Tissue-Specific and Genetic Regulation of Insulin Sensitivity-Associated Transcripts in African Americans

Abstract

Integrative multiomics analyses of adipose and muscle tissue transcripts, S, and genotypes revealed novel genetic regulatory mechanisms of insulin resistance in African Americans.

Figure 1.

Common and tissue-specific characteristics of adipose and muscle tissue transcripts associated with S_I in AAs. A stacked bar graph shows enrichment of adipose (A) and muscle (B) tissue transcripts associated with S_I in IPA biological pathway analysis. A Venn diagram (C) shows overlap of adipose and muscle tissue transcripts positively or negatively associated with S_I. Scatter plot (D) shows the concordance and discordance in direction of association (effect, β from regression analysis) of transcripts associated with S_I in both adipose and muscle tissue. Visualization of running sum statistics from advanced gene set enrichment analysis (GSEA, GeneTrail) shows (E) common and tissue-specific modulation of transcripts with S_I and enrichment in biological pathways.

Figure 2.

Ninjurin1 (NINJ1) transcript is associated with S_I and cis-eSNPs for this transcript also associate with S_I in AAs. The scatter plot shows association of NINJ1 transcript expression (ILMN_1815086) in adipose tissue with S_I and BMI (A, B). The box plot shows association of NINJ1 transcript expression (ILMN_1815086) in adipose with genotype of the cis-eSNP rs7033638 (C) and association of S_I and with genotype of the SNP rs7033638 (D). LocusZoom plots show regional association of NINJ1 cis-eQTL region SNPs (genotyped and imputed) with transcript expression and S_I (E, F). Significance level (-log10 P-values) indicated in LocusZoom plots are based on score test implemented in the program SNPTEST. LD plot shows LD relationship (r²) between genotyped SNPs in the marked region.

Figure 3.

Knockdown of NINJ1 expression in vitro in THP1 cells modulated expression of target genes. A, Relative expression of NINJ1 in pooled RNA samples from stromal vascular fractions compared with the adipocyte fraction of sc adipose tissue in AAs. B, Phorbol ester exposed (TPA/PMA, 10 ng/mL for 48 h) differentiated THP1 macrophages showed strong induction of NINJ1 expression compared with undifferentiated (control) cells. C, Transduction of THP1 cells by NINJ1 specific lentiviral shRNA stably knocked down its expression at baseline and in the TPA-induced differentiated state compared with control-shRNA lentiviral particle–treated cells. Stable knockdown efficiency of NINJ1 expression determined by qRT-PCR from two independent experiments (each with 2–3 biological replicates for each condition are shown. Expression of two other macrophage genes (CD68 and LCP1) was unchanged. D–K, ShRNA-mediated abrogation of NINJ1 induction in PMA/TPA treated THP1 macrophages significantly abrogated induction of several genes, while enhancing the expression of other genes. Validation of selected RNA-seq identified genes by qRT-PCR are shown. #, P < .01 lv-shRNA-control vs lv-shRNA-NINJ1 in basal or undifferentiated condition; *, P < .01 lv-shRNA-control vs lv-shRNA-NINJ1 in TPA treated or differentiated THP1 cells.