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Network-Based Integrative Analysis to Identify Key Genes and Corresponding Reporter Biomolecules for Triple-Negative

Pooja Singh1, Rupesh Chaturvedi2, Pallavi Somvanshi1

  • 1School of Computational & Sciences (SCIS), Jawaharlal Nehru University, New Delhi, India.

Cancer Medicine
|April 27, 2025
PubMed
Summary

Triple-negative breast cancer (TNBC) is a deadly disease with limited treatments. This study identified 13 key genes and associated molecules, offering potential new targets for TNBC diagnosis and drug development.

Keywords:
cumulative survival analysiskey genereporter biomoleculetriple negative breast cancer

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Area of Science:

  • Genomics and Bioinformatics
  • Molecular Oncology
  • Biomarker Discovery

Background:

  • Triple-negative breast cancer (TNBC) is a significant cause of cancer death in Indian women and globally, accounting for over 40% of breast cancer cases.
  • TNBC is defined by the lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) expression.
  • Limited targeted treatment options exist for TNBC due to the absence of specific molecular targets.

Purpose of the Study:

  • To identify key genes and elucidate molecular mechanisms underlying TNBC.
  • To explore potential therapeutic targets for improving TNBC treatment strategies.
  • To provide a foundation for future drug design and biomarker discovery in TNBC.

Main Methods:

  • Integration of Protein-Protein Interaction (PPI) and Weighted Gene Co-expression Network Analysis (WGCNA).
  • Analysis of TNBC-related gene expression datasets (GSE52194 and GSE58135).
  • Downstream analysis including identification of transcription factors (TFs) and microRNAs (miRNAs) associated with key genes.

Main Results:

  • Identification of 13 key genes (e.g., PLCG2, CXCL10, CDK1, STAT1, IL6, PLK1, CCNB1, AURKA, NDC80, EGFR, IL1B, FN1, BUB1B) as significant reporter biomolecules in TNBC.
  • Association of 6 transcription factors and 20 miRNAs with these key genes, including several miRNAs with previously reported links to other cancers.
  • Enrichment and cumulative survival analyses confirmed the disease association of the identified key genes with TNBC.

Conclusions:

  • The identified key genes, TFs, and miRNAs provide a potential platform for experimental validation.
  • This integrative analysis supports the discovery of novel biomarkers for TNBC diagnosis.
  • The findings offer promising avenues for developing targeted therapeutic strategies for TNBC.