PHD2020-20
An interdisciplinary approach to the study of lateralization in the nervous system.
Host laboratory and collaborators
Vincent Bertrand / IBDM / vincent.bertrand@univ-amu.fr
Paul Villoutreix / LIS / paul.VILLOUTREIX@univ-amu.fr
Pierre Recouvreux / IBDM / pierre.recouvreux@univ-amu.fr
Abstract
Although the nervous system is mainly left-right (L-R) symmetric at the structural level, some functional L-R asymmetries exist. Defects in the lateralization of the nervous system can lead to neurological disorders such as dyslexia. However, the extent of these functional L-R asymmetries and their origins remain poorly characterized. C. elegans is a good system to study this process as its nervous system is simple, and the position and lineage of every neuron has been mapped. Recently single cell RNAseq data have been generated for nearly all cells during embryogenesis and at larval stage. We propose here to combine these expression data with the lineage and the spatial localization of cells using applied mathematics approaches to identify novel molecular asymmetries in the nervous system. These asymmetries will then be experimentally validated using single molecule FISH expression profiling, and their consequences on the organization and function of the nervous system will be tested using CRISPR loss of function.
Keywords
Nervous system development, lateralization, C. elegans, single cell expression data, smFISH, CRISPR
Objectives
The objectives of the project are:
1) to map the molecular L-R asymmetries during nervous system development by mathematical integration of single cell expression profiles, lineage and position data, followed by experimental validation using single molecule FISH;
2) to functionally characterize the effects of these novel molecular L-R asymmetries on nervous system development and function using CRISPR loss of function approaches.
Proposed approach (experimental / theoretical / computational)
The team of P. Villoutreix is currently applying mathematical approaches (graph theory and high dimensional statistics) to integrate single cell RNAseq data with cell lineages and positions in order to develop an integrated view of C. elegans development. We propose here to use this global approach to measure the degree of molecular L-R asymmetry during nervous system development. Novel asymmetries will then be experimentally validated using single molecule RNA fluorescent in situ hybridization and reporter constructs. The team of V. Bertrand has previously identified by serendipity a transcription factor that is L-R asymmetrically expressed in a small subset of morphologically symmetric interneurons and motorneurons. This lineage will be used as a test case for mathematical data analysis. The role of newly identified molecular L-R asymmetries will then be characterised experimentally by analysing the effects of loss of function (using RNAi knockdown or CRISPR knockout) on nervous system organisation and function.
Interdisciplinarity
This project is based on a collaboration between teams of biologists (V. Bertrand), mathematicians (P. Villoutreix) and a biophysicist (P. Recouvreux of the team P. F. Lenne). The increased amount of large scale biological data generated in recent years (single cell expression profiles, lineage data, cell position data) requires the development of novel mathematical approaches to extract biologically meaningful information that can lead to experimentally testable hypothesis. Our project relies on this interdisciplinary logic to tackle an essential biological question: how is the functional lateralization of the brain established?
Expected profile
The student recruited on this project should have a background in experimental biology with an interest in computational biology. He/she will be involved in experimental work on C. elegans in the Bertrand lab and computational approaches in the Villoutreix lab. For computational analysis he/she will receive extensive support from Villoutreix lab members (including possibly but not necessarily a mathematics student recruited to develop mathematical approaches on a complementary project: Bridging morphogenesis and single cell transcriptomics during C. elegans early development, https://centuri-livingsystems.org/phd2020-12/).