Journal: Nature Communications
Article Title: Comprehensive promotion of iPSC-CM maturation by integrating metabolic medium with nanopatterning and electrostimulation
doi: 10.1038/s41467-025-58044-6
Figure Lengend Snippet: a Enrichment maps illustrating clustered pathways identified in gene set enrichment analysis (GSEA) based on canonical pathway database. The colour scale represents normalised enrichment score (NES). Pathways were filtered based on max. size of 500 genes, NES ≥ 1.5, false discovery rate (FDR) q -value ≤ 0.2 and cluster size of ≥ 2 pathways. b , c Enrichment plots and most regulated genes in TFAM and HMCES clusters. The colour scale represents z-score. d Quantification of Tom20 intensity detected in cTNT-positive CM populations. n = 10 independent experiments with 3 different iPSC lines. Log transformation was performed for statistical analysis. e , f Seahorse mean traces ( e ) and determined parameters ( f ) were performed with sequential addition of oligomycin (ATP synthase inhibitor), carbonyl cyanide-p-(trifluoromethoxy) phenylhydrazone (FCCP; mitochondrial uncoupler) and rotenone/antimycin A (complex 1 and 2 inhibitor). n = 4 (B27, MM + NP + ES) and 5 (MM, MM + NP) independent experiments using 2 iPSC lines. Orange, red, blue and green lines represent the four experimental groups: B27, MM, MM + NP, and MM + NP + ES, respectively. g Relative expression of OPA1 , PPARGC1α and PPARα determined using real-time PCR. HPRT is used as control. Data from 7 ( PPARα , PPARGC1α ) or 8 ( OPA1 ) independent experiments of 3 iPSC lines. Symbols in ( d , f , g ) denote iPSC lines: circles for isWT7, squares for iWTD2, and triangles for iBM76. h Heatmaps of selected genes encoding ion channels including those significantly differentially expressed genes among the three groups. The colour scale represents z-score. Source data are provided as a Source Data file. Statistical analysis was performed using linear mixed model (two-sided) with Tukey’s correction for multiple pairwise comparisons between the 4 groups ( d , f ), Kruskal-Wallis test with Dunn’s multiple comparison test ( g ), or the Wald test of DESeq2 (two-sided) in ( b , c , h ). Exact p values in ( b , c , h ) are provided in the Source Data file. Data are presented as mean ± SEM ( e ) and in box plots indicating median (middle line), 25th, 75th percentile (box) and min and max data points (whiskers) in ( d , f , g ).
Article Snippet: Gene set enrichment analysis (GSEA) was performed based on normalised count data using GSEA software v.4.3.2 and canonical pathways (CP) collection (C2, CP: c2.cp.v2023.2.Hs, https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=CP ) or TFT collection (C3, TFT: c3.tft.v2023.2, https://www.gsea-msigdb.org/gsea/msigdb/human/genesets.jsp?collection=TFT ), two Human Molecular Signatures Database (MSigDB) collections provided by the Broad institute with following parameters: weighted scoring, meandiv normalisation, max_probe mode, maximum gene set size 500 genes, minimum set size 15 genes, and 1000 permutations.
Techniques: Transformation Assay, Expressing, Real-time Polymerase Chain Reaction, Control, Comparison
