Genomic physiology of eukaryotes

About

Physiological and pathological regeneration of the respiratory tract epithelium

Our group aims to identify the cellular and molecular mechanisms involved in the regeneration of the human respiratory tract epithelium. We play an active role within the international consortium Human Lung Cell Atlas, Our goal is to create a comprehensive molecular map of human lung cells. Within this framework, we contributed to the creation of the first cellular atlas of the human airways using biopsies from healthy donors, leveraging single-cell RNA sequencing technologies. Our most recent work focuses on the molecular mechanisms underlying secretory cell hyperplasia, a pathological phenomenon observed in several chronic respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis.

Wastewater epidemiology (respiratory viruses)

We are developing approaches to optimize the detection and monitoring of human pathogenic viruses in wastewater, particularly respiratory viruses (coronavirus, influenza A H1N1 and H3N2, influenza B, RSV). One of the objectives of the national OBEPINE consortium, in which we participate, is to establish a public health surveillance system based on the virological analysis of wastewater networks, a task to which we have committed ourselves. dedicated since the 2020 pandemic, using samples collected Primarily at the Haliotis wastewater treatment plant, which treats wastewater from a catchment area of over 400,000 inhabitants in the Nice Côte d'Azur Metropolitan Area. We have developed and validated a complete processing chain, from sampling to results reporting, including the extraction of viral nucleic acids and the standardization of quantification and analysis methods. The combination of quantitative digital PCR and sequencing approaches allows us to characterize the diversity and evolution of viral strains detected in environmental samples. Current research focuses on monitoring major respiratory viruses, such as SARS-CoV-2 and influenza viruses, with the aim of more effectively anticipating the emergence or resurgence of epidemics. This approach represents an innovative tool for strengthening epidemiological surveillance and improving preparedness for future infectious threats.

Development of new methods in genomics

Our group aims to develop bioinformatics tools applied to transcriptomic data to better understand biological mechanisms, highlighting cellular interactions and dynamics. We work on two main areas: firstly, spatial transcriptomics, which allows us to analyze the expression of hundreds of genes in their native tissue context using Xenium (10x Genomics) and MERSCOPE (Vizgen) technologies; and secondly, single-cell transcriptomics using long-read sequencing, which offers the possibility of studying the expression of isoforms of all genes in the genome with Nanopore technology (Oxford Nanopore). Our tools, distributed as Python or R packages, are designed for ease of use by the scientific community and are based on standards established by the international scVerse consortium.

This theme applies directly to the data generated by our team, allowing us to map the cellular organization within the human respiratory system and to study the complexity of diseases such as chronic obstructive pulmonary disease (COPD).