Nutrigenetics, Nutrigenomics and Inflammatory Bowel Diseases
Nutrigenetics, Nutrigenomics and Inflammatory Bowel Diseases
Epigenetics research may be essential to understanding the potential role of environment, including diet, in IBD. Jenke and Zilbauer reviewed the results of recent studies on epigenetic events in IBD, considering both the challenges and also the opportunities for future research. They summarized the accumulating evidence that epigenetics may modulate some of the effects of genetic predisposition, as well as environment and intestinal microbiota on the pathogenesis of IBD.
DNA methylation is a primary epigenetic mechanism which modulates DNA transcription and thereby gene expression. Cooke et al. considered differences in methylation patterns in DNA from rectal biopsies, in relation to UC, CD and control status. They initially used a commercial Human Methylation Bead Chip microarray and then validated selected methylation signals in a replication panel by pyrosequencing, as well as looking for effects on gene expression. This set of studies enabled them to correlate methylation patterns with disease susceptibility and activity. Some of the affected genes showed a strong overlap with susceptibility loci identified by Jostins et al., and previous candidate gene studies by numerous authors. This group included CARD9, ICAM3 and IL-8RB. The strong statistical significance suggests a mechanistic role of these epigenetic effects in IBD pathogenesis.
In their study, Lin et al. used B cells from the peripheral blood of 18 IBD patients (9 CD and 9 UC), enabling them to identify IBD-associated changes in DNA methylation. They compared methylation profiles between B cell lines from IBD patients with those from their siblings who had not developed IBD, correlating 14 CD-specific methylation sites, and 24 UC-specific methylation sites with disease status. These sites included several loci within the IL-12/IL-23 pathway that has been previously associated with disease risk.
Nimmo et al. considered the methylation status of 27,578 CpG sites across the genome, using the Illumina Human Methylation27 assay on DNA, again from peripheral blood mononuclear cells. They studied 40 adult females (21 ileal CD, 19 healthy controls) and 16 girls with childhood-onset CD, all non-smokers. The data revealed a global methylation profile that was characteristic of ileal CD, whereby 1117 sites were differentially methylated. Affected genes included those altering immune activation (FASLG, IL-21R, MAPK13, PRF1, RIPK3 and S100A13). Immunity-related pathways appeared as targets of epigenetic modification, including immune system processes, immune response and defense responses to bacteria. Other analyses implicated dendritic cell activity and differential regulation of cytokines, especially IL-17. It appeared that methylation status was able to predict disease status, with good sensitivity and specificity.
Gene expression may also be related to chromatin modifications and effects on non-coding RNAs. Scarpa and Stylianou described how environment can lead to modifications to chromatin and effects on non-coding RNAs, including miRNAs. This thereby induces diverse families of enzymes with significant effects on transcription. By these means, environmentally induced changes to gene expression are likely to determine cell phenotype and function in IBD.
miRNAs are small non-coding RNAs with some ability to regulate gene expression. Paraskevi et al. harvested peripheral blood mononuclear cells of IBD patients in order to study the expression patterns of some miRNAs that are commonly deregulated in IBD patients. They considered the expression patterns of the selected miRNA species in 162 healthy controls in comparison with 128 CD and 88 UC patients. The expression levels were assayed quantitatively using reverse transcription and real-time RT-PCR. Eleven miRNAs were overexpressed in the peripheral blood mononuclear cells from CD patients in comparison with healthy controls: miR-16, miR-23a, miR-29a, miR-106a, miR-107, miR-126, miR-191, miR-199a-5p, miR-200c, miR-362-3p and miR-532-3p. In comparison, six miRNAs were overexpressed in the peripheral blood mononuclear cells from UC patients in comparison with healthy controls: miR-16, miR-21, miR-28-5p, miR-151-5p, miR-155 and miR-199a-5p. They suggested that this panel could provide a new non-invasive biomarker for distinguishing CD from UC at an early stage of investigation.
More generally, Clark et al. obtained gene and miRNA signatures for CD and UC, which they obtained through bioinformatics tools and high-throughput computations using data from a comprehensive literature search. Coupled with these data, a systematic review enabled the group to compare IBD with other autoimmune diseases, picking up potential drug targets in the process. Indeed, they suggest that several drugs already on the market for various disorders including gastrointestinal cancers and viral infections might potentially be useful in one or both of these diseases. The top upregulated genes in IBD have been previously associated with bacterial signals, diabetogenesis, innate immunity, inflammation and matrix metalloproteases. The downregulated genes encoded tight junction proteins, solute transporters and adhesion proteins. Several genes were differentially expressed in UC as compared with CD. A compromised metabolism for processing of androgen and estrogen drugs, nitrogen and lipids in IBD was associated with changes in the levels of specific miRNAs.
A total of 172 biopsies from 53 CD and 31 control subjects were studied by Noble et al. They collected paired biopsies from five different locations including the terminal ileum, and processed these for RNA extraction and histology. A comparison of biopsies from CD patients as compared with controls showed 259 sequences to be upregulated and 87 sequences downregulated. In colonic inflammatory CD, they showed downregulation of expression of the organic solute carrier genes: SLC38A4, SLC26A2 and OST alpha, and upregulation of IL-23A, JAK2 and STAT3.
Unaffected ileal mucosal biopsies of patients with ileal CD were studied using whole human genome expression profiling, in order to develop an ileal CD gene signature. Patients with ileal CD were compared with UC patients and also control subjects. The authors collected samples from the proximal margin of the resected ileum, using tissues that were unaffected by disease. Agilent whole human genome expression profiling was used on two independent sets of such samples. The expression of folate hydrolase (prostate-specific membrane antigen) 1 (FOLH1) emerged as a common feature that discriminated ileal CD from the other two groups.
Despite such individual studies, a meta-analysis of available data on gene expression patterns of colon mucosa failed to show convincing evidence of major differences in gene expression patterns between CD and UC.
Epigenetics & IBD
Epigenetics research may be essential to understanding the potential role of environment, including diet, in IBD. Jenke and Zilbauer reviewed the results of recent studies on epigenetic events in IBD, considering both the challenges and also the opportunities for future research. They summarized the accumulating evidence that epigenetics may modulate some of the effects of genetic predisposition, as well as environment and intestinal microbiota on the pathogenesis of IBD.
DNA methylation is a primary epigenetic mechanism which modulates DNA transcription and thereby gene expression. Cooke et al. considered differences in methylation patterns in DNA from rectal biopsies, in relation to UC, CD and control status. They initially used a commercial Human Methylation Bead Chip microarray and then validated selected methylation signals in a replication panel by pyrosequencing, as well as looking for effects on gene expression. This set of studies enabled them to correlate methylation patterns with disease susceptibility and activity. Some of the affected genes showed a strong overlap with susceptibility loci identified by Jostins et al., and previous candidate gene studies by numerous authors. This group included CARD9, ICAM3 and IL-8RB. The strong statistical significance suggests a mechanistic role of these epigenetic effects in IBD pathogenesis.
In their study, Lin et al. used B cells from the peripheral blood of 18 IBD patients (9 CD and 9 UC), enabling them to identify IBD-associated changes in DNA methylation. They compared methylation profiles between B cell lines from IBD patients with those from their siblings who had not developed IBD, correlating 14 CD-specific methylation sites, and 24 UC-specific methylation sites with disease status. These sites included several loci within the IL-12/IL-23 pathway that has been previously associated with disease risk.
Nimmo et al. considered the methylation status of 27,578 CpG sites across the genome, using the Illumina Human Methylation27 assay on DNA, again from peripheral blood mononuclear cells. They studied 40 adult females (21 ileal CD, 19 healthy controls) and 16 girls with childhood-onset CD, all non-smokers. The data revealed a global methylation profile that was characteristic of ileal CD, whereby 1117 sites were differentially methylated. Affected genes included those altering immune activation (FASLG, IL-21R, MAPK13, PRF1, RIPK3 and S100A13). Immunity-related pathways appeared as targets of epigenetic modification, including immune system processes, immune response and defense responses to bacteria. Other analyses implicated dendritic cell activity and differential regulation of cytokines, especially IL-17. It appeared that methylation status was able to predict disease status, with good sensitivity and specificity.
Gene expression may also be related to chromatin modifications and effects on non-coding RNAs. Scarpa and Stylianou described how environment can lead to modifications to chromatin and effects on non-coding RNAs, including miRNAs. This thereby induces diverse families of enzymes with significant effects on transcription. By these means, environmentally induced changes to gene expression are likely to determine cell phenotype and function in IBD.
miRNAs are small non-coding RNAs with some ability to regulate gene expression. Paraskevi et al. harvested peripheral blood mononuclear cells of IBD patients in order to study the expression patterns of some miRNAs that are commonly deregulated in IBD patients. They considered the expression patterns of the selected miRNA species in 162 healthy controls in comparison with 128 CD and 88 UC patients. The expression levels were assayed quantitatively using reverse transcription and real-time RT-PCR. Eleven miRNAs were overexpressed in the peripheral blood mononuclear cells from CD patients in comparison with healthy controls: miR-16, miR-23a, miR-29a, miR-106a, miR-107, miR-126, miR-191, miR-199a-5p, miR-200c, miR-362-3p and miR-532-3p. In comparison, six miRNAs were overexpressed in the peripheral blood mononuclear cells from UC patients in comparison with healthy controls: miR-16, miR-21, miR-28-5p, miR-151-5p, miR-155 and miR-199a-5p. They suggested that this panel could provide a new non-invasive biomarker for distinguishing CD from UC at an early stage of investigation.
More generally, Clark et al. obtained gene and miRNA signatures for CD and UC, which they obtained through bioinformatics tools and high-throughput computations using data from a comprehensive literature search. Coupled with these data, a systematic review enabled the group to compare IBD with other autoimmune diseases, picking up potential drug targets in the process. Indeed, they suggest that several drugs already on the market for various disorders including gastrointestinal cancers and viral infections might potentially be useful in one or both of these diseases. The top upregulated genes in IBD have been previously associated with bacterial signals, diabetogenesis, innate immunity, inflammation and matrix metalloproteases. The downregulated genes encoded tight junction proteins, solute transporters and adhesion proteins. Several genes were differentially expressed in UC as compared with CD. A compromised metabolism for processing of androgen and estrogen drugs, nitrogen and lipids in IBD was associated with changes in the levels of specific miRNAs.
Gene Expression Studies
A total of 172 biopsies from 53 CD and 31 control subjects were studied by Noble et al. They collected paired biopsies from five different locations including the terminal ileum, and processed these for RNA extraction and histology. A comparison of biopsies from CD patients as compared with controls showed 259 sequences to be upregulated and 87 sequences downregulated. In colonic inflammatory CD, they showed downregulation of expression of the organic solute carrier genes: SLC38A4, SLC26A2 and OST alpha, and upregulation of IL-23A, JAK2 and STAT3.
Unaffected ileal mucosal biopsies of patients with ileal CD were studied using whole human genome expression profiling, in order to develop an ileal CD gene signature. Patients with ileal CD were compared with UC patients and also control subjects. The authors collected samples from the proximal margin of the resected ileum, using tissues that were unaffected by disease. Agilent whole human genome expression profiling was used on two independent sets of such samples. The expression of folate hydrolase (prostate-specific membrane antigen) 1 (FOLH1) emerged as a common feature that discriminated ileal CD from the other two groups.
Despite such individual studies, a meta-analysis of available data on gene expression patterns of colon mucosa failed to show convincing evidence of major differences in gene expression patterns between CD and UC.