Genome and stem cell plasticity in ageing​

The global project of the team is to explore basic genetic and epigenetic mechanisms underlying tissue regeneration, a process that takes place from early development through the entire lifetime and decreasing in the elderly. We aim to unravel and to manipulate age-related molecular pathways for efficient somatic cell reprogramming and to apply this knowledge to rejuvenation of cell physiology and improve tissue regeneration in chronic and aged related diseases, which is a major objective of regenerative medicine.

Mutations in genes involved in DNA metabolism or nuclear architecture can cause premature aging syndromes. Moreover, epigenetic modifications are associated to cellular aging and senescence leading to a “chromatin related aging memory” revealed by specific gene expression signature in stem cells, progenitors or differentiated cells. However, we showed recently that altered cellular aging/senescence physiology is reversible using a specific reprogramming strategy, through an induced pluripotent state. This indicate that it should be possible to modulate the aging process by interventions at the level of critical genetically and epigenetically-regulated networks. Although induced Pluripotent Stem Cells (iPSCs) exhibit the main biological features of hESCs, numerous hurdles need to be overcome for therapeutics applications, like accurate genetic diseases modeling or to obtain iPSCs at clinical grade for cell therapy. This includes specific developments to ensure genetic and epigenetic stability, during reprogramming responsible for some of the differences observed between hiPSCs and hESCs, so far demonstrated to generate cellular stress and senescence by themselves.

The project of the team is to explore genetic and epigenetic mechanisms involved in physiological and pathological cellular aging/senescence and its reprogramming. We will integrate different levels of analysis, from DNA sequence to local chromatin organization and to nuclear architecture to evaluate the limits of the cell plasticity in terms of genomic stability and genome organization during aging and rejuvenation from human cells.

Axis 1: To explore the epigenetic control of stem cell reprogramming in senescence/ ageing

1. Evaluation of the epigenetic control of senescence by studying the role of gene candidates involved in genome metabolism, selected in a siRNA screen developed for senescence induction or reversion.
2. Study of replication stress in different senescence induction processes and during reprogramming into iPSC.
3. Manipulating  cell fate in cellular aging/senescence in human and mice model to improve tissue regeneration in in vitro reconstructed tissue models  and in vivo in animal models.

Axis 2: To understand the origin and the nature of the DNA lesions occurring in hPSC

1. Mapping mutagenic events that occur during cell culture of hPluripotent Stem Cells using whole genome sequencing and RNA-seq data analysis with a software CRAC developed by members the team.
2. Understanding the nature of the DNA lesions occurring in hESC and iPSC in following replicative stress and DNA damage response and development of reprogramming strategies to prevent genomic instability. 
3. Understanding the dynamic and implication of L1 mobile elements in the genomic plasticity observed in hPSC during reprogramming and differentiation processes.

Axis 3: Developing human developmental age related disease models using induced pluripotent stem cells reprogramming.
Taking advantage of the expertise of our group on stem cell reprogramming from senescent and centenarian human fibroblasts, the SAFE-iPS platform from the INGESTEM project (directed by Jean-Marc Lemaitre) will offers a complete service to reprogram human cells and provide fully qualified iPSC to the medical and research community.

The team project is organized in different axis harboring specific objectives:

1. IPSC derivation of premature aging syndromes due to genetic mutations in genes involved in genome metabolism (like DNA helicases….) and age related diseases (like osteoarthritis) for diseases modeling. 
2. Developing differentiation protocols of iPSC into specific lineages with the aim to recapitulate the pathologies and further the etiology of the pathologies and to implement strategies of drug screening to delay pathological and physiological aging.
3. Exploring strategies for functional organ reconstruction from iPSCs.