Transcriptome analysis of productive and unproductive pathways of in vitro megakaryocytopoiesis and their control by he AHR antagonist SR1

Human CD34+ progenitors can be in vitro differentiated into proplatelet-producing megakaryocytes (MKs) within 17 days. During this course, 4 cell populations emerge, phenotypically defined as CD34+CD41+ at day 7 (D7) and CD34+CD41+CD9- at D10 and D14 —qualified as “productive” because they can differentiate into proplatelet-forming cells during the D14-D17 period— and CD34-CD41+ or CD34+CD41+CD9+ at day 10 —qualified as “unproductive”, because unable to form proplatelets later. The productive pathway is boosted by the addition of SR1 at D0 and D7. To clarify the features of the productive and unproductive pathways, as well as the effect of SR1, the transcriptomes of the cell populations present at D0, 7, 10 and 14, generated in the presence of the absence of SR1 were determined by RNA-Seq. 95% pure human CD34+ cells were in vitro differentiated into megakaryocytes using a 14-day long protocol, in the absence or the presence of SR1. Cells populations were isolated according to their phenotype at D7, 10 or 14, their RNAs were extracted and processed for RNA-seq library preparation and analysis. For each condition (i.e. cell subpopulation, day of culture, SR1- or SR1+ condition), three independent biological replicates were processed.