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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