An increasing amount of data demonstrates that genetic alterations are involved in cell migration and cancer metastasis. Invasive breast carcinoma of no special type shows significant morphological heterogeneity represented by different types of architectural arrangements of tumor cells: tubular, alveolar, solid, trabecular, and torpedo-like structures, and small groups, as well as single tumor cells. In this study, we use intratumoral morphological heterogeneity, whole-exome sequencing (WES), and genome editing to identify mutational drivers of breast cancer invasion.

• Novikov N.M., Zolotaryova S.Y., Gautreau A.M., Denisov E.V. Mutational drivers of cancer cell migration and invasion. Br J Cancer 2021;124:102-114.
• Gerashchenko T.S., Zolotaryova S.Y., Kiselev A.M., Tashireva L.A., Novikov N.M., Krakhmal N.V., Cherdyntseva N.V., Zavyalova M.V., Perelmuter V.M., Denisov E.V. The Activity of KIF14, Mieap, and EZR in a New Type of the Invasive Component, Torpedo-Like Structures, Predetermines the Metastatic Potential of Breast Cancer. Cancers (Basel) 2020;12(7):1909.
• Tashireva L.A., Zavyalova M.V., Savelieva O.E., Gerashchenko T.S.,  Kaigorodova E.V., Denisov E.V., Perelmuter V.M. Single tumor cells with epithelial-like morphology are associated with breast cancer metastasis. Front Oncol 2020;10:50.
• Gerashchenko T.S, Novikov N.M, Krakhmal N.V, Zolotaryova S.Y, Zavyalova M.V, Cherdyntseva N.V, Denisov E.V, Perelmuter V.M.  Markers of Cancer Cell Invasion: Are They Good Enough? J Clin Med 2019;8(8):1092

Metastasis is initiated by tumor cells detached from the primary tumor and entering the bloodstream. Circulating tumor cells (CTCs) are presented by phenotypically and genetically distinct subpopulations. Deciphering CTC heterogeneity represents a promising instrument for the identification of the metastasis-initiating cells and developing therapeutic strategies against metastatic disease. In our study, we used single-cell RNA sequencing to assess CTC composition in patients with breast cancer and identify CTC populations associated with metastasis. The tumorigenic potential of CTCs is further analyzed using in vitro and in vivo models.

• Tashireva L.A., Savelieva O.E., Grigoryeva E.S., Nikitin Y.V., Denisov E.V., Vtorushin S.V., Zavyalova M.V., Cherdyntseva N.V., Perelmuter V.M. Heterogeneous Manifestations of Epithelial-Mesenchymal Plasticity of Circulating Tumor Cells in Breast Cancer Patients. Int J Mol Sci 2021;2;22(5):2504.
• Menyailo M.E., Tretyakova M.S., Denisov E.V. Heterogeneity of Circulating Tumor Cells in Breast Cancer: Identifying Metastatic Seeds. Int J Mol Sci 2020;21(5):1696.
• Menyailo M.E., Bokova U.A., Ivanyuk E.E., Khozyainova A.A., Denisov E.V.  Metastasis Prevention: Focus on Metastatic Circulating Tumor Cells. Molecular Diagnosis and Therapy, 2021; 25(5): 549-562
  

Non-small cell lung cancer (NSCLC) is highly fatal. Recurrence is one of the main causes of high mortality of NSCLC patients. The prognosis and prevention of NSCLC progression still remain an unresolved problem. Previous studies revealed a significant association between the premalignant bronchial changes distant from the primary tumor and NSCLC progression risk. In this study, we stratify NSCLC patients into low- and high-risk groups according to bronchial lesions and apply WES for the identification of germline variations and somatic alterations that are associated with locoregional and distant recurrence.

• Schegoleva A.A., Khozyainova A.A., Fedorov A.A., Gerashchenko T.S., Rodionov E.O., Topolnitsky E.B., Shefer N.A., Pankova O.V., Durova A.A., Zavyalova M.V., Perelmuter V.M., Denisov E.V. Prognosis of Different Types of Non-Small Cell Lung Cancer Progression: Current State and Perspectives. Cell Physiol Biochem 2021;55(S2):29-48.
• Pankova O.V., Rodionov E.O., Miller S.V., Tuzikov S.A., Tashireva L.A., Gerashchenko T.S., Denisov E.V., Perelmuter V.M., Neoadjuvant chemotherapy combined with intraoperative radiotherapy is effective to prevent recurrence in high-risk non- small cell lung cancer (NSCLC) patients. Transl Lung Cancer Res 2020;9(4):988-999.
• Schegoleva A.A., Khozyainova A.A., Gerashchenko T.S., Zhuikova L. D., Denisov E.V. Metastasis prevention: targeting causes and roots. Clinical & Experimental Metastasis. 2022.
  
• Tashireva L.A., Pankova O.V., Rodionov E.O., Miller S.V., Tuzikov S.A., Pismenny D.S., Gerashchenko T.S., Zavyalova M.V., Vtorushin S.V., Denisov E.V., Perelmuter V.M. Premalignant changes in the bronchial epithelium are prognostic factors of distant metastasis in NSCLC patients. Front. Oncol. 
  

Oral squamous cell carcinoma (OSCC) that is most commonly diagnosed in older adults is becoming increasingly prevalent in young adults. Early-onset OSCC is not related to tobacco, alcohol, and human papillomavirus infection and shows resistance to chemo- and radiotherapy and high rates of recurrence. In this study, we analyze metagenome, genetic, and immunoinflammatory features of OSCC in young adults using 16S rRNA sequencing, WES, and multicolor immunofluorescence staining.

Cervical cancer (CC) is one of the most common malignant neoplasms in women. Every fourth patient with CC has regional recurrences or distant metastases. Current therapeutic approaches for CC patients include surgical treatment, radiation therapy, chemoradiotherapy, and chemotherapy; however, cancer progression remains a major problem for patients and oncologists. In this regard, it is necessary to understand the mechanisms of CC progression in various therapies and to identify effective and reliable prognostic markers. Our study is aimed at identifying markers of CC recurrence and metastasis depending on the therapy type using bulk RNA-seq and further validation by PCR and immunohistochemistry staining.

• Larionova I, Rakina M, Ivanyuk E, Trushchuk Y, Chernyshova A, Denisov E. Radiotherapy resistance: identifying universal biomarkers for various human cancers. J Cancer Res Clin Oncol. 2022 Feb 3.
  

Next-generation sequencing (NGS) is widely used in clinical oncology to advance the personalized treatment of cancer patients. In our study, we develop oligonucleotide baits (probes) and NGS panels for simultaneous detection of single-nucleotide variations (SNV), insertion and deletion alterations, tumor mutation burden (TMB), and microsatellite instability (MSI) to predict cancer risk and prognosis as well as provide a rationale for appropriate targeted and immune therapy.

Metastasis can be realized through the phenomenon of tumor cell fusion. The fusion of tumor cells with other tumor or normal cells leads to the appearance of tumor hybrid cells (THCs) exhibiting novel properties such as increased proliferation and migration, drug resistance, decreased apoptosis rate, and avoiding immune surveillance. Experimental studies showed the association of THCs with a high frequency of cancer metastasis; however, the underlying mechanisms remain unclear. In this study, we analyze the phenotypic composition of THCs, their genetic and transcriptional features, and their association with clinical and pathological parameters of NSCLC using single-cell DNA and RNA-seq and multicolor immunofluorescence staining.

• Tretyakova M.S, Subbalakshmi AR, Menyailo ME, Jolly MK, Denisov EV. Tumor Hybrid Cells: Nature and Biological Significance. Front Cell Dev Biol. 2022 Feb 15;10:814714..

Triple negative breast cancer (TNBC) is a less common, but the most aggressive type of breast cancer. TNBC is difficult to treat due to the lack of targeted therapies, and chemotherapy remains the standard treatment. Although patients with TNBC have a high rate of clinical response to chemotherapy, they show poor prognosis and high risk of recurrence. In this project, we use scRNAseq to reveal immune cells and molecular mechanisms that modulate the effectiveness of neoadjuvant chemotherapy in TNBC.