Oncotarget

Research Papers:

Identification of skin-related lncRNAs as potential biomarkers that are involved in Wnt pathways in keloids

Xiao-Jie Sun, Qiang Wang, Baofeng Guo, Xian-Ying Liu and Bing Wang _

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Oncotarget. 2017; 8:34236-34244. https://doi.org/10.18632/oncotarget.15880

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Abstract

Xiao-Jie Sun1, Qiang Wang2, Baofeng Guo1, Xian-Ying Liu3, Bing Wang1

1Department of Plastic and Reconstruction Surgery, China-Japan Union Hospital of Jilin University, Changchun, China

2Department of Obstetrics and Gynecology, Second Hospital of Jilin University, Changchun, China

3Department of medication, Second Hospital of Jilin University, Changchun, China

Correspondence to:

Bing Wang, email: wangbing8630@163.com

Keywords: keloid, long noncoding RNA, Wnt pathway, biostatistics, microarray

Received: October 21, 2016     Accepted: January 24, 2017     Published: March 03, 2017

ABSTRACT

The long non-coding RNAs (lncRNAs) regulating encoding transcripts/genes involved in Wnt signalling pathway in keloids is largely unclear. We used a pathway-focused lncRNA microarray to detect the differentiated expression profiles of both lncRNAs and genes involved in Wnt pathway, thus a total of 116 Wnt-targeted genes and 69 Wnt-related lncRNAs aberrantly expressed in keloids were initially identified. A stepwise bioinformatics was further performed to find skin-related lncRNA/gene pairs in Wnt pathway in keloids. Firstly, an lncRNA/gene co-expression network with clustered functional modules was constructed; simultaneously, 114 Wnt-genes regarding to dermis were online enriched using Phenotype Enrichment. Secondly, 17 skin-related keloid-aberrant Wnt-genes were acquired by overlapping the 114 skin-related Wnt-genes with the 116 keloid-aberrant Wnt-genes. Thirdly, after co-expression coefficient of each lncRNA/gene profile being ranked respectively, 11 top co-expressed lncRNAs characterized with the highest co-expression coefficients to the 17 genes were identified. Fourthly, seven of the 11 top co-expressed lncRNAs exhibiting array-detected aberrant expression in keloids, together with their 12 most interactive Wnt-genes, were selected to undergo in-pair intracellularly quantitative PCR validation in keloids. As a result, four lncRNAs including CACNA1G-AS1, HOXA11-AS, LINC00312 and RP11-91I11.1 with their six paired Wnt-genes undergoing both array-and-qPCR as well as lncRNA-and-gene double validation were finally identified as skin-related lncRNA/gene pairs that involved in Wnt signalling pathway in keloids. In conclusion, in-depth exploration on these easily-accessible lncRNAs in keloids might aid to find the novel target on how to maintain highly recurrent tumours benign via Wnt-involved network regulation.


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PII: 15880