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Differential expression of miRNAs in colons of STC patients

ABSTRACT: To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE57969 | GEO | 2014/05/27

SECONDARY ACCESSION(S): PRJNA248616

REPOSITORIES: GEO

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Differential expression of miRNAs in colons of STC patients

Project description:To investigate the pathogenesis of slow transit constipation (STC), we have employed microarray-based miRNA analysis as a discovery platform to identify miRNAs potentially related with STC pathogenesis.Full-thickness specimens were obtained from colons of STC patients undergoing total colectomy and ileorectal anastomosis or subtotal colectomy with antiperistaltic cecoproctostomy. And patients undergoing radical surgery for non-obstructing colon cancer (left colon cancer) as control. These patients were not constipated and had no colonic dilatation. The control specimens were obtained at least 5 cm from the resection margin in tumor free areas. Expression of five miRNAs (miRNA-128, miRNA-129-3p, miRNA-20b,miRNA-27b and miRNA-30b) from this signature was identified by arbitrarily setting the threshold at a fold change of 1.3 or above combined with p < 0.05 in the same RNA samples. Expression of miRNAs in the colon may be involved in STC pathogenesis. The samples were obtained and washed with cold PBS, transported in liquid nitrogen and immediately stored in liquid nitrogen after removal. Total RNA was isolated from frozen histologic specimens using a mirVana™ RNA isolation Kit.

2014-05-27 | E-GEOD-57969 | biostudies-arrayexpress

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Project description:Seven carbon autotrophic fixation pathways were described so far. However, it is not common to find the co-existence of more than one cycle in a single cell. Here, we describe a thermophilic bacterium Carbonactinospora thermoautotrophica StC with a unique and versatile carbon metabolism. StC was isolated from a consortium found in a burning organic pile that exhibits an optimal growth temperature between 55° and 65° C. The genome analyses suggested that the strain StC potentially performs two-carbon fixation pathways, Calvin-Benson-Bassham (CBB) cycle and the Reductive citrate cycle (rTCA) and preserve a microcompartment related with CO2 concentration. To better understand the carbon fixation in StC strain, the expression of the genes of bacterial cells grown autotrophically and heterotrophically were analyzed. For our surprise the data showed the co-existing of the both carbon fixation pathways - CBB and rTCA cycles - in a cultivable thermophilic chemoautotrophic bacterium Carbonactinospora thermoautotrophica strain StC, based on integrated omics of genomics, transcriptomics, and proteomics. These two cycles working together may help microorganisms to improve the CO2 fixation. The knowledge about the co-occurrence of carbon cycle in a single cell leads open a question ‘why microorganisms use multiple pathways to fix carbon and what the advantage for this strategy?’. Advancing on this is a key to better understand the biological carbon fixation mechanism in thermophiles and prospecting the repurposing of enzymes in synthetic biology for biotechnological applications.

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