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.

Статус метилирования ДНК в геноме человека изменяется в патогенезе распространенных заболеваний и выступает в качестве предиктора ожидаемой продолжительности жизни. В связи с этим представляет интерес исследование уровня метилирования регуляторных регионов генов, отвечающих за общебиологические процессы, потенциально значимые для развития возраст-ассоциированных заболеваний. Среди них гены белков различных систем репарации ДНК, продукты которых характеризуются плейотропными эффектами. В исследовании представлены результаты таргетного анализа метилирования двух регионов генома (промоторного участка гена MLH1 и энхансерного ‒ вблизи гена ATM) в разных тканях пациентов с атеросклерозом сонных артерий. В результате анализа профилей метилирования исследованных генов в различных тканях одних и тех же индивидов выявлено наличие выраженных различий между лейкоцитами и тканями сосудистой стенки. Различия по уровням метилирования в нормальных и пораженных атеросклерозом тканям сонных артерий обнаружены только для двух исследованных CpG-сайтов в гене ATM (chr11:108089866 и chr11:108090020, сборка GRCh37/hg19). На основании этих данных можно предполагать участие ATM в развитии атеросклероза. “Нагруженность” изученных регионов сайтами связывания транскрипционных факторов (по данным ReMapp2022) свидетельствует о том, что тканеспецифичный характер метилирования регуляторных участков генов MLH1 и ATM может быть связан с уровнем их экспрессии в конкретной ткани. Показано, что межиндивидуальные различия в уровнях метилирования CpG-сайтов ассоциированы с достаточно удаленными нуклеотидными заменами.

miRNAs are vital molecules of gene expression. They are involved in the pathogenesis of various common diseases, including atherosclerosis, its risk factors, and its complications. A detailed characterization of the spectrum of functionally significant polymorphisms of miRNA genes in patients with advanced carotid atherosclerosis is an important research task. We analyzed miRNA expression and exome sequencing data of carotid atherosclerotic plaques of male patients (n = 8, 66–71 years of age, 67–90% degree of carotid artery stenosis). For further study and analysis of the association between the rs2910164 polymorphism of the MIR146A gene and advanced carotid atherosclerosis, we recruited 112 patients and 72 relatively healthy Slavic residents of Western Siberia. A total of 321 and 97 single nucleotide variants (SNVs) were detected in the nucleotide sequences of pre- and mature miRNAs in carotid atherosclerotic plaques. These variants were located in 206 and 76 miRNA genes, respectively. Integration of the data of exome sequencing and miRNA expression revealed 24 SNVs of 18 miRNA genes that were processed to mature form in carotid atherosclerotic plaques. SNVs with the greatest potential functional significance for miRNA expression predicted in silico were rs2910164:C>G (MIR146A), rs2682818:A>C (MIR618), rs3746444:A>G (MIR499A), rs776722712:C>T (MIR186), rs199822597:G>A (MIR363). The expression of miR-618 was lower in carotid atherosclerotic plaques of patients with the AC rs2682818 genotype of the MIR618 gene compared with the CC genotype (log2 FC = 4.8; p = 0.012). We also found an association of rs2910164:C (MIR146A) with the risk of advanced carotid atherosclerosis (OR = 2.35; 95% CI: 1.43-3.85; p = 0.001). Integrative analysis of polymorphisms in miRNA genes and miRNA expression is informative for identifying functionally significant polymorphisms in miRNA genes. The rs2682818:A>C (MIR618) is a candidate for regulating miRNA expression in carotid atherosclerotic plaques. The rs2910164:C (MIR146A) is associated with the risk of advanced carotid atherosclerosis.

МикроРНК, участвующие в регуляции экспрессии генов, вовлечены в патогенез широкого спектра многофакторных заболеваний, в том числе атеросклероза, его факторов риска и осложнений, что делает актуальным изучение функционально значимых полиморфных вариантов в генах микроРНК у пациентов с клинически выраженным атеросклерозом сонных артерий. Нами проведено секвенирование экзомов и микроРНК из одних и тех же образцов атеросклеротических бляшек сонных артерий мужчин (n = 8, возраст 66‒71 лет) с клинически выраженным атеросклерозом. В подтверждающем исследовании использовали расширенную выборку из 112 пациентов и 72 индивидов контрольной группы (этнических славян, жителей Западной Сибири). В образцах сонных артерий, пораженных атеросклерозом, обнаружены 206 пре-микроРНК и 76 зрелых микроРНК, содержащих 321 и 97 однонуклеотидных вариантов (SNV) соответственно. Объединение данных секвенирования экзомов и микроРНК показало, что 18 генов микроРНК, которые экспрессируются в атеросклеротических бляшках до зрелого состояния, несут 24 SNV. Из них наибольшей потенциальной функциональной значимостью в отношении экспрессии микроРНК, предсказанной in silico, обладали варианты rs2910164:C>G (MIR146A), rs2682818:A>C (MIR618), rs3746444:A>G (MIR499A), rs776722712:C>T (MIR186) и rs199822597:G>A (MIR363). В образцах, полученных от пациентов с генотипом АС rs2682818 гена MIR618, выявлено снижение уровня экспрессии miR-618 по сравнению с генотипом СС (log2 FC = 4.8; p = 0.012). Обнаружено, что rs2910164:C (MIR146A) ассоциирован с риском развития клинически выраженного атеросклероза сонных артерий (OR = 2.35; 95%CI: 1.43‒3.85; p = 0.001). Интегративный подход позволил выявить новые наиболее информативные с точки зрения предсказания функциональной значимости полиморфные варианты в генах микроРНК. Вариант rs2682818:A>C (MIR618) может быть связан с изменением экспрессии miR-618 в атеросклеротических бляшках сонных артерий, а rs2910164:C (MIR146A) ассоциирован с риском развития клинически выраженного атеросклероза.

A broad range of SNP markers associated with diseases and pathogenically significant features were identified in noncoding regions of the human genome. The mechanisms that underlie their associations are a pressing problem. A number of associations was previously observed between polymorphic variants of DNA repair proteins genes and common diseases. To clarify the possible mechanisms of the associations, a detailed annotation of the regulatory potential of the markers was carried out using online resources (GTX-Portal, VannoPortal, Ensemble, RegulomeDB, Polympact, UCSC, GnomAD, ENCODE, GeneHancer, EpiMap Epigenomics 2021, HaploReg, GWAS4D, JASPAR, ORegAnno, DisGeNet, and OMIM). The review characterizes the regulatory potential for the polymorphisms rs560191 (of the TP53BP1 gene), rs1805800, rs709816 (NBN), rs473297 (MRE11), rs189037, rs1801516 (ATM), rs1799977 (MLH1), rs1805321 (PMS2), and rs20579 (LIG1). General characteristics of the markers are considered, and data are summarized to describe their influence on expression of their own and co-regulated genes and binding affinity of transcription factors. The review additionally considers the data on adaptogenic and pathogenic potentials of the SNPs and co-localized histone modifications. A possible involvement in regulating the functions of both their own and nearby genes may explain the associations of the SNPs with diseases and their clinical phenotypes.

Выявление широчайшего спектра локализованных в некодирующих участках генома однонуклеотидных полиморфизмов (SNP), ассоциированных с заболеваниями человека и патогенетически значимыми признаками, остро поставило вопрос по идентификации механизмов, объясняющих эти связи. Ранее нами выявлен ряд ассоциаций полиморфных вариантов генов, кодирующих белки репарации ДНК, с многофакторными заболеваниями. Для выяснения возможных механизмов, лежащих в их основе, нами проведена подробная аннотация регуляторного потенциала изучаемых маркеров с использованием ряда on-line ресурсов (GTXPortal, VannoPortal, Ensemble, RegulomeDB, Polympact, UCSC, GnomAD, ENCODE, GeneHancer, EpiМap Epigenomics 2021, HaploReg, GWAS4D, JASPAR, ORegAnno, DisGeNet, OMIM). В статье охарактеризован регуляторный потенциал следующих полиморфных вариантов: rs560191 (в гене TP53BP1), rs1805800 и rs709816 (NBN), rs473297 (MRE11), rs189037 и rs1801516 (ATM), rs1799977 (MLH1), rs1805321 (PMS2), rs20579 (LIG1). Приведена как общая характеристика изученных маркеров, так и информация по их влиянию на экспрессию “своего” и корегулируемых генов, на аффинность связывания факторов транскрипции. Рассмотрены опубликованные данные по адаптогенному и патологическому потенциалу этих SNP и о колокализованных с ними модификациях гистонов. Потенциальная вовлеченность на различных уровнях в регуляцию функционирования не только генов, в состав которых входят исследованные маркеры, но и близлежащих генов может объяснять ассоциированность изученных SNP с заболеваниями и их клиническими фенотипами.

The Khamnigan are a small ethnic group that was once locally dominant in the Onon and Argun river basins, a region today politically divided between Mongolia, the Russian Federation, and the People’s Republic of China. Historically also known as the “Horse Tungus of Transbaikalia”, the Khamnigan are characterized by a rare type of ethnic bilingualism, in which two different languages, Khamnigan Mongol (Mongolic) and Khamnigan Ewenki (Tungusic), have been transmitted for several generations within a single ethnic group. Khamnigan Ewenki, which was first documented in two varieties by the Finnish linguist M. A. Castrén (1856), may be taxonomically placed in the context of the Ewenki language, as spoken widely in Siberia, while Khamnigan Mongol is today recognized as a separate ethnospecific Mongolic language whose principal property is that it lacks most of the Post-Proto-Mongolic innovations that distinguish its closest neighbours – Khalkha and Buryat – from each other and from other Mongolic languages. Khamnigan Mongol was first studied by the Buryat scholar Tsyben Zhamtsarano in the early 20th century, but most of his results remained unpublished at the time. It was only with the field work carried out by the Hungarian folklorist Katalin Uray-Kőhalmi (1959) that the Khamnigan became more widely known to the international scholarly community.

Disruption of neocortical circuitry and architecture in humans causes numerous neurodevelopmental disorders. Neocortical cytoarchitecture is orchestrated by various transcription factors such as Satb2 that control target genes during strict time windows. In humans, mutations of SATB2 cause SATB2 Associated Syndrome (SAS), a multisymptomatic syndrome involving intellectual disability, speech delay, epilepsy and craniofacial defects. We show that Satb2 controls neuronal migration and axonal outgrowth by inducing the expression of the GPI-anchored protein, Sema7A. We find that heterodimerization with Sema4D increases targeting of Sema4D to the membrane and is required for Sema7A function. Finally, we report that membrane localization and pos- translational modification of the Sema7A-Sema4D complex is disrupted by a novel de novo mutation in Sema4D (Q497P) that is associated with epilepsy in humans.

A new series of heterocyclic derivatives with a 1,7,7-trimethylbicyclo[2.2.1]heptane fragment was designed, synthesised and biologically evaluated. Synthesis of the target compounds was performed using the Cu(I) catalysed cycloaddition reaction. The key starting substances in the click reaction were an alkyne containing a 1,7,7-trimethylbicyclo[2.2.1]heptane fragment and a series of azides with saturated nitrogen-containing heterocycles. Some of the derivatives were found to exhibit strong antiviral activity against Marburg and Ebola pseudotype viruses. Lysosomal trapping assays revealed the derivatives to possess lysosomotropic properties. The molecular modelling study demonstrated the binding affinity between the compounds investigated and the possible active site to be mainly due to hydrophobic interactions. Thus, combining a natural hydrophobic structural fragment and a lysosome-targetable heterocycle may be an effective strategy for designing antiviral agents.

Viruses and genetics in pregnancy and birth Čulić Vida1,2, Robert Vulić1, Maja Radman3, Tamara Bošnjak4, Jasminka Rešić Karara5, Maria Lopatkina6 and Igor Lebedev6 1 Gynecology and Obstetrics Private Outpatient Clinic, Split, Croatia 2 Laboratory for Human Genetics, Department of Medical Genetics, Pediatrics Clinic, University Hospital Centre Split, Split, Croatia 3 Clinics for Internal Medicine, Department of Endocrinology, Diabetes and Metabolism, University Hospital Center Split, Split, Croatia 4Neonatology Department, Clinics for Gynecology and Obstetrics, University Hospital Centre Split, Split, Croatia 5Clinics for Gynecology and Obstetrics, University Hospital Centre Split, Split, Croatia 6Research Institute of Medical Genetics, Tomsk National Research Medical Center, Tomsk, Russia ABSTRACT In this study we presented several patients with genital infections during pregnancy, perinatal infection, de novo genetics syndromes, sterility problems and spontaneous abortions with HSV1, HSV2, CMV, Adeno, Parvo B19, RSV, EBV and Coxsackie virus. Spontaneous abortion were provoked (or at least associated) with viral infection. For some we had expected such pregnancy outcomes, and for some we observed chromosome breaks that by repetitive screening, after cessation of acute viral infection, could no longer been seen. Nonspecific chromosomal aberrations were associated with HSV type 2, herpes zoster and Ebstein Barr virus infection. SCIREA Journal of Biology http://www.scirea.org/journal/Biology October 30, 2023 Volume 8, Issue 5, October 2023 https://doi.org/10.54647/biology180326 139 EBV is a causative agent of autoimmune entities were polyclonality in serological findings is present, we are searching for the same answer in the cause of spontaneous abortion with or without chromosomes abnormalities with atypical serology values of those viruses at both partners.

Background: Squamous cell lung cancer (SCLC) arises from bronchial changes: basal cell hyperplasia (BCH), squamous metaplasia (SM), and dysplasia. However, the premalignant process preceding SCLC is not inevitable; it can stop at any of the bronchial lesions. Previously, we hypothesized that combinations of premalignant lesions observed in the small bronchi of SCLC patients can reflect the different "scenarios" of the premalignant process: BCHi-the stoppage at the stage of hyperplasia and BCHSM-the progression of hyperplasia to metaplasia.

Methods and results: In this study, using whole-genome bisulfite sequencing we analyzed the DNA methylome of two forms of BCH: isolated BCH (BCHi) and BCH co-occurred with SM (BCHSM) in the small bronchi of SCLC patients. It was shown that BCHi harbored differentially methylated regions (DMRs) affecting genes associated with regulating phosphatase activity. In BCHSM, DMRs were found in genes involved in PI3K-Akt and AMPK signaling pathways. DMRs were also found to affect specific miRNA genes: miR-34a and miR-3648 in BCHi and miR-924 and miR-100 in BCHSM.

Conclusions: Thus, this study demonstrated the significant changes in DNA methylome between the isolated BCH and BCH combined with SM. The identified epigenetic alterations may underlie different "scenarios" of the premalignant process in the bronchial epithelium.

Cohen syndrome is an autosomal recessive disorder caused by VPS13B (COH1) gene mutations. This syndrome is significantly underdiagnosed and is characterized by intellectual disability, microcephaly, autistic symptoms, hypotension, myopia, retinal dystrophy, neutropenia, and obesity. VPS13B regulates intracellular membrane transport and supports the Golgi apparatus structure, which is critical for neuron formation. We generated induced pluripotent stem cells from two patients with pronounced manifestations of Cohen syndrome and differentiated them into neural stem cells and neurons. Using transmission electron microscopy, we documented multiple new ultrastructural changes associated with Cohen syndrome in the neuronal cells. We discovered considerable disturbances in the structure of some organelles: Golgi apparatus fragmentation and swelling, endoplasmic reticulum structural reorganization, mitochondrial defects, and the accumulation of large autophagosomes with undigested contents. These abnormalities underline the ultrastructural similarity of Cohen syndrome to many neurodegenerative diseases. The cell models that we developed based on patient-specific induced pluripotent stem cells can serve to uncover not only neurodegenerative processes, but the causes of intellectual disability in general.

Pregnancy loss is often caused by chromosomal abnormalities of the conceptus. The prevalence of these abnormalities and the allocation of (ab)normal cells in embryonic and placental lineages during intrauterine development remain elusive. In this study, we analyzed 1,745 spontaneous pregnancy losses and found that roughly half (50.4%) of the products of conception (POCs) were karyotypically abnormal, with maternal and paternal age independently contributing to the increased genomic aberration rate. We applied genome haplarithmisis to a subset of 94 pregnancy losses with normal parental and POC karyotypes. Genotyping of parental DNA as well as POC extra-embryonic mesoderm and chorionic villi DNA, representing embryonic and trophoblastic tissues, enabled characterization of the genomic landscape of both lineages. Of these pregnancy losses, 35.1% had chromosomal aberrations not previously detected by karyotyping, increasing the rate of aberrations of pregnancy losses to 67.8% by extrapolation. In contrast to viable pregnancies where mosaic chromosomal abnormalities are often restricted to chorionic villi, such as confined placental mosaicism, we found a higher degree of mosaic chromosomal imbalances in extra-embryonic mesoderm rather than chorionic villi. Our results stress the importance of scrutinizing the full allelic architecture of genomic abnormalities in pregnancy loss to improve clinical management and basic research of this devastating condition.

HSPA8 is involved in many stroke-associated cellular processes, playing a pivotal role in the protein quality control system. Here we report the results of the pilot study aimed at determining whether HSPA8 SNPs are linked to the risk of ischemic stroke (IS). DNA samples from 2139 Russians (888 IS patients and 1251 healthy controls) were genotyped for tagSNPs (rs1461496, rs10892958, and rs1136141) in the HSPA8 gene using probe-based PCR. SNP rs10892958 of HSPA8 was associated with an increased risk (risk allele G) of IS in smokers (OR = 1.37; 95% CI = 1.07–1.77; p = 0.01) and patients with low fruit and vegetable consumption (OR = 1.36; 95% CI = 1.14–1.63; p =0.002). SNP rs1136141 of HSPA8 was also associated with an increased risk of IS (risk allele A) exclusively in smokers (OR = 1.68; 95% CI = 1.23–2.28; p = 0.0007) and in patients with a low fruit and vegetable intake (OR = 1.29; 95% CI = 1.05–1.60; p = 0.04). Sex-stratified analysis revealed an association of rs10892958 HSPA8 with an increased risk of IS in males (risk allele G; OR = 1.30; 95% CI =1.05–1.61; p = 0.01). Thus, SNPs rs10892958 and rs1136141 in the HSPA8 gene represent novel genetic markers of IS.

The study aimed to assess clinical pharmacology patterns of prescribed and taken medications in older cardiovascular patients using electronic health records (EHRs) (n = 704) (2019–2022). Medscape Drug Interaction Checker was used to identify pairwise drug–drug interactions (DDIs). Prevalence rates of DDIs were 73.5% and 68.5% among taken and prescribed drugs, respectively. However, the total number of DDIs was significantly higher among the prescribed medications (p < 0.05). Serious DDIs comprised 16% and 7% of all DDIs among the prescribed and taken medications, respectively (p < 0.05). Median numbers of DDIs between the prescribed vs. taken medications were Me = 2, IQR 0–7 vs. Me = 3, IQR 0–7 per record, respectively. Prevalence of polypharmacy was significantly higher among the prescribed medications compared with that among the taken drugs (p < 0.05). Women were taking significantly more drugs and had higher prevalence of polypharmacy and DDIs (p < 0.05). No sex-related differences were observed in the list of prescribed medications. ICD code U07.1 (COVID-19, virus identified) was associated with the highest median DDI number per record. Further research is warranted to improve EHR structure, implement patient engagement in reporting adverse drug reactions, and provide genetic profiling of patients to avoid potentially serious DDIs.