No evidence of an association between mitochondrial DNA variants and osteoarthritis in 7393 cases and 5122 controls

Impact of genetically predicted characterization of mitochondrial DNA quantity and quality on osteoarthritis

Background: Existing studies have indicated that mitochondrial dysfunction may contribute to osteoarthritis (OA) development. However, the causal association between mitochondrial DNA (mtDNA) characterization and OA has not been extensively explored. Methods: Two-sample Mendelian randomization was performed to calculate the impact of mitochondrial genomic variations on overall OA as well as site-specific OA, with multiple analytical methods inverse variance weighted (IVW), weighted median (WM), MR-Egger and MR-robust adjusted profile score (MR-RAPS). Results: Genetically determined mitochondrial heteroplasmy (MtHz) and mtDNA abundance were not causally associated with overall OA. In site-specific OA analyses, the causal effect of mtDNA abundance on other OA sites, including hip, knee, thumb, hand, and finger, had not been discovered. There was a suggestively protective effect of MtHz on knee OA IVW OR = 0.632, 95% CI: 0.425-0.939, p-value = 0.023. No causal association between MtHz and other different OA phenotypes was found. Conclusion: MtHz shows potential to be a novel therapeutic target and biomarker on knee OA development. However, the variation of mtDNA abundance was measured from leukocyte in blood and the levels of MtHz were from saliva samples rather than cartilage or synovial tissues. Genotyping samples from synovial and cartilage can be a focus to further exploration.

Precision mitochondrial medicine

Mitochondria play a key role in cell homeostasis as a major source of intracellular energy (adenosine triphosphate), and as metabolic hubs regulating many canonical cell processes. Mitochondrial dysfunction has been widely documented in many common diseases, and genetic studies point towards a causal role in the pathogenesis of specific late-onset disorder. Together this makes targeting mitochondrial genes an attractive strategy for precision medicine. However, the genetics of mitochondrial biogenesis is complex, with over 1,100 candidate genes found in two different genomes: the nuclear DNA and mitochondrial DNA (mtDNA). Here, we review the current evidence associating mitochondrial genetic variants with distinct clinical phenotypes, with some having clear therapeutic implications. The strongest evidence has emerged through the investigation of rare inherited mitochondrial disorders, but genome-wide association studies also implicate mtDNA variants in the risk of developing common diseases, opening to door for the incorporation of mitochondrial genetic variant analysis in population disease risk stratification.

Is osteoarthritis a mitochondrial disease? What is the evidence

PROPOSE OF REVIEW

To summarize the evidence that suggests that osteoarthritis (OA) is a mitochondrial disease.

RECENT FINDINGS

Mitochondrial dysfunction together with mtDNA damage could contribute to cartilage degradation via several processes such as: (1) increased apoptosis; (2) decreased autophagy; (3) enhanced inflammatory response; (4) telomere shortening and increased senescence chondrocytes; (5) decreased mitochondrial biogenesis and mitophagy; (6) increased cartilage catabolism; (7) increased mitochondrial fusion leading to further reactive oxygen species production; and (8) impaired metabolic flexibility.

SUMMARY

Mitochondria play an important role in some events involved in the pathogenesis of OA, such as energy production, the generation of reactive oxygen and nitrogen species, apoptosis, authophagy, senescence and inflammation. The regulation of these processes in the cartilage is at least partially controlled by retrograde regulation from mitochondria and mitochondrial genetic variation. Retrograde regulation through mitochondrial haplogroups exerts a signaling control over the nuclear epigenome, which leads to the modulation of nuclear genes, cellular functions and development of OA. All these data suggest that OA could be considered a mitochondrial disease as well as other complex chronic disease as cancer, cardiovascular and neurologic diseases.

Human genetic analyses of organelles highlight the nucleus in age-related trait heritability

Most age-related human diseases are accompanied by a decline in cellular organelle integrity, including impaired lysosomal proteostasis and defective mitochondrial oxidative phosphorylation. An open question, however, is the degree to which inherited variation in or near genes encoding each organelle contributes to age-related disease pathogenesis. Here, we evaluate if genetic loci encoding organelle proteomes confer greater-than-expected age-related disease risk. As mitochondrial dysfunction is a 'hallmark' of aging, we begin by assessing nuclear and mitochondrial DNA loci near genes encoding the mitochondrial proteome and surprisingly observe a lack of enrichment across 24 age-related traits. Within nine other organelles, we find no enrichment with one exception: the nucleus, where enrichment emanates from nuclear transcription factors. In agreement, we find that genes encoding several organelles tend to be 'haplosufficient,' while we observe strong purifying selection against heterozygous protein-truncating variants impacting the nucleus. Our work identifies common variation near transcription factors as having outsize influence on age-related trait risk, motivating future efforts to determine if and how this inherited variation then contributes to observed age-related organelle deterioration.

Mitochondrial Genetics and Epigenetics in Osteoarthritis

During recent years, the significant influence of mitochondria on osteoarthritis (OA), the most common joint disease, has been consistently demonstrated. Not only mitochondrial dysfunction but also mitochondrial genetic polymorphisms, specifically the mitochondrial DNA haplogroups, have been shown to have an important influence on different OA-related features, including the prevalence, severity, incidence, and progression of the disease. This influence could probably be mediated by the role of mitochondria in the regulation of different processes involved in the pathogenesis of OA, such as energy production, the generation of reactive oxygen and nitrogen species, apoptosis, and inflammation. The regulation of these processes is at least partially controlled by the bi-directional communication between the nucleus and mitochondria, which permits the regulation of adaptation to a wide range of stressors and the maintenance of cellular homeostasis. This bi-directional communication consists of an “anterograde regulation” by which the nucleus regulates mitochondrial biogenesis and activity and a “retrograde regulation” by which both mitochondria and mitochondrial genetic variation exert a regulatory signaling control over the nuclear epigenome, which leads to the modulation of nuclear genes. Throughout this mini review, we will describe the evidence that demonstrates the profound influence of the mitochondrial genetic background in the pathogenesis of OA, as well as its influence on the nuclear DNA methylome of the only cell type present in the articular cartilage, the chondrocyte. This evidence leads to serious consideration of the mitochondrion as an important therapeutic target in OA.

Mitochondrial DNA haplogroups participate in osteoarthritis: current evidence based on a meta-analysis

Mitochondrial genes' variants encoded in both the nuclear and mitochondrial genomes can disrupt mitochondrial function, resulting in losing of cartilage and generating osteoarthritis (OA). However, the association between mtDNA haplogroups and OA still lacks strength evidence supporting. The aim of this meta-analysis is to assess the role of mtDNA haplogroups in speculating the pathogenesis and progression of OA. PubMed, Embase, the Cochrane Central Register of Controlled Trials, and World Health Organization clinical trials' registry center were searched to identify relevant studies up to the end of March 2019. Inclusion citations required a case-control or cohort study to demonstrate the association between mtDNA haplogroups and OA's prevalence or progression. Title, abstract, and full-text screening were sequentially assessed by three reviewers. Data were analyzed using STATA. Besides, publication bias and meta-regression analysis were conducted to explore potential heterogeneities. We collected results from 7 articles. The cluster TJ cases showed a lower proportion in OA cases (RR = 0.83, 95% CI 0.72, 0.96). However, there is no evidence that revealed this kind of impact originated from neither type J nor type T individually. Besides, the type B and G analyses among Asian populations also elucidated a negative association. Moreover, the cluster TJ of mtDNA haplogroups revealed a lower cumulative probability of radiographic OA progression (ES = 0.77, 95% CI 0.63, 0.94), which was contributed by type T (ES = 0.61, 95% CI 0.45, 0.82).The mtDNA haplogroups do have impacts on the prevalence and progression of OA. Cluster TJ could help reduce the prevalence and slow down the radiographic changes; however, the impacts came from type J and type T, respectively.

Mitochondrial DNA variation and the pathogenesis of osteoarthritis phenotypes

Mitochondria and mitochondrial DNA (mtDNA) variation are now recognized as important factors in the development of osteoarthritis (OA). Mitochondria are the energy powerhouses of the cell, and also regulate different processes involved in the pathogenesis of OA including inflammation, apoptosis, calcium metabolism and the generation of reactive oxygen species (ROS) and reactive nitrogen species (RNS). Mitochondria contain their own genetic material, mtDNA, which evolved through the sequential accumulation of mtDNA variants to enable humans to adapt to different climates. The ROS and reactive metabolic intermediates that are by-products of mitochondrial metabolism are regulated in part by mtDNA and are among the signals that transmit information between mitochondria and the nucleus. These signals can alter nuclear gene expression and, when disrupted, affect a number of cellular processes and metabolic pathways, leading to disease. mtDNA variation influences OA-associated phenotypes, including those related to metabolism, inflammation and even ageing, as well as nuclear epigenetic regulation. This influence also enables the use of specific mtDNA haplogroups as complementary diagnostic and prognostic biomarkers of OA.

Background sequence characteristics influence the occurrence and severity of disease-causing mtDNA mutations

Inherited mitochondrial DNA (mtDNA) mutations have emerged as a common cause of human disease, with mutations occurring multiple times in the world population. The clinical presentation of three pathogenic mtDNA mutations is strongly associated with a background mtDNA haplogroup, but it is not clear whether this is limited to a handful of examples or is a more general phenomenon. To address this, we determined the characteristics of 30,506 mtDNA sequences sampled globally. After performing several quality control steps, we ascribed an established pathogenicity score to the major alleles for each sequence. The mean pathogenicity score for known disease-causing mutations was significantly different between mtDNA macro-haplogroups. Several mutations were observed across all haplogroup backgrounds, whereas others were only observed on specific clades. In some instances this reflected a founder effect, but in others, the mutation recurred but only within the same phylogenetic cluster. Sequence diversity estimates showed that disease-causing mutations were more frequent on young sequences, and genomes with two or more disease-causing mutations were more common than expected by chance. These findings implicate the mtDNA background more generally in recurrent mutation events that have been purified through natural selection in older populations. This provides an explanation for the low frequency of mtDNA disease reported in specific ethnic groups.

MtDNA mutations are a major cause of genetic disease. Many of these variants have recurred several times in different populations and on diverse haplogroup backgrounds, but the clinical presentation of mutations causing Leber Hereditary Optic Neuropathy (LHON: m.14484T>C, m.3460G>A, m.11778G>A) are strongly associated with a specific mtDNA haplogroup. This raises the possibility that many pathogenic mtDNA mutations are subject to the same effects. Here, our analysis of 30,506 human mtDNA sequences shows that the association between disease-causing mtDNA mutations and background mtDNA haplogroups is not only restricted to three disease-causing mtDNA mutations known to cause LHON. The frequent recurrence of the same mutations on a population clade, and the reduced frequency of European mtDNAs harboring two or more diseases-causing mutations, suggest that the population mtDNA background influences the risk of developing mtDNA mutations. Our analysis also shows that disease-causing mtDNA mutations also occur more frequently on younger mtDNAs. This implies that, once formed, the mutations are selected against. These findings indicate that the clinical interpretation of mtDNA variants should be performed within an ethnogeographic context.

Can Chronic Pain Be Prevented?

All chronic pain begins at some discrete point in time. Significant strides in the understanding of mechanisms and risk factors associated with the transition from a new, or acute, pain experience to a chronic pain condition have been made over the past 20 years. These insights provide the hope of one day being able to modify or even halt this pathophysiologic progression. This article reviews some of the current knowledge of this transition as well as the evidence currently available to best prevent and treat it using persistent surgical pain as a model.

Mitochondrial DNA haplogroups influence the risk of incident knee osteoarthritis in OAI and CHECK cohorts. A meta-analysis and functional study

Objective

To evaluate the influence of the mitochondrial DNA (mtDNA) haplogroups in the risk of incident knee osteoarthritis (OA) and to explain the functional consequences of this association to identify potential diagnostic biomarkers and therapeutic targets.

Methods

Two prospective cohorts contributed participants. The osteoarthritis initiative (OAI) included 2579 subjects of the incidence subcohort, and the cohort hip and cohort knee (CHECK) included 635, both with 8-year follow-up. The analysis included the association of mtDNA haplogroups with the rate of incident knee OA in subjects from both cohorts followed by a subsequent meta-analysis. Transmitochondrial cybrids harbouring haplogroup J or H were constructed to detect differences between them in relation to physiological features including specific mitochondrial metabolic parameters, reactive oxygen species production, oxidative stress and apoptosis.

Results

Compared with H, the haplogroup J associates with decreased risk of incident knee OA in subjects from OAI (HR=0.680; 95% CI 0.470 to 0.968; p<0.05) and CHECK (HR=0.728; 95% CI 0.469 to 0.998; p<0.05). The subsequent meta-analysis including 3214 cases showed that the haplogroup J associates with a lower risk of incident knee OA (HR=0.702; 95% CI 0.541 to 0.912; p=0.008). J cybrids show a lower free radical production, higher cell survival under oxidative stress conditions, lower grade of apoptosis as well as lower expression of the mitochondrially related pro-apoptotic gene BCL2 binding component 3 (BBC3). In addition, J cybrids also show a lower mitochondrial respiration and glycolysis leading to decreased ATP production.

Conclusions

The physiological effects of the haplogroup J are beneficial to have a lower rate of incident knee OA over time. Potential drugs to treat OA could focus on emulating the mitochondrial behaviour of this haplogroup.

A replication study and meta-analysis of mitochondrial DNA variants in the radiographic progression of knee osteoarthritis

OBJECTIVE

To conduct a replication study and meta-analysis involving the study of mtDNA variants in the radiographic progression of OA in different cohorts worldwide, including Cohort Hip and Cohort Knee (CHECK), the OA Initiative and a cohort from Spain.

METHODS

The influence of the haplogroups in the rate of radiographic progression at 96 months in 431 subjects from CHECK was assessed in terms of Kellgren and Lawrence (KL) grade. Progression was defined as a change from KL ⩾ 1 at baseline to any higher grade during the follow-up. Extended Cox proportional hazard models were used to analyse the influence of mtDNA variants in the rate of radiographic knee OA progression. A subsequent meta-analysis of 1603 subjects following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines was conducted to combine the data of individual studies. A sensitivity analysis was performed to validate the stability of the results.

RESULTS

CHECK subjects carrying the haplogroup T showed the lowest rate of radiographic knee OA progression [hazard ratio (HR) 0.645 (95% CI 0.419, 0.978); P < 0.05]. When pooled, subjects within the superhaplogroup JT showed the same trend [HR 0.707 (95% CI 0.501, 0.965); P < 0.05]. BMI [HR 1.046 (95% CI 1.018, 1.073); P < 0.05] and bilateral OA [HR 2.266 (95% CI 1.733, 2.954); P < 0.05] at baseline are risk factors for radiographic knee OA progression as well. In the meta-analysis there was a reduced rate of radiographic progression in subjects with haplogroup T [HR 0.612 (95% CI 0.454, 0.824); P = 0.001] or in the superhaplogroup JT [HR 0.765 (95% CI 0.624, 0.938); P = 0.009]. Sensitivity analysis revealed that the results were robust.

CONCLUSION

The mtDNA variants in the superhaplogroup JT associate with a reduced rate of radiographic OA progression. The mtDNA polymorphisms in the superhaplogroup JT emerge as potential complementary genetic biomarkers for disease progression.

Inherited mtDNA variations are not strong risk factors in human prion disease

Aside from variation in the prion protein gene, genetic risk factors for sporadic Creutzfeldt-Jakob disease remain elusive. Given emerging evidence implicating mitochondrial dysfunction in the pathogenesis of the disorders, we studied the role of inherited mitochondrial DNA variation in a 2255 sporadic prion disease cases and 3768 controls. Our analysis indicates that inherited mitochondrial DNA variation does not have a major role in the risk of developing the disorder.

Mitochondrial DNA (mtDNA) haplogroups influence the progression of knee osteoarthritis. Data from the Osteoarthritis Initiative (OAI)

OBJECTIVE

To evaluate the influence of the mtDNA haplogroups on knee osteoarthritis progression in Osteoarthritis Initiative (OAI) participants through longitudinal data from radiographs and magnetic resonance imaging (MRI).

METHODS

Four-year knee osteoarthritis progression was analyzed as increase in Kellgren and Lawrence (KL) grade, in addition to increase in OARSI atlas grade for joint space narrowing (JSN), osteophytes and subchondral sclerosis in the tibia medial compartment of 891 Caucasian individuals from the progression subcohort. The influence of the haplogroups on the rate of structural progression was also assessed as the four-year change in minimum joint space width (mJSW in millimetres) in both knees of (n = 216) patients with baseline unilateral medial-tibiofemoral JSN. Quantitative cartilage measures from longitudinal MRI data were those related to cartilage thickness and volume with a 24 month follow-up period (n = 381).

RESULTS

During the four-year follow-up period, knee OA patients with the haplogroup T showed the lowest increase in KL grade (Hazard Risk [HR] = 0.499; 95% Confidence Interval [CI]: 0.261-0.819; p<0.05) as well as the lowest cumulative probability of progression for JSN (HR = 0.547; 95% CI: 0.280-0.900; p<0.05), osteophytes (HR = 0.573; 95% CI: 0.304-0.893; p<0.05) and subchondral sclerosis (HR = 0.549; 95% CI: 0.295-0.884; p<0.05). They also showed the lowest decline in mJSW (standardized response means (SRM) = -0.39; p = 0.037) in those knees without baseline medial JSN (no-JSN knees). Normalized cartilage volume loss was significantly lower in patients carrying the haplogroup T at medial tibia femoral (SRM = -0.33; p = 0.023) and central medial femoral (SRM = -0.27; p = 0.031) compartments. Cartilage thickness loss was significantly lower in carriers of haplogroup T at central medial tibia-femoral (SRM = -0.42; p = 0.011), medial tibia femoral (SRM = -0.32; p = 0.018), medial tibia anterior (SRM = +0.31; p = 0.013) and central medial femoral (SRM = -0.19; p = 0.013) compartments.

CONCLUSIONS

Mitochondrial genome seems to play a role in the progression of knee osteoarthritis. mtDNA variation could improve identification of patients predisposed to faster or severe progression of the disease.

Role of mtDNA haplogroups in the prevalence of osteoarthritis in different geographic populations: a meta-analysis

Background

Osteoarthritis (OA) is the most common form of arthritis and has become an increasingly important public-health problem. However, the pathogenesis of OA is still unclear. In recent years, its correlation with mtDNA haplogroups attracts much attention. We aimed to perform a meta-analysis to investigate the association between mtDNA haplogroups and OA.

Methods

Published English or Chinese literature from PubMed, Web of Science, SDOS, and CNKI was retrieved up until April 15, 2014. Case-control or cohort studies that detected the frequency of mtDNA haplogroups in OA patients and controls were included. The quality of the included studies was evaluated by the Newcastle-Ottawa Scale (NOS) assessment. A meta-analysis was conducted to calculate pooled odds ratio (OR) with 95% confidence interval (CI) through the random or fixed effect model, which was selected based on the between-study heterogeneity assessed by Q test and I² test. Subgroup analysis was performed to explore the origin of heterogeneity.

Results

A total of 6 case-control studies (10590 cases and 7161 controls) with an average NOS score of 6.9 were involved. For the analysis between mtDNA haplogroup J and OA, random model was selected due to high heterogeneity. No significant association was found initially (OR = 0.73, 95%CI: 0.52–1.03), however, once any study from UK population was removed the association emerged. Further subgroup analysis demonstrated that there was a significant association in Spain population (OR = 0.57, 95%CI: 0.46–0.71), but not in UK population. Also, subgroup analysis revealed that there was a significant correlation between cluster TJ and OA in Spain population (OR = 0.70, 95%CI: 0.58–0.84), although not in UK population. No significant correlation was found between haplogroup T/cluster HV/cluster KU and OA.

Conclusions

Our current meta-analysis suggests that mtDNA haplogroup J and cluster TJ correlate with the risk of OA in Spanish population, but the associations in other populations require further investigation.

An exploratory analysis of mitochondrial haplotypes and allogeneic hematopoietic cell transplantation outcomes

Certain mitochondrial haplotypes (mthaps) are associated with disease, possibly through differences in oxidative phosphorylation and/or immunosurveillance. We explored whether mthaps are associated with allogeneic hematopoietic cell transplantation (HCT) outcomes. Recipient (n = 437) and donor (n = 327) DNA were genotyped for common European mthaps (H, J, U, T, Z, K, V, X, I, W, and K2). HCT outcomes for mthap matched siblings (n = 198), all recipients, and all donors were modeled using relative risks (RR) and 95% confidence intervals and compared with mthap H, the most common mitochondrial haplotypes. Siblings with I and V were significantly more likely to die within 5 years (RR = 3.0; 95% confidence interval [CI], 1.2 to 7.9; and RR = 4.6; 95% CI, 1.8 to 12.3, respectively). W siblings experienced higher acute graft-versus-host disease (GVHD) grades II to IV events (RR = 2.1; 95% CI, 1.1 to 2.4) with no events for those with K or K2. Similar results were observed for all recipients combined, although J recipients experienced lower GVHD and higher relapse. Patients with I donors had a 2.7-fold (1.2 to 6.2) increased risk of death in 5 years, whereas few patients with K2 or W donors died. No patients with K2 donors and few patients with U donors relapsed. Mthap may be an important consideration in HCT outcomes, although validation and functional studies are needed. If confirmed, it may be feasible to select donors based on mthap to increase positive or decrease negative outcomes.

Mitochondrial DNA haplogroups modulate the radiographic progression of Spanish patients with osteoarthritis

Not all patients with osteoarthritis (OA) show the same disease progression, as some of them remain relatively stable over time, while others progress to severe structural deterioration of the joint. In this sense, the main goal of both genetic and protein biomarkers in OA is to predict not only the risk of OA at an earlier stage of the disease but also which OA patients are more likely to progress to severe disease. Taking into account the incidence of the mitochondria and the mtDNA haplogroups in the pathogenesis of OA, the main objective of this work was to evaluate the incidence of the mtDNA haplogroups in the radiographic progression of the OA disease in a well-characterized follow-up cohort of Spanish patients. DNA from 281 OA patients from Hospital Universitario A Coruña was isolated to determine the European mtDNA haplogroups. Knee or hip radiographs from all affected joints were obtained at two time points with at least 36 months apart. Radiographs were evaluated using the Kellgren/Lawrence (K/L) scale; radiographic OA progression was defined as any radiographic worsening of the K/L joint score. Statistical analyses included Kaplan-Meier survival curves and Cox regression models. Patients belonging to the cluster TJ showed a slower radiographic OA progression than patients in the cluster KU (p = 0.036). Moreover, patients carrying the most common mtDNA haplogroup H are more apt to require total joint replacement surgery than non-H patients (p = 0.049). The inherited mitochondrial variants influence the radiographic progression of OA and could be considered among the genetic variants taken into account when the radiographic progression of OA is analyzed.

Accurate mitochondrial DNA sequencing using off-target reads provides a single test to identify pathogenic point mutations

PURPOSE

Mitochondrial disorders are a common cause of inherited metabolic disease and can be due to mutations affecting mitochondrial DNA or nuclear DNA. The current diagnostic approach involves the targeted resequencing of mitochondrial DNA and candidate nuclear genes, usually proceeds step by step, and is time consuming and costly. Recent evidence suggests that variations in mitochondrial DNA sequence can be obtained from whole-exome sequence data, raising the possibility of a comprehensive single diagnostic test to detect pathogenic point mutations.

METHODS

We compared the mitochondrial DNA sequence derived from off-target exome reads with conventional mitochondrial DNA Sanger sequencing in 46 subjects.

RESULTS

Mitochondrial DNA sequences can be reliably obtained using three different whole-exome sequence capture kits. Coverage correlates with the relative amount of mitochondrial DNA in the original genomic DNA sample, heteroplasmy levels can be determined using variant and total read depths, and-providing there is a minimum read depth of 20-fold-rare sequencing errors occur at a rate similar to that observed with conventional Sanger sequencing.

CONCLUSION

This offers the prospect of using whole-exome sequence in a diagnostic setting to screen not only all protein coding nuclear genes but also all mitochondrial DNA genes for pathogenic mutations. Off-target mitochondrial DNA reads can also be used to assess quality control and maternal ancestry, inform on ethnic origin, and allow genetic disease association studies not previously anticipated with existing whole-exome data sets.

Recent mitochondrial DNA mutations increase the risk of developing common late-onset human diseases

Mitochondrial DNA (mtDNA) is highly polymorphic at the population level, and specific mtDNA variants affect mitochondrial function. With emerging evidence that mitochondrial mechanisms are central to common human diseases, it is plausible that mtDNA variants contribute to the “missing heritability” of several complex traits. Given the central role of mtDNA genes in oxidative phosphorylation, the same genetic variants would be expected to alter the risk of developing several different disorders, but this has not been shown to date. Here we studied 38,638 individuals with 11 major diseases, and 17,483 healthy controls. Imputing missing variants from 7,729 complete mitochondrial genomes, we captured 40.41% of European mtDNA variation. We show that mtDNA variants modifying the risk of developing one disease also modify the risk of developing other diseases, thus providing independent replication of a disease association in different case and control cohorts. High-risk alleles were more common than protective alleles, indicating that mtDNA is not at equilibrium in the human population, and that recent mutations interact with nuclear loci to modify the risk of developing multiple common diseases.

There is a growing body of evidence indicating that mitochondrial dysfunction, a result of genetic variation in the mitochondrial genome, is a critical component in the aetiology of a number of complex traits. Here, we take advantage of recent technical and methodological advances to examine the role of common mitochondrial DNA variants in several complex diseases. By examining over 50,000 individuals, from 11 different diseases we show that mitochondrial DNA variants can both increase or decrease an individual's risk of disease, replicating and expanding upon several previously reported studies. Moreover, by analysing several large disease groups in tandem, we are able to show a commonality of association, with the same mitochondrial DNA variants associated with several distinct disease phenotypes. These shared genetic associations implicate a shared underlying functional effect, likely changing cellular energy, which manifests as distinct phenotypes. Our study confirms the important role that mitochondrial DNA variation plays on complex traits and additionally supports the utility of a GWAS-based approach for analysing mitochondrial genetics.

mtDNA haplogroups and osteoarthritis in different geographic populations

OBJECTIVE

To compare the frequency distribution of the mtDNA haplogroups in OA patients and healthy controls between the United Kingdom (UK) and Spain.

METHODS

We used the single base extension (SBE) assay to obtain the European mtDNA haplogroups in 1471 OA patients and 406 healthy controls from Spain, and 453 OA patients and 280 healthy controls from the UK. Some differential haplogroup J-related single nucleotide polymorphisms (SNPs) between both populations were analyzed. The whole data was analyzed with SPSS software (v.18) following appropriate approaches that included chi-square contingency tables and logistic regression models adjusting by gender and age.

RESULTS

The haplogroup J appeared underrepresented in OA patients from Spain when compared with healthy controls (OR=0.636; 95% CI: 0.444-0.911; p=0.013). Individuals from the UK carrying the haplogroup T showed a decreased risk of OA (OR=0.574; 95% CI: 0.350-0.939; p=0.027). The comparison of the frequency distribution of the haplogroup J between the UK and Spain showed a decreased presence of this haplogroup in healthy controls from the UK when compared with healthy controls from Spain that is in borderline of the statistical significance (p=0.06). The analysis of some haplogroup J-related SNPs in OA patients and healthy controls from Spain and the UK showed that the SNP m.3394t>c appeared underrepresented in the UK cohort (p=0.038).

CONCLUSIONS

The proposed mitochondrial uncoupling mechanism derived from the mtDNA haplogroups J and T could be behind their protective role against OA. The different association found in Spain and the UK could reflect the adaptation of the mtDNA haplogroups to different climatic patterns. The genetic composition of the haplogroup J between the UK and Spain seems to be slightly different, being the m.3394t>c SNP one of the differentially expressed haplogroup J-related polymorphisms.

Role of mtDNA haplogroups in the prevalence of knee osteoarthritis in a southern Chinese population

Mitochondrial DNA (mtDNA) has been implicated in various human degenerative diseases. However, the role of mtDNA in Osteoarthritis (OA) is less known. To investigate whether mtDNA haplogroups contribute to the prevalence of knee OA, we have carried out a comprehensive case-control study on 187 knee OA patients and 420 geographically matched controls in southern China. OA patients were classified on the Kellgren/Lawrence scale from two to four for the disease severity study and the data were analyzed by adjusting for age and sex. We found that patients with haplogroup G (OR = 3.834; 95% CI 1.139, 12.908; p = 0.03) and T16362C (OR = 1.715; 95% CI 1.174, 2.506; p = 0.005) exhibited an increased risk of OA occurrence. Furthermore, patients carrying haplogroup G had a higher severity progression of knee OA (OR = 10.870; 95% CI 1.307, 90.909; p = 0.007). On the other hand, people with haplogroup B/B4 (OR = 0.503; 95% CI 0.283, 0.893; p = 0.019)/(OR = 0.483; 95% CI 0.245, 0.954; p = 0.036) were less susceptible for OA occurrence. Interestingly, we found OA patients also exhibited a general increase in mtDNA content. Our study indicates that the mtDNA haplogroup plays a role in modulating OA development.

Osteoarthritis year 2013 in review: genetics and genomics

Progress in genetic research has delivered important highlights in the last year. One of the widest impact is the publication of the Encyclopedia of DNA Elements (ENCODE) project showing the impressive complexity of the human genome and providing information useful for all areas of genetics. More specific of osteoarthritis (OA) has been the incorporation of DOT1-like, histone H3 methyltransferase (DOT1L) to the list of 11 OA loci with genome-wide significant association, the demonstration of significant overlap between OA genetics and height or body mass index (BMI) genetics, and the tentative prioritization of HMG-box transcription factor 1 (HBP1) in the 7q22 locus based on functional analysis. In addition, the first large scale analysis of DNA methylation has found modest differences between OA and normal cartilage, but has identified a subgroup of OA patients with a very differentiated phenotype. The role of DNA methylation in regulation of NOS2, SOX9, MMP13 and IL1B has been further clarified. MicroRNA expression studies in turn have shown some replication of differences between OA and control cartilage from previous profiling studies and have identified potential regulators of TGFβ signaling and of IL1β effects. In addition, non-coding RNAs showed promising results as serum biomarkers of cartilage damage. Gene expression microarray studies have found important differences between studies of hip or knee OA that reinforce the idea of joint specificity in OA. Expression differences between articular cartilage and other types of cartilage highlighted the WNT pathway whose regulation is proposed as critical for maintaining the articular cartilage phenotype. Many of these results need confirmation but they signal the exciting progress that is taking place in all areas of OA genetics, indicate questions requiring more study and augur further interesting discoveries.

The genetics and functional analysis of primary osteoarthritis susceptibility

Recent genome-wide association scans (GWASs) along with several adequately powered candidate gene studies have yielded a number of risk alleles for osteoarthritis (OA). This number is now sufficiently large to allow conclusions to be drawn regarding the nature of genetic susceptibility, including the fact that the risk alleles have variable effects depending on sex, ethnicity and on the skeletal site of the disease. Several of the alleles that have emerged from the GWASs are within or close to highly plausible candidate genes, including RUNX2 and CHST11. However, the majority of risk alleles do not map to genes previously reported to play a role in musculoskeletal biology, indicating that the GWAS datasets are telling us something new about the OA disease process. Functional studies have so far revealed that effects on gene expression are likely to be one of the main mechanisms through which OA susceptibility is acting. Epigenetic mechanisms such as DNA methylation also influence OA risk, and integration of genetic, transcriptomic and epigenetic data will allow us to use the genetic discoveries for informed development of new OA biological treatments.