Non-pathogenic bacteria modulate colonic epithelial gene expression in germ-free mice

Organic Selenium Increased Gilts Antioxidant Capacity, Immune Function, and Changed Intestinal Microbiota

Selenium is an indispensable essential micronutrient for humans and animals, and it can affect biological functions by combining into selenoproteins. The purpose of this study was to investigate the effects of 2-hydroxy-4-methylselenobutanoic acid (HMSeBA) on the antioxidant performance, immune function, and intestinal microbiota composition of gilts. From weaning to the 19th day after the second estrus, 36 gilts (Duroc × Landrace × Yorkshire) were assigned to three treatments: control group, sodium selenite group (0.3 mg Se/kg Na₂SeO₃), and HMSeBA group (0.3 mg Se/kg HMSeBA). Dietary supplementation with HMSeBA improved the gilts tissue selenium content (except in the thymus) and selenoprotein P (SelP1) concentration when compared to the Na₂SeO₃ or control group. Compared with the control group, the antioxidant enzyme activity in the tissues from gilts in the HMSeBA group was increased, and the concentration of malondialdehyde in the colon had a decreasing trend (p = 0.07). Gilts in the HMSeBA supplemented group had upregulated gene expression of GPX2, GPX4, and SelX in spleen tissue, TrxR1 in thymus; GPX1 and SelX in duodenum, GPX3 and SEPHS2 in jejunum, and GPX1 in the ileum tissues (p < 0.05). In addition, compared with the control group, the expression of interleukin-1β (IL-1β), interleukin-6 (IL-6), interleukin-8 (IL-8), and monocyte chemotactic protein-1 (MCP-1) in the liver, spleen, thymus, duodenum, ileum, and jejunum of gilts in the HMSeBA group were downregulated (p < 0.05), while the expression of interleukin-10 (IL-10) and transforming growth factor-β (TGF-β) in the liver, thymus, jejunum, and ileum were upregulated (p < 0.05). Compared with the control group and the Na₂SeO₃ group, HMSeBA had increased concentration of serum cytokines interleukin-2 (IL-2) and immunoglobulin G (IgG; p < 0.05), increased concentration of intestinal immunoglobulin A (sIgA; p < 0.05), and decreased concentration of serum IL-6 (p < 0.05). Dietary supplementation with HMSeBA also increased the abundance of intestinal bacteria (Ruminococcaceae and Phascolarctobacterium; p < 0.05) and selectively inhibited the abundance of some bacteria (Parabacteroides and Prevotellaceae; p < 0.05). In short, HMSeBA improves the antioxidant performance and immune function of gilts, and changed the structure of the intestinal microflora. And this study provided data support for the application of HMSeBA in gilt and even pig production.

Genetic and transcriptional analysis of inflammatory bowel disease-associated pathways in patients with GUCY2C-linked familial diarrhea

OBJECTIVE

Activating mutations in the GUCY2C gene, which encodes the epithelial receptor guanylate cyclase C, cause diarrhea due to increased loss of sodium chloride to the intestinal lumen. Patients with familial GUCY2C diarrhea syndrome (FGDS) are predisposed to inflammatory bowel disease (IBD). We investigated whether genes in the guanylate cyclase C pathway are enriched for association with IBD and reversely whether genetic or transcriptional changes associated with IBD are found in FGDS patients.

METHODS

(1) A set of 27 genes from the guanylate cyclase C pathway was tested for enrichment of association with IBD by Gene Set Enrichment Analysis, using genome-wide association summary statistics from 12,882 IBD patients and 21,770 controls. (2) We genotyped 163 known IBD risk loci and sequenced NOD2 in 22 patients with FGDS. Eight of them had concomitant Crohn's disease. (3) Global gene expression analysis was performed in ileal tissue from patients with FGDS, Crohn's disease and healthy individuals.

RESULTS

The guanylate cyclase C gene set showed a significant enrichment of association in IBD genome-wide association data. Risk variants in NOD2 were found in 7/8 FGDS patients with concomitant Crohn's disease and in 2/14 FDGS patients without Crohn's disease. In ileal tissue, downregulation of metallothioneins characterized FGDS patients compared to healthy controls.

CONCLUSIONS

Our results support a role of guanylate cyclase C signaling and disturbed electrolyte homeostasis in development of IBD. Furthermore, downregulation of metallothioneins in the ileal mucosa of FGDS patients may contribute to IBD development, possibly alongside effects from NOD2 risk variants.

Insights into microbiome research 5: Mapping is first but function must come next

Several efforts identifying differential bacterial prevalence in the gut of multiple sclerosis (MS) patients have been reported and many more are underway. While these are critical first steps in determining the involvement of gut microbes in MS pathogenesis, functional assays (both in vitro and in vivo) are needed to explore the mechanisms underlying the observed changes and ultimately implementing interventional strategies to counter severity, progression or even reduce the chance that it develops in the first place.

Genetic and transcriptional analysis of human host response to healthy gut microbiota

The study of host-microbiota interactions in humans is largely limited to identifying associations between microbial communities and host phenotypes. While these studies have generated important insights on the links between the microbiota and human disease, the assessment of cause-and-effect relationships has been challenging. Although this relationship can be studied in germfree mice, this system is costly, and it is difficult to accurately account for the effects of host genotypic variation and environmental effects seen in humans. Here, we have developed a novel approach to directly investigate the transcriptional changes induced by live microbial communities on human colonic epithelial cells and how these changes are modulated by host genotype. This method is easily scalable to large numbers of host genetic backgrounds and diverse microbiota and can be utilized to elucidate the mechanisms of host-microbiota interactions. Future extensions may also include colonic organoid cultures.

Many studies have demonstrated the importance of the gut microbiota in healthy and disease states. However, establishing the causality of host-microbiota interactions in humans is still challenging. Here, we describe a novel experimental system to define the transcriptional response induced by the microbiota for human cells and to shed light on the molecular mechanisms underlying host-gut microbiota interactions. In primary human colonic epithelial cells, we identified over 6,000 genes whose expression changed at various time points following coculturing with the gut microbiota of a healthy individual. Among the differentially expressed genes we found a 1.8-fold enrichment of genes associated with diseases that have been previously linked to the microbiome, such as obesity and colorectal cancer. In addition, our experimental system allowed us to identify 87 host single nucleotide polymorphisms (SNPs) that show allele-specific expression in 69 genes. Furthermore, for 12 SNPs in 12 different genes, allele-specific expression is conditional on the exposure to the microbiota. Of these 12 genes, 8 have been associated with diseases linked to the gut microbiota, specifically colorectal cancer, obesity, and type 2 diabetes. Our study demonstrates a scalable approach to study host-gut microbiota interactions and can be used to identify putative mechanisms for the interplay between host genetics and the microbiota in health and disease.

IMPORTANCE The study of host-microbiota interactions in humans is largely limited to identifying associations between microbial communities and host phenotypes. While these studies have generated important insights on the links between the microbiota and human disease, the assessment of cause-and-effect relationships has been challenging. Although this relationship can be studied in germfree mice, this system is costly, and it is difficult to accurately account for the effects of host genotypic variation and environmental effects seen in humans. Here, we have developed a novel approach to directly investigate the transcriptional changes induced by live microbial communities on human colonic epithelial cells and how these changes are modulated by host genotype. This method is easily scalable to large numbers of host genetic backgrounds and diverse microbiota and can be utilized to elucidate the mechanisms of host-microbiota interactions. Future extensions may also include colonic organoid cultures.

Cross-talk between E. coli strains and a human colorectal adenocarcinoma-derived cell line

Although there is great interest in the specific mechanisms of how gut microbiota modulate the biological processes of the human host, the extent of host-microbe interactions and the bacteria-specific metabolic activities for survival in the co-evolved gastrointestinal environment remain unclear. Here, we demonstrate a comprehensive comparison of the host epithelial response induced by either a pathogenic or commensal strain of Escherichia coli using a multi-omics approach. We show that Caco-2 cells incubated with E. coli display an activation of defense response genes associated with oxidative stress. Indeed, in the bacteria co-culture system, the host cells experience an altered environment compared with the germ-free system that includes reduced pH, depletion of major energy substrates, and accumulation of fermentation by-products. Measurement of intracellular Caco-2 cell metabolites revealed a significantly increased lactate concentration, as well as changes in TCA cycle intermediates. Our results will lead to a deeper understanding of acute microbial-host interactions.

Intestinal colonization: how key microbial players become established in this dynamic process: microbial metabolic activities and the interplay between the host and microbes

In this review, we provide an overview of the dynamic changes within the microbiota and its metabolites that are implicated in establishing and maintaining gastrointestinal homeostasis during various stages of microbial colonization. The gradual conversion of the gut microbiota toward a mutualistic microbial community involves replacement of pioneer gut colonizers with bacterial taxa that are characteristic for the adult gut. An important microbial signature of homeostasis in the adult gut is the prevalence and activity of a diverse spectrum of bacterial species that produce beneficial metabolites through metabolic interactions between microbial groups. Deciphering these microbial signatures and their metabolites that govern short and long-term equilibrium, as well as imbalances in host-microbial relationships, may provide novel diagnostic tools and/or therapeutic targets for specific disorders associated with intestinal dysbiosis and loss of homeostasis.

Upregulation of superoxide dismutase activity in the intestinal tract mucosa of germ-free mice

Superoxide dismutase (SOD) catalyzes the breakdown of superoxide into hydrogen peroxide and oxygen in the antioxidant defense system. We had reported that the SOD activities in the ceca of germ-free (GF) mice were significantly higher than those in conventional (CV) mice. In this study, we confirmed the location where SOD activity and protein expression increased in the ceca of GF mice. An immunohistochemical analysis and total SOD activity assay were conducted using the mucosa and other remaining tissues in the ceca. In addition to SOD activity in the ceca, 4 sites of intestinal (duodenal, jejunal, ileal and colonic) mucosae in GF mice were compared with those of CV mice. Total SOD activity in the cecal mucosa of GF mice was significantly higher than that in CV mice (P<0.01), and the intensity of CuZnSOD-positive cells in cecal mucosa was increased in all GF mice. Total and CuZnSOD activities in the duodenal, jejunal, ileal, cecal and colonic mucosae of GF mice were significantly higher than those in CV mice (P<0.05, or P<0.01). Furthermore, CuZnSOD mRNA showed similar tendencies with respect to these activities. Our results suggest for the first time that upregulation of SOD activity occurs in the entire intestinal mucosa of GF mice.

Effects of intestinal microflora on superoxide dismutase activity in the mouse cecum

In the antioxidant defense system, superoxide dismutase (SOD) catalyzes the breakdown of superoxide into hydrogen peroxide and oxygen. In the cecum, the influence of intestinal microflora on SOD activity is unknown. In this study, we used germ-free (GF) mice to examine the effect of intestinal microflora on SOD activity in the cecum, and SOD activity was compared between GF and conventional (CV) mice. The activity of CuZnSOD and MnSOD was determined using the SOD Assay Kit-WST. Expressions of CuZnSOD mRNA and protein were determined by real-time PCR and western blot analyses, respectively. The activities of CuZnSOD and MnSOD were significantly higher in the ceca of GF IQI and FVB/N strain mice than in CV mice (P<0.01-0.05). The gene expressions of CuZnSOD mRNA in the ceca of GF mice were significantly higher than those in CV mice (P<0.05), and CuZnSOD protein expression showed similar tendencies. Consistent with the abovementioned results, the total SOD activity in conventionalized mice decreased to the level of total SOD activity observed in the ceca of CV mice. Furthermore, no differences between GF and CV mice were observed in the SOD activities in the liver and thymus. Our results suggest that the antioxidant defense system in the mouse cecum is influenced by the intestinal microflora that downregulate SOD activity.

Alteration of local microflora and α-defensins hyper-production in colonic adenoma mucosa

BACKGROUND AND AIM

Gut flora/host interactions are fundamental for the maintenance of homeostasis. Evidence of possible regulatory effect of commensal bacteria on proliferative disorders of the colon is mounting. In this study, we explored the hypothesis that precancerous lesions, such as adenomas, present alteration of the local microflora and lead to an overproduction of antibacterial molecules of the innate immunity, namely α-defensins. Thus, the host-bacteria misbalance could represent a potential procarcinogenic factor.

METHODS

Biopsies from adenomatous polyps and normal mucosa, in the rectum-sigmoid colon, were collected from 51 patients. Concentration of mucosal bacteria was evaluated by real-time polymerase chain reaction after extraction of total DNA. Total RNA was also extracted, and the defensin α-1, defensin-5, and defensin-6 gene expressions were evaluated by real-time polymerase chain reaction. Immunohistochemical study has been carried out to evaluate protein production and location. Antibacterial activity of adenomatous polyps mucosa was evaluated in vitro.

RESULTS

Biopsies from adenomatous polyps had a significant relative reduction of mucosa adherent bacteria compared with normal tissue (20-fold relative reduction, P<0.05). Concomitantly, α-defensin expression and production were significantly increased in adenomas. Adenoma mucosa showed increased antibacterial activity in vitro compared with normal mucosa.

CONCLUSIONS

Microflora dysbiosis occurs at the mucosal surface in colonic adenomas, and may represent a potential factor for dysplastic cell proliferation. Further studies are needed to confirm and define the role of this mechanism in colon carcinogenesis and the potential applications in the clinical setting.

Dietary selenium affects host selenoproteome expression by influencing the gut microbiota

Colonization of the gastrointestinal tract and composition of the microbiota may be influenced by components of the diet, including trace elements. To understand how selenium regulates the intestinal microflora, we used high-throughput sequencing to examine the composition of gut microbiota of mice maintained on selenium-deficient, selenium-sufficient, and selenium-enriched diets. The microbiota diversity increased as a result of selenium in the diet. Specific phylotypes showed differential effects of selenium, even within a genus, implying that selenium had unique effects across microbial taxa. Conventionalized germ-free mice subjected to selenium diets gave similar results and showed an increased diversity of the bacterial population in animals fed with higher levels of selenium. Germ-free mice fed selenium diets modified their selenoproteome expression similar to control mice but showed higher levels and activity of glutathione peroxidase 1 and methionine-R-sulfoxide reductase 1 in the liver, suggesting partial sequestration of selenium by the gut microorganisms, limiting its availability for the host. These changes in the selenium status were independent of the levels of other trace elements. The data show that dietary selenium affects both composition of the intestinal microflora and colonization of the gastrointestinal tract, which, in turn, influence the host selenium status and selenoproteome expression.

Depletion of murine intestinal microbiota: effects on gut mucosa and epithelial gene expression

Background

Inappropriate cross talk between mammals and their gut microbiota may trigger intestinal inflammation and drive extra-intestinal immune-mediated diseases. Epithelial cells constitute the interface between gut microbiota and host tissue, and may regulate host responses to commensal enteric bacteria. Gnotobiotic animals represent a powerful approach to study bacterial-host interaction but are not readily accessible to the wide scientific community. We aimed at refining a protocol that in a robust manner would deplete the cultivable intestinal microbiota of conventionally raised mice and that would prove to have significant biologic validity.

Methodology/Principal Findings

Previously published protocols for depleting mice of their intestinal microbiota by administering broad-spectrum antibiotics in drinking water were difficult to reproduce. We show that twice daily delivery of antibiotics by gavage depleted mice of their cultivable fecal microbiota and reduced the fecal bacterial DNA load by 400 fold while ensuring the animals' health. Mice subjected to the protocol for 17 days displayed enlarged ceca, reduced Peyer's patches and small spleens. Antibiotic treatment significantly reduced the expression of antimicrobial factors to a level similar to that of germ-free mice and altered the expression of 517 genes in total in the colonic epithelium. Genes involved in cell cycle were significantly altered concomitant with reduced epithelial proliferative activity in situ assessed by Ki-67 expression, suggesting that commensal microbiota drives cellular proliferation in colonic epithelium.

Conclusion

We present a robust protocol for depleting conventionally raised mice of their cultivatable intestinal microbiota with antibiotics by gavage and show that the biological effect of this depletion phenocopies physiological characteristics of germ-free mice.

An imbalance in mucosal cytokine profile causes transient intestinal inflammation following an animal's first exposure to faecal bacteria and antigens

Intestinal microflora play a critical role in the initiation and perpetuation of chronic inflammatory bowel diseases. In genetically susceptible hosts, bacterial colonization results in rapid-onset chronic intestinal inflammation. Nevertheless, the intestinal and systemic immune response to faecal bacteria and antigen exposure into a sterile intestinal lumen of a post-weaned animal with a mature immune system are not understood clearly. This study examined the effects of faecal bacteria and antigen exposure on the intestinal mucosal and systemic immune system in healthy axenic mice. Axenic wild-type mice were inoculated orally with a crude faecal slurry solution derived from conventionally raised mice and were analysed prior to and then at days 3, 7, 14 and 28 post-treatment. Ingestion of faecal slurry resulted in a transient, early onset of proinflammatory interferon (IFN)-gamma, tumour necrosis factor (TNF)-alpha and interleukin (IL)-17 response that was maximal at day 3. In contrast, the transient release of the anti-inflammatory cytokines IL-10 and IL-4 occurred later and was maximal at day 7. Both responses subsided by day 14. This early cytokine imbalance was associated with a brief rise in colonic and caecal histopathological injury score at day 7. The bacterial antigen-specific systemic response was found to follow the intestinal immune response with a maximal release of both pro- and anti-inflammatory cytokines at day 7. Thus, first exposure of healthy axenic wild-type mice to normal faecal flora and antigens results in an early proinflammatory cytokine response and transient colonic inflammation that then resolves in conjunction with a subsequent anti-inflammatory cytokine profile.

Bacterial population moves toward a colon-like community in the pouch after total proctocolectomy

BACKGROUND

Colonic transformation is defined by phenotypic alterations in the ileum after total proctocolectomy. Changes in microbiota of the ileal pouch and the roles of these microbes in colonic transformation, however, have not been addressed.

METHODS

A total of 151 stool samples were collected from patients with ulcerative colitis patients and an ileostomy, those with an ileal pouch, and healthy control volunteers. Bacterial DNA was extracted from stool, and the diversity of complex bacteria was assessed by terminal restriction fragment length polymorphism (T-RFLP) analysis, a novel DNA-based approach that enables us to investigate the presence of nonculturable bacteria. To determine whether ileal pouch bacterial communities shift to a more colon-like distribution, the relative abundance of terminal restriction fragments that could be classified as "colonic," "ileal," or "common" was investigated.

RESULTS

Cluster analysis demonstrated that most of the ileostomy samples were categorized into Cluster I or II and that less than 10% of ileostomy samples were classified into Cluster IV. In contrast, more than 90% of control samples were grouped in Cluster IV. In further analyses, the median lifetimes of pouches in Clusters I, II, III, and IV were significantly different at 11, 56, 265, and 310 days, respectively. T-RFLP patterns of the ileal pouch were characterized by a time-dependent decrease in "ileal" and increase in a part of "colonic" fragments, which represented mainly nonculturable bacteria such as the Clostridium coccoides group.

CONCLUSION

T-RFLP analysis demonstrated that a time-dependent shift to a "colon-like" bacterial community, including nonculturable bacteria, in the ileal pouch after total proctocolectomy.

Functional Genomics Approaches to Studies of the Cytochrome P450 Superfamily

Functional genomics approaches are widely implemented in current research and have found application in many areas of biology. This review will present research fields, novel findings and new tools developed in the cytochrome P450 field using the functional genomics techniques. The most widely used method is microarray technology, which has already greatly contributed to the understanding of the cytochromes P450 function and expression. Several focused CYP microarrays have been developed for genotyping, toxicogenomics and studies of CYP function of many different organisms. Our contribution to the CYP field by development of Steroltalk microarrays to study the cross-talk of cholesterol homeostasis and drug metabolism is also presented.

Commensal bacteria and "oncologic surveillance": suggestions from an experimental model

The relationship between resident intestinal flora and colon cancer development are not yet clear. Apoptosis induction could represent a mechanism by which commensal and/or probiotic bacteria could prevent proliferation of dysplastic cells. In the present study, the in vivo and in vitro proapoptotic effect of resident bacteria was evaluated in mouse colon mucosa. Preliminary results suggest that colonic apoptosis induction, by commensal bacteria, could possibly represent a physiologic "oncologic surveillance" mechanism for colonic proliferative disease prevention.

Importance of the interferon-alpha system in murine large intestine indicated by microarray analysis of commensal bacteria-induced immunological changes

Background

Although microbiota play a critical role in the normal development and function of host immune systems, the underlying mechanisms, especially those involved in the large intestine (LI), remain unknown. In the present study, we performed transcriptome analysis of the LI of germ-free (GF) and specific pathogen-free (SPF) mice of the IQI strain, an inbred strain established from ICR mice.

Results

GeneChip analysis, quantitative real-time RT-PCR, and reconfirmation using bacteria-inoculated GF mice revealed differences in the expression levels of several immune-related genes, such as cryptdin-related sequences (CRS), certain subsets of type 1 interferon (IFN)-related genes, class Ib MHC molecules, and certain complements. LI expressed no authentic cryptdins but predominantly expressed CRS2, 4, and 7. The mRNA levels of IFN-related genes, including Irf7, Isgf3g, Ifit1 and Stat1, were lower in SPF- and flora-reconstituted mice. When an oral IFN-α inducer tilorone analog, R11567DA, was administered to SPF mice, IFN-α was induced rapidly in the LI at 4 h, whereas no IFN-α protein was detected in the small intestine (SI) or blood. In situ hybridization and immunohistochemistry suggested that the IFN-α production originated from Paneth cells in the SI, and portions of lamina proprial CD11b- or mPDCA1-positive cells in the LI.

Conclusion

The present study suggests that microbial colonization, while inducing the expression of anti-microbial peptides, results in the down-regulation of certain genes responsible for immune responses, especially for type I IFN synthesis. This may reflect the adaptation process of the immune system in the LI to prevent excessive inflammation with respect to continuous microbial exposure. Further, the repertoire of anti-microbial peptides and the extraordinary role of interferon producing cells in the LI have been found to be distinct from those in the SI.

Probiotic bacteria change Escherichia coli-induced gene expression in cultured colonocytes: Implications in intestinal pathophysiology

AIM: To investigate the change in eukaryotic gene expression profile in Caco-2 cells after infection with strains of Escherichia coli and commensal probiotic bacteria.

METHODS: A 19200 gene/expressed sequence tag gene chip was used to examine expression of genes after infection of Caco-2 cells with strains of normal flora E. coli, Lactobacillus plantarum, and a combination of the two.

RESULTS: The cDNA microarray revealed up-regulation of 155 and down-regulation of 177 genes by E. coli. L. plantarum up-regulated 45 and down-regulated 36 genes. During mixed infection, 27 genes were up-regulated and 59 were down-regulated, with nullification of stimulatory/inhibitory effects on most of the genes. Expression of several new genes was noted in this group.

CONCLUSION: The commensal bacterial strains used in this study induced the expression of a large number of genes in colonocyte-like cultured cells and changed the expression of several genes involved in important cellular processes such as regulation of transcription, protein biosynthesis, metabolism, cell adhesion, ubiquitination, and apoptosis. Such changes induced by the presence of probiotic bacteria may shape the physiologic and pathologic responses they trigger in the host.

CARD15 status and familial predisposition for Crohn's disease and colonic gene expression

Familial disposition and mutations in the Caspase Recruitment Domain 15 (CARD15) have been associated with an increased risk for Crohn's disease (CD). This study investigated whether these risk factors correlate with colonic gene expression profiles generated by DNA-microarray technology. Tissue specimens from descending colon were obtained during colonoscopy from 45 CD patients (18 from areas with inflammation and 27 from noninflamed areas). Gene profiling analysis was performed using the Human Genome U133 Plus 2.0 GeneChip Array. Patients were classified according to their CARD15 status. Hybridization data were analyzed with dChip software. Nine patients with either one or two CARD15 mutations had no differentially expressed genes, compared to 36 patients with wild- type CARD15. There was only one differentially expressed EST between 8 patients who had familial disposition for inflammatory bowel disease (IBD) and 36 who did not, but hierarchical cluster analysis did not show group homogeneity. We conclude that gene expression profiling of mucosal biopsies from the descending colon of patients with CD could not be correlated with CARD15 status or with familial disposition for IBD.

Treatment response and colonic gene expression in patients with Crohn's disease

OBJECTIVE

Responses and adverse events to medication vary greatly among patients with Crohn's disease (CD). The aim of this study was to investigate whether global gene expression profiles could predict such responses and possible side effects.

MATERIAL AND METHODS

Tissue specimens from the descending colon were obtained from 32 CD patients (in 18 patients from areas without inflammation and in 14 patients from inflamed areas). Gene profiling was done using the Affymetrix Human Genome U133 Plus 2.0 GeneChip array. Hybridization data were analyzed with dChip software.

RESULTS

There were no differentially expressed genes between six patients who responded well to azathioprine and four who did not. No differences were found between 12 patients with adverse events to azathioprine and 9 patients who tolerated this drug. Sixteen patients who were not glucocorticoid-dependent had no differentially expressed genes as compared with 15 glucocorticoid-dependent patients. Six patients who responded well to infliximab had only one differentially expressed gene as compared to four patients who did not.

CONCLUSIONS

DNA microarray analyses did not show differentially expressed genetic profiles from colonic mucosal cells obtained from groups of patients classified according to therapeutic criteria.

Expression of the genes dual oxidase 2, lipocalin 2 and regenerating islet-derived 1 alpha in Crohn's disease

OBJECTIVE

A global gene expression profile of non-inflamed colonic mucosal cells from patients with Crohn's disease (CD) and of colonic mucosal cells from controls was performed.

MATERIAL AND METHODS

Tissue specimens from macroscopically non-inflamed descending colon were obtained colonoscopically from 33 CD patients and from 17 control subjects. All controls and 10 CD patients were medication-free at the time of colonoscopy. The Human Genome U133 Plus 2.0 GeneChip Array was used for gene profiling. Hybridization data were analysed with dChip software. Results were confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR). Protein product expression of selected genes was assessed by immunohistochemistry using the Envision+ visualization technique.

RESULTS

The expression profile was not homogeneous with the statistical cut-point settings applied. In comparison with controls, it was found that 19 CD patients had three differentially expressed genes, two of them related to the innate immune system: dual oxidase 2 on chromosome 15 (DUOX2, fold change 4.1) and lipocalin 2 on chromosome 9 (LCN2, fold change 3.1). The third gene, regenerating islet-derived 1 alpha (REG1A, fold change 3.9), codes for a mitogenic protein; this could not be confirmed by RT-PCR. Medication-free patients had no differentially expressed genes as compared with controls. Immunohistochemistry indicated that these proteins were produced by epithelial cells (REG1A, LCN2) and leucocytes (DUOX2 and LCN2).

CONCLUSIONS

As compared with controls, non-inflamed colonic mucosal cells contain two up-regulated genes related to the innate immune system. Up-regulation of these genes, known to be induced by microorganisms, suggests either increased microflora antigenicity or an altered function in mucosal barrier defence.

Gingival epithelial cell transcriptional responses to commensal and opportunistic oral microbial species

Transcriptional profiling and ontology tools were utilized to define the biological pathways of gingival epithelial cells modulated by coculture with the oral commensal Streptococcus gordonii and the opportunistic commensal Fusobacterium nucleatum. Overall, F. nucleatum and S. gordonii perturbed the gingival epithelial cell transcriptome much less significantly than the oral pathogens Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans perturbed the transcriptome, indicating that there was a greater degree of host adaptation by the commensal species (M. Handfield, J. J. Mans, G. Zheng, M. C. Lopez, S. Mao, A. Progulske-Fox, G. Narasimhan, H. V. Baker, and R. J. Lamont, Cell. Microbiol. 7:811-823, 2005). The biological pathways significantly impacted by F. nucleatum and S. gordonii included the mitogen-activated protein kinase (MAPK) and Toll-like receptor signaling pathways. Differential regulation of GADD45 and DUSP4, key components of the MAPK pathway, was confirmed at the protein level by Western blotting. Modulation of the MAPK pathway is likely to affect host cell proliferation and differentiation. In addition, both the MAPK and Toll-like receptor pathways ultimately converge on cytokine gene expression. An enzyme-linked immunosorbent assay of secreted interleukin-6 (IL-6) and IL-8 demonstrated that F. nucleatum induced production of these cytokines, whereas S. gordonii inhibited secretion from the epithelial cells. Stimulation of secretion of proinflammatory cytokines from epithelial cells may reflect the invasive phenotype of F. nucleatum and contribute to the greater pathogenic potential of F. nucleatum than of S. gordonii.

Clinical phenotype and gene expression profile in Crohn's disease

The clinical course varies significantly among patients with Crohn's disease (CD). This study investigated whether gene expression profiles generated by DNA microarray technology might predict disease progression. Biopsies from the descending colon were obtained colonoscopically from 40 CD patients. Gene profiling analyses were performed using a Human Genome U133 Plus 2.0 GeneChip Array, and summarization into a single expression measure for each probe set was performed using the robust multiple array procedure. Principal component analysis demonstrated that three components explain two-thirds of the total variation. The most important parameters for the determination of the colonic gene expression patterns were the presence of disease (CD) and presence of inflammation. Superimposition of clinical phenotype data revealed a grouping of the samples from patients with stenosis toward negative values on the axis of the second principal component. The functional annotation analysis suggested that the expression of genes involved in intracellular transport and cytoskeletal organization might influence the development of stenosis. In conclusion, even though most variation in the colonic gene expression patterns is due to presence or absence of CD and inflammation status, the development of stenosis is a parameter that affects colonic gene expression to some extent.

Distinct signals from the microbiota promote different aspects of zebrafish gut differentiation

All animals exist in intimate associations with microorganisms that play important roles in the hosts' normal development and tissue physiology. In vertebrates, the most populous and complex community of microbes resides in the digestive tract. Here, we describe the establishment of the gut microbiota and its role in digestive tract differentiation in the zebrafish model vertebrate, Danio rerio. We find that in the absence of the microbiota, the gut epithelium is arrested in aspects of its differentiation, as revealed by the lack of brush border intestinal alkaline phosphatase activity, the maintenance of immature patterns of glycan expression and a paucity of goblet and enteroendocrine cells. In addition, germ-free intestines fail to take up protein macromolecules in the distal intestine and exhibit faster motility. Reintroduction of a complex microbiota at later stages of development or mono-association of germ-free larvae with individual constituents of the microbiota reverses all of these germ-free phenotypes. Exposure of germ-free zebrafish to heat-killed preparations of the microbiota or bacterial lipopolysaccharide is sufficient to restore alkaline phosphatase activity but not mature patterns of Gal alpha1,3Gal containing glycans, indicating that the host perceives and responds to its associated microbiota by at least two distinct pathways.

An approach to analyze mechanisms of intestinal adaptation following total proctocolectomy

We hypothesized that epithelial cells of the remnant small intestine display "colonic" phenotype after total proctocolectomy. The aims of the present study were to identify preferentially expressed molecules in the colon or in the small intestine and to evaluate mRNA levels of those in the ileal pouch. Differential gene expression was investigated between the small intestine and the colon by using cDNA microarray and was confirmed by Northern blotting. Expression of three colonic mRNAs (3-hydroxy-3-methylglutaryl-coenzyme A synthase 2, deleted malignant brain tumors 1, carcinoembryonic antigen-related cell adhesion molecule 1) and one "small intestinal" (microsomal triglyceride transfer protein) mRNA were compared between the control and the ileal pouch mucosae by quantitative reverse transcriptase-polymerase chain reaction. Seventy-four clones were differentially expressed with more than a threefold difference. Differential expression was confirmed in all mRNAs examined, including 3-hydroxy-3-methylglutaryl-coenzyme A synthase 2 and microsomal triglyceride transfer protein. The mucosal expression of carcinoembryonic antigen-related cell adhesion molecule 1 mRNA in the ileal pouch was enhanced in humans. The remnant ileum develops some, but not all, colonic phenotype after total proctocolectomy. Comparative study of epithelial gene expression between the small intestine and the colon enables us to analyze mechanisms of intestinal adaptation after total proctocolectomy.

Gene expression profiling of jejunal Peyer’s patches in juvenile and adult pigs

Peyer's patches are organized lymphoid tissues of the small intestine that play a critical role in disease resistance and oral tolerance. Peyer's patches in the jejunum contain lymphocytes, dendritic cells, macrophages, villous epithelium, and specialized follicle-associated epithelium. Little is known about the mechanisms and processes by which cells of the Peyer's patches discriminate food nutrients and commensal microflora from pathogenic microbiota. We hypothesize that the jejunal Peyer's patches express genes that mediate and regulate its essential functions. Expression patterns of approximately 2600 cDNAs from a porcine Peyer's patch subtracted library were examined by microarray profiling. Individual mRNAs of interest were further examined by quantitative RT-PCR. Innate immunity-associated genes, including complement 3 and lysozyme, and the genes for epithelial chloride channel and trappin 1 were highly expressed by jejunal Peyer's patch in both juvenile and adult pigs. The growth- and apoptosis-associated genes CIDE-B, GW112, and PSP/Reg I (pancreatic stone protein or regenerating gene) were differentially expressed in juvenile pig Peyer's patches. Many sequences which were highly expressed in jejunal Peyer's patches have previously been described with functions in epithelial cells. Animal-to-animal variation in basal jejunal Peyer's patch gene expression was considerable and reflects the dynamic physiological environment of the gut in addition to genetic, epigenetic, and microbiological variation in the small intestine.

Gene expression in gastric biopsies from patients infected with Helicobacter pylori

BACKGROUND

Helicobacter pylori infection has protean effects on gene expression in the host gastric mucosa, which have been investigated by gene chip analysis in vitro. In this study the effects of H. pylori infection on host gene expression in the gastric antral mucosa in patients were examined.

METHODS

One gastric antral biopsy was obtained from a total of 18 untreated patients undergoing routine endoscopic evaluation of chronic abdominal complaints. Nine patients had histologic evidence of H. pylori infection and 9 age- and sex-matched patients had no histologic evidence of H. pylori infection. A microarray analysis was performed using a gene chip containing 35,000 human expressed sequence tags on RNA extracted from endoscopic, gastric antral biopsies, and average gene expression among infected and uninfected patients was compared.

RESULTS

Underexpressed genes in infected patients' mucosa included gastric intrinsic factor and several metallothionein isoforms. Overexpressed genes in infected patients' mucosa comprised MHC Class II molecules, immunoglobulin and B-cell activation genes, as well as genes known to induce apoptosis. Changes in expression were confirmed for a subset of genes by SYBR green real-time PCR.

CONCLUSIONS

Microarray analysis of antral biopsies from patients with and without H. pylori infection revealed differential expression of metal regulatory, immunity and inflammation-related genes.

Impact of commensal microbiota on murine gastrointestinal tract gene ontologies

The gastrointestinal tract (GIT) of eukaryotes is colonized by a vast number of bacteria, where the commensal microbiota play an important role in defining the healthy gut. To investigate the influence of commensal bacteria on multiple regions of the host GIT transcriptome, the gene expression profiles of the corpus, jejunum, descending colon, and rectum of conventional (n = 3) and germ-free mice (n = 3) were examined using the Affymetrix Mu74Av2 GeneChip. Differentially regulated genes were identified using the global error assessment model, and a novel method of Gene Ontology (GO) clustering was used to identify significantly modulated biological functions. The microbiota modify the greatest number of genes in the jejunum (267 genes with an alpha < 0.001) and the fewest in the rectum (137 genes with an alpha < 0.001). Clustering genes by GO biological process and molecular function annotations revealed that, despite the large number of differentially regulated genes, the residential microbiota most significantly modified genes involved in such biological processes as immune function and water transport all along the length of the mouse GIT. Additionally, region-specific communication between the host and microbiota were identified in the corpus and jejunum, where tissue kallikrein and apoptosis regulator activities were modulated, respectively. These findings identify important interactions between the microbiota and the mouse gut tissue transcriptome and, furthermore, suggest that interactions between the microbial population and host GIT are implicated in the coordination of region-specific functions.