Molekulyarnaya Biologiya最新文献

Age-associated transformation of methylation patterns is considered to be an important predictor of human biological age. Changes in the level of CpG-dinucleotide methylation contribute to a shift in the function of a number of genes, including those associated with the functioning of the immune system. One such gene is CSF1. The protein product of this gene is associated with inflammatory aging, making it an important biomarker of age-related diseases. We studied the methylation profile of the promoter-associated CpG island of the CSF1 gene by MALDI-TOF mass spectrometry. Dependences between the character of CpG-site methylation within the investigated regions and the relative level of the gene mRNA and its protein product in people of different age groups were sought. For two CpG sites, a high level of correlation with the studied parameters is shown. A search for the landing sites of transcription factor binding sites associated with gene transcription showed that these CpG dinucleotides are part of motifs for the NFI family transcription factors and the EGR1 factor. We hypothesize that these CpG sites play an important role in the regulation of CSF1 gene expression.

Transposable elements (TEs) increase the frequency of spontaneous mutations in the genome and are capable of altering the gene structure and expression. TE activities and genomic positions are therefore important to study. A combination of two sequencing methods proved advantageous in searching for TE insertions and chromosomal rearrangements, i.e., full-genome nanopore sequencing allowed detection of TE insertions, and transcriptome sequencing on the Illumina platform evaluated their effects on gene expression. Genome sequencing data were obtained for Drosophila melanogaster strains with the SS (w^(1), flamenco mutant) and MS (w^(1), flamenco mutant, active gypsy copy) flamenco phenotypes. The wild-type laboratory strain D32 was used as a control. TE insertions and deletions in euchromatin genome regions and gene introns were found in the mutant and wild-type strains as compared with a reference genome (NCBI GCF_000001215.4). The genomes under study were searched for insertions and deletions in RNA interference system genes and genes differentially expressed in the SS and MS strains. TE insertions were detected in various regions of the AGO3, CG17147, Su(var)3-3, Gasz, CG43348, moody, and CG17752 genes. A change in TE position did not correlate with a decrease or an increase in gene transcription in most genes. A chromosomal rearrangement affecting the 3'-untranslated region was observed in the vig gene. A de novo genome assembly was conducted for the MS strain based on the long-read sequencing data. Higher expression of CR45822 and pst in the SS and MS strains was found to be due to a triplication rather than to changes in regulatory sequences or a TE insertion.

Various age-related disorders accumulate during aging, causing a decline in tissue and organ function, raising the risk of disease development, and leading to death. Age-related phenotypes are tightly related to an increase in coordinated, progressive changes in the transcriptome, proteome, metabolome, microbiome, and epigenome. Age-dependent modifications of the transcriptome, caused by changes in epigenetic, transcriptional, and post-transcriptional regulation of gene expression, lead to the accumulation of age-related changes in the proteome and metabolome. In turn, dynamic changes in the microbiota during aging also affect gene expression and thus lead to age-related changes in the proteome and metabolome. Recent studies have shown that multi-omic rejuvenation technologies decrease age-related disorders and extend longevity. For example, the short-term induction of the expression of transcription factors that ensure the reprogramming of somatic cells into pluripotent stem cells is accompanied by the restoration of the DNA methylation pattern and transcriptome expression profile characteristic of younger tissues, resulting in an increased lifespan. In this review, we discuss existing multi-omic rejuvenation technologies and the prospects for extending and improving life.

Numerous regulatory cascades link the cell response to oxidative stress and the mechanisms that maintain homeostasis and cell viability. The review summarizes the molecular mechanisms of interaction of the autophagy protein p62 with cell defense systems, primarily through the NRF2/KEAP1/ARE pathway. Understanding the cross-regulation of antioxidant defense and autophagy pathways contributes to the search for promising molecular targets to prevent and treat age-related diseases.

Pancreatic Ductal AdenoCarcinoma (PDAC) is characterized by a poor prognosis and is poorly amenable to modern therapies. A range of cell cultures reflecting different degrees of tumor differentiation and malignancy can serve as a model of PDAC development. Highly differentiated cells with low malignancy are characterized by increased expression of the KLF5 gene. The KLF5 protein is a vivid representative of multifunctional transcription factors, and its involvement in a variety of cellular processes, particularly in the pathology of various cancers, has been demonstrated. We investigated the spatial organization of chromatin of the regulatory regions of the KLF5 gene using highly differentiated Capan2 PDAC cells with a high level of KLF5 expression and poorly differentiated MIA PaCa2 PDAC cells with a low level of expression of this gene by circular chromosome conformation capture (4C-seq). It was shown that the number and distribution of contacts of the KLF5 regulatory region with other chromatin regions are significantly different for these types of cells; the number of contacts is significantly higher for Capan2 cells. There is a correlation between the expression level of genes close to KLF5 and the intensity of their sequence contacts with the KLF5 regulatory region, indicating that their expression is coordinated, possibly within the transcriptional factory. Capan2 is characterized by a high level of contacts of the KLF5 regulatory region with the gene-free region containing a cluster of PDAC-associated single nucleotide polymorphisms (SNP/InDel). Thus, the total number of contacts of the promoter region of the KLF5 gene and the expression level of most of the surrounding KLF5 genes decrease as the grade of cell malignancy increases.

Human papillomavirus type 16 (HPV16) belongs to viruses of the high-risk type and is associated by overexpression of E6 and E7 oncoproteins, which determine the oncogenic properties of the virus, such as immortalization and malignant transformation of proliferating epithelial cells. The biogenesis of redox-sensitive proteins E6 and E7 at the early stages of viral infection leads to blocking of the cell antioxidant defense system and ubiquintin-dependent degradation of p53 and Rb tumor suppressors. Maintaining high rates of tumor cell proliferation contributes to an increase in the level of reactive oxygen species (ROS) and a shift in the redox balance towards oxidative processes. Reduced glutathione (GSH) provides antioxidant protection to tumor cells through S-glutathionylation of thiol groups of redox-sensitive proteins, which leads to the appearance of multidrug-resistant forms of cancer. In this regard, drugs restoring redox balance and increasing susceptibility to antitumor therapy are of particular importance. We have established that, Bacillus pumilus RNase (binase) modulates the redox-dependent regulatory mechanisms that ensure tumor cell resistance to apoptosis in HPV-16-positive SiHa cells of cervical squamous cell carcinoma. Binase in nontoxic concentrations initiates a number of pre-apoptogenic changes, i.e., decreases ROS and reduced glutathione (GSH) levels, suppresses the expression of the E6 oncoprotein, activates the expression of the p53 tumor suppressor, and reduces the mitochondrial potential of tumor cells. Binase-induced disruption of the integrity of the mitochondrial membrane is a signal for activation of the mitochondrial apoptosis pathway.

Transglutaminases are enzymes that carry out post-translational modifications of proteins and participate in the regulation of their activities. Here, we show for the first time that the transglutaminase genes in the basal metazoan, the sea sponge Halisarca dujardinii, are organized in a cluster, similarly to mammalian transglutaminases. The regulatory regions of six transglutaminase genes and their differential expression in the course of the life cycle of H. dujardinii suggest independent regulation of these genes. The decrease in transglutaminase activities by cystamine facilitates restoration of the multicellular structures of this sponge after its mechanical dissociation. For the first time we observed that this decrease in transglutaminase activities was accompanied by generation of the reactive oxygen species in the cells of a basal metazoan. The study of transglutaminases in the basal metazoans and other sea-dwelling organisms might provide better understanding of the evolution and specific functions of these enzymes in higher animals.

Chronic obstructive pulmonary disease (COPD) is a multifactorial heterogeneous chronic inflammatory respiratory disease. The molecular pathogenesis of COPD may include dysregulation of the stress responses that are associated with cell senescence and involve a wide range of signaling pathways and their epigenetic regulators, such as long noncoding RNAs (lncRNAs). To assess the contribution of genes involved in key signaling pathways related to cell senescence to the molecular pathogenesis of COPD, expression profiling of lncRNA (TP53TG1, LINC00342, H19, MALAT1, DNM3OS, and MEG3) and protein-coding (PTEN, TGFB2, FOXO3, and KEAP1) genes was performed in peripheral blood mononuclear cells of COPD patients (n = 92) and control subjects (n = 81). Significant downregulation of the TP53TG1 and DNM3OS lncRNAs and the TGFB2 mRNA was observed in the COPD patients, while the MALAT1 and LINC00342 were upregulated. A highly informative prognostic model was constructed based on the multiple regression and ROC analyses. The model included simultaneous assessment of the TP53TG1 and TGFB2 expression levels (AUC = 0.92). MALAT1, DNM3OS, TGFB2, FOXO3 and KEAP1 expression levels were found to positively correlate with lung function parameters, reflecting the disease progression. The lncRNA (TP53TG1, LINC00342, DNM3OS, and MALAT1) and protein-coding (TGFB2) genes that were differentially expressed in the COPD patients are functionally involved in regulating apoptosis, inflammation, fibrogenesis, and the epithelial-to-mesenchymal transition, implicating cell senescence processes in the molecular pathogenesis of COPD.

Vimentin intermediate filaments are dynamic structures that are able to move in cytoplasm owing to activity of the motor proteins, kinesin-1 and cytoplasmic dynein. How exactly motors interact with vimentin filaments remains unclear. In this work, I show that GRIP1 (Glutamate Receptor Interacting Protein 1), known as adapter for kinesin-1 on many cargoes in neurons, might also mediate kinesin-1 interaction with vimentin filaments. GRIP1 associates with vimentin filaments in various cells and co-immunoprecipitates with vimentin from cell lysates. Human endothelial cells knockout by GRIP1 gene lose focal adhesions and change their adhesive properties. Hypothetically, kinesin-1 engages GRIP1 to deliver vimentin filaments to the cell periphery so that they make contact with focal adhesions and stabilize them.

Obesity is associated with changes in the gut microbiota, as well as with increased permeability of the intestinal wall. In 130 non-obese volunteers, 57 patients with metabolically healthy obesity (MHO), and 76 patients with metabolically unhealthy obesity (MUHO), bacterial DNA was isolated from stool samples, and the 16S rRNA gene was sequenced. The metabolic profile of the microbiota predicted by PICRUSt2 (https://huttenhower.sph.harvard.edu/picrust/) was more altered in patients with MUHO than MHO. Obesity, especially MUHO, was accompanied by an increase in the ability of the gut microbiota to degrade energy substrates, produce energy through oxidative phosphorylation, synthesize water-soluble vitamins (B1, B6, B7), nucleotides, heme, aromatic amino acids, and protective structural components of cells. Such changes may be a consequence of the microbiota adaptation to the MUHO-specific conditions. Thus, a vicious circle is formed, when MUHO promotes the depletion of the gut microbiome, and further degeneration of the latter contributes to the pathogenesis of metabolic disorders. The concentration of the trefoil factor family (TFF) in the serum of the participants was also determined. In MHO and MUHO patients, the TFF2 and TFF3 levels were increased, but we did not find significant associations of these changes with the metabolic profile of the gut microbiota.