LncRNA expression during cell differentiation

Studying cell differentiation has been revolutionized by the advent of single cell technologies. Moving beyond a stepwise view, we now depict a continuum process containing a range of intermediate cell states expressing different transcriptomic programs. Up to now, the annotation and understanding of these intermediate states mostly relied on protein-coding genes. However, while 2/3 of the genome is transcribed, only 2% of it is made of protein-coding transcripts, the rest being composed of non-coding genetic sequences. Moreover, it is well known that lncRNAs have tissue- and cell-specific expression patterns, meaning that they are potential key regulators of cell fate.

In this project, we propose to investigate the temporal expression of lncRNAs in myeloid cell differentiation in inflammatory cancers, especially focusing on the highly abundant “MDSC” populations in hepatocellular carcinoma. We wish to elucidate the regulatory relationships between lncRNAs and genes or gene networks in this specific context. This is an interdisciplinary project that will rely on cellular, molecular and computational biology. In collaboration with ImmunoConcEpT, we analyze multi-omic datasets and we develop new computational methods to identify new lncRNA transcripts.