Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer

Yeye Fan; Chunyu Kao; Fu Yang; Fei Wang; Gengshen Yin; Yongjiu Wang; Yong He; Jiadong Ji; Liyuan Liu

doi:10.3389/fonc.2022.899900

Integrated Multi-Omics Analysis Model to Identify Biomarkers Associated With Prognosis of Breast Cancer

Front Oncol. 2022 Jun 10:12:899900. doi: 10.3389/fonc.2022.899900. eCollection 2022.

Authors

Yeye Fan¹, Chunyu Kao², Fu Yang², Fei Wang^{3

4}, Gengshen Yin^{3

4}, Yongjiu Wang^{3

4}, Yong He^{1

2}, Jiadong Ji², Liyuan Liu^{1

3

4}

Affiliations

¹ School of Mathematics, Shandong University, Jinan, China.
² Zhongtai Securities Institute for Financial Studies, Shandong University, Jinan, China.
³ Department of Breast Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China.
⁴ Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China.

Abstract

Background: With the rapid development and wide application of high-throughput sequencing technology, biomedical research has entered the era of large-scale omics data. We aim to identify genes associated with breast cancer prognosis by integrating multi-omics data.

Method: Gene-gene interactions were taken into account, and we applied two differential network methods JDINAC and LGCDG to identify differential genes. The patients were divided into case and control groups according to their survival time. The TCGA and METABRIC database were used as the training and validation set respectively.

Result: In the TCGA dataset, C11orf1, OLA1, RPL31, SPDL1 and IL33 were identified to be associated with prognosis of breast cancer. In the METABRIC database, ZNF273, ZBTB37, TRIM52, TSGA10, ZNF727, TRAF2, TSPAN17, USP28 and ZNF519 were identified as hub genes. In addition, RPL31, TMEM163 and ZNF273 were screened out in both datasets. GO enrichment analysis shows that most of these hub genes were involved in zinc ion binding.

Conclusion: In this study, a total of 15 hub genes associated with long-term survival of breast cancer were identified, which can promote understanding of the molecular mechanism of breast cancer and provide new insight into clinical research and treatment.

Keywords: breast cancer; differential network; multi-omics; prognosis; survival prediction.