Putative positive role of inflammatory genes in fat deposition supported by altered gene expression in purified human adipocytes and preadipocytes from lean and obese adipose tissues

Figures

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  Fig. 1. Overall schematic of the workflow. Workflow is depicted as a flowchart. Abbreviations used in this flowchart are as follows; AC, adipocyte; preAC, preadipocyte; DEG, differentially expressed gene; Le, lean extreme; Oe, obese extreme; Ag, AC differentiation; LS, lean AC differentiation-specific; OS, obese AC differentiation-specific; CA, commonly altered for both

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  Fig. 2. Classification of AC samples by DEGs. a Construction of the heatmap accompanied by unsupervised hierarchical clustering. Heatmap coupled with unsupervised hierarchical clustering is generated by the 1,198 DEGs that are estimated by comparing mRNA expression with P < 0.01 between 12 L-AC and 11 O-AC samples. Cyan and red bars located at top of the heatmap are replaced for the dendrograms generated by the clustering procedure where cyan and red bars represent lean and obese samples, respectively. ‘Le’, ‘I’, and ‘Oe’ represent extreme, intermediate, and obese extremes, respectively, as explained in the main text. The samples in blue and green ‘*’ indicate whether the patients have been treated with drugs for diabetes (DM) or hypertension (HTN), respectively. b GO analysis of ‘AC-DEGs’; the red and green bars represent upregulated (i.e., genes with higher levels in obese ACs than in lean ACs) and downregulated genes (i.e., genes with lower levels in obese ACs than in lean ACs), respectively. The functional terms with top significance by sorting P values in the GO analysis are represented only in the graph. The scale on the bottom indicates the -log10 P value of the significance of…

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  Fig. 3. Three classes of DEGs using the three redefined groups of samples. a Construction of heatmap coupled with unsupervised hierarchical clustering for three different classes of DEGs. A total of 2,657 ‘LO-DEGs’ (Q < 0.01), 1,474 ‘LI-DEGs’ (P < 0.01), and 1,324 ‘IO-DEGs’ (Q < 0.05) are used to construct a heatmap coupled with unsupervised clustering (refer to Additional file 4: Table S3). The same notations used for Fig. 2a are also used in this heatmap (refer to Fig. 2a legend). b Analysis of GO functional terms for each of the three classes of DEGs. ‘LO’, ‘LI’, and ‘IO’ represent ‘LO-DEGs’, ‘LI-DEGs’ and ‘IO-DEGs’, respectively. For each class of DEGs, genes are divided into upregulated genes (i.e., genes with higher levels in obese ACs than in lean ACs) and downregulated genes (i.e., genes with lower levels in obese ACs than in lean ACs). Wide red and blue boxes within the plot indicate upregulated and downregulated genes, respectively, for both ‘LO-DEGs’ and ‘IO-DEGs’. Narrow red and blue boxes within the plot indicate upregulated and downregulated genes, respectively, for the ‘LI-DEGs’

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  Fig. 4. Examination of changes in gene expression between lean ACs and obese ACs. Changes in gene expression are allocated into eight different categories: ‘progressive-up/down’, ‘initial-up/down’ ‘later-up/down’, and ‘up-to-down/down-to-up’. Each category of DEGs is obtained by intersecting ‘LI-DEGs’ and ‘IO-DEGs’ (refer to Additional file 6: Figure S3 for the detailed strategy for the subcategorization). A heatmap is generated for each category of DEGs with genes assigned to each category. The bars in the first column represent the trend of gene expression levels in each category, and the blue, gray, and red lines surrounding each bar represent genes in the Le, I, and Oe categories, respectively

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  Fig. 5. Differentiation of lean preAC samples and obese preAC samples by ‘Class II: preAC-DEGs’. a Construction of heatmap accompanied with unsupervised hierarchical clustering. A heatmap coupled with unsupervised hierarchical clustering is generated with a total of 213 ‘Class II: preAC-DEGs’ (P < 0.01) (Additional file 2: Table S1). Refer to the notations in the Fig. 2a legend. b GO analysis of ‘preAC-DEGs’; red and green bars represent upregulated (i.e., genes with higher levels in obese preACs than in lean preACs) and downregulated genes (i.e., genes with lower levels in obese preACs than in lean preACs), respectively. Refer to the Fig. 2b legend for how to select the functional terms and the meaning of the scale on the bottom

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  Fig. 6. Comparison of inflammatory gene expression in lean and obese adipogenesis. a A scatter plot was constructed with a total of 7,118 genes commonly altered in lean and obese adipogenesis (i.e., common DEGs between ‘Lean_Ag-DEGs’ and ‘Obese_Ag-DEGs’). Log2FC values of gene expression in ‘Lean_Ag-DEGs’ were plotted against log2FC values of gene expression in ‘Obese_Ag-DEGs’. The gray and red dots represent the total 7118 common DEGs and the inflammatory genes, respectively. The blue dashed diagonal line indicates a regression line for the values, while the black diagonal line indicates the line of equality (y = x). The correlation coefficient (γ) was calculated by Pearson correlation test. b Boxplots of gene expression values for three selected genes, i.e., IL-6, TNF-α, and IL-1β were constructed; the box plots in the left panel provide a comparison of the expression of these three genes in lean and obese AC samples, while the box plots in the right panel provide a comparison between ‘[AC/preAC]_lean’ (i.e., expression levels of these three genes in AC and preAC samples derived from the lean adipogenesis condition) and ‘[AC/preAC]_obese’ (i.e., expression levels of these three genes…