Expression of Toll-like receptor 9 and response to bacterial CpG oligodeoxynucleotides in human intestinal epithelium

Recognition of repeat CpG motifs, which are common in bacterial, but not in mammalian, DNA, through Toll-like receptor (TLR)9 is an integral part of the innate immune system. As the role of TLR9 in the human gut is unknown, we determined the spectrum of TLR9 expression in normal and inflamed colon and examined how epithelial cells respond to specific TLR9 ligand stimulation. TLR9 expression was measured in human colonic mucosal biopsies, freshly isolated human colonic epithelial cells and HT-29 cells by reverse transcriptase-polymerase chain reaction or Western blotting. Colonic epithelial cell cultures were stimulated with a synthetic CpG-oligodeoxynucleotide (ODN), exhibiting strong immunostimulatory effects in B cells. Interleukin (IL)-8 secretion was determined by enzyme-linked immunosorbent assay, nuclear factor-kappaB (NF-kB) activity by electrophoretic mobility shift assay and IkB phosphorylation by Western blotting. TLR9 mRNA was equally expressed in colonic mucosa from controls (n = 6) and patients with ulcerative colitis or Crohn's disease disease (n = 13). HT-29 cells expressed TLR9 mRNA and protein and responded to CpG-ODN (P < 0.01), but not to non-CpG-ODN stimulation, by secreting IL-8, apparently in the absence of NF-kB activation. Primary epithelial cells isolated from normal human colon expressed TLR9 mRNA, but were completely unresponsive to CpG-ODN stimulation in vitro. In conclusion, differentiated human colonic epithelial cells are unresponsive to TLR9 ligand stimulation in vitro despite spontaneous TLR9 gene expression. This suggests that the human epithelium is able to avoid inappropriate immune responses to luminal bacterial products through modulation of the TLR9 pathway.

Peroxisome proliferator-activated receptor expression and activation in normal human colonic epithelial cells and tubular adenomas

OBJECTIVE

Peroxisome proliferator-activated receptor (PPAR) ligands, widely used in type 2 diabetes treatment, have variably been shown to promote or prevent colon tumor formation in animal models and cell lines, but their role in normal human colon is unknown. The aim of this study was to determine PPAR expression and function in normal human colonic epithelial cells and tubular adenomas.

MATERIAL AND METHODS

Short-term cultures of normal human colonic epithelial cells were established from biopsies obtained in 42 patients with normal colonoscopy. PPAR and adipophilin mRNA expression was assessed by real-time RT-PCR. PPARs were activated by ligands for PPAR alpha (Wy-14643), PPAR delta (GW-501516) and PPAR gamma (rosiglitazone or troglitazone). Cell viability was measured using the methyltetrazoleum assay, proliferation by thymidine incorporation, and DNA profiles by flow cytometry. PPAR mRNA levels in tubular adenomas or metaplastic polyps (n=12) were compared with those in controls.

RESULTS

PPAR alpha and gamma were consistently expressed in normal colonocytes while no PPAR delta expression could be detected. PPAR gamma activation induced a 7.5-fold increase in adipophilin expression (a PPAR-activated gene). PPAR gamma activation had no effect on viability or DNA profiles, but led to a 25% significant decrease in cell proliferation. Finally, a selective and significant 2.5-fold decrease in PPAR alpha expression was observed in tubular adenomas, but not in metaplastic polyps, compared to controls.

CONCLUSIONS

Our findings support the view that PPAR gamma ligands act as anti-proliferative agents rather than as promoters of tumorigenesis in normal human colon. Moreover, they raise interest in investigation of PPAR alpha as a therapeutic target to prevent adenoma formation.

Array-A-Lizer: a serial DNA microarray quality analyzer

Background

The proliferate nature of DNA microarray results have made it necessary to implement a uniform and quick quality control of experimental results to ensure the consistency of data across multiple experiments prior to actual data analysis.

Results

Array-A-Lizer is a small and convenient stand-alone tool providing the necessary initial analysis of hybridization quality of an unlimited number of microarray experiments. The experiments are analyzed for even hybridization across the slide and between fluorescent dyes in two-color experiments in spotted DNA microarrays.

Conclusions

Array-A-Lizer allows the expedient determination of the quality of multiple DNA microarray experiments allowing for a rapid initial screening of results before progressing to further data analysis. Array-A-Lizer is directed towards speed and ease-of-use allowing both the expert and non-expert microarray researcher to rapidly assess the quality of multiple microarray hybridizations. Array-A-Lizer is available from the Internet as both source code and as a binary installation package.

BioWareDB: the biomedical software and database search engine

A wealth of bioinformatics tools and databases has been created over the last decade and most are freely available to the general public. However, these valuable resources live a shadow existence compared to experimental results and methods that are widely published in journals and relatively easily found through publication databases such as PubMed. For the general scientist as well as bioinformaticists, these tools can deliver great value to the design and analysis of biological and medical experiments, but there is no inventory presenting an up-to-date and easily searchable index of all these resources. To remedy this, the BioWareDB search engine has been created. BioWareDB is an extensive and current catalog of software and databases of relevance to researchers in the fields of biology and medicine, and presently consists of 2800 validated entries.

AVAILABILITY

BioWareDB is freely available over the Internet at http://www.biowaredb.org/

Affordable biocomputing for everyone: using the Internet, freeware and open-source software

How to build your own complete working biocomputing platform with nothing more than a desktop computer and an Internet connection.