Considerations on the application of microarray analysis in rhinology

Molecular biological tools are finding their way into modern rhinological research. This overview aims to discuss the merits and pitfalls of micro-array analysis as one of these molecular tools. The outcome of a micro-array experiment will describe which genes are active in a given cell type or tissue, allowing us to investigate healthy and diseased conditions on a large scale and in extreme detail. Although this will deepen our understanding of our disease of interest, we should not expect that micro-array analysis will resolve all our questions. In this overview we have indicated points that we feel are critical for any application of micro-array analysis in modern rhinological research. Choices on experimental design and patient inclusion will influence the outcome data of the experiment and the extend of the conclusions that can be drawn from these data. A second important issue is the size of the data set, which can comprise of hundreds of different genes, making it difficult to come to grips with the affected processes in a disease. New visualization and analysis tools for microarray data are discussed in this overview that deal with these complex issues.

How epithelial cells detect danger: aiding the immune response

The epithelial layer occupies a strategic important location between an organisms' interior and exterior environment. Although as such it forms a physical barrier between both environments, it became clear that the role of the epithelium extends far beyond this rather passive role. Through specialized receptors and other more general mechanisms, the epithelial layer is not only able to sense changes in its environment but also to actively respond to these changes. These responses allow the epithelium to contribute to wound and tissue repair, to the defense against micro-organisms, and to the control and regulation of the locale immune response. In this review, we focus on signals acting on epithelium from the exterior environment, how these signals are processed and identify research challenges.

Comparison of expression profiles induced by dust mite in airway epithelia reveals a common pathway

BACKGROUND

Airway epithelial cells have shown to be active participants in the defense against pathogens by producing signaling and other regulatory molecules in response to the encounter.

METHODS

In previous manuscripts, we have studied the effect of house dust mite (HDM) extract on both an epithelial cell-line (H292) and primary nasal epithelial cell. When we compare these responses we conclude that the H292 cells more closely resemble nasal epithelium of healthy controls (share 107 probe-sets) than of allergic individuals (share 17 probe-sets).

RESULTS

Interestingly, probably because of an absent intraindividual variation between samples, more probe-sets (8280) change expression significantly in H292 than in either healthy (555) or allergic (401) epithelium.

CONCLUSIONS

A direct comparison of all the responses in these epithelial cells reveals a core-response to HDM of just 29 genes. These genes (CCL20, IL-8, CXCL2, CXCL1, IL-1B, AREG, TNFAIP3, HBEGF, PTGS2, BMP2, LDLR, PLAUR, PLAU, NFKB2, NFKB1, JUN, ATF3, EGR1, NPC1, TICAM1, EPHA2, CTGF, DUSP1, SPRY1, TLR-3, complement factor C3, IVNS1ABP, SerpinB3, and PSAT1) have described links with allergy or inflammation and may even describe the well-established relationship between viral infections and allergic exacerbations or allergy development.

Allergen induced gene expression of airway epithelial cells shows a possible role for TNF-alpha

BACKGROUND

Epithelium is more than a physical barrier for pathogens and allergens, as it is also capable of producing mediators in response to these environmental factors. Some of these mediators have an immuno-modulatory function, suggesting that epithelium is an active component of the immune response. Here, we fully characterize the expression profile of airway epithelial cells in response to house dust mite (HDM) allergen.

METHODS

H292 cells were exposed to HDM extract for 24 h, RNA and supernatant was used for microarray analysis and multiplex enzyme-linked immunosorbent assay (ELISA) respectively.

RESULTS

A total of 38,500 genes, 813 were differentially expressed by more than twofold and 116 even more than fivefold. Interestingly, among the most up-regulated genes, a large number are involved in cell-to-cell communication. These include chemokines (CCL-8 and -20, CXCL-1, -2 and -3), cytokines (IL-1alpha, -6 and -11), anti-inflammatory factors [PTX-3, interleukin (IL)-13Ralpha, tumour necrosis factor (TNF)-alphaIP3], and factors that are involved in repair of the mucosal tissue (LOXL-2, NID-2, HBEGF, MUC-5AC and MUC-5B). Pathway analysis showed that a number of these genes are transcriptionally regulated by TNF-alpha, which we could detect by quantitative polymerase chain reaction at earlier time points after HDM exposure. In addition, we could detect increased protein levels for TNF-alpha, IL-6, IL8, granulocyte-macrophage colony-stimulating factor, granulocyte colony stimulating factor and interferon (IFN)-gamma using ELISA.

CONCLUSION

Our data show that a broad range of mediators produced upon allergen exposure by these mediators' epithelial cells can participate in the immune response via recruitment and activation of cells of the immune system.