RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study.
10.3346/jkms.2017.32.5.817
- Author:
Kyuwhan JUNG
1
;
InSong KOH
;
Jeong Hyun KIM
;
Hyun Sub CHEONG
;
Taejin PARK
;
So Hyun NAM
;
Soo Min JUNG
;
Cherry Ann SIO
;
Su Yeong KIM
;
Euiseok JUNG
;
Byoungkook LEE
;
Hye Rim KIM
;
Eun SHIN
;
Sung Eun JUNG
;
Chang Won CHOI
;
Beyong Il KIM
;
Eunyoung JUNG
;
Hyoung Doo SHIN
Author Information
1. Department of Surgery, Jeju National University Hospital, Jeju, Korea.
- Publication Type:Original Article
- Keywords:
Necrotizing Enterocolitis;
RNA-Seq;
Gene Expression
- MeSH:
Axons;
Colon;
Enterocolitis, Necrotizing*;
Gene Expression Profiling*;
Gene Expression*;
Gene Ontology;
Genome;
Humans*;
Infant, Newborn;
Infant, Premature;
Mortality;
Necrosis;
Nervous System;
Pilot Projects*;
Sample Size;
Sequence Analysis, RNA;
Thyroid Neoplasms;
Transcriptome
- From:Journal of Korean Medical Science
2017;32(5):817-824
- CountryRepublic of Korea
- Language:English
-
Abstract:
Necrotizing enterocolitis (NEC) characterized by inflammatory intestinal necrosis is a major cause of mortality and morbidity in newborns. Deep RNA sequencing (RNA-Seq) has recently emerged as a powerful technology enabling better quantification of gene expression than microarrays with a lower background signal. A total of 10 transcriptomes from 5 pairs of NEC lesions and adjacent normal tissues obtained from preterm infants with NEC were analyzed. As a result, a total of 65 genes (57 down-regulated and 8 up-regulated) revealed significantly different expression levels in the NEC lesion compared to the adjacent normal region, based on a significance at fold change ≥ 1.5 and P ≤ 0.05. The most significant gene, DPF3 (P < 0.001), has recently been reported to have differential expressions in colon segments. Our gene ontology analysis between NEC lesion and adjacent normal tissues showed that down-regulated genes were included in nervous system development with the most significance (P = 9.3 × 10⁻⁷; P(corr) = 0.0003). In further pathway analysis using Pathway Express based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, genes involved in thyroid cancer and axon guidance were predicted to be associated with different expression (P(corr) = 0.008 and 0.020, respectively). Although further replications using a larger sample size and functional evaluations are needed, our results suggest that altered gene expression and the genes' involved functional pathways and categories may provide insight into NEC development and aid in future research.
