MicroRNA expression in abdominal and gluteal adipose tissue is associated with mRNA expression levels and partly genetically driven

Abstract

To understand how miRNAs contribute to the molecular phenotype of adipose tissues and related traits, we performed global miRNA expression profiling in subcutaneous abdominal and gluteal adipose tissue of 70 human subjects and characterised which miRNAs were differentially expressed between these tissues. We found that 12% of the miRNAs were significantly differentially expressed between abdominal and gluteal adipose tissue (FDR adjusted p<0.05) in the primary study, of which 59 replicated in a follow-up study of 40 additional subjects. Further, 14 miRNAs were found to be associated with metabolic syndrome case-control status in abdominal tissue and three of these replicated (primary study: FDR adjusted p<0.05, replication: p<0.05 and directionally consistent effect). Genome-wide genotyping was performed in the 70 subjects to enable miRNA expression quantitative trait loci (eQTL) analysis. Candidate miRNA eQTLs were followed-up in the additional 40 subjects and six significant, independent cis-located miRNA eQTLs (primary study: p<0.001; replication: p<0.05 and directionally consistent effect) were identified. Finally, global mRNA expression profiling was performed in both tissues to enable association analysis between miRNA and target mRNA expression levels. We find 22% miRNAs in abdominal and 9% miRNAs in gluteal adipose tissue with expression levels significantly associated with the expression of corresponding target mRNAs (FDR adjusted p<0.05). Taken together, our results indicate a clear difference in the miRNA molecular phenotypic profile of abdominal and gluteal adipose tissue, that the expressions of some miRNAs are influenced by cis-located genetic variants and that miRNAs are associated with expression levels of their predicted mRNA targets.

Figure 1. Tissue differential expression (the tissue-related fixed-effects coefficients (β)), of the 59 miRNA that were replicated (p-value<0.05) in the replication study.

The coefficients (β) are sorted on effect-size, a positive value indicating higher expression in gluteal adipose tissue relative abdominal adipose tissue. Error-bars show the standard-error of β for each miRNA.

Figure 2. Locus plots for miRNA eQTLs that replicated.

P-values from the primary study are shown in figure (criteria for replication: p-value<0.001 in the primary study and p-value<0.05 in the replication study with a directionally consistent effect). A) Abdominal adipose tissue hsa-miR-1255a:rs1822168 (p-value = 1.83E-05 in primary study and p-value = 9.91E-03 in replication study) B) Abdominal adipose tissue hsa-miR-618: rs1716543 (p-value = 5.34E-04 in primary study and p-value = 5.80E-03 in replication study) C) Abdominal adipose tissue hsa-miR-146a*:rs2961920 (p-value = 5.87E-04e in primary study and p-value = 6.45E-06 in replication study) D) Gluteal adipose tissue hsa-miR-1255a:rs1822168 (p-value = 1.56E-05 in primary study and p-value = 1.65E-04 in replication study), E) Gluteal adipose tissue hsa-miR-1307:rs11191666 (p-value = 1.27E-04 in primary study and p-value = 3.55E-04 in replication study), F) Gluteal adipose tissue hsa-miR-330-3p:rs7252175 (p-value = 3.85E-04 in primary study and p-value = 4.04E-02 in replication study).

Figure 3. Genetic effects in replicated miRNA eQTLs in abdominal adipose tissue (see Materials and Methods section for criteria).

The violin-plot represents the density of miRNA expression relating to the SNP effect for each genotype (variability relating to the other fixed effects was regressed out); the line represents the fixed-effect coefficient (β) relating to the SNP effect. A) Primary study hsa-miR-1255a:rs1822168 B) Primary study hsa-miR-618:rs1716543 C) Primary study hsa-miR-146a*:rs2961920 D) Replication study hsa-miR-1255a:rs1822168 E) Replication study hsa-miR-618:rs1716543. F) Replication study hsa-miR-146a*:rs2961920.

Figure 4. Genetic effects in replicated miRNA eQTLs in gluteal adipose tissue (see Materials and Methods section for criteria).

The violin-plot represents the density of miRNA expression relating to the SNP effect for each genotype (variability relating to other fixed effects was regressed out); the line represents the fixed-effect coefficient (β) relating to the SNP effect. A) Primary study hsa-miR-1255a:rs1822168 B) Primary study hsa-miR-1307:rs11191666. C) Primary study hsa-miR-330-3p:rs7252175 D) Replication study hsa-miR-1255a:rs1822168. E) Follow up study hsa-miR-1307:rs11191666. F) Replication study hsa-miR-330-3p:rs7252175.

Figure 5. (A) Venn diagram showing the number of common and unique miRNAs with significant association to their target mRNAs in each adipose tissue type.

(B) Venn diagram showing the number of common and unique KEGG terms in each adipose tissue type.