Baseline Characteristics of Mitochondrial DNA and Mutations Associated With Short-Term Posttreatment CD4+T-Cell Recovery in Chinese People With HIV

BackgroundMitochondrial DNA (mtDNA) profiles and contributions of mtDNA variants to CD4+T-cell recovery in Euramerican people living with HIV (PLWH) may not be transferred to East-Asian PLWH, highlighting the need to consider more regional studies. We aimed to identify mtDNA characteristics and mutations that explain the variability of short-term CD4+T-cell recovery in East-Asian PLWH.MethodEight hundred fifty-six newly reported antiretroviral therapy (ART)-naïve Chinese PLWH from the Comparative HIV and Aging Research in Taizhou (CHART) cohort (Zhejiang Province, Eastern China) were enrolled. MtDNA was extracted from peripheral whole blood of those PLWH at HIV diagnosis, amplified, and sequenced using polymerase chain reaction and gene array. Characterization metrics such as mutational diversity and momentum were developed to delineate baseline mtDNA mutational patterns in ART-naïve PLWH. The associations between mtDNA genome-wide single nucleotide variants and CD4+T-cell recovery after short-term (within ~48 weeks) ART in 724 PLWH were examined using bootstrapping median regressions.ResultsOf 856 participants, 74.18% and 25.82% were male and female, respectively. The median age was 37 years; 94.51% were of the major Han ethnicity, and 69.04% and 28.62% were of the heterosexual and homosexual transmission, respectively. We identified 2,352 types of mtDNA mutations and mtDNA regions D-loop, ND5, CYB, or RNR1 with highest mutational diversity or volume. Female PLWH rather than male PLWH at the baseline showed remarkable age-related uptrends of momentum and mutational diversity as well as correlations between CD4+T <200 (cells/μl) and age-related uptrends of mutational diversity in many mtDNA regions. After adjustments of important sociodemographic and clinical variables, m.1005T>C, m.1824T>C, m.3394T>C, m.4491G>A, m.7828A>G, m.9814T>C, m.10586G>A, m.12338T>C, m.13708G>A, and m.14308T>C (at the Bonferroni-corrected significance) were negatively associated with short-term CD4+T-cell recovery whereas m.93A>G, m.15218A>G, and m.16399A>G were positively associated with short-term CD4+T-cell recovery.ConclusionOur baseline mtDNA characterization stresses the attention to East-Asian female PLWH at risk of CD4+T-cell loss-related aging and noncommunicable chronic diseases. Furthermore, mtDNA variants identified in regression analyses account for heterogeneity in short-term CD4+T-cell recovery of East-Asian PLWH. These results may help individualize the East-Asian immune recovery strategies under complicated HIV management caused by CD4+T-cell loss.

Mitochondrial Genome Variation and Metabolic Traits in a Maori Community

<p>The mitochondrion is the energy producing factory of cells and it has long been thought that disruption to mitochondrial systems is linked to energy metabolism dysfunction. Sequence variants in the mitochondrial genome are plausible candidate risk factors for numerous human diseases, and research has identified specific mitochondrial DNA (mtDNA) variants associated with metabolic disorders such as obesity and type-2 diabetes. As part of the Rakaipaaka Health and Ancestry Study (RHAS) it has been observed that the Maori community of Nuhaka (Ngati Rakaipaaka) have a high incidence of certain metabolic diseases, namely obesity and diabetes. The reason for this is not well understood, but is likely to be a combination of both current lifestyle (e.g. dietary) and ancestral genetic factors. This study set out to sequence the entire mitochondrial genome in a sample of RHAS Maori participants. The aim was to discover genetic variation that might be specific to this Maori community and test whether such variants are associated with diabetes and other metabolic traits. This study used a novel RFLP assay to screen the mtDNA control region for Polynesian mtDNA ancestry. This established an initial group (n=30) with high levels of Maori mtDNA. Hypervariable (HVRI) sequencing was then used to generate a large dataset of sequences (n=94). This dataset was representative of individuals showing high Maori ancestry and aided the selection of 20 mtDNA's for Mitochip analysis. Combining the RHAS Maori HVRI sequences with those from previous studies indicated elevated variation in Maori mtDNA. Haplotype analysis identified 17 unique Maori haplotypes, 10 more than previously recorded. Mitochip resequencing has provided the first complete Maori mtDNA sequences to date. When compared to other mtDNA sequences it was identified that RHAS Maori share similar haplotype markers with Polynesians. Seven novel undocumented variants were found, as well as four variants that had previously been associated with various metabolic disorders. Mitochip analysis of mtDNA sequences revealed three variants which created a RHAS Maori specific signature; C1185T, G4769A, and T16126C. These variants also defined 3 unique mtDNA haplotypes within RHAS Maori, which are the first Maori specific haplotypes reported. Variant genotyping and correlation with metabolic traits identified significant associations within the wider RHAS Maori community. It was identified that RHAS Maori with T16189C showed elevation in both vitamin B12 levels and mean diastolic blood pressure. Individuals with the G4769A variant were shown to have significant increases in specific metabolic risk factors for cardiovascular disease. Conversely individuals with the more common A4769G variant were 2 times less likely to be diagnosed with diabetes. The findings from this study have identified a series of potential markers of metabolic disease within the RHAS Maori community. The goal now is to understand how these markers interact with environmental variables to increase the risk of metabolic syndrome. Such an outcome may open the way to designing personalised intervention strategies (e.g. dietary) to increase the health and well-being of at risk individuals.</p>

Mitochondrial Genome Variation and Metabolic Traits in a Maori Community

<p>The mitochondrion is the energy producing factory of cells and it has long been thought that disruption to mitochondrial systems is linked to energy metabolism dysfunction. Sequence variants in the mitochondrial genome are plausible candidate risk factors for numerous human diseases, and research has identified specific mitochondrial DNA (mtDNA) variants associated with metabolic disorders such as obesity and type-2 diabetes. As part of the Rakaipaaka Health and Ancestry Study (RHAS) it has been observed that the Maori community of Nuhaka (Ngati Rakaipaaka) have a high incidence of certain metabolic diseases, namely obesity and diabetes. The reason for this is not well understood, but is likely to be a combination of both current lifestyle (e.g. dietary) and ancestral genetic factors. This study set out to sequence the entire mitochondrial genome in a sample of RHAS Maori participants. The aim was to discover genetic variation that might be specific to this Maori community and test whether such variants are associated with diabetes and other metabolic traits. This study used a novel RFLP assay to screen the mtDNA control region for Polynesian mtDNA ancestry. This established an initial group (n=30) with high levels of Maori mtDNA. Hypervariable (HVRI) sequencing was then used to generate a large dataset of sequences (n=94). This dataset was representative of individuals showing high Maori ancestry and aided the selection of 20 mtDNA's for Mitochip analysis. Combining the RHAS Maori HVRI sequences with those from previous studies indicated elevated variation in Maori mtDNA. Haplotype analysis identified 17 unique Maori haplotypes, 10 more than previously recorded. Mitochip resequencing has provided the first complete Maori mtDNA sequences to date. When compared to other mtDNA sequences it was identified that RHAS Maori share similar haplotype markers with Polynesians. Seven novel undocumented variants were found, as well as four variants that had previously been associated with various metabolic disorders. Mitochip analysis of mtDNA sequences revealed three variants which created a RHAS Maori specific signature; C1185T, G4769A, and T16126C. These variants also defined 3 unique mtDNA haplotypes within RHAS Maori, which are the first Maori specific haplotypes reported. Variant genotyping and correlation with metabolic traits identified significant associations within the wider RHAS Maori community. It was identified that RHAS Maori with T16189C showed elevation in both vitamin B12 levels and mean diastolic blood pressure. Individuals with the G4769A variant were shown to have significant increases in specific metabolic risk factors for cardiovascular disease. Conversely individuals with the more common A4769G variant were 2 times less likely to be diagnosed with diabetes. The findings from this study have identified a series of potential markers of metabolic disease within the RHAS Maori community. The goal now is to understand how these markers interact with environmental variables to increase the risk of metabolic syndrome. Such an outcome may open the way to designing personalised intervention strategies (e.g. dietary) to increase the health and well-being of at risk individuals.</p>

Mitochondrial DNA variants segregate during human preimplantation development into genetically different cell lineages that are maintained postnatally

Humans present remarkable mitochondrial DNA (mtDNA) variant mosaicism, not only across tissues but even across individual cells within one person. The timing of the first appearance of this mosaicism has not yet been established. In this study, we hypothesized it occurs during preimplantation development. To investigate this, we deep-sequenced the mtDNA of 254 oocytes from 85 donors, 158 single blastomeres of 25 day-3 embryos, 17 inner cell mass and trophectoderm samples of 7 day-5 blastocysts, 142 bulk DNA and 68 single cells of different adult tissues. We found that day-3 preimplantation embryos already present blastomeres that carry variants unique to that cell, showing that the first events of mtDNA mosaicism happen very early in human development. We classified the mtDNA variants based on their recurrence or uniqueness across sibling oocytes and embryos, and between single cells and samples from the same embryos or adult individuals. Variants that recurred across samples had higher heteroplasmic loads and more frequently resulted in synonymous changes or were located in non-coding regions than variants that were unique to one oocyte or single embryonic cell. These differences were maintained through developmental stages, suggesting that the mtDNA mosaicism arising in preimplantation development is maintained into adulthood. Further, the results support a model in which close clustering of mitochondria carrying specific mtDNA variants in the ooplasm leads to asymmetric distribution of these mitochondria throughout the cell divisions of the preimplantation embryo, resulting in the appearance of the first form of mtDNA mosaicism in human development.

EPID-12. MITOCHONDRIAL DNA SEQUENCE VARIATION AND MENINGIOMA

Meningiomas are the most common primary central nervous system tumors. Risk factors include female sex, African American race, a higher body mass index, and exposure to ionizing radiation. Genome-wide association studies have identified two risk loci for meningioma in the nuclear genome (rs12770228 and rs2686876). Whereas mitochondrial DNA (mtDNA) sequence variants and haplogroups have been linked with certain cancers, research on meningioma is lacking. We examined the association of 42 common (minor allele frequency ≥ 5%) germline mtDNA variants, haplogroups, and genes with meningioma risk in 1,080 controls and 478 cases from a case-control study conducted at medical centers in the southeastern US. Participant DNA samples were genotyped using the UK Biobank array that included a set of common and rare mtDNA variants. Risk associations were examined separately for meningioma overall, WHO grade 1 (n=409) and WHO grade 2/3 (n=69) meningiomas. Overall, meningioma risk was significantly higher among women (OR=2.86; 95% CI:2.21-3.71) compared to men, higher among African Americans (OR=2.37, 95% CI:1.41-3.99) compared to Caucasians, and higher among those who were overweight (OR=1.48; 95% CI:1.11-1.98) or obese (OR= 1.73; 95% CI:1.26-2.38) compared to those of normal weight. The variant m.16362T &gt;C (rs62581341) in the mitochondrial control region was positively associated with grade 2/3 meningiomas (OR=2.33; 95% CI: 1.14-4.79), but not with grade 1 tumors (OR=0.99; 95% CI:0.64-1.53). Haplogroup L, a marker for African ancestry, was identified among 3.6% of controls and 8.6% of cases and was associated with meningioma risk overall (OR=2.56; 95% CI:1.52-4.30). When stratifying by self-reported race, the association between haplogroup L and meningioma was only apparent among the small number of self-reported Caucasians with this haplogroup (OR=6.68; 95% CI=1.66-26.91) when compared to non-L haplogroups, combined. No other common mtDNA variant (minor allele &gt;5%), haplogroup, or gene was associated with meningioma risk. These findings merit further study.

Mitonuclear interactions affect locomotor activity and sleep in Drosophila melanogaster

Mitochondria are organelles that produce cellular energy in the form of ATP through oxidative phosphorylation, and this primary function is conserved between many taxa. Locomotion is a trait that is highly reliant on metabolic function and expected to be greatly affected by disruptions to mitochondrial performance. To this end, we aimed to examine how activity and sleep vary between Drosophila melanogaster strains with different geographic origins, how these patterns are affected by mitochondrial DNA (mtDNA) variation, and how breaking up co-evolved mito-nuclear gene combinations affect the studied activity traits. The results demonstrate that Drosophila strains from different locations differ in sleep and activity, and the extent of variation differs between sexes, females in general being more active. By comparing activity and sleep of mtDNA variants introgressed onto a common nuclear background in cytoplasmic hybrid (cybrid) strains, we establish that mtDNA variation affects both traits, sex specifically. Furthermore, by using previously published mtDNA copy number data, we detected a positive correlation between mtDNA copy number and the activity levels of the cybrid flies. Altogether, our study shows that both mtDNA variation and mitonuclear interactions affect activity and sleep patterns, highlighting the important role that both genomes play on life-history trait evolution.

Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China

Background Mitochondria have been shown to play vital roles during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) development. Currently, it is unclear whether mitochondrial DNA (mtDNA) variants, which define mtDNA haplogroups and determine oxidative phosphorylation performance and reactive oxygen species production, are associated with COVID-19 risk. Methods A population-based case–control study was conducted to compare the distribution of mtDNA variations defining mtDNA haplogroups between healthy controls (n = 615) and COVID-19 patients (n = 536). COVID-19 patients were diagnosed based on molecular diagnostics of the viral genome by qPCR and chest X-ray or computed tomography scanning. The exclusion criteria for the healthy controls were any history of disease in the month preceding the study assessment. MtDNA variants defining mtDNA haplogroups were identified by PCR-RFLPs and HVS-I sequencing and determined based on mtDNA phylogenetic analysis using Mitomap Phylogeny. Student’s t-test was used for continuous variables, and Pearson’s chi-squared test or Fisher’s exact test was used for categorical variables. To assess the independent effect of each mtDNA variant defining mtDNA haplogroups, multivariate logistic regression analyses were performed to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) with adjustments for possible confounding factors of age, sex, smoking and diseases (including cardiopulmonary diseases, diabetes, obesity and hypertension) as determined through clinical and radiographic examinations. Results Multivariate logistic regression analyses revealed that the most common investigated mtDNA variations (> 10% in the control population) at C5178a (in NADH dehydrogenase subunit 2 gene, ND2) and A249d (in the displacement loop region, D-loop)/T6392C (in cytochrome c oxidase I gene, CO1)/G10310A (in ND3) were associated with a reduced risk of severe COVID-19 (OR = 0.590, 95% CI 0.428–0.814, P = 0.001; and OR = 0.654, 95% CI 0.457–0.936, P = 0.020, respectively), while A4833G (ND2), A4715G (ND2), T3394C (ND1) and G5417A (ND2)/C16257a (D-loop)/C16261T (D-loop) were related to an increased risk of severe COVID-19 (OR = 2.336, 95% CI 1.179–4.608, P = 0.015; OR = 2.033, 95% CI 1.242–3.322, P = 0.005; OR = 3.040, 95% CI 1.522–6.061, P = 0.002; and OR = 2.890, 95% CI 1.199–6.993, P = 0.018, respectively). Conclusions This is the first study to explore the association of mtDNA variants with individual’s risk of developing severe COVID-19. Based on the case–control study, we concluded that the common mtDNA variants at C5178a and A249d/T6392C/G10310A might contribute to an individual’s resistance to developing severe COVID-19, whereas A4833G, A4715G, T3394C and G5417A/C16257a/C16261T might increase an individual’s risk of developing severe COVID-19.

Antigen receptor stimulation drives selection against pathogenic mtDNA variants that dysregulate lymphocyte responses

Pathogenic mitochondrial (mt)DNA molecules can exhibit heteroplasmy in single cells and cause a range of clinical phenotypes, although their contribution to immunity is poorly understood. Here, in mice carrying heteroplasmic C5024T in mt-tRNAAla – that impairs oxidative phosphorylation – we found a reduced mutation burden in peripheral T and B memory lymphocyte subsets, compared to their naïve counterparts. Furthermore, selection diluting the mutation was induced in vitro by triggering T and B cell antigen receptors. While C5024T dysregulated naïve CD8+ T cell respiration and metabolic remodeling post-activation, these phenotypes were partially ameliorated by selection. Analogous to mice, peripheral blood memory T and B lymphocyte subsets from human MELAS (Mitochondrial Encephalomyopathy with Lactic Acidosis and Stroke-like episodes) patients – carrying heteroplasmic A3243G in mt-tRNALeu – displayed a reduced mutation burden, compared to naïve cells. In both humans and mice, mtDNA selection was observed in IgG+ antigen-specific B cells after SARS-CoV-2 Spike vaccination, illustrating an on-going process in vivo. Taken together, these data illustrate purifying selection of pathogenic mtDNA variants during the oxidative phosphorylation checkpoints of the naïve-memory lymphocyte transition.HighlightsIn human MELAS patients (A3243G in mt-tRNALeu) and a related mouse model (C5024T in mt-tRNAAla), T and B memory subsets displayed a reduced mtDNA mutation burden compared to their naïve counterparts.Selection was observed in antigen-specific IgG+ B cells after SARS-CoV-2 Spike protein vaccination.T and B cell antigen receptor stimulation triggered purifying selection in vitro, facilitating mechanistic studies of mtDNA selection.Heteroplasmic pathogenic mutations in mtDNA dysregulated metabolic remodeling after lymphocyte activation and reduced macrophage OXPHOS capacity.

Gitelman-Like Syndrome Caused by Pathogenic Variants in mtDNA

Background: Gitelman syndrome (GS) is the most frequent hereditary salt-losing tubulopathy characterized by hypokalemic alkalosis and hypomagnesemia. GS is caused by biallelic pathogenic variants in SLC12A3, encoding the Na+-Cl- cotransporter (NCC) expressed in the distal convoluted tubule. Pathogenic variants of CLCNKB, HNF1B, FXYD2, or KCNJ10 may result in the same renal phenotype of GS, as they can lead to reduced NCC activity. For approximately 10 percent of patients with a GS phenotype, the genotype is unknown. Methods: We identified mitochondrial DNA (mtDNA) variants in three families with GS-like electrolyte abnormalities, then investigated 156 families for variants in MT-TI and MT-TF, which encode the transfer RNAs for phenylalanine and isoleucine. Mitochondrial respiratory chain function was assessed in patient fibroblasts. Mitochondrial dysfunction was induced In NCC-expressing HEK293 cells to assess the effect on thiazide-sensitive 22Na+ transport. Results: Genetic investigations revealed four mtDNA variants in 13 families: m.591C>T (n=7), m.616T>C (n=1), m.643A>G (n=1) (all in MT-TF) and m.4291T>C (n=4, in MT-TI). Variants were near homoplasmic in affected individuals. All variants were classified as pathogenic, except for m.643A>G, which was classified as a variant of uncertain significance. Importantly, affected members of six families with an MT-TF variant additionally suffered from progressive chronic kidney disease. Dysfunction of oxidative phosphorylation complex IV reduced maximal mitochondrial respiratory capacity in patient fibroblasts. In vitro pharmacological inhibition of complex IV, mimicking the effect of the mtDNA variants, inhibited NCC phosphorylation and NCC-mediated sodium uptake. Conclusion: Pathogenic mtDNA variants in MT-TF and MT-TI can cause a GS-like syndrome. Genetic investigation of mtDNA should be considered in patients with unexplained GS-like tubulopathies.