Lyudmila F. Gulyaeva

Tobacco smoking continues to represent the leading risk factor for multiple malignancies, most notably lung cancer (LC), which exhibits a complex molecular pathogenesis. While classical models prioritize direct DNA damage and mutagenesis, growing evidence points to the role of mechanisms not directly dependent on structural DNA lesions. In particular, dysregulation of oncogenic and tumor-suppressive microRNAs (miRNAs) has emerged as a promising area of research. Although numerous miRNAs potentially involved in LC pathogenesis have been reported to be altered by tobacco exposure, the available evidence is fragmented. This heterogeneity, compounded by the chemical complexity of tobacco smoke, prevents the formation of a comprehensive landscape of its pathogenetic mechanisms. This review aims to systematize existing data on tobacco smoke–induced changes in miRNA expression profiles in LC, with reference to individual tobacco smoke constituents, and to identify key biological processes likely modulated by these changes.

Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of advanced non-small cell lung cancer (NSCLC). However, the limited predictive value of PD-L1 expression as a biomarker underscores the urgent need for more reliable predictors of ICI response. Interferon regulatory factor 1 (IRF1) is a transcription factor that lies downstream of interferon-γ signaling and directly regulates CD274 (PD-L1) transcription. Here, we performed a comprehensive bioinformatic analysis to identify microRNAs (miRNAs) that may be associated with IRF1 expression in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Using data from The Cancer Genome Atlas (TCGA), we identified 20 miRNAs whose expression levels consistently and negatively correlated with IRF1 mRNA levels in both LUAD and LUSC. Among these, only hsa-miR-301b possesses conserved binding sites in the 3′UTR of IRF1 mRNA, suggesting direct post-transcriptional repression. For the remaining 19 miRNAs, we hypothesized an indirect mechanism of action. Further analysis revealed that hsa-miR-183 and hsa-miR-141 may target the transcription factor genes NFKB1 and STAT4, respectively, both of which positively correlate with IRF1 expression and are themselves associated with improved survival in ICI-treated patients. This study delineates a multi-layer miRNA regulatory network associated with IRF1 expression in NSCLC and identifies hsa-miR-301b, hsa-miR-183 and hsa-miR-141 as candidate upstream regulators of IRF1. Direct survival analysis for these miRNAs in ICI-treated cohorts was not feasible due to the lack of publicly available miRNA-seq data with treatment annotations; therefore, their clinical predictive value remains hypothetical, and experimental validation is required to assess their potential as predictors of ICI response.

The development of resistance to trastuzumab in HER2-positive breast cancer is a serious clinical problem that limits the effectiveness of targeted therapy. In a significant proportion of patients, the mechanisms in the development of resistance remain poorly understood. The BT-474 cell line was selected as an optimal model for study because it represents a HER2-positive luminal B subtype breast cancer cell line. To identify the molecular mechanisms of resistance, a comprehensive transcriptomic analysis based on RNA-seq data comparison of three independent datasets including both sensitive and trastuzumab-resistant variants was applied. The methodological approach included multistep bioinformatics analysis followed by identification of regulatory interactions. The study identified genes with increased expression (FUCA2, HSPE1, SHLD1, NMD3) and genes with decreased expression (GPC5, FSTL1, ATG16L2, POLD2) in resistant cells. Key transcription factors (E2F1, MYC, YBX1, HEY1, NFIC, TFAP2A, AP-1/JUN, NCOA1) regulating the expression of the detected genes during the development of resistance were identified. The changes identified indicate a complex reprogramming of transcriptional activity affecting cell cycle processes, DNA repair, metabolism, and the epithelial–mesenchymal transition. The findings expand our understanding of the molecular mechanisms of trastuzumab resistance and open prospects for the development of novel therapeutic strategies to overcome drug resistance in HER2-positive breast cancer.

Development of next generation sequencing technologies allows to identify a large number of genetic landscape types in various cancers including breast cancer. Frequent genetic abnormalities identified using whole genome sequencing are point mutations (missense, nonsense mutations), deletions, insertions, which usually lead to activation of protooncogenes and inactivation of tumor suppressor genes. Genome sequencing of malignant tumors allowed, on one hand, to identify driver mutations in carcinogenic genes in different organs, and on the other – to use mutated genes for targeted therapy. Study of biological functions of these genes from the point of view of their contribution to carcinogenesis allows to better understand its mechanism. In this review, signaling cascades of breast cancer with identified mutated genes – targets for therapy – are analyzed.

Metabolomics is a new approach in modern biomedical science, the purpose of which is to study unique chemicals specific to the processes occurring in living cells. Due to the continuous development of advanced analytical methods and bioinformatics, metabolomics is widely used as a new, holistic, diagnostic tool in clinical and biomedical research. Metabolic reprogramming is a hallmark of cancer. Studies have shown that in transformed cells, in-cluding the mammary gland, there are profound metabolic changes aimed at survival. The detection of oncometabolites is one of the important prob-lems of modern science today, as it allows understanding the metabolic pathways of the transformed cell, which is important both for diagnosis and the search for new therapeutic targets. In connection with the development of new chemical technologies, it became possible to determine the level of steroids and their metabolites, as well as fatty acids in the tumor. One such method, along with NMR spectrometry and liquid chromatography, in con-junction with mass spectrometry (LC-MS), is gas chromatography with GC-MS mass spectrometry. Enormous progress in the application of these modern analytical methods allows for a deeper and more accurate description of metabolic processes. This review article discusses some of the current and current hurdles in cancer metabolomics research. In addition, it reviews some of the most re-cent and exciting developments in metabolomics that may address some of these issues. The purpose of this article is to inform the oncometabo-lomics research community about the problems and possible solutions to these problems.

The development of resistance to trastuzumab in HER2-positive breast cancer is a serious clinical problem that limits the effectiveness of targeted therapy. In a significant proportion of patients, the mechanisms in the development of resistance remain poorly understood. The BT-474 cell line was selected as an optimal model for study because it represents a HER2-positive luminal B subtype breast cancer cell line. To identify the molecular mechanisms of resistance, a comprehensive transcriptomic analysis based on RNA-seq data comparison of three independent datasets including both sensitive and trastuzumab-resistant variants was applied. The methodological approach included multistep bioinformatics analysis followed by identification of regulatory interactions. The study identified genes with increased expression (FUCA2, HSPE1, SHLD1, NMD3) and genes with decreased expression (GPC5, FSTL1, ATG16L2, POLD2) in resistant cells. Key transcription factors (E2F1, MYC, YBX1, HEY1, NFIC, TFAP2A, AP-1/JUN, NCOA1) regulating the expression of the detected genes during the development of resistance were identified. The changes identified indicate a complex reprogramming of transcriptional activity affecting cell cycle processes, DNA repair, metabolism, and the epithelial-mesenchymal transition. The findings expand our understanding of the molecular mechanisms of trastuzumab resistance and open prospects for the development of novel therapeutic strategies to overcome drug resistance in HER2-positive breast cancer.

Cancer of women’s reproductive organs (gynecological cancers) and breast cancer affect women all over the world

Tyrosine protein kinase HER2 plays an important role in carcinogenesis. In breast cancer (BC), the HER2 gene is amplified in approximately 20% of cases. Trastuzumab is used to treat BC with HER2 gene amplification. Trastuzumab is not effective in treating tumors with low HER2 expression, but trastuzumab deruxtecan was recently found to significantly improve prognosis in these patients. Nonetheless, there are still difficulties with accurate diagnosis of HER2-low BC, especially at the preoperative stage. In this study, when comparing the results between core needle biopsies and resection specimens using three immunohistochemistry scores (0, 1+, and 3+) of the HER2 protein level, we observed only moderate agreement (66.2%, κ = 0.486) in patients who did not undergo neoadjuvant therapy (n = 71). Other miRNA- or protein-coding genes regulated by HER2 signaling pathways may be additional markers for the scoring of the HER2 level. We measured levels of HER2-regulated miR-378a, -205, and -21 and mRNA levels of their target genes TRPS1, ITGA2, BCL6, and PTEN in BC surgical specimens. For estrogen receptor-positive BC (n = 64), we confirmed that the expression of miR-21, miR-378a, TRPS1, PTEN, and BCL6 is associated with the HER2 protein level. Moreover, the expression profile of miR-378a, BCL6, and PTEN differed between HER2 1+ and HER2 3+ tumors. TRPS1 expression was significantly higher in HER2 3+ tumors compared with HER2 0 tumors, but there was no difference in the amount of TRPS1 mRNA between HER2 1+ and HER2 3+ tumors. Thus, an analysis of the expression of miR-21, miR-378a, TRPS1, PTEN, and BCL6 may help to distinguish between HER2-negative, HER2-positive, and HER2-low BCs.

NSCLC is a very aggressive solid tumor, with a poor prognosis due to post-surgical recurrence. Analysis of the specific tumor and immune signatures of NSCLC samples is a critical step in prognostic evaluation and management decisions for patients after surgery. Routine histological assays have some limitations. Therefore, new diagnostic tools with the capability to quickly recognize NSCLC subtypes and correctly identify various markers are needed. We developed a technique for ex vivo isolation of cancer and immune cells from surgical tumor and lung tissue samples of patients with NSCLC (adenocarcinomas and squamous cell carcinomas) and their examination on ex vivo cell preparations and, parallelly, on histological sections after Romanovsky–Giemsa and immunofluorescent/immunochemical staining for cancer-specific and immune-related markers. As a result, PD-L1 expression was detected for some patients only by ex vivo analysis. Immune cell profiling in the tumor microenvironment revealed significant differences in the immunological landscapes between the patients’ tumors, with smokers’ macrophages with simultaneous expression of pro- and anti-inflammatory cytokines, neutrophils, and eosinophils being the dominant populations. The proposed ex vivo analysis may be used as an additional diagnostic tool for quick examination of cancer and immune cells in whole tumor samples and to avoid false negatives in histological assays.

Smoking is an established risk factor for a variety of malignant tumors, the most well-known of which is lung cancer. Various molecular interactions are known to link tobacco smoke exposure to lung cancer, but new data are still emerging on the effects of smoking on lung cancer development, progression, and tumor response to therapy. In this study, we reveal in further detail the previously established association between smoking and hsa-mir-301a activity in lung squamous cell carcinoma, LUSC. Using different bioinformatic tools, we identified IRF1 as a key smoking-regulated target of hsa-mir-301a in LUSC. We further confirmed this relationship experimentally using clinical LUSC tissue samples and intact lung tissue samples. Thus, increased hsa-mir-301a levels, decreased IRF1 mRNA levels, and their negative correlation were shown in LUSC tumor samples. Additional bioinformatic investigation for potential pathways impacted by such a mechanism demonstrated IRF1’s multifaceted role in controlling the antitumor immune response in LUSC. IRF1 was then shown to affect tumor immune infiltration, the expression of immune checkpoint molecules, and the efficacy of immune checkpoint blockade therapy. As a result, here we suggest a smoking-regulated mir301a/IRF1 molecular axis that could modulate the antitumor immune response and immunotherapy efficacy in LUSC, opening up novel opportunities for future research.