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. 2017 Aug;14(2):1526-1530.
doi: 10.3892/ol.2017.6283. Epub 2017 May 31.

Analysis of long non-coding RNA expression profiles in ovarian cancer

Liang Shen  1 , Wei Liu  1 , Jing Cui  2 , Juan Li  1 , Changzhong Li  1
Affiliations

Analysis of long non-coding RNA expression profiles in ovarian cancer

Liang Shen et al. Oncol Lett. 2017 Aug.

Abstract

Ovarian cancer is one of the major threats to female health. Identifying cancer cases at an early stage and selecting effective therapeutic drugs for patients is challenging. The number of studies concerning long non-coding RNAs (lncRNAs) is increasing rapidly; there is a large body of evidence indicating that lncRNAs are crucial in oncogenic and tumor-suppression mechanisms. Therefore, in the present study, lncRNA expression in ovarian cancer was considered. All of the existing ovarian cancer microarray datasets in the Gene Expression Omnibus database were assessed and two met the criteria for the present study; these were designated the training and validation sets. A re-annotation pipeline method was established to annotate lncRNAs from existing probe sets. When comparing ovarian cancer with normal ovarian tissues, seven lncRNAs from the RefSeq database, based on their combined ability to classify tissue in the training set, were identified and validated with the validation set. Research into the molecular functions of the seven identified lncRNAs may contribute to the understanding of ovarian cancer oncogenesis; they may also be candidates for novel ovarian cancer biomarkers.

Keywords: long non-coding RNA; microarray; ovarian cancer.

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Figures

Figure 1.
Figure 1.
Organization of the training and validation datasets. Based on specific criteria, two datasets of OCS microarray data were selected from the Gene Expression Omnibus. Each dataset included data from OCS and normal ovarian tissue. OC, ovarian cancer; SBOC, ovarian borderline carcinoma specimens; SNO, normal ovary specimens; SC, ovarian serous carcinoma specimens; OCS, ovarian carcinoma specimens.
Figure 2.
Figure 2.
All detected lncRNA signatures in dataset (A) GSE36668 and (B) GSE18520. Samples are in columns and lncRNAs are in rows. Gene expression levels are indicated as follows: Red, upregulated; green, downregulated. lncRNA, long non-coding RNA; SBOC, ovarian borderline carcinoma specimens; SNO, normal ovary specimens; SC, ovarian serous carcinoma specimens.
Figure 3.
Figure 3.
FC of the expression levels of the seven identified differentially expressed lncRNAs in (A) GSE36668 and (B) GSE18520. The combined differential expression of the identified lncRNAs was sufficient to distinguish cancer and normal tissues. lncRNA, long non-coding RNA; FC, fold change.
Figure 4.
Figure 4.
Principle component analysis results of samples in (A) the training set, GSE36668 (green, serous carcinoma; red, borderline carcinoma; blue, normal ovary tissue) and (B) the validation set, GSE18520 (red, ovarian cancer; green, normal ovary tissue), based on the combined differential expression levels of seven lncRNAs. lncRNA, long non-coding RNA.
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