Nonalcoholic fatty liver disease (NAFLD) is the most prominent form of liver disease in the western world, affecting approximately one­third of the population, and is projected to become a major clinical and economic burden worldwide within the next decade. Chronic inflammation favors the perpetuation and aggravation of NAFLD, notably through the accumulation of activated macrophages. However, in inflamed tissues, macrophages are diverse. Indeed, two types of macrophages with different developmental origins cohabite: tissue resident macrophages (rMf) that self-maintain independently from circulating monocytes by proliferating locally, and inflammatory monocyte-derived macrophages (iMf) differentiated from circulating Ly-6C+ monocytes recruited to the inflamed tissue. While iMf are believed to play a detrimental role in NALFD and its complications, there is no available information on the specific roles played by rMf in these disorders. Such lack of knowledge is largely due to the absence of tools allowing to specifically target liver rMf, known as Kupffer cells (KCs), and this had precluded their appropriate study in physiology and physiopathology in general. To fill this gap, we have developed new mouse models and methods allowing us to study how KCs impact on liver metabolic diseases outcome. We will take advantage of these tools to study how specific modulation of pro and anti-inflammatory genes in KCs modulates NAFLD and its complications. In addition, our preliminary data also suggest that self-maintenance and activities of KCs are modulated by the environmental context of these pathologies (inflammation, lipid stress, …). Indeed, contrary to what is observed during healthy homeostasis, a significant part of KCs is replaced by cells of monocytic origin under conditions of NAFLD and steatohepatitis (NASH). We propose to further study this phenomenon. More specifically, our proposal entitled TARGETKC will allow us to: 1) Determine the mechanism underlying the participation of monocytes to the Kupffer cell pool under conditions of lipid stress, as well as the physiopathological role played by monocyte-derived KCs; 2) Determine how TLR4-mediated sensing of danger signals (gut-derived LPS, lipids, fetuin A, HMGB1, …) and tonic IL-10 production by KCs alter liver function, systemic inflammation as well as liver lipid metabolism in the context of NASH; and 3) Uncover molecular and lipid pathways induced in Kupffer cells under conditions of NASH using transcriptomic and lipidomics approaches.

A central problem in practical use of statistical models is the interpretability of a model. In many applications it is quite useful to construct a scoring system which can be defined as a sparse linear model where coefficients are simple, having few significant digits, or are even integers. Ideally, a scoring system is based on simple arithmetic operations, is sparse, and can be easily explained by human experts. In this project, we challenge the problem of automated interpretable score learning purely from data. Our main motivation from real applications is to construct simple rules which are meaningful for human experts and can be used by healthcare providers. Our goal is to introduce an original methodology to learn adaptive interpretable discretisation, and the scores associated with the learned categories (or thresholds). We aim to propose cost-sensitive heterogeneous cascading scoring systems taking into consideration the needs of physicians, costs of data acquisition, medical treatment, and introduce penalties for predicting wrong diagnosis. To realize this challenging task, we will develop multi-stage learning under budget. The project is extremely interdisciplinary, since there is a need to work on the intersection of statistical machine learning, decision making, optimization, and medicine. The DiagnoLearn unifies researchers whose expertise covers all mentioned domains.

Left ventricle hypertrophy (LVH) is an adaptive response of the heart to an increase workload. At the beginning, LVH is beneficial to maintain cardiac output by reducing wall stress, but it becomes maladaptive in the chronic phase, resulting in heart failure (HF). HF remains a deadly syndrome with 5-year mortality of 40-60%. Advancement of the understanding of the mechanisms underlying LV remodeling and the transition to HF is a prerequisite for the development of new efficient management strategies. A prominent and unique feature of cardiac muscle is the presence of intercalated discs (ID) at polarized ends of cardiomyocytes. ID are the “glue” which ensures mechanical and electrical coupling from one cardiomyocyte to another. Soon after birth, the cardiomyocytes elongate, ID are organizing toward a mature state. Human studies have shown that during LVH process, hypertrophied myocytes harbor dedifferentiated phenotype (ID destructuration, sarcomere depletion, glycogen accumulation, and alteration of mitochondria). It is proposed that these changes toward a fetal-like phenotype represent an adaptive programmed cell survival response. However, the biology of this phenomenon of recapitulation of an immature phenotype of the failing myocardium is largely unknown. The global objective of this proposal is to decipher new molecular mechanisms driving the LV remodeling and the transition to failure. Wnt/Planar Cell Polarity (PCP) pathway has recently emerged as a major regulator in adult organs for tissue morphogenesis. This ubiquitous system coordinates cellular communications; it involves polarized coupling between adjacent cells. By applying PCP features to heart morphogenesis, we hypothesize that the Wnt/PCP pathway may signal in the cardiomyocytes and control their polar organization and their remodeling and in fine the molecular balance from dedifferentiated immature toward a differentiated a phenotype and vice versa. Our working proposed model is that Wnt/PCP signaling is required during fetal maturation, for the organization of cardiomyocytes (immature phenotype) and is repressed when cardiomyocytes undergo differentiation In this project, we have asked whether Wnt/PCP signaling is reactivated during hypertrophic cardiomyopathy development and involved in HF. Our objective is to decrypt PCP signaling and its role in the process of cardiac morphogenesis. It will be the first demonstration that PCP signaling is involved in the physiopathology of the transition from LVH to HF. The core molecular machinery and regulation of PCP pathway is far to be known in mammals. We have recently identified a novel actor of PCP pathway: the ubiquitine E3 ligase, PDZRN3 and demonstrated its upstream critical role in the regulation of the Wnt/PCP signaling. To tackle this project, we have then developed original tools to overexpress and to delete specifically Pdzrn3 in cardiomyocytes in vivo (transgenic mice) and in vitro. In order to better understand the physiopathology basis of this reported phenotype of Pdzrn3 mutant mice, we have collected cardiac human tissues from patients suffering from various cardiomyopathies. Utilization of animal and cellular models to probe causes and mechanisms of cardiomyopathy disease will result in breakthroughs in diagnosis or prognosis tools or in development of novel treatments that will hopefully improve the outcome for HF patients.

At the back of the eye lies a monolayer of cells essential for vision: the retinal pigment epithelium (RPE). Apical microvilli from these polarized cells make close contact with the photosensitive photoreceptor outer segments (POS). POS are constantly renewed to fight the high levels of oxidative damage they are subjected to, and one of RPE cell main roles to maintain lifelong vision is the daily elimination of used POS tips by phagocytosis. Absence or failure to complete this task leads to the development of blinding diseases for which no treatment exists, such as early-onset retinal dystrophies or age-related macular degeneration (AMD). An important feature of RPE phagocytosis is its rhythmic activity. We showed previously that the alphavbeta5 integrin receptor controls the rhythmic activation of RPE phagocytosis. Subsequently, an intracellular signaling cascade activates the Mer tyrosine kinase (MerTK) internalization receptor. Our recent studies suggest that MerTK also controls the amounts of POS that can be tethered by RPE cells, including via the extracellular cleavage of MerTK. Interestingly, the known machinery for RPE phagocytosis is close to the clearance of apoptotic cells by macrophages. In macrophages, many molecules intervene in such processes, suggesting that similar intricate protein networks could operate in RPE cells. However, tissue specificity exists, including the permanent contact between photoreceptors and RPE cells, thus regulation of the machinery has to be controlled very tightly via several mechanisms to launch and stop phagocytosis at the proper time. Our recent data on the tissue-specific opposite role of MerTK ligands reinforce this idea. Moreover, several other receptors have been shown to be expressed by RPE cells, but their participation in POS phagocytosis has not been investigated yet. So far, studies on the phagocytic machinery have been performed on nocturnal rodent species using mostly rod photoreceptors sensitive to dim light. However, central vision in humans is mostly due to cones that give us details resolution and color vision. Rod and cone POS membrane structures are different and they are used for vision almost in exclusion of each other, either at night or during the day, respectively. Therefore, our hypothesis is that the elimination of used cone POS could take place at a different timing and with a different molecular machinery than for rod POS. For these reasons, with the REPHAGO project we plan on identifying the contribution of new membrane receptors in controlling the daily activation of rod (Aim 1) and cone (Aim 2) POS phagocytosis by RPE cells. Candidate receptors for rod POS phagocytosis will be validated in vitro and then in vivo for interesting candidates according to their implication during the phagocytic process. We will characterize cone-specific molecules for POS clearance using transcriptome studies associated with functional validation assays. For this project, we will use multiple state-of the art approaches (functional phagocytosis assays, in vivo phagocytosis assessment, RNAseq, visual animal phenotyping…) as well as new and innovative animal models (RPE-specific knockout mouse models for rod receptor candidates, cone-rich diurnal rodent model). Identified receptors will be then explored in other phagocytic cells. Understanding the complexity and specificity of protein networks and interactions to complete daily this crucial task will enlighten us both on normal retinal function and on the consequences of phagocytic defects. This will help us consider new avenues for therapies and therapeutic targets for these pathologies for which no treatment exists. As well, the sequential activation of the RPE machinery can help us decipher molecular pathways that are used in other phagocytic cells, and in particular macrophages. Thus, our results could contribute to the understanding of phagocytic processes occurring in other tissues or pathologies such as atherosclerosis.

Matrix Metalloproteinases (MMPs), as extracellular zinc-endopeptidase secreted by almost all hepatic cells, are directly involved in extracellular matrix remodeling and are implicated in the initiation, progression and resolution of liver diseases. In all liver diseases, these proteases' expression and activation patterns vary according to the pathological grade, making them relevant biomarkers for accurate diagnosis early liver fibrosis and monitoring of potential regression or progression to severe forms. The FibrosOr project tackles the development of non-invasive prognostics able to grade the severity of liver fibrosis. These diagnostic tools will consist of smart clearable gold nano-probes capable of responding to an MMP trigger (activity-based sensor) and producing a urinary signal detectable by the naked eye. The reticulation of small pegylated gold nanoparticles (AuNPs) with peptide linkers will result in gold-organic hybrid nanostructures (hAuNS). hAuNS will benefit from an extended blood circulation half-life and a hydrodynamic diameter (ca. 90 nm) to prevent their urinary elimination. In each hAuNS, AuNPs will be held together by MMP-cleavable peptides used as cross-linkers. After their injection in vivo, the “smart” hAuNS will accumulate preferentially in the liver tissue. Within the inflammatory environment, cleavage of the peptide sequence by the target MMP will result in the release of individual AuNPs with a much smaller hydrodynamic diameter (ca. 5 nm). A part of the free AuNPs will undergo exocytosis from the liver macrophages, escape the fibrotic tissue, and be eliminated by the renal route, thanks to their small size (below the glomerular filtration threshold which is about 8 nm). A dedicated colorimetric test will detect the actual presence of AuNPs in the urine and correlate to an uncontrolled MMP-catalyzed tissue remodeling within the liver. In addition, the concomitant use of three different hAuNS specific of MMP-9, MMP-12 or MMP-13, will allow multiplexed analysis to establish an MMP activity profile correlated to a particular grade of liver fibrosis.