Additional file 1:Experimental results of RS-SNP and GENGEN on MSigDB C2 collection. Tables repor... more Additional file 1:Experimental results of RS-SNP and GENGEN on MSigDB C2 collection. Tables reporting the experimental results obtained by the proposed method, RS-SNP, and by GENGEN on the MSigDB C2 pathway collection. (PDF 106 KB)
Additional file 3:RS-SNP package. The proposed RS-SNP software is contained in this compressed fi... more Additional file 3:RS-SNP package. The proposed RS-SNP software is contained in this compressed file, together with: • the help documentation, • example files with the SNP-gene mapping and gene-pathway mapping; • example of input files. (ZIP 3 MB)
Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methy... more Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methylation of candidate genes for inflammatory bowel disease (IBD) have demonstrated significant associations between genetic and epigenetic changes and IBD. Independent GWA studies have identified genetic variants in the , , , , and loci to be associated with both IBD and immunoglobulin G (IgG) glycosylation. Using bisulfite pyrosequencing, we analyzed CpG methylation in promoter regions of these five genes from peripheral blood of several hundred IBD patients and healthy controls (HCs) from two independent cohorts, respectively. We found significant differences in the methylation levels in the and genes between both Crohn's disease and ulcerative colitis when compared to HC. The same pattern of methylation changes was identified for both genes in CD19 B cells isolated from the whole blood of a subset of the IBD patients. A correlation analysis was performed between the and promoter met...
Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn... more Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn's disease (CD) and ulcerative colitis (UC), are sometimes hard to distinguish. Glycosylation of IgG has been associated with CD and UC. IgG Fc-glycosylation affects IgG effector functions. We evaluated changes in IgG Fc-glycosylation associated with UC and CD, as well as with disease characteristics in different patient groups. We analyzed 3441 plasma samples obtained from 2 independent cohorts of patients with CD (874 patients from Italy and 391 from the United States) or UC (1056 from Italy and 253 from the US and healthy individuals [controls]; 427 in Italy and 440 from the United States). IgG Fc-glycosylation (tryptic glycopeptides) was analyzed by liquid chromatography coupled to mass spectrometry. We analyzed associations between disease status (UC vs controls, CD vs controls, and UC vs CD) and glycopeptide traits, and associations between clinical characteristics and glycopep...
Crohn's disease (CD) is a pathologic condition with different clinical expressions that may r... more Crohn's disease (CD) is a pathologic condition with different clinical expressions that may reflect an interplay between genetics and environmental factors. Recently, it has been highlighted that three genetic markers, NOD2, MHC and MST1, were associated to distinct CD sites, supporting the concept that genetic variations may contribute to localize CD. Genetic markers, previously shown to be associated with inflammatory bowel disease (IBD), were tested in CD patients with the aim to better dissect the genetic relationship between ileal, ileocolonic and colonic CD and ascertain whether a different genetic background would support the three disease sites as independent entities. A panel of 29 SNPs of 19 IBD loci were analyzed by TaqMan SNP allelic discrimination method both evaluating their distinct contribute and analyzing all markers jointly. Seven hundred and eight CD patients and 537 healthy controls were included in the study. Of the overall population of patients, 237 patien...
Simultaneous analysis of the transcripts of thousands of genes by cDNA microarrays allows the ide... more Simultaneous analysis of the transcripts of thousands of genes by cDNA microarrays allows the identification of genetic regulatory mechanisms involved in disease pathophysiology. The circadian clock circuitry controls essential cell processes and the functioning of organ systems, which are characterized by rhythmic variations with 24-hour periodicity. The derangement of these processes is involved in the basic mechanisms of inflammatory, metabolic, degenerative and neoplastic diseases. We evaluated by genome-wide cDNA microarray analysis the transcriptome of endoscopic mucosal biopsies of patients with inflammatory bowel diseases (IBD) focusing on the expression of circadian genes in Crohn's disease (CD) and ulcerative colitis (UC). Twenty-nine IBD patients (15 with CD and 14 with UC) were enrolled and mucosal biopsies were sampled at either inflamed or adjacent non-inflamed areas of the colon. A total of 150 circadian genes involved in pathways controlling crucial cell processes and tissue functions were investigated. In CD specimens 50 genes were differentially expressed, and 21 genes resulted up-regulated when compared to healthy colonic mucosa. In UC specimens 50 genes were differentially expressed, and 27 genes resulted up-regulated when compared to healthy colonic mucosa. Among the core clock genes ARNTL2 and RORA were up-regulated, while CSNK2B, NPAS2, PER1 and PER3 were down-regulated in CD specimens. Conversely, ARNTL2, CRY1, CSNK1E, RORA and TIPIN were up-regulated, while NR1D2 and PER3 were down-regulated in UC. In conclusion, in CD and UC patients there are differences in the expression of circadian genes between normal and diseased intestinal mucosa. The deregulated genes evidenced by transcriptome analysis in the major IBDs may play a crucial role in the pathophysiological mechanisms and may suggest novel therapeutic approaches.
This paper focuses on the comparison of two different approaches to the analysis of Single Nucleo... more This paper focuses on the comparison of two different approaches to the analysis of Single Nucleotide Polymorphism (SNP) profiles data regarding Crohn's Disease; the first one is based on a single SNP analysis, conducted by means of classical statistical tools, to ...
Palmieri, O., Latiano, A., Maglietta, R., Palumbo, O., Carella, M., Ancona, N., Bossa, F., Andriu... more Palmieri, O., Latiano, A., Maglietta, R., Palumbo, O., Carella, M., Ancona, N., Bossa, F., Andriulli, A. and Annese, V.(2011), Dissecting the mucosal expression of human leucine-rich repeat family genes in inflammatory bowel disease patients. Inflammatory Bowel Diseases ...
Additional file 1:Experimental results of RS-SNP and GENGEN on MSigDB C2 collection. Tables repor... more Additional file 1:Experimental results of RS-SNP and GENGEN on MSigDB C2 collection. Tables reporting the experimental results obtained by the proposed method, RS-SNP, and by GENGEN on the MSigDB C2 pathway collection. (PDF 106 KB)
Additional file 3:RS-SNP package. The proposed RS-SNP software is contained in this compressed fi... more Additional file 3:RS-SNP package. The proposed RS-SNP software is contained in this compressed file, together with: • the help documentation, • example files with the SNP-gene mapping and gene-pathway mapping; • example of input files. (ZIP 3 MB)
Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methy... more Many genome- and epigenome-wide association studies (GWAS and EWAS) and studies of promoter methylation of candidate genes for inflammatory bowel disease (IBD) have demonstrated significant associations between genetic and epigenetic changes and IBD. Independent GWA studies have identified genetic variants in the , , , , and loci to be associated with both IBD and immunoglobulin G (IgG) glycosylation. Using bisulfite pyrosequencing, we analyzed CpG methylation in promoter regions of these five genes from peripheral blood of several hundred IBD patients and healthy controls (HCs) from two independent cohorts, respectively. We found significant differences in the methylation levels in the and genes between both Crohn's disease and ulcerative colitis when compared to HC. The same pattern of methylation changes was identified for both genes in CD19 B cells isolated from the whole blood of a subset of the IBD patients. A correlation analysis was performed between the and promoter met...
Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn... more Causes of inflammatory bowel diseases are not well understood and the most prominent forms, Crohn's disease (CD) and ulcerative colitis (UC), are sometimes hard to distinguish. Glycosylation of IgG has been associated with CD and UC. IgG Fc-glycosylation affects IgG effector functions. We evaluated changes in IgG Fc-glycosylation associated with UC and CD, as well as with disease characteristics in different patient groups. We analyzed 3441 plasma samples obtained from 2 independent cohorts of patients with CD (874 patients from Italy and 391 from the United States) or UC (1056 from Italy and 253 from the US and healthy individuals [controls]; 427 in Italy and 440 from the United States). IgG Fc-glycosylation (tryptic glycopeptides) was analyzed by liquid chromatography coupled to mass spectrometry. We analyzed associations between disease status (UC vs controls, CD vs controls, and UC vs CD) and glycopeptide traits, and associations between clinical characteristics and glycopep...
Crohn's disease (CD) is a pathologic condition with different clinical expressions that may r... more Crohn's disease (CD) is a pathologic condition with different clinical expressions that may reflect an interplay between genetics and environmental factors. Recently, it has been highlighted that three genetic markers, NOD2, MHC and MST1, were associated to distinct CD sites, supporting the concept that genetic variations may contribute to localize CD. Genetic markers, previously shown to be associated with inflammatory bowel disease (IBD), were tested in CD patients with the aim to better dissect the genetic relationship between ileal, ileocolonic and colonic CD and ascertain whether a different genetic background would support the three disease sites as independent entities. A panel of 29 SNPs of 19 IBD loci were analyzed by TaqMan SNP allelic discrimination method both evaluating their distinct contribute and analyzing all markers jointly. Seven hundred and eight CD patients and 537 healthy controls were included in the study. Of the overall population of patients, 237 patien...
Simultaneous analysis of the transcripts of thousands of genes by cDNA microarrays allows the ide... more Simultaneous analysis of the transcripts of thousands of genes by cDNA microarrays allows the identification of genetic regulatory mechanisms involved in disease pathophysiology. The circadian clock circuitry controls essential cell processes and the functioning of organ systems, which are characterized by rhythmic variations with 24-hour periodicity. The derangement of these processes is involved in the basic mechanisms of inflammatory, metabolic, degenerative and neoplastic diseases. We evaluated by genome-wide cDNA microarray analysis the transcriptome of endoscopic mucosal biopsies of patients with inflammatory bowel diseases (IBD) focusing on the expression of circadian genes in Crohn's disease (CD) and ulcerative colitis (UC). Twenty-nine IBD patients (15 with CD and 14 with UC) were enrolled and mucosal biopsies were sampled at either inflamed or adjacent non-inflamed areas of the colon. A total of 150 circadian genes involved in pathways controlling crucial cell processes and tissue functions were investigated. In CD specimens 50 genes were differentially expressed, and 21 genes resulted up-regulated when compared to healthy colonic mucosa. In UC specimens 50 genes were differentially expressed, and 27 genes resulted up-regulated when compared to healthy colonic mucosa. Among the core clock genes ARNTL2 and RORA were up-regulated, while CSNK2B, NPAS2, PER1 and PER3 were down-regulated in CD specimens. Conversely, ARNTL2, CRY1, CSNK1E, RORA and TIPIN were up-regulated, while NR1D2 and PER3 were down-regulated in UC. In conclusion, in CD and UC patients there are differences in the expression of circadian genes between normal and diseased intestinal mucosa. The deregulated genes evidenced by transcriptome analysis in the major IBDs may play a crucial role in the pathophysiological mechanisms and may suggest novel therapeutic approaches.
This paper focuses on the comparison of two different approaches to the analysis of Single Nucleo... more This paper focuses on the comparison of two different approaches to the analysis of Single Nucleotide Polymorphism (SNP) profiles data regarding Crohn's Disease; the first one is based on a single SNP analysis, conducted by means of classical statistical tools, to ...
Palmieri, O., Latiano, A., Maglietta, R., Palumbo, O., Carella, M., Ancona, N., Bossa, F., Andriu... more Palmieri, O., Latiano, A., Maglietta, R., Palumbo, O., Carella, M., Ancona, N., Bossa, F., Andriulli, A. and Annese, V.(2011), Dissecting the mucosal expression of human leucine-rich repeat family genes in inflammatory bowel disease patients. Inflammatory Bowel Diseases ...
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