Transcriptomic analysis of mRNA expression in giant congenital melanocytic nevi.

BACKGROUND AND OBJECTIVE

GCMN is a sporadic disease with an incidence ranging from 1/20,000 to 1/500000. So far, several studies have found that GCMN is related to somatic mutations, but most of them have focused on known pathogenic genes, and transcriptome sequencing based on large datasets is relatively uncommon. At present, the use of next-generation sequencing technologies and bioinformatics platforms makes genomic information study more comprehensive and efficient. In this study, the transcriptome differences between GCMN lesions and surrounding normal skin tissues were investigated using high-throughput transcriptome sequencing, and hub genes and pathways related to pathogenesis were identified, providing a theoretical foundation for further research into the pathogenesis of GCMN.

METHODS

Pathological skin tissue and surrounding normal skin tissue from GCMN patients, namely the pathological group (PG) and the control group (CG), were obtained. 1. All specimens were stained with HE to ensure that the samples met the experimental requirements. 2. Ten pairs of specimens were selected for high-throughput transcriptome sequencing, and the differentially expressed genes (DEGs) between the PG and the CG were obtained. The DEGs were analyzed by clusterProfiler R software for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The function of the subnetwork was analyzed and the hub genes were identified by the STRING database and Cytoscape software. 3. The expression differences of hub genes PTGS2, EGF, and SOX10 in pathological skin tissues and normal skin tissues were verified by qRT-PCR and immunofluorescence staining.

RESULTS

1. HE staining revealed a lot of melanocytes in the dermis and subcutaneous tissues. They were found around the hair follicles, sweat glands, sebaceous glands, and blood vessel walls, or in a specific pattern. 2. The screening threshold was set at p < 0.01 and |log2fc|<1, and a total of 1163 DEGs were discovered between the PG and CG, with 519 genes up-regulated and 644 genes down-regulated in the pathological tissues. According to the GO functional analysis, 29 biological processes, 18 cell compositions, and 17 molecular functions were significantly enriched, with the majority of them being related to keratinocytes and the extracellular matrix. There were 779 nodes and 2359 interactions in the protein interaction network. Using the MCODE plug-in, the network was divided into 25 functional clusters. According to ClueGO results, Cluster5 was involved in melanin biosynthesis and melanocyte proliferation. Using 11 operation methods in the Cytohubba plug-in, PTGS2, EGF, and SOX10 in Cluster5 were chosen as hub genes. 3. qRT-PCR and immunofluorescent staining revealed that compared to normal skin tissue, the expression of SOX10 was significantly up-regulated, and the expression of PTGS2 and EGF was significantly down-regulated in pathological skin tissue(P < 0.001).

CONCLUSIONS

In GCMN, keratinocytes and extracellular matrix may directly and indirectly affect melanocyte activity. PTGS2, EGF, and SOX10 are important genes and significantly differentially expressed in pathological and normal skin tissues. These findings may serve as a springboard for future research.