Genome Biology lab: research activities

Our lab is committed to unveil the complexities of the human transcriptome of T cell in the tumor microenvironment, with a particular focus on the annotation and functional role of retrotransposable elements (REs) —a largely uncharted territory in genomics. Since REs constitute nearly 43% of the human genome, incorporating them into gene annotation is essential to define the precise grammar that dictate cell differentiation and function.

However, studying these REs remains particularly challenging, as current bioinformatics tools often overlook them, leading to incomplete mapping and inaccurate quantification. To address these limitations, our team is dedicated to developing innovative technologies and computational approaches that allow for the precise annotation, quantification and interpretation of the REs and RE-derived transcripts in omics datasets and at single cell level. This is instrumental to unveiling their previously unrecognized roles in gene regulation and cellular function.

Cell identity is not a fixed state in space and time; rather, it is dynamic and multifaceted, constantly adapting to environmental stimuli. Epigenetics plays a fundamental role in enabling cells to respond to these changes, allowing them to reach a new state of balance or internal homeostasis. Studying epigenetic mechanisms involves unraveling a complex interplay of DNA sequences, RNA molecules, and proteins, which are intricately organized within chromatin in a highly structured nuclear topology to regulate gene expression. A comprehensive understanding of these regulatory networks must integrate Retrotransposable Elements (REs) which make up nearly half of the human genome and are pervasively transcribed, yet often overlooked. Our research has revealed that REs play a pivotal role in shaping gene expression and regulating T lymphocyte function under physiological conditions, within the tumor microenvironment, and throughout the human lifespan. Our mission is to fully elucidate the epigenetic mechanisms by which RE-transcripts regulate immune responses in both health and disease. By leveraging a broad spectrum of cutting-edge omics technologies, advanced computational tools, high-resolution imaging approaches, and functional assays, our lab is dedicated to deciphering the epigenetic role of REs in immune regulation. Given our expertise in this area, our lab is an active member of the FANTOM_6 consortium.