Purification methods to reduce interference by dextran sodium sulfate with quantification of gene expression in intestinal tissue samples from a piglet model of colitis

Dextran sodium sulfate (DSS) is commonly used to induce intestinal (i.e., colonic) inflammation in a variety of animal models. However, DSS is known to cause interference when using quantitative-real time polymerase chain reaction (qRT-PCR) methods, thereby invalidating accurate and precise measurement of tissue gene expression. Therefore, the goal of this study was to determine whether different mRNA purification methods would reduce DSS-interference. Colonic tissue samples were collected at postnatal days (PND) 27 or 28 from pigs that had not been administered DSS (Control), and two independent groups of pigs that received 1.25 g of DSS/kg of BW/d (DSS-1 and DSS-2) from PND 14 to 18. Tissue samples collected were subsequently stratified into three purification methods (i.e., 9 total treatment x method combinations), including: 1) no purification, 2) purification with lithium chloride (LiCl), or 3) purification using spin column filtration. All data were analyzed using a one-way ANOVA in the Mixed procedure of SAS. The average RNA concentrations across all treatments were between 1,300 and 1,800 mu g/mu L for all three in vivo groups. Although there were statistical differences among purification methods, the 260/280 and 260/230 ratios fell between acceptable limits of 2.0 to 2.1 and 2.0 to 2.2, respectively, for all treatment groups. This confirms the RNA quality was adequate and not influenced by purification method in addition to suggesting the absence of phenol, salts, and carbohydrate contamination. For pigs in the Control group that did not receive DSS, qRT-PCR Ct values of four cytokines were achieved, though these values were not altered by purification method. For pigs that had undergone DSS dosing, those tissues subjected to either no purification or purification using LiCl did not generate applicable Ct values. However, when tissues derive from DSS-treated pigs underwent spin column purification, half of the samples from DSS-1 and DSS-2 groups generated appropriate Ct estimates. Therefore, spin column purification appeared to be more effective than LiCl purification, but no method was 100% effective, so caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis. Gene expression can be inhibited by a variety of substrates, including dextran sodium sulfate (DSS), a commonly used compound for inducing tissue-level inflammation. We tested whether this interference could be overcome by applying sample purification methods. Lithium chloride purification was not completely effective at removing DSS-induced interference, whereas spin column purification yielded appreciably better results when quantifying the expression of immune-related genes in tissues of pigs experiencing DSS-induced colitis. Lay Summary Dextran sodium sulfate (DSS) is a chemical used to experimentally induce colonic inflammation in animal models. However, DSS causes chemical inhibition of processes involved with quantitative real-time polymerization chain reaction, thereby inhibiting the measurement of gene expression in tissues. In this study, differing methods of RNA purification were applied to remove DSS inhibition. Because no purification methods were 100% effective in alleviating this interference, caution should be exercised when interpreting gene expression results from studies where animals are exposed to DSS-induced colitis.

Automated summary

This study aims to determine if different mRNA purification methods can reduce interference caused by DSS. The results show that spin column purification is more effective than LiCl purification, but no method can completely eliminate interference. Therefore, caution should be exercised when interpreting gene expression results in animal studies using DSS-induced colitis.