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Thuong NT, et al. (2008) PLoS Pathog 4(12):e1000229

Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles.

Thuong NT, Dunstan SJ, Chau TT, Thorsson V, Simmons CP, Quyen NT, Thwaites GE, Thi Ngoc Lan N, Hibberd M, Teo YY, Seielstad M, Aderem A, Farrar JJ, Hawn TR

Although host genetics influences susceptibility to tuberculosis (TB), few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of Mycobacterium tuberculosis (Mtb) infection would have distinct gene expression profiles and that polymorphisms in these genes may also be associated with susceptibility to TB. We measured gene expression levels of >38,500 genes from ex vivo Mtb-stimulated macrophages in 12 subjects with 3 clinical phenotypes: latent, pulmonary, and meningeal TB (n = 4 per group). After identifying differentially expressed genes, we confirmed these results in 34 additional subjects by real-time PCR. We also used a case-control study design to examine whether polymorphisms in differentially regulated genes were associated with susceptibility to these different clinical forms of TB. We compared gene expression profiles in Mtb-stimulated and unstimulated macrophages and identified 1,608 and 199 genes that were differentially expressed by >2- and >5-fold, respectively. In an independent sample set of 34 individuals and a subset of highly regulated genes, 90% of the microarray results were confirmed by RT-PCR, including expression levels of CCL1, which distinguished the 3 clinical groups. Furthermore, 6 single nucleotide polymorphisms (SNPs) in CCL1 were found to be associated with TB in a case-control genetic association study with 273 TB cases and 188 controls. To our knowledge, this is the first identification of CCL1 as a gene involved in host susceptibility to TB and the first study to combine microarray and DNA polymorphism studies to identify genes associated with TB susceptibility. These results suggest that genome-wide studies can provide an unbiased method to identify critical macrophage response genes that are associated with different clinical outcomes and that variation in innate immune response genes regulate susceptibility to TB.

MESH: Chemokine CCL1/*genetics/metabolism; Oligonucleotide Array Sequence Analysis; Case-Control Studies; Databases, Genetic; Macrophages/*immunology; Mycobacterium tuberculosis/*immunology; Gene Expression Regulation; Reproducibility of Results; RNA, Messenger/genetics/metabolism; Tuberculosis/*genetics/*immunology; Tuberculosis, Pulmonary/genetics/immunology; Humans; Polymerase Chain Reaction; *Genetic Predisposition to Disease; Macrophage Activation; *Polymorphism, Single Nucleotide; Cluster Analysis; Tuberculosis, Meningeal/genetics/immunology
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Associated Experiment Sets Options
Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles (CEL data) view cluster image download a pre-clustering (PCL) file view data retrieval and analysis summary view experiment set details display data data retrieval and analysis data for individual sample download raw dataset  (192.12 Mbytes)
Identification of tuberculosis susceptibility genes with human macrophage gene expression profiles (Probe Set data) view cluster image download a pre-clustering (PCL) file view data retrieval and analysis summary view experiment set details display data data retrieval and analysis data for individual sample download raw dataset  (10.93 Mbytes)