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Medical Oncology

, 35:147 | Cite as

DNA methylation marker to estimate the breast cancer cell fraction in DNA samples

  • Hiroki Ishihara
  • Satoshi Yamashita
  • Satoshi Fujii
  • Kazunari Tanabe
  • Hirofumi Mukai
  • Toshikazu Ushijima
Original Paper
  • 21 Downloads

Abstract

Estimation of the cancer cell fraction in breast cancer tissue is important for exclusion of samples unsuitable for multigene prognostic assays and a variety of molecular analyses for research. Here, we aimed to establish a breast cancer cell fraction marker based on DNA methylation. First, we screened genes unmethylated in non-cancerous mammary tissues and methylated in breast cancer tissues using microarray data from the TCGA database, and isolated 12 genes. Among them, four genes were selected as candidate marker genes without a high incidence of copy number alterations and with broad coverage across patients. Bisulfite pyrosequencing analysis of additional breast cancer biopsy specimens purified by laser capture microdissection (LCM) excluded two genes, and a combination of SIM1 and CCDC181 was finally selected as a fraction marker. In further additional specimens without LCM purification, the fraction marker was substantially methylated (≥ 20%) with high incidence (50/51). The cancer cell fraction estimated by the fraction marker was significantly correlated with that estimated by microscopic examination (p < 0.0001). Performance of a previously established marker, HSD17B4 methylation, which predicts therapeutic response of HER2-positive breast cancer to trastuzumab, was improved after the correction of cancer cell fraction by the fraction marker. In conclusion, we successfully established a breast cancer cell fraction marker based on DNA methylation.

Keywords

DNA methylation Cancer cell fraction Breast cancer Trastuzumab HER2 Cancer cell content HSD17B4 

Notes

Acknowledgements

The authors are grateful to Drs. K. Ichimura, Y. Matsushita, and M. Kitahara of Division of Brain Tumor Translational Research in the National Cancer Center Research Institute for their technical assistance with the usage of the PSQ 96 Pyrosequencing System.

Funding

This research was supported by the Program for Promoting Platform of Genomics based Drug Discovery (Grant Number 18kk0305004h0003) from the Japan Agency for Medical Research and Development, AMED.

Compliance with ethical standards

Conflict of interest

The authors state no conflicts of interest regarding this work.

Ethical approval

Written informed consent was obtained from all participants.

Supplementary material

12032_2018_1207_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 14 KB)
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Supplementary material 2 (TIFF 447 KB)
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Supplementary material 3 (TIFF 760 KB)
12032_2018_1207_MOESM4_ESM.xlsx (28 kb)
Supplementary material 4 (XLSX 28 KB)

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Division of EpigenomicsNational Cancer Center Research InstituteTokyoJapan
  2. 2.Department of UrologyTokyo Women’s Medical UniversityTokyoJapan
  3. 3.Division of Pathology, Exploratory Oncology Research and Clinical Trial CenterNational Cancer CenterKashiwaJapan
  4. 4.Department of Breast and Medical OncologyNational Cancer Center Hospital EastKashiwaJapan

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