Éva Schád1, Beáta Szabó1, Eszter Bajtai1, András Füredi2 and Ágnes Tantos1*
1HUN-REN Research Centre for Natural Sciences, Institute of Molecular Life Sciences
2HUN-REN Research Centre for Natural Sciences, Institute of Molecular Life Sciences, HUN-REN Centre of Energy Research, Institute of Technical Physics and Materials Science, Obuda University, University Research and Innovation Center, Physiological Controls Research Center
tantos.agnes [at] ttk.hu
Abstract
Therapy-induced senescence (TIS) is considered a permanent cell cycle arrest following DNA-damaging treatments; however, its irreversibility has been challenged in our recent publication, where we demonstrated that escape from TIS is universal across breast cancer cells. Moreover, TIS provides a reversible drug resistance mechanism that ensures survival of the population, and could contribute to relapse.
The experimental setup was to induce TIS in four different breast cancer cell lines with high-dose chemotherapy and culture the cells until they escape TIS. Parental (CTR), TIS and repopulating (REPOP) cells were analysed by bulk and single-cell RNA sequencing and surface proteomics. Cells in the TIS state showed a remarkable resistance to a broad panel of anticancer agents and different senolytic drugs. Our results revealed that TIS, as a transient drug resistance mechanism, could contribute to overcome the immune response and to relapse by reverting to a proliferative stage.
In order to better understand the molecular mechanisms driving TIS induction and escape, we performed a deep analysis of the transcriptomic changes that accompany these processes, with specific focus on the non-coding RNAs. Our main goal in the present work was to identify regulatory RNA interactions that orchestrate large-scale transcriptomic deregulation of genes necessary for the survival and later repopulation of cancer cells undergoing TIS.
Regulatory RNA networks consist of lncRNA sponges that bind a large amount of miRNAs, releasing the miRNA-target mRNAs from translational repression. Using the transcriptomic data from the bulk RNA sequencing of the different states, we reconstructed the regulatory RNA networks that exist in CTR, TIS and REPOP cells. These revealed cell type-specific and generally existing networks and showed a strong upregulation in the TIS state. Comparison of the different networks revealed general, but also specific RNA networks that are exclusively present in the TIS cells. The lncRNAs with the highest connectivity in these networks may serve as new target candidates in a possible TIS-specific treatment. Importantly we also identified RNA networks that remain active in the REPOP cells – these may be used as TIS history markers and may facilitate the escape from TIS during a repeated treatment cycle.
Keywords: ceRNA networks, TIS, breast cancer
Acknowledgement: The project received funding from National Research, Development and Innovation Office (ADVANCED 152119, STARTING 149496 and 2023-1.2.4-TÉT-2023-00107), the European Commission’s Marie Skłodowska-Curie Actions (Grant agreement ID: 101065044), the Research Grant Hungary (RGH- 151536).