RNA-Seq reveals strain-specific immune gene expression by epithelial cells infected with Mycobacterium tuberculosis strains of varying pathogenicity

Background: An insight into host mechanisms, genes and pathways, at the molecular level, is essential for our understanding of the host immune response to infection, especially with different strains of M. tuberculosis. Therefore, this study was undertaken in order to gain a better understanding of differential and strain specific immune responses of epithelial cells during infection by Mycobacterium tuberculosis strains of varying pathogenicity. Methods & Materials: Transcriptomics was used to investigate changes in gene expression of immune related genes by directly sequencing RNA transcripts from pulmonary epithelial cells infected with strains belonging to four different genotypes and a Unique strain of M. tuberculosis associated with drug resistance in KwaZulu-Natal. RNA was extracted from infected and uninfected epithelial cells at 48 hr after infection. The Illumina HiSeq 2000 platform was used to sequence 50 bp reads that were mapped to the human genome (hg19) using Tophat (2.0.10). Differential expression between the uninfected and infected cells, as well as among the different strains, was quantified using Cufflinks (2.1.0). Results: Enrichment analysis revealed differential expression of a varying number of immune-related genes by the different strains: F15/LAM4/KZN (KZN) (450), Beijing (319), F11 (422), F28 (325), Unique (334) and H37Rv (383). All strains induced 178 immune related genes in common at different levels. These included surface receptors (TLRs), interleukins, cell differentiation markers and genes involved in signalling pathways for cytokine production and immune response pathways. Additionally, changes were induced in a number of immune related genes distinct for the different strains: KZN (49), Unique (34), H37Rv (16), F11 (14), F28 (3), Beijing (0). Conclusion: The highly virulent Beijing strain failed to induce genes specific to its genotype in contrast to other strains. The KZN strain displayed the highest number of genotype-specific immune related genes compared to the others. Strain-specific gene expression signature patterns during infection by different strains of M. tuberculosis may reflect varying pathogenicity and represent potential biomarkers that can be exploited for vaccine development. However, this will need to be confirmed in vivo.