Genome-wide expression profiling identifies type 1 interferon response pathways in active tuberculosis - PubMed (original) (raw)

doi: 10.1371/journal.pone.0045839. Epub 2012 Sep 21.

Ranjeeta Hari Dass, Ninghan Yang, Mingzi M Zhang, Hazel E E Wong, Edhyana Sahiratmadja, Chiea Chuen Khor, Bachti Alisjahbana, Reinout van Crevel, Sangkot Marzuki, Mark Seielstad, Esther van de Vosse, Martin L Hibberd

Affiliations

Genome-wide expression profiling identifies type 1 interferon response pathways in active tuberculosis

Tom H M Ottenhoff et al. PLoS One. 2012.

Abstract

Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb), remains the leading cause of mortality from a single infectious agent. Each year around 9 million individuals newly develop active TB disease, and over 2 billion individuals are latently infected with M.tb worldwide, thus being at risk of developing TB reactivation disease later in life. The underlying mechanisms and pathways of protection against TB in humans, as well as the dynamics of the host response to M.tb infection, are incompletely understood. We carried out whole-genome expression profiling on a cohort of TB patients longitudinally sampled along 3 time-points: during active infection, during treatment, and after completion of curative treatment. We identified molecular signatures involving the upregulation of type-1 interferon (α/β) mediated signaling and chronic inflammation during active TB disease in an Indonesian population, in line with results from two recent studies in ethnically and epidemiologically different populations in Europe and South Africa. Expression profiles were captured in neutrophil-depleted blood samples, indicating a major contribution of lymphocytes and myeloid cells. Expression of type-1 interferon (α/β) genes mediated was also upregulated in the lungs of M.tb infected mice and in infected human macrophages. In patients, the regulated gene expression-signature normalized during treatment, including the type-1 interferon mediated signaling and a concurrent opposite regulation of interferon-gamma. Further analysis revealed IL15RA, UBE2L6 and GBP4 as molecules involved in the type-I interferon response in all three experimental models. Our data is highly suggestive that the innate immune type-I interferon signaling cascade could be used as a quantitative tool for monitoring active TB disease, and provide evidence that components of the patient's blood gene expression signature bear similarities to the pulmonary and macrophage response to mycobacterial infection.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1

Figure 1. Differential gene expression in blood from TB patients and controls determined by microarrays.

Heat map of 875 transcripts which were statistically different in one condition from the other condition, using ANOVA and were hierarchically clustered. active = patients with active disease, treatment = patients after 8 weeks of treatment, recovered = patients after 28 weeks of treatment and controls = healthy controls. Red represents an increase in gene expression and green represents a decrease in gene expression.

Figure 2

Figure 2. Cluster analysis using self-organizing map with further Panther analysis.

Genespring GX10 was used to analyse transcripts which were significantly different between the four conditions (Active disease, Treatment, Recovered and Controls) using one-way ANOVA and subsequently subjected to self-organizing map clustering analysis. Upregulated transcripts (left panel) and downregulated transcripts (right panel) were subjected to further analysis through Panther.

Figure 3

Figure 3. Comparison of differential gene expression between M.tb infected patients and BCG infected THP-1 cells.

Venn diagram representing the 875 significantly differentially expressed in TB patients and 461 transcripts significantly differentially expressed in THP-1 BCG in vitro model. A total of 95 transcripts were found to be in common between these two systems. Red – transcripts for active TB patients only; Green – Common between TB patients and BCG-infected THP-1 cell line; Blue – transcripts for BCG-infected THP-1 only.

Figure 4

Figure 4. Comparison of differential gene expression between patients with active TB and mice infected M.tb in vivo model.

Venn diagram representing the 875 significantly differentially expressed in TB patients and 1674 transcripts significantly differentially expressed in TB actively infected mice. A total of 121 transcripts were found to be in common between these two systems. Red – transcripts for TB patient only; Green – Common between TB patients and mice infected with TB; Blue – transcripts for mice infected with TB only.

Figure 5

Figure 5. Comparison of differential gene expression from all three models.

Venn diagram representing the 875 significantly differentially expressed in TB patients, 461 significantly differentially expressed in BCG-infected THP-1 cells and 1674 transcripts significantly differentially expressed in TB actively infected mice. A total of 33 transcripts (representing 26 genes) were found to be in common between all three systems. Red – transcripts for patients with active TB; Blue – transcripts for BCG-infected THP-1 cells; yYellow – transcripts for mice infected with active TB.

Figure 6

Figure 6. Validating microarray data by qRT-PCR.

Microarray results were validated by qRT-PCR. 17 genes from the 26 genes were found to be significantly different between TB patients with active disease and healthy controls, 15 genes from the 26 genes were found to be significantly different between live BCG-infected THP-1 cells at 20 hours compared to uninfected controls, and 5 genes from 26 genes were found to be significantly different between mice infected with active TB and mock infected mice, using student’s T test (P<0.05). Three genes which were common to all 3 models show similar levels of expression with both techniques applied. The fold increase for microarray technique (blue, orange and yellow) and qRT-PCR technique (light blue, light orange and light yellow) for patients, THP-1 cells and mice respectively. Microarray data (and their corresponding qRT-PCR data) that were not validated by qRT-PCR are not shown.

Figure 7

Figure 7. Ingenuity pathway analysis of the key genes identified.

Ingenuity pathway analysis of the genes differentially regulated and common to the three systems described above (in orange). Network of genes in the interferon 1 signaling pathways that were found to be common in active TB patients, BCG-infected THP-1 cells at 20 hours and mice infected with active TB are illustrated. The lines in between genes represent known interactions, with solid lines representing direct interactions and dashed lines representing indirect interactions.

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