Ethnicity-specific distribution of TRPM8 gene variants in Eurasian populations: signs of selection.

The TRPM8 gene encodes the ion channel, which is a cold receptor in afferent neurons of the mammalian somatosensory system. We studied the frequency of haplotype distribution from six SNPs in the TRPM8 gene in Eurasian human populations, including Russians, Kazakhs and Chukchi. Four of the six SNPs are located in exon 7 (rs13004520, rs28901637, rs11562975, rs17868387), rs7593557 is in exon 11. These exons encode parts of the N-terminus, which is necessary for channel functioning in the plasma membrane of neurons. The rs11563071 is in exon 23 encoding part of the C-terminus. The primary difference in population distribution of haplotypes determines the SNP from exon 11 which leads to Ser419Asn substitution in protein. The most pronounced differences in the patterns of diversity and frequencies of haplotypes were observed between Chukchi and Russians. The frequency of major H1 haplotype encompassing the 419Ser gene variant differs in examined populations; 0.738 (Russians), 0.507 (Kazakhs) and 0.337 (Chukchi), p < 0.001. The TRPM8 gene variants encoding 419Asn and carrying the minor alleles of rs28901637 (P249P) and rs11562975 (L250L) in exon 7 are characteristic of Asian populations. The frequency of all 419Asn variants in Chukchi is comparable to that in Africans, however, the minor allele frequencies of rs28901637, rs11562975 in Africans is low. Apparently in the process of human colonization of Eurasia, minor alleles of these SNPs diverged depending on rs7593557 structure in exon 11. We analyzed sequences of five TRPM8 mRNA isoforms extracted by researchers from different tissues. Sequence analysis demonstrates that they are transcribed from major H1 variant of the TRPM8 gene but contain different translation start codons, which are generated by alternative splicing from pro-mRNA.

Associations of cold receptor TRPM8 gene single nucleotide polymorphism with blood lipids and anthropometric parameters in Russian population.

We analyzed associations of single nucleotide polymorphisms rsl13004520 (R247T), rs11562975 (L250L), rs7593557 (S419N), rs11563208 (I1016I), and rs11563071 (V1058V) of the cold receptor TRPM8 (2q37.1) gene with blood plasma lipids and anthropometric parameters in Russian population (randomly chosen residents of Novosibirsk: 507 women and 459 men, mean age 57 years). The studied polymorphisms are localized in regions encoding NH2-terminal (R247T, L250L, S419N) and COOH-terminal (I1016I, V1058V) cytoplasmic domains of the channel. We showed association of single nucleotide polymorphism V1058V with the levels of total cholesterol and LDL and HDL cholesterol, and association of I1016I polymorphism with triglyceride content. Polymorphisms L250L and S419N correlated with anthropometric parameters (body mass index and waist and hip circumferences).

[Evaluation of association between 9 genetic polymorphism and myocardial infarction in the Siberian population].

AIM: to evaluate association between genetic polymorphism (SNPs) and myocardial infarction (identified in recent GWAS) as markers of high risk of myocardial infarction (MI) in Siberian population. Patients were divided into 2 groups - MI patients and control group (ratio 1:2) and presented the sapmle of population of Novosibirsk (9400 patients, 45-69 years) within international project HAPIEE (Health, Alcohol and Psychosocial factors In Eastern Europe). 200 patients with MI (129 men, 71 women) were included. Control group - individuals without MI (420) matched for age and sex. Genomic DNA was extracted from venous blood by phenol-chloroform extraction. Gene polymorphism of genes tested by real-time PCR according to protocol (probes TaqMan, Applied Biosystems, USA) with the use of ABI 7900HT. The following SNPs were studied: rs28711149, rs499818, rs619203, rs10757278 and rs1333049 (hr. 9), rs1376251, rs2549513, rs4804611, rs17465637. The association of SNP and MI was confirmed for 4 of 9 studied SNPs: rs1333049 (hr. 9), rs10757278 (hr. 9), rs499818 (hr. 6), rs619203 gene ROS1. Heart rate was associated with rs1333049 and rs10757278. Glucose level was associated with rs619203, rs28711149 and rs1376251. Total cholesterol and atherogenic index was associated with rs28711149. For the first time in Russian population the associations of GWAS with myocardial infarction SNPs was detected for rs619203, rs499818, rs1333049 and rs10757278. These genetic markers can be used for assessing the risk of myocardial infarction in Russian population.

[CCR5, CCR2, apoe, p53, ITGB3 and HFE gene polymorphism in Western Siberia long-livers].

In order to estimate the distribution of some polymorphisms for the CCR5, CCR2, apoE, p53, ITGB3, and HFE genes in Russian long-livers from Western Siberia, a sample of 271 individuals (range 90-105 years) was examined. It was demonstrated that carriage of the delta32 polymorphism for the CCR5 gene, V64/polymorphism for the CCR2 gene, e2/e3/e4 for the apoE gene, L33P for the ITGB3 gene, as well as H63D and S65C polymorphisms for the HFE gene does not influence on predisposition to the longevity; carriage of the 282 Y allele for the HFE gene negatively influences on the longevity; carriage of the heterozygous genotype for the R72P polymorphism for the p53 gene correlates with the longevity of elderly people.

[HFE gene polymorphism in the population of Northern Asia].

Human HFE gene haplotype analysis with reference to IVS2(+4)t/c, IVS4(-44)t/c, IVS5(-47)a/g polymorphic sites was performed in different North Asian ethnic groups. Of the eight possible intronic haplotypes, TTG, TTA, CTA and CCA were identified. High frequency of the CCA haplotype appears to be a characteristic feature of all Asian native populations. Potential functional importance of IVS4(-44)t/c polymorphism is demonstrated. Patients presenting with iron overload syndrome are shown to have low frequency of IVS4(-44)c.

[Relationship of single-nucleotide polymorphism rs11562975 in thermo-sensitive ion channel TRPM8 gene with human sensitivity to cold and menthol].

The examination of people belonging to the Russian ethnic group revealed that 20.3% of subjects had heterozygous genotype, containing the C-allele in single nucleotide polymorphism rs11562975, located in exon 7 of the gene encoding the temperature-sensitive ion channel TRPM8. Functional differences, associated with sensitivity to cold and menthol were identified between subjects with different genotypes of the polymorphism rs11562975 (GG and GC). Subjects with heterozygous genotype GC were characterized by increased sensitivity to cold and reduced sensitivity to menthol, agonist of the ion channel TRPM8, compared with subjects with homozygous genotype GG.

Association of cold receptor TRPM8 gene polymorphism with blood lipid indices and anthropometric parameters in Shorians.

We analyzed single nucleotide polymorphisms of the cold receptor TRPM8 gene as genetic markers of blood serum lipid indices in Shorians. Associations were found between rs11562975 (L250L) TRPM8 gene mononucleotide polymorphism with total cholesterol and LDL cholesterol and between rs28901637 (P249P) and HDL cholesterol. No associations of P249P and L250L with triglyceride level were found. L250L polymorphism was associated with anthropometric parameters characterizing lipid metabolism (hip and waist circumferences). The TRPM8 gene is likely to be involved in the regulation of lipid metabolism.

[Analysis of the gene polymorphism of matrix metalloproteinase-2 and -9 in patients with coronary heart disease].

AIM: To analyze the gene polymorphisms of matrix metalloproteinase-2 and -9 in patients with coronary heart disease (CHD). MATERIALS AND METHODS: The influence of single nucleotide polymorphism in the promoter region of the gene of matrix metalloproteinase (MMP)-2 at position -1306 and that of MMP-9 at position -1562 on the development of complications was studied in 181patients with atherosclerosis by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of amplification products. RESULTS: A significant genotype increase with enhanced MMP-9 gene transcriptional activity was found in the patients aged 55 years inclusively who had been diagnosed as having myocardial infarction as compared with an older age group and, on the contrary, a rise in the MMP-2 genotype with a high promoter activity in the older age group. CONCLUSION: The findings suggest that the functional polymorphism in the promoter region of the MMP-2 and MMP-9 genes plays a certain role in the development of acute coronary events.

[Analysis of polymorphism of three positions of promoter region of TNF- gene in patients with ischemic heart disease, unstable angina and myocardial infarction].

We studied polymorphism of three positions of promoter region of TNF alpha gene in patients with ischemic heart disease (IHD), development of unstable angina (UA) and acute myocardial infarction (MI). Analysis of frequencies of genotypes in position A308 showed that heterozygotness in patients with cardiovascular diseases significantly decreased. Lowering of risk of development of MI in carriers of heterozygous variant of the gene in position A308 was shown. In the group of patients with Q wave MI frequency of A308 AA genotype rose.

[Polymorphism in the human 2'-5'-oligoadenylate synthetase genes (OAS), associated with predisposition to severe forms of tick-borne encephalitis, in populations from North Eurasia].

2'-5'-oligoadenylate synthetases are a family of interferon-induced enzymes which play an important role in the antiviral defense in mammals. In human genome three genes encoding functional synthetases (OAS1, OAS2 and OAS3) form a cluster. Previously we found that particular genotypes and/or alleles of five single nucleotide polymorphisms (SNPs) located within OAS2 and OAS3 genes are associated with predisposition to severe forms of tick-borne encephalitis (TBE) in Russian population. In current study we investigated the distribution of three of that SNPs (OAS3rs2285932 (C/T Ile438Ile), OAS3rs2072136 (G/A, Ser567Ser) and OAS2 rs15895 (G/A, Trp720Ter relative to p71 isoform)) in seven populations from North Eurasia: Caucasians (Russians and Germans (from Altai region)), Central Asian Mongoloids (Altaians, Khakasses, Tuvinians and Shorians) and Arctic Mongoloids (Chukchi). Differences between populations in genotype, allele and haplotype frequencies and in linkage disequilibrium structure for these SNPs were detected. We found that these frequencies correlate with the ethnicity of the populations and with their supposed differential exposure to TBE virus. Particularly, the lowest frequencies of G/G genotype for OAS3 gene rs2072136 SNP (that according to our previously obtained data is associated with predisposition to severe forms of TBE) were found in Altaians, Khakasses, Tuvinians and Shorians who may highly contact with TBE virus in places of their habitation. Thus, data obtained allow to suppose that TBE virus might act as a selection factor for particular OAS genes variants in Central Asian Mongoloids.

[Genetics of atrial fibrillation].

We carried out examination of 103 probands with atrial fibrillation (AF) and 301 their 1st, 2nd, and 3rd degree relatives (main group). In addition we examined 82 probands without clinical electrocardiographic signs of heart disease and 163 their 1st and 2nd degree relatives (control group). We found accumulation of AF in families of probands with this pathology. Segregation analysis of idiopathic forms of AF allowed to reveal autosomal dominant type of inheritance of this pathology. Heterozygous variant of Ser49Gly of betai-adrenoreceptor gene can be considered as one of genetic predictors of development of how primary and secondary AF.

[The spectrum of mutations in the low-density lipoprotein receptor gene in the Russian population].

The spectrum of mutations in the low-density lipoprotein (LDL) receptor gene was studied in a sample of hypercholesterolemia patients of Caucasoid origin from the population of Russia. The examined patients were 45 to 49-years-old and had the highest level of total serum cholesterol in this age group. Seven previously non-described mutations have been revealed in exon 9 (R410G; M412V) and in exon 12 (Y/Y576; N/N591; L605V; L605R; A612G). Twelve previously described mutations have been identified in exons 2 (C/C27), 5 (C261F; E240X), 6 (E288K), 8 (A391T), 9 (E418G; L432R; D433E), 11 (G/G549; E558K; L/L568), and 12 (G592E). Only one of these mutations was previously described in Russia in a clinical sample of patients with familial hypercholesterolemia. The spectrum of LDL receptor gene mutations in the population sample of patients with hypercholesterolemia significantly differs from the mutation spectrum in patients with familial hypercholesterolemia (clinical samples). Sequencing of the LDL receptor gene is a highly efficient method for identifying the markers of hypercholesterolemia predisposition in a population.

[Deletional polymorphism of the 11th intron of the human c-fms gene: allele frequency in certain Russian populations and possible functional significance]. / Deletsionnyi polimorfizm 11-go introna gena c-fms cheloveka: chastoty allelei v nekotorykh populiatsiiakh Rossii i vozmozhnaia funktsional'naia znachimost'.

Analysis of deletion polymorphism of human c-fms gene intron 11 (approximately 425-bp deletion) is of particular interest because of the increased proportion of the deletion heterozygotes among the infants born from the parents, one of which lacks the deletion allele, and the other is heterozygous for the deletion. In this study, allele and haplotype frequencies of the polymorphism examined were assessed in a number of Caucasoid and Mongoloid populations of Russia. In all populations tested, relatively high prevalence of the deletion-bearing allele, ranging from 9.45% in ethnic Germans to 20.75% in Altaians, was detected. Russians and Kazakhs were characterized by intermediate frequencies of the rare allele, constituting in these populations 12.89 and 14.93%, respectively. Hardy-Weinberg expectations were met in all populations examined, pointing to a stable level of polymorphism at the c-fms intron 11. It was established by the context analysis of DNA of the deleted fragment along with the flanking sequences that this region contained a number of transcription factor motifs (Ets, SRF, and Myc), potentially capable of the regulation of the M-CFF-dependant c-fms transcription. The deletion breakpoint was localized within the CArG motif, which, together with the neighboring ets motif, form the potential CArG/ets composite element. It was suggested that allele lacking the fragment of intron 11 could be restricted in its ability to modulate the level of the c-fms transcription in response to the action of M-CSF. The data of molecular epidemiological survey serve as the indirect evidence favoring the suggestion on the possible functional value of this gene fragment. It was demonstrated that in the samples of acute bronchitis and trichomoniasis patients allelic and genotype frequencies were statistically significantly different from those in the population sample. In case of trichmoniasis, the frequency of rare allele was 2.4 times lower, and in case of acute bronchitis it was 2.1 times higher than in the control sample.

[Polymorphism of the HFE gene associated with hereditary hemochromatosis in populations of Russia]. / Polimorfizm gena HFE, assotsiirovannogo s nasledstvennym gemokhromatozom, v populiatsiiakh Rossii.

Expression of hereditary hemochromatosis as well as predisposition to iron overload syndrome and sporadic porphyria cutanea tarda are currently believed to be associated with the inheritance of certain allelic variants of the HFE gene. Allele frequencies of the C282Y (845A) and H63D (187G) mutations in the HFE gene in human populations of different races are remarkably different, and the prevalence of the S65C (193T) mutation is still poorly studied. In the present study we estimated allele frequencies of HFE mutations in Russians and in a number of Siberian ethnic indigenous populations. In Russians, allele frequencies of the C282Y, H63D and S65C mutations were 3.7, 13.3 and 1.7%, respectively. These values were similar to those observed in populations of Europe. The C282Y mutation was not detected in the population samples of Siberian ethnic groups, including Mansis, Khantys (Finno-Ugric group), Altaians, and Nivkhs (Mongoloids), suggesting that the frequency of this allele in the populations examined was lower than 1%. The frequency of the C282Y allele in the Tuvinian and Chukchi samples (Mongoloids) constituted 0.45 and 0.8%, respectively. Furthermore, pedigree analysis of both Chukchi carriers discovered showed that some of their ancestors were from other ethnic groups. Low frequencies of this allelic variant is typical of many Eastern Asian populations, which are also characterized by rather low frequencies of the H63D variant. In contrast, in some ethnic groups of Western Siberia allelic frequency of the H63D mutation is rather high, constituting 8.7% in Altaians, 15.5% in Mansis, and 11.3% in Khantys. The frequency of this allele in Tuvinians, Nivkhs, and Chukchis constituted 5, 4.7, and 0.8%, respectively. These findings make it possible to estimate the proportion of individuals predisposed to iron overload syndrome in different Russian ethnic groups. The HFE allele frequency distribution patterns observed in the populations examined pointed to pre-Celtic appearance of the CY82 allele. It also provides elucidation of the evolutionary genetic relationships between Siberian ethnic groups and the contemporary populations of Eastern and Western Europe.

[Polymorphism of the gene of angiotensin-converting enzyme and apolipoprotein E gene in long-livers of Novosibirsk city]. / Polimorfizm gena angiotensin-prevrashchaiushchego fermenta i gena apolipoproteina E u dolgozhitelei goroda Novosibirska.

The levels of polymorphism of genes of angiotensin converting enzyme (ACE) and apolipoprotein E (Apo E) were studied in elderly and long-living people in Novosibirsk. The results of the study in the investigated group (97 subjects) were compared with polymorphism of these genes in Novosibirsk population group aged 25-64 who were investigated in MONICA Project survey and had DNA data base formed. Frequency of D/D genotype among senile and long-living men was 5.9%. It is 5 times lower than in men 55-64 years of age (p = 0.04). Similar decrease of this gene frequency was also found in women of the same age. In men older than 83 years of age 4 times lowering of 3/4 genotype of Apo E gene and 2 times increasing of frequency of 2/3 genotype were revealed when comprising frequency of these genotypes in people of middle age. In subjects of senile age and long-livers of both sexes genotype 4/4 was not revealed. Lipid levels were more favorable in women with genotype 2/3 of Apo E gene (comparatively lower mean level of total cholesterol and higher level of HDL cholesterol) if compared with genotypes 3/3 and 3/4.

[Detection of two polymorphic sites in the human c-fms gene: allele frequency and genotype in some populations of Russia]. / Obnaruzhenie dvukh polimorfnykh saitov v gene c-fms cheoveka: chastoty allelei i genotipov v nekotorykh populiatsiiakh Rossii.

Two polymorphic sites were found in the human c-fms gene: one (G-->A) was in position 34,047 in the last intron, and the other (dinucleotide TC-->CA) was in positions 34,293 and 34,294 in the 3'-untranslated gene region, 34 bp downstream of the translation stop codon. The polymorphic dinucleotide appeared to be immediately upstream of an octamer showing 100% homology to cis element -CAAACTTC-, which is responsible for controlled instability of mRNAs of several genes. Based on these data, functional significance was assumed for this polymorphism of the c-fms gene. Allele frequencies were established for several populations. The mutant allele of the polymorphism located in the intron were detected only in one family of ethnic Germans from the Altaiskii krai. Polymorphism of the second site, which is in the 3'-untranslated region of the c-fms gene, was observed in all Caucasoid and Mongoloid populations examined. Frequency of the rare allele varied from 19.7-25% in Arctic Mongoloids to 31-42.6% in Central Asian Mongoloids and was similar in two Caucasoid populations (22.6% in ethnic Russians and 26.5% in ethnic Germans). The wide distribution of the mutant allele in human populations of the two races was considered indicative of an adaptive role of the polymorphism in providing a certain level of the gene product, a receptor, in certain cell processes.

Transcription Regulatory Regions Database (TRRD): its status in 2002.

Transcription Regulatory Regions Database (TRRD) is an informational resource containing an integrated description of the gene transcription regulation. An entry of the database corresponds to a gene and contains the data on localization and functions of the transcription regulatory regions as well as gene expression patterns. TRRD contains only experimental data that are inputted into the database through annotating scientific publication. TRRD release 6.0 comprises the information on 1167 genes, 5537 transcription factor binding sites, 1714 regulatory regions, 14 locus control regions and 5335 expression patterns obtained through annotating 3898 scientific papers. This information is arranged in seven databases: TRRDGENES (general gene description), TRRDLCR (locus control regions); TRRDUNITS (regulatory regions: promoters, enhancers, silencers, etc.), TRRDSITES (transcription factor binding sites), TRRDFACTORS (transcription factors), TRRDEXP (expression patterns) and TRRDBIB (experimental publications). Sequence Retrieval System (SRS) is used as a basic tool for navigating and searching TRRD and integrating it with external informational and software resources. The visualization tool, TRRD Viewer, provides the information representation in a form of maps of gene regulatory regions. The option allowing nucleotide sequences to be searched for according to their homology using BLAST is also included. TRRD is available at http://www.bionet.nsc.ru/trrd/.

Transcription regulatory regions database (TRRD): its status in 2000.

Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure-function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. TRRD 4.2.5 is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation.

COMPEL is a database on composite regulatory elements, the basic structures of combinatorial regulation. Composite regulatory elements contain two closely situated binding sites for distinct transcription factors and represent minimal functional units providing combinatorial transcriptional regulation. Both specific factor-DNA and factor-factor interactions contribute to the function of composite elements (CEs). Information about the structure of known CEs and specific gene regulation achieved through such CEs appears to be extremely useful for promoter prediction, for gene function prediction and for applied gene engineering as well. The structure of the relational model of COMPEL is determined by the concept of molecular structure and regulatory role of CEs. Based on the set of a particular CE, a program has been developed for searching potential CEs in gene regulatory regions. WWW search and browse routines were developed for COMPEL release 3.0. The COMPEL database equipped with the search and browse tools is available at http://compel.bionet.nsc.ru/. The program for prediction of potential CEs of NFAT type is available at http://compel.bionet.nsc. ru/FunSite.html and http://transfac.gbf.de/dbsearch/funsitep/ s_comp.html

[Characteristics of the mitochondrial genome of russian germans]. / Osobennosti mitokhondrial'nogo genofonda rossiiskikh nemtsev.

Nucleotide sequences of the mitochondrial DNA (mtDNA) control region were studied in Germans living in the Altai, Russia. Although this ethnic group has been living in Russia for a long time, the obtained data indicate that its mitochondrial gene pool retains the main characteristics of the Western and Central European gene pools. Regarding the mitochondrial gene pool, Russian Germans were more similar to Germans living in Germany than to Russians with regard to the frequency of the Cambridge nucleotide sequence, frequencies and composition of five European haplotypic groups (classification of Richards et al.), and average intra- and interpopulation pairwise nucleotide differences. However, the mitochondrial gene pool of Altaian Germans also differed from that of Western European populations. The gene pool of Altaian Germans contained the ancestral variants of the main haplotypic groups. To date, these variants have not been found in modern Western and Central European populations, which is apparently due to their lower frequencies. In addition, some previously unknown mtDNA variants with specific nucleotide substitutions were found in Altaian Germans. The obtained results suggest that the modern mitochondrial gene pool of Europeans, including Germans from Germany, was largely affected by the demographic processes that occurred in the past two centuries. The Germans that lived in Russia were relatively isolated and, hence, retained more characteristics of the ancestral gene pool.