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Updated: Dec 30, 2025
Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
Published on: December 9, 2016
Deep Sequencing Analysis Reveals Distinctive Non-Coding RNAs When Comparing Tumor Multidrug-Resistant Cells and
Diana Sousa1,2,3, Rune Matthiesen4, Raquel T Lima1,5,6
1i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.
Abstract:
Multidrug resistance (MDR) is one of the main limitations of cancer treatment. The overexpression of drug-efflux pumps, such as P-glycoprotein (P-gp), is a major cause of MDR. Importantly, different studies have shown that extracellular vesicles (EVs) participate in the communication between MDR cells and drug-sensitive counterparts, promoting dissemination of the MDR phenotype. In the present work, we aimed to identify RNA species present in MDR cells and in EVs released by those cells, which may be associated with the MDR phenotype. The RNA content from two pairs (leukemia and lung cancer) of MDR (P-gp overexpressing) cells and their drug-sensitive counterparts, as well as from their EVs, was analyzed by deep sequencing. Our results showed distinctive transcripts for MDR cells and their EVs, when compared with their drug-sensitive counterparts. Remarkably, two pseudogenes (a novel pseudogene and RNA 5.8S ribosomal pseudogene 2) were found to be increased in EVs released by MDR cells in both leukemia and lung cancer models. Moreover, six miRs (miR-204-5p, miR-139-5p, miR-29c-5p, miR-551b-3p, miR-29b-2-5p, and miR-204-3p) exhibited altered levels in lung cancer MDR cells and their EVs. This study provides insights into the contribution of EVs to MDR.
Insights
Multidrug resistance (MDR) hinders cancer treatment. Extracellular vesicles (EVs) from MDR cells carry specific RNA, including pseudogenes and microRNAs, which may spread the MDR trait to other cancer cells.
Area of Science:
- Oncology
- Molecular Biology
- Biochemistry
Background:
- Multidrug resistance (MDR) is a significant challenge in cancer therapy.
- Overexpression of drug-efflux pumps like P-glycoprotein (P-gp) is a primary driver of MDR.
- Extracellular vesicles (EVs) are implicated in intercellular communication and the spread of MDR phenotypes.
Purpose of the Study:
- To identify RNA species in MDR cells and their released EVs that contribute to the MDR phenotype.
- To compare RNA content between P-gp overexpressing MDR cells and their drug-sensitive counterparts.
- To investigate the role of EVs in the dissemination of MDR.
Main Methods:
- Deep sequencing was employed to analyze RNA content.
- Samples included two pairs of MDR (P-gp overexpressing) and drug-sensitive cells (leukemia and lung cancer).
- EVs isolated from these cell lines were also subjected to deep sequencing analysis.
Main Results:
- Distinctive RNA transcripts were identified in MDR cells and their EVs compared to drug-sensitive counterparts.
- Two pseudogenes, a novel pseudogene and RNA 5.8S ribosomal pseudogene 2, were significantly increased in EVs from MDR cells in both leukemia and lung cancer models.
- Six microRNAs (miRs) showed altered levels in lung cancer MDR cells and their EVs, including miR-204-5p, miR-139-5p, miR-29c-5p, miR-551b-3p, miR-29b-2-5p, and miR-204-3p.
Conclusions:
- EVs carry specific RNA signatures associated with the MDR phenotype.
- Increased pseudogene and altered miR levels in EVs suggest a mechanism for MDR dissemination.
- This research provides novel insights into the molecular mechanisms by which EVs contribute to multidrug resistance in cancer.
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