DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations

doi:10.1016/j.ebiom.2021.103446

	DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations
	Yang, Mei 1; Fan, Yanhui 2,3; Wu, Zhi-Yong 4; Gu, Jin 13; Feng, Zhendong 2; Zhang, Qiangzu 2; Han, Shunhua 2,6; Zhang, Zhonghai 7; Li, Xu 7; Hsueh, Yi-Ching 2; Ni, Yanxiang 14,15; Li, Xiaoling 1; Li, Jieqing 1; Hu, Meixia 1; Li, Weiping 1; Gao, Hongfei 1; Yang, Ciqiu 1; Zhang, Chunming 2,7; Zhang, Liulu 1; Zhu, Teng 1; Cheng, Minyi 1; Ji, Fei 1; Xu, Juntao 2; Cui, Hening 2; Tan, Guangming 7; Zhang, Michael Q.8,9,10,11; Liang, Changhong 12; Liu, Zaiyi 12; Song, You-Qiang 5; Niu, Gang 2,16; Wang, Kun 1
	2021-07-01
发表期刊	EBIOMEDICINE
ISSN	2352-3964
卷号	69 页码:11
摘要	Background: Breast cancers can be divided into HER2-negative and HER2-positive subtypes according to different status of HER2 gene. Despite extensive studies connecting germline mutations with possible risk of HER2-negative breast cancer, the main category of breast cancer, it remains challenging to obtain accurate risk assessment and to understand the potential underlying mechanisms. Methods: We developed a novel framework named Damage Assessment of Genomic Mutations (DAGM), which projects rare codingmutations and gene expressions into Activity Profiles of Signalling Pathways (APSPs). Findings: We characterized and validated DAGM framework at multiple levels. Based on an input of germline rare coding mutations, we obtained the corresponding APSP spectrum to calculate the APSP risk score, which was capable of distinguish HER2-negative from HER2-positive cases. These findings were validated using breast cancer data from TCGA (AUC = 0.7). DAGM revealed that HER2 signalling pathway was up-regulated in germline of HER2-negative patients, and those with high APSP risk scores had exhibited immune suppression. These findings were validated using RNA sequencing, phosphoproteome analysis, and CyTOF. Moreover, using germline mutations, DAGM could evaluate the risk for HER2-negative breast cancer, not only in women carrying BRCA1/2 mutations, but also in those without known disease-associated mutations. Interpretation: The DAGM can facilitate the screening of subjects at high risk of HER2-negative breast cancer for primary prevention. This study also provides new insights into the potential mechanisms of developing HER2-negative breast cancer. The DAGM has the potential to be applied in the prevention, diagnosis, and treatment of HER2-negative breast cancer. (C) 2021 The Authors. Published by Elsevier B.V.
关键词	HER2-negative breast cancer Germline rare coding mutations Damage assessment of genomic mutations (DAGM) Risk assessment Activity profiles of signalling pathways (APSP) HER2 signalling pathway Immune suppression
DOI	10.1016/j.ebiom.2021.103446
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFC0910406] ; National Key Research and Development Program of China[2018AAA0103302] ; National Natural Science Foundation of China[81202076] ; National Natural Science Foundation of China[82072939] ; National Natural Science Foundation of China[81871513] ; Guangzhou Science and Technology Program key projects[2014J2200007] ; Guangzhou Science and Technology Program key projects[202002030236] ; National Key R&D Program of China[2017YFC1309100] ; Shenzhen Science and Technology Planning Project[JCYJ20170817095211560] ; Natural Science Foundation of Guangdong Province[2017A030313882] ; Natural Science Foundation of Guangdong Province[S2013010012048] ; Natural Science Foundation of Guangdong Province[KF2020009] ; RGC General Research Fund[17114519]
WOS研究方向	General & Internal Medicine ; Research & Experimental Medicine
WOS类目	Medicine, General & Internal ; Medicine, Research & Experimental
WOS记录号	WOS:000684979000017
出版者	ELSEVIER
引用统计	被引频次：2[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/17262
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Niu, Gang; Wang, Kun
作者单位	1.Guangdong Acad Med Sci, Guangdong Prov Peoples Hosp, Canc Ctr, Dept Breast Canc, Guangzhou, Guangdong, Peoples R China 2.Phil Rivers Technol, Beijing 100095, Peoples R China 3.Phil Rivers Technol, Shenzhen, Peoples R China 4.Shantou Cent Hosp, Diag & Treatment Ctr Breast Dis, Shantou, Guangdong, Peoples R China 5.Univ Hong Kong, Sch Biomed Sci, Hong Kong, Peoples R China 6.Univ Georgia, Inst Bioinformat, Athens, GA 30602 USA 7.Chinese Acad Sci, Inst Comp Technol, State Key Lab Comp Architecture, Beijing, Peoples R China 8.Tsinghua Univ, MOE Key Lab Bioinformat, TNLIST, Beijing, Peoples R China 9.Tsinghua Univ, Bioinformat Div, TNLIST, Beijing, Peoples R China 10.Tsinghua Univ, Ctr Synthet & Syst Biol, TNLIST, Beijing, Peoples R China 11.Tsinghua Univ, Sch Med, Beijing, Peoples R China 12.Guangdong Acad Med Sci, Guangdong Prov Peoples Hosp, Dept Radiol, Guangzhou, Guangdong, Peoples R China 13.Tsinghua Univ, Dept Automat, BNRIST Bioinformat Div, Beijing, Peoples R China 14.Shenzhen Univ, Nanophoton Res Ctr, Shenzhen Key Lab Microscale Opt Informat Technol, Shenzhen, Peoples R China 15.Shenzhen Univ, Inst Microscale Optoelect, Shenzhen, Peoples R China 16.Chinese Acad Sci, Western Inst Adv Technol, Chongqing, Peoples R China
推荐引用方式 GB/T 7714	Yang, Mei,Fan, Yanhui,Wu, Zhi-Yong,et al. DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations[J]. EBIOMEDICINE,2021,69:11.
APA	Yang, Mei.,Fan, Yanhui.,Wu, Zhi-Yong.,Gu, Jin.,Feng, Zhendong.,...&Wang, Kun.(2021).DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations.EBIOMEDICINE,69,11.
MLA	Yang, Mei,et al."DAGM: A novel modelling framework to assess the risk of HER2-negative breast cancer based on germline rare coding mutations".EBIOMEDICINE 69(2021):11.