Gene and protein expression in human megakaryocytes derived from induced pluripotent stem cells

Abstract

Background There is interest in deriving megakaryocytes (MKs) from pluripotent stem cells (iPSC) for biological studies. We previously found that genomic structural integrity and genotype concordance is maintained in iPSC‐derived MKs. Objective To establish a comprehensive dataset of genes and proteins expressed in iPSC‐derived MKs. Methods iPSCs were reprogrammed from peripheral blood mononuclear cells (MNCs) and MKs were derived from the iPSCs in 194 healthy European American and African American subjects. mRNA was isolated and gene expression measured by RNA sequencing. Protein expression was measured in 62 of the subjects using mass spectrometry. Results and Conclusions MKs expressed genes and proteins known to be important in MK and platelet function and demonstrated good agreement with previous studies in human MKs derived from CD34+ progenitor cells. The percent of cells expressing the MK markers CD41 and CD42a was consistent in biological replicates, but variable across subjects, suggesting that unidentified subject‐specific factors determine differentiation of MKs from iPSCs. Gene and protein sets important in platelet function were associated with increasing expression of CD41/42a, while those related to more basic cellular functions were associated with lower CD41/42a expression. There was differential gene expression by the sex and race (but not age) of the subject. Numerous genes and proteins were highly expressed in MKs but not known to play a role in MK or platelet function; these represent excellent candidates for future study of hematopoiesis, platelet formation, and/or platelet function.

Modeling genetic platelet disorders with human pluripotent stem cells: mega-progress but wanting more on our plate(let)

“…Most importantly, the authors found a very high concordance of tissue-specific expression quantitative trait loci in both iMKs and platelets, validating this platform for studying the genetics of platelet-related phenotypes. In support, an extension of this study by demonstrated very good agreement between gene expression in iMKs and previous studies in which megakaryocytes were derived from cord blood or bone marrow sources, confirming that iMKs are a relevant model for native megakaryocytes [26 ▪ ]. They also observed that both sex and race have significant effects on differential gene expression but not differential protein expression.…”

“…In native megakaryocytes, these characteristics are lowest in yolk sac-derived megakaryocytes and higher in fetal liver-derived, cord blood-derived, and bone marrow-derived megakaryocytes [54,55,57,58]. (Bottom) Pluripotent stem cell-derived megakaryocytes (iMKs) are strong models for yolk-sac hematopoiesis [26 ▪ ,60]. For disease modeling, induced pluripotent stem cells are particularly advantageous because they are patient-specific and can be edited with technology such as CRISPR-Cas9 to produce isogenic controls.…”

resVAE ensemble: Unsupervised identification of gene sets in multi-modal single-cell sequencing data using deep ensembles

“…and mediators of immune relevance ( IL1B , IL8 , CXCL1 , CXCL2 , TGFBI etc.) ( Cunin and Nigrovic, 2019 ; Kammers et al, 2021 ). resVAE also managed to identify other biologically meaningful genes missed by Seurat, including a cell surface receptor on B cells involved in isotype switching ( CD40 ; Bishop and Hostager, 2001 ), a cell adhesion molecule expressed on T cells that is a well-known marker for naïve and memory cells ( SELL ; Yang et al, 2011 ), a pro-inflammatory cytokine expressed on NK cells ( IL32 ; Yang et al, 2019 ) and more ( Figure 3E ).…”

Secondary analyses for genome‐wide association studies using expression quantitative trait loci

“…Details on the iPSC derived MK and PLT samples used in the RNA sequencing are described in detail elsewhere (Kammers et al, 2017; Kammers, Taub, Mathias, et al, 2021; Kammers, Taub, Rodriguez, et al, 2021). Briefly, for 185 iPSC‐derived MK cell lines and for 290 PLT samples with WGS data we also obtained RNA‐seq data from extracted nonribosomal RNA.…”