Unbiased detection of driver mutations in extramammary paget disease

Yoshihiro Ishida, Nobuyuki Kakiuchi, Kenichi Yoshida, Yoshikage Inoue, Hiroyuki Irie, Tatsuki R. Kataoka, Masahiro Hirata, Takeru Funakoshi, Shigeto Matsushita, Hiroo Hata, Hiroshi Uchi, Yuki Yamamoto, Yasuhiro Fujisawa, Taku Fujimura, Ryunosuke Saiki, Kengo Takeuchi, Yuichi Shiraishi, Kenichi Chiba, Hiroko Tanaka, Atsushi OtsukaSatoru Miyano, Kenji Kabashima, Seishi Ogawa

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)

Abstract

Purpose: Extramammary Paget disease (EMPD) is an uncommon skin malignancy whose genetic alterations are poorly characterized. Previous reports identified mutations in chromatin remodeling genes and PIK3CA. In order to unambiguously determine driver mutations in EMPD, we analyzed 87 EMPD samples using exome sequencing in combination with targeted sequencing. Experimental Design: First, we analyzed 37 EMPD samples that were surgically resected using whole-exome sequencing. Based on several in silico analysis, we built a custom capture panel of putative driver genes and analyzed 50 additional formalin-fixed, paraffin-embedded samples using target sequencing. ERBB2 expression was evaluated by HER2 immunohisotochemistry. Select samples were further analyzed by fluorescence in situ hybridization. Results: A median of 92 mutations/sample was identified in exome analysis. A union of driver detection algorithms identified ERBB2, ERBB3, KMT2C, TP53, PIK3CA, NUP93, AFDN, and CUX1 as likely driver mutations. Copy-number alteration analysis showed regions spanning CDKN2A as recurrently deleted, and ERBB2 as recurrently amplified. ERBB2, ERBB3, and FGFR1 amplification/ mutation showed tendency toward mutual exclusivity. Copy-number alteration load was associated with likelihood to recur. Mutational signatures were dominated by aging and APOBEC activation and lacked evidence of ultraviolet radiation. HER2 IHC/fluorescence in situ analysis validated ERBB2 amplification but was underpowered to detect mutations. Tumor heterogeneity in terms of ERBB2 amplification status was observed in some cases. Conclusions: Our comprehensive, unbiased analysis shows EMPD is characterized by alterations involving the PI3K-AKT pathway. EMPD is distinct from other skin cancers in both molecular pathways altered and etiology behind mutagenesis.

Original languageEnglish
Pages (from-to)1756-1765
Number of pages10
JournalClinical Cancer Research
Volume27
Issue number6
DOIs
Publication statusPublished - 2021 Mar

ASJC Scopus subject areas

  • Oncology
  • Cancer Research

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