Hypervariable Region II Research Articles

Nucleotide sequence analysis of mitochondrial DNA hypervariable region II and inter HVR in Thais

ABSTRACT In this study, the nucleotide sequences of the mitochondrial DNA hypervariable region II (HVRII) and inter HVR in the Thai population were investigated. Buccal swab samples were randomly collected from 100 unrelated healthy individuals residing in Thailand. The analysis of HVRII revealed a total of 65 different haplotypes of which 47 were unique and 18 were found in more than one individual. The most frequent haplotype observed was A73G-A249D-A263G-309.1C–315.1C (7%). Nucleotide transition from adenine (A) to guanine (G) was the most frequent substitution. Nucleotide transversions were also observed but with a lower frequency compared to nucleotide transitions. Insertions of C (57%), CC (14%), and CCC (1%) were found at position 309. Twenty-six samples were found to exhibit nucleotide deletion at position 249. The haplotype diversity, random match probability, and discrimination power were calculated to be 0.9859, 0.0240, and 0.976 respectively. In addition, the outside HVR fragment within the control region at positions 16381–72 (inter HVRI/HVRII) and 341–437 (inter HVRII/HVRIII) were sequenced in order to examine the polymorphic sites. High polymorphism was found at positions 16519, 150, 249, and 309. It was concluded that the nucleotide sequence variations in HVRII and inter HVRI/HVRII would be useful for forensic identification.

Emergence of a novel highly pathogenic porcine reproductive and respiratory syndrome virus in China.

From 2014 to 2015, four novel highly pathogenic PRRS virus (HP-PRRSV) strains named 14LY01-FJ, 14LY02-FJ 15LY01-FJ, and 15LY02-FJ were isolated from high morbidity (100%) and mortality (40%-80%) in piglets and sows in Fujian Province. To further our knowledge about these novel virus strains, we characterized their complete genomes and determined their pathogenicity in piglets. Full-length genome sequencing analysis showed that these four isolates were closely related to type 2 (North American type, NA-type) isolates, with 88.1%-96.3% nucleotide similarity, but only 60.6%-60.8% homology to the Lelystad virus (LV) (European type, EU-type). The full length of the four isolates was determined to be 15017 or 15018 nucleotides (nt), excluding the poly(A) tail. Furthermore, the four isolates had three discontinuous deletions (aa 322-432, aa 483, and aa 504-522) within hypervariable region II (HV-II) of Nsp2, as compared to the reference strain VR-2332. This deletion pattern in the four isolates is consistent with strain MN184 and strain NADC30 isolated from America. Phylogenetic and molecular evolutionary analyses indicated that these virulent strains originated from a natural recombination event between the JXA1-like HP-PRRSV (JXA-1 is one of the earliest Chinese HP-PRRSV strains; sublineage 8.7) and the NADC30-like (lineage 1) PRRSV. Animal experiments demonstrated that these four strains caused significant weight loss and severe histopathological lung lesions as compared to the negative control group. High mortality rate (40% or 80%) was found in piglets infected with any one of the four strains, similar to that found with other Chinese HP-PRRSV strains. This study showed that the novel variant PRRSV was HP-PRRSV, and it is therefore critical to monitor PRRSV evolution in China and develop a method for controlling PRRS.

Vitamin E Protects against Lipid Peroxidation and Rescues Tumorigenic Phenotypes in Cowden/Cowden-like Patient-Derived Lymphoblast Cells with Germline SDHx Variants

Cowden syndrome (CS), a Mendelian autosomal-dominant disorder, predisposes to breast, thyroid, and other cancers. Germline variations in succinate dehydrogenase genes (SDHx) occur in approximately 10% PTEN mutation-negative CS and CS-like (CSL) individuals (SDH(var+)). We previously showed that SDHx variants result in elevated reactive oxygen species (ROS), disruption of nicotinamide adenine dinucleotide (NAD) equilibrium, and destabilization of p53 hence apoptosis resistance in CS/CSL patient-derived lymphoblastoid cells. In the present study, we sought to address the tumorigenic impacts of increased ROS and the potential of protecting SDH(var+) cells with antioxidants. We measured the lipid peroxidation levels in patient-derived SDH(var+) lymphoblastoid cells and sequenced 74 controls or SDH(var+) germline DNA samples for mitochondrial hypervariable region II (HVRII) polymorphisms. SDH(var+) lymphoblastoid cells were treated with various antioxidants to check p53 expression and sub-G(1) cell population with cell-cycle analysis. We showed that elevated ROS results in higher lipid peroxidation in SDH(var+) cells. Accumulation of polymorphisms in mitochondrial HVRII was observed in SDH(var+) samples. Interestingly, α-tocopherol (vitamin E) treatment, but not other antioxidants, rescued SDH(var+) cells from apoptosis resistance and protected SDH(var+) cells from oxidative damage such as decreased lipid peroxidation as well as partially recovered p53 expression and NAD/NADH levels. We conclude that disruption of complex II because of SDHx variants leads to increased ROS generation, specifically accompanied by lipid peroxidation. The lipid soluble antioxidant α-tocopherol can selectively protect SDH(var+) cells from oxidative damage, apoptosis resistance, and rebalance redox metabolites NAD/NADH.

Abstract 1120: α-Tocopherol protects cells from lipid peroxidation and rescues tumorigenic phenotypes in CS/CSL patients with germline SDHx variants

Abstract Cowden syndrome (CS), a Mendelian autosomal-dominant disorder, predisposes to breast, thyroid, and other cancers. Germline mutations in phosphatase and tensin homolog (PTEN) have been found in 25% of classic CS individuals accrued from the community. Additionally, we have shown that germline variations in succinate dehydrogenase genes (SDHx) occur in 8% of 608 PTEN mutation-negative CS and CS-like (CSL) individuals (SDHvar+), compared to 0/700 controls (p<0.0001, Fisher's 2-tailed exact test). SDHx genes encode for mitochondrial complex II which lies at the crossroads of electron transport and the tricarboxylic acid cycle. We previously showed that SDHx variants result in elevated reactive oxygen species (ROS) and in disruption of such mitochondrial metabolites as flavin adenine dinucleotide (FAD) and nicotinamide adenine dinucleotide (NAD) equilibrium in CS/CSL patient-derived lymphoblastoid cells. Consequently, improper NADH quinone oxidoreductase 1 (NQO1)-p53 interaction results in destabilization of p53 and apoptosis resistance. Here we further demonstrate that elevated ROS production results in higher lipid peroxidation in SDHvar+ cells compared to healthy control cells. This increased oxidative stress led to increased mutation accumulation in mitochondrial hypervariable region II (HVRII) in samples with SDHx variants compared to controls. Interestingly, α-tocopherol treatment, but not other antioxidants, can rescue SDHvar+ cells from apoptosis resistance. This lipid soluble vitamin E, functions as a peroxyl-radical scavenger, protecting SDHvar+ cells from oxidative damage. We observed down regulated lipid peroxidation in SDHvar+ cells after α-tocopherol exposure, as well as recovered p53 expression and FAD/NAD levels. We conclude that α-tocopherol selectively protects SDHvar+ cells from redox stress and downstream tumorigenic reprogramming, which may have intriguing clinical implications such as using vitamin E as a potential preventive adjunct for CS/CSL individuals with SDHx variants. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1120. doi:1538-7445.AM2012-1120

Mitochondrial DNA sequence analysis of a native Bolivian population

Mitochondrial DNA analysis is very useful for the interpretation of the history of human migration and to estimate the frequency of a haplotype in the forensic context. From a human settlement perspective, La Paz area is greatly interesting since the first planned city of the region is located there. Samples from 110 individuals from La Paz were studied analysing the polymorphisms in the D-loop, hypervariable region I (HVI) and hypervariable region II (HVII) in order to verify the genetic diversity. The aim of this study was to start the creation of a population database in order to obtain the genetic interpopulation variability and classify haplotypes into characteristic haplogroups of South America. A total of 97 different haplotypes were identified, 90 being unique, expressed by 122 polymorphic nucleotide positions. Nucleotide and sequence diversity were estimated to be 0.015 ± 0.0075 and 0.996, respectively. Haplogroup distribution in the samples was 57.27% B4, 19.09% C1, 10.00% A2, 3.64% D1, 2.73% D4h3, 1.82% H, and 0.91% for each of the haplogroups A4, B4c1a, CZ, D4J, M7a and M8/N9b. The rate of length heteroplasmy was 36.36% in HVI and 52.73% in HVII. Phylogenetic analysis reveals proximity to the Korean, Chilean aboriginal, Japanese and Australian populations. The estimated genetic variability of the studied population was high, suggesting an early settlement.

Genetic variability of HVRII mtDNA in cord blood and respiratory morbidity in children

Genetic polymorphisms were examined using direct sequencing of the hypervariable region II (HVRII) in the D-loop of mtDNA in the cord blood of 355 children living in two areas of the Czech Republic – the industrial district of Teplice and the agricultural district of Prachatice. The incidence of the most frequent nucleotide variants of HVRII, C150T (10.1%), T152C (19.7%), T195C (19.7%) and 309.nC (41.4% for 309.2C and 13.8% for 309.3C), and the respiratory morbidity at the ages of 0–2 years and 2–6 years were investigated, considering many other factors such as locality, gender, ethnicity, heating by coal in household, maternal age, asthma bronchiale, allergic rhinitis, pollinosis, conjunctivitis and maternal tobacco exposure during and after pregnancy. We found that the T195C transversion in HVRII is connected with an increased risk of early childhood (0–2 years) bronchitis (RR 1.38, p = 0.034, 95% CI 1.04–1.85) and with increased risk of otitis media in children aged 2–6 years (RR 1.62, p = 0.032, 95% CI 1.04–2.53). Another polymorphism, 309.nC, is associated with an increased risk of bronchitis in children aged 2–6 years (RR 1.46, p = 0.030, 95% CI 1.04–2.06). The results indicate that genetic polymorphisms in mtDNA may be an important factor not only for various types of cancers and neurodegenerative diseases, but also for respiratory morbidity in children.

Frequency and Pattern of Heteroplasmy in the Control Region of Human Mitochondrial DNA

In this work, we present the results of the screening of human mitochondrial DNA (mtDNA) heteroplasmy in the control region of mtDNA from 210 unrelated Spanish individuals. Both hypervariable regions of mtDNA were amplified and sequenced in order to identify and quantify point and length heteroplasmy. Of the 210 individuals analyzed, 30% were fully homoplasmic and the remaining presented point and/or length heteroplasmy. The prevalent form of heteroplasmy was length heteroplasmy in the poly(C) tract of the hypervariable region II (HVRII), followed by length heteroplasmy in the poly(C) tract of hypervariable region I (HVRI) and, finally, point heteroplasmy, which was found in 3.81% of the individuals analyzed. Moreover, no significant differences were found in the proportions of the different kinds of heteroplasmy in the population when blood and buccal cell samples were compared. The pattern of heteroplasmy in HVRI and HVRII presents important differences. Moreover, the mutational profile in heteroplasmy seems to be different from the mutational pattern detected in population. The results suggest that a considerable number of mutations and, particularly, transitions that appear in heteroplasmy are probably eliminated by drift and/or by selection acting at different mtDNA levels of organization. Taking as a whole the results reported in this work, it is mandatory to perform a broad-scale screening of heteroplasmy to better establish the heteroplasmy profile which would be important for medical, evolutionary, and forensic proposes.

The relationship between HVRII mutation of mitochondrial DNA and squamous cell carcinoma of the lung

Mitochondrial DNA (mtDNA) is the only hereditary substance besides nucleus, which is composed of a code region and a non-code D-loop region. The aim of this study is to investigate the hypervariable region II (HVRII) mutation of mtDNA in peripheral blood leucocyte, pericancerous tissues and cancer tissues of lung squamous cell carcinoma patients, and to explore its significance. White blood cells, pericancerous tissues and cancer tissues were obtained from 15 cases of lung squamous cell carcinoma patients and mtDNA were extracted by one step method. HVRII fragments were amplified by PCR. Mutations were determined by DNA sequencing and the mutations of HVRII were analysed. In 15 lung squamous cell carcinoma patients, 14 patients showed mutation in HVRII(93.33%), 88 mutations were found totally. Eighty-seven mutations located in H-strand origin region, especially in the conserved sequence blocks and the mtTF1, 2 binding site (TFX and TFY). The results suggest that the mutation frequency of HVRII in cancer tissues of lung squamous cell carcinoma patients is very high and it might play an important role in carcinogenesis of the lung.

HvrBase++: a phylogenetic database for primate species

HvrBase++ is the improved and extended version of HvrBase. Extensions are made by adding more population-based sequence samples from all primates including humans. The current collection comprises 13 873 hypervariable region I (HVRI) sequences and 4940 hypervariable region II (HVRII) sequences. In addition, we included 1376 complete mitochondrial genomes, 205 sequences from X-chromosomal loci and 202 sequences from autosomal chromosomes 1, 8, 11 and 16. In order to reduce the introduction of erroneous data into HvrBase++, we have developed a procedure that monitors GenBank for new versions of the current data in HvrBase++ and automatically updates the collection if necessary. For the stored sequences, supplementary information such as geographic origin, population affiliation and language of the sequence donor can be retrieved. HvrBase++ is Oracle based and easily accessible by a web interface (). As a new key feature, HvrBase++ provides an interactive graphical tool to easily access data from dynamically created geographical maps.

MtDNA hypervariable region II (HVII) sequences in human evolution studies.

Variation in human mitochondrial DNA (mtDNA) has been used to infer the origin and migration patterns in human populations. mtDNA analysis has been focused mainly on the first hypervariable region (HVI). Nevertheless, although many studies of the second hypervariable region (HVII) have been carried out during recent years, the correlation between the first and the second hypervariable regions has not been well established. We have analysed 71 individuals from a relatively isolated region at the westernmost edge of continental Europe (Galicia, NW Iberian peninsula) and we have used available HVII sequence information from another 17 European and African populations. The results show high concordance between the two hypervariable regions, not only in variability levels but also in other phylogenetic aspects. The study of the population structure through an AMOVA analysis shows a low level of heterogeneity in the European populations. Nevertheless, we have found some inconsistency in the results, which are related to the mutation rate in these two hypervariable regions. These results are compatible with a high heterogeneity of mutation rates across the HVII region and stress the interest of HVII in population and forensic genetics.

The Frequency of Heteroplasmy in the HVII Region of mtDNA Differs across Tissue Types and Increases with Age

An immobilized sequence-specific oligonucleotide (SSO) probe system consisting of 16 SSO probes that detect sequence polymorphisms within five regions of the mtDNA control region was used to investigate the frequency of heteroplasmy in human mtDNA. Five regions of hypervariable region II (HVII) of the control region were studied in blood-, muscle-, heart-, and brain-tissue samples collected from 43 individuals during autopsy. An initial search for heteroplasmy was conducted by use of the SSO probe system. Samples in which multiple probe signals were detected within a region were sequenced for the HVII region, to verify the typing-strip results. The frequency of heteroplasmy was 5 of 43 individuals, or 11.6%. The frequency of heteroplasmy differed across tissue types, being higher in muscle tissue. The difference in the frequency of heteroplasmy across different age groups was statistically significant, which suggests that heteroplasmy increases with age. As a test for contamination and to confirm heteroplasmy, the samples were sequenced for the HVI region and were typed by use of a panel of five polymorphic nuclear markers. Portions of the tissues that appeared to be heteroplasmic were extracted at least one additional time; all gave identical results. The results from these tests indicate that the multiple sequences present in individual samples result from heteroplasmy and not from contamination.

Pattern of nucleotide substitution and rate heterogeneity in the hypervariable regions I and II of human mtDNA.

This study provides a comprehensive survey of the complex pattern of nucleotide substitution in the control region of human mtDNA, which is of central importance to the studies of human evolution. A total of 1229 different hypervariable region I (HVRI) and 385 different hypervariable region II (HVRII) sequences were analyzed using a complex substitution model. Moreover, we suggest a new method to assign relative rates to each site in the sequence. Estimates are based on maximum-likelihood methods applied to randomly selected subsets of sequences. Our results indicate that the rate of substitution in HVRI is approximately twice as high as in HVRII and that this difference is mainly due to a higher frequency of pyrimidine transitions in HVRI. However, rate heterogeneity is more pronounced in HVRII.

Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay.

Several populations were typed for the hypervariable region II (HVRII) of the mitochondrial DNA (mtDNA) control region using immobilised sequence-specific oligonucleotide (SSO) probes. A total of 16 SSO probes was used to type 1081 individuals from eight different ethnic groups (African Americans, Somali, US Europeans, US Hispanics, Bosnians, Finns, Saami and Japanese). Data was compared with already published sequence data by analysis of principal components, genetic distances and analysis of the molecular variance (AMOVA). The analyses performed group the samples in several clusters according to their geographical origins. Most of the variability detected is assigned to differences between individuals and only 7% is assigned to differences among groups of populations within and between geographical regions. Several features are patent in the samples studied: Somali, as a representative East African population, seem to have experienced a detectable amount of Caucasoid maternal influence; different degrees of admixture in the US samples studied are detected; Finns and Saami belong to the European genetic landscape, although Saami present an outlier position attributable to a strong maternal founder effect. The technique used is a rapid and simple method to detect human variation in the mtDNA HVRII in a large number of samples, which might be useful in forensic and population genetic studies.

HvrBase: compilation of mtDNA control region sequences from primates.

HvrBase is a compilation of human and ape mtDNA control region sequences. Sequences and related information on individuals, such as from where the sequences were obtained, is stored in three ASCII files as described previously. Moreover, the collection is also available as Mac/PC database application with a graphical user interface. It can be accessed through the WWW at URL http://www.eva.mpg.de/hvrbase. The current collection comprises 5846 human sequences from hypervariable region I (HVRI) and 2302 human sequences from hypervariable region II (HVRII). From apes, 295 HVRI sequences and 13 HVRII sequences are available.

Compilation of human mtDNA control region sequences.

This paper describes the organisation of a database for human mitochondrial control-region sequences. The data are divided into three ASCII files that contain aligned sequences from the hypervariable region I (HVRI), from the hypervariable region II (HVRII), and the available information about the individuals, from whom the sequences stem. The current collection comprises 4079 HVRI and 969 HVRII sequences. From 728 individuals sequences of both HVRI and HVRII are available. For easy access, the collection is made available to the scientific community via World Wide Web at URL http://www.zi.biologie.uni-muenchen.de/[symbol: see text]meyers/mtdna.html

Airway hyperresponsiveness (AHR) and lymphocyte subsets in BAL and peripheral blood among patients with seasonal pollinosis exacerbation

Genetic polymorphisms were examined using direct sequencing of the hypervariable region II (HVRII) in the D-loop of mtDNA in the cord blood of 355 children living in two areas of the Czech Republic – the industrial district of Teplice and the agricultural district of Prachatice. The incidence of the most frequent nucleotide variants of HVRII, C150T (10.1%), T152C (19.7%), T195C (19.7%) and 309.nC (41.4% for 309.2C and 13.8% for 309.3C), and the respiratory morbidity at the ages of 0–2 years and 2–6 years were investigated, considering many other factors such as locality, gender, ethnicity, heating by coal in household, maternal age, asthma bronchiale, allergic rhinitis, pollinosis, conjunctivitis and maternal tobacco exposure during and after pregnancy. We found that the T195C transversion in HVRII is connected with an increased risk of early childhood (0–2 years) bronchitis (RR 1.38, p = 0.034, 95% CI 1.04–1.85) and with increased risk of otitis media in children aged 2–6 years (RR 1.62, p = 0.032, 95% CI 1.04–2.53). Another polymorphism, 309.nC, is associated with an increased risk of bronchitis in children aged 2–6 years (RR 1.46, p = 0.030, 95% CI 1.04–2.06). The results indicate that genetic polymorphisms in mtDNA may be an important factor not only for various types of cancers and neurodegenerative diseases, but also for respiratory morbidity in children.