Gene Expression Analysis of Peripheral Cells for Subclassification of Pediatric Inflammatory Bowel Disease in Remission

Objective

In current clinical practice, optimal treatment of inflammatory bowel disease (IBD) aims at the induction and maintenance of clinical remission. Clinical remission is apparent when laboratory markers of inflammation are normal and clinical symptoms are absent. However, sub-clinical inflammation can still be present. A detailed analysis of the immune status during this inactive state of disease may provide a useful tool to categorize patients with clinical remission into subsets with variable states of immune activation.

Design

By using Affymetrix GeneChips, we analysed RNA gene expression profiles of peripheral blood leukocytes from pediatric IBD patients in clinical remission and controls. We performed (un)supervised clustering analysis of IBD-associated genes and applied Ingenuity® pathway software to identify specific molecular profiles between patients.

Results

Pediatric IBD patients with disease in clinical remission display heterogeneously distributed gene expression profiles that are significantly distinct from controls. We identified three clusters of IBD patients, each displaying specific expression profiles of IBD-associated genes.

Conclusion

The expression of immune- and IBD-associated genes in peripheral blood leukocytes from pediatric IBD patients in clinical remission was different from healthy controls, indicating that sub-clinical immune mechanisms are still active during remission. As such, RNA profiling of peripheral blood may allow for non-invasive patient subclassification and new perspectives in treatment regimes of IBD patients in the future.     

毕赤酵母表达系统优化策略概述

毕赤酵母(Pichia pastor)表达系统是近年发展起来的一种高效表达外源蛋白的系统,利用该系统表达外源基因具有良好的应用前景。尽管毕赤酵母表达系统具有比较完备的基因表达调控机制和对真核基因表达产物的加工修饰能力,但由于基因本身及表达系统等诸多因素,仍然存在外源蛋白表达产量很低甚至不表达的情况。针对毕赤酵母表达系统这一因素,对表达载体的优化,毕赤酵母菌株优化及发酵条件优化进行了综述,以期为外源基因在毕赤酵母中的高效表达提供理论基础。     

SHIP在炎症性肠病结肠组织中的表达及其临床意义

目的：观察SHIP 在溃疡性结肠炎(UC)和克罗恩病(CD)患者结肠组织标本中的表达情况,探讨其在炎症性肠病发生过程中 所起的作用及意义。方法：收集活动期UC患者,活动期CD 患者,及结直肠癌旁正常粘膜组织（NC组）标本各20 例。将活检标本 进行苏木精- 伊红染色及SHIP 免疫组化染色观察;利用Western blot 半定量比较分析SHIP 蛋白表达及组间差异;Real-time RT-PCR 分析SHIP在RNA水平的表达情况和组间差异。统计学处理采用Student''s t检验。结果：免疫组化染色示UC组SHIP阳 性表达积分为（7.20± 2.53）,CD 组积分为（6.50± 2.76）,对照组积分为（1.10± 0.74）。t 检验组间比较UC组和CD组无统计学差异 (t=0.59,P＞0.05);而UC组与NC组（t=7.32,P＜0.05）,CD组与NC组（t=5.98, P＜0.05）,差异均有统计学意义。Western blot 检测 结肠组织SHIP表达,UC组SHIP 相对表达量为（0.314± 0.021）,CD组（0.301± 0.019）,NC 组（0.163± 0.027）。UC和CD组表达 无差异(t=1.44,P＞0.05),而UC组,CD组与NC 组相比表达明显升高（t=13.88、13.16, P均＜0.05）。Real-time RT PCR 检测UC 组 结肠粘膜SHIP mRNA相对表达量为（0.649± 0.028）,CD 组为（0.645± 0.021）,NC 组为（0.140± 0.015）。同样,UC组与CD 组没 有统计学差异,而其相较对照组表达均升高（P＜0.05）。结论：炎症性肠病患者结肠组织SHIP 表达明显高于正常结肠组织,但其在 溃疡性结肠炎和克罗恩病间没有明显差异;提示SHIP可能在炎症性肠病的发病中发挥重要作用。     

Human Blood and Mucosal Regulatory T Cells Express Activation Markers and Inhibitory Receptors in Inflammatory Bowel Disease

Background

FOXP3⁺ regulatory T cells (Tregs) are critical for preventing intestinal inflammation. However, FOXP3⁺ T cells are paradoxically increased in the intestines of patients with the inflammatory bowel disease (IBD) ulcerative colitis (UC) or Crohn’s disease (CD). We determined whether these FOXP3⁺ cells in IBD patients share or lack the phenotype of such cells from patients without IBD.

Methods

We quantified and characterized FOXP3⁺ Treg populations, as well as FOXP3^- CD4⁺ T cells, in the lamina propria lymphocytes (LPL) of intestine surgically resected from patients with and without IBD, and in the blood of controls or Crohn’s patients with or without disease activity.

Results

In all samples, a similar fraction of FOXP3⁺ cells expressed the “natural” Treg (nTreg) marker Helios, suggesting that, in IBD, these cells are not entirely “induced” Tregs (iTregs) derived from activated effector T cells. Helios⁺ and Helios^- FOXP3⁺ T cells demonstrated similar expression of maturation markers, activation markers, and inhibitory molecules between IBD patients and controls, while FOXP3^- cells paradoxically expressed more of the inhibitory receptors CD39, CTLA4, and PD-1 in inflamed mucosa. Greater expression of activation markers was also seen in both Helios⁺ and Helios^- Tregs, relative to FOXP3^- cells, in both IBD patients and controls, indicating that Tregs are effectively activated by antigen in IBD.

Conclusions

Extensive immunophenotyping revealed that Helios⁺ and Helios^- mucosal Tregs exist at a similar frequency, and have a similar expression of inhibitory molecules and activation markers in patients with IBD as in healthy controls.     

A Modular Organization of the Human Intestinal Mucosal Microbiota and Its Association with Inflammatory Bowel Disease

Abnormalities of the intestinal microbiota are implicated in the pathogenesis of Crohn''s disease (CD) and ulcerative colitis (UC), two spectra of inflammatory bowel disease (IBD). However, the high complexity and low inter-individual overlap of intestinal microbial composition are formidable barriers to identifying microbial taxa representing this dysbiosis. These difficulties might be overcome by an ecologic analytic strategy to identify modules of interacting bacteria (rather than individual bacteria) as quantitative reproducible features of microbial composition in normal and IBD mucosa. We sequenced 16S ribosomal RNA genes from 179 endoscopic lavage samples from different intestinal regions in 64 subjects (32 controls, 16 CD and 16 UC patients in clinical remission). CD and UC patients showed a reduction in phylogenetic diversity and shifts in microbial composition, comparable to previous studies using conventional mucosal biopsies. Analysis of weighted co-occurrence network revealed 5 microbial modules. These modules were unprecedented, as they were detectable in all individuals, and their composition and abundance was recapitulated in an independent, biopsy-based mucosal dataset 2 modules were associated with healthy, CD, or UC disease states. Imputed metagenome analysis indicated that these modules displayed distinct metabolic functionality, specifically the enrichment of oxidative response and glycan metabolism pathways relevant to host-pathogen interaction in the disease-associated modules. The highly preserved microbial modules accurately classified IBD status of individual patients during disease quiescence, suggesting that microbial dysbiosis in IBD may be an underlying disorder independent of disease activity. Microbial modules thus provide an integrative view of microbial ecology relevant to IBD.     

Genetic Association Analysis of the Functional c.714T>G Polymorphism and Mucosal Expression of Dectin-1 in Inflammatory Bowel Disease

Background

Dectin-1 is a pattern recognition receptor (PRR) expressed by myeloid cells that specifically recognizes β-1,3 glucan, a polysaccharide and major component of the fungal cell wall. Upon activation, dectin-1 signaling converges, similar to NOD2, on the adaptor molecule CARD9 which is associated with inflammatory bowel disease (IBD). An early stop codon polymorphism (c.714T>G) in DECTIN-1 results in a loss-of-function (p.Y238X) and impaired cytokine responses, including TNF-α, interleukin (IL)-1β and IL-17 upon in vitro stimulation with Candida albicans or β-glucan. The aim of the present study was to test the hypothesis that the DECTIN-1 c.714T>G (p.Y238X) polymorphism is associated with lower disease susceptibility or severity in IBD and to investigate the level of dectin-1 expression in inflamed and non-inflamed colon tissue of IBD patients.

Methodology

Paraffin embedded tissue samples from non-inflamed and inflamed colon of IBD patients and from diverticulitis patients were immunohistochemically stained for dectin-1 and related to CD68 macrophage staining. Genomic DNA of IBD patients (778 patients with Crohn''s disease and 759 patients with ulcerative colitis) and healthy controls (n = 772) was genotyped for the c.714T>G polymorphism and genotype-phenotype interactions were investigated.

Principal Findings

Increased expression of dectin-1 was observed in actively inflamed colon tissue, as compared to non-inflamed tissue of the same patients. Also an increase in dectin-1 expression was apparent in diverticulitis tissue. No statistically significant difference in DECTIN-1 c.714T>G allele frequencies was observed between IBD patients and healthy controls. Furthermore, no differences in clinical characteristics could be observed related to DECTIN-1 genotype, neither alone, nor stratified for NOD2 genotype.

Conclusions

Our data demonstrate that dectin-1 expression is elevated on macrophages, neutrophils, and other immune cells involved in the inflammatory reaction in IBD. The DECTIN-1 c.714T>G polymorphism however, is not a major susceptibility factor for developing IBD.     

Association of IRGM Gene Mutations with Inflammatory Bowel Disease in the Indian Population

Background

Mutations in the IRGM gene have been associated with Crohn''s disease in several populations but have not been explored in Indian patients with this disease. This study examined the association of IRGM mutations with ulcerative colitis and Crohn''s disease in Indian patients with inflammatory bowel disease.

Methods

The IRGM gene was amplified in four segments and Sanger-sequenced in 101 participants (42 Crohn''s disease, 39 ulcerative colitis, and 20 healthy controls). Ten single nucleotide polymorphisms (SNP) were genotyped in 1200 participants (352 Crohn''s disease, 400 ulcerative colitis, and 448 healthy controls) using Sequenom MassARRAY iPLEX. Disease associations were evaluated for each of the ten SNPs.

Results

Thirty one mutations were identified in the IRGM gene, of which two had not hitherto been reported (150226250- ss947429272 & 150227858- ss947429273). Ten SNPs (6 from the above and 4 from the literature) were evaluated. Significant associations with Crohn''s disease were noted with the T allele of rs1000113 (OR 1.46, 95% CI 1.12–1.90), T allele of rs9637876 (OR 1.25, 95% CI 1.005–1.561) and C allele of rs 13361189 (OR 1.33, 95% CI 1.07–1.669). Two SNPs – rs11747270 and rs180802994 – did not exhibit Hardy-Weinberg equilibrium but were associated with both Crohn''s disease and ulcerative colitis in this population. The remaining SNPs did not show significant associations with either Crohn''s disease or ulcerative colitis.

Conclusions

Association of IRGM gene SNPs with Crohn''s disease is reported for the first time in Indian patients. We also report, for the first time, an association of rs 9637876 in the IRGM gene with Crohn''s disease.     

Whole Genome Gene Expression Meta-Analysis of Inflammatory Bowel Disease Colon Mucosa Demonstrates Lack of Major Differences between Crohn's Disease and Ulcerative Colitis

Background

In inflammatory bowel disease (IBD), genetic susceptibility together with environmental factors disturbs gut homeostasis producing chronic inflammation. The two main IBD subtypes are Ulcerative colitis (UC) and Crohn’s disease (CD). We present the to-date largest microarray gene expression study on IBD encompassing both inflamed and un-inflamed colonic tissue. A meta-analysis including all available, comparable data was used to explore important aspects of IBD inflammation, thereby validating consistent gene expression patterns.

Methods

Colon pinch biopsies from IBD patients were analysed using Illumina whole genome gene expression technology. Differential expression (DE) was identified using LIMMA linear model in the R statistical computing environment. Results were enriched for gene ontology (GO) categories. Sets of genes encoding antimicrobial proteins (AMP) and proteins involved in T helper (Th) cell differentiation were used in the interpretation of the results. All available data sets were analysed using the same methods, and results were compared on a global and focused level as t-scores.

Results

Gene expression in inflamed mucosa from UC and CD are remarkably similar. The meta-analysis confirmed this. The patterns of AMP and Th cell-related gene expression were also very similar, except for IL23A which was consistently higher expressed in UC than in CD. Un-inflamed tissue from patients demonstrated minimal differences from healthy controls.

Conclusions

There is no difference in the Th subgroup involvement between UC and CD. Th1/Th17 related expression, with little Th2 differentiation, dominated both diseases. The different IL23A expression between UC and CD suggests an IBD subtype specific role. AMPs, previously little studied, are strongly overexpressed in IBD. The presented meta-analysis provides a sound background for further research on IBD pathobiology.     

No Induction of Thiopurine Methyltransferase During Thiopurine Treatment in Inflammatory Bowel Disease

The aim of this study was to follow, during standardized initiation of thiopurine treatment, thiopurine methyltransferase (TPMT) gene expression and enzyme activity and thiopurine metabolite concentrations, and to study the role of TPMT and ITPA 94C > A polymorphisms for the development of adverse drug reactions. Sixty patients with ulcerative colitis or Crohn's disease were included in this open and prospective multi-center study. Thiopurine naïve patients were prescribed azathioprine (AZA), patients previously intolerant to AZA received 6-mercaptopurine (6-MP). The patients followed a predetermined dose escalation schedule, reaching target dose at Week 3; 2.5 and 1.25 mg/kg body weight for AZA and 6-MP, respectively. The patients were followed every week during Weeks 1–8 from baseline and then every 4 weeks until 20 weeks. TPMT activity and thiopurine metabolites were determined in erythrocytes, TPMT and ITPA genotypes, and TPMT gene expression were determined in whole blood. One homozygous TPMT-deficient patient was excluded. Five non compliant patients were withdrawn during the first weeks. Twenty-seven patients completed the study per protocol; 27 patients were withdrawn because of adverse events. Sixty-seven percent of the withdrawn patients tolerated thiopurines at a lower dose at Week 20. There was no difference in baseline TPMT enzyme activity between individuals completing the study and those withdrawn for adverse events (p = 0.45). A significant decrease in TPMT gene expression (TPMT/huCYC ratio, p = 0.02) was found, however TPMT enzyme activity did not change. TPMT heterozygous individuals had a lower probability of remaining in the study on the predetermined dose (p = 0.039). The ITPA 94C > A polymorphism was not predictive of adverse events (p = 0.35).     

细胞因子在炎症性肠病中的作用

炎症性肠病(inflammatory bowel disease,IBD)是一组病因未明的以慢性胃肠道炎症为特征的疾病,包括克罗恩病(Crohn's disease,CD)和溃疡性结肠炎(ulcerative colitis,UC)。细胞因子在IBD肠道炎症反应和黏膜免疫反应中起重要作用,目前已成为研究IBD发病机制的热点,本文就其在IBD中的作用作一综述。     

抗菌肽的基因工程研究进展

近年来细菌耐药性问题日趋严峻,寻找新型抗生素已迫在眉睫。抗菌肽是生物体产生的一种阳离子短肽,具有天然的抗菌活性。由于抗菌肽具有与传统抗生素不同的作用机制,不产生耐药性,因而具有重要的临床应用价值。但实践表明,抗菌肽的开发并非易事。针对近年来抗菌肽开发的基因工程策略和实践,尤其是大肠杆菌表达系统和酵母表达系统,进行了简要综述。     

Antimicrobial Peptides in Health and Disease (Review)

The review describes the latest data on the role of antimicrobial peptides (AMPs) in health and disease, as well as their structure and mechanisms of action. AMPs mediate protection by both direct lysis of bacteria and also by regulation of inflammation and chemotaxis, thus demonstrating immunomodulatory properties. A large amount of data shows that AMPs play an important role in the pathogenesis of multiple chronic diseases with genetic predisposition, such as atopic dermatitis, rosacea, and scleroderma.     

The Vitamin D Status in Inflammatory Bowel Disease

Context

There is no consensus on the vitamin D status of children and adolescents with inflammatory bowel disease (IBD).

Aim

To determine the vitamin D status of patients with IBD by comparing their serum 25(OH)D concentration to that of healthy controls.

Hypothesis

Serum 25(OH)D concentration will be lower in patients with IBD compared to controls.

Subjects and Methods

A case-controlled retrospective study of subjects with IBD (n = 58) of 2–20 years (male n = 31, age 16.38±2.21 years; female n = 27, age16.56±2.08 years) and healthy controls (n = 116; male n = 49, age 13.90±4.59 years; female n = 67, age 15.04±4.12years). Study subject inclusion criteria: diagnosis of Crohn’s disease (CD) or ulcerative colitis (UC). Vitamin D deficiency was defined as 25(OH)D of (<20 ng/mL) (<50 nmol/L), overweight as BMI of ≥85^th but <95^th percentile, and obesity as BMI ≥95^th percentile. Data were expressed as mean ± SD.

Results

Patients with CD, UC, and their controls had mean serum 25(OH)D concentrations of 61.69±24.43 nmol/L, 53.26±25.51, and 65.32±27.97 respectively (ANOVA, p = 0.196). The overweight/obese controls had significantly lower 25(OH)D concentration compared to the normal-weight controls (p = 0.031); whereas 25(OH)D concentration was similar between the normal-weight and overweight/obese IBD patients (p = 0.883). There was no difference in 25(OH)D between patients with UC and CD, or between subjects with active IBD and controls. However, IBD subjects with elevated ESR had significantly lower 25(OH)D than IBD subjects with normal ESR (p = 0.025), as well as controls (65.3±28.0 nmol/L vs. 49.5±25.23, p = 0.045).

Conclusion

There is no difference in mean serum 25(OH)D concentration between children and adolescents with IBD and controls. However, IBD subjects with elevated ESR have significantly lower 25(OH)D than controls. Therefore, IBD subjects with elevated ESR should be monitored for vitamin D deficiency.     

Consumption of Dental Treatment in Patients with Inflammatory Bowel Disease,a Register Study

Objective

The aim of this study was to compare the consumption of dental treatment among patients with Crohn´s disease (CD) or ulcerative colitis (UC) compared to age and gender matched control groups.

Design

The study group comprised 2085 patients with CD and 3161 with UC from the Uppsala-Örebro region and from the Stockholm region. The patients in the cohort were diagnosed between 1960 and 1989. Patients up to 70 years of age were included in the study. The two patients groups were compared to age- and gender-matched, randomly selected control groups from the same geographic area comprising a corresponding number of participants.

Results

CD patients had significantly higher total number of procedures registered (p < 0.000). The difference was most pronounced for removable dentures (+65%), fillings in front teeth (+52%) and endodontic treatment (+46%) when Crohn’s patients were compared to controls (p<0.001). The corresponding figures for UC patients were also a significantly higher total number of procedures (p < 0.005), more clinical examinations (p<0.000), fillings in canines and incisors (p < 0.001) and fillings in bicuspids and molars (p < 0.000).

Conclusion

This study demonstrate that CD and UC individuals use more dental treatment compared to an age-gender matched control group, and more caries-related treatments. The difference was most pronounced for restorative treatment in patients with Crohn’s.