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Novel data integration approaches identify concordant and discordant immune responses between mice and humans [mouse]

ABSTRACT: We have conducted experiments to compare transcriptional response to tuberculosis (TB) in whole blood in two different TB murine models (susceptible 129S2 strain and resistant C57BL/6 strain) in time points day 1, day 7, day 14 and day 21 after infection.

ORGANISM(S): Mus musculus

PROVIDER: GSE89389 | GEO | 2017/09/21

SECONDARY ACCESSION(S): PRJNA352057

REPOSITORIES: GEO

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Project description:Although host genetics influences susceptibility to tuberculosis, few genes determining disease outcome have been identified. We hypothesized that macrophages from individuals with different clinical manifestations of tuberculosis 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 tuberculosis (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 1608 and 199 genes that were differentially expressed by >2 and >5-fold, respectively. Using cluster analysis, we identified gene expression patterns that distinguished the different clinical forms of tuberculosis. 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 tuberculosis. Experiment Overall Design: Latent TB (LTB) subjects were healthy nursing staff members who had worked at a tuberculosis hospital, for more than 20 years and were positive in ESAT-6 and CFP-10- specific IFN-ï?§ ELISPOT assays. All subjects with pulmonary (PTB) and meningeal (TBM) disease had been treated and were free of symptoms at the time of venipuncture. Gene expression of monocyte derived macrophages (MDMs) from subjects with three clinical forms of TB including LTB, PTB and TBM (n = 4 in each group) was examined by microarray. MDMs were stimulated either with a whole cell lysate of M. tuberculosis H37Rv or PBS for 4 hours. RNA expression was analyzed using a Human Genome U133 Plus 2.0 Array (Affymetrix, USA) which contains probe sets for 47,000 transcripts including 38,500 well-characterized human genes.

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Novel data integration approaches identify concordant and discordant immune responses between mice and humans [mouse]

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