Genetic alterations in seborrheic keratoses

Abstract

Seborrheic keratoses are common benign epidermal lesions that are associated with increased age and sun-exposure. Those lesions despite harboring multiple somatic alterations in contrast to malignant tumors appear to be genetically stable. In order to investigate and characterize the presence of recurrent mutations, we performed exome sequencing on DNA from one seborrheic keratosis lesion and corresponding blood cells from the same patients with follow up investigation of alterations identified by exome sequencing in 24 additional lesions from as many patients. In addition we investigated alterations in all lesions at specific genes loci that included FGFR3, PIK3CA, HRAS, BRAF, CDKN2A and TERT and DHPH3 promoters. The exome sequencing data indicated three mutations per Mb of the targeted sequence. The mutational pattern depicted typical UV signature with majority of alterations being C>T and CC>TT base changes at dipyrimidinic sites. The FGFR3 mutations were the most frequent, detected in 12 of 25 (48%) lesions, followed by the PIK3CA (32%), TERT promoter (24%) and DPH3 promoter mutations (24%). TERT promoter mutations associated with increased age and were present mainly in the lesions excised from head and neck. Three lesions also carried alterations in CDKN2A. FGFR3, TERT and DPH3 expression did not correlate with mutations in the respective genes and promoters; however, increased FGFR3 transcript levels were associated with increased FOXN1 levels, a suggested positive feedback loop that stalls malignant progression. Thus, in this study we report overall mutation rate through exome sequencing and show the most frequent mutations seborrheic keratosis.

Keywords: exome-sequencing; seborrheic keratosis; skin cancer; somatic mutations.

Figure 1

(A) Mutational signature from exome sequencing data dominated by characteristic UV-signature mutations at dipyrimidinic sites. (B) Proportion ofnon-synonymous versus synonymous mutations from exome exome sequencing (C) Integrative Genomics Viewer screenshots of a somatic trinucleotide mutation in AQP11 (D) Integrative Genomics Viewer screenshots of a 2 bp insertion in WDR44 that results a stop codon after 10 (KMCLKLKQKY) residues.

Figure 2. Relative gene expression in seborrheic keratosis measured by quantitative real-time PCR

(A) Differences in the levels of DPH3 expression with and without mutations in the DPH3 promoter. (B) Measurement of FGFR3 expression based on presence or absence of activating FGFR3 mutations. Comparison of FOXN1 expression according to (C) presence of FGFR3 mutations melanoma and (D) expression levels of FGFR3 (according to median expression).