title: Canonical pathways, networks and transcriptional factor regulation by clinical strains of Mycobacterium tuberculosis in pulmonary alveolar epithelial cells.
abstract: Limited knowledge exists on pathways, networks and transcriptional factors regulated within epithelial cells by diverse Mycobacterium tuberculosis genotypes. This study aimed to elucidate these mechanisms induced in A549 epithelial cells by dominant clinical strains in KwaZulu-Natal, South Africa. RNA for sequencing was extracted from epithelial cells at 48 h post-infection with 5 strains at a multiplicity of infection of approximately 10:1. Bioinformatics analysis performed with the RNA-Seq Tuxedo pipeline identified differentially expressed genes. Changes in pathways, networks and transcriptional factors were identified using Ingenuity Pathway Analysis (IPA). The interferon signalling and hepatic fibrosis/hepatic stellate cell activation pathways were among the top 5 canonical pathways in all strains. Hierarchical clustering for enrichment of cholesterol biosynthesis and immune associated pathways revealed similar patterns for Beijing and Unique; F15/LAM4/KZN and F11; and, F28 and H37Rv strains, respectively. However, the induction of top scoring networks varied among the strains. Among the transcriptional factors, only EHL, IRF7, PML, STAT1, STAT2 and VDR were induced by all clinical strains. Activation of the different pathways, networks and transcriptional factors revealed in the current study may be an underlying mechanism that results in the differential host response by clinical strains of M. tuberculosis.
authors.affiliation: School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville 3630, South Africa. Electronic address: 207500550@stu.ukzn.ac.za.
authors.forename: Nontobeko E
authors.initials: NE
authors.lastname: Mvubu
authors.affiliation: School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Westville 3630, South Africa. Electronic address: pillayb1@ukzn.ac.za.
authors.forename: Balakrishna
authors.initials: B
authors.lastname: Pillay
authors.affiliation: South African National Bioinformatics Institute/MRC Unit for Bioinformatics Capacity Development, University of the Western Cape, Bellville 7530, South Africa. Electronic address: junaid@sanbi.ac.za.
authors.forename: Junaid
authors.initials: J
authors.lastname: Gamieldien
authors.affiliation: Department of Medicine, Division of Infectious Diseases, Johns Hopkins School of Medicine, 1550 Orleans St., Baltimore, MD, United State of America. Electronic address: wbishai1@jhmi.edu.
authors.forename: William
authors.initials: W
authors.lastname: Bishai
authors.affiliation: Medical Microbiology and Infection Control, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Private Bag 7, Congella 4013, Durban, South Africa. Electronic address: pillayc@ukzn.ac.za.
authors.forename: Manormoney
authors.initials: M
authors.lastname: Pillay
mesh_terms: D045744:Cell Line, Tumor; D016000:Cluster Analysis; D019295:Computational Biology; D030541:Databases, Genetic; D004847:Epithelial Cells / Q000378:metabolism / Q000382:microbiology*; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D054884:Host-Pathogen Interactions; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000472:pathogenicity*; D060066:Protein Interaction Maps; D011650:Pulmonary Alveoli / Q000378:metabolism / Q000382:microbiology*; D015398:Signal Transduction / Q000235:genetics; D013997:Time Factors; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D014157:Transcription Factors
keywords: Canonical pathways; Epithelial cells; Mycobacterium tuberculosis; Networks; RNA sequencing; Transcriptional factors