Identification of single nucleotide polymorphisms in the TNFRSF17 gene and their association with gastrointestinal disorders

Identification of the key genes and pathways involved in B cells in primary Sjögren' s syndrome

Primary Sjögren’ s syndrome (pSS) is a relatively common autoimmune disease, which mainly involves the exocrine glands, causing dry eye, dryness of mouth, fatigue and pain in the joints, thus severely affecting the normal lives of patients. B cell populations are considered to play an important role in their pathogenesis and pSS patients are generally characterized by exhibiting biological signs of B cell activation. Moreover, another important characterized change in the peripheral blood of pSS patients is found to be the decreased number of circulating memory B cells. However, the mechanisms underlying the B cell activation and the decreased level of circulating memory B cells in pSS patients are still unclear. Therefore, we identified key genes and pathways involved in B cells in pSS through a combination of several bioinformatic approaches including Cell-type Identification By Estimating Relative Subsets Of RNA Transcripts (CIBERSORT) and weighted gene co-expression network analysis (WGCNA) using gene expression data of pSS patients and controls from an open database Gene Expression Omnibus (GEO). The results may provide some novel insights into the pathogenesis of pSS. Moreover, we constructed and validated a diagnostic model for pSS by using the expression patterns of these key genes, which may assist clinicians in diagnosing pSS.

9q34 & 16p13 chromosome duplications in autism

Epigenetic mechanisms, genetic factors, and environment influence the diversity of phenotypes developed in various diseases. Duplications in several chromosomes are well characterized in the scientific literature, but partial duplications, in some cases, present with milder forms of a disease and are yet to be understood. Fortunately, the identification of genetic diseases has now become more feasible due to several cytogenetic techniques such as microarray analysis and karyotyping. With these tools, together with other laboratory results and clinical examination, we are able to report the first case in the medical literature of double partial trisomy of chromosome 9q34 and 16p13.

Bone Morphogenetic Protein 6 Polymorphisms are Associated With Systemic Lupus Erythematosus Susceptibility in the Korean Population

Objectives

This study aims to investigate whether bone morphogenetic protein 6 (BMP6) single-nucleotide polymorphism (SNP) is associated with susceptibility to systematic lupus erythematosus (SLE).

Patients and methods

We analyzed the genotype and allele frequencies of BMP6 SNPs using genomic deoxyribonucleic acid isolated from 119 SLE patients (9 males, 110 females; mean age 36.4 years; range 19 to 59 years) and 509 healthy controls (323 males, 186 females; mean age 42.1 years; range 19 to 61 years). Genomic deoxyribonucleic acid was extracted from peripheral blood leukocytes using a standard phenol-chloroform method or by using a genomic deoxyribonucleic acid extraction kit. Erythrocyte sedimentation rate, C-reactive protein, and antinuclear antibody levels of SLE patients were recorded.

Results

Our results showed that the genotype frequencies of rs17557 and rs9505273 for BMP6 in SLE patients significantly differed from those of the control group (p=0.01 and p=0.04, respectively). The genotype frequencies of the rs17557 and rs9505273 for BMP6 in female SLE patients were also significantly different from those in female healthy controls (p=0.04 and p=0.03, respectively). We also revealed that the distribution of the main haplotypes of BMP6 SNPs in SLE patients was significantly different from their distribution in healthy controls.

Conclusion

These results suggested that SNPs in BMP6 might be associated with susceptibility to SLE and that haplotypes of BMP6 polymorphisms might represent useful genetic markers for SLE.

Genetic polymorphism in pathogenesis of irritable bowel syndrome

Irritable bowel syndrome (IBS) is a complex symptom-based disorder without established biomarkers or putative pathophysiology. IBS is a common functional gastrointestinal disorder which is defined as recurrent abdominal pain or discomfort that has at least two of the following symptoms for 3 d per month in the past 3 mo according to ROME III: relief by defecation, onset associated with a change in stool frequency or onset with change in appearance or form of stool. Recent discoveries revealed genetic polymorphisms in specific cytokines and neuropeptides may possibly influence the frequencies and severity of symptoms, as well as the therapeutic responses in treating IBS patients. This review gives new insights on how genetic determinations influence in clinical manifestations, treatment responses and potential biomarkers of IBS.

Pathogen-specific risk of celiac disease following bacterial causes of foodborne illness: a retrospective cohort study

BACKGROUND

The US CDC recently estimated over 2 million foodborne illnesses annually are caused by 4 major enteropathogens: non-typhoid Salmonella spp., Campylobacter spp., Shigella spp., and Yersinia enterocolitica. While recent data suggest functional gastrointestinal disorders are associated with these infections, studies linking foodborne illness to celiac disease (CD) are limited. We utilized a US Department of Defense medical encounter database to evaluate the risk of CD following select foodborne infections.

METHODS

We identified subjects with acute gastroenteritis between 1998 and 2009 attributed to Salmonella (nontyphoidal) spp., Shigella spp., Campylobacter spp., or Y. enterocolitica and matched each with up to 4 unexposed subjects. Exposed and unexposed subjects were followed for incident CD diagnosis for their entire military record duration (or a minimum of 1 year). Relative risks were calculated using modified Poisson regression to determine the relationship between pathogen-attributable gastroenteritis and CD while controlling for covariates.

RESULTS

A total of 1,753 pathogen-specific gastroenteritis cases (Campylobacter: 738; Salmonella: 624; Shigella: 376; Yersinia: 17) were identified and followed for a median of 3.8 years. The incidence (per 100,000 person-years) of CD was 0.05. We found a suggested risk of CD after Campylobacter, but not other foodborne infection etiologies.

CONCLUSIONS

These data support a previous study demonstrating increased risk of CD following Campylobacteriosis and highlight the need for additional research into how infections might trigger CD in susceptible individuals.

Identification of the polymorphisms in IFITM1 gene and their association in a Korean population with ulcerative colitis

Interferon inducible transmembrane protein (IFITM) family genes have been implicated in several cellular processes such as the homotypic cell adhesion functions of IFNs and cellular anti-proliferative activities. We previously showed that the IFITM3 single nucleotide polymorphisms (SNPs) associated with susceptibility to ulcerative colitis (UC). The present study aimed to investigate whether the polymorphisms in the IFITM1 gene are associated with susceptibility to UC. We also evaluated the expression levels in the putative functional promoter polymorphisms to determine the change of their activity. Gene expression profiles in the tissues obtained from human digestive tracts by RT-PCR, and the possible variation sites and SNPs of IFITM1 were identified by direct sequencing method. Genotype analysis in the IFITM1 SNPs was performed by high resolution melting and TaqMan probe analysis, and the haplotype frequencies of IFITM1 SNPs for multiple loci were estimated using the expectation maximization (EM) algorithm. The expression levels in the putative functional promoter polymorphisms were evaluated by performing a luciferase reporter assay. We identified two SNPs and two variation sites, g.-1920G>A (rs77537847), g.-1547delA (novel) and g.-416C>G (rs11246062) in the promoter region, and g.364delA (rs200576757) in intron 1. The genotype and allele frequencies of the g.-1920G>A polymorphism of IFITM1 gene in the UC patients were significantly different from those of the healthy controls (P=0.002 and 0.042, respectively). These results suggest that the g.-1920G>A polymorphism in IFITM1 may be associated with susceptibility to UC.

EED gene polymorphism in patients with colorectal cancer

BACKGROUND

Our previous work indicated that, first, the embryonic ectoderm development (EED) gene is a candidate gene associated with the pathogenesis of ulcerative colitis (UC) and, second, that the haplotypes of the EED polymorphism are one of the markers for UC susceptibility. The risk of developing colorectal cancer (CRC) increases in patients with inflammatory bowel disease. 


AIM

The present study aimed at determining the association between polymorphisms in the EED gene and CRC. 


METHODS

Genotype analysis of EED single nucleotide polymorphisms (SNPs) was performed with high-resolution melting analysis, and the genotype and allele frequencies of the EED SNPs were compared between CRC patients and healthy controls. The haplotype frequencies of EED for multiple loci were estimated using the expectation maximization (EM) algorithm. 


RESULTS

Our study had a power of 76.6% at a 0.05 significance level. Genotype and allele frequencies of the SNPs and haplotype frequencies of the EED gene in CRC patients were not significantly different from those in healthy controls. Only the allele frequency of g.-1850G>C in the rectal cancer (RC) patient group was significantly different from that of the control group (p=0.04). Similarly, the genotype and allelic frequencies of the EED SNPs for either tumor site (left or right) or tumor stage were not significantly different from those in healthy controls. However, our data show an association between the g.-993G>C polymorphism in the EED gene and the presence of lymph node metastasis in CRC.


CONCLUSIONS

These results suggest that the SNPs of the EED gene might not be associated with susceptibility to CRC. However, this study shows that the allele frequency of g.-1850G>C in the RC patient group was significantly different from that in the control group (p=0.04) and that g.-993G>C may play a role in the lymph node metastatic process of CRC.

Peripheral blood derived gene panels predict response to infliximab in rheumatoid arthritis and Crohn's disease

Background

Biological therapies have been introduced for the treatment of chronic inflammatory diseases including rheumatoid arthritis (RA) and Crohn's disease (CD). The efficacy of biologics differs from patient to patient. Moreover these therapies are rather expensive, therefore treatment of primary non-responders should be avoided.

Method

We addressed this issue by combining gene expression profiling and biostatistical approaches. We performed peripheral blood global gene expression profiling in order to filter the genome for target genes in cohorts of 20 CD and 19 RA patients. Then RT-quantitative PCR validation was performed, followed by multivariate analyses of genes in independent cohorts of 20 CD and 15 RA patients, in order to identify sets ofinterrelated genes that can separate responders from non-responders to the humanized chimeric anti-TNFalpha antibody infliximab at baseline.

Results

Gene panels separating responders from non-responders were identified using leave-one-out cross-validation test, and a pool of genes that should be tested on larger cohorts was created in both conditions.

Conclusions

Our data show that peripheral blood gene expression profiles are suitable for determining gene panels with high discriminatory power to differentiate responders from non-responders in infliximab therapy at baseline in CD and RA, which could be cross-validated successfully. Biostatistical analysis of peripheral blood gene expression data leads to the identification of gene panels that can help predict responsiveness of therapy and support the clinical decision-making process.

The incidence and risk of celiac disease in a healthy US adult population

OBJECTIVES

Celiac disease (CD) is an increasingly common disease that may affect as many as 1% of the North American population. Recent population-based data suggest a substantial increase in the prevalence of CD over the last several decades. Several factors are hypothesized as possible disease triggers including intercurrent illnesses, such as gastroenteritis, surgeries, and trauma. We used the active duty US military, a unique healthy worker population with essentially complete medical diagnostic coding, as an opportunity to describe trends in CD and deployment-related risk factors.

METHODS

Using electronic medical encounter data (1999-2008) on active duty US military (over 13.7 million person-years), a matched, nested case-control study describing the epidemiology and risk determinants of CD (based on ≥2 ICD-9 medical encounters) was conducted. Incidence and duration of CD-related medical care were estimated, and conditional logistic regression was utilized to evaluate CD risk following infectious gastroenteritis (IGE) occurring within 3 years before CD diagnosis while controlling for other risk factors.

RESULTS

A total of 455 incident cases of CD were identified and age, gender, and time matched to 1,820 controls. The incidence of CD increased five-fold from 1.3 per 100,000 in 1999 to 6.5 per 100,000 in 2008, with the highest rates of increase among those over 34 years of age (average annual increase of 0.8 cases per 100,000). A total of 172 IGE episodes, predominately of "viral etiology" (60.5%), were documented. In multivariate models, a significant association between IGE and CD was found (Odds ratio (OR): 2.06, 95% confidence interval (CI) 1.43, 2.97). Risk generally increased with temporal proximity to, and non-viral etiology of, exposure. Other notable risk factors for CD in multivariate models were Caucasian race (OR: 3.1, P<0.001), non-Army service (OR: 1.5, P=0.001), and greater than a high-school education (OR: 1.3, P=0.05).

CONCLUSIONS

Incidence of CD diagnosis in the US military is increasing, particularly among those in the fourth and fifth decades of life and appears higher than other population-based estimates. An association between antecedent IGE and risk of CD was noted, but the potential for exposure misclassification cannot be ruled out and further study is needed to link pathogen-specific exposure to incident CD anti-gluten antibody development or symptom onset.

Chronic gastrointestinal consequences of acute infectious diarrhea: evolving concepts in epidemiology and pathogenesis

Acute infectious diarrhea is a frequent occurrence both in the developing world, where it results in considerable mortality, and in developed countries, where it accounts for a significant number of health visits, hospitalizations, and medical and non-medical losses. Recent evidence in basic, clinical, and epidemiological science domains has emerged that suggest that the burden caused by these infections is not limited to the acute illness, but may result in triggering or contributing to the pathogenesis of a number of chronic health problems. This review considers the breadth of this information for the purpose of consolidating what is currently known, identifying gaps in knowledge, and describing future directions and policy implications related to the chronic consequences of acute infectious diarrhea. A unifying hypothesis of this review is that infections may trigger a number of long-lasting changes in gut physiology and immunity that can increase the risk to a variety of chronic gastrointestinal diseases, particularly in genetically susceptible individuals.

The TNF family member APRIL promotes colorectal tumorigenesis

The tumor necrosis factor (TNF) family member APRIL (A proliferation inducing ligand) is a disease promoter in B-cell malignancies. APRIL has also been associated with a wide range of solid malignancies, including colorectal cancer (CRC). As evidence for a supportive role of APRIL in solid tumor formation was still lacking, we studied the involvement of APRIL in CRC. We observed that ectopic APRIL expression exacerbates the number and size of adenomas in Apc(Min) mice and in a mouse model for colitis-associated colon carcinogenesis. Furthermore, knockdown of APRIL in primary spheroid cultures of colon cancer cells and both mouse and human CRC cell lines reduced tumor clonogenicity and in vivo outgrowth. Taken together, our data therefore indicate that both tumor-derived APRIL and APRIL produced by non-tumor cells is supportive in colorectal tumorigenesis.

The haplotypes of TNFRSF17 polymorphisms are associated with colon cancer in a Korean population

PURPOSE

We previously found that the haplotypes of TNFRSF17 single nucleotide polymorphisms (SNPs) were associated with the susceptibility to inflammatory bowel disease on Korean population. The present study aimed to investigate whether the polymorphisms in the TNFRSF17 gene are associated with susceptibility to colorectal cancer (CRC).

METHODS

Genotype analysis in the TNFRSF17 SNPs was performed by high-resolution melting and TaqMan probe analysis, and the genotype and allele frequencies of TNFRSF17 SNPs were compared between the CRC patients and the healthy controls. The haplotype frequencies of TNFRSF17 for multiple loci were estimated using the expectation maximization algorithm.

RESULTS

Although, the genotype and allelic frequencies of these SNPs, in the colon cancer and rectal cancer patients, were not significantly different from those in the healthy controls, the genotype and allele frequency of g.2493G>A was significantly different between the healthy controls and the right colon cancer patients (P = 0.014 and 0.004, respectively). Moreover, the haplotypes frequencies in the healthy controls were significantly different from those in the colon cancer patients.

CONCLUSION

Our results suggest that TNFRSF17 may be a candidate gene associated with the pathogenesis of colon cancer, and the haplotypes of the TNFRSF17 polymorphisms might be one of the markers for colon cancer susceptibility.

Promoter polymorphism of the EED gene is associated with the susceptibility to ulcerative colitis

BACKGROUND

Embryonic ectoderm development (EED) protein is involved in multiple cellular protein complexes. EED mediates the repression of gene activity through histone deacetylation, and it may act as a specific regulator of integrin's function. This gene was identified as a candidate gene for the susceptibility to IBD by our previous cDNA microarray analysis.

AIM

The present study aimed to validate the expression level of the EED gene in patients with IBD by performing RT-PCR, and we investigated whether the polymorphisms in the EED gene are associated with the susceptibility to UC, and whether a functional EED promoter polymorphism is related to UC.

METHODS

Genotype analysis of the EED SNPs was performed by single-base extension analysis. The haplotype frequencies of the EED gene for multiple loci were estimated using the expectation maximization algorithm. The promoter region of the human EED gene, including the g.-1850G>C allele, was isolated by PCR. The amplified PCR products were inserted into the pGL3-basic vector and the luciferase activity was analyzed.

RESULTS

The expression level of the EED gene was significantly decreased in both the UC and CD patients and it was significantly higher in the liver and ileum than in the other tissues of the human digestive system. The genotype and allele frequencies of the g.-1850G>C polymorphism of the EED gene in the UC patients were significantly different from those of the healthy controls (p = 0.018 and 0.017, respectively). The luciferase activity assay showed that the promoter activity was decreased about twofold in the construct containing the g.-1850G allele compared to that of the construct containing the g.-1850C allele, which means that the allele G could produce less EED mRNA.

CONCLUSIONS

These results suggest that the g.-1850G>C polymorphism in the EED gene might be associated with the susceptibility to UC by the change of the EED expression level.

Risk of inflammatory bowel disease following a diagnosis of irritable bowel syndrome

BACKGROUND

Irritable bowel syndrome (IBS) and inflammatory bowel disease (IBD) symptoms often overlap. In some IBS cases there are subtle inflammatory changes similar to the immune-mediated pathophysiology of IBD, and the risk of both increases after infectious gastroenteritis (IGE).

METHODS

To evaluate the effect of IBS and IGE on IBD risk utilizing US Department of Defense medical encounter data, active duty personnel with IBS were matched to subjects without IBS. Medical encounter history was analyzed to assess for incident IBD. IGE was identified from documented medical encounters and by self-report. Relative risks were calculated using Poisson regression models.

RESULTS

We identified 9,341 incident IBS cases and 18,678 matched non-IBS subjects and found an 8.6-fold higher incidence (p < 0.0001) of IBD among those with IBS (238.1 per 100,000 person-years) compared to our referent population (27.8 per 100,000 person-years). In a subset (n = 2,205) of well-defined IBS cases, IBD risk was 15 times that of subjects without IBS. The median time between IBS and IBD diagnoses was 2.1 years. IGE also increased IBD risk approximately 2-fold ( p < 0.05) after controlling for IBS.

CONCLUSIONS

These data reflect a complex interaction between illness presentation and diagnosis of IBS and IBD and suggest intercurrent IGE may increase IBD risk in IBS patients. Additional studies are needed to determine whether IBS lies on the causal pathway for IBD or whether the two are on a pathophysiological spectrum of the same clinical illness. These data suggest consideration of risk reduction interventions for IGE among IBS patients at high disease risk.

Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation

The identification of true causal loci to unravel the statistical evidence of genotype-phenotype correlations and the biological relevance of selected single-nucleotide polymorphisms (SNPs) is a challenging issue in genome-wide association studies (GWAS). Here, we introduced a novel method for the prioritization of SNPs based on p-values from GWAS. The method uses functional evidence from populations, including phenotype-associated gene expressions. Based on the concept of genetic interactions, such as perturbation of gene expression by genetic variation, phenotype and gene expression related SNPs were prioritized by adjusting the p-values of SNPs. We applied our method to GWAS data related to drug-induced cytotoxicity. Then, we prioritized loci that potentially play a role in druginduced cytotoxicity. By generating an interaction model, our approach allowed us not only to identify causal loci, but also to find intermediate nodes that regulate the flow of information among causal loci, perturbed gene expression, and resulting phenotypic variation.

Role of TNFR-related 2 mediated immune responses in dextran sulfate sodium-induced inflammatory bowel disease

Previous work has suggested that the LIGHT-TR2 costimulatory pathway plays a role in the acute and chronic stages of dextran sulfate sodium (DSS)-induced colitis [Steinberg et al. (2008); Wang et al. (2005)]. To clarify the role of TNFR-related 2 (TR2) signaling in the maintenance of intestinal homeostasis, we generated a TR2 knock-out (KO) mouse. Using DSS to induce colitis, we compared the colitic symptoms and pathological changes in wild type (WT) and TR2 KO mice, and the production of cytokines by the diseased colons. We also studied the role of TR2 in suppressing innate and adaptive immunity in the DSS model. TR2 deficient mice were characterized by reduced symptoms of intestinal inflammation compared with wild-type mice, and reduced production of cytokines. We therefore generated a monoclonal antibody against mouse TR2 which was specific to TR2 and capable of blocking TR2 signals. With this antibody, we demonstrated that antagonizing TR2 during the development of DSS-induced colitis reduced the symptoms of inflammation. Our findings suggest that TR2 is an important mediator in colitis, and may serve as a therapeutic target in inflammatory bowel disease.