Related Experiment Video
Updated: Mar 12, 2026
Sequencing Small Non-coding RNA from Formalin-fixed Tissues and Serum-derived Exosomes from Castration-resistant Prostate Cancer Patients
Published on: November 19, 2019
Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in
Yuanjun Ma1, Yali Miao2, Zhuochun Peng1
1Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
Abstract:
Docetaxel has been the standard first-line therapy in metastatic castration resistant prostate cancer. The survival benefit is, however, limited by either primary or acquired resistance. In this study, Du145 prostate cancer cells were converted to docetaxel-resistant cells Du145-R and Du145-RB by in vitro culturing. Next generation RNAseq was employed to analyze these cell lines. Forty-two genes were identified to have acquired mutations after the resistance development, of which thirty-four were found to have mutations in published sequencing studies using prostate cancer samples from patients. Fourteen novel and 2 previously known fusion genes were inferred from the RNA-seq data, and 13 of these were validated by RT-PCR and/or re-sequencing. Four in-frame fusion transcripts could be transcribed into fusion proteins in stably transfected HEK293 cells, including MYH9-EIF3D and LDLR-RPL31P11, which were specific identified or up-regulated in the docetaxel resistant DU145 cells. A panel of 615 gene transcripts was identified to have significantly changed expression profile in the docetaxel resistant cells. These transcriptional changes have potential for further study as predictive biomarkers and as targets of docetaxel treatment.
Insights
Docetaxel resistance in prostate cancer limits treatment effectiveness. This study identified gene mutations and fusions in resistant cells, offering potential new biomarkers and therapeutic targets for advanced prostate cancer.
Area of Science:
- Oncology
- Genomics
- Molecular Biology
Background:
- Docetaxel is a standard first-line therapy for metastatic castration-resistant prostate cancer.
- Treatment efficacy is often limited by primary or acquired docetaxel resistance.
- Understanding resistance mechanisms is crucial for improving patient outcomes.
Purpose of the Study:
- To investigate the genetic and transcriptional changes associated with docetaxel resistance in prostate cancer cells.
- To identify potential novel biomarkers and therapeutic targets for overcoming docetaxel resistance.
Main Methods:
- In vitro culturing of Du145 prostate cancer cells to establish docetaxel-resistant cell lines (Du145-R and Du145-RB).
- Next-generation RNA sequencing (RNAseq) to analyze gene mutations and expression profiles.
- Validation of identified gene fusions using RT-PCR and re-sequencing.
- Functional assessment of fusion transcripts in transfected cell lines.
Main Results:
- Forty-two genes acquired mutations in resistant cells, with 34 overlapping with mutations found in patient samples.
- Fourteen novel and 2 known gene fusions were identified, with 13 validated.
- Specific fusion transcripts, such as MYH9-EIF3D and LDLR-RPL31P11, were identified or upregulated in resistant cells.
- A panel of 615 gene transcripts showed significantly altered expression profiles in docetaxel-resistant cells.
Conclusions:
- Docetaxel resistance in prostate cancer is associated with specific gene mutations and novel fusion events.
- Transcriptional changes in resistant cells may serve as predictive biomarkers.
- Identified fusion genes and altered expression profiles represent potential therapeutic targets for docetaxel-resistant prostate cancer.
