Cluster analysis of genome-wide expression differences in disease-unaffected ileal mucosa in inflammatory bowel diseases.
ABSTRACT Whole human genome (Agilent) expression profiling was conducted on disease-unaffected ileal RNA collected from the proximal margin of resected ileum from 47 ileal Crohn's disease (CD), 27 ulcerative colitis (UC) and 25 control patients without inflammatory bowel diseases (IBD). Cluster analysis combined with significance analysis of microarrays (SAM) and principal component analysis (PCA) and was used to reduce the data dimension to identify gene- probe clusters associated with early pathogenic changes in ileal CD and UC. Ingenuity Pathway Analysis (IPA) was used to identify the biological pathways associated with each cluster. We reduced the dimensions of the 26,765 gene probe set to 43 gene-probe clusters. Most of these clusters could be labeled as related to different biological pathways, such as Paneth cell antimicrobial peptides, the formation of organized lymphoid structures, or nuclear receptor signaling and xenobiotic metabolism. Molecular phylogenetic 16S rRNA sequence analysis was completed on 83 DNA samples from the same samples used to generate the gene expression profiles. We conducted an exploratory study to determine if the first principle component (PC1) of these clusters could be linked to specific phyla/subphyla taxa. patients undergoing either right hemicolectomy or total colectomy. Of these 99 subjects, we have completed molecular phylogenetic analysis of the same biopsy samples based on 16S rRNA sequence analysis in 83 subjects. To identify biological pathways associated with early pathogeneic changes in the disease unaffected ileum, we aim to construct a system model including clinical information, genetic data and microbiota composition. In order to integrate these large data sets, we developed a dimension reduction scheme combining several computational tools, including cluster analysis, significance analysis of microarray (SAM) (4) and principal component analysis (PCA), to summarize information from our whole expression profiling experiments. Cluster analysis of microarray data based on similarity of gene expression values has been used for dimension reduction purpose (5-7), but has been criticized for lacking of statistical significance (4). IPA as well as direct inspection of the gene lists within each cluster was used to identify biological pathways. To illustrate the use of this approach towards demonstration - reduction, we present an exploratory analysis integrating the results of our cluster analysis with genotype, phenotype and human microbiome data.
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ABSTRACT: In this paper, we propose a computationally efficient approach -space(Sparse PArtial Correlation Estimation)- for selecting non-zero partial correlations under the high-dimension-low-sample-size setting. This method assumes the overall sparsity of the partial correlation matrix and employs sparse regression techniques for model fitting. We illustrate the performance of space by extensive simulation studies. It is shown that space performs well in both non-zero partial correlation selection and the identification of hub variables, and also outperforms two existing methods. We then apply space to a microarray breast cancer data set and identify a set of hub genes which may provide important insights on genetic regulatory networks. Finally, we prove that, under a set of suitable assumptions, the proposed procedure is asymptotically consistent in terms of model selection and parameter estimation.Journal of the American Statistical Association 06/2009; 104(486):735-746. · 1.83 Impact Factor
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ABSTRACT: Interactions between the colonic lymphoid system and the genetic background in Crohn's disease are unexplored. This study analysed variations of colonic lymphoid follicles (CLFs) according to the nucleotide-binding oligomerization domain 2 (NOD2) and caspase recruitment domain-containing protein 15 (CARD15) gene in patients with Crohn's disease. CLFs were characterized by histology and immunohistochemistry in the specimens of 41 patients undergoing colonic resection for Crohn's disease. Variants of the NOD2/CARD15 gene were assessed by denaturing high performance liquid chromatography and confirmed by DNA sequencing. Eleven patients had a heterozygous variant of the NOD2/CARD15 gene. The uninvolved colon of mutants had significantly lower CLF density (0.9 versus 2.7 follicles per cm(2); P < 0.001) and proportion of those with a germinal centre (9 versus 22 per cent; P = 0.040) than in non-mutants. In active disease, CLF density increased similarly in patients with and without the mutation. The proportion of extramucosal CLFs was higher in mutants than in non-mutants (34 versus 22 per cent; P = 0.030). No significant difference between groups was recorded for cellular profile and proliferation. Patients with Crohn's disease and the NOD2/CARD15 mutation show a remodelling of CLFs in both uninvolved and actively inflamed intestines. These subjects may have a defective immune response by organized lymphoid structures.British Journal of Surgery 06/2009; 96(6):655-62. · 4.84 Impact Factor
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ABSTRACT: NOD2 single nucleotide polymorphisms have been associated with increased risk of ileal Crohn's disease (CD). This exploratory study was conducted to compare ileal mucosal gene expression in CD patients with and without NOD2 risk alleles. Ileal samples were prospectively collected from 18 nonsmoking CD patients not treated with anti-TNF-α biologics and 9 nonsmoking control patients without inflammatory bowel disease undergoing initial resection and genotyped for the 3 major NOD2 risk alleles (Arg702Trp, Gly908Arg, Leu1007fs). Microarray analysis was performed in samples from 4 NOD2(R) (at least 1 risk allele) CD patients, 4 NOD2(NR) (no risk alleles) CD patients, and 4 NOD2(NR) controls. Candidate genes selected by significance analysis of microarrays (SAM) were confirmed by quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) assays of all the samples. SAM detected upregulation of 18 genes in affected ileum in NOD2(R) compared to NOD2(NR) CD patients, including genes related to lymphocyte activation. SAM also detected altered ileal gene expression in unaffected NOD2(NR) ileal mucosal CD samples compared to NOD2(NR) control samples. qRT-PCR conducted on all the samples confirmed that increased CD3D expression in affected samples was associated with NOD2(R) status, and that increased MUC1, DUOX2, DMBT1 and decreased C4orf7 expression in unaffected samples was associated with CD, independent of NOD2 status. The results support the concept that NOD2 risk alleles contribute to impaired regulation of inflammation in the ileum. Furthermore, altered ileal gene expression, independent of NOD2 status, is detected in the unaffected proximal margin of resected ileum from CD patients.Inflammatory Bowel Diseases 02/2010; 16(10):1649-57. · 5.12 Impact Factor