Mitochondrial DNA Single Nucleotide Polymorphisms Research Articles

A naturally occurring variant of SHLP2 is a protective factor in Parkinson’s disease

Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) have been associated with a reduced risk of developing Parkinson’s disease (PD), yet the underlying mechanisms remain elusive. In this study, we investigate the functional role of a PD-associated mtSNP that impacts the mitochondrial-derived peptide (MDP) Small Humanin-like Peptide 2 (SHLP2). We identify m.2158 T > C, a mtSNP associated with reduced PD risk, within the small open reading frame encoding SHLP2. This mtSNP results in an alternative form of SHLP2 (lysine 4 replaced with arginine; K4R). Using targeted mass spectrometry, we detect specific tryptic fragments of SHLP2 in neuronal cells and demonstrate its binding to mitochondrial complex 1. Notably, we observe that the K4R variant, associated with reduced PD risk, exhibits increased stability compared to WT SHLP2. Additionally, both WT and K4R SHLP2 show enhanced protection against mitochondrial dysfunction in in vitro experiments and confer protection against a PD-inducing toxin, a mitochondrial complex 1 inhibitor, in a mouse model. This study sheds light on the functional consequences of the m.2158 T > C mtSNP on SHLP2 and provides insights into the potential mechanisms by which this mtSNP may reduce the risk of PD.

The Revolution of Animal Genomics in Forensic Sciences.

Nowadays, the coexistence between humans and domestic animals (especially dogs and cats) has become a common scenario of daily life. Consequently, during a forensic investigation in civil or criminal cases, the biological material from a domestic animal could be considered "evidence" by law enforcement agencies. Animal genomics offers an important contribution in attacks and episodes of property destruction or in a crime scene where the non-human biological material is linked to the victim or perpetrator. However, only a few animal genetics laboratories in the world are able to carry out a valid forensic analysis, adhering to standards and guidelines that ensure the admissibility of data before a court of law. Today, forensic sciences focus on animal genetics considering all domestic species through the analysis of STRs (short tandem repeats) and autosomal and mitochondrial DNA SNPs (single nucleotide polymorphisms). However, the application of these molecular markers to wildlife seems to have gradually gained a strong relevance, aiming to tackle illegal traffic, avoid the loss of biodiversity, and protect endangered species. The development of third-generation sequencing technologies has glimmered new possibilities by bringing "the laboratory into the field", with a reduction of both the enormous cost management of samples and the degradation of the biological material.

Mitochondrial Genome Study Identifies Association Between Primary Open-Angle Glaucoma and Variants in MT-CYB, MT-ND4 Genes and Haplogroups

Background and purpose: Primary open-angle glaucoma (POAG) is an optic neuropathy characterized by death of retinal ganglion cells and atrophy of the optic nerve head. The susceptibility of the optic nerve to damage has been shown to be mediated by mitochondrial dysfunction. In this study, we aimed to determine a possible association between mitochondrial SNPs or haplogroups and POAG. Methods: Mitochondrial DNA single nucleotide polymorphisms (mtSNPs) were genotyped using the Illumina Infinium Global Screening Array-24 (GSA) 700K array set. Genetic analyses were performed in a POAG case-control study involving the cohorts, Groningen Longitudinal Glaucoma Study-Lifelines Cohort Study and Amsterdam Glaucoma Study, including 721 patients and 1951 controls in total. We excluded samples not passing quality control for nuclear genotypes and samples with low call rate for mitochondrial variation. The mitochondrial variants were analyzed both as SNPs and haplogroups. These were determined with the bioinformatics software HaploGrep, and logistic regression analysis was used for the association, as well as for SNPs. Results: Meta-analysis of the results from both cohorts revealed a significant association between POAG and the allele A of rs2853496 [odds ratio (OR) = 0.64; p = 0.006] within the MT-ND4 gene, and for the T allele of rs35788393 (OR = 0.75; p = 0.041) located in the MT-CYB gene. In the mitochondrial haplogroup analysis, the most significant p-value was reached by haplogroup K (p = 1.2 × 10−05), which increases the risk of POAG with an OR of 5.8 (95% CI 2.7–13.1). Conclusion: We identified an association between POAG and polymorphisms in the mitochondrial genes MT-ND4 (rs2853496) and MT-CYB (rs35788393), and with haplogroup K. The present study provides further evidence that mitochondrial genome variations are implicated in POAG. Further genetic and functional studies are required to substantiate the association between mitochondrial gene polymorphisms and POAG and to define the pathophysiological mechanisms of mitochondrial dysfunction in glaucoma.

SUN-453 Association study of mitochondrial genome with sepsis

Sepsis is a clinical syndrome of high mortality and morbidity and still has a lot of controversy in mechanism. Mitochondria are the core part of the cell oxygen metabolism and mitochondrial dysfunction may have a profound impact on sepsis and multiple organ damage. Mitochondrial single nucleotide polymorphisms, in Europe and in the Han nationality have been shown to affect the prognosis of sepsis, however, similar to many complex diseases, the exact effect of mtDNA variation on sepsis and how to influence is not clear. With the development of genome sequencing technology and biological information, it is possible to use the next generation sequencing (NGS) to deal with that. To investigate the relationship between mitochondrial haplotypes and the prognosis of severe sepsis, and to screen the mitochondrial DNA single nucleotide polymorphisms associated with severe sepsis. Peripheral blood DNA from 151 sepsis patients and 103 healthy people were obtained. Mitochondrial genome wide association study of sepsis was conducted based on the mitochondrial DNA barcode sequencing method. We compared the mitochondrial haplotype distribution in the disease and control group, and the relationship between haplotype and prognosis of disease. Single nucleotide polymorphisms associated with disease onset and prognosis were screened. Association analysis based on the mitochondrial DNA sequencing found 9 loci associated with sepsis and controls: A (OR=0.2186, p=4.06E-05), B (OR=0.2271, p=0.001107), C (OR=0.2274, p=0.003112), D (OR=5.221, p=0.003419), E (OR=2.532, P=0.02615), F (OR=0.2478, p=0.02668), G (OR=0.2478, p=0.02668), H(OR=2.327, p=0.02913) and I (OR= 0.2256, p=0.03349). And 1 loci associated with in-hospital mortality of sepsis patients. J was associated with in-hospital mortality (OR=2.469, p=0.04966). There was no difference in the distribution of mitochondrial haplotypes among the groups. mitochondrial SNP A/B/C/D/E/F/G/H and I are associated with sepsis, while J is associated with the in-hospital deaths in sepsis patients.

Variability of the Mitochondrial Genome and Development of the Primary Progressing form of Multiple Sclerosis

Recently, it has been shown that dysfunction of mitochondria is an important component of the molecular mechanisms of the development of many neurodegenerative diseases. These include multiple sclerosis, a chronic autoimmune and neurodegenerative disease of the central nervous system, which is characterized by clinical heterogeneity. The role of genetic variability of mitochondrial DNA in the development of various clinical forms of multiple sclerosis is poorly understood. The aim of present study was to analyze the association often mitochondrial DNA single nucleotide polymorphisms and the nine most common European mitochondrial haplogroups (H, J, K, U, T, I, V, W and X) with a severe and relatively rare multiple sclerosis disease form-primary progressive multiple sclerosis. 110 patients with primary progressive multiple sclerosis and 406 healthy controls were enrolled in the study, all ethnic Russians. For the first time association of the m.12308*G (rs2853498) variant (P = 0.024) and haplogroup U (P = 0.0004, passes the adjustment for multiple comparisons: Pcorr = 0.0076) with primary progressive multiple sclerosis was shown. Comparison of these data with the results of our previous study [1], that was focused on the role of mitochondrial genome variability in susceptibility to the most common form of multiple sclerosis, relapsing-remitting multiple sclerosis, leads to the conclusion that two different mitochondrial haplogroups, U and J, are involved in the development of two different clinical forms of multiple sclerosis. The results may contribute to the identification of new targets for the treatment of primary progressive multiple sclerosis, for which there is no effective pathogenetic treatment at the moment.

Using Machine Learning to Predict the Development of Diabetes and Potential Biomarkers Linked to Cardiac Risk

BackgroundDiabetes mellitus is a chronic, debilitating disease that continues to affect a greater percentage of people each year. Among its systemic comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While glycosylated hemoglobin (HbA1c) remains the primary diagnostic for diabetes mellitus onset, predicting health outcomes through a single measure is difficult, with disparities existing between ethnic and demographic groups. The purpose of this study was to use machine learning algorithms to develop personalized prognostics in predicting the development and progression of diabetes mellitus in the heart.MethodsRight atrial appendages from 48 patients, 29 non‐diabetic and 19 type 2 diabetic, were procured from the WVU Ruby Memorial Hospital. Machine learning was applied to physiological (sex, BMI, HbA1c, comorbidities), biochemical (total methylation and mitochondrial bioenergetics functional parameters), and sequencing data (mitochondrial genomic DNA single nucleotide polymorphisms (SNPs) and nuclear genomic DNA CpG island methylation) for each patient. Supervised (including HbA1c) and unsupervised (without HbA1c) learning evaluated the efficiency of testing and training sets through classification and regression trees, logistic regression, support vector machines, and k nearest neighbors.ResultsNuclear 5‐methylcytosine content and s‐adenosyl methionine activity matched diagnostic accuracy of HbA1c (~91% testing) for all patients. Mitochondrial DNA SNPs found in the D‐Loop region (SNP‐152C, ‐16126C, and ‐16362C) were significantly associated with diabetes incidence. The CpG island for the mitochondrial transcription factor A (TFAM) revealed specific CpG sites (chr10:58384915 and 58385262) that showed high accuracy (~89% testing) in predicting diabetes incidence. Unsupervised learning, both binary (diabetic or non‐diabetic) and multi‐classification (diabetic, pre‐diabetic, or non‐diabetic), confirmed these results.ConclusionsUsing machine learning, we were able to predict health outcomes through the combination of multiple physiological, biochemical, and sequencing approaches, assessing the development and progression of diabetes. Linking mitochondrial and genomic/epigenomic data, we detail how learning algorithms can be applied to forwarding personalized medicine and developing novel, more advanced prognostics in the heart.Support or Funding InformationR01 HL‐128485 (JMH), AHA‐17PRE33660333 (QAH), WV‐INBRE support by NIH Grant P20GM103434, WVU Flow Cytometry & Single Cell Core supported by MBRCC CoBRE Grant GM103488 and Fortessa S10 Grant OD016165, and the Community Foundation for the Ohio Valley Whipkey Trust. We would like to acknowledge the WVU Genomics Core Facility, Morgantown WV for support provided to help make this work possible.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Horizontal Transmission of Clonal Cancer Cells Causes Leukemia in Soft-Shell Clams

Outbreaks of fatal leukemia-like cancers of marine bivalves throughout the world have led to massive population loss. The cause of the disease is unknown. We recently identified a retrotransposon, Steamer, that is highly expressed and amplified to high copy number in neoplastic cells of soft-shell clams (Mya arenaria). Through analysis of Steamer integration sites, mitochondrial DNA single-nucleotide polymorphisms (SNPs), and polymorphic microsatellite alleles, we show that the genotypes of neoplastic cells do not match those of the host animal. Instead, neoplastic cells from dispersed locations in New York, Maine, and Prince Edward Island (PEI), Canada, all have nearly identical genotypes that differ from those of the host. These results indicate that the cancer is spreading between animals in the marine environment as a clonal transmissible cell derived from a single original clam. Our findings suggest that horizontal transmission of cancer cells is more widespread in nature than previously supposed.

Mitochondrial DNA variation and HIV-associated sensory neuropathy in CHARTER

HIV-associated sensory neuropathy remains an important complication of combination antiretroviral therapy and HIV infection. Mitochondrial DNA haplogroups and single nucleotide polymorphisms (SNPs) have previously been associated with symptomatic neuropathy in clinical trial participants. We examined associations between mitochondrial DNA variation and HIV-associated sensory neuropathy in CNS HIV Antiretroviral Therapy Effects Research (CHARTER). CHARTER is a USA-based longitudinal observational study of HIV-infected adults who underwent a structured interview and standardized examination. HIV-associated sensory neuropathy was determined by trained examiners as ≥1 sign (diminished vibratory and sharp-dull discrimination or ankle reflexes) bilaterally. Mitochondrial DNA sequencing was performed and haplogroups were assigned by published algorithms. Multivariable logistic regression of associations between mitochondrial DNA SNPs, haplogroups, and HIV-associated sensory neuropathy were performed. In analyses of associations of each mitochondrial DNA SNP with HIV-associated sensory neuropathy, the two most significant SNPs were at positions A12810G [odds ratio (95 % confidence interval) = 0.27 (0.11-0.65); p = 0.004] and T489C [odds ratio (95 % confidence interval) = 0.41 (0.21-0.80); p = 0.009]. These synonymous changes are known to define African haplogroup L1c and European haplogroup J, respectively. Both haplogroups were associated with decreased prevalence of HIV-associated sensory neuropathy compared with all other haplogroups [odds ratio (95 % confidence interval) = 0.29 (0.12-0.71); p = 0.007 and odds ratio (95 % confidence interval) = 0.42 (0.18-1.0); p = 0.05, respectively]. In conclusion, in this cohort of mostly combination antiretroviral therapy-treated subjects, two common mitochondrial DNA SNPs and their corresponding haplogroups were associated with a markedly decreased prevalence of HIV-associated sensory neuropathy.

Mitochondrial bioenergetics and drug-induced toxicity in a panel of mouse embryonic fibroblasts with mitochondrial DNA single nucleotide polymorphisms

Mitochondrial DNA (mtDNA) variations including single nucleotide polymorphisms (SNPs) have been proposed to be involved in idiosyncratic drug reactions. However, current in vitro and in vivo models lack the genetic diversity seen in the human population. Our hypothesis is that different cell strains with distinct mtDNA SNPs may have different mitochondrial bioenergetic profiles and may therefore vary in their response to drug-induced toxicity. Therefore, we used an in vitro system composed of four strains of mouse embryonic fibroblasts (MEFs) with mtDNA polymorphisms. We sequenced mtDNA from embryonic fibroblasts isolated from four mouse strains, C57BL/6J, MOLF/EiJ, CZECHII/EiJ and PERA/EiJ, with the latter two being sequenced for the first time. The bioenergetic profile of the four strains of MEFs was investigated at both passages 3 and 10. Our results showed that there were clear differences among the four strains of MEFs at both passages, with CZECHII/EiJ having a lower mitochondrial robustness when compared to C57BL/6J, followed by MOLF/EiJ and PERA/EiJ. Seven drugs known to impair mitochondrial function were tested for their effect on the ATP content of the four strains of MEFs in both glucose- and galactose-containing media. Our results showed that there were strain-dependent differences in the response to some of the drugs. We propose that this model is a useful starting point to study compounds that may cause mitochondrial off-target toxicity in early stages of drug development, thus decreasing the number of experimental animals used.

Mitochondrial bioenergetics and drug-induced toxicity in a panel of mouse embryonic fibroblasts with mitochondrial DNA single nucleotide polymorphisms

Mitochondrial DNA (mtDNA) variations including single nucleotide polymorphisms (SNPs) have been proposed to be involved in idiosyncratic drug reactions. However, current in vitro and in vivo models lack the genetic diversity seen in the human population. Our hypothesis is that different cell strains with distinct mtDNA SNPs may have different mitochondrial bioenergetic profiles and may therefore vary in their response to drug-induced toxicity. Therefore, we used an in vitro system composed of four strains of mouse embryonic fibroblasts (MEFs) with mtDNA polymorphisms. We sequenced mtDNA from embryonic fibroblasts isolated from four mouse strains, C57BL/6J, MOLF/EiJ, CZECHII/EiJ and PERA/EiJ, with the latter two being sequenced for the first time. The bioenergetic profile of the four strains of MEFs was investigated at both passages 3 and 10. Our results showed that there were clear differences among the four strains of MEFs at both passages, with CZECHII/EiJ having a lower mitochondrial robustness when compared to C57BL/6J, followed by MOLF/EiJ and PERA/EiJ. Seven drugs known to impair mitochondrial function were tested for their effect on the ATP content of the four strains of MEFs in both glucose- and galactose-containing media. Our results showed that there were strain-dependent differences in the response to some of the drugs. We propose that this model is a useful starting point to study compounds that may cause mitochondrial off-target toxicity in early stages of drug development, thus decreasing the number of experimental animals used.

Genotyping mitochondrial DNA single nucleotide polymorphisms by PCR ligase detection reactions

The identification of human mitochondrial DNA (mtDNA) sequence variations, especially single nucleotide polymorphisms (SNPs), is important for many applications. The PCR-ligase detection reaction (LDR) method can reduce false-positives and eliminate the need for both post-PCR and post-ligation purifications in SNP analyses. In addition, it has been successfully employed to detect point mutations in various nuclear genes. In this study, we used the PCR-LDR platform to characterize mtDNA SNPs. Multiplex PCR-LDRs were used to genotype 19 mtDNA single nucleotide polymorphic sites from 812 samples. Performance of the method was assessed by direct sequencing of 44 samples. We established an overall 97.4% success rate with 99.2% accuracy using the multiplex PCR-LDR methodology. The PCR-LDR mtDNA genotyping technique is simple, highly accurate, has high-throughput, and is cost-effective. Therefore, this method is applicable to mtDNA haplotyping in various applications.

Optimization and validation of 10 mitochondrial DNA SNPs using SNaPshot Kit

In some forensic cases, nuclear DNA is degraded and cannot be analyzed. In such a case mitochondrial DNA (mtDNA) is usually used in forensic cases for identification because of its special features as high number of copies per cell, maternal inheritance and high mutation rate. Single nucleotide polymorphisms (SNPs) represent the most abundant class of human polymorphisms. The aim of this study was optimization of 10 mtDNA SNPs by using SNaPshot minisequencing technique on ABI310 genetic analyser in forensic molecular genetics laboratory. At the end of this study, the optimization of minisequencing technique was done by changing some assay parameters. Also, during the optimization of 10 mtSNP loci in our laboratory.

The Use of Mitochondrial DNA Single Nucleotide Polymorphisms to Assist in the Resolution of Three Challenging Forensic Cases

Mitochondrial DNA (mtDNA) single nucleotide polymorphisms (SNPs) in an 11-plex assay were typed in three missing person cases involving highly degraded human remains. Unlike the traditional forensic approach to analyzing mtDNA which focuses on sequencing portions of the noncoding Control Region, this assay targets discriminatory SNPs that reside principally in the coding region. In two of the cases, the SNP typing successfully excluded one of two reference families that could not be excluded on the basis of mtDNA hypervariable region sequencing alone, and resulted in the final resolution of both decades-old cases. In a third case, SNP typing confirmed the sorting and reassociation of multiple commingled skeletal elements. The application of a specific mtDNA SNP assay in these cases demonstrates its utility in distinguishing samples when the most common Caucasian hypervariable region type is encountered in forensic casework.

Characterization of 19 single nucleotide polymorphism markers for coho salmon

AbstractWe report 39 single nucleotide polymorphisms (SNPs) observed in 23 nuclear DNA sequences in coho salmon Oncorhynchus kisutch. High‐throughput genotyping assays based on the 5′‐nuclease reaction were developed for 17 of these nuclear SNPs and for two previously published mitochondrial DNA SNPs. Minor allele frequency differences (Δq) among collections were between 5.2% and 51.2%, resulting in per locus FST estimates of 0.00–0.24 with an average of 0.09.

Beyond HV1 and HV2—identification of valuable mitochondrial DNA single nucleotide polymorphisms

The degree of polymorphism characteristic for hypervariable segments of mitochondrial DNA (mtDNA) is sometimes too low to enable differentiation between individuals revealing most frequent HV1 and HV2 haplotypes. An acceptable solution in such a situation seems to be analysis of additional variation present outside the control region. For practical and ethical reasons, analysis of variation present in the coding part of mitochondrial DNA should be limited to selected single nucleotide polymorphisms. Before selective SNP analysis is possible, those particular valuable mutations, which occur appropriately frequently in a population and are free of medical information, must be determined.