The non-invasive exfoliated transcriptome (exfoliome) reflects the tissue-level transcriptome in a mouse model of NSAID enteropathy

Scientific Reports
Canaan M Whitfield-CargileRobert S Chapkin

Abstract

Non-steroidal anti-inflammatory drugs (NSAIDs) are among the most frequently used classes of medications in the world, yet they induce an enteropathy that is associated with high morbidity and mortality. A major limitation to better understanding the pathophysiology and diagnosis of this enteropathy is the difficulty of obtaining information about the primary site of injury, namely the distal small intestine. We investigated the utility of using mRNA from exfoliated cells in stool as a means to surveil the distal small intestine in a murine model of NSAID enteropathy. Specifically, we performed RNA-Seq on exfoliated cells found in feces and compared these data to RNA-Seq from both the small intestinal mucosa and colonic mucosa of healthy control mice or those exhibiting NSAID-induced enteropathy. Global gene expression analysis, data intersection, pathway analysis, and computational approaches including linear discriminant analysis (LDA) and sparse canonical correlation analysis (CCA) were used to assess the inter-relatedness of tissue (invasive) and stool (noninvasive) datasets. These analyses revealed that the exfoliated cell transcriptome closely mirrored the transcriptome of the small intestinal mucosa. Thus, the exfoliome ...Continue Reading

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Citations

Jul 4, 2019·The American Journal of Clinical Nutrition·Stephen J D O'Keefe
Mar 17, 2020·PloS One·Michelle C ColemanRobert S Chapkin
May 23, 2020·Current Zoology·Tania P GuerreroAlexandra Weyrich
Oct 12, 2019·Scientific Reports·Ana M Chamoun-EmanuelliCanaan M Whitfield-Cargile
Dec 10, 2020·Journal of Animal Science and Biotechnology·Johan S Osorio
Feb 7, 2020·The Journal of Nutritional Biochemistry·Samuel T WestreichDanielle G Lemay
May 6, 2021·American Journal of Physiology. Gastrointestinal and Liver Physiology·Grace YoonRobert S Chapkin

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Datasets Mentioned

BETA
PRJNA290483

Methods Mentioned

BETA
RNA-Seq
MDS
IECs
scrapings
biopsy
biopsies
chip

Software Mentioned

exfoliome
QIAGEN
edgeR
IPA Knowledgebase
Ingenuity® Pathway Analysis ( IPA
Fastqc
Spliced Transcripts Alignment to a Reference ( STAR )
IPA
Ensembl
mathop

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