Sex-specific regulation of mitochondrial DNA levels: genome-wide linkage analysis to identify quantitative trait loci

Abstract

Altered mitochondrial DNA (mtDNA) levels have been associated with common diseases in humans. We investigated the genetic mechanism that controls mtDNA levels using genome-wide linkage analyses in families from the Genetic Analysis of Idiopathic Thrombophilia Project (GAIT). We measure mtDNA levels by quantitative real-time PCR in 386 subjects from 21 extended Spanish families. A variance component linkage method using 485 microsatellites was conducted to evaluate linkage and to detect quantitative trait loci (QTLs) involved in the control of mtDNA levels. The heritalibility of mtDNA levels was 0.33 (p=1.82e-05). We identified a QTL on Chromosome 2 (LOD=2.21) using all of the subjects, independently on their sex. When females and males were analysed separately, three QTLs were identified. Females showed the same QTL on Chromosome 2 (LOD=3.09), indicating that the QTL identified in the analysis using all of the subjects was a strong female QTL, and another one on Chromosome 3 (LOD=2.67), whereas in males a QTL was identified on Chromosome 1 (LOD=2.81). These QTLs were fine-mapped to find associations with mtDNA levels. The most significant SNP association was for the rs10888838 on Chromosome 1 in males. This SNP mapped to the gene MRPL37, involved in mitochondrial protein translation. The rs2140855 on Chromosome 2 showed association in the analysis using all of the subjects. It was near the gene CMPK2, which encodes a mitochondrial enzyme of the salvage pathway of deoxyribonucleotide synthesis. Our results provide evidence of a sex-specific genetic mechanism for the control of mtDNA levels and provide a framework to identify new genes that influence mtDNA levels.

Figure 1. Linkage analysis for mtDNA levels in subjects of both sexes.

There is a linkage signal in Chromosome 2 with a peak LOD score of 2.21 (p = 7.09e-04) defining a quantitative trait locus for mtDNA levels in a region that maps to 2p25.3-2p24.3.

Figure 2. Linkage analysis for mtDNA levels in females only.

The linkage signal detected in Chromosome 2 in the first analysis including the subjects of both sexes remains in the analysis performed with females only. However, this linkage signal in the sex-specfic analysis becomes better defined and more significant (LOD score of 3.09; p = 8.11e-05). In addition, a new quantitative trait locus for mtDNA levels is detected in Chromosome 3 only in females (LOD score of 2.67; p = 2.27e-04). Fine-mapping of the female-specific QTLs detected on Chromosome 2 and Chromosome 3 was carried with a set of 790 and 2687 SNPs, respectively.

Figure 3. Linkage analysis for mtDNA levels in males only.

The linkage signal detected in Chromosome 2 in the first analysis including the subjects of both sexes completely disappears in the analysis performed with males only. However, a new significant linkage signal for mtDNA levels is detected in Chromosome 1 only in males (LOD score of 2.81). Fine-mapping in this linkage region with 971 SNPs reveals the most significant SNP association with mtDNA levels for the rs10888838 (MAF = 0.1133; p = 4.01e-06) in the analysis with males only. This SNP was located in the gene MRPL37, which emerges as a strong candidate gene for the control of mtDNA levels in males.