The mtDNA replication-related genes TFAM and POLG are associated with leprosy in Han Chinese from Southwest China

https://doi.org/10.1016/j.jdermsci.2017.09.001Get rights and content

Highlights

  • TFAM and POLG affect risk to leprosy in Han Chinese.

  • Rs1049432 and rs3176238 are cis eQTLs in human tissues.

  • Differential mRNA expression of POLG in leprotic skin lesions.

Abstract

Background

The pathogen Mycobacterium leprae of leprosy is heavily dependent on the host energy metabolites and nutritional products for survival. Previously we and others have identified associations of several mitochondrion-related genes and mitochondrial DNA (mtDNA) copy number alterations with leprosy and/or its subtype. We hypothesized that genetic variants of mtDNA replication-related genes would affect leprosy.

Objective

We aimed to identify genetic associations between the mtDNA replication-related genes TFAM, POLG and leprosy.

Methods

Genetic association study was performed in 2898 individuals from two independent sample sets in Yunnan Province, China. We first screened 7 tag SNPs of TFAM and POLG in 527 leprosy cases and 583 controls (Sample I). Expression quantitative trait loci (eQTL) analysis and differential mRNA expression were analyzed to discern potential effect of risk variants. The entire exon region of TFAM and POLG were further analyzed in 798 leprosy cases and 990 controls (Sample II; 4327 East Asians from the ExAC dataset was included as a reference control) by using targeted gene sequencing for fine mapping potentially causal variants.

Results

Two tag SNPs of TFAM (rs1049432, P = 0.007) and POLG (rs3176238, P = 0.006) were associated with multibacillary leprosy (MB) in Sample I and the significance survived correction for multiple comparisons. SNPs rs1937 of TFAM (which was linked with rs1049432) and rs61756401 of POLG were associated with leprosy, whereas no potentially causative coding variants were identified in Sample II. The eQTL analysis showed that rs1049432 was a significant cis eQTL for TFAM in nerve tissue (P = 1.20 × 10−12), and rs3176238 was a significant cis eQTL for POLG in nerve (P = 3.90 × 10−13) and skin tissues (P = 2.50 × 10−11). Consistently, mRNA level of POLG was differentially expressed in leprotic skin lesions.

Conclusions

Genetic variants of TFAM and POLG were associated with leprosy in Han Chinese, presumably by affecting gene expression.

Introduction

Leprosy is a chronic infectious and neurological disease [1], [2] that affects around 200,000 people each year [3]. The pathogen, Mycobacterium leprae (M. leprae), is an obligate intracellular parasite with an extremely eroded genome [4], [5]. Nearly 50% of coding genes in M. leprae genome, especially these genes in energy metabolic pathways, were pseudogenized or lost [4], [5]. This evolutionary event led to an essential dependence of the host energy metabolites and nutritional products for the survival of M. leprae.

Mitochondria play key roles in cellular energy supply and antimicrobial immune response [6], [7] and may be actively involved in the infection of M. leprae given its eroded genome and dependence on host metabolism [8]. An increasing number of studies showed that mitochondrial dysfunction could cause heart, nervous and immune system diseases [6], [7], [9]. Recently, we found that the mitochondrion-related genes that were encoded by chromosomal genes, such as OPA1 [10], LRRK2 [11], PINK1 and PARL [12] were associated with leprosy per se and/or clinical subtypes, but the mitochondrion-related antimicrobial/antiviral immune genes MAVS, MITA and MFN2 were not associated with leprosy [13]. In patients with lepromatous leprosy (LL), there was a higher mitochondrial DNA (mtDNA) copy number than those with the other clinical subtypes [8], which might be caused by the alteration of the host mtDNA replication effect or autophagy [14] after the load of M. leprae and different host immune reactions. In this study, we hypothesized that mtDNA replication-related genes mitochondrial transcription factor A (TFAM) and mtDNA polymerase gamma (POLG) were associated with leprosy and this might explain the altered mtDNA copy number in lepromatous leprosy [8]. TFAM is an essential protein component of the mitochondrial nucleoid core complex [15]. It plays a key role in mtDNA transcription, replication and repair [16], [17]. Previous association study showed that rs2306604 of TFAM affects the risk for Alzheimer's disease (AD) [18], and mtDNA copy number was increased in TFAM transgenic animals [19]. The POLG gene is located in chromosome 15q26 and encodes a catalytic subunit of mtDNA polymerase [20]. It also plays an essential role in mtDNA replication and repair [21]. Dysfunction of POLG has been reported in Parkinson’s disease (PD) [22], [23] and other mitochondrial syndromes [24]. Leprosy was regarded as a neurological disease [2] and it would be naturally to test potential associations of TFAM and POLG with leprosy given the roles of these two genes in neurological diseases [18], [22], [23].

In this study, we performed a genetic association study to discern potential association of TFAM and POLG with leprosy in two independent sample sets from Yunnan Province, China. Seven tag single nucleotide polymorphisms (SNPs) of TFAM and POLG were analyzed in Sample I (527 leprosy cases and 583 controls). Together with expression quantitative trait loci (eQTL) analysis and differential mRNA expression analysis of leprotic skin lesions, we aimed to characterize the roles of TFAM and POLG in leprosy. We also directly sequenced the complete coding region of TFAM and POLG in Sample II (798 leprosy cases and 990 controls) using the next-generation sequencing (NGS) technologies to validate the association and to identify potential causal variants. Our results indicated that TFAM and POLG confer genetic susceptibility to leprosy in Han Chinese.

Section snippets

Subjects

A total of 2898 individuals were collected from the Yuxi Prefecture and Wenshan Prefecture, Yunnan Province of Southwest China. The Yuxi sample served as Sample I and had been described in our previous studies [10], [11]. In brief, 527 leprosy patients (onset age from 2 to 67 years, 387 males and 140 females, 279 multibacillary [MB] and 248 paucibacillary [PB] patients) and 583 healthy control subjects (age from 4 to 88 years, 365 males and 218 females) were collected from the same geographic

TFAM rs1049432 and POLG rs3176238 conferred genetic susceptibility to leprosy

The MAF of the 7 tag SNPs in TFAM and POLG ranged from 11.2% to 49.5% in our Sample I (Table 1). Assuming an odds ratio (OR) value as 1.6 for risk allele, the power was expected to be above 89.5% (Fig. S1). All the tag SNPs were in HWE in both controls and cases (Table S2). The observed distributions of allele and genotype frequencies in leprosy patients and controls were summarized in Tables 1 and S3, respectively. The TFAM rs1049432 was associated with leprosy per se (T allele, P = 0.002, OR

Discussion

Increasing evidence suggests that mitochondrion-related genes play important roles of in antimicrobial immune response and energy production [6], [47]. Under an evolutionary hypothesis of host energy dependence of M. leprae due to its eroded genome, we and others speculated that genetic variants of host mitochondrion-related genes would affect risk to leprosy. Indeed, there are many reports for association of mitochondrion-related genes with leprosy [10], [11], [12], [48], [49], albeit there is

Conflict of interest

The authors declare no conflict of interest.

Acknowledgements

This study was supported by the National Natural Science Foundation of China (81573034, 31271346), Yunnan Province (2014FB177) and West Light Foundation of the Chinese Academy of Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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