Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin

Dai Shimizu; Kenzui Taniue; Yusuke Matsui; Hiroshi Haeno; Hiromitsu Araki; Fumihito Miura; Mitsuko Fukunaga; Kenji Shiraishi; Yuji Miyamoto; Seiichi Tsukamoto; Aya Komine; Yuta Kobayashi; Akihiro Kitagawa; Yukihiro Yoshikawa; Kuniaki Sato; Tomoko Saito; Shuhei Ito; Takaaki Masuda; Atsushi Niida; Makoto Suzuki; Hideo Baba; Takashi Ito; Nobuyoshi Akimitsu; Yasuhiro Kodera; Koshi Mimori

doi:10.1038/s41417-021-00401-w

Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin

Dai Shimizu, Kenzui Taniue, Yusuke Matsui, Hiroshi Haeno, Hiromitsu Araki, Fumihito Miura, Mitsuko Fukunaga, Kenji Shiraishi, Yuji Miyamoto, Seiichi Tsukamoto, Aya Komine, Yuta Kobayashi, Akihiro Kitagawa, Yukihiro Yoshikawa, Kuniaki Sato, Tomoko Saito, Shuhei Ito, Takaaki Masuda, Atsushi Niida, Makoto SuzukiHideo Baba, Takashi Ito, Nobuyoshi Akimitsu, Yasuhiro Kodera, Koshi Mimori

Research output: Contribution to journal › Article › peer-review

6 Citations (Scopus)

Abstract

The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

Original language	English
Pages (from-to)	428-436
Number of pages	9
Journal	Cancer Gene Therapy
Volume	29
Issue number	5
DOIs	https://doi.org/10.1038/s41417-021-00401-w
Publication status	Published - May 2022

All Science Journal Classification (ASJC) codes

Molecular Medicine
Molecular Biology
Cancer Research

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1038/s41417-021-00401-w

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Shimizu, D., Taniue, K., Matsui, Y., Haeno, H., Araki, H., Miura, F., Fukunaga, M., Shiraishi, K., Miyamoto, Y., Tsukamoto, S., Komine, A., Kobayashi, Y., Kitagawa, A., Yoshikawa, Y., Sato, K., Saito, T., Ito, S., Masuda, T., Niida, A., ... Mimori, K. (2022). Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin. Cancer Gene Therapy, 29(5), 428-436. https://doi.org/10.1038/s41417-021-00401-w

Shimizu, D, Taniue, K, Matsui, Y, Haeno, H, Araki, H , Miura, F, Fukunaga, M, Shiraishi, K, Miyamoto, Y, Tsukamoto, S, Komine, A, Kobayashi, Y, Kitagawa, A, Yoshikawa, Y, Sato, K, Saito, T, Ito, S, Masuda, T, Niida, A, Suzuki, M, Baba, H, Ito, T, Akimitsu, N, Kodera, Y & Mimori, K 2022, 'Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin', Cancer Gene Therapy, vol. 29, no. 5, pp. 428-436. https://doi.org/10.1038/s41417-021-00401-w

@article{3621ffd724624fee880d7aa7455d1a6c,

title = "Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin",

abstract = "The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.",

author = "Dai Shimizu and Kenzui Taniue and Yusuke Matsui and Hiroshi Haeno and Hiromitsu Araki and Fumihito Miura and Mitsuko Fukunaga and Kenji Shiraishi and Yuji Miyamoto and Seiichi Tsukamoto and Aya Komine and Yuta Kobayashi and Akihiro Kitagawa and Yukihiro Yoshikawa and Kuniaki Sato and Tomoko Saito and Shuhei Ito and Takaaki Masuda and Atsushi Niida and Makoto Suzuki and Hideo Baba and Takashi Ito and Nobuyoshi Akimitsu and Yasuhiro Kodera and Koshi Mimori",

note = "Funding Information: D.S. was supported by JSPS KAKENHI Grant Number 19K16868. K.M. received funding from the Platform Project for Supporting Drug Discovery, Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP20am0101103 (support number 0958), P-CREATE from AMED (20cm0106475h0001(e-Rad ID: 20317791)), JSPS KAKENHI (20H05039, 19H03715, 19K09220), Grant-in-Aid for Scientific Research on Innovative Areas (15H05912), Priority Issue on Post-K computer (hp170227, hp160219), the Project for Cancer Research and Therapeutic Evolution (19cm0106504h0004), Research Grant of the Princess Takamatsu Cancer Research, and SRL, Miraka Research Institute and Takeda Science Foundation. K.T. was supported by the Kobayashi Foundation, Takeda Science Foundation and JSPS KAKENHI Grant Number (21H02758 and 21K19402). Publisher Copyright: {\textcopyright} 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.",

year = "2022",

month = may,

doi = "10.1038/s41417-021-00401-w",

language = "English",

volume = "29",

pages = "428--436",

journal = "Cancer Gene Therapy",

issn = "0929-1903",

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TY - JOUR

T1 - Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin

AU - Shimizu, Dai

AU - Taniue, Kenzui

AU - Matsui, Yusuke

AU - Haeno, Hiroshi

AU - Araki, Hiromitsu

AU - Miura, Fumihito

AU - Fukunaga, Mitsuko

AU - Shiraishi, Kenji

AU - Miyamoto, Yuji

AU - Tsukamoto, Seiichi

AU - Komine, Aya

AU - Kobayashi, Yuta

AU - Kitagawa, Akihiro

AU - Yoshikawa, Yukihiro

AU - Sato, Kuniaki

AU - Saito, Tomoko

AU - Ito, Shuhei

AU - Masuda, Takaaki

AU - Niida, Atsushi

AU - Suzuki, Makoto

AU - Baba, Hideo

AU - Ito, Takashi

AU - Akimitsu, Nobuyoshi

AU - Kodera, Yasuhiro

AU - Mimori, Koshi

N1 - Funding Information: D.S. was supported by JSPS KAKENHI Grant Number 19K16868. K.M. received funding from the Platform Project for Supporting Drug Discovery, Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED under Grant Number JP20am0101103 (support number 0958), P-CREATE from AMED (20cm0106475h0001(e-Rad ID: 20317791)), JSPS KAKENHI (20H05039, 19H03715, 19K09220), Grant-in-Aid for Scientific Research on Innovative Areas (15H05912), Priority Issue on Post-K computer (hp170227, hp160219), the Project for Cancer Research and Therapeutic Evolution (19cm0106504h0004), Research Grant of the Princess Takamatsu Cancer Research, and SRL, Miraka Research Institute and Takeda Science Foundation. K.T. was supported by the Kobayashi Foundation, Takeda Science Foundation and JSPS KAKENHI Grant Number (21H02758 and 21K19402). Publisher Copyright: © 2021, The Author(s), under exclusive licence to Springer Nature America, Inc.

PY - 2022/5

Y1 - 2022/5

N2 - The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

AB - The accurate and early diagnosis and classification of cancer origin from either tissue or liquid biopsy is crucial for selecting the appropriate treatment and reducing cancer-related mortality. Here, we established the CAncer Cell-of-Origin (CACO) methylation panel using the methylation data of the 28 types of cancer in The Cancer Genome Atlas (7950 patients and 707 normal controls) as well as healthy whole blood samples (95 subjects). We showed that the CACO methylation panel had high diagnostic potential with high sensitivity and specificity in the discovery (maximum AUC = 0.998) and validation (maximum AUC = 1.000) cohorts. Moreover, we confirmed that the CACO methylation panel could identify the cancer cell type of origin using the methylation profile from liquid as well as tissue biopsy, including primary, metastatic, and multiregional cancer samples and cancer of unknown primary, independent of the methylation analysis platform and specimen preparation method. Together, the CACO methylation panel can be a powerful tool for the classification and diagnosis of cancer.

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JO - Cancer Gene Therapy

JF - Cancer Gene Therapy

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ER -

Pan-cancer methylome analysis for cancer diagnosis and classification of cancer cell of origin

Abstract

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