Background/Objectives: Pharmacogenetic variability plays a crucial role in determining both the efficacy and toxicity of chemotherapy for gastrointestinal cancers. However, data on allele frequencies and their clinical relevance in Russian populations remain scarce. Methods: We conducted a prospective observational study of 412 patients with gastrointestinal malignancies between 2020 and 2023. Pharmacogenetic testing was performed prior to the initiation of chemotherapy using real-time allele-specific PCR and microarray hybridization technology. Polymorphisms in the DPYD, UGT1A1, CYP2C8, CYP3A5, GSTP1, ERCC1, XPC, CDA, MTHFR, TYMS, and SLC31A1 genes were analyzed. Results: The frequency of most variants was consistent with those reported in European populations, reflecting the ethnic proximity of the studied cohort. Several clinically relevant variants were identified: DPYD rs2297595 occurred more frequently than in European cohorts, and UGT1A1 rs8175347 was observed at a higher prevalence, underscoring the potential risk of irinotecan-related neutropenia and diarrhea. CYP2C8 rs10509681 was present at frequencies comparable to European populations and is associated with an increased risk of taxane-induced peripheral neuropathy. Other markers (GSTP1, ERCC1, CDA, SLC31A1, MTHFR, TYMS) demonstrated variable associations with chemotherapy efficacy and toxicity, consistent with findings from previous international studies. Conclusions: This study provides the first comprehensive description of pharmacogenetic polymorphisms in a Russian cohort of patients with gastrointestinal cancers. Our findings confirm the clinical importance of DPYD and UGT1A1 testing and highlight additional variants of potential interest.

To reduce severe fluoropyrimidine-related toxicity, pharmacogenetic guidelines recommend a dose reduction for carriers of four high-risk variants in the DPYD gene (*2A, *13, c.2846A>T, HapB3). The polymorphism in the MIR27A gene has been shown to enhance the predictive value of these variants. Our study aimed to explore whether rs895819 in the MIR27A gene modifies the effect of five common DPYD variants: c.1129-5923C>G (rs75017182, HapB3), c.2194G>A (rs1801160, *6), c.1601G>A (rs1801158, *4), c.496A>G (rs2297595), and c.85T>C (rs1801265, *9A). The study included 370 Caucasian patients with gastrointestinal tumors who received fluoropyrimidine-containing chemotherapy. Genotyping was performed using high-resolution melting analysis. The DPYD*6 allele was associated with overall severe toxicity and neutropenia with an increased risk particularly pronounced in patients carrying the MIR27A variant. All carriers of DPYD*6 exhibited an association with asthenia regardless of their MIR27A status. The increased risk of neutropenia in patients with c.496G was only evident in those co-carrying the MIR27A variant. DPYD*4 was also significantly linked to neutropenia risk in co-carriers of the MIR27A variant. Thus, we have demonstrated the predictive value of the *6, *4, and c.496G alleles of the DPYD gene, considering the modifying effect of the MIR27A polymorphism.

Stenotrophomonas maltophilia is an opportunistic pathogen intrinsically resistant to multiple and broad-spectrum antibiotics. Although the bacterium is considered a low-virulence pathogen, it can cause various severe diseases and contributes significantly to the pathogenesis of multibacterial infections. During the COVID-19 pandemic, S. maltophilia has been recognized as one of the most common causative agents of respiratory co-infections and bacteremia in critically ill COVID-19 patients. The high ability to adapt to unfavorable environments and new habitat niches, as well as the sophisticated switching of metabolic pathways, are unique mechanisms that attract the attention of clinical researchers and experts studying the fundamental basis of virulence. In this review, we have summarized the current knowledge on the molecular aspects of S. maltophilia virulence and putative virulence factors, partially touched on interspecific bacterial interactions and iron uptake systems in the context of virulence, and have not addressed antibiotic resistance.

AIMS The aim of this study was to develop a rapid PCR-based method for spoligotyping of Mycobacteria in the microarray format and to compare it to conventional spoligotyping by hybridization. METHODS AND RESULTS The method employs the on-Chip PCR technique with primers specific for 43 spacers that separate direct repeats (DRs) in the DR region of mycobacterial DNA. The primers were immobilized on gel-based microarrays, and PCR was performed directly on the chips. The PCR fluorescence images were acquired and processed using a portable fluorescence analyzer equipped with dedicated software. Analysis takes 1.5-2 hours and can be carried out on clinical samples without additional handling. The analytical sensitivity of the method was 103 copies of target DNA. The spoligotyping results of 51 samples produced by the proposed method and by conventional reverse hybridization approach were in full concordance. CONCLUSIONS High throughput capacity, computerized data analysis, compact equipment, and reliable results make the on-Chip PCR an attractive alternative to intra- and interspecific spoligotyping of Mycobacterium tuberculosis complex bacteria. SIGNIFICANCE AND IMPACT OF STUDY Fast microarray-based spoligotyping technique using on-Chip PCR was developed.

Introdiction . Systemic chemotherapy (CT) based on oxaliplatin, 5-fluorouracil, capecitabine is the standard of treatment for advanced gastric, colorectal and rectal cancer, which is characterized by frequent development of severe adverse events (AEs). The results of translational studies in the Russian patient population are limited, it is necessary to study pharmacogenetic markers. Aim. To study the frequency of carrying allelic variants of DPYD, GSTP1, MTHFR, XPC, ERCC1, TYMS genes and their association with the development of AEs during palliative treatment with FOLFOX/XELOX. Materials and methods . A total of 166 patients (67 gastric cancer, 99 colorectal cancer) were included in the prospective observational study. All patients underwent pharmacogenetic testing by hybridization analysis on biological microarrays ( DPYD (rs2297595 and rs75017182), MTHFR (rs1801133), XPC (rs2228001), TYMS (rs11280056), ERCC1 (rs3212986)) and PCR ( GSTP1 (rs1695), ERCC1 (rs11615)) before starting CT. The genotype frequency distribution was analyzed between the groups of patients with and without the development of severe AEs. Results . AEs developed in 97.7% of patients, severe AEs accounting for 54.2%. According to the results of univariate analysis, TC genotype of DPYD gene rs2297595 OR = 3.0 (95% CI 1.2–7.3, p = 0.025), GG genotype of GSTP1 gene rs1695 OR = 2.9 (95% CI 1.02–8.6, p = 0.038) were associated with the development of severe neutropenia. In multivariate analysis TT genotype rs2297595 of the DPYD gene remained the only predictor of severe neutropenia (B ± SE = -1.103 ± 0.503; DI [-2.090; -0.116]; p = 0.028). Conclusions . The results of this study allowed us to identify possible markers of toxicity of FOLFOX/XELOX chemotherapy.

Introduction. Stenotrophomonas maltophilia is an opportunistic pathogen that is intrinsically resistant to a wide range of antibiotics. The bacterium is associated with a number of serious diseases and makes a significant contribution to the pathogenesis of polymicrobial infections. S. maltophilia has a wide range of virulence factors, information about which is currently presented in the form of scattered and unconsolidated data. Purposes and objectives: critically analyze and summarize current data regarding the molecular-genetic aspects of S. maltophilia virulence for better understanding of the pathogenesis of infections associated with this pathogen. Materials and methods. An analysis of information from 80 modern literary sources devoted to the study of the virulent properties of S. maltophilia at the molecular-genetic level has been carried out. The analysis focuses on the mechanisms of production of virulence factors and their genetic determinants. Results.The molecular mechanisms of virulence that determine the infectious process caused by S. maltophilia have been analyzed and summarized, including the adhesive function of the surface structures of the bacterial cell (lipopolysaccharides, pili/fimbriae, flagella), the production of extracellular enzymes, the ability to form biofilms on abiotic surfaces and on the tissues of the macroorganism, the functioning of efflux pumps, secretion of small molecules into the external environment by the intercellular information exchange system Quorum Sensing, as well as the influence of iron metabolism on the virulence properties of S. maltophilia. Conclusion. The adaptation mechanisms that allow S. maltophilia to adapt to new habitat niches and survive in the human body and unfavorable environmental conditions have been poorly studied. An analytical review summarizing current information on the molecular-genetic aspects of S. maltophilia virulence will be of interest to clinicians and researchers studying the fundamental mechanisms of virulence.

Background: Mutations in homologous recombination (HR) and Fanconi anemia (FA) genes may predispose to pancreatic cancer (PC) and enable the prediction of sensitivity to platinum-based chemotherapy. FOLFIRINOX is a standard treatment option for non-selected PC patients and could be effective due to undiagnosed DNA repair deficiency. Here, we aimed to determine the frequency of mutations in genes involved in the HR and FA pathways, evaluate their clinical implications, and determine the objective response rate (ORR), progression-free survival (PFS), and overall survival (OS) of PC patients treated with platinum. Methods: We performed targeted DNA sequencing of 30 genes ( ABRAXAS1 , ATM , ATR , BARD1 , BLM , BRCA1 , BRCA2 , BRIP1 , CDKN2A , CHEK1 , CHEK2 , FANCC , FANCF , FANCG , FANCI , FANCL , FANCM , MRE11A , NBN , PALB2 , PTEN , RAD50 , RAD51C , RAD51D , RAD52 , RAD54B , RBBP8 , RINT1 , SLX4 , and XRCC2 ) for 543 PC patients. Results: In BRCA/PALB2 -mutated patients with advanced PC (33 patients, 6.1%), the PFS and OS were higher for first-line platinum therapy than for non-platinum therapy [PFS: HR = 0.28, 95% confidence interval (CI) = 0.10–0.81, p = 0.02; OS: HR = 0.31, 95% CI = 0.08–1.16, p = 0.08]. Among 93 patients (17.1%) with mutations in other HR/FA genes, no statistically significant difference in PFS and OS was observed between first-line platinum therapy and non-platinum therapy (PFS: HR = 0.83, 95% CI = 0.43–1.62, p = 0.59; OS: HR = 0.58, 95% CI = 0.28–1.22, p = 0.15). For patients with early PC, no prognostic value was observed for BRCA1/2 , PALB2 , or other HR/FA genes mutations. Moreover, a personal history of breast, ovarian, pancreatic, or prostate cancer was identified as the only independent predictor of the risk of BRCA/PALB2 mutations (HR = 5.83, 95% CI = 2.16–15.73, p < 0.01). Conclusion: Mutations in the BRCA1/2 and PALB2 genes increase the sensitivity of PC to platinum agents. Thus, alterations in these genes in PC patients must be determined prior to anticancer therapy.

Pancreatic ductal adenocarcinoma (PDAC) is a highly fatal malignancy that has the worst 5-year survival rate of all of the common malignant tumors. Surgery, chemotherapy, and/or chemoradiation remain the main tactics for PDAC treatment. The efficacy of chemotherapy is often compromised because of the substantial risk of severe toxicities. In our study, we focused on identification of polymorphisms in the genes involved in drug metabolism, DNA repair and replication that are associated with inter-individual differences in drug-induced toxicities. Using the microarray, we genotyped 12 polymorphisms in the DPYD, XPC, GSTP1, MTHFR, ERCC1, UGT1A1, and TYMS genes in 78 PDAC patients treated with FOLFIRINOX. It was found that the TYMS rs11280056 polymorphism (6 bp-deletion in TYMS 3′-UTR) predicted grade 1–2 neurotoxicity (p = 0.0072 and p = 0.0019, according to co-dominant (CDM) and recessive model (RM), respectively). It is the first report on the association between TYMS rs11280056 and peripheral neuropathy. We also found that PDAC patients carrying the GSTP1 rs1695 GG genotype had a decreased risk for grade 3–4 hematological toxicity as compared to those with the AA or AG genotypes (p = 0.032 and p = 0.014, CDM and RM, respectively). Due to relatively high p-values, we consider that the impact of GSTP1 rs1695 requires further investigation in a larger sample size.

Aim. To assess the association between the carriage of minor allelic variants of 8 genes that encode key enzymes involved in the metabolism of anticancer drugs (DPYD, GSTP1, MTHFR, UGT1A1) and cell repair (XPC, ERCC1, TYMP, NQO1) and the severity of adverse drug events in patients with common gastrointestinal tumors. Tasks. To study the frequency of minor allelic variants of the DPYD, GSTP1, MTHFR, UGT1A1, XPC, ERCC1, TYMP, NQO1 genes; to assess the frequency and severity of adverse drug events of chemotherapy treatment in the study population. Materials and methods. For the period from October 2020 to April 2021, 56 patients (women 29, men 27) with verified malignant tumors of the gastrointestinal tract were included in a prospective clinical study as a part of the RSF grant No. 20-75-10158. The mean age was 62.311.4 years. Colon cancer was detected in 24 patients, tumors of the esophagus and stomach in 19 patients, tumors of pancreas and biliary tract in 13 patients. First-line palliative chemotherapy was given to 27 patients, adjuvant 19 patients, neoadjuvant 10 patients. All patients had not previously received cytotoxic or radiation treatment. Point nucleotide variants of genes DPYD, XPC, GSTP1, MTHFR, ERCC1, UGT1A1, TYMPS, NQO1 were determined by hybridization analysis on biological microchips. Differences in the tolerance of cytotoxic therapy (5-fluorouracil, platinum preparations, irinotecan) depending on the genotype were assessed using Fishers exact test. Results. The average number of chemotherapy courses received was 4.22.6 (112). There was a statistically significant difference in the tolerability of chemotherapy in patients with minor allelic variants of the GSTP1 rs1695 (p=0.03), ERCC1 rs11615 (p=0.01), and UGT1A1 rs8175347 (p=0.003) genes. Conclusion. The use of hybridization analysis on biological microchips to assess allelic variants responsible for the tolerability of cytotoxic therapy is reasonable and requires further prospective assessment.

The survival of bacteria under antibiotic therapy varies in nature and is based on the bacterial ability to employ a wide range of fundamentally different resistance mechanisms. This great diversity requires a disambiguation of the term 'resistance' and the development of a more precise classification of bacterial survival strategies during contact with antibiotics. The absence of a unified definition for the terms 'resistance', 'tolerance' and 'persistence' further aggravates the imperfections of the current classification system. This review suggests a number of original classification criteria that will take into account (1) the bacterial ability to replicate in the presence of antimicrobial agents, (2) existing evolutionary stability of a trait within a species, and (3) the presence or absence of specialized genes that determine the ability of a microorganism to decrease its own metabolism or switch it completely off. This review describes potential advantages of the suggested classification system, which include a better understanding of the relationship between bacterial survival in the presence of antibiotics and molecular mechanisms of cellular metabolism suppression, the opportunity to pinpoint targets to identify a true bacterial resistance profile. The true resistance profile in turn, could be used to develop effective diagnostic and antimicrobial therapy methods, while taking into consideration specific bacterial survival mechanisms.

BACKGROUND:Circulating tumor DNA (ctDNA) holds great potential for cancer therapy and can provide diagnostic and prognostic information before and during treatment.METHODS:Plasma DNA samples from 97 melanoma patients, 20 healthy donors and 3 patients with benign skin tumors were analyzed by microarray analysis and droplet digital PCR (ddPCR).RESULTS:A microarray for simultaneous detection of six BRAF V600 mutations in ctDNA has been developed. The method allows the detection of 0.05% mutated DNA from WT DNA background. For paired samples (pre-surgery plasma and tumor tissue) isolated from 74 patients, the concordance of genotypes between tumor DNA and ctDNA was 65% (48/74). BRAF mutations in ctDNA were detected in 27/50 patients with BRAF-positive tumors and in 3/24 patients with BRAF wild-type tumors. The presence of ctDNA BRAF mutations in 23 plasma samples from melanoma patients undergoing therapy correlated significantly with tumor progression (P=0.005). The increase in cell-free DNA levels measured by ddPCR also correlated with disease progression (P=0.02). The concordance of results obtained by microarray identification of BRAF mutations and those obtained by ddPCR was 91%.CONCLUSION:The novel microarray-based approach can be a useful non-invasive tool for accurate identification of ctDNA BRAF mutations to monitor disease progression.

A individual approach to the treatment of cancer patients, which takes the genetic features of the patient’s metabolism into account, allows one to choose an appropriate drug and its dose, that increases the efficiency of therapy and prevents the development of side toxic effects. For this purpose, we developed a biological microarray-based method for studying the primary structure of patient DNA and identifying polymorphisms in the UGT1A1, DPYD, GSTP1, and ABCB1 genes associated with alterations in xenobiotic metabolism. Genotyping of samples from 89 cancer patients and 15 healthy donors was carried out using the developed microarray. The results of determination of the primary structure of DNA samples coincided completely with the control sequencing. To increase the specificity of determination of polymorphic variants of the UGT1A1 gene, we used hybridization probes containing LNA nucleotides. The frequencies of polymorphic allelic variants of the UGT1A1*28, DPYD*2A, GSTP1 (I105V), and ABCB1 (C3435T) genes in the studied sample were 0.39, 0, 0.33, and 0.57, respectively.

В черте города Москвы из фекалий диких водоплавающих птиц изолировали 42 штамма вируса гриппа птиц и проанализировали их на микрочипах «Биогрипп», которые содержат 176 зондов к различным участкам генома вирусов гриппа. Микрочип позволяет определять: 1) субтип поверхностных белков гемагглютинина и нейраминидазы; 2) структуру С-концевой последовательности вирусного белка NS1, влияющую на степень ингибирования транскрипции клеточных хозяйских генов, в том числе ответственных за синтез интерферона; 3) наличие стоп-кодонов и мутацию N66S в рамке считывания вирусного белка PB1-F2, 4) наличие полиосновного сайта протеолитического расщепления гемагглютинина. Среди изолятов от диких птиц идентифицированы вирусы гриппа субтипов H3N1, H3N6, H3N8, H4N6, H1N1, H5N3 и H11N9. Все они содержали последовательность ESEV на С-конце белка NS1, полноразмерную рамку считывания для белка PB1-F2. Замена N66S в PB1-F2 обнаружена у шести штаммов. Однако такие маркеры патогенности, как последовательность ESEV (лиганд PDZ-домена) в вирусном белке NS1 и замена N66S PB1-F2 в контексте генома вирусов гриппа диких уток, не делали вирус патогенным для мышей. Все изоляты были высокоурожайны в куриных эмбрионах, инфекционны и иммуногенны для мышей, но не вызывали у этих животных клинических симптомов заболевания.

Forty-two strains of avian influenza viruses were isolated from the wild waterfowl’s feces in the city of Moscow. These viruses as well as reference strains and some experimental reassortants were analyzed by microarrays. The used microarrays contained 176 probes to the different segments of influenza virus genome. The microarray allows to determine 1) the hemagglutinin and neuraminidase proteins subtype; 2) the primary structure of the C-terminal sequence of the viral NS1 protein, which serves as a ligand for the PDZ domain; 3) the presence of stop codons and substitution N66S in the reading frame of the viral protein PB1-F2; 4) the presence of the polybasic site for hemagglutinin cleavage. The viruses of H3N1, H3N6, H3N8, H4N6, H1N1, H5N3 and H11N9 subtypes were identified from the group of wild bird’s isolates. All isolates contained the ESEV sequence at the C-terminus of the NS1 protein and the full-length reading frame for the PB1-F2 protein. The replacement of N66S in PB1-F2 was found in six strains. However, the presence of ESEV sequence (ligand of PDZ domain) in the NS1 virus protein and the N66S substitution in PB1-F2 did not lead to the pathogenicity of these viruses for mice. All isolates demonstrated high yield growth in chicken embryos, were infectious and immunogenic for mice, but did not induce any clinical symptoms.

BACKGROUND Improving the efficacy of anticancer therapy remains an urgent and very important task. Screening of the individual genetic metabolism of cancer patients allows for prescribing adequate medication in the correct dose as well as for decreasing side effects associated with drug toxicity. OBJECTIVE Estimation of a microarray-based method for genotyping of the UGT1A1, DPYD, GSTP1, and ABCB1 metabolic regulation genes to evaluate for an increased risk of toxicity of anticancer drugs. METHODS The microarray was used to conduct genotyping of specimens taken from 115 cancer patients and 31 healthy donors. RESULTS A microarray-based method for identification of the rs8175347, rs3918290, rs1695, and rs1045642 polymorphisms in the corresponding UGT1A1, DPYD, GSTP1, and ABCB1 genes has been developed for genotyping. The results obtained were in full concordance with those obtained using control sequencing. The frequencies of the rs8175347, rs3918290, rs1695, and rs1045642 genetic variations were 0.38, 0, 0.35, and 0.56, respectively. CONCLUSION The implementation of this biochip-based method in diagnostic practice should increase the overall survival and quality of life of cancer patients, decrease the length of their hospital stay, and reduce treatment costs.

We describe the development and evaluation of a rotary-based platform with multiple disposable fluidic modules for simultaneous automatic nucleic acid (NA) isolation from up to 24 biological samples. The procedure is performed inside insulated individual disposable modules, which minimizes both the risk of infection of personnel and laboratory cross-contamination. Each module is a segment of a circular cylinder containing a leak-proof inlet port for sample input, reservoirs with lyophilized chemicals and solvents, fluidic channels, stoppers, valves, a waste reservoir and an outlet port equipped with the standard micro test tube for NA collection. The entire platform, apart from the rotor that accommodates 24 modules, consists of functional elements that provide spinning of the rotor, reagent mixing, pressure delivery, and heating of reaction mixtures. The transfer of the reaction mixtures inside the modules is performed either with rotation of the rotor or with excessive air pressure applied to the module's reservoirs. The entire process takes less than 40 min, starting from the sample loading to the recovery of the purified NA, and it allows NA isolation both from bacterial cells and viral particles. The feasibility and reproducibility of the developed platform was demonstrated by the NA isolation from suspensions of Bacillus thuringiensis and Mycobacterium tuberculosis cells within a concentration range of 10(8) to 10(2) cells/ml. Isolation of NAs from blood plasma samples with varying concentration of hepatitis B and C viruses from 10(7) to 10(2) particles/ml were also successful. The purity and integrity of the extracted NAs were both reliable for performing quantitative PCR.

Steadily growing resistance of the tuberculosis causative agent towards a broad spectrum of anti-tuberculosis drugs calls for rapid and reliable methods for identifying the genetic determinants responsible for this resistance. In this study, we present a biochip-based method for simultaneous identification of mutations within rpoB gene associated with rifampin resistance, mutations in katG, inhA, ahpC genes responsible for isoniazid resistance, mutations within the regions of gyrA and gyrB genes leading to fluoroquinolones resistance, and mutations in the rrs gene and the eis promoter region associated with the resistance to kanamycin, capreomycin and amikacin. The oligonucleotide microchip, as the core element of this assay, provides simultaneous identification of 99 mutations in the format "one sample--one PCR--one microchip", and it makes it possible to complete analysis of multi-drug-resistant and extensively drug-resistant tuberculosis within a single day. The tests on 63 Mycobacterium tuberculosis clinical isolates with different resistance profiles using the developed approach allows us to reveal the spectrum of drug-resistance associated mutations, and to estimate the significance of the inclusion of extra genetic loci in the determination of M. tuberculosis drug resistance.

Species of the genus Acinetobacter represent opportunistic bacteria with a growing clinical significance. In this literature review, we focus on the current role of Acinetobacter in infectious pathology and describe physiology, taxonomy, ecology, pathogenicity, and antibiotic resistance of these bacteria. Molecular pathogenesis and regulation of virulence factors in Acinetobacter spp. are described in detail. The majority of acinetobacterial infections are associated with A. baumannii and occur predominantly in an immunocompromised host. Usually, acinetobacterial infections are characterized by local purulent inflammation; in severe cases, meningitis and sepsis may develop. Antibiotic resistance ofAcinetobacter is a major clinical problem; therefore we give special attention to laboratory testing of resistance as well as identification of Acinetobacter. In addition, treatment and prophylaxis of acinetobacterial infections are discussed.