Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cells: Implication of endothelin-1 in inflammatory bowel disease

Wei Yu, Zhenwu Lin, John P. Hegarty, Gerrit John, Xi Chen, Pieter W. Faber, Ashley A. Kelly, Yunhua Wang, Lisa S. Poritz, Stefan Schreiber, Walter A. Koltun

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

Nkx2-3 gene variants are strongly associated with inflammatory bowel disease (IBD) and its expression is up-regulated in Crohn's disease (CD). However, the nature of its role underlying IBD pathogenesis is unknown. We investigated the genes regulated by Nkx2-3 using cDNA microarray. A small interfering RNA (siRNA)-mediated knockdown of Nkx2-3 in a B cell line from a CD patient was generated. Gene expression was profiled on high-density cDNA microarrays representing over 25,000 genes. Ingenuity pathway analysis (IPA) was used to identify gene networks according to biological functions and associated pathways. Expression profiling analysis by cDNA microarray showed that 125 genes were regulated by Nkx2-3 knockdown (fold change ≥3.0, p < 0.01), among which 51 genes were immune and inflammatory response genes. Microarray results were validated by RT-PCR and further confirmed in a B cell line expressing siRNA of Nkx2-3 from an additional CD patient. The results showed that Nkx2-3 was up-regulated (p < 0.05) and EDN1 was down-regulated (p < 0.05) in B cell lines from CD patients. mRNA expression levels of Nkx2-3 were negatively correlated with those of EDN1 (r = -0.6044, p < 0.05). EDN1 was also down-regulated in intestinal tissues from UC patients (p < 0.05). Our present results demonstrate that a decrease in Nkx2-3 gene expression level can profoundly alter the expression of genes and cellular functions relevant to the pathogenesis and progression of IBD, such as EDN1.

Original languageEnglish (US)
Pages (from-to)88-95
Number of pages8
JournalMolecular Genetics and Metabolism
Volume100
Issue number1
DOIs
StatePublished - May 1 2010
Externally publishedYes

Fingerprint

Endothelin-1
Inflammatory Bowel Diseases
Small Interfering RNA
B-Lymphocytes
Genes
Cells
Crohn Disease
Microarrays
Oligonucleotide Array Sequence Analysis
Gene Expression
Cell Line
Complementary DNA
Gene expression
Gene Regulatory Networks
Polymerase Chain Reaction
Messenger RNA
Tissue

Keywords

  • cDNA microarray
  • EDN1
  • Gene regulation
  • IBD
  • Nkx2-3

ASJC Scopus subject areas

  • Endocrinology, Diabetes and Metabolism
  • Biochemistry
  • Molecular Biology
  • Genetics
  • Endocrinology

Cite this

Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cells : Implication of endothelin-1 in inflammatory bowel disease. / Yu, Wei; Lin, Zhenwu; Hegarty, John P.; John, Gerrit; Chen, Xi; Faber, Pieter W.; Kelly, Ashley A.; Wang, Yunhua; Poritz, Lisa S.; Schreiber, Stefan; Koltun, Walter A.

In: Molecular Genetics and Metabolism, Vol. 100, No. 1, 01.05.2010, p. 88-95.

Research output: Contribution to journalArticle

Yu, W, Lin, Z, Hegarty, JP, John, G, Chen, X, Faber, PW, Kelly, AA, Wang, Y, Poritz, LS, Schreiber, S & Koltun, WA 2010, 'Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cells: Implication of endothelin-1 in inflammatory bowel disease', Molecular Genetics and Metabolism, vol. 100, no. 1, pp. 88-95. https://doi.org/10.1016/j.ymgme.2010.02.001
Yu, Wei ; Lin, Zhenwu ; Hegarty, John P. ; John, Gerrit ; Chen, Xi ; Faber, Pieter W. ; Kelly, Ashley A. ; Wang, Yunhua ; Poritz, Lisa S. ; Schreiber, Stefan ; Koltun, Walter A. / Genes regulated by Nkx2-3 in siRNA-mediated knockdown B cells : Implication of endothelin-1 in inflammatory bowel disease. In: Molecular Genetics and Metabolism. 2010 ; Vol. 100, No. 1. pp. 88-95.
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AU - Faber, Pieter W.

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