Related Experiment Video
Updated: Jan 7, 2026
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
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.
Background/Aim:
Pathologic complete response (pCR) to neoadjuvant chemotherapy (NACT) is a strong prognostic indicator in triple-negative breast cancer (TNBC). However, reliable predictive biomarkers for pCR remain limited. This study aimed to identify gene expression signatures associated with pCR in TNBC to facilitate more precise treatment stratification.
Materials And Methods:
Tumor samples from 16 TNBC patients treated with NAC at the Kaohsiung Medical University Hospital (KMUH) were analyzed, including 5 pCR and 11 non-pCR cases. RNA sequencing (RNA-seq) was performed, and differentially expressed genes (DEGs) were identified using DESeq2 (|log2FC| ≥2, adjusted p<0.05). Gene expression profiles were compared with a validation cohort of 27 NAC-responsive TNBC cases from The Cancer Genome Atlas (TCGA). Overlapping DEGs were identified using Venn diagram analysis, and drug-gene interaction databases were queried to explore therapeutic relevance.
Results:
In the KMUH cohort, 175 DEGs were identified, including 146 up-regulated and 29 down-regulated genes in non-pCR tumors. Fifteen DEGs demonstrated consistent differential expression patterns between KMUH and TCGA datasets, showing enrichment in pCR samples. These genes may serve as predictive biomarkers for NAC response. Notably, several of these genes are potentially druggable, suggesting opportunities for targeted therapy in chemoresistant TNBC.
Conclusion:
We identified and validated a 15 gene signature associated with pCR in TNBC across independent cohorts. These findings offer a promising basis for improving patient stratification, guiding treatment decisions, and developing targeted therapies for NAC-resistant TNBC.
