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Updated: Oct 15, 2025
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Transcriptional landscape associated with TNBC resistance to neoadjuvant chemotherapy revealed by single-cell RNA-seq
Radhakrishnan Vishnubalaji1, Nehad M Alajez1,2
1Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
Abstract:
Triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy (NAC) represents a major clinical challenge; therefore, delineating tumor heterogeneity can provide novel insight into resistance mechanisms and potential therapeutic targets. Herein, we identified the transcriptional landscape associated with TNBC resistance to NAC at the single-cell level by analyzing publicly available transcriptome data from more than 5,000 single cells derived from four extinction (responders) and four persistence (non-responders) patients, revealing remarkable tumor heterogeneity. Employing iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP), we classified TNBC single cells into several clusters based on their distinct gene signatures. The presence of clusters indicative of immune cell activation was a hallmark of the extinction group pre-NAC, while post NAC, the extinction tissue consisted mostly of breast, omental fat, and fibroblasts. The persistent gene signatures of pre-NAC resembled the gene signature of lung epithelial, mammary, and salivary glands and acute myeloid leukemia blast cells, which were associated with enhanced cellular movement and activation of FOXM1, NOTCH1, and MYC and suppression of tumor necrosis factor (TNF) and IFNG mechanistic networks. Multivariate survival analysis identified persistence-derived three-gene signature (KIF5BhighHLA-ClowIGHG2low) predictive of relapse-free survival (hazard ratio [HR]: 2.2 [1.6-3.2, p < 0.0001]) in a second cohort of 360 TNBC patients. Mechanistically, loss of function of several upregulated genes in the persistent group (BYSL, FDPS, ENO1, MED20, MRPL9, MRPL37, NDUFB11, PMVK, MYC, and GSTP1) inhibited MDA-MB-231 and BT-549 TNBC models' colony-forming unit (CFU) potential and enhanced their sensitivity to paclitaxel. Our data unraveled the transcriptional portrait associated with NAC resistance, identified several key genes, and suggested their potential utilization as prognostic markers and therapeutic targets in TNBC.
Insights
Triple-negative breast cancer (TNBC) resistance to neoadjuvant chemotherapy (NAC) is a challenge. Single-cell analysis revealed distinct gene signatures in resistant tumors, identifying potential therapeutic targets and prognostic markers for TNBC.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Triple-negative breast cancer (TNBC) exhibits significant resistance to neoadjuvant chemotherapy (NAC), posing a major clinical hurdle.
- Understanding tumor heterogeneity is crucial for uncovering resistance mechanisms and identifying novel therapeutic strategies in TNBC.
Purpose of the Study:
- To delineate the transcriptional landscape of TNBC at the single-cell level in response to NAC.
- To identify key genes and molecular pathways associated with chemotherapy resistance in TNBC.
- To discover potential prognostic markers and therapeutic targets for TNBC.
Main Methods:
- Analysis of publicly available transcriptome data from over 5,000 single cells from NAC responders and non-responders.
- Application of iterative clustering and guide-gene selection (ICGS) and uniform manifold approximation and projection (UMAP) for cell classification.
- Multivariate survival analysis on a cohort of 360 TNBC patients to identify predictive gene signatures.
Main Results:
- Single-cell analysis revealed significant tumor heterogeneity in TNBC, with distinct gene signatures differentiating responders from non-responders.
- Pre-NAC immune cell activation characterized responders, while non-responders showed signatures resembling lung, mammary, salivary glands, and acute myeloid leukemia cells, with enhanced cellular movement and activation of FOXM1, NOTCH1, and MYC.
- A three-gene signature (KIF5BhighHLA-ClowIGHG2low) was identified as predictive of relapse-free survival in TNBC patients.
- Functional studies demonstrated that loss of function of upregulated genes in resistant tumors inhibited colony formation and increased sensitivity to paclitaxel.
Conclusions:
- The study unraveled the transcriptional portrait associated with NAC resistance in TNBC at the single-cell level.
- Key genes and pathways linked to TNBC chemoresistance were identified, offering insights into resistance mechanisms.
- The identified three-gene signature holds potential as a prognostic marker, and specific genes represent potential therapeutic targets for TNBC.
