Plenary conferences
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.
Liquid, epigenetic biopsies – Charlotte PROUDHON, Irset, Rennes
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.
Charlotte Proudhon is a researcher at INSERM in genetics and genomics, expertise that she demonstrates in the field of research on liquid biopsies and the development of non-invasive tests for precision oncology.
Charlotte Proudhon completed her doctorate in molecular genetics at the Institut Curie in Paris under the supervision of Déborah Bourc’his. During this period, she trained in the study of DNA methylation, and in particular its role as an epigenetic vector of information between generations in the mouse model. She then completed a postdoctoral fellowship at New York University in the laboratory of Jane Skok, where she specialized in three-dimensional analysis of the genome in cells of the immune system. Through these two experiences, Charlotte Proudhon has built solid expertise in genetics, epigenetics and genomics. On her return to France, Charlotte Proudhon co-supervised a team in translational research at the Institut Curie where, drawing on her scientific background, she set about developing innovative tests based on circulating tumor DNA, a field emerging and truly revolutionary in precision medicine. Charlotte Proudhon obtained a position as a research manager at INSERM in 2020. In 2022, her ambition and talent were doubly recognized: by her selection as team leader during an international call for tenders intended to the recruitment of new teams at IRSET in Rennes, and by obtaining prestigious “Starting Grant” funding from the European Research Council (ERC). During her career, C. Proudhon has co-signed 43 publications, she holds 4 patents, she has obtained numerous funding (including the prestigious ERC named above).
Unraveling the secrets of bacterial Type 4 Secretion Systems: from pilus biogenesis to pathogenicity – Kevin MACE – IGDR, Rennes
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.
Kevin Mace is a prominent microbiologist and structural biologist. Currently, as the Chair Junior Fellow at CNRS in France, he specializes in cryo-electron microscopy (cryo-EM) to explore the Type IV Secretion System’s role in antibiotic resistance and virulence at the T4-SECRET Lab. Previously, during a six-year postdoctoral stint at the Waksman Lab in London, he focused on cryo-EM structural studies of the Type IV Secretion System and its mechanisms. Kevin’s academic journey began with a PhD thesis at the Université Rennes 1, investigating protein synthesis and trans-translation.
His research career also includes notable internships and work as a microbiology and biochemical technician, contributing significantly to the study of bacterial systems, antibiotic resistance, and virulence mechanisms.
Transgenic rat models of Pulmonary Hypertension – Frédéric PERROS, CarMeN, Lyon
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.
Frédéric Perros, Ph.D.-HDR is research director at INSERM. He is a specialist in the pathophysiology of pulmonary hypertension (PH). In September 2022, he joined the CarMeN laboratory, a renowned center of excellence in Lyon, France, dedicated to cutting-edge research in cardiovascular diseases, metabolism and nutrition. Prior to his assignment at CarMeN, Dr. Perros led the “Pulmonary Hypertension: From Susceptibility Genes to Pathophysiology” team at UMRS-999 in Plessis Robinson, France. He also enriched his experience as a guest researcher in the pulmonary hypertension research group of the University Institute of Cardiology and Pneumology of Quebec (IUCPQ), Université Laval, Quebec, Canada, during the 2015-2016 academic year. . Dr. Perros has made significant contributions to the field, focusing on the identification and analysis of risk factors for PH, including inflammation and autoimmune mechanisms, drug-induced PH and toxins, as well as genetic predispositions such as mutations in BMPR2, KCNK3 et EIF2AK4. His focus is on understanding how alterations in pathways dependent on these genes contribute to both heritable and non-heritable forms of PH. In addition, he is actively involved in the identification and validation of biomarkers in PH and in therapeutic innovation through preclinical studies on animal models of the disease.
Spatial characterization of invasive cutaneous squamous cell carcinoma by high-dimensional mass cytometry imaging – Fabienne ANJUERE, IPMC, Valbonne
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.
A chemist by training, Dr. Fabienne Anjuère has been interested in the immunology of healthy and cancerous epithelial tissues since the beginning of his career. She is an INSERM researcher and currently head of the “Regulation of immune responses to muco-cutaneous surfaces” team with Dr. Véronique Braud at the Institute of Molecular and Cellular Pharmacology of Sophia-Antipolis.
Between 2001 and 2010, she developed recognized expertise in the biology of cutaneous and mucosal dendritic cells and their role in the induction of immune responses against mucosal infections. Since 2010, she has sought to understand in a spatial and integrative manner the immunosuppression mechanisms involved in the progression of cutaneous and mucosal carcinomas of the head and neck. Recently, she has developed fundamental and translational research aimed at deciphering the dialogue between pathological epithelium, non-immune stromal cells and immune cells by relying on innovative mass cytometry imaging technology in order to identify new therapeutic targets and targeted immunotherapies against cutaneous and oral squamous cell carcinomas. She has recognized expertise in translational research in ENT oncology (Expert for UNICANCER since 2018). She is the inventor of several patents in oncoimmunology.
How the study of spatial biology reveals the intimate interactions of cells in oncology – Henri-Alexandre MICHAUD, Montpellier Cancer Research Institute
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.
A trained pharmacist and doctor in immunology, Henri-Alexandre Michaud first studied the immunosuppressive mechanisms put in place during viral infections or the development of cancers as well as the therapeutic strategies allowing them to be circumvented. His thesis work (IGMM, Montpellier) contributed to characterizing the immunomodulatory and vaccine effects of antiviral monoclonal antibodies. in vivo in preclinical mouse models. During his postdoc (UCSF, San Francisco), he transposed this work into the context of HIV-1 infection by isolating an antibody directed against an immunosuppressive viral protein and demonstrating its ability to target infected immune cells.
In 2013, he joined the Immunity and Cancer team at the Montpellier Cancer Research Institute (IRCM) where he characterized a therapeutic monoclonal antibody targeting the adenosine pathway. This molecule is a powerful inhibitor of the immune system in the tumor microenvironment, significantly participating in tumor escape and resistance to anticancer treatments, mainly immunotherapies.
His work and new issues in oncology have shown the need to study the tumor microenvironment in a global, deep and spatial manner. It has become essential to identify and localize all the cellular players present in the tumor to deduce their interactions. It is with this aim that he developed and took charge of the management of the SIMCaT (Spatial Imaging Mass Cytometry and Trancriptomic) core facility of the IRCM which is based on two innovative technologies, mass cytometry imaging and transcriptomics. spatial at the single cell scale. At the same time, he continues his research work aimed at better describing tumor heterogeneity and response to treatments in breast, ovarian, uterine and esophagogastric junction cancers, in close collaboration with oncologists from the Montpellier Cancer Institute. The ambition of this work is to identify signatures predictive of response to treatment as well as to develop new avenues for therapeutic innovation.