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High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays |
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| Authors: | Yuker Wang Victoria EH Carlton George Karlin-Neumann Ronald Sapolsky Li Zhang Martin Moorhead Zhigang C Wang Andrea L Richardson Robert Warren Axel Walther Melissa Bondy Aysegul Sahin Ralf Krahe Musaffe Tuna Patricia A Thompson Paul T Spellman Joe W Gray Gordon B Mills Malek Faham |
| Institution: | 1. Jenner Institute, ORCRB, University of Oxford, Churchill Hospital, Oxford, OX3 7DQ, UK 2. South African Tuberculosis Vaccine Initiative, Institute of Infectious Diseases and Molecular Medicine, and School of Child and Adolescent Health, University of Cape Town, South Africa 3. Trudeau Institute Inc., Saranac Lake, NY, USA 4. Laboratory of Mycobacterial Immunity and Pathogenesis, Public Health Research Institute, Newark, NJ, USA |
| Abstract: | BackgroundNovel tuberculosis (TB) vaccines recently tested in humans have been designed to boost immunity induced by the current vaccine, Mycobacterium bovis Bacille Calmette-Guérin (BCG). Because BCG vaccination is used extensively in infants, this population group is likely to be the first in which efficacy trials of new vaccines will be conducted. However, our understanding of the complexity of immunity to BCG in infants is inadequate, making interpretation of vaccine-induced immune responses difficult.MethodsTo better understand BCG-induced immunity, we performed gene expression profiling in five 10-week old infants routinely vaccinated with BCG at birth. RNA was extracted from 12 hour BCG-stimulated or purified protein derivative of tuberculin (PPD)-stimulated PBMC, isolated from neonatal blood collected 10 weeks after vaccination. RNA was hybridised to the Sentrix® HumanRef-8 Expression BeadChip (Illumina) to measure expression of >16,000 genes.ResultsWe found that ex vivo stimulation of PBMC with PPD and BCG induced largely similar gene expression profiles, except that BCG induced greater macrophage activation. The peroxisome proliferator-activated receptor (PPAR) signaling pathway, including PPAR-γ, involved in activation of the alternative, anti-inflammatory macrophage response was down-regulated following stimulation with both antigens. In contrast, up-regulation of genes associated with the classic, pro-inflammatory macrophage response was noted. Further analysis revealed a decrease in the expression of cell adhesion molecules (CAMs), including integrin alpha M (ITGAM), which is known to be important for entry of mycobacteria into the macrophage. Interestingly, more leukocyte genes were down-regulated than up-regulated.ConclusionOur results suggest that a combination of suppressed and up-regulated genes may be key in determining development of protective immunity to TB induced by vaccination with BCG. |
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