Abstract
In an attempt to find the correlation of aberrant expression of long intergenic noncoding RNAs (lincRNAs) with cancer, twenty-five samples of breast cancer tissue and respective adjacent normal tissue were studied for the expression of lincRNAs by RNA-seq. Among the 538 lincRNAs studied, 124 lincRNAs were exclusively expressed in cancer adjacent tissues and 62 lincRNAs were exclusively expressed in the cancer tissues. Furthermore, the expression of 134 lincRNAs was higher while 272 lower in breast cancer tissue compared with adjacent tissue. The expression of four selected lincRNAs (BC2, BC4, BC5, and BC8) was validated by semi-quantitative and real-time PCR. It was revealed that expression of lincRNA-BC5 was positively correlated with patients' age, pathological stage, and progesterone receptor concentration, while lincRNA-BC8 was negatively correlated with progesterone receptor expression. Higher expression of lincRNA-BC4 was seen in advanced breast cancer grade. LincRNA-BC2 showed no specific changes in the pathological features studied. Interactions between selected lincRNAs and breast cancer associated proteins were highly suggested by RPIseq based on the specific secondary structure. The results demonstrated that this group of lincRNAs was aberrantly expressed in breast cancer. They might play important roles in the function of oncogenes or tumor suppressors affecting the development and progression of breast cancer.
Highlights
The human genome contains only 20,000 protein-coding genes, representing,2% of the total genome
We found that a group of lincRNAs was aberrantly expressed in twenty five breast cancer tissues compared with matched adjacent tissues
RNA-Seq and Reads mapping PolyA-minus RNAs were fractionated from total RNA samples isolated from pooled breast cancer tissues and matched adjacent tissues
Summary
The human genome contains only 20,000 protein-coding genes, representing ,2% of the total genome. Long intergenic ncRNAs (lincRNAs) range in size from several hundred to tens of thousands of bases ($200). They belong to a newly discovered class of ncRNAs. more than 3,000 human lincRNAs have been identified, less than 1% of them have been characterized [2]. NcRNA, lincRNAs, have emerged as a new regulatory molecule exemplified by their frequent cell-type specific expression and subcellular compartment localization. They may play important roles in numerous systems, and interact with cancer related genes. Several well-described examples, such as HOTAIR [3], Xist [4], lincRNA-p21 [5], and MALAT-1 [6], indicate that lincRNAs may be essential factors in occurrences and developments of cancer [7,8]
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