Intrinsic abilities and nutrition in population : the role of Reactive Oxygen Species analyzed by mathematical modelling

PhD proposal

Supervisors: S. Guyonnet & N. Davezac

Team S. Andrieu (U1027)

The objective is to study the relationship between nutrition and intrinsic capacities and understand the impact of Reactive Oxygen Species (ROS) metabolism in this context. For this, different approaches will be carried out within the framework of the INSPIRE platform to promote healthy aging. First, the epidemiological component will be made from data from human cohorts, aged 70 and over, randomized with multi-domain interventions in order to analyze the link between the nutrition and intrinsic abilities. Existing cohorts (MAPT, NOLAN, COGFRAIL) will be analyzed as well as the ongoing cohort of the INSPIRE project. We developed a mathematical model centred on the mitochondrial dysfunctions and more precisely on the dysfunction of mitochondrial respiratory chain (MRC) as it was shown to be a major point in ROS production (80% of total ROS production).

 

The MRC can be divided in two models, one concerning Complex I and the other concerning Complex III as they are the principal providers of ROS. Detoxification of ROS in the mitochondria and then in the cytoplasm is being added. The PhD student will perform biological experiments to determine biological parameters with different quantities of NADH substrates of the MRC and different antioxidant component to mimic the different food intakes and modulate ROS metabolism. This sysiugiuguygtem-level model, which has been built taking into account the desired level of detail, is then used to explain, predict and analyse the behaviours of the biological system. Thus, it becomes possible to use the model as a way of proving hypothesis and performing predictions. This translational study will help to better understand the fundamental mechanisms of aging associating alimentation and intrinsic abilities as well as molecular level with ROS production, and in the long term, to offer treatments as well as predict and / or prevent the onset of pathologies in humans.

Key words: ROS, nutrition, mathematics

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PhD program

The PhD program is devoted to enroll students in various transdisciplinary research topics from very basic science to clinical or pharmacological outcomes. PhD research proposals are under the supervision of CARe-associated research teams from academic laboratories or partner companies. PhD proposals are selected by CARe committees and on line in spring every year. Candidates must send a complete biosketch and will be selected by a mixed board. PhD student will spend a part of the PhD abroad.

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Investigate the importance of mitochondria in cognitive processes during aging

PhD proposal

PhD supervisor : Claire Rampon & Marie-Christine Miquel – CRCA

PhD co-supervisor : Kevin Richetin – CHUV Lausanne, Swiss

 

The maintenance of healthy mitochondria is critical for brain functions throughout adult life. Aging is associated with a decrease in mitochondrial quality, the decline of biological functions and the development of several diseases. 

In the mammalian brain, considerable evidence shows that mitochondrial dysfunction occurs early and contributes to the loss of synaptic function and plasticity. In this context, the two research groups involved in this project (CNRS UNIV. Toulouse 3 and CHUV Lausanne, Switzerland) recently demonstrated that mitochondrial disorders play a primordial role in hippocampal function and memory performances during Alzheimer’s disease. However, it remains unclear how aging per se affects mitochondrial dynamics and functions in the hippocampus and whether mitochondrial defects are causal in neuronal dysfunction.

This project aims to understand the importance of mitochondria in cognition during healthy and pathological aging. Through access to primate and human brain biobanks (K Richetin) combined with the manipulation of mitochondrial dynamics targeting hippocampal neural cell populations in mice (MC Miquel/ C Rampon), we will seek for new crucial information linking mitochondria to brain plasticity and cognitive functions throughout aging. We expect that this study will shed light on an unexplored aspect of cognitive diseases, possibly leading to novel diagnostic approaches.

Key words: mitochondria, aging

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The mouth and the biological ageing process: bidirectional influences and biological markers

PhD proposal

Supervisor: Jean-Noel Vergnes

Team S. andrieu (U1027)

Biological ageing is a complex process, influenced by genetic and environmental
factors. Factors influencing the ageing of the mouth are in part genetic, but are mainly related to lifestyles habits, and hence often depend on socio-economic status. Numerous diseases of the oral cavity share common risk factors with other non-communicable diseases like diabetes or cancer. There is a bidirectional relationship between oral health and biological ageing. On one hand, age-related diseases, like dementia, cancer or geriatric depression, are frequent in elderly persons, and might have a direct impact on oral health. For example, oral health status may be jeopardised by frailty, disability, care dependency or limited access to professional oral health care. Another example is the side effect of several medications in causing xerostomia and hyposalivation. On the other hand, oral health problems such as periodontitis, unstable removable dentures, insufficient chewing or dysphagia are related to low Oral Health Reported Quality of Life scores, and nutritional state in geriatric individuals.

 

Besides this bidirectional relationship, the mouth also represents a potential source of biomarkers that can be collected in a non-invasively and cost-effectively way. We hypothesize that oral biomarkers (particularly salivary markers) can be integrated into predictive models for estimating biological age and/or detecting age-related diseases. Biomarkers represent an attractive measure of biological ageing and may potentially improve our understanding of underlying ageing processes and age-related disease.

The aims of this thesis will be 1) to better understand the bidirectional influences between oral health and biological ageing and 2) to explore how biomarkers from the mouth could be used as diagnostic tools to identify altered aging profiles.

In order to achieve these objectives, we plan to undertake two research phases. 

  • During the first phase, we will explore and synthesize the current literature in order to generate new knowledge (meta-synthesis of the literature).
  • During the second phase, we will analyse data from on-going cohorts, basing the choice of research criteria on the knowledge acquired from the first phase, in order to produce new primary knowledge.

Key words: biological aging, biomarkers, oral health, meta-research, clinical epidemiology, predictive model

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Automatic knowledge extraction and structuration in digital pathology images: applications to decision support tools for diagnosis and complex immunostaining analysis

PhD proposal

Supervisors: Pierre Brousset

Team P. Brousset (CRCT)

Deep convolutional neural networks (CNN) have been tackling, with impressive results, most of the pattern recognition challenges of the past few decades. With the advent of efficient digitization techniques for microscopy slides (Whole slide images, WSI), the use of deep learning models on histopathology images has been widely explored as it may save time and reduce errors in the diagnosis, prognosis or response to therapy predictions.

In that field, most of the clinically relevant tasks have been addressed under the framework of supervised classification [1]–[3]. Yet, despite countless efforts of design and optimization, the clinical use and deployment of the developed solutions remain difficult mostly due to domain adaption issues [4].

To override these limitations, the idea is to considerably widen the dictionary of structures and lesions to be recognized by supervised classifiers [5], [6]. Label comprehensiveness is a key-concept to produce any type of decision in a reliable, explainable and interpretable way that would fit with clinical routine [8]–[10].

Indeed, in the classical supervised framework, this can only be done at the cost of making highly qualified experts label tremendous amounts of images.

Therefore, this work has the ambition to lay the foundation of automated diagnosis and multiplex/complex immunostaining analysis with minimal supervision. Related to data mining approaches, that remain under-explored in the field of WSIs analysis [12]–[14]. Statistical models developed in this study will mix auto-supervised strategies [15], [16] with metric learning or generative models [17]–[21], as well as general-purpose feature transfer methods [22]–[25] to gather general and widely re-usable knowledge in large sets of raw unannotated WSIs.

Beyond statistical learning, this work will focus on the structure of the results. Inspired by the Knowledge Graph, the semantic web and graph databases technologies, AI tools will handle multiple decisional contexts and will take decisions based on logic and deduction. While the models will rely on « symbolic » AI, one major theoretical aspect is to formulate graph generation as an optimization problem that is compatible with gradient descent and backpropagation algorithm.

Key words: Digital Pathology, automated diagnosis, immunostaining analysis, data mining, auto-supervised learning, metric learning, generative models, structured knowledge.

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Intrinsic abilities and nutrition in population : the role of Reactive Oxygen Species analyzed by mathematical modelling

PhD proposal

Supervisors: S. Guyonnet & N. Davezac

Team S. Andrieu (U1027)

The objective is to study the relationship between nutrition and intrinsic capacities and understand the impact of Reactive Oxygen Species (ROS) metabolism in this context. For this, different approaches will be carried out within the framework of the INSPIRE platform to promote healthy aging. First, the epidemiological component will be made from data from human cohorts, aged 70 and over, randomized with multi-domain interventions in order to analyze the link between the nutrition and intrinsic abilities. Existing cohorts (MAPT, NOLAN, COGFRAIL) will be analyzed as well as the ongoing cohort of the INSPIRE project. We developed a mathematical model centred on the mitochondrial dysfunctions and more precisely on the dysfunction of mitochondrial respiratory chain (MRC) as it was shown to be a major point in ROS production (80% of total ROS production).

 

The MRC can be divided in two models, one concerning Complex I and the other concerning Complex III as they are the principal providers of ROS. Detoxification of ROS in the mitochondria and then in the cytoplasm is being added. The PhD student will perform biological experiments to determine biological parameters with different quantities of NADH substrates of the MRC and different antioxidant component to mimic the different food intakes and modulate ROS metabolism. This system-level model, which has been built taking into account the desired level of detail, is then used to explain, predict and analyse the behaviours of the biological system. Thus, it becomes possible to use the model as a way of proving hypothesis and performing predictions. This translational study will help to better understand the fundamental mechanisms of aging associating alimentation and intrinsic abilities as well as molecular level with ROS production, and in the long term, to offer treatments as well as predict and / or prevent the onset of pathologies in humans.

Key words: ROS, nutrition, mathematics

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Role of the myelomonocytic lineage in Noonan syndrome-associated clinical traits

PhD proposal

Supervisor: A. Yart

Team P. Valet – I2MC

The general aim of the thesis project is to better understand the pathophysiology of Noonan syndrome (NS), a relatively frequent (1/2000 live births) genetic disorder associating cranio-facial features, cardiopathies, short stature and learning disability. Beside these congenital involvements, patients with NS also display a wide range of clinical traits that are reminiscent of early ageing, the pathophysiology of which is misunderstood: bone defects (e.g. decreased bone mass), muscle weakness, predisposition to myeloproliferative disorders (e.g. juvenile myelomonocytic leukaemia, JMML) and metabolic imbalance (e.g. insulin resistance). Interestingly, we and other obtained striking evidences that many of NS impairments are related to the dysfunction of cells from the myelomonocytic lineage : myeloid precursors in JMML, osteoclast in bone defects, monocytes/macrophages in insulin resistance. As a result, our project now aims

  1. to understand the cellular and molecular mechanisms that confer on these cells their pathophysiological potential with a particular focus on the pro-senescent potential of RAS/MAPK hyperactivation,
  2. to assess the relative contribution of myelomonocytic cells to the development of the different traits of the disease, and
  3. to translate the obtained observations to the clinics.

For this, we will favour a translational, comprehensive approach taking advantage of our expertise on the pathophysiology of NS, a wide range of approaches to specifically alter myeloid cells in pre-clinical models (knock in mouse and zebrafish) and evaluate the consequences on major postnatal/evolutive symptoms of the disease and a large and well-documented cohort of patients associated to a full biological collection and results from ongoing clinical trials.

 We expect to demonstrate that a dysfunction of cells from the myeloid lineage, in line with increased senescence, participates to multiple traits of NS, thereby highlighting a founding pathophysiological mechanism which could pave the way for the development of “many birds/one stone” therapeutic strategies. Beyond rare diseases, these results could help better understanding monocyte/macrophage biology and provide new insights into frequent pathologies involving myelomonocytic cells.

Key words: genetic diseases, macrophage, senescence, inflammation

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Modeling TNF-induced ceramide metabolism changes in T-cell immuno-senescence and resistance of melanoma patients to immune checkpoint inhibitors

PhD proposal

Supervisor: B. Segui

Team T. Levade – CRCT

Cutaneous melanoma is a very aggressive and immunogenic skin cancer that can be treated by immunotherapy based on the administration of antibodies neutralizing CTLA-4 and PD-1, two immune checkpoints expressed on the surface of activated T lymphocytes, acting as a real brake on lymphocyte activation. To date, the best clinical responses in patients with advanced melanoma have been obtained with the combination of ipilimumab (anti-CTLA-4) and nivolumab (anti-PD-1). However, almost half of patients with metastatic melanoma do not respond to this treatment and there are no biomarkers predictive of resistance. In this context, cellular senescence, a process of genetic, epigenetic and metabolic reprogramming as well as morphological modifications of the cell during aging, seems to play a dual role in resistance to immunotherapy.

While the senescence of cancer cells and regulatory T cells appears to facilitate the response to immunotherapies in mice and humans, the senescence of effector T cells may contribute to resistance mechanisms. Among the mechanisms of cellular senescence, a distinction is made between replicative senescence, linked to the shortening of telomeres as cell divisions progress, premature senescence induced by stressors such as pro-inflammatory cytokines (IFNg and TNF) and senescence induced by oncogenes such as BRAFV600E, which is expressed in 50% of melanomas.

Our laboratory has demonstrated two mechanisms of resistance to immunotherapies in murine melanoma models, one based on the production of TNF in the tumor microenvironment, the other dependent on the expression in melanoma cells of sphingosine kinase 1 (SK1), a lipid metabolism enzyme from the ceramide family. In addition, we have shown that the expression of SK1 in human tumor biopsies is a predictive biomarker of resistance to anti-PD-1. Our work constitutes the scientific rationale of two clinical trials in patients with advanced melanoma, TICIMEL and IMMUSPHINX, which aim to assess the impact of anti-TNF agents in melanoma immunotherapy and to identify in the biological samples of patients (blood and tumor biopsies) of biomarkers of resistance / response to immunotherapies. Biomarkers are sought among cytokines and metabolites of ceramide in plasma (measured by mesoscale and mass spectrometry, respectively), profile, gene expression and methylation of peripheral blood mononuclear cells (evaluated by flow cytometry, RNA Seq / CITE Seq single Seq RNA Seq, methyloma), leukocyte infiltrate of tumors (evaluated by immunohistochemistry) and the expression of enzymes of the metabolism of ceramide in tumors (evaluated by in situ hybridization).

The thesis work will consist of developing computer modeling approaches of all the big data collected in the two clinical trials TICIMEL and IMMUSPHINX in order to identify signatures of senescence in regulatory T lymphocytes and effectors predictive of response and resistance to immunotherapies, respectively. In addition, we will study whether these signatures are associated with alterations in the metabolism of ceramide dependent on TNF signaling.

Key words: Cancer, immunotherapy, Clinical trials, Biomarkers, big data, bioinformatics

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Blood platelets, Thrombosis and Aging: deciphering novel molecular mechanisms for therapy

PhD proposal

Supervisor: S. SEVERIN

Team B. Payrastre – I2MC

The thrombotic risk, mainly due to blood platelet dysfunctions, has a considerable impact in the cardiovascular complications in elderly. However, the mechanisms involved in the increased thrombotic risk and platelet dysfunctions associated to aging are still poorly characterized and therapeutic strategies are very limited. In this context, it seems urgent (i) to better understand the mechanisms involved in the dysfunction of platelet production and activation in an aging context and (ii) to find new pharmacological platelet targets or biomarkers in order to prevent and limit thrombotic complications. The research PhD project aims to finely study the processes of production and activation of blood platelets, from molecular mechanisms to pathophysiology, in an aging context. This project will use transgenic mouse models and a panel of in vivo experimental procedures in mice as well as in vitro and ex vivo imaging and biochemical techniques.

Key words: Blood platelets, Megakaryocytes, Thrombosis, Aging

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Multiomics analysis and modeling to predict metabolic response in the resistance to leukemia therapies

PhD proposal

Supervisor: J.E. SARRY

Team J.E. Sarry – CRCT

Despite a high rate of complete remission after treatment with genotoxic agents, the prognosis is poor in human acute myeloid leukemia (AML). Front-line chemotherapy is highly effective in ablating leukemic cells, but relapses caused by tumor regrowth initiated by resistant leukemic clones (RLCs) are observed in the majority of patients. The biology of therapeutic resistance currently represents an active area of research. However, the molecular mechanisms underlying drug resistance are still poorly understood in AML, especially in the in vivo context. To address this issue and to characterize chemoresistance and minimal residual disease (MRD), we established a robust patient-derived xenograft (PDX)-based preclinical model that predicts response to chemothepeutics in AML patients. Taking advantage of these in vivo models, we demonstrated that in vivo drug tolerant/resistant AML cells present an enhanced mitochondrial oxidative metabolism. Furthermore, our studies shown that the catabolic flexibility, the inflammatory response, and the metabolic cooperation between stromal and leukemic compartments are key players of mitochondrial activities of chemoresistant AML cells13,14. Therefore our previous results provide not only new targets but also a strong scientific rationale for ongoing clinical trials that assessed emerging combinatory therapies with different mitochondrial inhibitors in AML. Altogether, our work suggests that the mitochondrial function, the metabolic cooperation and symbiosis between the stromal and leukemic compartments inside the bone marrow niche, and inflammatory/stress responses, play a crucial role in drug resistance of AML.

 In light of our current results and evidences, our working hypothesis is that the microenvironment-tumor interplay regulates mitochondrial metabolism of AML cells through the activation of key transcriptional factors and regulons, and of stress responses, leading to drug resistance in vivo. To address this hypothesis and to further decipher the heterogeneity of these drug resistance pathways at both single cell and tissue levels, our methodological strategy is based on functional approaches using well-characterized AML cell lines and primary patient samples in vitro and in our xenograft NSG model coupled to bulk and single cell omics and computational approaches. Finally, our preliminary single cell transcriptomic analysis of cells collected from PDX and patients at diagnosis and relapse uncovered a subpopulation endowed with a specific transcriptional profile implicated into (and predictive of) the relapse in AML.

Key Words: AML, drug resistance, metabolism, in silico modeling, computational prediction

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