Identification of hub genes and molecular pathways in human T-lymphotropic virus type 1 associated diseases using protein-protein interactions networks

Amin Ebadi; Navid Momenifar; Shaghayegh Yazdani; Omid Gholizadeh; Vahdat Poortahmasebi

doi:10.18502/ijm.v14i1.8814

Identification of hub genes and molecular pathways in human T-lymphotropic virus type 1 associated diseases using protein-protein interactions networks

Iran J Microbiol. 2022 Feb;14(1):125-132. doi: 10.18502/ijm.v14i1.8814.

Authors

Amin Ebadi^{1

2}, Navid Momenifar³, Shaghayegh Yazdani⁴, Omid Gholizadeh^{2

5}, Vahdat Poortahmasebi^{2

5

6}

Affiliations

¹ Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
² Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
³ Human and Animal Cell Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran.
⁴ Department of Microbiology, Faculty of Advanced Science & Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
⁵ Department of Bacteriology and Virology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
⁶ Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran.

Abstract

Background and objectives: Human T-lymphotropic virus type 1 (HTLV-1) is the cause of adult T-cell leukemia (ATL) and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). The present study aims to analyze gene expression patterns in ATL and HAM/TSP.

Materials and methods: Microarray gene expression profiling of T-lymphocytes from HTLV-1 associated disease and healthy control were obtained from Gene Expression Omnibus (GEO). Several bioinformatics tools were used to identify differentially expressed genes (DEGs). Among the generated DEGs, we constructed protein-protein interaction (PPI) between HAM/TSM and ATL in comparison to asymptomatic carriers (ACs). Subsequently, gene ontology (GO) and topological analysis were performed.

Results: We found that the majority of DEGs in ATL and HAM/TSP were importantly implicated in immune response categories. The nodes and edges number of normal-AC, AC-ATL and ATL-HAM/TSP PPIs were 168 and 145, 116 and 97, and 275 and 327, respectively. Based on the topological analyses of protein-protein interaction networks, APP (Amyloid Beta Precursor Protein) was detected as a critical player in progression of HTLV-1 disease.

Conclusion: Dysregulation of immune response associated transcripts play a critical role in HTLV-1 disease progression. Immune response associated genes may be biomarker for prognosis in cancer development and therapeutic targets.

Keywords: Adult T-cell leukemia; DEGs; Gene expression; Gene ontology; Human T lymphotropic virus type 1 (HTLV-1)-associated myelopathy/tropical spastic paraparesis; Human T-lymphotropic virus 1.