Vol 58, No 4 (2024)

Modern genetic engineering technologies, such as base editing (BE) and prime editing (PE), have proven to be effective and reliable genome editing tools that do not require the introduction of double-strand breaks in DNA and the presence of donor templates. Relatively new, they quickly gained recognition for their accuracy, simplicity and multiplexing capabilities. This review summarizes new literature on these technologies: architecture and methods for creating editors, specificity, efficiency and versatility. The advantages, disadvantages and prospects for using these editors in basic and applied research are discussed. The information presented in the review may be useful for planning genome editing studies and for analyzing their results when solving various problems in fundamental biology, biotechnology, medicine and agriculture.

The E6 and E7 proteins of human papillomavirus (HPV) play a key role in the oncogenesis of papillomavirus infection. Data on the variability of these proteins are limited, and the factors affecting their variability are poorly understood. We analyzed the variability of the currently known sequences of HPV type 16 (HPV16) E6 and E7 proteins, taking into account their geographic origin and year of sample collection, as well as the direction of their evolution in major geographic regions of the world. All sequences belonging to HPV16 genome fragments encoding E6 and E7 oncoproteins were downloaded from the NCBI GenBank database on October 6, 2022. Samples were filtered according to the following parameters: the sequence includes at least one of the two whole open reading frames, the collection date and the country of origin are known. A total of 3,651 full-genome nucleotide sequences encoding the E6 protein and 4,578 full-genome nucleotide sequences encoding the E7 protein were sampled. The nucleotide sequences obtained after sampling and alignment were converted to amino acid sequences and analyzed using MEGA11, R, RStudio, Jmodeltest 2.1.20, BEAST v1.10.4, Fastcov, and Biostrings software. The highest variability in E6 protein structure was recorded at positions 17, 21, 32, 85, and 90, while in E7, positions 28, 29, 51, and 77 were the most variable. The samples were divided geographically into 5 heterogeneous groups: African, European, American, Southwest and South Asia and Southeast Asia. Unique amino acid substitutions (AA-substitutions) in the E6/E7 proteins of HPV16, presumably characteristic of certain ethnic groups, were identified for a number of countries. They are mainly localized in sites of known B- and T-cell epitopes and relatively rarely in structural and functional domains. The revealed differences in AA-substitutions in different ethnic groups and their colocalization with clusters of B- and T-cell epitopes suggest their possible relationship with the geographical distribution of alleles and haplotypes of the major histocompatibility complex (HLA). This may lead to the recognition of a different set of B- and T-cell epitopes of the virus, resulting in regional differences in the direction of epitope drift. Phylogenetic analysis of the nucleotide sequences encoding the E6 protein of HPV16 revealed a common ancestor, confirmed regional clustering of the E6 protein gene sequences by the set of the most common AA-substitutions, and identified cases of reversion of individual AA-substitutions when the virus distribution region changed. For the E7 protein, a similar analysis was not possible due to high sequence homology. Covariance analysis of the pooled sample revealed that there was no relationship between amino acid residues in the E6 protein, in the E7 protein, and between E6 and E7. Data obtained are important for the development of therapeutic vaccines against HPV of high carcinogenic risk.

The low efficiency of knock-in, especially in primary human cells, limits the use of genome editing technology for therapeutic purposes, which makes it important to develop approaches for increasing knock-in levels. In this work, using a knock-in model of the peptide fusion inhibitor of HIV MT-C34 into the human CXCR4 locus in the CEM/R5 T cell line, we analyzed the effectiveness of several approaches to increasing knock-in levels. First, donor DNA modification aimed at improving the efficiency of plasmid transport into the nucleus was evaluated, namely the introduction into the donor plasmid of the SV40 DNA transport sequence (DTS) or the binding sites for the transcription factor NF-κB, whose effects on knock-in levels have not been described. In the MT-C34 knock-in model into the CXCR4 locus, this modification was ineffective. The second approach, modifying the Cas9 nuclease by introducing two additional nuclear localization signals (NLS), increased the knock-in level by 30%. Finally, blocking DNA repair via the nonhomologous end joining pathway using DNA-dependent protein kinase inhibitors caused a 1.8-fold increase in knock-in. The combination of the last two approaches caused an additive effect. Thus, increasing the number of NLSs in the Cas9 protein and inhibiting DNA repair via the nonhomologous end joining pathway significantly increased the level of knock-in of the HIV-1 peptide fusion inhibitor into the clinically relevant locus CXCR4, which can be used to develop effective gene therapy approaches for the treatment of HIV infection.

The sensitivity of human glioblastoma cells to virus-mediated oncolysis was investigated on five patient-derived cell lines. Primary glioblastoma cells (Gbl13n, Gbl16n, Gbl17n, Gbl25n, and Gbl27n) were infected with 10-fold serial dilutions of the Leningrad-3 strain of mumps virus, virus reproduction and cytotoxicity were monitored for 96–120 hours. Immortalized human non-tumor NKE cells were used as controls to determine virus specificity. Four out of the five glioblastoma cell lines examined were susceptible to mumps virus infection, whereas no virus reproduction was observed in the non-tumor cell line. Moreover, the level of proapoptotic caspase-3 activity was increased in all infected cells 48 hours after infection. The kinetics of viral RNA accumulation in the studied glioblastoma cell lines was comparable with the rate of cell death. The data suggest that glioblastoma cell lines are permissive for mumps virus. Glioblastoma cell lines differed in type I IFN production in response to mumps virus infection. In addition, it was shown that MV infection was able to induce immunogenic death of glioblastoma cells.

In previous studies, we purified the DUB-module of the Drosophila SAGA complex and showed that a number of zinc proteins interact with it, including Aef1 and CG10543. In this work, we conducted a genome-wide study of the Aef1 and CG10543 proteins and showed that they are localized predominantly on the promoters of active genes. The binding sites of these proteins colocalize with the SAGA and dSWI/SNF chromatin modification and remodeling complexes, as well as with the ORC replication complex. It has been shown that the Aef1 and CG10543 proteins are involved in the regulation of the expression of some genes on the promoters of which they are located. Thus, the Aef1 and CG10543 proteins are new participants in the cell transcriptional network and colocalize with the main transcription and replication complexes of Drosophila.

Obesity is associated with changes in the gut microbiota, as well as 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 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, TFF2 and TFF3 levels were increased, but we did not find significant associations of these changes with the metabolic profile of the gut microbiota.

Drug molecules that block the functional cycle of influenza A and SARS-CoV-2 viruses are proposed. The blocker molecules effectively binding inside the M2 and E-channels of influenza A and SARS-CoV-2 viruses and blocking the diffusion of H+/K+ ions destroy the functional cycle of viruses. A family of positively charged, +2 e. u., molecular blockers of H+ /K+ ion diffusion through M2 and E-channels is proposed. The blocker molecules, derivatives of diazabicyclooctane, was investigated for its binding affinity to the channels M2 and E. Thermal dynamics and binding affinity were modeled by the exhaustive docking method sites. Blocker molecules with higher affinity for the blocking sites were proposed. The most probable mutations of amino acids of protein M2 and E channels are considered, the effectiveness of channel blocking are analyzed and optimal structures of blocker molecules are proposed.