Transcriptome profiling of megakaryocytes and platelets: Application to GP9- and IKZF5-related thrombocytopenia

Platelets are anucleate cells produced in the bone marrow and derived from large progenitor cells called megakaryocytes (MKs). Platelets receive RNA transcripts from their progenitorial MKs during thrombopoiesis. However, the correspondence between platelet and MK transcriptomes is poorly understood, particularly in the context of germline mutations that cause platelet formation defects or thrombocytopenia. We have studied the effects of two such mutations on MK and platelet transcriptomes. We generated immortalized MK cell line (imMKCL)-based models of Bernard–Soulier syndrome and IKZF5-related thrombocytopenia. MKs derived from imMKCLs with either a homozygous deletion of GP9 (GP9^−/−) or a heterozygous Y121F variant in IKZF5 (IKZF5^WT/Y121F) exhibited reduced proplatelet formation (reductions of 96% and 57%, respectively). Platelets from patients with either GP9^−/− or IKZF5^WT/Y121F genotypes had broad transcriptomic dysregulation, suggesting that (pro)platelet formation defects due to mutations in glycoprotein receptor and transcription factor genes such as GP9 and IKZF5 already affect the MK transcriptome. RNA-seq data from MKs at four stages of differentiation revealed widespread but distinct changes in expression over time between the GP9^−/− and the IKZF5^WT/Y121F genotypes. Dysregulated genes in GP9^−/− MKs were enriched for RNA metabolism and actin/tubulin folding pathways, whereas those in IKZF5^WT/Y121F MKs were enriched for cell cycle pathways. Most of these genes were also dysregulated in the platelets of patients with the corresponding diseases. Our results suggest that patients with inherited forms of thrombocytopenia present with specific transcriptomic changes during platelet formation.