J Korean Med Sci.  2017 May;32(5):817-824. 10.3346/jkms.2017.32.5.817.

RNA-Seq for Gene Expression Profiling of Human Necrotizing Enterocolitis: a Pilot Study

• Jung K
• Koh I
• Kim JH
• Cheong HS
• Park T
• Nam SH
• Jung SM
• Sio CA
• Kim SY
• Jung E
• Lee B
• Kim HR
• Shin E
• Jung SE
• Choi CW
• Kim BI
• Jung E
• Shin HD

• KMID: 2375083
• DOI: http://doi.org/10.3346/jkms.2017.32.5.817

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.

Keyword

Necrotizing Enterocolitis; RNA-Seq; Gene Expression

MeSH Terms

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

Figure

• 

  Fig. 1 NEC tissues for experiment and histological features. Arrows indicate 2 tissue sections (NEC lesion and adjacent normal regions) from the resected small bowel segment and each histological examination. NEC = necrotizing enterocolitis.

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