Genome-wide analysis of Chinese keloid patients identifies novel causative genes

BACKGROUND: Keloids are benign skin tumors that appears on skin lesions in humans. Keloids are characterized by invasive tumor growth and are highly prone to recurrence after treatment. The incidence of keloids is ethnically specific; however, the molecular mechanism underlying the incidence of keloids in the Chinese population remains unclear. To date, no reports appear to have been published on the molecular characteristics underlying keloids in the Chinese population from the perspective of whole-genome sequencing. METHODS: In this study, we collected keloid samples from 9 keloid patients underwent surgery in the Department of Dermatology, The First Affiliated Hospital of Soochow University, paired them to normal skin tissues, and performed whole-exome sequencing. The average depth of the samples was 1,200×, and the average exome coverage was 98.90%. RESULTS: The bioinformatics analysis identified 3,125 single nucleotide variants (SNVs) and 299 insertions/deletions (InDels). The major mutation characteristics of the SNVs were C > A and C > T. The non-synonymous SNV types included stopgain, and stoploss. The non-synonym InDels included frameshift deletion, frameshift insertion, and stopgain. We also found a total of 67,873 copy number variations (CNVs) in the samples. The genes with the highest mutation frequency included mucin 4 (MUC4) (55.6%), tubulin tyrosine ligase like 12 (TTLL12) (33.3%), calcium voltage-gated channel subunit alpha1 (CACNA1C) (33.3%), and mucin 12 (MUC12) (33.3%). The average tumor mutation burden (TMB) was 289 mutations/million base pair (MB). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that the mutated genes were mainly concentrated in micro ribonucleic acids in cancer and the calcium signaling pathway. The Gene Ontology (GO) analysis showed that mutant genes were mainly concentrated in binding cells, cell parts, and cellular processes. CONCLUSIONS: Whole-exome sequencing was performed in the Chinese keloid patients and some potential candidate genes related to keloid occurrence and development were identified, which may provide new molecular targets for the clinical diagnosis and treatment of keloid patients.