Abstract 18159: Transcriptomic Profiling of Isogenic PBMC-derived and iPSC-derived Macrophages and Their Polarization
iPSC technology has demonstrated enormous potential for in vitro disease modeling. However, an important issue in the field is to what extent iPSC-differentiated cells adopt the transcriptomic characteristics of the primary somatic cells. To address this question, we performed deep RNA-seq in PBMC-derived iPSC-differentiated macrophages (IPSDM, >95% purity, n=4) and their isogenic human PBMC-derived macrophages (HMDM, by M-CSF) counterparts that were validated to be phenotypically and functionally highly comparable. Multidimensional scaling and hierarchical clustering revealed marked transcriptome changes during iPSC transition to IPSDM, which led to 100 to >4,000-fold decreases in the expression of key pluripotency genes and a concomitant increase in that of key macrophage functional genes with an over-representation of GO terms associated with immune response, defense response, and inflammatory response. Compared with isogenic HMDM, IPSDM revealed ~90% genes to be similarly expressed, but 1,632 genes (~10% of detectable genes at 1st percentile FPKM) to be differentially expressed (DE) (FDR-adjusted P<0.01, fold-change>2). Genes expressed at higher levels in IPSDM include typical fibroblast markers and genes encoding collagen and extracellular matrix, but not lineage markers of other hematopoietic cells. M1-polarized (by LPS+IFN) cells showed distinct profile from non-polarized and M2-polarized (by IL-4) cells that were relatively less separated. There were marked overlap (>70%) of DE genes between non-polarized and M1-polarized cells in HMDM and IPSDM. Many of the genes expressed at lower levels in non-polarized IPSDM compared with HMDM were upregulated during subsequent polarization to levels comparable to that of M1- or M2- HMDM suggesting that polarization leads to greater convergence of ISPDM and HMDM transcriptome. In summary, at the transcriptome level, IPSDM and HMDM were similar with marked differences between IPSDM and their iPSC precursors. M1 polarization was associated with a dramatic and similar change in the transcriptome of IPSDM and HMDM.
Author Disclosures: H. Zhang: None. C. Xue: None. R. Shah: None. K. Bermingham: None. C.C. Hinkle: None. W. Yang: None. S.J. Gosai: None. D. VanDorn: None. S.T. Chou: None. B.D. Gregory: None. E.E. Morrisey: None. M. Li: None. D.J. Rader: None. M.P. Reilly: None.
- © 2014 by American Heart Association, Inc.