Refinement in localization and identification of gene regions associated with Crohn disease

A New Differential Gene Expression Based Simulated Annealing for Solving Gene Selection Problem: A Case Study on Eosinophilic Esophagitis and Few Other Gastro-intestinal Diseases

Identifying the set of genes collectively responsible for causing a disease from differential gene expression data is called gene selection problem. Though many complex methodologies have been applied to solve gene selection, formulated as an optimization problem, this study introduces a new simple, efficient, and biologically plausible solution procedure where the collective power of the targeted gene set to discriminate between diseased and normal gene expression profiles was focused. It uses Simulated Annealing to solve the underlying optimization problem and termed here as Differential Gene Expression Based Simulated Annealing (DGESA). The Ranked Variance (RV) method has been applied to prioritize genes to form reference set to compare with the outcome of DGESA. In a case study on Eosinophilic Esophagitis (EoE) and other gastrointestinal diseases, RV identified the top 40 high-variance genes, overlapping with disease-causing genes from DGESA. DGESA identified 40 gene pathways each for EoE, Crohn's Disease (CD), and Ulcerative Colitis (UC), with 10 genes for EoE, 8 for CD, and 7 for UC confirmed in literature. For EoE, confirmed genes include KRT79, CRISP2, IL36G, SPRR2B, SPRR2D, and SPRR2E. For CD, validated genes are NPDC1, SLC2A4RG, LGALS8, CDKN1A, XAF1, and CYBA. For UC, confirmed genes include TRAF3, BAG6, CCDC80, CDC42SE2, and HSPA9. RV and DGESA effectively elucidate molecular signatures in gastrointestinal diseases. Validating genes like SPRR2B, SPRR2D, SPRR2E, and STAT6 for EoE demonstrates DGESA's efficacy, highlighting potential targets for future research.

Unravelling the Oral-Gut Axis: Interconnection Between Periodontitis and Inflammatory Bowel Disease, Current Challenges, and Future Perspective

As the opposite ends of the orodigestive tract, the oral cavity and the intestine share anatomical, microbial, and immunological ties that have bidirectional health implications. A growing body of evidence suggests an interconnection between oral pathologies and inflammatory bowel disease [IBD], implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an 'oral-gut' axis, marked by a higher prevalence of periodontitis and other oral conditions in IBD patients and vice versa. We present an in-depth examination of the interconnection between oral pathologies and IBD, highlighting the shared microbiological and immunological pathways, and proposing a 'multi-hit' hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.

Unraveling the Link between Periodontitis and Inflammatory Bowel Disease: Challenges and Outlook

Periodontitis and Inflammatory Bowel Disease (IBD) are chronic inflammatory conditions, characterized by microbial dysbiosis and hyper-immunoinflammatory responses. Growing evidence suggest an interconnection between periodontitis and IBD, implying a shift from the traditional concept of independent diseases to a complex, reciprocal cycle. This review outlines the evidence supporting an "Oral-Gut" axis, marked by a higher prevalence of periodontitis in IBD patients and vice versa. The specific mechanisms linking periodontitis and IBD remain to be fully elucidated, but emerging evidence points to the ectopic colonization of the gut by oral bacteria, which promote intestinal inflammation by activating host immune responses. This review presents an in-depth examination of the interconnection between periodontitis and IBD, highlighting the shared microbiological and immunological pathways, and proposing a "multi-hit" hypothesis in the pathogenesis of periodontitis-mediated intestinal inflammation. Furthermore, the review underscores the critical need for a collaborative approach between dentists and gastroenterologists to provide holistic oral-systemic healthcare.

The hazards of genotype imputation in chromosomal regions under selection: A case study using the Lactase gene region

Although imputation of missing SNP results has been widely used in genetic studies, claims about the quality and usefulness of imputation have outnumbered the few studies that have questioned its limitations. But it is becoming clear that these limitations are real-for example, disease association signals can be missed in regions of LD breakdown. Here, as a case study, using the chromosomal region of the well-known lactase gene, LCT, we address the issue of imputation in the context of variants that have become frequent in a limited number of modern population groups only recently, due to selection. We study SNPs in a 500 bp region covering the enhancer of LCT, and compare imputed genotypes with directly genotyped data. We examine the haplotype pairs of all individuals with discrepant and missing genotypes. We highlight the nonrandom nature of the allelic errors and show that most incorrect imputations and missing data result from long haplotypes that are evolutionarily closely related to those carrying the derived alleles, while some relate to rare and recombinant haplotypes. We conclude that bias of incorrectly imputed and missing genotypes can decrease the accuracy of imputed results substantially.

Linkage disequilibrium maps for European and African populations constructed from whole genome sequence data

Quantification of linkage disequilibrium (LD) patterns in the human genome is essential for genome-wide association studies, selection signature mapping and studies of recombination. Whole genome sequence (WGS) data provides optimal source data for this quantification as it is free from biases introduced by the design of array genotyping platforms. The Malécot-Morton model of LD allows the creation of a cumulative map for each choromosome, analogous to an LD form of a linkage map. Here we report LD maps generated from WGS data for a large population of European ancestry, as well as populations of Baganda, Ethiopian and Zulu ancestry. We achieve high average genetic marker densities of 2.3-4.6/kb. These maps show good agreement with prior, low resolution maps and are consistent between populations. Files are provided in BED format to allow researchers to readily utilise this resource.

MACC1-the first decade of a key metastasis molecule from gene discovery to clinical translation

Deciphering the paths to metastasis and identifying key molecules driving this process is one important issue for understanding and treatment of cancer. Such a key driver molecule is Metastasis Associated in Colon Cancer 1 (MACC1). A decade long research on this evolutionarily conserved molecule with features of a transcription factor as well as an adapter protein for versatile protein-protein interactions has shown that it has manifold properties driving tumors to their metastatic stage. MACC1 transcriptionally regulates genes involved in epithelial-mesenchymal transition (EMT), including those which are able to directly induce metastasis like c-MET, impacts tumor cell migration and invasion, and induces metastasis in solid cancers. MACC1 has proven as a valuable biomarker for prognosis of metastasis formation linked to patient survival and gives promise to also act as a predictive marker for individualized therapies in a broad variety of cancers. This review discusses the many features of MACC1 in the context of the hallmarks of cancer and the potential of this molecule as biomarker and novel therapeutic target for restriction and prevention of metastasis.

Myeloid-Derived Suppressor Cells Produce IL-10 to Elicit DNMT3b-Dependent IRF8 Silencing to Promote Colitis-Associated Colon Tumorigenesis

IL-10 functions as a suppressor of colitis and colitis-associated colon cancer, but it is also a risk locus associated with ulcerative colitis. The mechanism underlying the contrasting roles of IL-10 in inflammation and colon cancer is unknown. We report here that inflammation induces the accumulation of CD11b+Gr1+ myeloid-derived suppressor cells (MDSCs) that express high levels of IL-10 in colon tissue. IL-10 induces the activation of STAT3 that directly binds to the Dnmt1 and Dnmt3b promoters to activate their expression, resulting in DNA hypermethylation at the Irf8 promoter to silence IRF8 expression in colon epithelial cells. Mice with Irf8 deleted in colonic epithelial cells exhibit significantly higher inflammation-induced tumor incidence. Human colorectal carcinomas have significantly higher DNMT1 and DNMT3b and lower IRF8 expression, and they exhibit significantly higher IRF8 promoter DNA methylation than normal colon. Our data identify the MDSC-IL-10-STAT3-DNMT3b-IRF8 pathway as a link between chronic inflammation and colon cancer initiation.

High-Resolution Genetic Maps Identify Multiple Type 2 Diabetes Loci at Regulatory Hotspots in African Americans and Europeans

Interpretation of results from genome-wide association studies for T2D is challenging. Only very few loci have been replicated in African ancestry populations and the identification of the implicated functional genes remain largely undefined. We used genetic maps that capture detailed linkage disequilibrium information in European and African Americans and applied these to large T2D case-control samples in order to estimate locations for putative functional variants in both populations. Replicated T2D locations were tested for evidence of being regulatory hotspots using adipose expression. We validated a sample of our co-location intervals using next generation sequencing and functional annotation, including enhancers, transcription, and chromatin modifications. We identified 111 additional disease-susceptibility locations, 93 of which are cosmopolitan and 18 of which are European specific. We show that many previously known signals are also risk loci in African Americans. The majority of the disease locations appear to confer risk of T2D via the regulation of expression levels for a large number (266) of cis-regulated genes, the majority of which are not the nearest genes to the disease loci. Sequencing three cosmopolitan locations provided candidate functional variants that precisely co-locate with cell-specific chromatin domains and pancreatic islet enhancers. These variants have large effect sizes and are common across populations. Results show that disease-associated loci in different populations, gene expression, and cell-specific regulatory annotation can be effectively integrated by localizing these effects on high-resolution genetic maps. The cis-regulated genes provide insights into the complex molecular pathways involved and can be used as targets for sequencing and functional molecular studies.

ErbB4 signaling stimulates pro-inflammatory macrophage apoptosis and limits colonic inflammation

Efficient clearance of pro-inflammatory macrophages from tissues after resolution of a challenge is critical to prevent prolonged inflammation. Defects in clearance can contribute to conditions such as inflammatory bowel disease, and thus may be therapeutically targetable. However, the signaling pathways that induce termination of pro-inflammatory macrophages are incompletely defined. We tested whether the ErbB4 receptor tyrosine kinase, previously not known to have role in macrophage biology, is involved in this process. In vitro, pro-inflammatory activation of cultured murine and human macrophages induced ErbB4 expression; in contrast, other ErbB family members were not induced in pro-inflammatory cells, and other innate immune lineages (dendritic cells, neutrophils) did not express detectable ErbB4 levels. Treatment of activated pro-inflammatory macrophages with the ErbB4 ligand neuregulin-4 (NRG4) induced apoptosis. ErbB4 localized to the mitochondria in these cells. Apoptosis was accompanied by loss of mitochondrial membrane potential, and was dependent upon the proteases that generate the cleaved ErbB4 intracellular domain fragment, suggesting a requirement for this fragment and mitochondrial pathway apoptosis. In vivo, ErbB4 was highly expressed on pro-inflammatory macrophages but not neutrophils during experimental DSS colitis in C57Bl/6 mice. Active inflammation in this model suppressed NRG4 expression, which may allow for macrophage persistence and ongoing inflammation. Consistent with this notion, NRG4 levels rebounded during the recovery phase, and administration of exogenous NRG4 during colitis reduced colonic macrophage numbers and ameliorated inflammation. These data define a novel role for ErbB4 in macrophage apoptosis, and outline a mechanism of feedback inhibition that may promote resolution of colitis.

Whole genome sequences are required to fully resolve the linkage disequilibrium structure of human populations

BACKGROUND

An understanding of linkage disequilibrium (LD) structures in the human genome underpins much of medical genetics and provides a basis for disease gene mapping and investigating biological mechanisms such as recombination and selection. Whole genome sequencing (WGS) provides the opportunity to determine LD structures at maximal resolution.

RESULTS

We compare LD maps constructed from WGS data with LD maps produced from the array-based HapMap dataset, for representative European and African populations. WGS provides up to 5.7-fold greater SNP density than array-based data and achieves much greater resolution of LD structure, allowing for identification of up to 2.8-fold more regions of intense recombination. The absence of ascertainment bias in variant genotyping improves the population representativeness of the WGS maps, and highlights the extent of uncaptured variation using array genotyping methodologies. The complete capture of LD patterns using WGS allows for higher genome-wide association study (GWAS) power compared to array-based GWAS, with WGS also allowing for the analysis of rare variation. The impact of marker ascertainment issues in arrays has been greatest for Sub-Saharan African populations where larger sample sizes and substantially higher marker densities are required to fully resolve the LD structure.

CONCLUSIONS

WGS provides the best possible resource for LD mapping due to the maximal marker density and lack of ascertainment bias. WGS LD maps provide a rich resource for medical and population genetics studies. The increasing availability of WGS data for large populations will allow for improved research utilising LD, such as GWAS and recombination biology studies.

Phenolyzer: phenotype-based prioritization of candidate genes for human diseases

Prior biological knowledge and phenotype information may help to identify disease genes from human whole-genome and whole-exome sequencing studies. We developed Phenolyzer (http://phenolyzer.usc.edu), a tool that uses prior information to implicate genes involved in diseases. Phenolyzer exhibits superior performance over competing methods for prioritizing Mendelian and complex disease genes, based on disease or phenotype terms entered as free text.

Association of IL23R and ATG16L1 with susceptibility of Crohn's disease in Chinese population

OBJECTIVES

To investigate whether gene polymorphisms of ATG16L1 and IL23R are associated with the susceptibility of Crohn's disease (CD) in Chinese population.

METHODS

A total of 420 patients with CD and 450 age- and sex-matched healthy volunteers from Chinese Han population were included in this study. Single nucleotide polymorphisms (SNPs) rs2241880 of ATG16L1 and rs11209026, rs1004819, and rs1495965 of IL23R were genotyped. The differences of genotype and allele distributions between CD patients and healthy controls were assessed using the Chi-squared test. Besides, subgroup analysis of disease groups was performed using the Chi-squared test.

RESULTS

For ATG16L1, patients were found to have significantly higher proportion of genotype GG (18.3%), when compared with the normal controls (12.4%). Allele G was found to be the risk allele for the disease (34.3% vs. 29.0%, p = 0.016) with an odds ratio of 1.18. For IL23R, all three SNPs were found not to be associated with the development of CD. None of these four SNPs was found to be associated with the clinical features of the patients, including age at diagnosis, disease location, and behavior.

CONCLUSION

The original genome-wide association studies finding on ATG16L1 gene should be robust and this gene does play a role in the pathogenesis of CD in the Chinese population. However, the role of IL23R gene in the occurrence of CD remains obscure.

ABCC5 transporter is a novel type 2 diabetes susceptibility gene in European and African American populations

Numerous functional studies have implicated PARL in relation to type 2 diabetes (T2D). We hypothesised that conflicting human association studies may be due to neighbouring causal variants being in linkage disequilibrium (LD) with PARL. We conducted a comprehensive candidate gene study of the extended LD genomic region that includes PARL and transporter ABCC5 using three data sets (two European and one African American), in relation to healthy glycaemic variation, visceral fat accumulation and T2D disease. We observed no evidence for previously reported T2D association with Val262Leu or PARL using array and fine-map genomic and expression data. By contrast, we observed strong evidence of T2D association with ABCC5 (intron 26) for European and African American samples (P = 3E-07) and with ABCC5 adipose expression in Europeans [odds ratio (OR) = 3.8, P = 2E-04]. The genomic location estimate for the ABCC5 functional variant, associated with all phenotypes and expression data (P = 1E-11), was identical for all samples (at Chr3q 185,136 kb B36), indicating that the risk variant is an expression quantitative trait locus (eQTL) with increased expression conferring risk of disease. That the association with T2D is observed in populations of disparate ancestry suggests the variant is a ubiquitous risk factor for T2D.

Higher revision and complication rates following total hip arthroplasty in patients with inflammatory bowel disease

The purpose of this study was to compare the clinical outcomes of total hip arthroplasty in patients with and without inflammatory bowel disease (IBD). Between 2001 and 2010, all total hip arthroplasties performed at a single institution were reviewed to identify patients who had IBD. There were 23 total hip arthroplasties in the study group, which were matched in a 1:3 ratio to 69 additional hips. At a mean follow-up of 49 months (range, 24-96 months), patients with IBD had an overall significantly lower survivorship of 87% (n = 3 revisions), compared to 98.5% (n = 1 revision) in the matched group who had a mean follow-up of 47 months (range, 24-94 months). In addition, there were significantly higher major complications in the study group (5 patients) compared to the matched group (2 patients). These results indicate that patients with IBD had an overall higher revision and complication rate.

The role of Klebsiella in Crohn's disease with a potential for the use of antimicrobial measures

There is a general consensus that Crohn's disease (CD) develops as the result of immune-mediated tissue damage triggered by infections with intestinal microbial agents. Based on the results of existing microbiological, molecular, and immunological studies, Klebsiella microbe seems to have a key role in the initiation and perpetuation of the pathological damage involving the gut and joint tissues in patients with CD. Six different gastroenterology centres in the UK have reported elevated levels of antibodies to Klebsiella in CD patients. There is a relationship between high intake of starch-containing diet, enhanced growth of gut microbes, and the production of pullulanases by Klebsiella. It is proposed that eradication of these microbes by the use of antibiotics and low starch diet, in addition to the currently used treatment, could help in alleviating or halting the disease process in CD.

IRF5, but not TLR4, DEFB1, or VDR, is associated with the risk of ulcerative colitis in a Han Chinese population

OBJECTIVE. IRF5, TLR4, DEFB1, and VDR genetic variations have been associated with ulcerative colitis (UC) in several European patient cohorts. As distinct genetic backgrounds may play a role in different ethnicities, we evaluated the effects of single-nucleotide polymorphisms (SNPs) in these genes and their interactions in UC patients of Han Chinese descent. MATERIAL AND METHODS. DNA samples from 300 UC patients and 302 healthy control subjects from Peking Union Medical College Hospital were genotyped for 14 tag SNPs, which were selected based on haplotype analysis of IRF5, TLR4, DEFB1, and VDR. Multidimensionality reductions were used to explore gene-gene interactions. RESULTS. The only observed association with UC was for IRF5. On an allelic level, SNP rs3807306 was associated with UC risk (p = 6.7 × 10(-3)). On a genotypic level, the CC genotype of SNP rs3807306 (p = 0.03) was associated with protection from UC, and the AA genotype of SNP rs4728142 (p = 7.6 × 10(-3)) was associated with a risk of UC. In the haplotype analysis, GGATT was highly correlated with UC risk (p-Value = 2.0 × 10(-4)). No significant multilocus interactions were detected among these four genes. CONCLUSIONS. Our study confirmed the association of IRF5 with UC in Han Chinese patients. Han Chinese UC patients share part of their genetic susceptibility with Caucasian patients.

MACC1 - a novel target for solid cancers

INTRODUCTION

The metastatic dissemination of primary tumors is directly linked to patient survival in many tumor entities. The previously undescribed gene metastasis-associated in colon cancer 1 (MACC1) was discovered by genome-wide analyses in colorectal cancer (CRC) tissues. MACC1 is a tumor stage-independent predictor for CRC metastasis linked to metastasis-free survival.

AREAS COVERED

In this review, the discovery of MACC1 is briefly presented. In the following, the overwhelming confirmation of these data is provided supporting MACC1 as a new remarkable biomarker for disease prognosis and prediction of therapy response for CRC and also for a variety of additional forms of solid cancers. Lastly, the potential clinical utility of MACC1 as a target for prevention or restriction of tumor progression and metastasis is envisioned.

EXPERT OPINION

MACC1 has been identified as a prognostic biomarker in a variety of solid cancers. MACC1 correlated with tumor formation and progression, development of metastases and patient survival representing a decisive driver for tumorigenesis and metastasis. MACC1 was also demonstrated to be of predictive value for therapy response. MACC1 is a promising therapeutic target for anti-tumor and anti-metastatic intervention strategies of solid cancers. Its clinical utility, however, must be demonstrated in clinical trials.

The link between ankylosing spondylitis, Crohn's disease, Klebsiella, and starch consumption

Both ankylosing spondylitis (AS) and Crohn's disease (CD) are chronic and potentially disabling interrelated conditions, which have been included under the group of spondyloarthropathies. The results of a large number of studies support the idea that an enteropathic pathogen, Klebsiella pneumoniae, is the most likely triggering factor involved in the initiation and development of these diseases. Increased starch consumptions by genetically susceptible individuals such as those possessing HLA-B27 allelotypes could trigger the disease in both AS and CD by enhancing the growth and perpetuation of the Klebsiella microbes in the bowel. Exposure to increased levels of these microbes will lead to the production of elevated levels of anti-Klebsiella antibodies as well as autoantibodies against cross-reactive self-antigens with resultant pathological lesions in the bowel and joints. Hence, a decrease of starch-containing products in the daily dietary intake could have a beneficial therapeutic effect on the disease especially when used in conjunction with the currently available medical therapies in the treatment of patients with AS and CD.