|Mr Charles Plessy, Ph. D.
Senior scientist - Genomics Miniaturization Technology Unit
Building on the projects and achievements described below, I am now leading the Genomics Miniaturization Technology Unit in RIKEN's new Center for Life Science Technologies. This page will not be updated anymore; you can follow our work on single cells and population transcriptomics on our new website at the following address.
Population transcriptomics. We are developing high-troughput methods to profile the transcriptional activity of single cells. My goal is to establish a new field, population transcriptomics, where a biological sample (blood sample, dissociated cells, biopsy, microdissected tissue, etc.) is studied in terms of the population of cell it harbors, grouped by cell types, and the activities of these cells (for instance division, signalling, etc.). In that purpose, I am modifying the nanoCAGE technology that we have developed here, with the aim of 10,000 single cells per sample, that is, up to hundreds of thousands of cells in experimental setups with multiple replicated samples, or millions of cells when aiming at covering a broad number of cell types.
The CAGE method developed at the OSC (see the "Technologies" section of our website) is ideal for studying the regulatory mechanisms that govern cell differentiation and homeostasis, as it focuses on measuring the activity of gene promoters (transcription start sites), in an unbiased way open to the discovery of novel transcripts, with no pre-conceived limit on size, polyadenylation coding potential, etc. We are excited develop new CAGE protocols to produce data that will question many assumptions that were made when working complex mixtures, which will now isolate in single cells. Among the challenges ahead, there are the definition of gene promoters at the single-cell level, where stochastic transcript counts are expected, or the classification of single-cell profiles of promoter activitiy in overlapping categories extending the classical definitions from cell biology, such as cell type, position in the cell cycle, etc. Our role will be to find the novel and the unexpected at the single-cell resolution.
In parallel, I am also studying T and B lymphocytes by high-troughput sequencing, again with single-cell population transcriptomics as a goal, this time defining the cells by the sequence of their receptors.