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Is GeneMind Genolab M suitable for spatial transcriptomics?
The article «Comparison of the Illumina NextSeq 2000 and GeneMind Genolab M sequencing platforms for spatial transcriptomics» prepared by our laboratory together with Tomsk State University, Peoples’ Friendship University of Russia (RUDN University) and Genomed has been recently published in BMC Genomics.
In October 2020 a new sequencing instrument (GenoLab M) was released by GeneMind, which is fully compatible with Illumina based libraries and does not require library conversion. However, the performance of the GenoLab M platform in other applications has not yet been tested for single cell sequencing including spatial transcriptomics.
This article confirms that GeneMind Genolab M sequencing platform generates consistent with Illumina NextSeq 2000 sequencing results: sequencing quality metrics indicate highly comparable base calling accuracy in UMI sequence, spatial barcode sequence, and probe read sequence. Also identical spot clusters were identified in each sample and spatial distribution of spot clusters was predominantly similar without obvious differences.
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Complex analysis of single-cell RNA sequencing data
The article «Complex Analysis of Single-Cell RNA Sequencing Data» prepared by our laboratory together with Lomonosov Moscow State University, Pirogov Russian National Medical University, Tomsk State University, Dmitry Rogachev National Research Center of Pediatric Hematology, Oncology and Immunology and Koltzov Institute of Developmental Biology of the Russian Academy of Sciences has been recently published in Biochemistry (Moscow).
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features of cells, opens up the possibility to analyze the trajectories/phylogeny of cell differentiation and cell–cell interactions, and helps in discovery of new cell types and previously unexplored processes.
This review describes different approaches to the analysis of scRNA-seq data, discusses the advantages and disadvantages of bioinformatics tools, provides recommendations and examples of their successful use, and suggests potential directions for improvement.
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How to catch metastatic seeds
The review article «Metastasis prevention: How to catch metastatic seeds» prepared by our laboratory has been recently published in Biochimica et Biophysica Acta (BBA) - Reviews on Cancer.
Despite considerable advances in the evolution of anticancer therapies, metastasis still remains the main cause of cancer mortality. Targeting metastatic pathways represents a promising therapeutic opportunity aimed at obstructing tumor cell dissemination and metastatic colonization. This review recapitulates preclinical studies and clinical trials over the last five years that showed high efficacy in suppressing metastasis through targeting lymph node dissemination, tumor cell extravasation, reactive oxygen species, pre-metastatic niche, exosome machinery, and dormancy.
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New equipment for imaging and data analysis
We purchased the CELENA S Digital Imaging System (Logos Bio) that makes capturing high resolution images of cells and tissues. Simple software supports multicolor fluorescence imaging, brightfield imaging, phase contrast imaging, live cell time lapse imaging, and Z-stack imaging.
Identifying functional features of circulating monocytes in breast cancer patients
The article «Changes in blood monocyte functional profile in breast cancer» prepared by our laboratory together with Tomsk State University has been recently published in Siberian Journal of Oncology.
Peripheral blood monocytes are important components of innate immunity, as they are involved in maintaining tissue homeostasis. Their main function in malignant neoplasms is to replenish the pool of tumor-associated macrophages, dendritic cells, and myeloid suppressor cells. Currently, it is assumed that monocytes can have certain transcriptome programs mediated by the tumor.
This article confirms the concept of the formation of a pool of monocytes with the ability to support tumor growth in breast cancer, especially by programming them into macrophages with tumor supporting capacity.
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Online seminar on education and work in bioinformatics
Dr. Evgeny Denisov presented two talks at the online seminar on education and work in bioinformatics which was organized by Bioinformatics Institute (Saint-Petersburg) and held on 18 February 2023. In the first talk, Evgeny told about the experience of our laboratory in the organization of the workshop on single-cell sequencing and the establishment of Association for Single Cell Analysis. The second one was devoted to the applications of NGS for understanding cancer origin and progression mechanisms.

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Our laboratory joined the VII All-Russian Conference on Molecular Oncology, which was held on December 21-23, 2022 in Moscow
Dr. Tatiana Gerashchenko talked about dynamics of immune cell population composition in blood and breast tumor during chemotherapy. Maria Tretiakova and Elizaveta Prostakishina presented poster talks about migration and invasive potential of different cell populations in breast cancer and the role of dual specificity phosphatases DUSP in the functional polarization of monocytes in breast cancer.
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Single cell and spatial transcriptomics: applications in cancer research
Dr. Evgeny Denisov joined the online meeting organized by the Oncology Institute of Istanbul University and told about our laboratory projects and how we use single cell and spatial sequencing technologies and what results are obtained.
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Is there ideal method for isolation of viable circulating tumor cells?
The article «Technologies for Viable Circulating Tumor Cell Isolation» prepared by our laboratory has been recently published in International Journal of Molecular Sciences.
The spread of tumor cells throughout the body by traveling through the bloodstream is a critical step in metastasis. The detection and analysis of circulating tumor cells (CTCs) is important for understanding the biology of metastasis and the development of antimetastatic therapy. However, most methods for CTC isolation lead to CTC damage.
This review summarizes the available literature on methods for isolating viable CTCs cells, which are of most interest for assessing anticancer drug efficacy and studying the mechanisms of cancer metastasis in vitro, ex vivo and in vivo models.
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Oral squamous cell carcinoma in young adults - problems and prospects
The review article «Early-onset oral cancer as a clinical entity: aetiology and pathogenesis» prepared by our laboratory together with Department of Head and Neck Cancer of Cancer Research Institute has been recently published in the International Journal of Oral and Maxillofacial Surgery.
Oral squamous cell carcinoma (OSCC) is one of the most important medical and socio-economic problems in many developed countries of the world, due to the high mortality. It is known that the incidence of OSCC among persons under 45 years of age is growing every year. However, aetiological factors and pathogenetic mechanisms are currently insufficiently understood. This review summarizes the available information regarding clinicopathological features, extrinsic and intrinsic aetiological factors, and the molecular and immune landscape of early-onset OSCC.
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