Adipose co-expression networks across Finns and Mexicans identify novel triglyceride-associated genes

Abstract

Background: High serum triglyceride (TG) levels is an established risk factor for coronary heart disease (CHD). Fat is stored in the form of TGs in human adipose tissue. We hypothesized that gene co-expression networks in human adipose tissue may be correlated with serum TG levels and help reveal novel genes involved in TG regulation.

Methods: Gene co-expression networks were constructed from two Finnish and one Mexican study sample using the blockwiseModules R function in Weighted Gene Co-expression Network Analysis (WGCNA). Overlap between TG-associated networks from each of the three study samples were calculated using a Fisher's Exact test. Gene ontology was used to determine known pathways enriched in each TG-associated network.

Results: We measured gene expression in adipose samples from two Finnish and one Mexican study sample. In each study sample, we observed a gene co-expression network that was significantly associated with serum TG levels. The TG modules observed in Finns and Mexicans significantly overlapped and shared 34 genes. Seven of the 34 genes (ARHGAP30, CCR1, CXCL16, FERMT3, HCST, RNASET2, SELPG) were identified as the key hub genes of all three TG modules. Furthermore, two of the 34 genes (ARHGAP9, LST1) reside in previous TG GWAS regions, suggesting them as the regional candidates underlying the GWAS signals.

Conclusions: This study presents a novel adipose gene co-expression network with 34 genes significantly correlated with serum TG across populations.

Figure 1

Finnish twin WGCNA results indicate that the blue module is associated with serum TG levels. Each row represents a module (labeled by color), and each column represents a trait. The value at the top of each square represents the correlation coefficient between the module eigengene and the trait with the correlation p-value in parentheses. The red color represents a positive correlation between the module eigengene and trait, and the green color represents a negative correlation. The number of gene expression probes present in each module and the percent of probes correlated with TGs (p<0.05, Pearson correlation) are listed in parenthesis next to the module color. To prevent potential confounding factors influencing expression values, gene expression values were corrected for age, sex, and twin relatedness using the Microarray Quality Control Pipeline as described previously [10]. TG values were log transformed and corrected for age, sex, disconcordant BMI status, and BMI using stepwise linear regression. BMI values were corrected for age, sex, disconcordant BMI status, and TG using stepwise linear regression. Genes that could not be clustered into one of the modules were assigned to the grey module, thus grey denotes background genes outside of modules. The blue module associated with TGs passed the Bonferroni correction for the 16 statistical tests performed (8 modules, 2 traits); the Bonferroni p-value cut-off = 3.1 x 10^-3.

Figure 2

Finnish twin WGCNA blue TG module is preserved in Mexican TG cases/controls. Each data point represents a Finnish twin WGCNA module. A Zsummary value over 2 represents a moderately preserved module. A Zsummary value over 10 provides strong evidence of module preservation. To prevent potential confounding factors influencing expression values, Finnish twin gene expression values were corrected for age, sex, and twin relatedness using the Microarray Quality Control Pipeline as described previously [10].

Figure 3

Genes in the Finnish and Mexican TG modules significantly overlap. The blue square represents Finnish TG module genes (n=320), and the pink square represents Mexican TG modules genes (n=123) determined by WGCNA. Area represented is proportional to the number of genes present in each group. P-value was calculated using a Fisher’s Exact test.