Aleksei Aleksandrovich Shefer

Mr. Aleksei Aleksandrovich Shefer

Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Novosibirskaya Oblast’, Russia
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orcid

Research Focus & Metrics

Academic Career Length

5Years (2022-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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NYNatalia v Yunusova
Natalia v Yunusova
ЕДЕкатерина Джугашвили
Екатерина Джугашвили
AYAlena Yalovaya
Alena Yalovaya
LKLarisa Kolomiets
Larisa Kolomiets
Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
STSvetlana Tamkovich
Svetlana Tamkovich
Ovarian cancer (OC) is one of the most common and fatal types of gynecological cancer. In the early phase of OC detection, the current treatment and diagnostic methods are not efficient and sensitive enough. Therefore, it is crucial to explore the mechanisms of OC metastasis and discover valuable factors for early diagnosis of female cancers and novel therapeutic strategies for metastasis. Exosomes are known to be involved in the development, migration, and invasion of cancer cells, and their cargo could be useful for the non-invasive biopsy development. CD151- and Tspan8-positive exosomes are known to support the degradation of the extracellular matrix, and are involved in stroma remodeling, angiogenesis and cell motility, as well as the association of miR-24 and miR-101 with these processes. The objective of this study was to explore the relationship of these components of exosomal cargo, in patients with OC, to clarify the clinical significance of these markers in liquid biopsies. The levels of tetraspanins Tspan8+ and CD151+ exosomes were significantly higher in plasma exosomes of OC patients compared with healthy females (HFs). The relative levels of miR-24 and miR-101 in plasma exosomes of HFs were significantly higher than in plasma exosomes of OC patients, while the levels of these microRNAs in exosomes from plasma and ascites of ill females showed no difference. Our study revealed a strong direct correlation between the change in the ascites exosomes CD151+Tspan8+ subpopulation level and the expression levels of the ascites (R = 0.81, p < 0.05) and plasma exosomal miR-24 (R = 0.74, p < 0.05) in OC patients, which confirms the assumption that exosomal cargo act synergistically to increase cellular motility, affecting cellular processes and signaling. Bioinformatics analysis confirmed the involvement of CD151 and Tspan8 tetraspanins and genes controlled by miR-24-3p and miR-101 in signaling pathways, which are crucial for carcinogenesis, demonstrating that these tetraspanins and microRNAs are potential biomarkers for OC screening, and predictors of poor clinicopathological behavior in tumors.

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Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
AYAlena Yalovaya
Alena Yalovaya
STSvetlana Tamkovich
Svetlana Tamkovich
In women, breast cancer (BC) is the most commonly diagnosed cancer (24.5%) and the leading cause of cancer death (15.5%). Understanding how this heterogeneous disease develops and the confirm mechanisms behind tumor progression is of utmost importance. Exosomes are long-range message vesicles that mediate communication between cells in physiological conditions but also in pathology, such as breast cancer. In recent years, there has been an exponential rise in the scientific studies reporting the change in morphology and cargo of tumor-derived exosomes. Due to the transfer of biologically active molecules, such as RNA (microRNA, long non-coding RNA, mRNA, etc.) and proteins (transcription factors, enzymes, etc.) into recipient cells, these lipid bilayer 30–150 nm vesicles activate numerous signaling pathways that promote tumor development. In this review, we attempt to shed light on exosomes’ involvement in breast cancer pathogenesis (including epithelial-to-mesenchymal transition (EMT), tumor cell proliferation and motility, metastatic processes, angiogenesis stimulation, and immune system repression). Moreover, the potential use of exosomes as promising diagnostic biomarkers for liquid biopsy of breast cancer is also discussed.

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OTOleg Tutanov
Oleg Tutanov
Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
YTYuri Tsentalovich
Yuri Tsentalovich
STSvetlana Tamkovich
Svetlana Tamkovich
Cell-free DNA (cfDNA) circulates in the bloodstream packed in membrane-coated structures (such as apoptotic bodies) or bound to proteins. To identify proteins involved in the formation of deoxyribonucleoprotein complexes circulating in the blood, native complexes were isolated using affinity chromatography with immobilized polyclonal anti-histone antibodies from plasma of healthy females (HFs) and breast cancer patients (BCPs). It was found that the nucleoprotein complexes (NPCs) from HF plasma samples contained shorter DNA fragments (~180 bp) than BCP NPCs. However, the share of DNA in the NPCs from cfDNA in blood plasma in HFs and BCPs did not differ significantly, as well as the share of NPC protein from blood plasma total protein. Proteins were separated by SDS-PAGE and identified by MALDI-TOF mass spectrometry. Bioinformatic analysis showed that in the presence of a malignant tumor, the proportion of proteins involved in ion channels, protein binding, transport, and signal transduction increased in the composition of blood-circulating NPCs. Moreover, 58 (35%) proteins are differentially expressed in a number of malignant neoplasms in the NPCs of BCPs. Identified NPC proteins from BCP blood can be recommended for further testing as breast cancer diagnostic/prognostic biomarkers or as being useful in developing gene-targeted therapy approaches.

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Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
OTOleg Tutanov
Oleg Tutanov
MBMaxim Belenikin
Maxim Belenikin
YTYuri Tsentalovich
Yuri Tsentalovich
STSvetlana Tamkovich
Svetlana Tamkovich
Circulating DNA (cirDNA) is a promising tool in translational medicine. However, studies of cirDNA have neglected its association with proteins, despite ample evidence that this interaction may affect the fate of DNA in the bloodstream and its molecular functions. The goal of the current study is to shed light on the differences between the proteomic cargos of histone-containing nucleoprotein complexes (NPCs) from healthy female (HFs) and breast cancer patients (BCPs), and to reveal the proteins involved in carcinogenesis. NPCs were isolated from the blood samples of HFs and BCPs using affinity chromatography. A total of 177 and 169 proteins were identified in NPCs from HFs and BCPs using MALDI-TOF mass spectrometry. A bioinformatics analysis revealed that catalytically active proteins, as well as proteins that bind nucleic acids and regulate the activity of receptors, are the most represented among the unique proteins of blood NPCs from HFs and BCPs. In addition, the proportion of proteins participating in ion channels and proteins binding proteins increases in the NPCs from BCP blood. However, the involvement in transport and signal transduction was greater in BCP NPCs compared to those from HFs. Gene ontology term (GO) analysis revealed that the NPC protein cargo from HF blood was enriched with proteins involved in the negative regulation of cell proliferation, and in BCP blood, proteins involved in EMT, invasion, and cell migration were observed. The combination of SPG7, ADRB1, SMCO4, PHF1, and PSMG1 NPC proteins differentiates BCPs from HFs with a sensitivity of 100% and a specificity of 80%. The obtained results indirectly indicate that, in tandem with proteins, blood cirDNA is an important part of intercellular communication, playing a regulatory and integrating role in the physiology of the body.

17 April 2025 in Diagnostics
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Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
LYLyudmila Yanshole
Lyudmila Yanshole
KPKsenia Proskura
Ksenia Proskura
OTOleg Tutanov
Oleg Tutanov
NYNatalia v Yunusova
Natalia v Yunusova
STSvetlana Tamkovich
Svetlana Tamkovich
Background: Breast cancer (BC) is the most common cancer among women worldwide; therefore, the efforts of many scientists are aimed at finding effective biomarkers for this disease. It is known that exosomes are nanosized extracellular vesicles (EVs) that are released from various cell types, including cancer cells. Exosomes are directly involved in governing the physiological and pathological processes of an organism through the horizontal transfer of functional molecules (proteins, microRNA, etc.) from producing to receiving cells. Since the diagnosis and treatment of BC have been improved substantially with exosomes, in this study, we isolated breast carcinoma cell-derived exosomes, primary endotheliocyte-derived exosomes, and blood exosomes from BC patients (BCPs) in the first stage of disease and investigated their proteomic profiles. Methods: Exosomes were isolated from the samples by ultrafiltration and ultracentrifugation, followed by mass spectrometric and bioinformatics analyses of the data. The exosomal nature of vesicles was verified using transmission electron microscopy and flow cytometry. Results: Exosome proteins secreted by MCF-7 and BT-474 cells were found to form two clusters, one of which enhanced the malignant potential of cancer cells, while the other coincided with a cluster of HUVEC-derived exosome proteins. Despite the different ensembles of proteins in exosomes from the MCF-7 and BT-474 lines, the relevant portions of these proteins are involved in similar biological pathways. Comparison analysis revealed that more BC-associated proteins were found in the exosomal fraction of blood from BCPs than in the exosomal fraction of conditioned medium from cells mimicking the corresponding cancer subtype (89% and 81% for luminal A BC and MCF-7 cells and 86% and 80% for triple-positive BC and BT-474 cells, respectively). Conclusions: Tumor-associated proteins should be sought not in exosomes secreted by cell lines but in the composition of blood exosomes from cancer patients, while the contribution of endotheliocyte exosomes to the total pool of blood exosomes can be neglected.

16 October 2025 in Molecules
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Aleksei Aleksandrovich SheferAleksei Aleksandrovich Shefer
Aleksei Aleksandrovich Shefer
LYLyudmila Yanshole
Lyudmila Yanshole
AGAlina Grigor'eva
Alina Grigor'eva
NYNatalia v Yunusova
Natalia v Yunusova
IKIrina V. Kondakova
Irina V. Kondakova
STSvetlana Tamkovich
Svetlana Tamkovich
Mitochondrial proteins (mtPs) packaged into extracellular vesicles (EVs), particularly exosomes, have emerged as promising biomarkers and functional mediators in cancer biology. In this study, we investigated whether breast cancer (BC)-derived exosomes selectively incorporate mtPs, thereby providing insights into their diagnostic potential and role in tumor progression. Exosomes were isolated from conditioned media of multiple BC cell lines and non-tumorigenic breast epithelial cells using ultracentrifugation and were characterized by transmission electron microscopy and flow cytometry for canonical markers CD9 and CD81. Proteomic profiling by MALDI-TOF mass spectrometry revealed a distinct enrichment of mtPs in exosomes derived exclusively from tumor cells, while non-tumorigenic cells lacked such cargo. Identified proteins were predominantly associated with the oxidative phosphorylation system, with Complex I subunits most frequently detected, whereas Complex II components were entirely absent. These findings highlight a cancer-specific mechanism of exosomal mtP incorporation, potentially reflecting altered energy metabolism and stress responses in malignant cells. We conclude that mtPs in exosomes represent both functional contributors to tumor progression and promising candidates for liquid biopsy-based BC diagnostics.