RNAseq experimental analysis

To study the molecular mechanisms involved in fate decision for liver and pancreas, which originate from a common progenitor, we profiled gene expression in liver and pancreas progenitors from two time points using RNAseq [1]. The non-canonical Wnt pathway was identified and found to be able to induce the pancreatic lineage. One of the genes observed to be differentially expressed in pancreatic or hepatic lineage commited cells was the TALE homeodomain-containing transcription factor TGIF2. As a follow up of this study, we were able to use the TGIF2 protein (using a lentiviral expression vector) to reprogram adult mouse hepatocytes into pancreatic progenitors in vitro and in vivo [2], characterized using RNAseq of the transformed cells.

The sea urchin is a non-chordate deuterostome that is used as a model for embryonic development. We measured gene expression at eleven time points during embryonic and larval development of Lytechinus variegatus. the sea urchin Atlantic species, which is currently not so well studied as Strongylocentrotus purpuratus, the Pacific species. Expression changes are observed not to be gradual but rather separated by three abrupt transitions (hatching, gastrulation and morphogenesis) in four stages during which expression is rather stable [3]. We propose to investigate if punctuated changes in expression are an organizational feature of the development of all animal and plant embryos.

Huntington's disease is a neurodegenerative disease caused by a mutation in the huntingtin gene that causes neuronal death in the brains of older people. To search for potential marker genes in blood, we produced and analysed the transcriptome of peripheral blood from patients and matched controls [4]. We found a number of genes significantly dysregulated, prominently, the upregulation of genes related to inflammatory and immune response, indicating that the progression of the disease in the brain can indeed be detected in the blood. This result implies that the effect of therapies could potentially be assessed using blood tests.


[1] Rodriguez-Seguel, E., N. Mah, H. Naumann, I.M. Pongrac, N. Cerdá-Esteban, J.F. Fontaine, Y. Wang, W. Chen, M.A. Andrade-Navarro, F.M. Spagnoli. 2013. Mutually exclusive signaling signatures define the hepatic and pancreatic progenitor cell lineages divergence. Genes and Development27, 1932-1946. Seguel13_cover

[2] Cerdá-Esteban, N., H. Naumann, S. Ruzittu, N. Mah, I.M. Pongrac, C. Cozzicorto, A. Hommel, M.A. Andrade-Navarro, E. Bonifacio, F.M. Spagnoli. 2017. Stepwise reprogramming of liver cells to a pancreas progenitor state by the transcriptional regulator Tgif2. Nature Communications. 8, 14127.

[3] Hogan, J.D., J.L. Keenan, L. Luo, J. Ibn-Salem, A. Lamba, D. Schatzberg, M.L. Piacentino, D.T. Zuch, A.B. Core, C. Blumberg, B. Timmermann, J.H. Grau, E. Speranza, M.A. Andrade-Navarro, N. Irie, A.J. Poustka and C.A. Bradham. 2020. The developmental transcriptome for Lytechinus variegatus exhibits temporally punctuated gene expression changes. Dev. Biol. 460, 139-154.

[4] Andrade-Navarro, M.A., K, Muehlenberg, E. Spruth, N. Mah, A. González-López, T. Andreani, J. Russ, M.R. Huska, E.M. Muro, J.F. Fontaine, V. Amstislavskiy, A. Soldatov, W. Nietfeld, E.E. Wanker, J. Priller. 2020. RNA sequencing of human peripheral blood cells indicates upregulation of immune-related genes in Huntington’s disease. Frontiers in Neurology. 11, 573560.