Transposable Elements: from epigenomics to precision oncology

Join us for two back-to-back, interactive seminars by prominent group leaders conducting cutting-edge research on the role of transposable elements (TEs) in cancer. In the wake of the Next Generation Sequencing revolution, TEs are starting to reveal their not-so-subtle effects on tumor biology: they drive oncogene expression, disrupt tumor suppressors and potentiate immunotherapies through viral mimicry and the generation of neoantigens.

The schedule has been set so as to save time for discussions animated by members of the Trono Lab, to which all are invited to participate.

Program:
Özgen Deniz: Multi-faceted roles of retrotransposons in cancer genomes
Gael Cristofari: The epigenetic and transcriptional interplay between L1 retrotransposons and their integration sites

Özgen Deniz has recently launched her group at the Barts Cancer Institute in London. There, she and her team aim to understand the epigenetic regulation of TEs and how their dysregulation contributes to the generation and development of blood cancers. In particular, they investigate the role of TEs as gene regulators and triggers of anti-tumor immunity in blood cancers, with their eyes set on novel anti-cancer therapies. During her postdoctoral stay in Miguel Branco’s group, Özgen has notably co-pioneered a CRISPR-based biotechnology allowing the simultaneous epigenetic perturbation of thousands of phylogenetically related TE integrants, which she then leveraged to show that TE-located epigenetic marks control growth in models of acute myeloid leukemia.

Gael Cristofari is a renowned figure in the field and leads the Retrotransposons and Genome Plasticity group at the Institute for Research on Cancer and Aging in Nice. There, he and his team study L1HS, the only TE subfamily still capable of autonomous self-replication in the human genome. Despite contributing to human genetic variation - including pro-tumorigenic neo-insertions - L1HS remain understudied, as non-reference insertions and extreme levels of sequence similarity confound standard NGS approaches. Gael and his team have established a deep-sequencing method tailored for comprehensively mapping the position of L1 elements in individual human genomes, as well as variations of this technique to assess the DNA methylation level of each L1 copy genome-wide. Gael is an alumnus of the Lingner Lab here at EPFL, where he completed postdoctoral research on telomere extension which, like retrotransposition, relies on reverse transcription.

Chairs: Danica Milovanovic & Romain Forey | Trono Lab EPFL