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

J Genet Genomics. 2024 Apr;51(4):443-453. doi: 10.1016/j.jgg.2023.09.010. Epub 2023 Sep 30.

Authors

Shuyu Liang¹, Sicheng Xu², Shichong Zhou³, Cai Chang³, Zhiming Shao⁴, Yuanyuan Wang¹, Sheng Chen⁵, Yunxia Huang⁶, Yi Guo⁷

Affiliations

¹ Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China; The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai, Shanghai 200032, China.
² Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai 200433, China.
³ Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
⁴ Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China.
⁵ Department of Breast Surgery, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China. Electronic address: 0456177@fudan.edu.cn.
⁶ Department of Ultrasound, Fudan University Shanghai Cancer Center, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China. Electronic address: applewinwin@sina.com.
⁷ Department of Electronic Engineering, School of Information Science and Technology, Fudan University, Shanghai 200433, China; The Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention (MICCAI) of Shanghai, Shanghai 200032, China. Electronic address: guoyi@fudan.edu.cn.

PMID: 37783335
DOI: 10.1016/j.jgg.2023.09.010

Abstract

Investigating 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.

Keywords: Breast cancer; IMAGGS; Molecular subtypes; Radiogenomic framework; “Image–gene–gene set” associations.

MeSH terms

Breast Neoplasms* / diagnostic imaging
Breast Neoplasms* / genetics
Female
Genomics / methods
Glioblastoma* / genetics
Humans
Magnetic Resonance Imaging / methods
Phenotype