Biomarkers of human gastrointestinal tract regions

Dysregulation of intestinal epithelial cell performance is associated with an array of pathologies whose onset mechanisms are incompletely understood. While whole-genomics approaches have been valuable for studying the molecular basis of several intestinal diseases, a thorough analysis of gene expression along the healthy gastrointestinal tract is still lacking. The aim of this study was to map gene expression in gastrointestinal regions of healthy human adults and to implement a procedure for microarray data analysis that would allow its use as a reference when screening for pathological deviations. We analyzed the gene expression signature of antrum, duodenum, jejunum, ileum, and transverse colon biopsies using a biostatistical method based on a multivariate and univariate approach to identify region-selective genes. One hundred sixty-six genes were found responsible for distinguishing the five regions considered. Nineteen had never been described in the GI tract, including a semaphorin probably implicated in pathogen invasion and six novel genes. Moreover, by crossing these genes with those retrieved from an existing data set of gene expression in the intestine of ulcerative colitis and Crohn's disease patients, we identified genes that might be biomarkers of Crohn's and/or ulcerative colitis in ileum and/or colon. These include CLCA4 and SLC26A2, both implicated in ion transport. This study furnishes the first map of gene expression along the healthy human gastrointestinal tract. Furthermore, the approach implemented here, and validated by retrieving known gene profiles, allowed the identification of promising new leads in both healthy and disease state

Consequences of Exchanging Carbohydrates for Proteins in the Cholesterol Metabolism of Mice Fed a High-fat Diet

Consumption of low-carbohydrate, high-protein, high-fat diets lead to rapid weight loss but the cardioprotective effects of these diets have been questioned. We examined the impact of high-protein and high-fat diets on cholesterol metabolism by comparing the plasma cholesterol and the expression of cholesterol biosynthesis genes in the liver of mice fed a high-fat (HF) diet that has a high (H) or a low (L) protein-to-carbohydrate (P/C) ratio. H-P/C-HF feeding, compared with L-P/C-HF feeding, decreased plasma total cholesterol and increased HDL cholesterol concentrations at 4-wk. Interestingly, the expression of genes involved in hepatic steroid biosynthesis responded to an increased dietary P/C ratio by first down-regulation (2-d) followed by later up-regulation at 4-wk, and the temporal gene expression patterns were connected to the putative activity of SREBF1 and 2. In contrast, Cyp7a1, the gene responsible for the conversion of cholesterol to bile acids, was consistently up-regulated in the H-P/C-HF liver regardless of feeding duration. Over expression of Cyp7a1 after 2-d and 4-wk H-P/C-HF feeding was connected to two unique sets of transcription regulators. At both time points, up-regulation of the Cyp7a1 gene could be explained by enhanced activations and reduced suppressions of multiple transcription regulators. In conclusion, we demonstrated that the hypocholesterolemic effect of H-P/C-HF feeding coincided with orchestrated changes of gene expressions in lipid metabolic pathways in the liver of mice. Based on these results, we hypothesize that the cholesterol lowering effect of high-protein feeding is associated with enhanced bile acid production but clinical validation is warranted. (246 words

A short noncoding viral DNA element showing characteristics of a replication origin confers Bacteriophage resistance to Streptococcus thermophiles.

A 302-bp noncoding DNA fragment from the DNA replication module of phage φSfi21 was shown to protect theStreptococcus thermophilusstrainSfi1 from infection by 17 of 25 phages. The phage-inhibitory DNA possesses two determinants, each of which individually mediated phage resistance. The phage-inhibitory activity was copy number dependent and operates by blocking the accumulation of phage DNA. Furthermore, when cloned on a plasmid, the φSfi21 DNA acts as an origin of replication driven by phage infection. Protein or proteins in the φSfi21-infected cells were shown to interact with this phage-inhibitory DNA fragment, forming a retarded protein–DNA complex in gel retardation assays. A model in which phage proteins interact with the inhibitory DNA such that they are no longer available for phage propagation can be used to explain the observed bacteriophage resistance. Genome analysis of φSfi19, a phage that is insensitive to the inhibitory activity of the φSfi21-derived DNA, led to the characterisation of a variant putative phage replication origin that differed in 14 of 302 nucleotides from that of φSfi21. The variant origin was cloned and exhibited an inhibitory activity toward phages that were insensitive to the φSfi21-derived DNA

The Role of Prophage for Genome Diversification within a Clonal Lineage of Lactobacillus johnsonii: Characterization of the Defective Prophage LJ771▿ †

Two independent isolates of the gut commensal Lactobacillus johnsonii were sequenced. These isolates belonged to the same clonal lineage and differed mainly by a 40.8-kb prophage, LJ771, belonging to the Sfi11 phage lineage. LJ771 shares close DNA sequence identity with Lactobacillus gasseri prophages. LJ771 coexists as an integrated prophage and excised circular phage DNA, but phage DNA packaged into extracellular phage particles was not detected. Between the phage lysin gene and attR a likely mazE (“antitoxin”)/pemK (“toxin”) gene cassette was detected in LJ771 but not in the L. gasseri prophages. Expressed pemK could be cloned in Escherichia coli only together with the mazE gene. LJ771 was shown to be highly stable and could be cured only by coexpression of mazE from a plasmid. The prophage was integrated into the methionine sulfoxide reductase gene (msrA) and complemented the 5′ end of this gene, creating a protein with a slightly altered N-terminal sequence. The two L. johnsonii strains had identical in vitro growth and in vivo gut persistence phenotypes. Also, in an isogenic background, the presence of the prophage resulted in no growth disadvantage

Amelioration of dyslipidemia by H-P/C-HF feeding.

<p>Plasma triglyceride (TG) (A), free fatty acids (FFA) (B), total cholesterol (C) and HDL cholesterol (D) concentrations in mice consuming the L-P/C-HF or the H-P/C-HF diet for 2-d and 4-wk. Data are median ± semedian, n = 12/group except for H-P/C-HF 2-d, n = 11. * p<0.05 by Wilcoxon test.</p

Body weight gain and energy intake of mice fed different high-fat diets.

<p>Data are mean ± sem, n = 12/group.</p>*<p>p<0.05 vs. L-P/C-HF group. BW, body weight. EI, energy intake.</p

A model of Cyp7a1 regulation by H-P/C-HF feeding.

<p>Graphic illustration of a network of transcription regulators and <i>Cyp7a1</i> in the H-P/C-HF group compared with the L-P/C/HF group after 2-d (A) and 4-wk (B) of treatment. All transcription regulators that had statistically significant association with <i>Cyp7a1</i> in the present datasets were selected to build a network. Genes are represented as nodes and the expression levels of genes were overlaid on the network of nodes. Node color indicates the direction of regulation, green for down- and red for up-regulation. Fold change of differentially regulated genes is indicated by the number below gene name. Lines in between genes represent known interactions and the red color lines indicated the positive contributions. Red and green border colors of nodes indicate the putative transcription activity as “active” and “inhibit”, respectively. The image was created using IPA software.</p

Top 5 differentially regulated canonical pathways between H-P/C-HF and L-P/C-HF feeding for 2-d.

<p>Top 5 differentially regulated canonical pathways between H-P/C-HF and L-P/C-HF feeding for 2-d.</p