The E6 and E7 proteins of the high risk human papillomaviruses (HR HPVs) play a key role in the oncogenesis associated with papillomavirus infection. Data on the variability of these proteins are limited, and the factors affecting their variability are still poorly understood. We analyzed the variability of the currently known sequences of the 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 the major geographic regions of the world. All sequences belonging to HPV16 genome fragments encoding the 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 has to include at least one of the two whole open reading frames, and given date of collection, and the country of origin. A total of 3651 full-genome nucleotide sequences encoding the E6 protein and 4578 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 the MEGA11, R, RStudio, Jmodeltest 2.1.20, BEAST v1.10.4, Fastcov, and Biostrings software. The highest variability in the E6 protein was recorded for amino acid (AA) residues in the positions 17, 21, 32, 85, and 90. The most variable in E7 were aa positions 28, 29, 51, and 77. The samples were divided geographically into five heterogeneous groups as derived from Africa, Europe, America, South-West and South Asia, and South-East Asia. Unique amino acid substitutions (AA-substitutions) in the E6/E7 proteins of HPV16, presumably characteristic to certain ethnic groups, were identified for a number of countries. They weare mainly localized in the sites of known B- and T-cell epitopes and relatively rarely the domains critical for in structure and protein function. The revealed differences in AA-substitutions in different ethnic groups and their colocalization with the clusters of B- and T-cell epitopes suggested their possible relation to 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 in different geographic areas, resulting in the regional differences in the direction of epitopic drift. Phylogenetic analysis of the nucleotide sequences encoding the E6 protein of HPV16 revealed a common ancestor, confirmed regional clustering of the E6 protein sequences sharing common AA-substitutions, and identified cases of reversion of individual AA-substitutions when the change of geographical localization. For the E7 protein, such analysis was not possible due to the high sequence homology. Covariance analysis of the pooled of E6 and E7 sequences revealed that there was no associations between amino acid residues in any aa position within E6 or E7 as well as aa positions of E6 and E7 proteins. The data presented here are important for the development of universal therapeutic vaccines against HPV of high carcinogenic risk.

Randomized clinical trials (RCTs) are the gold standard of evidence-based medicine. However, it is no less evident that real practice presents many new and important questions that are difficult to answer in the RCT. To what extent does the real patient meet the criteria for inclusion in the study? What are the efficacy and safety of the drug in comorbid and elderly patients? How deviations from the treatment regimen affect safety, etc. The introduction of innovative oncology approaches is disproportionately faster than in other fields. That is why a balanced analysis of the effects of innovation in real-world practice is relevant. Regulatory authorities are aware of this and demonstrate a willingness to consider and actively support real-world evidence research as part of drug applications, which is a powerful incentive for developing this area. The purpose of the article is to analyze the regulatory approaches in the United States and Europe to real-world studies when considering drug applications and to discuss the experience of organizing an observational study of the effectiveness of individual drugs for the treatment of oncological diseases in Moscow as a unique example of interaction between regulatory authorities and the expert community of oncologists.

Carboxypeptidase A3 (CPA3) is a specific protease of mast cells (MC) with variable expression and appears to be one of the preformed components of the secretome. CPA3 is involved in regulation of the state of a specifi tissue microenvironment and components of the integrative-buffer metabolic environment in adaptive and pathological processes; it affects implementation of the innate immunity, mechanisms of angiogenesis, processes of the extracellular matrix remodeling, etc. CPA3 identification using protocols of multiplex immunohistochemistry allows specifying details of the organ-specific mast cell population features, including the protease phenotype, mechanisms of biogenesis with cytoand histotopographic criteria, and features of secretory pathways. Numerous biological effects of CPA3, including participation in the regulation of the pulmonary parenchyma and systemic blood flow, in biogenesis and remodeling of the fibrous component of the extracellular matrix, in epigenetic reprogramming, determine the importance of fundamental investigation of the physiological activity of protease and its involvement in the implementation of pathological processes. Further studies will contribute to the detection of the translational value of the mast cell CPA3 expression features as a prognostic factor and a promising molecular target for treatment of socially significant diseases.

Background. The effective treatment of oncological diseases requires the proper organization of interdisciplinary communication between specialists. Such an approach should be implemented in educational events organized by professional communities. Aim. To analyze the effectiveness of interaction between professional oncology communities and expert physicians on the platforms of educational events in Russia as a response to the unprecedented growth of scientific knowledge in oncology. Materials and methods. We studied educational events programs organized by oncological communities. The keywords of the report titles in 2012 and 2021 and the features of the networking structure of the speakers at the educational events in 2021 were analyzed. Results. In 2021, there was a significant expansion of the range of topics discussed compared to 2012, while experts began to use the terms "diagnosis", "prevention", "radiotherapy", and others much less frequently. The network structure of professional community interactions and interdisciplinary connections of experts at educational events is heterogeneous; some communities actively cooperate, while others show a closed position. At the level of systematic multidisciplinary expert interaction, there is also an underrepresentation of pathologists, geneticists, and other specialists. Conclusion. The oncology professional community needs to regularly work on multidisciplinary consolidation of competencies and broad discussion of clinical experience at scientific and educational events.

Cell transmembrane receptors and extracellular matrix components play a pivotal role in regulating cell activity and providing for the concerted integration of cells in the tissue structures. We have assessed DNA methylation in the promoter regions of eight integrin genes, two nidogen genes, and the dystroglycan gene in normal breast tissues and breast carcinomas (BC). The protein products of these genes interact with the basement membrane proteins LAMA1, LAMA2, and LAMB1; abnormal hypermethylation of the LAMA1 , LAMA2 , and LAMB1 promoters in BC has been described in our previous publications. In the present study, the frequencies of abnormal promoter hypermethylation in BC were 13% for ITGA1 , 31% for ITGA4 , 4% for ITGA7 , 39% for ITGA9 , 38% for NID1 , and 41% for NID2 . ITGA2, ITGA3, ITGA6, ITGB1 , and DAG1 promoters were nonmethylated in normal and BC samples. ITGA4, ITGA9 , and NID1 promoter hypermethylation was associated with the HER2 positive tumors, and promoter hypermethylation of ITGA1, ITGA9 , NID1 and NID2 was associated with a genome-wide CpG island hypermethylated BC subtype. Given that ITGA4 is not expressed in normal breast, one might suggest that its abnormal promoter hypermethylation in cancer is non-functional and is thus merely a passenger epimutation. Yet, this assumption is not supported by our finding that it is not associated with a hypermethylated BC subtype. ITGA4 acquires expression in a subset of breast carcinomas, and methylation of its promoter may be preventive against expression in some tumors. Strong association of abnormal ITGA4 hypermethylation with the HER2 positive tumors (p = 0.0025) suggests that simultaneous presence of both HER2 and integrin α4 receptors is not beneficial for tumor cells. This may imply HER2 and integrin α4 signaling pathways interactions that are yet to be discovered.

Matrix metalloproteinases (MMPs) and their tissue inhibitors (TIMPs) substantially contribute to the regulation of intercellular interactions and thereby play a role in maintaining the tissue structure and function. We examined methylation of a subset of 5'-cytosine-phosphate-guanine-3' (CpG) dinucleotides in promoter regions of the MMP2, MMP11, MMP14, MMP15, MMP16, MMP17, MMP21, MMP23B, MMP24, MMP25, MMP28, TIMP1, TIMP2, TIMP3, and TIMP4 genes by methylation-sensitive restriction enzyme digestion PCR. In our collection of 183 breast cancer samples, abnormal hypermethylation was observed for CpGs in MMP2, MMP23B, MMP24, MMP25, and MMP28 promoter regions. The non-methylated status of the examined CpGs in promoter regions of MMP2, MMP23B, MMP24, MMP25, and MMP28 in tumors was associated with low HER2 expression, while the group of samples with abnormal hypermethylation of at least two of these MMP genes was significantly enriched with HER2-positive tumors. Abnormal methylation of MMP24 and MMP25 was significantly associated with a CpG island hypermethylated breast cancer subtype discovered by genome-wide DNA bisulfite sequencing. Our results indicate that abnormal hypermethylation of at least several MMP genes promoters is a secondary event not directly functional in breast cancer (BC) pathogenesis. We suggest that it is elevated and/or ectopic expression, rather than methylation-driven silencing, that might link MMPs to tumorigenesis.

Introduction. Adjuvant systemic therapy remains one of the main options for treating breast cancer. Results of standard immunohistochemical studies are not always a criterion for selecting systemic therapy. Nowadays, multigene expression analysis is actively used to predict the response to chemotherapy in patients with earlystage breast cancer. We studied a 24-gene multi-gene panel for typing breast cancer. Material and Methods. A prospective analysis of 199 breast cancer patients (T1–3N0–3M0) was carried out. Surgical specimens were studied using the standard immunohistochemistry (IHC) and RT-PCR for detecting expression of 24 genes. Results. According to the IHC results, breast cancer was divided into 5 molecular subtypes: luminal A was detected in 59 (30 %) patients; luminal B (HER2-negative) in 52 (26 %); luminal B (HER2-positive) in 19 (9 %); triple-negative in 28 (14 %); HER2-positive 41 (21 %). RT-PCR showed that ST K15, MYC, MYBL2, BIRCC 5, BCL2, TERT, ESRP1, PGR, HER2, GBR7, MGB1 and MMP11 were the most significant genes in subtype distribution. The total percentage of matches between the two studies was 61.7 %. Conclusion. Studies have shown the need to add additional typing methods for breast cancer to a standard IHC study, which will undoubtedly increase the information content of diagnostic measures and will improve the effectiveness of the treatment.

Introduction. Adjuvant systemic therapy remains one of the main options for treating breast cancer. Results of standard immunohistochemical studies are not always a criterion for selecting systemic therapy. Nowadays, multigene expression analysis is actively used to predict the response to chemotherapy in patients with earlystage breast cancer. We studied a 24-gene multi-gene panel for typing breast cancer.Material and Methods. A prospective analysis of 199 breast cancer patients (T1–3N0–3M0) was carried out. Surgical specimens were studied using the standard immunohistochemistry (IHC) and RT-PCR for detecting expression of 24 genes.Results. According to the IHC results, breast cancer was divided into 5 molecular subtypes: luminal A was detected in 59 (30 %) patients; luminal B (HER2-negative) in 52 (26 %); luminal B (HER2-positive) in 19 (9 %); triple-negative in 28 (14 %); HER2-positive 41 (21 %). RT-PCR showed that ST K15, MYC, MYBL2, BIRCC 5, BCL2, TERT, ESRP1, PGR, HER2, GBR7, MGB1 and MMP11 were the most significant genes in subtype distribution. The total percentage of matches between the two studies was 61.7 %.Conclusion. Studies have shown the need to add additional typing methods for breast cancer to a standard IHC study, which will undoubtedly increase the information content of diagnostic measures and will improve the effectiveness of the treatment.

The purpose of systemic treatment in patients with breast cancer is based largely on the molecular characteristics of the primary tumor, but many clinical recommendations suggest also the study of metastatic nodes with an assessment of their receptor status (estrogen receptor ER, progesterone receptor RP, human epidermal growth factor receptor 2 Her2/neu). This is due to the fact that according to numerous studies, the discrepancy between the status of the primary tumor and the secondary nodes can reach high rates: 3–54 % for ER, 5–78 % for RP, and 0–34 % for Her2/neu. At the same time, more and more data actively demonstrate the imperfection of immunohistochemical analysis and the need to study additional parameters to improve the quality of diagnosis of patients with breast cancer. Material and methods. A morphological and immunohistochemical study of the tumor tissue of the primary node and axillary lymph nodes was performed in 199 patients with breast cancer (T1-3N0-3M0) using standard methods, and RT-PCR was also studied with the expression of 24 genes. Results. The incidence of differences between the molecular phenotypes of the main tumor and metastatic axillary lymph nodes was 26 (26 %) of 99 cases. Most often, differences were noted in cases of breast cancer with luminal A type – 13 cases (50 %). According to the results of a comparative PCR analysis of tissue samples from the primary tumor and metastatic regional lymph nodes, only the expression of the CD68, ERSR1, GRB7 and MMD11 receptors was statistically significant. Conclusion. The results indicate the need for an integrated approach and additional methods for the diagnosis of breast cancer, which will undoubtedly improve the quality of planning and the effectiveness of systemic treatment in patients with breast cancer.

Aim: To provide a breast cancer (BC) methylotype classification by genome-wide CpG islands bisulfite DNA sequencing. Materials & methods: XmaI-reduced representation bisulfite sequencing DNA methylation sequencing method was used to profile DNA methylation of 110 BC samples and 6 normal breast samples. Intrinsic DNA methylation BC subtypes were elicited by unsupervised hierarchical cluster analysis, and cluster-specific differentially methylated genes were identified. Results & conclusion: Overall, six distinct BC methylotypes were identified. BC cell lines constitute a separate group extremely highly methylated at the CpG islands. In turn, primary BC samples segregate into two major subtypes, highly and moderately methylated. Highly and moderately methylated superclusters, each incorporate three distinct epigenomic BC clusters with specific features, suggesting novel perspectives for personalized therapy.

Matrix metalloproteinases (MMPs) responsible for the extracellular matrix remodeling, the activation of various growth factors, and angiogenesis play an important role in the colorectal cancer (CRC) development. In the present work the comparative analysis of MMP-7, -8, -9, and -11 mRNA as well mRNA of the Ki-67 proliferation marker in tissue samples obtained from CRC patients and healthy individuals. Employing the real time PCR method the expression levels of several MMPs (MMP-7, -8, -9, and -11) and cell proliferation marker, Ki-67, were simultaneously measured in 256 tissue samples obtained from 112 patients with CRC: 112 samples of the primary tumor (CRC), 112 samples of the most distant border of morphologically normal colonic mucosa (MNT), 16 samples of liver metastases) and from 16 healthy volunteers who underwent colonoscopy and biopsy. The expression of both MMPs studied and Ki-67 was found to be elevated in CRC primary tumors and liver metastases compared with the normal mucosa. CRC tumor and metastatic cells exhibited similar proliferative activity. The metastases are characterized by the highest cross-correlation of MMPs among tissue types tested. For the first time it was shown that normal mucosa from healthy individuals and CRC patients varied in the MMP-8 expression level. They also had dissimilar MMP correlation patterns thus suggesting that epithelial cells adjusted to CRC tumor differ from mucosal epithelial cells of healthy individuals.

РЕФЕРАТ Болезнь Паркинсона (БП) – одно из наиболее распространенных двигательных расстройств, диагностика которого до настоящего времени остается, главным образом, клинической. Для разработки патогенетического лечения БП важна точная диагностика БП на самых ранних стадиях, в связи с чем необходим поиск потенциальных биомаркеров заболевания. Нами оценена диагностическая значимость ряда микроРНК и их взаимосвязь с клиническими характеристиками БП. В исследование включены 70 пациентов с БП и 40 здоровых добровольцев. В лейкоцитах крови оценивали экспрессию 15 микроРНК, отобранных на основании опубликованных данных и современных представлений о молекулярном патогенезе БП. Всем пациентам проведена оценка по клиническим шкалам Hoehn–Yahr, UPDRS, NMSQ, PDQ-39. По результатам исследования выявлено статистически значимое повышение экспрессии miR-7-1-5p, miR-29c-3p и miR-185-5p и снижение экспрессии miR-29a-3p и miR-30c-1-5p в лейкоцитах при БП. Однако показано, что измененный профиль микроРНК обладает умеренной диагностической значимостью. Изменения экспрессии микроРНК были ассоциированы с моторными и немоторными фенотипическими особенностями БП и изменялись на фоне приема противопаркинсонических препаратов. Также показана связь ряда изученных микроРНК с длительностью и тяжестью БП, что потенциально может использоваться в мониторировании прогрессирования заболевания. КЛЮЧЕВЫЕ СЛОВА болезнь Паркинсона, микроРНК, биомаркеры. СПИСОК СОКРАЩЕНИЙ БП – болезнь Паркинсона; REM-фаза – фаза быстрых движений глаз (rapid eye movement); UPDRS – унифицированная рейтинговая шкала оценки болезни Паркинсона (Unified Parkinson’s Disease Rating Scale); NMSQ – опросник немоторных симптомов (Non-Motor Symptoms Questionnaire); HADS – госпитальная шкала тревоги и депрессии (Hospital Anxiety and Depression Scale); MоCA – Монреальская шкала когнитивной оценки (Montreal Cognitive Assessment); PDQ-39 – опросник качества жизни пациентов с болезнью Паркинсона (Parkinson’s Disease Questionnaire).

Matrix metalloproteinases and their inhibitors contribute to the regulation of cell-cell interactions and maintain tissue structure and function. We have analyzed DNA methylation at the promoter regions of 11 matrix metalloproteinases genes ( MMP2, MMP11, MMP14, MMP15, MMP16, MMP17, MMP21, MMP23B, MMP24, MMP25, MMP28 ), and 4 inhibitors of matrix metalloproteinases genes ( TIMP1, TIMP2, TIMP3, TIMP4 ). Collectively members of these families take part in regulation of matrix proteins degradation, signal transduction, adhesion, migration, cell differentiation, apoptosis and angiogenesis. Abnormal methylation frequencies at the promoter regions of genes MMP2, MMP23B, MMP24, MMP25, MMP28 in breast cancer accounted for 7,7%, 17%, 11,9%, 15,4% and 4,9% respectively. Promoter regions of genes TIMP1, TIMP4, MMP14 MMP21 were constitutively methylated in breast tissue.

Currently, no molecular biological markers do exist for early diagnosis of breast cancer. One of the possible candidates for the marker of early breast cancer is mammaglobin (MGB1) or SCGB2A2 (secretoglobin, family 2A, member 2), characterized by the maximal expression level in early breast cancer. Using the RT-PCR method MGB1 mRNA expression was examined in 57 tumor tissue samples and 57 samples of morphologically non-malignant tissue (MNT) of breast cancer (BC) patients. Specificity and sensitivity of the MGB1 mRNA assay in peripheral blood of BC patients was evaluated by nested PCR. 169 blood samples (from 95 BC patients, 22 from patients with benign breast tumors, 28 from patients with tumors of other localizations, and 24 samples from healthy donors) have been analyzed. MGB1 expression was significantly higher in BC tissue samples compared to MNT (p = 0.0019). The maximal expression level was in the samples T1 (p = 0.013), stage I BC (p = 0.037), GI (p = 0.0019). MGB1 expression positively correlated with expression of estrogen (p = 0.034) and progesterone (p = 0.0004) receptors. Sensitivity and specificity of the MGB1 mRNA assay in peripheral blood were 60.6 and 92.3%, respectively. Expression of MGB1 was higher in BC than MNT and it decreased during BC progression. The sensitivity and specificity of the MGB1 mRNA assay may be used as an additional diagnostic method.

Purpose: to analyze the expression levels of 21 genes participating in cell proliferation control, apoptosis activation, cell differentiation and adhesion in FFPE in breast cancer (BC) tumor samples from patients with and without local relapse after breast-conserving surgery. Additionally we tried to develop prognostic model for local relapse risk assessment after breast-conserving surgery on the basis of tumor gene expression profile. Materials and methods: Study included 53 BC samples received from patients after breast-conserving surgery. Locoregional relapse was observed in 14 (26%) cases. Results: We analyzed expression level of 21 genes by RT-PCR and used those data to distinguish retrospectively the relapsed and nonrelapsed patients. Analysis allowed us to predict locoregianal recurrence in 71,4 % of the cases and we could exclude it in 94,8 % cases. Conclusion: Comparative genes expression analysis allows to create the algorithm of locoregional recurrence prediction after breast-conserving surgery.

Extracellular glycoproteins of the laminin family are essential components of basement membranes involved in a number of biological processes, including tissue differentiation, wound healing, and tumorigenesis. We present the first comprehensive study of promoter methylation status of the genes encoding laminin chains in normal tissues (peripheral blood leucocytes, buccal epithelial cells, autopsy breast tissue samples) and in breast carcinoma samples. Based on the results of this study, we divide laminin genes into three categories. Genes, constitutively methylated in breast tissues include LAMA3A, LAMB2, LAMB3, and LAMC2. Genes prone to abnormal methylation in breast carcinoma include LAMA1, LAMA2, LAMA3B, LAMA4, LAMB1, and LAMC3. Genes that are rarely if ever methylated in breast carcinoma include LAMA5 and LAMC1. The constitutively methylated group includes all of the genes that encode subunits of laminin-5 (the historical name of laminin 332), the promoters of which were previously considered unmethylated in normal tissues and prone to abnormal methylation in breast cancer.

In normal cell apoptosis and proliferation are strictly controlled by intra- and extracell mechanisms. These signals interfere with cell pathways through cell receptors, estrogen, progesterone, HER2/neu receptors in the case of breast cancer. Expression of apoptotic and proliferative genes is different in breast cancer depending on hormonal status. Besides correlation analysis shows different role of cell receptors in proliferation control in normal and breast tissue.

Cervical cancer is one of the most common diseases in women and a role of human papilloma virus (HPV) as the trigger of malignization is considered to be proved. Virus replication influence alterations in gene expression pattern provoking proliferative and antiapoptotic activity of infected cell - fundamental features of malignization. We analyzed KI67, Aurora A, Birc5, cyclin B1, CTSL2, MMP11, Her2/neu, GRB7, BCL2, BAG1, BAX, NDRG1, ESR, PRG, PTEN, MGB and hTERT expression by qPCR in normal HPV positive/negative cervical epithelium (CE), through cervical intraepithelial neoplasia progression (CIN I-III) and in cervical cancer (CC).