How does a cell control the expression of its genome? How does this control support the development of a multicellular organism? What are the consequences of defective control mechanisms? How can these defects result in human diseases? These questions are far from being resolved. We have chosen to address them by focusing on the controls on RNA. While it was long thought that the bulk of gene expression controls were carried out on transcription, it is now clear that regulations on RNA, called post-transcriptional regulations, are at least as important. These regulations take place at many levels: (alternative) splicing, mRNA stability and location, and translation.
The "Gene expression and development" (GED) team studies post-transcriptional regulations, mainly using the amphibian Xenopus (Why Xenopus?), cultured cells and mice as models. This research has a strong impact on the understanding of human diseases.
Lens development and cataract
CELF1 is an RNA binding protein that plays many roles in RNA metabolism. We have observed that mice conditionally inactivated for the Celf1 gene suffer from congenital cataract. The cataract consists of ocular lens clouding, where ocular lens normally allows light to converge on the retina. Cataract is currently the leading cause of blindness in the world.
The transparency of the ocular lens is obtained by the very regular assembly of the lens fibers and by the loss of all their intracellular organelles, including their nuclei. These features, which are crucial for the functions of the crystalline lens, are lost in mice lacking the CELF1 protein.
We are currently characterising the CELF1-dependent gene regulatory network in the ocular lens, in order to identify the regulations that are important for lens physiopathology. Using functional genomics approaches, we systematically identify CELF1 RNA ligands by "CLIPseq" and differentially regulated genes by "RNAseq". Using imaging and biophysical approaches in CELF1-deficient lenses, we characterize their cellular organization and their biomechanical and optical properties. We use different cataract models (Xenopus larvae and lens spheroids) to decipher how changes in gene expression in the absence of CELF1 lead to cataract. These data will provide a better understanding of the lens diseases.
TP63 alternative splicing and head and neck squamous cell carcinoma
Alternative splicing of transcription factors greatly modifies gene expression networks. How do these mutiple isoforms of a single transcription factor affect cell physiology and how are their syntheses regulated ?
Head and neck cancers are the fourth most frequent cancer, with nearly 14,000 new cases each year in France. The vast majority are squamous cell carcinomas. The TP63 gene is frequently over-expressed in these cancers. It encodes a transcription factor, p63, of the same family as p53. This transcription factor is central in the biology of epithelial tissues and more particularly in the development and homeostasis of the epidermis. Two alternative promoters and multiple alternative splicing events allow the expression of at least eight different isoforms with different functional domains. Although the functions of these different isoforms have not been clearly described, it is clear that they have distinct properties. Understanding the link between the p63 factor and tumorigenesis or aggressiveness linked to the production of metastases is therefore complicated by the existence of these numerous isoforms.
The different isoforms of TP63 have different impacts on the survival of patients with head and neck squamous cell carcinomas. Currently, we are characterizing the role of RNA-binding proteins in the control of TP63 splicing and the impact of these different isoforms on cell physiology. We investigate the control of TP63 splicing using splicing reporter minigenes that recapitulate the regulation of TP63 by functionally inactivating RNA binding proteins. For phenotype analysis, we are evaluating the impact of modifying the relative proportions of different isoforms on cell proliferation and migration, and on the expression of TP63 markers and targets in 2D and 3D cell culture models.