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Hum Pathol. 2018 Oct;80:1-10. doi: 10.1016/j.humpath.2018.03.008. Epub 2018 Mar 17.

Whole-exome sequencing identified mutational profiles of squamous cell carcinomas of anus.

Author information

1
Department of Microbiology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
2
Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
3
Department of Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
4
Department of Hospital Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
5
Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea.
6
Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Department of Pathology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea. Electronic address: suhulee@catholic.ac.kr.
7
Department of Microbiology, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Cancer Evolution Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea; Precision Medicine Research Center, The Catholic University of Korea, Seoul, 06591, Republic of Korea. Electronic address: yejun@catholic.ac.kr.

Abstract

Anal squamous cell carcinoma (ASCC), either with human papillomavirus (+) or (-), is a neoplastic disease with frequent recurrence and metastasis. To characterize ASCC genomes, we attempted to disclose novel alterations of ASCC genomes and other genetic features including mutation signatures. We performed whole-exome sequencing and copy number alteration (CNA) profiling for 8 ASCC samples from 6 patients (2 cases with primary and recurrent/metastatic tumors). We found known ASCC mutations (TP53, CDKN2A, and PIK3CA) and CNAs (gains on 3q and 19q and losses on 11q and 13q). In addition, we discovered novel mutations in HRAS and ARID1A and CNAs (gain on 8q and losses 5q, 9p, 10q, and 19p) that had not been reported in ASCCs. We identified 4 signature patterns of the mutations (signatures 1 and 2 with deamination of 5-methyl-cytosin, signature 3 with APOBEC, and signature 4 with mismatch repair) in the ASCCs. Although signatures 1 to 3 have been detected in other SCCs, signature 4 was first identified in ASCCs. In addition, we first found that ASCCs harbored chromothripsis, copy-neutral losses of heterozygosity, and focal amplification of KLF5 super-enhancer. Analyses of primary and recurrent/metastatic pair genomes revealed that driver events in development and progression of ASCC might not be uniform. Our data indicate that ASCCs may have similar mutation and CNA profiles to other SCCs, but that there are unique genomic features of ASCCs as well. Our data may provide useful information for ASCC pathogenesis and for developing clinical strategies for ASCC.

KEYWORDS:

Anus; Cancer; Copy number alteration; Mutation signature; Squamous cell carcinoma; Whole-exome sequencing

PMID:
29555573
DOI:
10.1016/j.humpath.2018.03.008
[Indexed for MEDLINE]

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