Probing the origins of cancer stem cells Cancer stem cells may remain in an individual’s body even after they have been successfully treated, and the presence of these cells can then lead to the formation of a new tumour. We spoke to Dr Francesca Rapino about her research into the cellular origin of cancer stem cells and its wider implications for the diagnosis of cancer. A certain proportion of cells in a tumour are cancer stem cells (CSCs), which aren’t eradicated by chemotherapy or radiotherapy and so remain in the body even after a course of treatment has finished. While a patient may be considered to be tumour-free after treatment, they still have a very small population of cells that do not divide normally and can cause health problems later on. “When treatment is removed, those cells are able to re-grow a new tumour and cause metastasis,” explains Dr Francesca Rapino, Research Associate at the FNRS and Welbio researcher at the University of Liege. As the Principal Investigator of the tRNAtoGO project, Dr Rapino is investigating how these CSCs are formed, focusing on the role of tRNAs, molecules which play an important role in the production of proteins. “tRNAs are secreted in the blood. They are very abundant in cells in general, and extremely abundant in cancer,” she outlines.
TRNAtoGo “tRNA actors” heterogeneity: a new identifier of cancer stem cells The TRNAtoGo project is funded under the European Research Council Starting Grant agreement number 948170. Project Coordinator, Dr Rapino Francesca, PhD GIGA-Stem Cell Laboratory of Cancer Stemness T: +32 4 366 25 48 E: Francesca.Rapino@uliege.be W: https://cordis.europa.eu/ project/id/948170 W: www.uliege.be Dr Francesca Rapino, PhD is an Associate Professor at FRS-FNRS and WelBio researcher at the University of Liege, and Head of the lab of Cancer stemness. She is interested in understanding how tRNA heterogeneity affects the establishment of pathological phenotypes. In particular, she aims to identify the background context to oncogenic transformation.
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RNAtoGO experimental approach
Cancer stem cells The process by which some stem cells become CSCs is unclear, a topic at the core of the project. The working hypothesis is that certain sub-groups of tRNAs effectively prime cells to transform into CSCs when a genetic mutation is present, now Dr Rapino and her colleagues in the lab are looking to gain deeper insights. “We are using genetically modified mouse models to isolate and characterize the healthy and cancerous stem cells in the intestine,” she says. When researchers have the populations of healthy stem cells and CSCs, they can then profile them using sequencing techniques. “We use proteomics to see the proteins, RNA-seq for the RNAs, as well as other techniques like Ribo-seq and transcriptome RNA sequencing to focus on specific changes in translation dynamics,” continues Dr Rapino. “We’re looking at the different actors involved in translation, such as the ribosome and tRNAs. From this we generate algorithms to essentially highlight the actors involved, we’re using bioinformatics techniques in the project.” Researchers are also using machine learning techniques to try and identify the tRNAs that make the difference between the situation of a healthy stem cell and a CSC. This only produces a prediction however, so Dr Rapino is also using gene-editing techniques like CrisprCas9 to build a fuller picture. “We pull out these tRNAs that we predict to be important for the transformation of healthy stem cells
into CSCs. We then investigate whether a healthy stem cell can survive without this specific tRNA, and if the CSC cannot. We aim to identify a group of tRNA genes that are not essential for healthy stem cells, but then become extremely important for CSCs,” she explains. This research could hold important implications for the way cancer is diagnosed, opening up the possibility of a blood test. “Cancers produce a lot of proteins and tRNAs. There are so many of these tRNAs that at some points they enter the blood,” says Dr Rapino. A test capable of detecting tRNAs known to be important in CSCs could help diagnose cancer earlier and improve the prospects of treating it effectively. This is a topic Dr Rapino is exploring in her research. “We are developing tools to detect specific signatures of tRNAs, first in cells and then in the blood of mice,” she outlines. Alongside this more diagnostic dimension of research, Dr Rapino also plans to continue investigating the nature of CSCs over the remainder of the project’s funding term. “We’ve profiled stem cells and CSCs. We’ve also built the first version of this bioinformatic pipeline and have the first results from our functional screen,” she continues. “We will validate those tRNAs that come out from our screen in mouse models. We will generate new mouse models that do not have those tRNAs, to see how a tumour progresses – we want to see how cell translation is changed when you don’t have specific tRNAs.”
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