Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis

Koji Tsumura, Eri Arai, Ying Tian, Ayako Shibuya, Hiroshi Nishihara, Takuya Yotani, Yuriko Yamada, Yoriko Takahashi, Akiko Miyagi Maeshima, Hiroyuki Fujimoto, Tohru Nakagawa, Haruki Kume, Yukio Homma, Teruhiko Yoshida, Yae Kanai

Research output: Contribution to journalArticle

Abstract

The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.

Original languageEnglish
Pages (from-to)1308-1319
Number of pages12
JournalCarcinogenesis
Volume40
Issue number11
DOIs
Publication statusPublished - 2019 Nov 25

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Urothelium
DNA Methylation
Genome
Neoplasms
Carcinoma
Sensitivity and Specificity
ROC Curve
Learning
Urine
Mutation
Health
Genes

ASJC Scopus subject areas

  • Cancer Research

Cite this

Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. / Tsumura, Koji; Arai, Eri; Tian, Ying; Shibuya, Ayako; Nishihara, Hiroshi; Yotani, Takuya; Yamada, Yuriko; Takahashi, Yoriko; Maeshima, Akiko Miyagi; Fujimoto, Hiroyuki; Nakagawa, Tohru; Kume, Haruki; Homma, Yukio; Yoshida, Teruhiko; Kanai, Yae.

In: Carcinogenesis, Vol. 40, No. 11, 25.11.2019, p. 1308-1319.

Research output: Contribution to journalArticle

Tsumura, K, Arai, E, Tian, Y, Shibuya, A, Nishihara, H, Yotani, T, Yamada, Y, Takahashi, Y, Maeshima, AM, Fujimoto, H, Nakagawa, T, Kume, H, Homma, Y, Yoshida, T & Kanai, Y 2019, 'Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis', Carcinogenesis, vol. 40, no. 11, pp. 1308-1319. https://doi.org/10.1093/carcin/bgz112
Tsumura, Koji ; Arai, Eri ; Tian, Ying ; Shibuya, Ayako ; Nishihara, Hiroshi ; Yotani, Takuya ; Yamada, Yuriko ; Takahashi, Yoriko ; Maeshima, Akiko Miyagi ; Fujimoto, Hiroyuki ; Nakagawa, Tohru ; Kume, Haruki ; Homma, Yukio ; Yoshida, Teruhiko ; Kanai, Yae. / Establishment of permutation for cancer risk estimation in the urothelium based on genome-wide DNA methylation analysis. In: Carcinogenesis. 2019 ; Vol. 40, No. 11. pp. 1308-1319.
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AU - Arai, Eri

AU - Tian, Ying

AU - Shibuya, Ayako

AU - Nishihara, Hiroshi

AU - Yotani, Takuya

AU - Yamada, Yuriko

AU - Takahashi, Yoriko

AU - Maeshima, Akiko Miyagi

AU - Fujimoto, Hiroyuki

AU - Nakagawa, Tohru

AU - Kume, Haruki

AU - Homma, Yukio

AU - Yoshida, Teruhiko

AU - Kanai, Yae

PY - 2019/11/25

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N2 - The aim of this study was to establish permutation for cancer risk estimation in the urothelium. Twenty-six samples of normal control urothelium obtained from patients without urothelial carcinomas (C), 47 samples of non-cancerous urothelium without noticeable morphological changes obtained from patients with urothelial carcinomas (N), and 46 samples of the corresponding cancerous tissue (T) in the learning cohort and 64 N samples in the validation cohort, i.e. 183 tissue samples in total, were analyzed. Genome-wide DNA methylation analysis was performed using the Infinium HumanMethylation 450K BeadChip, and DNA methylation levels were verified using pyrosequencing and MassARRAY. Amplicon sequencing was performed using the GeneRead DNAseq Targeted Panels V2. Although N samples rarely showed genetic mutations or copy number alterations, they showed DNA methylation alterations at 2502 CpG sites compared to C samples, and such alterations were inherited by or strengthened in T samples, indicating that DNA methylation alterations may participate in field cancerization in the urothelium. Receiver operating characteristic curve analysis confirmed the feasibility of cancer risk estimation to identify urothelium at the precancerous stage by DNA methylation quantification. Cancer risk estimation permutation was established using a combination of two marker CpG loci on the HOXC4, TENM3 and TLR1 genes (sensitivity and specificity 96-100%). Among them, the diagnostic impact of 10 patterns of permutation was successfully validated in the validation cohort (sensitivity and specificity 94-98%). These data suggest that cancer risk estimation using procedures such as urine tests during health checkups might become applicable for clinical use.

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