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Bulk RNA sequencing dataset of Claudin-low breast cancer cell lines with Neuropilin-1 knockdown
Layla-Rose Lynam1, Anja Rockstroh1, Melanie Lehman1,2
1Australian Prostate Cancer Research Centre - Queensland, Centre for Genomics and Personalised Health, Faculty of Health, School of Biomedical Sciences, Translational Research Institute, Queensland University of Technology, Brisbane, QLD, Australia.
Abstract:
Triple-negative breast cancers (TNBC) are a particularly aggressive breast cancer subtype with poor prognosis and high relapse rates. Due to a lack of identified targeted therapies, chemotherapy currently remains as the primary treatment for TNBC. Approximately 25-39% of TNBC are claudin-low breast cancers, which are mainly defined by low expression of cell-cell adhesion proteins and enrichment of mesenchymal signatures. Functional studies have demonstrated the potential role of the transmembrane-coreceptor, Neuropilin-1 (NRP1) in regulating the progression of these tumours. However, there have been no high-throughput studies to date that comprehensively investigate NRP1-modulated cell-signalling across multiple claudin-low cell lines. Therefore, we treated HS578T, MDA-MB-231 and SUM159PT claudin-low cell lines with either a non-targeting (NT) control or two NRP1-targeting small-interfering RNA (siRNA) or short-hairpin RNA (shRNA) sequences and followed this with bulk-RNA sequencing. We present this comprehensive transcriptomic dataset which provides a valuable resource for understanding both the transcriptomic landscape of claudin-low breast cancer and NRP1-regulated signalling pathways. Therefore, paving the way for future studies of its potential as a therapeutic target.
Insights
Triple-negative breast cancer (TNBC) is aggressive, often treated with chemotherapy. This study explores Neuropilin-1 (NRP1) in claudin-low TNBC, identifying NRP1-regulated pathways for potential new therapies.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Triple-negative breast cancer (TNBC) is an aggressive subtype with limited targeted therapies.
- Claudin-low TNBC, characterized by low cell adhesion and mesenchymal features, comprises a significant portion of TNBC cases.
- Neuropilin-1 (NRP1) is implicated in tumor progression, but its signaling pathways in claudin-low TNBC are not fully understood.
Purpose of the Study:
- To comprehensively investigate Neuropilin-1 (NRP1)-modulated cell signaling in claudin-low breast cancer cell lines.
- To generate a transcriptomic dataset for understanding claudin-low TNBC and NRP1-regulated pathways.
- To explore NRP1 as a potential therapeutic target in TNBC.
Main Methods:
- Treatment of three claudin-low cell lines (HS578T, MDA-MB-231, SUM159PT) with non-targeting control or NRP1-targeting small-interfering RNA (siRNA) or short-hairpin RNA (shRNA).
- High-throughput bulk-RNA sequencing to analyze transcriptomic changes.
- Bioinformatic analysis of gene expression data.
Main Results:
- A comprehensive transcriptomic dataset was generated from NRP1-modulated claudin-low breast cancer cell lines.
- Identification of key signaling pathways regulated by NRP1 in this subtype.
- Provides a resource for further investigation into NRP1's role.
Conclusions:
- The study provides valuable transcriptomic data on claudin-low breast cancer.
- NRP1-regulated signaling pathways have been elucidated, offering insights into TNBC progression.
- This research lays the groundwork for future therapeutic strategies targeting NRP1 in TNBC.
