Cancer predisposition syndromes (CPSs) account for 8.5-18% of all childhood cancer cases. Most of them are inherited in an autosomal dominant pattern; consequently, there is a 50% risk of transmission to offspring. Early detection of CPSs is crucial for choosing patient treatment strategies and for counseling in the family. This study enrolled 886 pediatric patients with hematologic and solid neoplasms from prospective and retrospective cohorts (2018-2025). Clinical exome or multigene panel sequencing was used to analyze blood DNA. Overall, 186 pathogenic/likely pathogenic (PLP) variants in cancer-associated genes were identified in 176/886 (20%) of patients, and the most frequently mutated were the NF1 (n = 35) and TP53 (n = 18) genes. Among the 186 PLP variants, 126/886 (14.2%) were causative for pediatric neoplasms, while 56/886 (6.3%) were heterozygous mutations associated with adult-onset CPSs affecting DNA repair. The highest total mutation rate was revealed in retinoblastoma (80%), peripheral nerve sheath tumors (60%), and pheochromocytoma/paraganglioma (47%), while the lowest rate was found in hematologic malignancies (4.6%) and neuroblastoma (12%). The wide range and high frequency of deleterious variants in pediatric patients, especially in those with solid tumors, highlights the importance of multigene panel sequencing for the accurate determination of CPSs.

The white poplar (Populus alba L.) is an economically significant tree species with a natural distribution spanning an extensive region of Eurasia. Nevertheless, there is currently no hypothesis regarding the historical shaping of this range. In this study, we collected and sequenced 36 individuals of white poplar from disparate regions of Russia and Kazakhstan. Additionally, we employed available genomic data of white poplars from Italy, Hungary, and China. A genomic approach was employed to collate data on the location of glaciers in different periods, along with information on the natural and artificial distribution of white poplar. This enabled the formulation of the first hypothesis regarding the formation of the modern range of this plant. It is hypothesized that during the period of maximum glaciation, three refugia existed: the South European, Transcaucasian, and Altai–Middle Asian refugia. Postglacial migration from these refugia led to the formation of modern populations of P. alba in Eastern Europe (including the European part of Russia), the Caucasus, and Siberia, respectively.

1IntroductionSea buckthorn (Hippophae rhamnoides L.) is a woody oil tree known for its fruits, which are a rich source of bioactive compounds, including carotenoids and flavonoids (Ciesarova et al., 2020; Mihal et al., 2023). In addition, the unique fatty acid composition of the fruit pulp oil, especially the high content of omega-7 monounsaturated palmitoleic acid, which is rare in plants, contributes to the nutritional benefits of its products (Sola Marsinach and Cuenca, 2019). In this regard, sea buckthorn products are used in medicine, cosmetics, and nutraceuticals (Gatlan and Gutt, 2021; Guo et al., 2022; Zuchowski, 2023). In addition to cultivation for fruit production, sea buckthorn is also used for ecological restoration due to its high resistance to extreme conditions (Ruan et al., 2013).Sea buckthorn is mainly cultivated in China (2.07 million ha), India (0.02 million ha), Romania (0.02 million ha), Mongolia (0.02 million ha), Russia (0.01 million ha), and Pakistan (0.01 million ha) (Nybom et al., 2023). Thus, 90% of sea buckthorn resources are located in China (Singh, 2022). However, the pioneer in sea buckthorn breeding was Russia, where selection of H. rhamnoides ssp. mongolica Rousi started in 1933 and allowed the development of a wide range of high-yield varieties with high-quality fruits (Singh and Zubarev, 2014). In contrast, breeding of sea buckthorn in China started later, mainly with H. rhamnoides ssp. sinensis Rousi (Nybom et al., 2023). Varieties of H. rhamnoides ssp. mongolica are characterized by large fruits, high yield, high oil content, and lower acidity compared to H. rhamnoides ssp. sinensis varieties, which are better adapted to abiotic and biotic stressors (Nybom et al., 2023). Sea buckthorn breeding does not stand still, new improved varieties are being developed and genetic data can contribute to this. However, only a few DNA markers potentially useful for sea buckthorn breeding are known. Markers were proposed to distinguish Hippophae species and subspecies, including H. rhamnoides ssp. sinensis and H. rhamnoides ssp. mongolica (Liu et al., 2015; Liu et al., 2016; Liu et al., 2018; Piao et al., 2022). Hippophae species are dioecious, and attempts were made to develop DNA markers to identify sex, but these markers do not always work in genetically diverse material (Korekar et al., 2012; Das et al., 2017; Zhou et al., 2018; Zeng et al., 2024a; Zeng et al., 2024b). Markers associated with oil content in fruits (Ding et al., 2016) and genes involved in flavonoid biosynthesis (Zhang et al., 2024) were identified. Several works were performed to search for genes associated with resistance of Hippophae species to biotic and abiotic stressors (Nybom et al., 2023). In recent years, high-quality genome assemblies of H. rhamnoides (with sizes of 849, 730, and 919 Mb) (Wu et al., 2022; Yu et al., 2022; Yang et al., 2024), Hippophae tibetana (957 and 1453 Mb) (Wang et al., 2022b; Zhang et al., 2024), and Hippophae gyantsensis (716 Mb) (Chen et al., 2024) were obtained. However, a very limited number of sea buckthorn genotypes were studied using whole-genome sequencing. Whole-genome sequencing of only 40 wild H. rhamnoides ssp. mongolica and H. rhamnoides ssp. sinensis representatives and 15 cultivated H. rhamnoides ssp. mongolica varieties was performed by Chinese researchers (Yu et al., 2022). Therefore, there is a lack of genomic data for varieties of sea buckthorn. The aim of the present study was to fill this gap by performing whole-genome sequencing of the unique set of 55 varieties of Russian breeding, which are likely to be significantly different from the Chinese varieties and characterized by valuable traits. These data can significantly expand the knowledge of the diversity of H. rhamnoides at the whole-genome level and provide the necessary data for the development of genetic technologies for sea buckthorn breeding.2Materials and Methods2.1Plant MaterialTo cover the diversity of sea buckthorn cultivated in Russia, a set of 56 accessions representing 55 varieties of H. rhamnoides L. was formed: one replicate for 54 varieties (one tree for each variety) and two biological replicates for the variety Elizaveta (two different trees). The following valuable characteristics were considered: weight, flavor, shape, and color of the fruits and differences in origin (Table 1). Characteristics of sea buckthorn varieties were assessed according to Kondrashov et al. (Kondrashov et al., 1999). Dormant shoots of the selected genotypes were collected at the Federal Altai Scientific Center of Agrobiotechnologies (Barnaul, Russia) in April 2023. The shoots were placed in containers with water in a room with a temperature of ~22 °C for one week. When the leaves appeared, they were collected in tubes, frozen in liquid nitrogen, and stored in a low-temperature freezer until DNA extraction.2.2DNA ExtractionDNA was extracted using the Magen HiPure Plant DNA Mini Kit (Magen, Guangzhou, China). The quality and quantity of DNA were evaluated using NanoDrop 2000C (Thermo Fisher Scientific, Waltham, MA, USA), Qubit 4.0 (Thermo Fisher Scientific), and agarose gel electrophoresis (2% agarose).2.3Whole-Genome SequencingThe QIAseq FX DNA Library UDI Kit (Qiagen, Chatsworth, CA, USA) was used for DNA library preparation. Quantity and quality of DNA libraries were assessed using Qubit 4.0 (Thermo Fisher Scientific) and Qsep1-Plus (Bi-Optic, New Taipei City, Taiwan). Genome sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, CA, USA) with a read length of 150 + 150 bp.2.4Sequencing Data AnalysisThe obtained Illumina reads were processed with Trimmomatic 0.39 (TRAILING:28, SLIDINGWINDOW:4:17, MINLEN:40) (Bolger et al., 2014). The processed reads were mapped to the annotated H. rhamnoides genome from the CNGB Nucleotide Sequence Archive (https://db.cngb.org/cnsa), project ID CNP0001846 (Wu et al., 2022), and VAF (Variant Allele Frequencies) values were calculated for genome regions corresponding to genes (exons and introns) using PPLine (Krasnov et al., 2015). Genetic distances between sea buckthorn varieties were calculated and clustered with Ward's method (ward.D2) in PPLine (Krasnov et al., 2015).3Preliminary Data AnalysisA representative set of 56 accessions comprising 55 sea buckthorn varieties (for the variety Elizaveta, two different trees were analyzed) was formed from the unique collection of the Federal Altai Scientific Center of Agrobiotechnologies (Barnaul, Russia). The selected varieties had different fruit characteristics and different origins in order to maximize the diversity of the analyzed set (Table 1).Whole-genome sequencing was performed and at least 23 Gbases of raw Illumina data were obtained for each accession, which corresponded to more than 25× genome coverage (raw Illumina reads were deposited to NCBI SRA, BioProject PRJNA1177110). After mapping the reads to the annotated H. rhamnoides reference genome, data on about 4 million DNA polymorphisms in genes were obtained (lists of DNA polymorphisms were deposited to Zenodo, https://zenodo.org/records/13999625). These data are useful for studying the diversity of allelic variants for specific genes, especially those that may be associated with valuable traits, such as the content of bioactive compounds and other fruit characteristics and resistance to stressors. It is worth noting that a significant part of the identified DNA polymorphisms was present in all analyzed sea buckthorn varieties, indicating that they are genetically distinct from the used reference genome. In addition, genetic distances between the accessions were calculated to evaluate their relationships (Supplementary Table 1).To visualize the relationships of the studied varieties based on DNA polymorphisms in gene sequences, a dendrogram was constructed (Figure 1). Cluster I was the most distinct and included KP-686 (Kyrgyz ecotype), Dunayskaya, and Yantarnaya Yagoda, which are not varieties of Altai breeding and probably have significant differences at the genome level from the other studied accessions. The same cluster included 175-02-01, obtained by crossing varieties of Altai breeding, and its position in the dendrogram is not expected and requires additional research.The remaining sea buckthorn varieties were divided into four clusters. Cluster II included Afina and all studied progenies of this variety, namely 625-08-01, 625-14-1, 762-14-1, and 763-14-1. It can be assumed that Afina and sea buckthorn genotypes obtained with its participation are genetically quite different from the other studied varieties of Altai breeding. In addition, 111-05-01, 258-03-01, and 42-68-2, which are believed to be unrelated to Afina, were in Cluster II, which is difficult to explain from a genealogical point of view.Cluster III clearly distinguished a group of sea buckthorn varieties with Panteleevskaya in their lineages. Thus, this group is likely to be significantly different from other studied sea buckthorn genotypes at the genome level.Cluster IV included 14 varieties, among which the genetic relationships were not as clear as in the first three clusters, but they were still present. Thus, a group of four Novosibirsk accessions was isolated: Triumf, Zarnitsa, 681-09-01, and 708-13-1, with Triumf being the parental form for 681-09-01 and 708-13-1. Ulala and its progeny 125-02-01 were also in this cluster. Two varieties with Panteleevskaya in their lineages were also in Cluster IV: 22-02-2003 and 226-00-01. In general, however, this cluster contained a mixture of quite different sea buckthorn varieties.Cluster V contained 23 accessions. In this cluster, as in other clusters, some relationships corresponding to lineages were observed. For example, Rosinka and Sudarushka, which entered this cluster, have common roots. In addition, varieties Essel and 218-03-06 have the genotype 89-72-6a in their lineages. 89-72-6a is very interesting in terms of strong inheritance of large fruit size. In this respect, it is the progenitor of many varieties, most of which were present in Cluster V. The exception was the variety Aureliya, which was in Cluster IV. Other relationships can also be traced in Cluster V. For example, Lyubimaya clone is a seedless mutant of the variety Lyubimaya. Several closely related groups were also isolated: Elizaveta (two biological replicates) and its progeny 2016-00-1, Chechek and its progeny Ognivo, Chuyskaya and its progeny Klavdiya and 111-10-2, and Panteleevskaya and its progeny 114-13-1.In general, the dendrogram obtained by us on the basis of DNA polymorphisms in all sea buckthorn genes annotated in the used reference genome (Wu et al., 2022) reflected well the known data on the relationship of the studied genotypes. The research on H. rhamnoides performed by Yu et al. using whole-genome sequencing allowed the authors to separate wild genotypes of H. rhamnoides ssp. mongolica from cultivated ones, as well as to separate H. rhamnoides ssp. sinensis accessions into a separate group (Yu et al., 2022). However, we were unable to find any other work that characterized representative sets of sea buckthorn genotypes using whole-genome sequencing (NCBI PubMed, https://pubmed.ncbi.nlm.nih.gov/; Google Scholar, https://scholar.google.com; accessed October 28, 2024). Meanwhile, whole-genome sequencing and linkage mapping is an urgent need for sea buckthorn studies (Sharma, 2022).Data on the diversity of sea buckthorn varieties at the genomic level are of great value in understanding the extent to which selection has affected the gene pool of this crop and what patterns can be traced by analyzing the genetic data. We studied the sea buckthorn varieties of Russian breeding, which has a long history. The forms with valuable traits created by Russian breeders became the progenitors of many varieties all over the world (Singh, 2022), so the obtained by us data are of special value. In addition, the evaluation of genetic relationships of different accessions is important for breeders when selecting parental forms for crosses.Recently, there has been an increasing number of articles devoted to the beneficial properties of sea buckthorn (Wang et al., 2022a; Chen et al., 2023; Mihal et al., 2023; Nybom et al., 2023; Teng et al., 2024; Xu et al., 2024), but in terms of genetics, this crop is still relatively understudied (Sharma, 2022). Indeed, several high-quality genome assemblies of H. rhamnoides were obtained (Wu et al., 2022; Yu et al., 2022; Yang et al., 2024) and some transcriptome studies were performed (Bansal et al., 2018; Ye et al., 2018; Gao et al., 2022; Lyu et al., 2022; Yu et al., 2022). A number of works were also devoted to fatty acid synthesis in sea buckthorn and genes/microRNAs involved in this process (Ding et al., 2018; Ding et al., 2019; Ding et al., 2022; Yu et al., 2022; Arkhipov et al., 2024). However, the genetic determinants and their diversity remain unknown for most of the key traits that define the value of sea buckthorn varieties, including carotenoid content, fruit shape and flavor. In this context, data on DNA polymorphisms in gene sequences obtained for a representative set of accessions characterized by phenotype will allow the search for associations between allelic variants of genes and valuable traits. These data are the basis for the development of marker-assisted and genomic selection of sea buckthorn, which are increasingly used in breeding practice for other agricultural plants (Xu et al., 2020; Hasan et al., 2021; Thudi et al., 2021; Dmitriev et al., 2022; Werner et al., 2023; Mangal et al., 2024).4ConclusionsH. rhamnoides is a valuable crop whose fruits are rich in bioactive compounds with health benefits. To date, there is a lack of genetic data for varieties of sea buckthorn. This fact hinders the identification of genetic determinants of valuable traits and limits the efficiency of breeding. In the present study, we analyzed a representative set of 55 valuable H. rhamnoides varieties of Russian breeding with different fruit characteristics and diverse lineages. Whole-genome sequencing was performed on the Illumina platform, and at least 25× genome coverage was obtained for each accession. Based on the sequencing data, DNA polymorphisms were identified in genomic regions corresponding to genes. These polymorphisms were used to evaluate the genetic relationships of the studied sea buckthorn varieties. We revealed genetically distinct groups of accessions that mostly corresponded to the lineages of the genotypes. Our data are important for assessing the effect of selection on sea buckthorn diversity and for evaluating the genetic relationship of different varieties, which is useful for breeders when selecting parental forms for crosses. The obtained data on genomic sequences of 55 H. rhamnoides varieties in combination with information on valuable traits of their fruits are the basis for identification of quantitative trait loci (QTL) and quantitative trait nucleotides (QTN) for further development of DNA tests. This will be the basis for marker-assisted selection of sea buckthorn. The obtained information on DNA polymorphisms is also necessary to study the diversity of genes, including those that may determine valuable traits, such as fruit characteristics. This will help to promote genomic breeding of H. rhamnoides. Thus, our data can benefit both basic and applied research on sea buckthorn.

Sestrin1 and Sestrin2 (SESN1 2) are evolutionarily conserved, stress-responsive proteins that regulate cell growth and viability. The primary target of Sestrins is the mTORC1 protein kinase, an activator of anabolic processes and an autophagy inhibitor. Our previous studies showed that inactivating SESN1 2 in lung adenocarcinoma A549 cells accelerates cell proliferation and confers resistance to cell death without affecting mTORC1 activity, suggesting that SESN1 2 modulate cellular processes via mTORC1-independent mechanisms. This work describes a new mechanism through which SESN1 2 regulate cell proliferation and death by suppressing the STAT3 transcription factor. Normally activated in response to stress and inflammation, STAT3 is frequently overactivated in human cancers. This overactivation promotes the expression of pro-proliferative and anti-apoptotic genes that drive carcinogenesis. We demonstrate that SESN1 2 inactivation stimulates STAT3 by downregulating the PTPRD phosphatase, a protein responsible for STAT3 dephosphorylation. Our study demonstrates that SESN1 2 deficiency may cause STAT3 activation and facilitate carcinogenesis and drug resistance, making SESN1 2 reactivation a potential cancer treatment strategy.

Gliomas are a heterogeneous group of brain tumors, among which the most aggressive subtype is glioblastoma, accounting for 60% of cases in adults. Available systemic treatment options are few and ineffective, so new approaches to therapies for glioblastoma are in high demand. In total, 131 patients with diffuse glioma were studied. Paired tumor–normal samples were sequenced on the Illumina platform; the panel included 812 genes associated with cancer development. Molecular profiles in clinically distinct groups were investigated. In low-grade glioma (LGG) patients (n = 18), the most common mutations were IDH1/2 (78%), ATRX (33%), TP53 (33%), PIK3CA (17%), and co-deletion 1p/19q (22%). In high-grade glioma (HGG) patients (n = 113), more frequently affected genes were CDKN2A/B (33%), TERTp (71%), PTEN (60%), TP53 (27%), and EGFR (40%). The independent predictors of better prognosis were tumor grade and IDH1/2 mutations. In IDH—wildtype glioblastoma patients, a history of other precedent cancer was associated with worse overall survival (OS), while re-operation and bevacizumab therapy increased OS. Also, among genetic alterations, TERTp mutation and PTEN deletion were markers of poor prognosis. Nine patients received molecular targeted therapy, and the results were evaluated. The search for molecular changes associated with tumor growth and progression is important for diagnosis and choice of therapy.

Our aim was to study the association of endothelial dysfunction biomarkers with cirrhosis manifestations, bacterial translocation, and gut microbiota taxa. The fecal microbiome was assessed using 16S rRNA gene sequencing. Plasma levels of nitrite, big endothelin-1, asymmetric dimethylarginine (ADMA), presepsin, and claudin were measured as biomarkers of endothelial dysfunction, bacterial translocation, and intestinal barrier dysfunction. An echocardiography with simultaneous determination of blood pressure and heart rate was performed to evaluate hemodynamic parameters. Presepsin, claudin 3, nitrite, and ADMA levels were higher in cirrhosis patients than in controls. Elevated nitrite levels were associated with high levels of presepsin and claudin 3, the development of hemodynamic circulation, hypoalbuminemia, grade 2–3 ascites, overt hepatic encephalopathy, high mean pulmonary artery pressure, increased abundance of Proteobacteria and Erysipelatoclostridium, and decreased abundance of Oscillospiraceae, Subdoligranulum, Rikenellaceae, Acidaminococcaceae, Christensenellaceae, and Anaerovoracaceae. Elevated ADMA levels were associated with higher Child–Pugh scores, lower serum sodium levels, hypoalbuminemia, grade 2–3 ascites, milder esophageal varices, overt hepatic encephalopathy, lower mean pulmonary artery pressure, and low abundance of Erysipelotrichia and Erysipelatoclostridiaceae. High big endothelin-1 levels were associated with high levels of presepsin and sodium, low levels of fibrinogen and cholesterol, hypocoagulation, increased Bilophila and Coprobacillus abundances, and decreased Alloprevotella abundance.

Head and neck paragangliomas (HNPGLs) are rare neoplasms arising from paraganglia of the parasympathetic nervous system. HNPGLs are characterized by high vascularity and are located in proximity to major vessels and nerves, which may be potential sources of microbial invasion in these tumors. There have been no studies in the literature on the microbiota in HNPGLs. Investigation of the microbiome associated with paragangliomas is important for understanding tumor pathogenesis. In this study, we investigated the microbiome composition in two sets of HNPGLs. First, 29 fresh frozen (FF) tissues were subjected to 16S rRNA gene sequencing; concurrently, a panel of candidate laboratory-derived contaminants was investigated. Second, we analyzed microbial reads from whole transcriptome sequencing data obtained for 82 formalin-fixed paraffin-embedded (FFPE) HNPGLs. The bacterial diversity in FF tumors was found to be significantly lower than that observed in FFPE HNPGLs. Based on 16S rRNA gene sequencing, only seven bacterial families were identified as potential tumor inhabitants: Bryobacteraceae, Enterococcaceae, Neisseriaceae, Legionellaceae, Vibrionaceae, Obscuribacteraceae, and Mycobacteriaceae. However, RNA-Seq demonstrated higher sensitivity for identifying microbiome composition and revealed abundant bacterial families that partially correlated with those previously described in pheochromocytomas and extra-adrenal paragangliomas. No viruses were found in HNPGLs. In summary, our findings indicated the presence of a microbiome in HNPGLs, comprising a number of bacterial families that overlap with those observed in pheochromocytomas/paragangliomas and glioblastomas.

Boreal peatlands store most of their carbon in layers deeper than 0.5 m under anaerobic conditions, where carbon dioxide and methane are produced as terminal products of organic matter degradation. Since the global warming potential of methane is much greater than that of carbon dioxide, the balance between the production rates of these gases is important for future climate predictions. Herein, we aimed to understand whether anaerobic methane oxidation (AMO) could explain the high CO2/CH4 anaerobic production ratios that are widely observed for the deeper peat layers of boreal peatlands. Furthermore, we quantified the metabolic pathways of methanogenesis to examine whether hydrogenotrophic methanogenesis is a dominant methane production pathway for the presumably recalcitrant deeper peat. To assess the CH4 cycling in deeper peat, we combined laboratory anaerobic incubations with a pathway -specific inhibitor, in situ depth patterns of stable isotopes in CH4, and 16S rRNA gene amplicon sequencing for three representative boreal peatlands in Western Siberia. We found up to a 69 % reduction in CH4 production due to AMO, which largely explained the high CO2/CH4 anaerobic production ratios and the in situ depth -related patterns of delta 13C and delta D in methane. The absence of acetate accumulation after inhibiting acetotrophic methanogenesis and the presence of sulfate- and nitratereducing anaerobic acetate oxidizers in the deeper peat indicated that these microorganisms use SO42  and NO3  as electron acceptors. Acetotrophic methanogenesis dominated net CH4 production in the deeper peat, accounting for 81 +/- 13 %. Overall, anaerobic oxidation is quantitatively important for the methane cycle in the deeper layers of boreal peatlands, affecting both methane and its main precursor concentrations.

Vagal paraganglioma (VPGL) is a rare neuroendocrine tumor that originates from the paraganglion associated with the vagus nerve. VPGLs present challenges in terms of diagnostics and treatment. VPGL can occur as a hereditary tumor and, like other head and neck paragangliomas, is most frequently associated with mutations in the SDHx genes. However, data regarding the genetics of VPGL are limited. Herein, we report a rare case of a 41-year-old woman with VPGL carrying a germline variant in the FH gene. Using whole-exome sequencing, a variant, FH p.S249R, was identified; no variants were found in other PPGL susceptibility and candidate genes. Loss of heterozygosity analysis revealed the loss of the wild-type allele of the FH gene in the tumor. The pathogenic effect of the p.S249R variant on FH activity was confirmed by immunohistochemistry for S-(2-succino)cysteine (2SC). Potentially deleterious somatic variants were found in three genes, SLC7A7, ZNF225, and MED23. The latter two encode transcriptional regulators that can impact gene expression deregulation and are involved in tumor development and progression. Moreover, FH-mutated VPGL was characterized by a molecular phenotype different from SDHx-mutated PPGLs. In conclusion, the association of genetic changes in the FH gene with the development of VPGL was demonstrated. The germline variant FH: p.S249R and somatic deletion of the second allele can lead to biallelic gene damage that promotes tumor initiation. These results expand the clinical and mutation spectra of FH-related disorders and improve our understanding of the molecular genetic mechanisms underlying the pathogenesis of VPGL.

Head and neck paragangliomas (HNPGLs) are rare neoplasms that, along with pheochromocytomas and extra-adrenal paragangliomas, are associated with inherited mutations in at least 12 susceptibility genes in approximately 40% of cases. However, due to the rarity of HNPGLs, only a series of small-scale studies and individual cases have reported mutations in additional genes that may be involved in tumorigenesis. Consequently, numerous disease-causing mutations and genes responsible for the pathogenesis of HNPGLs remain poorly investigated. The aim of this study was to gain a deeper understanding of the genetic basis of HNPGLs by focusing on variants in genes that were not previously identified as well-known drivers. A whole-exome data analysis was conducted on a representative set of 152 HNPGLs. In 30% of the tumors examined, 53 potentially deleterious variants were identified in 36 different genes. The analysis identified pathogenic or likely pathogenic variants in the ARNT, IDH2, L2HGDH, MYH3, PIK3CA, and TERT genes. A functional network analysis of the mutated genes revealed numerous associations and a list of metabolic pathways (e.g., the TCA cycle, carbon metabolism, pyruvate metabolism, etc.) and signaling pathways (e.g., HIF1, PI3K-Akt, FoxO, AMPK, MAPK, etc.) that may play an important role in the development of HNPGLs. The identified range of genetic alterations affecting multiple genes and, potentially, influencing diverse cellular pathways provides an enhanced molecular genetic characterization of HNPGLs.

Introduction. Epidermal growth factor receptor (EGFR) is a transmembrane protein of the receptor tyrosine kinase family that is activated in various cancers (non-small cell lung cancer, colorectal cancer, head and neck tumors). In glial brain tumors, increased EGFR expression levels are characteristic of the most aggressive subtype, glioblastoma. Frequent structural changes of EGFR in glioblastoma are amplification of the chromosome region where the EGFR gene is located, point mutations, as well as deletion of exons 2–7 of the EGFR gene leading to the formation of EGFRvIII transcript.Aim. To determine structural changes of the EGFR gene (point mutations and amplification of the EGFR gene, EGFRvIII transcript) in tumor samples using different methods and to evaluate their potential clinical significance.Materials and methods. The study included 75 patients with brain gliomas (70 of them glioblastoma) aged 34 to 78 years (mean age 56 years). DNA and RNA isolation was performed from fresh frozen tumor tissue, as well as from peripheral blood leukocytes. EGFR gene mutations were determined by next-generation sequencing (NGS), and β allele frequency (BAF) comparative analysis (normal-tumor) was performed to determine the copy number of chromosome 7 regions. Quantitative polymerase chain reaction was used to confirm the EGFR gene amplification in tumor samples, and reverse transcription-PCR was used to detect EGFRvIII variant.Results. The NGS method revealed 11/70 (16 %) mutations in coding regions of EGFR gene in glioblastoma samples, the EGFR gene amplification was detected in 26/70 (37 %) cases; no structural changes of the EGFR gene were detected in 5 glioma samples (astrocytoma, oligodendroglioma). All cases of EGFR gene amplification detected by NGS were confirmed by quantitative polymerase chain reaction. To search for EGFRvIII transcript, 31 tumor RNA samples were examined, of which EGFR amplification was present in 12 samples. EGFRvIII transcript was detected only in samples with EGFR gene amplification – 4/12 (33 %). To assess the clinical significance of structural gene alterations, the frequency of occurrence in primary and recurrent glioblastoma samples was compared.Conclusion. The NGS method allows to detect both point mutations and amplification of the EGFR gene. The EGFR gene amplification was associated with EGFRvIII mutation in 33 % of cases. No statistically significant differences in the frequency of structural changes in the EGFR gene between primary and relapsed glioblastomas were found.

Background and Aims: Gut dysbiosis and abnormal cytokine profiles are common in cirrhosis. This study aimed to evaluate the correlations between them. Methods: In the blood plasma of cirrhosis patients and controls, 27 cytokines were examined using a multiplex assay. The plasma levels of nitrites (stable metabolites of the endothelial dysfunction biomarker nitric oxide) and lipopolysaccharide (LPS) were examined. The fecal microbiota was assessed by 16S rRNA gene sequencing. Results: Levels of IL -1b, IL2, IL -6, IL -13, IP -10, IFN-g, TNF-a, LPS, and nitrites were higher in cirrhosis patients than in controls, while levels of IL -4, IL -7, and PDGF-BB were lower. The LPS level was directly correlated with the levels of IL -1b, IL1-Ra, IL -9, IL17, PDGF-BB, IL -6, TNF-a, and nitrites. The nitrite level was significantly directly correlated with the levels of TNF-a, GM-CSF, IL -17, and IL -12, and inversely correlated with the IL -7 level. TNF-a levels were directly correlated with ascites severity and the abundance of Negativicutes, Enterobacteriaceae, Veillonellaceae, and Klebsiella, while inversely correlated with the abundance of Firmicutes, Clostridia, and Subdoligranulum. IFN-g levels were directly correlated with the abundance of Bacteroidaceae, Lactobacillaceae, Bacteroides, and Megasphaera, and inversely correlated with the abundance of Verrucomicrobiota, Akkermansiaceae, Coriobacteriaceae, Akkermansia, Collinsella, and Gemella. IL -1b levels were directly correlated with the abundance of Comamonadaceae and Enterobacteriaceae and inversely correlated with the abundance of Marinifilaceae and Dialister. IL -6 levels were directly correlated with the abundance of Enterobacteriaceae, hepatic encephalopathy, and ascites severity, and inversely correlated with the abundance of Peptostreptococcaceae, Streptococcaceae, and Streptococcus. Conclusions: The abundance of harmful gut micro biota taxa and endotoxinemia directly correlates with the levels of proinflammatory cytokines.

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BACKGROUND The gut-liver axis and bacterial translocation are important in cirrhosis, but there is no available universal biomarker of cellular bacterial translocation, for which presepsin may be a candidate. AIM To evaluate the relationship of the blood presepsin levels with the state of the gut microbiota in cirrhosis in the absence of obvious infection. METHODS This study included 48 patients with Child-Pugh cirrhosis classes B and C and 15 healthy controls. The fecal microbiome was assessed using 16S rRNA gene sequencing. Plasma levels of presepsin were measured. A total of 22 patients received a probiotic (Saccharomyces boulardii) for 3 months. RESULTS Presepsin levels were higher in patients with cirrhosis than in healthy individuals [342 (91-2875) vs 120 (102-141) pg/mL; P = 0.048]. Patients with elevated presepsin levels accounted for 56.3% of all included patients. They had lower levels of serum albumin and higher levels of serum total bilirubin and overall severity of cirrhosis as assessed using the Child-Pugh scale. Patients with elevated presepsin levels had an increased abundance of the main taxa responsible for bacterial translocation, namely Bacilli and Proteobacteria (including the main class Gammaproteobacteria and the minor taxa Xanthobacteraceae and Stenotrophomonas), and a low abundance of bacteria from the family Lachnospiraceae (including the minor genus Fusicatenibacter), which produce short-chain fatty acids that have a positive effect on intestinal barrier function. The presepsin level directly correlated with the relative abundance of Bacilli, Proteobacteria, and inversely correlated with the abundance of Lachnospiraceae and Propionibacteriaceae. After 3 months of taking the probiotic, the severity of cirrhosis on the Child-Pugh scale decreased significantly only in the group with elevated presepsin levels [from 9 (8-11) to 7 (6-9); P = 0.004], while there were no significant changes in the group with normal presepsin levels [from 8 (7-8) to 7 (6-8); P = 0.123]. A high level of presepsin before the prescription of the probiotic was an independent predictor of a greater decrease in Child-Pugh scores (P = 0.046), as well as a higher level of the Child-Pugh scale (P = 0.042), but not the C-reactive protein level (P = 0.679) according to multivariate linear regression analysis. CONCLUSION The level of presepsin directly correlates with the abundance in the gut microbiota of the main taxa that are substrates of bacterial translocation in cirrhosis. This biomarker, in the absence of obvious infection, seems important for assessing the state of the gut-liver axis in cirrhosis and deciding on therapy targeted at the gut microbiota in this disease.

Gut dysbiosis and subclinical intestinal damage are common in cirrhosis. The aim of this study was to examine the association of intestinal damage biomarkers (diamine oxidase [DAO], claudin 3, and intestinal fatty acid binding protein [I-FABP; FABP2]) with the state of the gut microbiota in cirrhosis. The blood levels of DAO were inversely correlated with blood levels of claudin 3, lipopolysaccharide (LPS), presepsin, TNF-α, and the severity of cirrhosis according to Child–Pugh scores. The blood level of I-FABP was directly correlated with the blood level of claudin 3 but not with that of DAO. Patients with small intestinal bacterial overgrowth (SIBO) had lower DAO levels than patients without SIBO. There was no significant difference in claudin 3 levels and I-FABP detection rates between patients with and without SIBO. The DAO level was directly correlated with the abundance of Akkermansiaceae, Akkermansia, Allisonella, Clostridiaceae, Dialister, Lactobacillus, Muribaculaceae, Negativibacillus, Ruminococcus, Thiomicrospiraceae, Verrucomicrobiae, and Verrucomicrobiota; and it was inversely correlated with the abundance of Anaerostipes, Erysipelatoclostridium, and Vibrio. The I-FABP level was directly correlated with Anaerostipes, Bacteroidia, Bacteroidota, Bilophila, Megamonas, and Selenomonadaceae; and it was inversely correlated with the abundance of Brucella, Pseudomonadaceae, Pseudomonas, and Vibrionaceae. The claudin 3 level was directly correlated with Anaerostipes abundance and was inversely correlated with the abundance of Brucella, Coriobacteriia, Eggerthellaceae, and Lactobacillus.

The white poplar (Populus alba) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes.

Hippophae rhamnoides is a valuable crop whose fruits are rich in bioactive compounds with health benefits. To date, there is a lack of genetic data for varieties of sea buckthorn. This fact hinders the identification of genetic determinants of valuable traits and limits the efficiency of breeding. In the present study, we analyzed a representative set of 55 valuable H. rhamnoides varieties of Russian breeding with different fruit characteristics and diverse lineages. Whole-genome sequencing was performed on the Illumina platform and at least 25x genome coverage was obtained for each accession. Based on the sequencing data, DNA polymorphisms were identified in genome regions corresponding to genes. These polymorphisms were used to evaluate the genetic relationships of the studied sea buckthorn varieties. We revealed genetically distinct groups of accessions that mostly corresponded to the lineages of the genotypes. Our data are important for assessing the effect of selection on sea buckthorn diversity and for evaluating the genetic relationship of different varieties, which is useful for breeders when selecting parental forms for crosses. The obtained information on DNA polymorphisms is also necessary to study the diversity of genes, including those that may determine valuable sea buckthorn traits, including fruit characteristics. Thus, our data can benefit both basic and applied research on sea buckthorn. ### Competing Interest Statement The authors have declared no competing interest.

Assessments of breast cancer (BC) risk in carriers of pathogenic variants identified by gene panel testing in different populations are highly in demand worldwide. We performed target sequencing of 78 genes involved in DNA repair in 860 females with BC and 520 age- and family history-matched controls from Central Russia. Among BC patients, 562/860 (65.3%) were aged 50 years or less at the time of diagnosis. In total, 190/860 (22%) BC patients were carriers of 198 pathogenic/likely pathogenic (P/LP) variants in 30 genes, while among controls, 32/520 (6.2%) carriers of P/LP variants in 17 genes were identified. The odds ratio [95% confidence interval] was 16.3 [4.0-66.7] for BRCA1; 12.0 [2.9-45.9] for BRCA2; and 7.3 [0.9-56.7] for ATM (p < 0.05). Previously undescribed BRCA1/2, ATM, and PALB2 variants, as well as novel recurrent mutations, were identified. The contribution to BC susceptibility of truncating variants in the genes BARD1, RAD50, RAD51C, NBEAL1 (p. E1155*), and XRCC2 (p. P32fs) was evaluated. The BLM, NBN, and MUTYH genes did not demonstrate associations with BC risk. Finding deleterious mutations in BC patients is important for diagnosis and management; in controls, it opens up the possibility of prevention and early diagnostics.

The application of manure has the potential to enhance soil health by increasing organic matter content and stimulating dormant soil-borne microorganisms. However, this treatment also carries the risk of side effects, including the invasion and spread of manure-borne pathogens. To assess the survival of manure-borne microbes in soil and their introduction into the soil microbiome, a laboratory experiment was conducted. Fresh cattle, swine, and poultry manures were applied at a rate of 50 t/ha to two different soil types: Chernozem and Retisol. The soil samples, including both control and manure-amended soils, were incubated in microcosms for a period of 6 months. Analysis of the samples was performed prior to fertilization, as well as at 1-and 6-months intervals following manure application. The analysis involved determining the gene numbers of archaea, bacteria, and fungi, as well as examining the taxonomic and physiological profiles of the microbial communities. The response of the microbial communities in the two soils to the manure application varied. In Chernozem, there was an increase in microbial abundance, activation of archaea and bacteria, and a moderate shift in the structure of prokaryotic community. On the other hand, the microbial community in Retisol did not show significant acti-vation due to the manure amendments, but notable changes in both community structure and functioning were observed during the experiment. It was found that more manure-borne genera survived after 6 months in Retisol compared to Chernozem. Consequently, manure amendments could pose a greater risk of microbial contami-nation in soils characterized by low microbial activity and abundance.