Genomic Studies Of Keratoacanthoma And Cutaneous Squamous Cell Carcinoma

Cutaneous Squamous Cell Carcinoma(cSCC)is the second most common malignant tumor in skin cancer,with an annual increase of 500,000 patients worldwide.If cSCC is not treated,it will metastasis and kill the patient.Keratoacanthoma(KA)is a benign tumor that will regress spontaneously without treatment.Although the prognosis of these two tumors is very different,KA and cSCC are highly similar in clinical characteristics and histopathology,and are difficult to distinguish,so misdiagnosis often occurs clinically.We urgently need biomarkers that can accurately distinguish these two tumors to aid diagnosis.In this study,a total of 31 KA,18 cSCC tumor tissues and some corresponding peripheral blood control samples were collected.DNA was extracted for whole-genome sequencing to obtain mutation and copy number information.After the mutation information is filtered by GATK’s hard-filter standard,ANNOVAR was used for gene annotation and 6 database filtering annotation including 1000 Genome,Ex AC and COSMIC to obtain somatic mutations.Next,the identification of driver genes and pathway enrichment analysis were performed on the obtained somatic mutations,and the whole-genome and whole-exon sequencing data analysis of all cSCC published in Pub Med were integrated to find the similarities and differences between KA and cSCC in the genome.After detecting copy number variations using ichor CNA and ascat NGS,run GISTIC to obtain gene fragments with significant number variation.TP53 and NOTCH1 are the two genes with the highest mutation frequency in most cancers.In KA and cSCC,these two genes also have a high mutation frequency.In KA,the mutation frequencies of TP53 and NOTCH1 in KA at different stages are different.The mutation frequency of these two genes in KA in the regress period is lower(1/13;3/13),while the mutation frequency of the KA in the proliferation period and cSCC is higher(TP53:11/18,6/18;NOTCH1:9/18,10/18).For the mutations in TP53,we also further determined that these mutations caused damage changes in protein structure through protein analysis software Schrodinger.In addition,KA define driver genes DYNC1H1,DPYSL2,DUSP5/16,OSBP2 and cSCC define driver genes CDKN2 A,CDH10,ADGRL2,MMP24,EPHB6,etc.We selected 10 sites for Sanger sequencing verification and obtained an 80% verification rate.The amplification of CDH18 and CYFIP1 fragments in copy number variations analysis provides a certain explanation for the reason that KA is not to metastasize.In addition,we analyzed the virus information in the KA and cSCC sequencing data.In KA and cSCC,in addition to human papilloma virus,we have also discovered sequences of other tumor-associated viruses,such as human herpes virus.We speculate that the virus may play a role in the development and progression of two types of tumors.This study provides some biomarkers for the diagnosis of KA and cSCC,which can clinically assist in the differential diagnosis of these two tumors.