Journal: Communications Biology

Article Title: Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency

doi: 10.1038/s42003-022-03942-4

Figure Lengend Snippet: a Heatmap and Venn diagram illustrating cardiac DEGs (ANOVA, p < 0.05, |FC| ≥ 1.2, n = 3) identified across the genotypes relative to WT by microarray analysis. For the heatmap, DEGs were first sorted from most up-regulated to most down-regulated in KI:KO hearts compared to WT prior to unsupervised sample clustering using Euclidean distance measure and average linkage. b Gene Set Enrichment Analysis showing an up-regulated hallmark inflammatory gene signature in ERRα KO and KI:KO cardiac transcriptomes vs WT. Normalized enrichment scores (NES), representative plots and gene heatmaps are shown. c Representative images and quantification of Aif-1 staining of mouse heart sections as a marker of macrophage infiltration ( n = 3). Scale bar, 50 μm. d Heatmap of matrisome DEGs. Arrows adjacent to genes signify that their expression was validated by RT-qPCR in ( e ). e Cardiac RT-qPCR analysis of key genes in ( d ) linked to TGF-β activation and signaling (n = 6). Data are normalized to Rplp0 levels. f Immunoblot analysis of α-SMA in heart tissue extracts ( n = 3). Vinculin levels are shown as a loading control. g Representative images and quantification of α-SMA staining of mouse heart sections ( n = 3). Scale bar, 50 μm. Data in ( c , e , and g ) represent means ± SEM; * p < 0.05 by ANOVA relative to WT controls, unless otherwise indicated. See also Supplementary Fig. .

Article Snippet: Volcano plots and heatmap were generated using GraphPad Prism (version 9) and Morpheus ( https://software.broadinstitute.org/morpheus/ ), respectively.

Techniques: Microarray, Staining, Marker, Expressing, Quantitative RT-PCR, Activation Assay, Western Blot, Control

Journal: Communications Biology

Article Title: Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency

doi: 10.1038/s42003-022-03942-4

Figure Lengend Snippet: a Simultaneous multi-comparison analysis of mouse heart transcriptomes integrated into metabolic networks identified 7 significantly perturbed metabolic modules among the genotypes. Genes found with the greatest correlation in expression and distance in a metabolic reaction network are scored higher and the relative expression of metabolic modules identified for a pattern of scoring genes was calculated across the groups. Heatmap expression patterns for each metabolic module across the groups are shown. b , c Gene signature heatmap and gene/metabolic network for 5 metabolic modules found in ( a ) displaying the strongest down-regulation ( b ) and up-regulation ( c ) upon the loss of both ErbB2 and ERRα signaling. Key significantly enriched pathways associated with DEGs within the metabolic networks are also shown. See also Supplementary Fig. .

Article Snippet: Volcano plots and heatmap were generated using GraphPad Prism (version 9) and Morpheus ( https://software.broadinstitute.org/morpheus/ ), respectively.

Techniques: Comparison, Expressing

Journal: Communications Biology

Article Title: Integrated multi-omics analysis of adverse cardiac remodeling and metabolic inflexibility upon ErbB2 and ERRα deficiency

doi: 10.1038/s42003-022-03942-4

Figure Lengend Snippet: a Bar chart and Venn diagram illustrating cardiac DEMs identified across genotypes relative to WT using a large-scale unbiased LC/MS-based screen (ANOVA, p < 0.05, n = 8). b Heatmap and pie charts of the cardiac mouse metabolomes subdivided into 8 major metabolic pathways. For the heatmap, DEMs were sorted from most up-regulated to most down-regulated in KI:KO hearts compared to WT within each metabolic category prior to unsupervised hierarchical sample clustering using Euclidean distance measure and average linkage. c , d Heatmap of cardiac fatty acid ( c ) and fatty acyl-carnitine ( d ) levels detected among the genotypes. e Box plot of free carnitine levels in mouse hearts ( n = 8). f Heatmap of relative glycogen metabolite and glycolytic intermediate levels in the mouse hearts and box plot of heart lactate levels ( n = 8). g RT-qPCR analysis of Ldha expression in mouse hearts ( n = 6). Data are normalized to Rplp0 levels. h Bar chart of circulating lactate levels in the mice ( n = 24). i , j Heatmap of amino acid ( i ) and dipeptide ( j ) profiles in the mouse hearts. k Box plot of mouse cardiac acetyl-CoA levels ( n = 8), produced by the breakdown and oxidation of lipids, carbohydrates, and protein. Data in ( e , f , and k ) are shown as box and whiskers plots: center line denotes median, box extends from 25th to 75th percentiles, and whiskers extend to the lowest and highest values; * p < 0.05 by ANOVA relative to WT controls, unless otherwise indicated. Data in ( g and h ) represent means ± SEM; * p < 0.05 by ANOVA relative to WT controls, unless otherwise indicated. Metabolites with an asterix (*) in the heatmap representations ( c , d , f , i , j ) were found significantly altered in the indicated mouse model versus WT, * p < 0.05 by ANOVA. See also Supplementary Fig. and .

Article Snippet: Volcano plots and heatmap were generated using GraphPad Prism (version 9) and Morpheus ( https://software.broadinstitute.org/morpheus/ ), respectively.

Techniques: Liquid Chromatography with Mass Spectroscopy, Quantitative RT-PCR, Expressing, Produced