Fig. 5

Subcellular RNA localization changes upon Doxorubicin treatment in iPSC-derived cardiomyocytes. A Cardiomyocytes derived from human iPSCs were treated with DMSO or 2.5 μM DOX for 12 h. The localizations of 100 genes relevant to cardiomyocyte health and function were measured using Molecular Cartography. Cell boundaries were determined using ClusterMap and nuclei were segmented using Cellpose. B Top 10 differentially upregulated and downregulated genes in vehicle versus treatment. T-test was used for comparisons. All genes shown are significant given an adjusted p-value threshold of p < 0.01. Benjamini–Hochberg correction was used to control for the false discovery rate. Vehicle and treatment conditions have n = 7159 and 6260 cells respectively. C APEX-seq location-specific gene enrichment of fluxmap domains for the cytosol, endoplasmic reticulum membrane (ERM), endoplasmic reticulum lumen (ER Lumen), nuclear lamina, nucleus, nucleolus, nuclear pore, and outer mitochondrial matrix (OMM). D Fluxmap domains visualized for a representative field of view of cardiomyocytes for vehicle and treatment respectively highlighting cellular nuclei, ERM/OMM, ER Lumen, and cytosol. E RNAflux fluxmap enrichment of each gene averaged across vehicle and treatment cardiomyocytes captures changes in subcellular RNA localization. Top 10 genes are labeled and ranked by the largest shifts between compartment compositions. Shifts are quantified by Wasserstein distance. F Average gene enrichment in each fluxmap across vehicle and treatment conditions colored by log-fold expression demonstrates population-level shifts in transcript subcellular localization. G Visualization of RBM20, CACNB2, and LAMP2 transcripts confirms the depletion of transcripts from the perinuclear and cytosolic compartments of cardiomyocytes upon DOX treatment