Ageing-related diseases are tightly correlated with the accumulation of senescent cells. While the selective elimination of senescent cells is a primary therapeutical goal in the field, no clinically approved treatment currently exists, which constitutes an important research gap. Abundant evidence highlights how changes in mitochondria and cellular metabolism can be both cause and consequence of the senescent phenotype and suggests a possible role of this organelle in the specific targeting of these cells. Through a CRISPR/Cas9-based screening, Serrano’s laboratory identified Cyclophilin D (CypD) as a promising candidate target, since its inactivation leads to the selective elimination of senescent cells while being non-toxic for control proliferating cells. CypD is a matrix isomerase involved in various mitochondrial functions, including the regulation of cell death and the opening of the mitochondrial permeability transition pore, a non-specific pore in the inner mitochondrial membrane, by sensitising it to calcium and reactive oxygen species. Interestingly, additional functions have been described for CypD, including proteins scaffolding, as it binds to several mitochondrial proteins, apoptosis and mitophagy control, and regulation of the electron transport chain activity. This project will study CypD as a novel, non-invasive senolytic target and provide a molecular understanding of its modulation in senescence biology, taking advantage of the various well-established senescence models developed in Serrano’s laboratory, including human and mouse cells and in vivo models. The ultimate goal is to improve the therapeutic outcome of senescence-associated diseases by developing new strategies for the detection and elimination of senescent cells in patients.

The gene-environment interaction paradigm has long provided a framework for understanding the contribution of environmental cues to cancer initiation. However, recent perspectives reveal that even amongst genetically identical cells, responses to environmental variation can be remarkably diverse. When and how pathogenic gene-environment interactions effectively ignite cancer remains ambiguous. IGNITE aims to explain what drives cancer initiation beyond genetics by dissecting (mal)adaptive responses to environmental variation at the cell, tissue, and organismal level, taking inflammation-driven pancreatic cancer as a disease paradigm. I hypothesize that qualitatively distinct forms of local and systemic inflammation, which I refer to as “inflammatory contexts”, direct tumor evolution in ways that are largely predetermined by epigenetic fingerprints integrating cells’ lineage, mutational, and environmental exposure history. Hence, I will (1) identify epigenetic determinants underlying the differential potential of pre-malignant and malignant cell states to sense, communicate and evolve within distinct inflammatory contexts; (2) define tissue-level hallmarks of pathogenic vs homeostatic inflammatory contexts, and develop new approaches to engineer immune cell states distinguishing each; and (3) dissect poorly understood links between pancreatic cancer risk and distal inflammatory disorders to uncover organismal mechanisms. IGNITE’s multi-layered perspective of cancer susceptibility and evolution will integrate methodologies to map and functionally interrogate molecular, cellular, tissue, and systemic traits in human samples and physiological models to establish causal relations. In sum, IGNITE will unmask yet-unknown contextual determinants of cancer beyond genetic susceptibility. The project’s results, new methods and concepts will make it possible to rationally harness inflammatory cues for steering tumor evolution towards clinically manageable states.

Mutations are the fuel of any evolutionary process, and this also applies to carcinogenesis. The advent of affordable DNA sequencing has enabled mutagenic processes in the human soma to be quantified genome-wide, revealing a striking occurrence of hypermutated tumors. They exhibit an extreme load of somatic changes, often harbouring hundreds of single-nucleotide variants and/or indels per megabase. The HYPER-INSIGHT project is organized into three objectives, which aim to take advantage of the unique opportunity provided by genome sequences of hypermutated and ultramutated tumors. In particular, this work planned in this project aims to further our knowledge on (i) the regional organization of the DNA replication and repair program in human cells, and the determinants thereof, (ii) the extent of selection which acts on somatic variants in various pathways or complexes and (iii) opportunities for selectively targeting DNA repair deficiencies that manifest as hypermutation. Methodologically, our work will employ a three-pronged approach. First, we will perform a multitude of rigorous statistical analyses that draw on the rich and still-expanding resources provided by cancer genomics consortia. Second, we will perform exome and genome sequencing, focusing on ultramutated tumors caused by specific defects in the DNA maintenance machinery. Third, the project involves conditional essentiality screens on cancer cell lines with hypermutant backgrounds. Their goal is to discover synthetic lethality relationships, useful for targeting hypermutating cells, while sparing healthy ones. In summary, one of the promises of cancer genome sequencing projects was to elucidate the mechanisms underlying mutational processes in the human soma, advancing our understanding of this important facet of cancer biology. We will work towards realizing this promise, thereby strengthening the EU’s position in the global scientific endeavour.