Gene expression profile in response to HIF-1a inhibition together with PPARa activation and the postnatal factors (T3, IGF-1 and dexamethasone) in hiPSC-CMs

Methods: RNA-seq libraries were prepared using the Illumina TruSeq technology. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq2500 system. Reads were mapped on the Human Genome Reference (GRCh38) and normalized expression table was generated. Results: Among differentially expressed genes, compared with DMSO-treated hiPSC-CMs, 505 genes were upregulated in FM+WY+TID-treated hiPSC-CMs, with 72 genes commonly upregulated in both FM+WY+TID-treated hiPSC-CMs and LV groups and 949 genes were downregulated in FM+WY+TID-treated hiPSC-CMs and 2137 genes were downregulated in LV, with 437 genes downregulated in both FM+WY+TID-treated hiPSC-CMs and LV compared with DMSO-treated hiPSC-CMs . Conclusions: Data demonstrate increased expression of genes associated with many metabolic processes which are also highly enriched in human pediatric heart samples including many interconnected metabolic processes that are upstream of lipid metabolism and FAO, agreeing with the shift to FAO for energy utilization in more mature CMs, and decreased expression of genes involved in developmental processes, adhesion and signaling in both FM+WY+TID-treated hiPSC-CMs and LV. The overlap in both upregulated and downregulated genes in both groups confirmed an advanced degree of cardiomyocyte maturation in response to FM+WY+TID. Overall design: RNA-sequencing analysis was performed to compare global gene expression profiles of hiPSC-CMs at differentiation day 28 with maturation factors (FM+WY+TID) treatment (Treat) vs. DMSO treatment (DMSO) vs. left ventricle tissue sample (LV).

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Gentillon C, Li D, Duan M, Yu WM, Preininger MK, Jha R, Rampoldi A, Saraf A, Gibson GC, Qu CK, Brown LA, Xu C