title: Identification of skin-related lncRNAs as potential biomarkers that involved in Wnt pathways in keloids.
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.
authors.affiliation: Department of Plastic and Reconstruction Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
authors.forename: Xiao-Jie
authors.initials: XJ
authors.lastname: Sun
authors.affiliation: Department of Obstetrics and Gynecology, Second Hospital of Jilin University, Changchun, China.
authors.forename: Qiang
authors.initials: Q
authors.lastname: Wang
authors.affiliation: Department of Plastic and Reconstruction Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
authors.forename: Baofeng
authors.initials: B
authors.lastname: Guo
authors.affiliation: Department of medication, Second Hospital of Jilin University, Changchun, China.
authors.forename: Xian-Ying
authors.initials: XY
authors.lastname: Liu
authors.affiliation: Department of Plastic and Reconstruction Surgery, China-Japan Union Hospital of Jilin University, Changchun, China.
authors.forename: Bing
authors.initials: B
authors.lastname: Wang
mesh_terms: D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005819:Genetic Markers / Q000235:genetics*; D006801:Humans; D007627:Keloid / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D062085:RNA, Long Noncoding / Q000235:genetics*; D012867:Skin / Q000737:chemistry*; D060449:Wnt Signaling Pathway
chemical_list: D005819:Genetic Markers; D062085:RNA, Long Noncoding
keywords: Wnt pathway; biostatistics; keloid; long noncoding RNA; microarray