Non-invasive analysis of intestinal development in preterm and term infants using RNA-Sequencing

Abstract

The state and development of the intestinal epithelium is vital for infant health, and increased understanding in this area has been limited by an inability to directly assess epithelial cell biology in the healthy newborn intestine. To that end, we have developed a novel, noninvasive, molecular approach that utilizes next generation RNA sequencing on stool samples containing intact epithelial cells for the purpose of quantifying intestinal gene expression. We then applied this technique to compare host gene expression in healthy term and extremely preterm infants. Bioinformatic analyses demonstrate repeatable detection of human mRNA expression, and network analysis shows immune cell function and inflammation pathways to be up-regulated in preterm infants. This study provides incontrovertible evidence that whole-genome sequencing of stool-derived RNA can be used to examine the neonatal host epithelial transcriptome in infants, which opens up opportunities for sequential monitoring of gut gene expression in response to dietary or therapeutic interventions.

Nutrient-Gene Interaction in Colon Cancer, from the Membrane to Cellular Physiology

“…Our group has developed methodology to extract host mRNA from stool samples for the purpose of RNA sequencing to examine gene expression profiles of the host organism (107). Indeed, we have demonstrated that the effects of chemotherapeutic diets on epithelial cell expression can be monitored noninvasively throughout the tumorigenic process (33).…”

Noninvasive molecular fingerprinting of host–microbiome interactions in neonates

“…We next applied our exfoliated cell transcriptomic approach to the preterm infant [48]. Preterm birth, which affected 15 million children in 2010, is a major determinant of neonatal morbidity and is the second leading cause of death in children under 5 years [64,65].…”

“…To determine whether sufficient exfoliated epithelial cells could be isolated from preterm infants and whether they would inform developmental differences, host transcript abundance in healthy full term (>38 weeks GA) and extremely preterm (24–30 weeks GA) infants were measured using RNA‐Seq [48]. Approximately, 5500 genes were detected (FPKM > 1) on average in both preterm and term samples.…”

“…Second, exfoliated cells express genes associated with specific intestinal cell types including absorptive enterocytes (lactase and sucrose–isomaltase), Goblet cells (mucin‐2), enteroendocrine cells (chromogranin A), and Paneth cells (lysozyme). Lastly, the transcriptional landscape is dramatically altered in the preterm versus term infant intestine [48].…”

Comprehensive site-specific whole genome profiling of stromal and epithelial colonic gene signatures in human sigmoid colon and rectal tissue

“…Reads [Ͼ200 bp in an intronic and intergenic (lincRNA) region] mapping against these additional regions were then included in our edgeR differential expression tests in addition to the coding genes. We considered all these results simultaneously when performing multiple testing correction as described previously (31,48).…”