Vol 58, No 1 (2024)

UV radiation of sunlight induces in cellular DNA of different organisms photochemical reactions, which may lead to the development of series biological responses to arising lesions, including apoptosis, mutagenesis, and carcinogenesis. The chemical nature and the amount of DNA lesions depend on the wavelength of UV radiation. Photons of UV radiation in the region B (UVB, 290–320 nm) cause the production of two main defects, namely, cyclobutane pyrimidine dimers and, with a less yield, pyrimidine (6-4) pyrimidone photoproducts; their formation is the result of the direct UVB photon absorption by DNA bases. Photons of UV radiation in the region A (UVA, 320–400 nm) induce only cyclobutane dimers that can be formed by triplet-triplet energy transfer from cellular chromophores, absorbing photons of this UV region, to DNA thymine bases. UVA is much more effective than UVB in the sensitized oxidatively lesion formation in DNA such as single strand breaks and oxidized bases; among those, 8-oxo-dihydroguanine is the most frequent since it can be produced from several oxidation processes. In recent years, multiple papers, reporting novel, more detailed information about molecular mechanisms of photochemical reactions underlying the formation of different lesions in DNA were published. The present review mainly aims at summarizing and analyzing data contained in these publications, particularly regarding oxidative reactions that are initiated by reactive oxygen species and radicals generated by potential endogenous photosensitizers such as pterins, riboflavin, protoporphyrin IX, NADH, and melanin. The role of specific DNA photoproducts in genotoxic processes induced in living systems by UV radiation of different wavelengths, including human skin carcinogenesis, is discussed.

Peripheral blood biomarkers are of particular importance to diagnose certain diseases including coronary artery disease (CAD) due to their non-invasiveness. Investigating the expression of noncoding RNAs (ncRNAs) paves the way to early disease diagnosis, prognosis, and treatment. Consequently, in this research, we aimed to investigate a panel of ncRNAs as potential biomarkers in patients with coronary artery disease. Two different groups have been designed (control and CAD). All participants were subjected to interviews and clinical examinations. Peripheral blood samples were collected, and plasma was extracted. At the same time, target ncRNAs have been selected based on literature review and bioinformatic analysis, and later they underwent investigation using quantitative real-time PCR. The selected panel encompassed the long non-coding RNAs (lncRNAs) MEG3, TUG1, and SRA1, and one related microRNA (miRNA): hsa-miR-21-3p. We observed statistically significant upregulation in MEG3, TUG1, and hsa-miR21-3p in CAD patients compared to control participants (p-value < 0.01). Nevertheless, SRA1 exhibited downregulation with no statistical significance (p-value > 0.05). All ncRNAs under study displayed a significantly strong correlation with disease incidence, age, and smoking. Network construction revealed a strong relationship between MEG3 and TUG1. ROC analysis indicated high potentiality for hsa-miR-21-3p to be a promising biomarker for CAD. Moreover, MEG3 and TUG1 displayed distinguished diagnostic discrimination but less than hsa-miR-21-3p, all of them exhibited strong statistical significance differences between CAD and control groups. Conclusively, this research pinpointed that MEG3, TUG1, and hsa-miR-21-3p are potential biomarkers of CAD incidence and diagnosis.

DNA transposons of the IS630/Tc1/mariner (ITm) are widespread representatives of DNA transposons that make a significant contribution to the evolution of eukaryotic genomes. With the start of large-scale application of next generation sequencing (NGS) technologies and the emergence of many new whole genome sequences of organisms in nucleotide collections, ITm elements have been identified in most taxa of the eukaryotic tree of life. Despite the rather detailed study of the diversity of ITm representatives, elements are still found that contribute to the expansion and revision of the classification of this group of DNA transposons. This paper presents for the first time a detailed analysis of the L31 elements of bivalves, which resulted in a description of the structure, diversity, distribution, and phylogenetic position among the ITm elements. It was found that L31 transposons are an independent superfamily in the ITm group, which has an ancient origin. Within the L31 clade, rather high diversity was observed: five phylogenetic clusters were identified. At the moment, the presence of L31 transposons in molluscs has been revealed only in bivalves in the subclass Autobranchia, with a predominance in diversity and quantity in the infraclass Pteriomorphia. It has also been shown that the protein encoded by the second open reading frame (ORF2) is an integral structural component of almost all full-length L31 elements. The data obtained contribute to a better understanding of the evolution of representatives of ITm transposons. Further study of L31 transposons in other taxa (cnidaria), as well as the study of the function of the second ORF protein, will provide an opportunity to better understand the evolution of DNA transposons, the mechanisms of horizontal transfer, and the contribution to eukaryotic biodiversity.

Stress can play a significant role in the development of arterial hypertension and many other complications of cardiovascular diseases. Considerable attention is paid to the study of the molecular mechanisms involved in the body’s response to stressful influences, but there are still many blank spots in understanding the details. ISIAH rats model a stress-sensitive form of arterial hypertension. ISIAH rats are characterized by genetically determined enhanced hypothalamic-adrenal-cortical and sympathetic adrenomedullary systems activity, which suggests a functional state of increased stress reactivity. In the present study, for the first time, the time course of the Fos and several related genes’ expression was studied in the hypothalamus of adult male hypertensive ISIAH rats after exposure to a single restraint stress of different duration (30, 60, and 120 minutes). The results of the study showed the activation of Fos transcription with a peak 1 hour after the onset of restraint stress. The dynamics of Fos gene activation coincides with the dynamics of blood pressure increase after stress. Restraint stress also alters the transcription of several other genes encoding transcription factors (Jun, Nr4a3, Jdp2, Ppargc1a) associated with the development of cardiovascular diseases. Since Fos induction is a marker of brain neuron activation, we can conclude that increased stress reactivity of the hypothalamic-pituitary-adrenocortical and sympathoadrenal systems of hypertensive ISIAH rats during short-term restriction is accompanied by activation of hypothalamic neurons and increased blood pressure level.

Regulation of retrotransposon activity in somatic tissues is a complex mechanism that is still not studied in details. It is strongly believed that siRNA interference is main mechanism of retrotransposon activity regulation outside the gonads, but recently was demonstrated that piRNA interference participates in retrotransposon repression during somatic tissue development. In this work, using RT-PCR, we demonstrated that during ontogenesis piRNA interference determinates retrotransposon expression level on imago stage and retrotransposons demonstrate tissue-specific expression. The major factor of retrotransposon tissue-specific expression is presence of transcription factor binding sites in their regulatory regions.

Epigenetic alterations associated with cancer have been shown to facilitate tumorigenesis and promote metastasis. In the study of cancer metastasis, epigenetics has been revealed to play a crucial role in supporting tumour immune evasion. As a result, epigenetic drugs have been identified as potential agents to activate anti-tumour immune responses and reverse tumour immunologically tolerant states. Mounting evidence is showing aberrant expression of MHC class I antigen processing molecules in cancers and their upregulation as a potential indicator for anti-tumour immunity. In this study, we demonstrate that the epigenetic drug Trichostatin A (TSA), a histone deacetylase inhibitor, can restore MHC I antigen presentation machinery (MHC I APM) genes in human breast cancer cells (MCF-7). Treatment with TSA resulted in the upregulation of MHC I, B2M, and PSMB9 in MCF-7 monolayer cells, and MHC I, B2M, PSMB9, PSMB8, TAP1, and TAP2 in MCF-7 spheroid cells. Interestingly, treatment with TSA also increased CD274 expression in these cells and enhanced the invasion ability of the MCF-7 spheroid. This aggressive behaviour was confirmed by increased expression of metastatic-related genes, SCN5A (nNav1.5 protein) and MMP1. In summary, although the restoration of MHC I APM expression was achieved by TSA, the upregulation of metastatic genes and CD274 also enhanced the invasion ability of breast cancer cells. These findings suggest the need for careful consideration when utilizing epigenetic drugs for breast cancer therapy.

Currently, data on the molecular mechanisms of fibrosis and cirrhosis of the liver do not allow us to fully understand all the stages in the development of these pathological processes. It is known that individual genes and signaling pathways do not function independently. Relations between them play a huge role in the implementation of their functions. Due to the complexity of studying this factor, information about their relationship is insufficient and often contradictory. In the present work, for the first time at different stages of thioacetamide-induced fibrosis in the liver of Wistar rats, mRNA expression of Notch1, Notch2, Yap1, Tweak (Tnfsf12), Fn14 (Tnfrsf12a), Ang, Vegfa, Cxcl12 (Sdf), Nos2, and Mmp-9 genes was studied in detail. Using factor analysis, three factors were obtained that combined highly correlated target genes with each other. The first factor includes four genes: Cxcl12 (r = 0.829, p < 0.05), Tweak (r = 0.841, p < 0.05), Notch1 (r = 0.848, p < 0.05), Yap1 (r = 0.921, p < 0.05). The second factor describes the correlations between the Mmp-9 (r = 0.791, p < 0.05) and Notch2 (r = 0.836, p < 0.05) genes. The third factor included genes Ang (r = 0.748, p < 0.05) and Vegfa (r = 0.679, p < 0.05). The Nos2 and Fn14 genes were not included in any of the factors. The selected genes classified on the basis of mRNA expression levels suggest that their products have a pathogenetic relationship in the processes of fibrotic changes in the liver of toxic etiology. Undoubtedly, the results obtained are of fundamental interest and require further expansion in the study of fibrosis and cirrhosis of the liver.

Murine gammaherpesvirus 68 (MHV68) establishes latency mainly in B cells and causes lymphomas reminiscent of human gammaherpesvirus diseases in laboratory mice. To study the molecular mechanism of virus infection and how the viral determinants control cell and eventually cause tumorigenesis, readily available latently infected cell lines are essential. For in vitro MHV68 latency studies, only two cell culture systems have been available. Gammaherpesviruses are known to infect developing B cells and macrophages, therefore we aimed to expand the MHV68 latently infected cell line repertoire. Here, several latently infected immature B cell and macrophage-like cell line clones were generated. Hygromycin-resistant recombinant MHV68 was isolated from a laboratory-made latent cell line, HE2.1, and propagated to develop stable cell lines that carry the viral genome under hygromycin selection. Subclones of these cells lines were analyzed for viral miRNA expression by TaqMan qPCR and assessed for expression of a lytic viral transcript M3. The cell lines maintain the viral genome as an episome shown by the digestion-circularization PCR assay. Latently infected cell lines generated here do not express viral miRNAs higher than the parental cell line. However, these cell lines may provide an alternative tool to study latency mechanisms and miRNA target identification studies.

CRISPR/Cas systems are perspective molecular tools for targeted manipulation with genetic materials, including gene editing, regulation of gene transcription, modification of epigenome etc. While CRISPR/Cas systems proved to be highly effective for correcting genetic disorders and treating infectious diseases and cancers in experimental settings, the clinical translation of these results is hampered by the lack of efficient CRISPR/Cas delivery vehicles. Modern synthetic nanovehicles based on organic and inorganic polymers have many disadvantages, including toxicity issues, the lack of targeted delivery, complex and expensive production pipelines. In turn, exosomes are secreted biological nanoparticles exhibiting high biocompatibility, physico-chemical stability, and ability to cross biological barriers. Early clinical trials found no toxicity associated with exosome injections. In recent years, exosomes have been considered as perspective delivery vehicles for CRISPR/Cas systems in vivo. The aim of this study was to analyze the efficacy of CRISPR/Cas stochastic packaging into exosomes at several human cell lines. Here, we show that Cas9 protein is effectively localized into the compartment of intracellular exosome biogenesis, but stochastic packaging of Cas9 into exosomes turns to be very low (~1%). As such, stochastic packaging of Cas9 protein is very ineffective, and cannot be used for gene editing purposes. Developing novel tools and technologies for loading CRISPR/Cas systems into exosomes is required.

Many viruses, including SARS-CoV-2, the coronavirus responsible for the COVID-19 pandemic, enter host cells through a process cell-viral membrane fusion that is activated by proteolytic enzymes. Typically, these enzymes are host cell proteases. Identifying the proteases that activate the virus is not a simple task but is important for the development of new antiviral drugs. In this study, we developed a bioinformatics method for identifying proteases that can cleave viral envelope glycoproteins. The proposed approach involves the use of predictive models for the substrate specificity of human proteases and the application of structural analysis method for predicting the vulnerability of protein regions to proteolysis based on their 3D structures. Specificity models were constructed for 169 human proteases using information on their known substrates. A previously developed method for structural analysis of potential proteolysis sites was applied in parallel with specificity models. Validation of the proposed approach was performed on the SARS-CoV-2 spike protein, the proteolysis sites of which had been well studied.

Production of extracellular membrane vesicles plays an important role in communication in bacterial populations and in bacteria - host interaction. Vesicles as carriers of various regulatory and signaling molecules may be potentially used as disease biomarkers and promising therapeutic agents, including vaccine preparations. The composition of membrane vesicles has been deciphered for a limited number of Gram-negative and Gram-positive bacteria. In this work, for the first time, extracellular membrane vesicles of a streptomycin-resistant strain Bacillus pumilus 3-19, a producer of extracellular guanyl-preferring ribonuclease binase, are isolated, visualized, and characterized by their genome and proteome composition. It has been established that there is no genetic material in the vesicles, and the spectrum of proteins differs depending on the phosphate content in the culture medium of the strain. Vesicles from a phosphate-deficient medium carry 49 unique proteins in comparison with 101 from a medium with the high phosphate content. The two types of vesicles had 140 mutual proteins. Flagellar proteins, RNase J – the main enzyme of RNA degradosomes, phosphatases, peptidases, iron transporters, signal peptides, were identified in vesicles. Antibiotic resistance proteins and amyloid-like proteins whose genes are present in B. pumilus 3-19 cells are absent. Phosphate deficiency-induced binase was found only in vesicles from a phosphate-deficient medium.