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

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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.

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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.

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Authors and Affiliations

  1. Division of Epigenomics, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo, 104-0045, Japan

    Hiroki Ishihara, Satoshi Yamashita & Toshikazu Ushijima

  2. Department of Urology, Tokyo Women’s Medical University, Tokyo, Japan

    Hiroki Ishihara & Kazunari Tanabe

  3. Division of Pathology, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan

    Satoshi Fujii

  4. Department of Breast and Medical Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan

    Hirofumi Mukai

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  1. Hiroki Ishihara
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Correspondence to Toshikazu Ushijima.

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Ishihara, H., Yamashita, S., Fujii, S. et al. DNA methylation marker to estimate the breast cancer cell fraction in DNA samples. Med Oncol 35, 147 (2018). https://doi.org/10.1007/s12032-018-1207-3

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  • DOI: https://doi.org/10.1007/s12032-018-1207-3

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