus will have mild to moderate respiratory symptoms. Multiple studies have proved that there is a substantial pathophysiological link between COVID-19 disease and patients having comorbidities such as cystic fibrosis and chronic kidney disease. In this study, we attempted to identify differentially expressed genes as well as genes that intersected among them in order to comprehend their compatibility. Gene expression profiling indicated that 849 genes were mutually exclusive and functional analysis was done within the context of gene ontology and key pathways involvement. Three genes (PRPF31, FOXN2, and RIOK3) were commonly upregulated in the analysed datasets of three disease categories. These genes could be potential biomarkers for patients with COVID-19 and cystic fibrosis, and COVID-19 and chronic kidney disease. Further extensive analyses have been performed to describe how these genes are regulated by various transcription factors and microRNAs. Then, our analyses revealed six hub genes (PRPF31, FOXN2, RIOK3, UBC, HNF4A, and ELAVL). As they were involved in the interaction between COVID-19 and the patient with CF and CKD, they could help researchers identify potential therapeutic molecules. Some drugs have been predicted based on the upregulated genes, which may have a significant impact on reducing the burden of these diseases in the future.

Keywords: Bioinformatics; COVID-19; Chronic kidney disease; Cystic fibrosis; Differentially expressed genes; Gene regulatory networks; Protein-protein interaction; SARS-CoV-2; System biology; Transcriptomic profiling.