After completing my PhD, I was employed on a fixed term contract by the “Host-Retrotransposon Interactions” team at the French National Institute for Agricultural Research (INRA). I have worked on a project aimed to investigate associations between retrotransposons and host adjacent genes in tobacco. The outcome of this work helped me secure a position as Junior Researcher in the team. Since then, I have focused on studying interactions between transposable elements and host gene expression as a consequence of host stress response. The award of a Cascade Fellowship has provided me with the opportunity to transfer my skills to a mammalian system in the context of human disease. The project will generate novel tools that will benefit the research community by providing valuable toolkits to understand the contribution of these sequences to normal development and disease.
Brief description of research project
Transcriptome RNA-seq analysis from the noncancerous and cancerous tissues allow us to gather wide information important to understand function, expression and regulation of virtually every nucleotide in the cancer. List of differentially expressed genes from this analysis would be fertile sources of putative cancer biomarkers. However, such lists of differentially expressed genes can be highly variable for multiple reasons, including, age, sex and stage of the tumour as well as the specific methods used for the identification of such genes. To overcome these limitations, in this project, we focused our analyses on matched normal and tumour tissues from a well-defined group of male patients aged 53-67 diagnosed with Dukes’ B colorectal cancers. Moreover, we generated a list of differentially expressed genes that resulted from the overlap of those obtained using the different analysis methods that are commonly used in isolation. We show that this approach provides a robust list of biomarker candidates for the early detection of colorectal cancer.