A New Leu714Arg Variant in the Converter Domain of MYH7 is Associated with a Severe Form of Familial Hypertrophic Cardiomyopathy

BACKGROUND

Hypertrophic cardiomyopathy is the most frequent autosomal dominant disease, yet due to genetic heterogeneity, incomplete penetrance, and phenotype variability, the prognosis of the disease course in pathogenic variant carriers remains an issue. Identifying common patterns among the effects of different genetic variants is important.

METHODS

We investigated the cause of familial hypertrophic cardiomyopathy (HCM) in a family with two patients suffering from a particularly severe disease. Searching for the genetic variants in HCM genes was performed using different sequencing methods.

RESULTS

A new missense variant, p.Leu714Arg, was identified in exon 19 of the beta-myosin heavy chain gene (MYH7). The mutation was found in a region that encodes the 'converter domain' in the globular myosin head. This domain is essential for the conformational change of myosin during ATP cleavage and contraction cycle. Most reports on different mutations in this region describe severe phenotypic consequences. The two patients with the p.Leu714Arg mutation had heart failure early in life and died from HCM complications.

CONCLUSIONS

This case presents a new likely pathogenic variant in MYH7 and supports the hypothesis that myosin converter mutations constitute a subclass of HCM mutations with a poor prognosis for the patient.

[Methylation of Regulatory Regions of DNA Repair Genes in Carotid Atherosclerosis]

The status of DNA methylation in the human genome changes during the pathogenesis of common diseases and acts as a predictor of life expectancy. Therefore, it is of interest to investigate the methylation level of regulatory regions of genes responsible for general biological processes that are potentially significant for the development of age-associated diseases. Among them there are genes encoding proteins of DNA repair system, which are characterized by pleiotropic effects. Here, results of the targeted methylation analysis of two regions of the human genome (the promoter of the MLH1 gene and the enhancer near the ATM gene) in different tissues of patients with carotid atherosclerosis are present. Analysis of the methylation profiles of studied genes in various tissues of the same individuals demonstrated marked differences between leukocytes and tissues of the vascular wall. Differences in methylation levels between normal and atherosclerotic tissues of the carotid arteries were revealed only for two studied CpG sites (chr11:108089866 and chr11:108090020, GRCh37/hg19 assembly) in the ATM gene. Based on this, we can assume the involvement of ATM in the development of atherosclerosis. "Overload" of the studied regions with transcription factor binding sites (according to ReMapp2022 data) indicate that the tissue-specific nature of methylation of the regulatory regions of the MLH1 and ATM may be associated with expression levels of these genes in a particular tissue. It has been shown that inter-individual differences in the methylation levels of CpG sites are associated with sufficiently distant nucleotide substitutions.

Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area

BACKGROUND

The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path.

RESULTS

Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines.

CONCLUSIONS

Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.

[Analysis of Heteroplasmy in the Major Noncoding Region of Mitochondrial DNA in the Blood and Atherosclerotic Plaques of Carotid Arteries]

For identification of somatic mitochondrial DNA (mtDNA) mutations, the mtDNA major noncoding region (D-loop) sequence in blood samples and carotid atherosclerosis plaques from patients with atherosclerosis was analyzed. Five point heteroplasmic positions were observed in 4 of 23 individuals (17%). Only in two cases could heteroplasmy have resulted from somatic mutation, whereas three heteroplasmic positions were found in both vascular tissue and blood. In addition, length heteroplasmy in a polycytosine stretches was registered at nucleotide positions 303-315 in 16 individuals, and also in the 16184-16193 region--in four patients. The results suggest that somatic mtDNA mutations can occur during atherosclerosis, but some heteroplasmic mutations may appear in all tissues, possibly being inherited.

[Genes for Fibrogenesis in the Determination of Susceptibility to Myocardial Infarction]

A group of patients with ischemic heart disease and myocardial infarction (N = 156) and a reference population sample (N = 300) were genotyped for 58 single nucleotide polymorphisms (SNPs) in the genes involved in extracellular matrix function and collagen metabolism or associated with cardiovascular diseases and atherosclerotic plaque stability. Genotyping was performed by mass-spectrometry with two multiplex sets of 27 and 31 SNPs. The study revealed different genetic composition of predisposition to cardiovascular disease continuum (CVDC) syntropy (patients with concomitant conditions: hypercholesterolemia, hypertension, and type-II diabetes mellitus, N = 96) and to isolated myocardial infarction (without these conditions, N = 60). Only the KIAA1462 gene (rs3739998) showed associations with both CVDC syntropy (OR = 1.71; 95% CI 1.19-2.45; р = 0.003) and isolated infarction (OR = 1.58; 95% CI 1.05-2.40; р = 0.028). Isolated myocardial infarction was also associated with LIG1 (rs20579) (OR = 2.08; 95% CI 1.06-4.17; р = 0.028) and ADAMDEC1 (rs3765124) (OR = 1.63; 95% CI 1.07-2.50; р = 0.020). CVDC syntropy was associated with CDKN2BAS1 (rs1333049) (OR = 1.48; 95% CI 1.03-2.12; р = 0.029) and APOA2 (rs5082) (OR = 1.47; 95% CI 1.02-2.11; р = 0.035). So, genes involved in fibrogenesis contribute to predisposition to the myocardial infarction as well. Isolated myocardial infarction and CVDC syntropy can be considered as pathogenetically different cardiovascular conditions, with different genes that contribute to the susceptibility.

[ Mitochondrial DNA polymorphism association with myocardial infarction and prognostic signs for atherosclerosis]

We have performed association analysis for mtDNA most common variants and haplogroups with myocardial infarction and some prognostic characteristics in patients. Comparison of patients (N=406) and controls (N=183) has shown higher frequency of HV0 haplogroup in patients (6.9% vs. 2.2%; p=0.033). Patients with early infarction (before age 55), comparing to patiens older than 55 and the first infarction, had higher frequency of 16189C variant (24.1 vs. 12.5%; p=0.008); also, haplogroup U2e was registered only in the subgroup with early infarction (4.4%; p=0.004). On the other side, haplogroup U5 was less frequent in the patients with early infarction (5.1% vs. 15.4%; p=0.002). The patients with recurring cardiovascular incidents during one year follow-up had higher frequency of haplogroup H1 (20% versus 4.5% in the patients without complications, p=0.002) and variant 16189C (30% versus 13.5%; p=0.018). Haplogroup U5 was more frequent in the group of patients with left ventricular ejection fraction less than 40%: 17.1% comparing to 8.2% in the group with ejection fraction>40%; p=0.034. The results suggest that mtDNA polymorphism contributes to coronary atherosclerosis. The associations could be explained by the polymorphism effect on oxidative phosphorylation and reactive oxygen production in mitochondria.

[The Study of Associations of Polymorphisms of Candidate Gene of Cardiovascular Diseases With Reduction of Glomerular Filtration Rate in Patients With ST Segment Elevation Myocardial Infarction]

AIM

to study associations of polymorphic genetic variants of inflammatory response, endothelial function, lipid metabolism, and blood coagulation with impaired renal function in patients with ST elevation myocardial infarction (STEMI).

MATERIAL AND METHODS

We enrolled in the study 171 patients admitted to the Kemerovo Cardiology Dispensary within 24 hours after onset of STEMI. All patients underwent genotype identification of 25 polymorphic variants of 18 major candidate genes for cardiovascular disease. Genotyping was performed with DNA chip SINKAR-1 (Institute of Medical Genetics and LLC "Genomic Diagnosis"). Glomerular filtration rate (GFR) was estimated using serum creatinine level measured at admission.

RESULTS

Comparison of allelic and genotype frequencies of the studied polymorphisms revealed that angiotensin-converting enzyme (ACE) gene rs4291 was associated with decreased GFR: odds ratio (OR) for carriers of rare TT genotype was 2.31 [1.01-5.25], =0.043. Analysis of genotype combinations of ACE rs4343 polymorphism and hepatic lipase gene (LIPC) rs1800588 showed that AA genotype of rs4343 polymorphism in combination with CC genotype of rs1800588 polymorphism was associated with lowest risk of renal dysfunction, whereas GG and AG genotypes of ACE rs4343 in combination with TT and CT genotypes of LIPC rs1800588.

[TOMM40 gene polymorphism association with lipid profile]

The distribution of the allele and genotype frequency for the TOMM40 gene polymorphic variants rs741780, rs157580, rs1160985, rs2075650, and rs8106922 was analyzed in a sampling of ethnic Russians from the city of Kemerovo. The study of the structure of linkage disequilibrium in terms of five studied polymorphic variants showed the presence ofa haplotype block 2 Kb in length, which includes three polymorphic variants, i.e., rs741780, rs1160985, and rs8106922. The differences in the frequencies of alleles and genotypes in terms of the polymorphic rs2075650 and rs157580 variants between ethnic Russians from the city of Kemerovo and other European populations were detected. It was discovered that polymorphic variants of TOMM40 rs741780, rs1160985, and rs8106922 are associated with serum triglyceride concentrations. In men, the polymorphic variant rs2075650 is associated with low-density lipoprotein cholesterol levels. In women, the polymorphic variant rs741780 is associated with diastolic blood pressure levels.

[Association between 242C > T polymorphism of NADPH oxidase p22phox gene (CYBA) and longevity in Russian population]

Life span depends on many factors, including the level of reactive oxygen species, like superoxide radical. Superoxide radical is produced from oxygen in the course of the oxidation of NADPH to NADP+. The process is catalyzed by NADPH oxidase. In this study, genotype and allele distributions of the C242T polymorphism in the CYBA gene, which encodes the alpha subunit ofNADPH oxidase (p22phox), were examined in the sample of long livers and in the population sample of the city of Tomsk. Statistically significantly higher frequency of T allele among female long livers (34.62%), compared to the females from Russian population (26.32%) was demonstrated (chi2 = 5.226; p = 0.022; OR = 1.48). Thus, the T allele is associated with a high life expectancy in females from the Russian population. No such association was observed for males from the same population.

[The role of genetic factors in the prediction of myocardial infarction complications within one year follow up]

A sample of 165 patients with myocardial infarction (MI) with ST segment elevation has been studied to construct a prediction model for one-year period complications (recurrent nonfatal IM or cardiac death). Polymorphic genetic markers (n = 32) with confirmed role in pathogenesis of cardiovascular disease were analyzed. The best model to stratify patients by risk of post-IM complications included variants rs4291 (A-240T) in the ACE gene, rs6025 (G1691A, Leiden mutation) in the F5, and rs5918 (Leu59Pro) in the IGTB3. C statistics for the genetic model was 0.75 (0.64; 0.86), p = 0.001, which is comparable with characteristics of the GRACE scale for the same patients' population: 0.73 (0.61; 0.85). Thereby, analysis of a limited number of genetic markers was sufficient to create risk prediction model for post-MI complications with comparable effectiveness to the model, which is currently in use in clinical practice. To confirm the clinical validity, the predictive model obtained in the study should be evaluated in independent samples of MI patients. Association analysis of individual genetic markers with patients' outcomes has revealed that T allele carrier status (AT and TT genotypes) rs4291 of the ACE and CG genotype rs328 of the LPL gene are risk factors for cardiac death during one year after MI; Leiden mutation (rs6025) of the F5 gene is related to the higher risk of recurrent non-fatal MI or death during one year; CC genotype of the rs10811661, located in 9p21 locus has a protective effect against recurrent MI or death within one year after acute event.

[The glutathione peroxidase 1 (GPX1) single nucleotide polymorphism pro198Leu: association with life span and coronary artery disease]

In this study we genotyped polymorphism in GPX1 Pro198Leu (C > T) rs 1050450 in four groups: patients with coronary artery disease, long-livers - above 90 years, early died peoples (before 55 years) from cardiovascular diseases and Russian population as control group. We have found significant higher allele T frequency in men with coronary artery disease -34.84% (Chi2 = 5.228, p = 0.022; OR = 1.46) and in early died men from cardiovascular diseases--38.16% (Chi2 = 6.461, p = 0.011; OR = 1.69) compared with control men--26.8%. Moreover, significantly higher genotype TT frequency has been shown in patients with coronary artery disease and myocardial infarction before age 50--19.44% in comparison with control group--7.28% (Chi2 = 9.55, p = 0.002). The TT frequency in long-livers (4.39%) was the lowest and significantly different from coronary artery disease group--12.79% (Chi2 = 8.07, p = 0.0045) and from coronary artery disease subgroup with myocardial infarction before 50--19.44% (Chi2 = 14.49, p = 0.0001). Thus our results indicate that allele T (Leu) of GPX1 Pro198Leu (C > T) polymorphism is unfavorable for successful ageing. It predisposes to coronary heart disease, earlier myocardial infarction (before age 50) and earlier death (before age 55).

Planning the human variome project: the Spain report

The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Because variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; http://www.humanvariomeproject.org/) was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008.

Beringian standstill and spread of Native American founders

Native Americans derive from a small number of Asian founders who likely arrived to the Americas via Beringia. However, additional details about the intial colonization of the Americas remain unclear. To investigate the pioneering phase in the Americas we analyzed a total of 623 complete mtDNAs from the Americas and Asia, including 20 new complete mtDNAs from the Americas and seven from Asia. This sequence data was used to direct high-resolution genotyping from 20 American and 26 Asian populations. Here we describe more genetic diversity within the founder population than was previously reported. The newly resolved phylogenetic structure suggests that ancestors of Native Americans paused when they reached Beringia, during which time New World founder lineages differentiated from their Asian sister-clades. This pause in movement was followed by a swift migration southward that distributed the founder types all the way to South America. The data also suggest more recent bi-directional gene flow between Siberia and the North American Arctic.

[ACE and AGTR1 genes polymorphisms in left ventricular hypertrophy pathogenesis in humans]

The role of A2350G polymorphism in exon 17 of the ACE gene and A1166C - in 3'-UTR of the AGTR1 in the pathogenesis of left ventricular hypertrophy was studied in patients with essential hypertension (EH) and arterial hypertension combined with diabetes mellitus type 2 (AH + DM2). Patients with EH and AH + DM2 did not differ from the control sample of healthy individuals by allele or genotype frequencies. However, an association of both polymorphisms with LVH was detected in EH patients. The frequency of 1166C allele was higher in patients with LVH (33.6% vs 20.7% without LVH). A1166C polymorphism determined the magnitude of left ventricular mass index (LVMI) in EH patients as well (p = 0.007). 2350G allele frequency of the ACE gene was in 1.5, and GG genotype--in 3.5-fold higher in EH patients with LVH, as compared without LVH. LVMI was significantly higher in patients with GG genotype as compared with heterozygotes and AA homozygotes (p = 0.002). Thus the presence of 1166C allele of AGTR1 and 2350G allele of ACE can be considered as predisposing factors for LVH development in EH. In contrast, association of studied polymorphisms with presence or LVH degree was not detected in patients with arterial hypertension combined with DM2. This may indicate another structure of genetic component of predisposition to LVH in different causes.

[MtDNA and Y-chromosome lineages in the Yakut population]

The structure of female (mtDNA) and male (Y-chromosome haplotypes) lineages in the Yakut population was examined. To determine mtDNA haplotypes, sequencing of hypervariable segment I and typing of haplotype-specific point substitutions in the other parts of the mtDNA molecule were performed. Y haplogroups were identified through typing of biallelic polymorphisms in the nonrecombining part of the chromosome. Haplotypes within haplogroups were analyzed with seven microsatellite loci. Mitochondrial gene pool of Yakuts is mainly represented by the lineages of eastern Eurasian origin (haplogroups A, B, C, D, G, and F). In Yakuts haplogroups C and D showing the total frequency of almost 80% and consisting of 12 and 10 different haplopypes, respectively, were the most frequent and diverse. The total part of the lineages of western Eurasian origin ("Caucasoid") was about 6% (4 haplotypes, haplogroups H, J, and U). Most of Y chromosomes in the Yakut population (87%) belonged to haplogroup N3 (HG16), delineated by the T-C substitution at the Tat locus. Chromosomes of haplogroup N3 displayed the presence of 19 microsatellite haplotypes, the most frequent of which encompassed 54% chromosomes of this haplogroup. Median network of haplogroup N3 in Yakuts demonstrated distinct "starlike phylogeny". Male lineages of Yakuts were shown to be closest to those of Eastern Evenks.

[Relationship between polymorphism of non-coding regions of human mitochondrial genome and primary cardiac conduction disorders]

AIM

Analysis of associations between idiopathic disturbances of cardiac conduction (DCC) and polymorphism of mitochondrial genome.

MATERIAL AND METHODS

A family examination was performed in 431 probands with various DCC and 1347 relatives of the first, second and third degree of kinship (the study group). All the examinees were divided into four subgroups. These included 158 probands with atrioventricular block (AVB) of various degree and their 518 relatives (subgroup 1); 50 probands with a complete right bundle-branch block (BBB) and their 161 relatives (subgroup 2); 108 probands with a complete left BBB and left anterior branch of the His bundle and their 152 relatives (subgroup 3); 115 probands with sick sinus syndrome (SSS) and their 327 relatives (subgroup 4). The control group consisted of 104 probands without clinical ECG manifestations of cardiac diseases and their 321 relatives. All the examinees have undergone ECG, atropin test, echocardioscopy, electrophysiological examination of the heart and mitochondrial DNA (mDNA).

RESULTS

Comparison of the incidence of mDNA D-loop restriction sites in the group of patients with idiopathic DCC and controls has found higher frequency of the Hae III 16517 site in the group of the patients (p = 0.0480). By location of the blocks (atrioventricular and intraventricular), the site occurred more frequently in patients with AVB (86.36%). The variant "+" by the site of Hae III 16517 mDNA was found to associate with disturbances of cardiac conduction, more closely in AVB.

CONCLUSION

Variability of mDNA may be an etiological factor of idiopathic DCC pathogenesis.

[The realm of mitochondrial genetics competence]

The paper discusses the main applications of achievements of mitochondrial genetics: human pathology (mitochondrial diseases, complex disease susceptibility genes) and population genetics (evolution of mankind, demographic history, and migration ways of populations). Awareness of the physiological properties of the well-known nucleotide sequences of mitochondrial DNA is ascertained to be a strategy for studying the functional organization of nuclear genome whose structure is all but completely decoded.

[Distribution of a deletion-insertion polymorphism in intergenic region V of mitochondrial DNA among the aboriginal population of Tuva]

Mitochondrial DNA region V deletion-insertion polymorphism was examined in three Tuvinian populations inhabiting western, northeastern, and southeastern parts of the republic. The 9-bp deletion was characterized by nonrandom distribution across the Tuva territory: its frequency in the western population (13.37%) was statistically significantly higher than that in the northeastern (4.62%), and southeastern populations, as well as in Mongols, who are territorially and ethnically close to Tuvinians. The insertion mutation in the region V was detected with a frequency of about 3% in two out of the three populations tested.

[Restriction polymorphism of the major noncoding region of mtDNA in the indigenous population of the TUVA republic]

Mitochondrial DNA sequence variation was examined in three rural populations of the indigenous inhabitants from the Tuva Republic. The frequencies of restriction sites within the D-loop region of mtDNA were determined. The three populations studied demonstrated similar patterns of mtDNA polymorphism. Like other Siberian populations, Tuvinians were characterized by high frequencies of the HaeIII 16517 and AspS9I (Cfr13I) 16516 restriction sites (about 75%). Moreover, in Tuvinians, a relatively low (71 to 81%) frequency of the KpnI 16129 restriction site was observed. The frequency of the mitotype differing from the Cambridge sequence by the HaeIII 16517 and KpnI 16129 sites in Tuvinians was higher than in Mongols and Russians. The features of mtDNA polymorphism point to the similarity between Tuvinians and other Siberian ethnic groups (Sel'kups in particular). This can be explained by the contribution of the Samoyed component, along with the Turkic and Mongoloid ones, to the formation of the Tuvinian ethnic group.

[Polymorphism of noncoding regions of the mitochondrial genome in the indigenous population of Southeastern Tuva Republic]

Deletion-insertion polymorphism of the V region and restriction polymorphism of D-loop for seven restriction enzymes--AspS9I (Cfr3I isoschizomere), BamHI, Bme18I (AvaII), EcoRV, HaeIII, KpnI, and Kzo9I (Sau3AI)--in mitochondrial DNA (mt DNA) were studied in the indigenous population of southeastern Tuva Republic. The results were compared with the data on Russians, Mongols, Buryats, and Altaians. Tuvinians significantly differed from Mongols in the frequency of the 9-bp deletion of the V region (1.89 and 8.07%, respectively). Additionally, significant differences between Tuvinians and samples of Mongols and Russians were obtained for frequencies of the AspS9I, HaeIII, and KpnI restriction sites. A comparison of the polymorphism of mitochondrial genome in individuals of different sexes and ages was performed in the studied sample.