Ultra-Deep Sequencing Reveals the microRNA Expression Pattern of the Human Stomach

Ândrea Ribeiro-Dos-Santos,André S Khayat,Dayse O Alencar,Leonardo Varuzza,Sylvain Darnet,Wilson A Silva,Dalila L Zanette,Monica Assumpção,Paulo Assumpção,Artur Silva,Sidney Santos,Larissa Luz,Jessé Lobato,Daniel G Pinheiro,Rommel Burbano

doi:10.1371/journal.pone.0013205

Abstract

BackgroundWhile microRNAs (miRNAs) play important roles in tissue differentiation and in maintaining basal physiology, little is known about the miRNA expression levels in stomach tissue. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia.Methodology/Principal FindingsA small RNA library of stomach tissue was sequenced using high-throughput SOLiD sequencing technology. We obtained 261,274 quality reads with perfect matches to the human miRnome, and 42% of known miRNAs were identified. Digital Gene Expression profiling (DGE) was performed based on read abundance and showed that fifteen miRNAs were highly expressed in gastric tissue. Subsequently, the expression of these miRNAs was validated in 10 healthy individuals by RT-PCR showed a significant correlation of 83.97% (P<0.05). Six miRNAs showed a low variable pattern of expression (miR-29b, miR-29c, miR-19b, miR-31, miR-148a, miR-451) and could be considered part of the expression pattern of the healthy gastric tissue.Conclusions/SignificanceThis study aimed to validate normal miRNA profiles of human gastric tissue to establish a reference profile for healthy individuals. Determining the regulatory processes acting in the stomach will be important in the fight against gastric cancer, which is the second-leading cause of cancer mortality worldwide.

Highlights

Friedman et al, 2009 demonstrated that the majority of human genes are under the control of miRNAs
Discussion miRNAs regulate the majority of human genes; only a few miRNAs have had their targets and specific functions identified [14]
Precancerous lesions such as gastritis lead to genomic hypomethylation in the stomach that could modify the expression pattern of miRNAs [15]

Summary

Introduction

Friedman et al, 2009 demonstrated that the majority of human genes are under the control of miRNAs. MiRNAs are small, non-coding sequences of 17–25 bp that regulate gene expression by binding to the 39 end of target mRNAs, resulting in the inhibition of translation of the mRNAs [2,3]. 14,000 miRNAs have been identified in animals, plants and fungi [4,5,6]. Mechanisms that involve miRNAs as negative regulators of gene expression are similar in animals and plants; they regulate fundamental cellular processes [6]. Approximately 3% of all genes are predicted to encode miRNA precursors, and over .60% of protein-coding genes could be regulated by miRNAs [1]. Alterations in miRNA expression contribute to human diseases such as cancers [7,8]. Alterations in the miRNA profile can lead to cell deregulation, which can induce neoplasia

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