Detection and Analysis of the Hedgehog Signaling Pathway-Related Long Non-Coding RNA (lncRNA) Expression Profiles in Keloid

Abstract

BACKGROUND Hedgehog (Hh) signaling pathway-related genes have important roles in several physiological and disease processes that involve cell proliferation. Long non-coding region RNAs (lncRNAs) have a regulatory role on gene expression. Keloid is characterized by excessive proliferation of scar tissue following trauma. The aims of this study were to evaluate the Hh signaling pathway in keloid skin tissues and its downstream gene expression and lncRNAs, compared with normal skin. MATERIAL AND METHODS Four pairs of keloids and adjacent normal skin epidermis underwent total RNA extraction. Gene chip high-throughput real-time quantitative polymerase chain reaction (qPCR) was used to examine the differential expression profiles of the Hh signaling pathway-related lncRNAs and mRNAs in the human keloid and normal skin. The differentially expressed mRNAs were analyzed by Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) to identify their biological roles. RESULTS In keloid tissue, differential expression of 33 mRNAs and 30 lncRNAs relating to the Hh pathway, were verified by gene chip qPCR. The results of GO and KEGG analysis showed that the upregulated mRNAs were involved in cell proliferation, cell growth, and tissue repair, and down-regulated mRNAs were involved in apoptosis. The lncRNA, AC073257.2, affected cell keloid growth and proliferation by its upstream target the GLI2 gene at the transcriptional level. The lncRNA, HNF1A-AS1, affected cell keloid growth and proliferation by its neighboring target gene, HNF1A. CONCLUSIONS Differential expression occurred in Hh signaling pathway-related lncRNAs and mRNAs, which may provide further insight into the development of keloid.

Figure 1

Expression of Hedgehog (Hh) signaling pathway-related long non-coding region RNAs (lncRNAs). (A) Thirty long non-coding region RNAs (lncRNAs) were differentially expressed relating to the Hedgehog (Hh) pathway. (B) Thirty-three lncRNAs were differentially expressed relating to the Hh pathway. There are 30 color bars in A and 33 color bars in B. Each color bar in the heat maps represent a lncRNA or mRNA, and the name of lncRNA or mRNA is on the right of the Figure. The red bar indicates upregulation of lncRNA or mRNA and the green bar indicates the down-regulation. [N] represents normal skin epidermis, and [K] represents the keloid epidermis. A is the lncRNA heat map and B is the mRNA heat map.

Figure 2

The biological effects of mRNA determined by enrichment of fold-change by Gene Ontology (GO) with FunRich software analysis. Seven enriched metabolic processes were identified, which mainly participated in embryonic development, gene expression, epigenetic inheritance, cell growth or communication, maintenance of cell morphology, and signal transduction.

Figure 3

The biological effects of mRNA determined by enrichment of fold-change by the Kyoto Encyclopedia of Genes and Genomes (KEGG) with FunRich software analysis. Ten enriched metabolic pathways were identified, which mainly involved the activation of the Notch signaling pathway, control of apoptosis, and regulation of gene expression.

Figure 4

Comparison of gene chip analysis and high-throughput real-time quantitative polymerase chain reaction (qPCR).