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Comparative Transcriptomic Analysis Identifies Predictive Biomarkers of Pathological Complete Response in
Fang-Ming Chen1, Chung-Liang Li1, Mei-Ren Pan2,3
1Division of Breast Oncology and Surgery, Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan, R.O.C.
Cancer Genomics & Proteomics
|January 2, 2026
Summary
Researchers identified a 15-gene signature that predicts response to neoadjuvant chemotherapy (NACT) in triple-negative breast cancer (TNBC). This discovery aids in stratifying patients and developing targeted therapies for chemoresistant TNBC.
Area of Science:
- Oncology
- Genomics
- Biomarker Discovery
Background:
- Pathologic complete response (pCR) is a key prognostic indicator in triple-negative breast cancer (TNBC).
- Predictive biomarkers for pCR in TNBC are currently limited.
- Accurate prediction of pCR is crucial for effective treatment stratification.
Purpose of the Study:
- To identify gene expression signatures predictive of pCR in TNBC patients receiving neoadjuvant chemotherapy (NACT).
- To establish a reliable biomarker for stratifying TNBC patients based on NACT response.
- To explore potential therapeutic targets for chemoresistant TNBC.
Main Methods:
- RNA sequencing (RNA-seq) was performed on tumor samples from 16 TNBC patients (5 pCR, 11 non-pCR).
- Differentially expressed genes (DEGs) were identified using DESeq2.
- Results were validated against a TCGA cohort; overlapping DEGs were analyzed for therapeutic relevance.
Main Results:
- 175 DEGs were identified in the primary cohort; 15 DEGs showed consistent differential expression in both cohorts.
- These 15 genes were enriched in pCR samples, suggesting their potential as predictive biomarkers for NACT response.
- Several identified genes are druggable, indicating potential for targeted therapies in chemoresistant TNBC.
Conclusions:
- A 15-gene signature associated with pCR in TNBC was identified and validated across independent cohorts.
- This signature provides a promising tool for improving patient stratification and guiding treatment decisions.
- The findings support the development of targeted therapies for NACT-resistant TNBC.
