A bias reduction small RNA deep sequencing protocol reveals signature miRNAs

To explore the role of miRNAs in colorectal cancers (CRC), researchers from the Beckman Research Institute of the City of Hope have deep sequenced 48 pairs of frozen CRC samples, of which 44 pairs produced high quality sequencing data. By using a combined approach of their bias reduction small RNA (smRNA) deep sequencing protocol and Illumina small RNA TruSeq method for sample bar coding, they have obtained data from samples of relatively large size with bias reduced digital profile results. This novel approach allowed the researchers 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 their 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.

rna-seq

Hierarchical cluster analysis classifies tumor versus normal tissues. Dendrogram of miRNAs with p<0.05 cluster normal tissue versus tumor tissue (44 pairs sample set). miRNAs are clustered into two groups that are either correlated with normal tissue or tumor tissue. There are several cases of tumor tissues are classified into normal tissues.

Sun G, Cheng YW, Lai L, Huang TC, Wang J, Wu X, Wang Y, Huang Y, Wang J, Zhang K, Hu S, Yang JR, Yen Y. (2015) Signature miRNAs in colorectal cancers were revealed using a bias reduction small RNA deep sequencing protocol. Oncotarget [Epub ahead of print]. [article]
Sun G, Wu X, Wang J, Li H, Li X, Gao H, Rossi J, Yen Y. (2011) A bias-reducing strategy in profiling small RNAs using Solexa. RNA 17(12):2256-62. [article]

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