Discovery of new long noncoding RNAs associated with ulcerative colitis with a novel general microarray expression...

Area of Science:

• Genomics
• Molecular Biology
• Gastroenterology

Background:

• Ulcerative colitis (UC) is a chronic inflammatory bowel disease with unknown causes, increasing bowel cancer risk.
• Long noncoding RNAs (lncRNAs) are increasingly recognized for their roles in disease pathogenesis.
• Microarray technology provides a platform for large-scale gene expression analysis.

Purpose of the Study:

• To develop a computational method for identifying functionally conserved lncRNAs in ulcerative colitis (UC) using cDNA microarray probe genomics data.
• To investigate the potential roles of specific lncRNAs in the pathogenesis of UC.
• To establish a novel approach for re-annotating transcriptome expression profiles from existing microarray data.

Main Methods:

• Analysis of 12,593 microarray probes from Ensembl, OMIM, UniGene, and Gene Ontology databases.
• Computational identification of evolutionary conserved lncRNAs associated with UC.
• Validation of lncRNA expression in colon tissue samples from UC patients.
• In vitro validation in Caco2/bbe and T84 cell lines treated with TNF-α.

Main Results:

• lncRNA n385775 was significantly upregulated (P < 0.001) in active UC patients.
• lncRNAs n336281 (P = 0.017), n341081 (P = 0.041), and n387236 (P = 0.006) were significantly downregulated in UC patients.
• lncRNA n38775 showed significant upregulation in Caco2/bbe cells after TNF-α treatment (P = 0.002).

Conclusions:

• A novel computational method can effectively re-annotate transcriptome expression profiles from existing cDNA microarray data to study lncRNA function in UC.
• Specific lncRNAs (n385775, n336281, n341081, n387236) show altered expression in UC and inflammatory conditions, suggesting their involvement in disease pathogenesis.
• This approach offers a valuable strategy for uncovering the functional roles of lncRNAs in complex diseases like UC.