IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

Shuyu Liang; Sicheng Xu; Shichong Zhou; Cai Chang; Zhiming Shao; Yuanyuan Wang; Sheng Chen; Yunxia Huang; Yi Guo

doi:10.1016/j.jgg.2023.09.010

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

doi: 10.1016/j.jgg.2023.09.010

a Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China;
b The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention(MICCAI) of Shanghai, Shanghai 200032, China;
c Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200433, China;
d Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China;
e Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China

基金项目:

This work was supported by the National Natural Science Foundation of China (Grant 81830058,82071945, 91959207, 92159301, and 82302212) and the Science and Technology Commission of Shanghai Municipality (Grant 22ZR1404800)

详细信息

通讯作者:
Sheng Chen,0456177@fudan.edu.cn

Yunxia Huang,applewinwin@sina.com

Yi Guo,guoyi@fudan.edu.cn

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出版历程
- 收稿日期: 2023-09-04
- 修回日期: 2023-09-18
- 网络出版日期: 2023-09-30

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

Shuyu Liang^a,b,
Sicheng Xu^c,
Shichong Zhou^d,
Cai Chang^d,
Zhiming Shao^e,
Yuanyuan Wang^a,b,
Sheng Chen^{e
, ,},
Yunxia Huang^{d
, ,},
Yi Guo^{a,b
, ,}

a Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China;
b The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention(MICCAI) of Shanghai, Shanghai 200032, China;
c Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200433, China;
d Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China;
e Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China

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摘要

摘要:
The investigation of correlations between radiomic and genomic profiling in breast cancer (BC) molecular subtypes is crucial for understanding disease mechanisms and providing personalized treatment. We present a well-designed radiogenomic framework—image-gene-gene set (IMAGGS), which detects multi-way associations in BC subtypes by integrating radiomic and genomic features.Our dataset consists of 721 patients, each of whom has 12 ultrasound (US) images captured from different angles and gene mutation data. To better characterize tumor traits, 12 multi-angle US images are fused using two distinct strategies. Then, we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm, deviating from the prevalent one-to-one relationship pattern observed in previous studies. Key radiomic and genomic features are screened using these associations. In addition, gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC subtypes. We further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and diseases. Taken together, IMAGGS provides a comprehensive characterization for diseases by associating imaging, genes, and gene sets, paving the way for biological interpretation of radiomics and development of targeted therapy.
- IMAGGS /
- radiogenomic framework /
- “image-gene-gene set” associations /
- molecular subtypes /
- breast cancer
Abstract:
The investigation of correlations between radiomic and genomic profiling in breast cancer (BC) molecular subtypes is crucial for understanding disease mechanisms and providing personalized treatment. We present a well-designed radiogenomic framework—image-gene-gene set (IMAGGS), which detects multi-way associations in BC subtypes by integrating radiomic and genomic features.Our dataset consists of 721 patients, each of whom has 12 ultrasound (US) images captured from different angles and gene mutation data. To better characterize tumor traits, 12 multi-angle US images are fused using two distinct strategies. Then, we analyze complex many-to-many associations between phenotypic and genotypic features using a machine learning algorithm, deviating from the prevalent one-to-one relationship pattern observed in previous studies. Key radiomic and genomic features are screened using these associations. In addition, gene set enrichment analysis is performed to investigate the joint effects of gene sets and delve deeper into the biological functions of BC subtypes. We further validate the feasibility of IMAGGS in a glioblastoma multiforme dataset to demonstrate the scalability of IMAGGS across different modalities and diseases. Taken together, IMAGGS provides a comprehensive characterization for diseases by associating imaging, genes, and gene sets, paving the way for biological interpretation of radiomics and development of targeted therapy.
- IMAGGS /
- radiogenomic framework /
- “image-gene-gene set” associations /
- molecular subtypes /
- breast cancer

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IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

doi: 10.1016/j.jgg.2023.09.010

通讯作者:
Sheng Chen,0456177@fudan.edu.cn

Yunxia Huang,applewinwin@sina.com

Yi Guo,guoyi@fudan.edu.cn

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IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

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留言板

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

doi: 10.1016/j.jgg.2023.09.010

通讯作者: Sheng Chen,0456177@fudan.edu.cn Yunxia Huang,applewinwin@sina.com Yi Guo,guoyi@fudan.edu.cn

计量

出版历程

IMAGGS: a radiogenomic framework for identifying multi-way associations in breast cancer subtypes

计量

出版历程

目录

通讯作者:
Sheng Chen,0456177@fudan.edu.cn

Yunxia Huang,applewinwin@sina.com

Yi Guo,guoyi@fudan.edu.cn