Oncotarget

Research Papers:

Signature miRNAs in colorectal cancers were revealed using a bias reduction small RNA deep sequencing protocol

Guihua Sun, Ya-Wen Cheng, Lily Lai, Tsui-Chin Huang, Jinhui Wang, Xiwei Wu, Yafan Wang, Yasheng Huang, Jinghan Wang, Keqiang Zhang, Shuya Hu, Ji-Rui Yang and Yun Yen _

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Oncotarget. 2016; 7:3857-3872. https://doi.org/10.18632/oncotarget.6460

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Abstract

Guihua Sun1, Ya-Wen Cheng4, Lily Lai2, Tsui-Chin Huang4, Jinhui Wang3, Xiwei Wu3, Yafan Wang1, Yasheng Huang1, Jinghan Wang1, Keqiang Zhang1, Shuya Hu1, Ji-Rui Yang4 and Yun Yen1,4

1 Department of Molecular Pharmacology, Beckman Research Institute of the City of Hope, Duarte, CA, USA

2 Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, USA

3 Integrated Genome Core, Beckman Research Institute of the City of Hope, Duarte, CA, USA

4 Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan

Correspondence to:

Guihua Sun, email:

Yun Yen, email:

Keywords: microRNA, colorectal cancer, small RNA deep sequencing, miR-21, miR-143

Received: August 19, 2015 Accepted: November 16, 2015 Published: December 04, 2015

Abstract

To explore the role of miRNAs in colorectal cancers (CRC), we have deep sequenced 48 pairs of frozen CRC samples, of which 44 pairs produced high quality sequencing data. By using a combined approach of our bias reduction small RNA (smRNA) deep sequencing protocol and Illumina small RNA TruSeq method for sample bar coding, we have obtained data from samples of relatively large size with bias reduced digital profile results. This novel approach allowed us to validate many previously published results using various techniques to profile miRNAs in CRC tissues or cell lines and to characterize ‘true’ miRNA signatures highly expressed in colon/rectum (CR) or CRC tissues. According to our results, miR-21, a miRNA that is up-regulated in CRC, and miR-143, a miRNA that is down-regulated in CRC, are the two miRNAs that dominated the miRNA population in CR tissues, and probably are also the most important miRNAs in CRCs. These two miRNAs, together with the other eight miRNAs, miR-148a, -194, -192, 200b, -200c, -10b, -26a, and -145, with descending expressing levels, constituted the top 10 highly expressed miRNAs in CR/CRC. Using TaqMan miRNA qPCR, we detected the relative expression of some of the CRC miRNAs in 10 CRC cell lines, validated their dysregulation under cancer condition, and provided possible explanation for their dysregulation, which could be caused by APC, KRAS, or TP53 mutations. We believe these results will provide a new direction in future miRNA-related CRC development studies, and application of miRNAs in CRC diagnosis/prognosis, and therapy.


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