Sequence polymorphisms within the human mitochondrial genes MTATP6, MTATP8 and MTND4

Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways

Alzheimers disease (AD) is the main cause of dementia and it is defined by cognitive decline coupled to extracellular deposit of amyloid-beta protein and intracellular hyperphosphorylation of tau protein. Historically, efforts to target such hallmarks have failed in numerous clinical trials. In addition to these hallmark-targeted approaches, several clinical trials focus on other AD pathological processes, such as inflammation, mitochondrial dysfunction, and oxidative stress. Mitochondria and mitochondrial-related mechanisms have become an attractive target for disease-modifying strategies, as mitochondrial dysfunction prior to clinical onset has been widely described in AD patients and AD animal models. Mitochondrial function relies on both the nuclear and mitochondrial genome. Findings from omics technologies have shed light on AD pathophysiology at different levels (e.g., epigenome, transcriptome and proteome). Most of these studies have focused on the nuclear-encoded components. The first part of this review provides an updated overview of the mechanisms that regulate mitochondrial gene expression and function. The second part of this review focuses on evidence of mitochondrial dysfunction in AD. We have focused on published findings and datasets that study AD. We analyzed published data and provide examples for mitochondrial-related pathways. These pathways are strikingly dysregulated in AD neurons and glia in sex-, cell- and disease stage-specific manners. Analysis of mitochondrial omics data highlights the involvement of mitochondria in AD, providing a rationale for further disease modeling and drug targeting.

The variation of mitochondrial NADH dehydrogenase subunit 4 (mtND4) and molecular dynamics simulation of SNPs among Iranian women with breast cancer

Breast cancer is the second cause of death among women all around the world. One out of every eight women is diagnosed with breast cancer in Iran. There are many reasons for cancer, one of which is the mutations in the mitochondrial genome observed in most breast cancer studies. However, the aim of this study is to evaluate the genetic region of NADH dehydrogenase subunit 4 in patients with breast cancer. First, the genomic DNA was extracted from a tissue. The NADH dehydrogenase subunit 4 coding region was amplified by PCR, and then the SSCP was sequenced. After that, the molecular dynamics were employed. The association between the mutations and the prognostic factors such as ER, PR, HER-2, and age were statistically examined. The sequence of the ND4 area was determined in 24 suspected patients, and 15 nucleotide changes were reported. The role of this variations was investigated by in-silico. The harmful mutations were predicted based on some servers. The molecular dynamics results showed that there is a significant relationship between the mutant protein and the changes in the structural conformation. Our results showed that the mutation in the ND4 area plays an important role in developing breast cancer. So, it can be concluded that the mitochondrial NADH dehydrogenase analysis may help to detect breast cancer in the early stages.

Titanic's unknown child: the critical role of the mitochondrial DNA coding region in a re-identification effort

This report describes a re-examination of the remains of a young male child recovered in the Northwest Atlantic following the loss of the Royal Mail Ship Titanic in 1912 and buried as an unknown in Halifax, Nova Scotia shortly thereafter. Following exhumation of the grave in 2001, mitochondrial DNA (mtDNA) hypervariable region 1 sequencing and odontological examination of the extremely limited skeletal remains resulted in the identification of the child as Eino Viljami Panula, a 13-month-old Finnish boy. This paper details recent and more extensive mitochondrial genome analyses that indicate the remains are instead most likely those of an English child, Sidney Leslie Goodwin. The case demonstrates the benefit of targeted mtDNA coding region typing in difficult forensic cases, and highlights the need for entire mtDNA sequence databases appropriate for forensic use.

Study of the cytochrome b gene sequence in populations of Taiwan

The cytochrome b gene (MTCYB) has been widely used in taxonomic research. In this study, the sequence polymorphism of the MTCYB gene was determined in 417 subjects of eight populations living in Taiwan (Taiwanese Han, indigenous Taiwanese, Tao, mainland Chinese, Filipino, Thai, Vietnamese, and Caucasian). Sequence variation from the revised Cambridge Reference Sequence and genetic distance between these populations were analyzed. There were 108 variable positions with a total of 99 haplotypes. Population-specific positions of MTCYB gene were noted in Tao and Caucasian populations. There were statistically significant differences of genetic distance between Taiwanese Han and Caucasian, between Taiwanese Han and Tao, and between Taiwanese Han and Filipino. A phylogenetic tree presents the genetic distances between these populations. In conclusion, there are sufficient sequence polymorphisms of the MTCYB gene in individuals of different populations, which may be used in the analyses of human ethnic groups in forensic casework.

Extended guidelines for mtDNA typing of population data in forensic science

Mitochondrial DNA analysis has become a vital niche in forensic science as it constitutes a powerful technique for low quality and low quantity DNA samples. For the forensic field it is important to employ standardized procedures based on scientific grounds, in order to have mtDNA evidence be accepted in court. Here, we modify and extend recommendations that were spelled out previously in the absence of solid knowledge about the worldwide phylogeny. Refinement of those earlier guidelines became necessary in regard to sample selection, amplification and sequencing strategies, as well as a posteriori quality control of mtDNA profiles. The notation of sequence data should thus reflect this growing knowledge.

Identification of human-specific adaptation sites of ATP6

Mitochondria play an essential role in forming ATP and generating heat. The proportion of these two depends on the coupling efficiency of electrochemical gradient to synthesize ATP. Therefore, an increased basal metabolic rate caused by partial uncoupling of the mitochondria can be balanced by a high caloric intake provided by a high-fat diet. The recent study by Mishmar et al. (Proc. Natl. Acad. Sci. USA 2003; 100: 171-176) suggested that ATP6 was the most variable gene among human mitochondrial DNAs and probably resulted from the adaptation of Homo sapiens to the colder climate during the migration out of Africa. According to this adaptation theory, the ATP6 of Homo sapiens (omnivorous animals consuming fat-containing diet) should be significantly different from that of other primates for permitting human adaptation to the dietary conditions. On the basis of this rationale, we analyzed ATP6 sequences of 136 unrelated Taiwanese subjects, which then were compared with 1,130 reported sequences. The obtained human consensus from 1,266 individuals was compared with that derived from 42 species of primates other than human. The alignment showed that human ATP6 harbored 80 variable residues, among which 25 amino acids were conserved in other primates, suggesting that adaptation constraints operating at the amino acid level results in the species-specific difference of ATP6. Therefore, these 25 amino acids are probably the human-specific adaptation residues of ATP6.

V-MitoSNP: visualization of human mitochondrial SNPs

BACKGROUND

Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers. Unfortunately, providing relevant mtSNP genotyping information in mtDNA databases in a neatly organized and transparent visual manner still remains a challenge. Amongst the many methods reported for SNP genotyping, determining the restriction fragment length polymorphisms (RFLPs) is still one of the most convenient and cost-saving methods. In this study, we prepared the visualization of the mtDNA genome in a way, which integrates the RFLP genotyping information with mitochondria related cancers and diseases in a user-friendly, intuitive and interactive manner. The inherent problem associated with mtDNA sequences in BLAST of the NCBI database was also solved.

DESCRIPTION

V-MitoSNP provides complete mtSNP information for four different kinds of inputs: (1) color-coded visual input by selecting genes of interest on the genome graph, (2) keyword search by locus, disease and mtSNP rs# ID, (3) visualized input of nucleotide range by clicking the selected region of the mtDNA sequence, and (4) sequences mtBLAST. The V-MitoSNP output provides 500 bp (base pairs) flanking sequences for each SNP coupled with the RFLP enzyme and the corresponding natural or mismatched primer sets. The output format enables users to see the SNP genotype pattern of the RFLP by virtual electrophoresis of each mtSNP. The rate of successful design of enzymes and primers for RFLPs in all mtSNPs was 99.1%. The RFLP information was validated by actual agarose electrophoresis and showed successful results for all mtSNPs tested. The mtBLAST function in V-MitoSNP provides the gene information within the input sequence rather than providing the complete mitochondrial chromosome as in the NCBI BLAST database. All mtSNPs with rs number entries in NCBI are integrated in the corresponding SNP in V-MitoSNP.

CONCLUSION

V-MitoSNP is a web-based software platform that provides a user-friendly and interactive interface for mtSNP information, especially with regard to RFLP genotyping. Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies.

Forensic mass screening using mtDNA

At the forensic autopsy of a sexual murder victim, some trace hairs, possibly belonging to the perpetrator, were saved. Initially, the analysis of a pubic hair shaft only revealed the presence of the mitochondrial (mt) DNA haplotype profile consisting of the (CA)(6) allele and the complete hypervariable region 1 (HV1) and 2 (HV2) sequence. Later, typing of some further telogene trace hairs, which had been stored for several years, yielded a nuclear short tandem repeat (STR) profile. We used both the mtDNA haplotype and the STR profile to start a DNA mass screening project involving 2,335 male citizens of the relevant communities. MtDNA screening was carried out by using the CA repeat amplification in combination with an SNP typing procedure based on the restriction site analysis of amplified d-loop sequences. The aim of our paper is to put mass screening with mtDNA up for discussion.

Evolutional Analysis in Determining Pathogenic versus Nonpathogenic Mutations of ATPase 6 in Human Mitochondriopathy

Because mitochondrial ATPase 6 plays an important role in ATP synthesis, mutations affecting ATPase 6 can undoubtedly cause human diseases. In contrast, the ATPase 6 gene is known to be a fast-evolving gene and has generated enough polymorphisms to allow identity investigation for forensic casework. To investigate these seemingly opposite views, we analyzed amino acid sequences of ATPase 6 in at least 1,266 humans, 102 mammals, and 213 vertebrates. The result showed that the amino acids of human ATPase 6 could be divided into the following four groups. Amino acid residue 192 (affected by alteration at nt 9101) and 79 other residues were variable, and therefore substitutions of these residues would not be pathogenic. Amino acid residue 156 (affected by alteration at nt 8993) and 93 other residues were conserved in Homo sapiens, but not in Mammalia. Therefore, they were potentially pathogenic if altered. Function studies would be necessary to confirm their role in pathogenesis. Amino acid residue 217 (affected by alteration at nt 9176) and 9 other residues were conserved across all species, including S. cerevisiae and E. coli. Mutations involving these residues would be pathogenic, some of which might even be life threatening. The remainder (42 residues) were conserved in Mammalia, but not in yeast and E. coli. They were probably pathogenic if mutated. The classification proposed in this study may, therefore, provide an algorithm for a diagnostic approach when a newly identified change of ATPase 6 is suspected for human mitochondriopathy.

Effective strategies for forensic analysis in the mitochondrial DNA coding region

Recently, it has been recognized that accessing information in the mtDNA coding region can provide additional forensic discrimination with respect to the standard typing of the D-loop region, augmenting the sometimes rather limited forensic power of mtDNA testing. Here, we discuss considerations relating to maximally effective approaches for recovering additional discrimination in the coding region, bearing in mind that (1) DNA quality and quantity in typical mtDNA casework usually restrict the amount of additional sequence that can be obtained, and (2) the need for additional discrimination primarily arises when common HV1/HV2 types are encountered. Most investigators have sought additional discrimination by sequencing short segments of coding region that are thought to be particularly variable. Unfortunately, efforts in this regard have generally failed to appreciate that most variation in the coding region is redundant with information already present in HV1/HV2 and have therefore overvalued the potential of this approach for providing additional discrimination. An alternative single nucleotide polymorphism-based approach [Int J Legal Med 118:137-146, 2004] has been to identify specific bases that provide resolution in specific common HV1/HV2 types (and related sequences). We investigate several highly relevant data sets wherein the latter approach performs appreciably better than sequencing selected short portions of the coding region. This is true even when only synonymous variation is targeted to minimize the potential for problems arising from discovery of mutations that have reportedly been related to disease.

Evaluating the forensic informativeness of mtDNA haplogroup H sub-typing on a Eurasian scale

The impact of phylogeographic information on mtDNA forensics has been limited to the quality control of published sequences and databases. In this work we use the information already available on Eurasian mtDNA phylogeography to guide the choice of coding-region SNPs for haplogroup H. This sub-typing is particularly important in forensics since, even when sequencing both HVRI and HVRII, the discriminating power is low in some Eurasian populations. We show that a small set (eight) of coding-region SNPs resolves a substantial proportion of the identical haplotypes, as defined by control-region variation alone. Moreover, this SNP set, while substantially increasing the discriminating efficiency in most Eurasian populations by roughly equal amounts, discloses population-specific profiles.

Artificial recombination in forensic mtDNA population databases

Artificial recombination of two or more mitochondrial DNA fragments from different samples would constitute a serious cause of error in forensic DNA typing, and yet one can demonstrate that such events have happened in the preparation of several published mtDNA databases. Focussed database searches, phylogenetic analysis, and network representations can highlight mosaic patterns and thus pinpoint sample mix-up. Therefore, we suggest that this approach should be applied to data prior to publication in order to uncover such errors in time.

Single nucleotide polymorphisms over the entire mtDNA genome that increase the power of forensic testing in Caucasians

We have sequenced the entire mtDNA genome (mtGenome) of 241 individuals who match 1 of 18 common European Caucasian HV1/HV2 types, to identify sites that permit additional forensic discrimination. We found that over the entire mtGenome even individuals with the same HV1/HV2 type rarely match. Restricting attention to sites that are neutral with respect to phenotypic expression, we have selected eight panels of single nucleotide polymorphism (SNP) sites that are useful for additional discrimination. These panels were selected to be suitable for multiplex SNP typing assays, with 7-11 sites per panel. The panels are specific for one or more of the common HV1/HV2 types (or closely related types), permitting a directed approach that conserves limiting case specimen extracts while providing a maximal chance for additional discrimination. Discrimination provided by the panels reduces the frequency of the most common type in the European Caucasian population from approximately 7% to approximately 2%, and the 18 common types we analyzed are resolved to 105 different types, 55 of which are seen only once.

The impact of mtDNA analysis between positions nt8306 and nt9021 for forensic casework

Identification in forensic casework by mtDNA sequencing is predominantly done by sequencing the non-coding control region (HVI and HVII). In an attempt to further increase the discriminatory power of mtDNA analysis, we sequenced a coding region between nt8306 and nt9021 to identify additional polymorphisms in a group of 61 unrelated German individuals who had mtDNA profiles that occurred more than two times each, as well as a control group of 119 unrelated Germans whose profiles occurred one or two times each. Within these 180 individuals, 38 different polymorphisms in this region were observed; 64.4% of these individuals displayed the Cambridge reference sequence profile plus A8860G. For 28 individuals with the two most common profiles, A263G-315.1insC (N = 18) and A263G-309.1insC-315.1insC (N = 10), additional polymorphisms in this coding region permitted further discrimination of 56 and 40% of the individuals, respectively.