Transcriptomic analysis of giant congenital melanocytic nevi across different anatomic sites

Abstract Background: Giant congenital melanocytic nevus (GCMN) is a skin disorder characterized by extensive abnormal proliferation and migration of melanocytes, which has the potential to be malignantly transformed into melanoma. Most studies have focused on revealing somatic mutation in GCMN. However, the specific alterations in gene expression across different anatomic sites of GCMN remain ambiguous. Methods: A total of 18 GCMNs including eight from the trunk, six from the head, and four from the extremities, as well as eight normal skin tissues were collected for transcriptome sequencing. Differential expression gene (DEG) analysis and a series of bioinformatics analyses were employed to explore the distinct expression pattern and involved pathways among different anatomic sites of GCMN. Results: A total of 258 (head), 1,472 (trunk), and 185 (extremities) site-specific DEGs were identified respectively, with a total of 368 up-regulated and 312 down-regulated DEGs in three tissues. Among them, ALB, CNTN2, GLI1, POU5F1 and CACNA1Dwere identified as core genes in head, as well as ERBB2, PPARA, VEGFA, FOSand IL1B in trunk, PRF1, STAT1, CXCR4, CD8A and CXCL8 in extremities, and SOX10, TYR, GRIN1, GRIA1 and PLP1 in all three tissues. Conclusion: This study mined the specific and common DEGs in the head, trunk, and extremities of GCMN and systematically explored the possible mechanism of action of these genes based on transcriptome sequencing data, which could provide insights for the research of GCMN and afford new therapeutic targets for GCMN patients.