Statistics and network-based approaches to identify molecular mechanisms that drive the progression of breast cancer

Md Shahin Alam; Md Matiur Rahaman; Adiba Sultana; Guanghui Wang; Md Nurul Haque Mollah

doi:10.1016/j.compbiomed.2022.105508

Statistics and network-based approaches to identify molecular mechanisms that drive the progression of breast cancer

Comput Biol Med. 2022 Jun:145:105508. doi: 10.1016/j.compbiomed.2022.105508. Epub 2022 Apr 14.

Authors

Md Shahin Alam¹, Md Matiur Rahaman², Adiba Sultana³, Guanghui Wang⁴, Md Nurul Haque Mollah⁵

Affiliations

¹ Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, China; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
² Department of Statistics, Faculty of Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, 8100, Bangladesh; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
³ Center for Systems Biology, Soochow University, Suzhou, 215006, China; Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh.
⁴ Laboratory of Molecular Neuropathology, Department of Pharmacology, Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, 199 Ren'ai Road, Suzhou, 215123, Jiangsu, China. Electronic address: wanggh@suda.edu.cn.
⁵ Bioinformatics Lab. (Dry), Department of Statistics, University of Rajshahi, Rajshahi, 6205, Bangladesh. Electronic address: mollah.stat.bio@ru.ac.bd.

PMID: 35447458
DOI: 10.1016/j.compbiomed.2022.105508

Abstract

Breast cancer (BC) is one of the most malignant tumors and the leading cause of cancer-related death in women worldwide. So, an in-depth investigation on the molecular mechanisms of BC progression is required for diagnosis, prognosis and therapies. In this study, we identified 127 common differentially expressed genes (cDEGs) between BC and control samples by analyzing five gene expression profiles with NCBI accession numbers GSE139038, GSE62931, GSE45827, GSE42568 and GSE54002, based-on two statistical methods LIMMA and SAM. Then we constructed protein-protein interaction (PPI) network of cDEGs through the STRING database and selected top-ranked 7 cDEGs (BUB1, ASPM, TTK, CCNA2, CENPF, RFC4, and CCNB1) as a set of key genes (KGs) by cytoHubba plugin in Cytoscape. Several BC-causing crucial biological processes, molecular functions, cellular components, and pathways were significantly enriched by the estimated cDEGs including at-least one KGs. The multivariate survival analysis showed that the proposed KGs have a strong prognosis power of BC. Moreover, we detected some transcriptional and post-transcriptional regulators of KGs by their regulatory network analysis. Finally, we suggested KGs-guided three repurposable candidate-drugs (Trametinib, selumetinib, and RDEA119) for BC treatment by using the GSCALite online web tool and validated them through molecular docking analysis, and found their strong binding affinities. Therefore, the findings of this study might be useful resources for BC diagnosis, prognosis and therapies.

Keywords: Breast cancer; Drug repositioning; Functional and pathway enrichment analysis; Integrated statistics and network-based approaches; Key genes (KGs); Regulatory network analysis; Transcriptomics analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Breast Neoplasms* / genetics
Breast Neoplasms* / pathology
Computational Biology / methods
Female
Gene Expression Profiling / methods
Gene Expression Regulation, Neoplastic
Gene Regulatory Networks
Humans
Molecular Docking Simulation