Gene regulation drives metabolic responses to environmental cues, such as fasting. Yet, the molecular mechanisms of this metabolic rewiring in highly sensitive organs such as liver is still poorly understood. Nuclear metabolism impacts gene expression through allosteric interactions, provision of energy, building blocks and co-factor supply crucial for epigenetic regulation. Thus, nuclear metabolism stands as a critical yet unknown link to transcriptional regulation. We also largely do not know how nutrient availability is sensed and signal transduction interplays with nuclear metabolism in transcription. These knowledge gaps are partially due to limitations of the existing computational tools for integrating diverse omics data and ignore of nuclear metabolome. Notably, current computational tools struggle with specificity, relying on pre-existing knowledge, do not encompass metabolic compartmentalization and falter in predicting dynamics of transcriptional responses under complex physiological conditions. The interdisciplinary CoMeT project will develop novel Computational methods with the aim to unravel new mechanistic connections between nuclear Metabolism and Transcriptional regulation in adaptation to fasting. CoMeT synergies complementary expertise from three partners in computational data analysis (Lutter lab), machine learning and data integration (Büttner lab), nutrient signaling, and transcriptional regulation (Panasyuk lab). By systematically exploring nuclear metabolomics, understanding predictability based on nuclear vs total metabolome, and adapting computational approaches, CoMeT commits to illuminating connections between metabolism and transcriptional regulation. Through interdisciplinary collaboration, innovative methodologies, and comprehensive multi-omics datasets, CoMeT aspires to deepen our understanding of metabolic adaptation to fasting, with three major objectives. First, CoMeT will develop prediction tools for metabolic impact on gene regulations in chronic fasting (calorie restriction) by integrating in prediction models nuclear metabolome, transcriptome and epigenetic profiles of H3K4me3 at the nexus of nuclear metabolism and active transcription. Second, largely supported by preliminary work, we will conduct mechanistic studies in reproducible cell models employing innovative molecular tools to establish the role of nuclear metabolism and nutrient sensing PI3K-3 signaling in transcriptional rewiring in fasting. Finally, we will employ developed computational models and new datasets to make predictions of sex-dimorphic transcriptional regulators in responses to fasting in liver. Altogether, CoMeT will advance our understanding of gene regulation. It will also provide cutting-edge machine learning methods and computational tools that will be instrumental for better comprehension of metabolic orchestration in health and disease.

At present, while there are innovative non-invasive biomarkers developed to diagnose acute rejection, there are no sufficiently reliable non-invasive biomarkers to assess the lesional state of the graft. Serum creatinine is not specific for renal allograft injury and does not clearly distinguish loss of function from acute rejection from another cause. In parallel, with the emergence of molecular biology technologies such as Next-Generation Sequencing (NGS), another approach using the quantification of Single Nucleotides Polymorphisms (SNPs) present on the donor's circulating DNA (dd-cfDNA) has been studied. . Data from several studies suggest that dd-cfDNA levels in blood and urine can detect rejection in heart, lung, liver and kidney allografts. However, it is currently not possible to identify the cellular origin of graft damage with these technologies. To make a diagnosis on the type of rejection, the use of solid biopsy is mandatory. The Banff classification established by different consortia is used as a reference method to characterize and diagnose the typology of renal transplant rejection.

While obesity has emerged as a pandemic in the past decades, underlying biological mechanisms are still unclear and therapeutic solutions remain poor. Macrophages are immune cells which reside in every organ including the ones involved in metabolic regulation such as the pancreas, adipose tissue and liver. Our aim is to gain insights into the biology of liver resident macrophages which have identified as key drivers of metabolic-associated fatty liver diseases, known as NAFLD or NASH currently. By combining a fundamental approach based on original mouse models with human samples from patients suffering from such disorders, we aim at identifying key pathways in liver macrophages involved in obesity-associated liver disorders. We will identify targets which can be used in new therapy development to face this rising global health challenge.

Asthma is a chronic disease affecting approximately 235 million people worldwide, and the number is rising. Asthma is not just a public health problem for developed countries; its incidence is also elevated in developing countries. Asthma concerns all age groups, but often starts in childhood. Severe asthma (SA) in children is infrequent, affecting 2-5% of the asthmatic paediatric population. Children with SA experience frequent SA attacks and have a reduced quality of life. Asthma has long been thought to be a single disease but is now considered to encompass various conditions characterized by the same symptoms (wheeze, cough, shortness of breath, chest tightness), variable degrees of airflow limitation, and different pattern of inflammation. Recent studies highlighted the heterogeneity of asthma, and the potential influence of various pathogenic mechanisms, including airway inflammation, remodelling, and immune and metabolic pathways in a specific microbial environment. However, there is very little data concerning the pathological process, especially in children. Most of the data describing different asthma endotypes in children are derived from large observational prospective cohorts. Although very informative, these studies were designed to analyse a small number of easily measured parameters, mainly lung function and atopy. The complexity of asthma pathogenesis was therefore underestimated and the individuals’ specificities only partially considered. In clinical practice, children with SA require an endoscopy, with broncho-alveolar lavage fluids (BALF) collection and bronchial biopsies to exclude a differential diagnosis and assess airway inflammation and remodelling. This approach also underestimates other components of the endotypes and results in “one size fits all” management based on high doses of inhaled steroids and the use of expensive biotherapy, such as anti-IgE therapy. Thus, although hospital admission and mortality rates for asthma decreased until the early 2000’s, they have remained stable over the past 10 years. It is therefore imperative to develop new approaches that incorporate relevant parameters analysed in the airways. Our project proposes an in-depth analysis, not only of clinical and functional parameters, but also of inflammation and remodelling, immune cells, metabolomic compounds, and microbiota present in the airways of children with SA. The project, scheduled for 4 years, is divided into five Tasks that will be performed by the following three teams: M. Leite-de-Moraes and G. Lezmi (Partner 1 and coordinator), K. Adel-Patient (Partner 2) and M. Thomas (Partner 3). Ethical approval has already been obtained for the project allowing the consortium to obtain preliminary data confirming the feasibility of the project.

Renal insufficiency is a frequent disorder affecting 10% of the population. It is associated with elevated risks of cardiovascular death at any stage of the disorder. The causes of the high cardiovascular morbidity remain uncertain and are only weakly associated with the traditional risk factors. In clinical studies elevated Fibroblast Growth Factor 23 (FGF23) plasma concentrations have been consistently associated with an increased risk of death even at the early stage of kidney disease. Few data obtained in animals suggest that intact-FGF23 could directly induce heart hypertrophy. FGF23 is a hormone-like FGF synthesized by osteocytes. It controls phosphate and vitamin D homeostasis. Its physiological effects are restricted to the kidney and the parathyroid gland. In the kidney FGF23 decreases calcitriol production, which consequently lowers intestinal phosphate absorption and inhibits phosphate reabsorption from urine in the renal proximal tubule. FGF23 plasma concentration increases at the very early stage of renal insufficiency in order to maintain normal serum phosphate concentration. Physiological FGF23 effects require the co-expression at the cell surface of a FGF receptor (FGFR) and aKlotho, a protein that acts as a co-receptor. aKlotho expression is restricted to few organs including the kidney and the parathyroid glands but in is absent in cardiomyocytes. A circulating form of aKlotho is present in the plasma. Its function is unknown. FGF23 can be cleaved in N and C-terminal peptides that have no physiological effect but could interfere with intact-FGF23 actions. Preliminary results obtained in collaboration by the two partners of this project have shown that intact-FGF23 can alter various functions of rat ventricular cardiomyocytes. These effects are mediated by a FGFR in the absence of aKlotho. The aim of this project is to further characterize the effects of intact FGF23 on cardiomyocyte and to determine if soluble aKlotho or the fragments of FGF23 can interfere with FGF23 effects on cardiomyocytes. In a first step we will perform experiments on primary culture of rat ventricular cardiomyocytes to determine if soluble aKlotho or FGF23 fragments alone can modify cardiomyocyte size, the kinetics of contraction, and calcium current transients. Using a proteomic platform we will assess the modifications of protein expression induced by the incubation of cardiomyocytes with soluble aKlotho or FGF23 fragments. We will check if aKlotho and FGF23 fragment can interfere with intact FGF23 action on cardiomyocytes. On the basis of the results obtained we will carry out in vivo experiments in rats with renal insufficiency to determine if overexpression of soluble aKlotho or FGF23 fragments alone or in combination could prevent intact FGF23 off-target effects on heart. aKlotho and FGF23 proteins will be expressed using adeno-associated viruses. We will measure heart conduction and functions using ECG, echocardiography, and cardiac MRI. We will perform histology analysis. We will check the occurrence of arrhythmia and heart performance with Langendorff apparatus. We will control if these treatments affect FGF23 function on phosphate and vitamin D homeostasis. Our result will determine if intact FGF23 can be a therapeutic target and if soluble aKlotho or FGF23 fragments can be used to design new therapeutic strategies to prevent the high rate of cardiovascular death observed in chronic kidney disease, which is a public health concern. Decreasing FGF23 concentration using blocking antibodies cannot be used to lower FGF23 effects on heart. In animals this strategy augments the mortality since it results in an increase in plasma phosphate concentration and subsequent vascular calcifications due to the suppression of the beneficial effect of intact FGF23 on the kidney to regulate phosphate homeostasis. This project aims at finding methods to prevent intact FGF23 action on heart without altering its effects on the kidney.