Role of trisomy 21, GATAs mutation and associated mutations in the development of a DS-AMKL model from IPSC: RNAseq

Acute megakaryoblastic leukemia of Down syndrome (DS-AMKL) is a model of clonal evolution from a preleukemic transient myeloproliferative disorder requiring both a trisomy 21 (T21) and a GATA1s mutation to a leukemia driven by additional driver mutations. We modeled this leukemic evolution through step-wise gene editing of GATA1s, SMC3+/- and MPLW515K providing 20 different trisomy or disomy 21 iPSC clones. For RNAseq, each condition was represented by a randomly selected clone and all the clones were isogenically compared. Cells were labeled with APC, BV421 and PE-conjugated antibodies against CD41a, CD42b and CD33 (see Table S5), respectively. In order to obtain a highly purified megakaryocytes, CD33+ cells were removed from the double positive CD41, CD42 population during cell sorting. After sorting, the purity was verified and corresponded to 98-100% of CD41+, CD42+, CD33. Total RNA was extracted using RNA/DNA/Protein Purification Plus Kit (Proteigene, St Marcel, France). Whole transcriptome sequencing was performed at the GenomEast Platform (Illkirch, France). cDNA libraries were synthesized from 250 ng total RNA using TruSeq Strandard mRNA Kit (Illumina). Libraries were verified for their amount and quality by capillary electrophoresis using a 2100 Bioanalyzer (Agilent Technologies). Sequencing was performed at 2100 bp using the Illumina HiSeq 4000 technology, yielding > 40 million reads per sample.