The application of differential display as a gene profiling tool

Identification of Differentially Expressed Genes in Nocardia brasiliensis Induced by Progesterone and Dihydrotestosterone Using Differential Display PCR

Sex steroid hormones have an important physiological role in humans. They can also affect the gene expression of many organisms, including bacteria. In Mexico, Nocardia brasiliensis is the main causative agent of actinomycetoma, a granulomatous disease more frequent in men than women, which is thought to be related to a higher occupational risk in men. Therefore, it has been suggested that differences in clinical presentation could be related to sex steroid hormone levels. Attempting to explain the differences in actinomycetoma prevalence between men and women, in this work, the effect of progesterone and dihydrotestosterone on the genetic expression of N. brasiliensis was investigated using a differential display polymerase chain reaction assay. The results showed that both hormones affected the expression of genes encoding proteins related to central metabolism and hypothetical proteins with unknown functions. This study also demonstrated the utility of differential display in this modern era and provided a first approach to the effect of sex hormones on N. brasiliensis gene expression.

AGR2 is a SMAD4-suppressible gene that modulates MUC1 levels and promotes the initiation and progression of pancreatic intraepithelial neoplasia

The mechanisms controlling expression of the putative oncogene AGR2 in pancreatic ductal adenocarcinoma (PDAC) are not well understood. We now show that AGR2 is a TGF-β-responsive gene in human pancreatic cancer cells, whose down-regulation is SMAD4-dependent. We also provide evidence supporting a role for AGR2 as an ER-chaperone for the cancer-associated mucin, MUC1. AGR2 is both sufficient and required for MUC1 expression in pancreatic cancer cells. Furthermore, AGR2 is co-expressed with MUC1 in mouse pancreatic intraepithelial neoplasia (mPanIN)-like lesions and in the cancer cells of four distinct genetically engineered mouse models of PDAC. We also show that Pdx1-Cre/LSL-Kras^G12D/Smad4^lox/lox mice heterozygous for Agr2 exhibit a delay in mPanIN initiation and progression to PDAC. It is proposed that loss of Smad4 may convert TGF-β from a tumor suppressor to a tumor promoter by causing the up-regulation of AGR2, which then leads to increased MUC1 expression, at which point both AGR2 and MUC1 facilitate mPanIN initiation and progression to PDAC.

Differential expression of a set of genes in follicular and classic variants of papillary thyroid carcinoma

Fine-needle aspiration biopsy (FNA) is currently the best initial diagnostic test for evaluation of a thyroid nodule. FNA cytology cannot discriminate between benign and malignant thyroid nodules in up to 30% of thyroid nodules. Therefore, an adjunct to FNA is needed to clarify these lesions as benign or malignant. Using differential display-polymerase chain reaction method, the gene expression differences between follicular and classic variants of papillary thyroid carcinoma (PTC) and benign thyroid nodules were evaluated in a group of 42 patients. Computational gene function analyses via Cytoscape, FuncBASE, and GeneMANIA led us to a functional network of 17 genes in which a core sub-network of five genes coexists. Although the exact mechanisms underlying in thyroid cancer biogenesis are not currently known, our data suggest that the pattern of transformation from healthy cells to cancer cells of PTC is different in follicular variant than in classic variant.

RNA arbitrarily primed PCR and fourier transform infrared spectroscopy reveal plasticity in the acid tolerance response of Streptococcus macedonicus

We have previously reported that an acid tolerance response (ATR) can be induced in Streptococcus macedonicus cells at mid-log phase after autoacidification, transient exposure to acidic pH, or acid habituation, as well as at stationary phase. Here, we compared the transcriptional profiles of these epigenetic phenotypes, by RNA arbitrarily primed PCR (RAP-PCR), and their whole-cell chemical compositions, by Fourier transform infrared spectroscopy (FT-IR). RAP-PCR fingerprints revealed significant differences among the phenotypes, indicating that gene expression during the ATR is influenced not only by the growth phase but also by the treatments employed to induce the response. The genes coding for the mannose-specific IID component, the 1,2-diacylglycerol 3-glucosyltransferase, the 3-oxoacyl-acyl carrier protein, the large subunit of carbamoyl-phosphate synthase, and a hypothetical protein were found to be induced at least under some of the acid-adapting conditions. Furthermore, principal component analysis of the second-derivative-transformed FT-IR spectra segregated S. macedonicus phenotypes individually in all spectral regions that are characteristic for major cellular constituents like the polysaccharides of the cell wall, fatty acids of the cell membrane, proteins, and other compounds that absorb in these regions. These findings provide evidence for major changes in cellular composition due to acid adaptation that were clearly different to some extent among the phenotypes. Overall, our data demonstrate the plasticity in the ATR of S. macedonicus, which reflects the inherent ability of the bacterium to adjust the response to the distinctiveness of the imposed stress condition, probably to maximize its adaptability.