RNA sequencing and proteomic analysis upon mitochondrial stress. (A) Schematic representation of the omics experiments. HeLa cells were treated with compounds for 24 h, and the transcriptome, proteome, and metabolome were analyzed. Control cells were treated with DMSO. (B) Pie charts representing the total number of genes and proteins identified in all conditions by RNA sequencing and TMT quantitative proteomic analysis. Number of mitochondrial genes and proteins are represented in both charts, as well as the percentage relative to the total. (C) Heatmap analysis of the transcriptome (top) and proteome (bottom). Hierarchical clustering of samples (columns) and genes/proteins (rows) was based on Pearson’s correlation coefficient to measure the distance and the mean to cluster the samples. (D) Multidimensional scaling (MDS) using the distances between transcript expression profiles (top) and principal-component analysis (PCA) of the proteomic profiles (bottom) show a similar clustering between the duplicates and treatments. BCV, biological coefficient of variation; Comp, principal component. (E) Bar plots representing the number of differentially expressed (DE) genes (top) and proteins (bottom) in each condition (FDR 5%). Percentage of DE mitochondrial genes and proteins is shown, observing a greater impact on the mitochondrial proteome than on the mitochondrial transcriptome. Acti, actinonin; Dox, doxycycline; MB, MitoBloCK-6.