Spatial and temporal gene expression patterns in the microenvironment promoting hematopoietic stem cell generation in vivo

Every day, hematopoietic stem cells (HSCs) produce billions of new blood cells essential for life. Defects in HSCs lead to blood-related disorders and various cancers (e.g. anemia, leukemia). The transplantation of healthy donor HSCs to replace the patient defective ones is an important part of the treatment. Less than 30% of the patients have matched donors in their family. Therefore successful transplantation in most patients relies on finding unrelated volunteer donors with the highest compatibility (the chance of an optimal match being very low). Since the number of transplantations increases every year, the availability of HSCs has become a major hurdle. To circumvent this shortage, huge efforts have been made to expand donor HSCs ex vivo or to generate new sources of HSCs in vitro (e.g. from pluripotent stem cells or somatic cells). Success has been limited so far mainly because the extrinsic events promoting HSC production in vivo remain largely unknown, and therefore difficult to reproduce in vitro. HSCs are initially generated during embryonic development. Others and we have proven that HSCs are first produced in the aorta from specialized endothelial precursors. Identifying the regulatory factors produced by the aortic microenvironment, which constitutes the physiological niche for HSC generation, would certainly help to design optimal in vitro HSC culture conditions in the future. The genome-wide RNA tomography technique (tomo-seq) was recently developed by the van Oudenaarden lab to combine RNA-Sequencing data and spatial information. Notably, it was used to generate a high-resolution genome-wide 3D atlas of gene expression in the whole zebrafish embryo. The originality of our approach will be to use the tomo-seq technique to accurately determine spatial gene expression patterns in restricted regions of the aorta of mouse and chicken embryos (and human embryos when available) isolated at different developmental stages. It will allow to infer the spatio-temporal dynamics of gene expression and to identify key genes responsible for HSC generation in the embryo. The advantage of using embryos is that the timing and location of HSC production within the aorta are precisely known. Moreover, the tomo-seq data obtained from different species will be compared to find conserved candidate genes and pathways (and therefore most likely relevant for humans). Our approach will have the unique advantage to provide a global view of the gene expression patterns in the whole microenvironment (as it is organized in vivo around the aorta). We will further test the inhibition/activation potential of selected and validated candidate genes on HSC generation, both in vitro and in vivo. I anticipate that our study will significantly advance our knowledge of the complex network of factors and pathways involved in the microenvironment supporting HSC production in vivo. It should prove useful in the future for engineering appropriate in vitro culture conditions to produce autologous HSC grafts needed to treat inherited and acquired blood disorders.