Gen2Bio 2024 will offer five plenary conferences with “health” as the common theme. These conferences will present innovative perspectives and key advancements in healthcare, providing in-depth insight into the sector's current challenges and opportunities.

The detection of circulating tumor DNA allows to non-invasively retrieve tumor molecular profiles and follow disease evolution. It promises optimal and individualized management of patients with cancer. However, despite remarkable progress, several technological obstacles still limit liquid biopsy widespread application. Indeed, detecting small fractions of tumor DNA released when the tumor burden is reduced remains a challenge and detectable recurrent mutations do not cover all patients.

We aimed to assess the universal potential of DNA methylation as circulating tumor biomarker using new highly sensitive strategies to detect common cancer-specific signatures in blood. We targeted hypomethylation of LINE-1 elements, a shared feature of multiple cancers, using a multiplex PCR-based targeted bisulfite method coupled to deep sequencing, together with computational tools to accurately align sequencing data in a genome reference-free manner. We implemented machine learning-based classifiers, integrating methylation patterns at single CpG sites and at the single molecular level, to discriminate cancer from healthy plasma samples.

We detected 30-40,000 LINE-1 elements scattered throughout the genome, covering abound 100,000 CpG sites. Methylation of these LINE-1 elements showed an extremely efficient ability to discriminate between healthy and tumor plasmas from 6 different types of cancers with an area under the curve (AUC) of 0.95 (NHealthy = 123; Ncancers = 383). This includes metastatic colorectal, breast, lung and uvea cancers but also non metastatic ovarian, gastric and breast cancers. These results have been validated on an independent cohort (NHealthy = 29; Ncancers = 216) including metastatic colorectal, breast, gastric and lung cancers and non-metastatic ovarian and breast cancers (AUC = 0.98).

Our method allows to dramatically increase the sensitivity of ctDNA detection in a cost-effective manner, providing an optimal trade-off between the number of targeted regions and sequencing depth. These results have important biomedical implications and should lead to the development of more efficient non-invasive diagnostic tests adapted to all types of cancers, based on the universality of these factors.

Bacteria Type 4 Secretion Systems (T4SS) are nanomachines that transfer substrates from a “donor” cell to a recipient “cell” via a long extracellular filament, termed conjugative pilus. T4SS have two main roles: i) DNA transfer between bacteria, in a mechanism called “conjugation”; ii) injection of virulence proteins and DNA by some pathogenic bacteria into pro-and eukaryotic cells. Conjugation is the major driver of genome dynamics and evolution, including playing a critical role in the rapid dissemination of antibiotic resistance. In this talk, I will present the first high-resolution structure of a 2.8 MegaDalton conjugative T4SS (11 PDB/EMDB depositions). This structure was validated by a new state-of-the-art method based on co-evolution analysis, using deep-learning AlphaFOLD2/RoseTTAFold software. The structure of this massive complex, spanning both bacterial membranes, not only describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS but also sheds unprecedented light on the unique mechanism by which they elaborate conjugative pili.

Pulmonary arterial hypertension (PAH) is a rare disease that primarily targets the pre-capillary pulmonary vascular bed. It is generally characterized by obstructive remodeling of the pulmonary arterioles, coupled with vascular rarefaction. This phenomenon increases right ventricular afterload, thus leading to right heart failure. Despite advances in understanding the pathobiology of PAH, the triggers and factors leading to pulmonary vascular obstruction remain unknown. Genetic mutations, particularly in genes regulating endothelial homeostasis such as BMPR2, genes encoding ion channels like KCNK3, or even genes involved in pulmonary vascular development such as SOX17, have been identified in certain forms of PAH. These mutations often follow an autosomal dominant mode of inheritance with incomplete penetrance. Rarer forms of PAH combine veinular and pulmonary capillary remodeling, presenting signs of venular and/or capillary damage (veno-occlusive disease and/or pulmonary capillary hemangiomatosis). This variant of PAH is characterized by autosomal recessive genetic transmission, linked to biallelic mutations of the gene EIF2AK4.

To better understand the mechanisms of the disease, Dr. Perros developed genetically modified rats using TRIP-Nantes, targeting the genes Bmpr2, Kcnk3, Eif2ak4, and recently Sox17. These rat models present a relevant alternative to existing preclinical models, particularly those based on mice. Unlike mice, rats develop severe PAH, with marked pulmonary vascular remodeling and right heart failure, thus providing a more faithful representation of the characteristics of human PAH. However, current rat models, induced by monocrotaline or Sugen+Hypoxia, are limited to acute toxic endothelial damage, not reproducing the chronicity and complex vascular lung damage observed in humans. The emergence of reliable tools for transgenesis in rats has opened promising perspectives in the development of more comprehensive and genetically modified models for PAH. During his presentation, Dr. Perros will share the results of his studies on rats Bmpr2+/-, Kcnk3+/-, Eif2ak4- / -, as well as his perspectives regarding rats Sox17+/- newly created.

Invasive cutaneous squamous cell carcinoma (cSCC) is the second deadliest skin cancer. There is currently no curative treatment for advanced, inoperable and/or metastatic tumors and no specific prognostic biomarker to identify patients who will develop local or lymph node relapse. We previously identified immunosuppressive mechanisms associated with increased aggressiveness of cutaneous carcinoma in mouse models of cSCC and human cSCC involving macrophages, neutrophils and NK cells (Bourdely-22; Luci-21; Khou-20). However, the interactions between these cells and the non-immune components of the tumor microenvironment remained to be explored to better understand the complexity of these tumors and to identify prognostic biomarkers associated with the risk of relapse. Our objective was to characterize and compare in a spatial and integrative manner the immune cells of the tumor microenvironment of primary cutaneous carcinomas which relapse or do not relapse within two years post-surgery. To answer this question, we rely on sections of tissue preserved in paraffin (FFPE) from primary and recurrent tumors of patients belonging to a cohort established in collaboration with the Biological Resources Center of the Antoine Lacassagne Center (Nice), and on a mass cytometry (BMI) imaging approach and a panel of 39 targets recently developed to characterize these tumors (Elaldi-21).

We determined the immunological profile of these tumors and identified immunological patterns making it possible to distinguish skin carcinomas which recur from those which do not recur, notably with a subpopulation of macrophages characteristic of healthy skin and enriched in tumors with a good prognosis. This work represents the first comprehensive spatial characterization of the human cSCC tumor microenvironment and identifies markers associated with cSCC relapse. The analysis of a validation cohort will make it possible to validate the prognostic value of the macrophage population described, in order to improve the selection of “high risk” patients and improve their care.

The success of immunotherapies aimed at awakening the anti-tumor immune response in patients with advanced metastatic cancer has revolutionized oncology. On the one hand, they demonstrated the possibility of inducing lasting complete responses (>10 years) in patients experiencing therapeutic failure and, on the other hand, that understanding the cellular interactions governing tumors represented real therapeutic avenues, in this case tumor cell – immune cell interactions. However, these treatments do not benefit all patients. Some cancers are completely refractory and for others, only 15 to 50% of patients show responses, from partial to complete. This difference in response is essentially based on a very strong heterogeneity between types of cancers, within cancers identified as similar and also between different tumor sites for the same patient. This last component, called intratumoral heterogeneity (HTI), has become a major area of ​​research as it is linked to tumor evolution and resistance to treatments. This HTI has many components, phenotypic, functional, genetic, epigenetic, metabolic and spatial heterogeneity.

To understand this HTI, we have developed a SIMCaT (Spatial Imaging Mass Cytometry and Trancriptomic) technological core facility based on two highly multiparametric technologies, Hyperion and Xenium, which make it possible to investigate protein profiles (40 markers) and transcriptomic profiles (500 genes) very diverse at the scale of the single cell. These technologies can thus identify and localize complex and unanticipated cellular phenotypes to determine their interaction networks. Through the example of different projects carried out by the core facility and in collaboration with several teams from the Montpellier Regional Cancer Center (ICM) site and the Montpellier Cancer Research Institute (IRCM), I will illustrate the major current issues in oncology such as patient stratification, the study of complex biological mechanisms such as metabolism or the remodeling of the tumor microenvironment by anti-cancer treatment.