Reference : UMR7275-GEOVAS-005
Workplace : VALBONNE
Date of publication : Monday, August 1, 2022
Scientific Responsible name : Georges Vassaux
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 3 October 2022
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Description of the thesis topic
Objective: The aim of this project is to develop a test to identify a non-genotoxic carcinogen (NGTxC) in the lung. The data generated, interpreted from a basic perspective, will provide a better understanding of the very early stages of carcinogenesis.
Techniques used: This research programme combines a well-established cellular model (3D lung epithelium cultured in an air/liquid interface (ALI)) and a state-of-the-art technique (single cell transcriptomics; sc-RNAseq). Sc-RNAseq is used to analyse the gene response of an ALI culture to carcinogens. The long-read sequencing technique will also be used. These new transcriptomics techniques were chosen because the more traditional approaches (global transcriptomic analysis) did not give any results that could be used in an industrial context.
Project update: This research programme started at the experimental level in 2018. The experiments carried out to date have enabled us to set up the experimental protocols and carry out the first sc-RNAseq experiments. This pilot study, carried out using three NGTxC substances, allowed us to set up an experimental and analysis platform that will be exploited for the entire project. The results obtained validated the basic hypothesis of the project, by demonstrating that the different cell types making up the ALI culture respond differently to the NGTxCs tested.
Thesis programme: We will build on this experience to increase the number of NGTxCs tested. Acute and chronic exposures are also planned. A "meta-analysis" of all the data obtained in sc-RNAseq will be carried out using techniques based on systems biology and artificial intelligence. This will allow the emergence of a characteristic signature common to all the NGTxCs tested in one or several cell types of the pulmonary epithelium.
Competence: He/she will be in charge of the bioinformatics analysis.
- Proven knowledge of transcriptomic analysis
- Biology (in-depth knowledge)
- English language: >B2 (Common European Framework of Reference for Languages)
- Implement transcriptomic analysis pipelines in R
- Knowledge of Python is a plus
- Oral and written communication skills (French/English)
- Ability to work in close collaboration with various French and foreign collaborators in the field.
The position is available at the Institute of Molecular and Cellular Pharmacology in Valbonne - Sophia Antipolis (Alpes Maritimes). The IPMC has 20 research teams and common services for a total staff of more than 220 people. The person recruited will work in the "Non-coding genome and pulmonary pathologies" research team. He/she will work closely with the IPMC's genomics platform, UCAGenomiX.
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