Ресурсный центр

@article{Bardakova2025,

title = {4D printing of novel polybenzimidazole-containing structures with exceptional radiation resistance and mechanical properties},

author = {Kseniia N. Bardakova and Bato Ch. Kholkhoev and Zakhar A. Matveev and Evgenii O. Epifanov and Yuri M. Efremov and Nikolay A. Verlov and Elena Gorenskaia and Anastasiya A. Akovantseva and Peter S. Timashev and Vitaliy F. Burdukovskii},

doi = {10.1016/j.apmt.2025.102734},

issn = {2352-9407},

year  = {2025},

date = {2025-06-00},

journal = {Applied Materials Today},

volume = {44},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Burdakov2025,

title = {Investigation of the structure of the nuclei of the Ehrlich adenocarcinoma cell line with a radioresistant phenotype},

author = {Vladimir S. Burdakov and Ignaty A. Kulakov and Lyubov A. Ivanova and Yulia E. Gorshkova and Gennady P. Kopitsa and Dmitry V. Lebedev and Alexey A. Bogdanov and Nikolay A. Verlov},

doi = {10.17816/maj635503},

issn = {2687-1378},

year  = {2025},

date = {2025-05-31},

journal = {Medical academic journal},

volume = {1},

number = {1},

pages = {54--61},

publisher = {ECO-Vector LLC},

abstract = {BACKGROUND: One of the obstacles in successful radiation therapy of malignant tumors is the emergence of cell subpopulation that have lower radiosensitivity than the original tumor. Use of fractionated irradiation in this case leads to a possibility of the radioresistant cells to substitute the initial cell population. We assume that changes in epigenetic profile of a cell affect chromatin packaging in the cell nucleus. This in turn represents changes leading to formation of the radioresistant phenotype.

AIM: The aim is to study the structure of nuclei of a subpopulation of Ehrlich adenocarcinoma cells with a radioresistant phenotype.

METHODS: In the present study the cells of ascitic Erlich adenocarcinoma have been sequentially irradiated in the PX-γ-30 (source is 60Co, dose output is 0.87 Gy/min). Then the cells have been inoculated into female outbred mice ICR (CD-1). Irradiation of the original population of Erlich adenocarcinoma showed that cells were losing an ability to transplantation after a dose of 20 Gy. In the series of irradiations with a gradual dose increase (from 10 to 40 Gy) there was obtained a cell subpopulation that retains an ability to transplantation after a dose of 40 Gy. The original and radioresistant cell subpopulations were tested for sensitivity to ionizing radiation. Nuclei were collected from these cells for further structure investigation with the method of small angle X-ray scattering (SAXS).

RESULTS: Analysis of SAXS data of the nuclei showed no significant changes in nucleus structures of Erlich adenocarcinoma initial cells that survived irradiation with doses of 20 and 30 Gy. At the same time, Erlich adenocarcinoma cells that survived irradiation with a dose of 40 Gy demonstrated abnormally low fractal dimension on mass fractal mode (in a size of 40–200 nm).

CONCLUSION: Observations of chromatin packing variations well conform with data obtained by biological characterization of researched samples and appear as a crucial aspect of understanding mechanisms of radioresistance occurrence.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ryzhov2025,

title = {Nonlinear Magnetic Response Measurements in Study of Magnetic Nanoparticles Uptake by Mesenchymal Stem Cells},

author = {Vyacheslav Ryzhov and Yaroslav Marchenko and Vladimir Deriglazov and Natalia Yudintceva and Oleg Smirnov and Alexandr Arutyunyan and Tatiana Shtam and Evgenii Ivanov and Stephanie E. Combs and Maxim Shevtsov},

doi = {10.3390/nano15090675},

issn = {2079-4991},

year  = {2025},

date = {2025-05-00},

urldate = {2025-05-00},

journal = {Nanomaterials},

volume = {15},

number = {9},

publisher = {MDPI AG},

abstract = {<jats:p>Stem cells therapies offer a promising approach in translational oncology, as well as in regenerative medicine due to the tropism of these cells to the damage site. To track the distribution of stem cells, the latter could be labeled by MRI-sensitive superparamagnetic (SPM) iron oxide nanoparticles. In the current study, magnetic properties of the magnetic nanoparticles (MNPs) incorporated into the bone marrow-derived fetal mesenchymal stem cells (FetMSCs) were evaluated employing nonlinear magnetic response measurements. Synthesized dextran-coated iron oxide nanoparticles were additionally characterized by X-ray diffraction, transmission electron microscopy, and dynamic light scattering. The MNP uptake by the FetMSCs 24 h following coincubation was studied by longitudinal nonlinear response to weak alternating magnetic field with registration of the second harmonic of magnetization. Subsequent data processing using a formalism based on the numerical solution of the Fokker–Planck kinetic equation allowed us to determine magnetic and dynamic parameters and the state of MNPs in the cells, as well as in the culture medium. It was found that MNPs formed aggregates in the culture medium; they were absorbed by the cells during coincubation. The aggregates exhibited SPM regime in the medium, and the parameters of the MNP aggregates remained virtually unchanged in the cells, indicating the preservation of the aggregation state of MNPs inside the cells. This implies also the preservation of the organic shell of the nanoparticles inside FetMSCs. The accumulation of MNPs by mesenchymal stem cells gradually increased with the concentration of MNPs. Thus, the study confirmed that the labeling of MSCs with MNPs is an effective method for subsequent cell tracking as incorporated nanoparticles retain their magnetic properties.</jats:p>},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Titova2025,

title = {Effect of E-Beam Irradiation on Solutions of Fullerene C60 Conjugate with Polyvinylpyrrolidone and Folic Acid},

author = {Anna V. Titova and Zhanna B. Lyutova and Alexandr V. Arutyunyan and Aleksandr S. Aglikov and Mikhail V. Zhukov and Lyudmila V. Necheukhina and Darya V. Zvyagina and Victor P. Sedov and Maria A. Markova and Anton V. Popugaev and Alina A. Borisenkova},

doi = {10.3390/polym17091259},

issn = {2073-4360},

year  = {2025},

date = {2025-05-00},

journal = {Polymers},

volume = {17},

number = {9},

publisher = {MDPI AG},

abstract = {The radiation sterilization of polymer-based drug solutions can change the characteristics that determine the efficiency of drug targeting, such as particle sizes in the solution and their surface potential. The effect of E-beam treatment at doses of 3 and 8 kGy in a Xe or air atmosphere on the hydrodynamic properties of dilute solutions of polyvinylpyrrolidone (PVP) conjugate with fullerene C60 and folic acid (FA-PVP-C60) was studied and compared with native PVP K30. The capillary viscometry method was used to determine the intrinsic viscosity of solutions. The particle sizes (Rh) were determined using the DLS method. The zeta potential of the particles was determined using the PALS method. The morphological features of the conjugate surface irradiated in a Xe atmosphere with a dose of 8 kGy FA-PVP-C60 were studied by AFM. The functionalization of FA-PVP-C60 and PVP during E-beam treatment was examined using UV- and FTIR-spectrometry. When the diluted solutions of FA-PVP-C60 and PVP were irradiated in air with a dose of 3 kGy, destruction of polymer chains occurred predominantly, but when the dose was increased to 8 kGy, intermolecular cross-linking occurred, leading to an increase in the characteristic viscosity and particle size in the solution. It was shown that the average particle sizes, amounting to 3 and 8 nm for PVP and 4 and 20 nm for FA-PVP-C60, did not change significantly under E-beam irradiation in a Xe atmosphere in the considered dose range. The zeta potential of the particles remained virtually unchanged for both PVP and FA-PVP-C60 under all irradiation conditions. The obtained results indicate the possibility of performing radiation sterilization of FA-PVP-C60 conjugate solutions in an inert gas atmosphere in the range of studied doses.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kurkin2025,

title = {Neurotropic Effects of Cortexin on Models of Mental and Physical Developmental Delay},

author = {Denis V. Kurkin and Dmitry A. Bakulin and Evgeny I. Morkovin and Vladimir I. Petrov and Andrei V. Strygin and Alexey V. Smirnov and Maksim V. Shmidt and Julia V. Gorbunova and Yury A. Kolosov and Olga V. Ivanova and Ivan S. Krysanov and Marina A. Dzhavakhyan and Andrew V. Zaborovsky and Valeria B. Saparova and Igor E. Makarenko and Roman I. Drai and Ilia A. Lugovik and Nikolay A. Verlov and Vladimir S. Burdakov},

doi = {10.3390/biomedicines13040860},

issn = {2227-9059},

year  = {2025},

date = {2025-04-00},

journal = {Biomedicines},

volume = {13},

number = {4},

publisher = {MDPI AG},

abstract = {Objective: To evaluate the efficacy of the neurotropic action of cortexin in models of mental and physical developmental delays in rat offspring. Methods: The neurotropic properties of bovine brain cortex polypeptides were studied using two models of mental and physical developmental delays in rats: toxic CNS damage (oral administration of ethanol during the last week of pregnancy) and neonatal trauma (ischemia-hypoxia). The drug was administered intramuscularly or rectally as suppositories for 20 days. Treatment efficacy was evaluated using the mNSS scale, open field, rotarod, and adhesive removal tests. A histological examination of the brain was subsequently performed. In a separate series of experiments in mice, the concentration of the test drug cortexin and the reference drug cerebrolysin was determined in blood and brain tissue samples using radioactive iodine (Na125I) labeling of these preparations. Results: Modeling developmental delay in rat offspring (due to the toxic effect of ethanol in late pregnancy or neonatal trauma) led to pronounced neurological deficits, manifested by decreased motor activity, and sensorimotor, and coordination disorders. Administration of cortexin in all forms reduced the severity of neurological deficits as measured by mNSS scores, improved motor activity in the Open Field test, enhanced performance in the Adhesive Removal and Rotarod tests, and decreased structural changes in brain tissues. Histological examination revealed reduced neuronal damage in multiple cortical regions, with a significant increase in normal, unchanged neurons compared to placebo groups. Comparison of the blood concentrations of labeled Na125I cortexin depending on the type of administration showed similar distribution profiles in brain tissues, primarily dependent on its blood concentration, which was influenced by the route of administration. Conclusions: The results indicate that brain polypeptides (cortexin), administered either intramuscularly or rectally, can reach the systemic circulation and cross the blood-brain barrier, as demonstrated by our distribution studies using radiolabeled preparations. These polypeptides exert comparable neurotropic effects in models of mental and physical developmental delays in offspring caused by neonatal trauma or the toxic effect of ethanol in late pregnancy in rats.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zorina2025,

title = {Biomarkers of hepatocellular carcinoma: status and prospects},

author = {E.S. Zorina and S.N. Naryzhny},

doi = {10.18097/pbmcr1543},

issn = {2310-6905},

year  = {2025},

date = {2025-00-00},

journal = {BIOMED KHIM},

volume = {71},

number = {1},

pages = {7--18},

publisher = {Institute of Biochemistry},

abstract = {Hepatocellular carcinoma (HCC) also known as hepatocellular cancer is one of the most common and aggressive types of primary malignant liver neoplasms. This type of cancer accounts for up to 90% of all primary liver tumors and is the third leading cause of cancer death worldwide. Despite the advances in modern medicine, diagnostics and treatment of HCC remain challenging, especially in the later stages, when the patient's prognosis significantly worsens and treatment options are very limited. More than half a century has passed since Yu.S. Tatarinov discovered embryo-specific α-globulin in the blood of people with primary liver cancer in 1963, which was later called alpha-fetoprotein (AFP), but unfortunately, the number of specific and sensitive biomarkers for HCC remains very limited. In this regard, many scientific papers are devoted to the search and study of potential HCC biomarkers, which are essential for early diagnostics, prognosis, and development of new therapeutic strategies. Proteomic studies represent one of the promising approaches to investigate both molecular mechanisms of HCC occurrence and HCC biomarkers. Identification of specific protein profiles characteristic of tumor cells can contribute to the identification of new biomarkers that can be used not only for early detection of the disease, but also for monitoring its progression, assessing the response to therapy and predicting the clinical outcome. This review discusses current achievements in the search for potential biomarkers of HCC, as well as the prospects for their clinical use.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Borisenkova2024b,

title = {Fullerenol C60(OH)36: Antioxidant, Cytoprotective, Anti-Influenza Virus Activity, and Self-Assembly in Aqueous Solutions and Cell Culture Media},

author = {Alina A. Borisenkova and Mikhail Y. Eropkin and Nadezhda I. Konovalova and Anna V. Titova and Maria A. Markova and Zhanna B. Lyutova and Anton S. Mazur and Victor P. Sedov and Vera A. Orlova and Anna N. Lykholay and Diana N. Orlova and Alexandr V. Arutyunyan},

doi = {10.3390/antiox13121525},

issn = {2076-3921},

year  = {2024},

date = {2024-12-00},

journal = {Antioxidants},

volume = {13},

number = {12},

publisher = {MDPI AG},

abstract = {Viral infections and many other dangerous diseases are accompanied by the development of oxidative stress, which is a consequence of an increase in the level of the reactive oxygen species (ROS). In this regard, the search for effective antioxidants remains highly relevant. We tested fullerenol C60(OH)36 in the context of the connection between its self-assembly in aqueous solutions and cell culture media, antiradical activity, UV cytoprotective action, and antiviral activity against international reference strains of influenza virus A(H1N1)pdm09, A(H3N2), and B subtypes in vitro on the MDCK cell line. Various characterization techniques, including Fourier-transform infrared spectroscopy (FTIR), Raman spectroscopy, NMR and ESR spectrometry, MALDI-TOF mass spectrometry, thermal analysis (TGA and DSC), dynamic light-scattering (DLS), and ζ-potential measurements, were used to confirm the production of fullerenol and study its self-assembly in aqueous solutions and cell culture media. Fullerenol C60(OH)36 demonstrated the ability to scavenge •DPPH, •OH, O2•− radicals and 1O2 and was non-toxic in the range of the studied concentrations (up to 200 μg/mL) when incubated with MDCK cells for 24 h. In addition, fullerenol exhibited a cytoprotective effect under UV irradiation (EC50 = 29.7 ± 1.0 μM) and showed moderate activity against human influenza viruses of subtypes A(H1N1)pdm09 (SI = 9.9 ± 4.6) and A(H3N2) (SI = 12.5 ± 1.3) when determined by the hemagglutination assay (HA-test) and the MTT assay. At the same time, C60(OH)36 was ineffective in vitro against the actual strain of influenza B virus (Victoria lineage). The high bioavailability of fullerenol in combination with its cytoprotective effect, as well as its antiradical and antiviral activity combined with a relatively low toxicity, allows to consider it a promising compound for biomedical applications.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ryzhov2024,

title = {Study of Dextran Coated Magnetic Nanoparticles Incorporation into Glioblastoma Cells},

author = {V. A. Ryzhov and V. V. Deriglazov and N. H. Tran and A. V. Volnitskiy and T. A. Shtam and A. V. Arutyunyan and A. S. Spitsyna and O. P. Smirnov and Yu. P. Chernenkov and V. G. Zinoviev and D. A. Rumyantseva and A. L. Konevega and Ya. Yu. Marchenko},

doi = {10.1134/s2635167624601736},

issn = {2635-1684},

year  = {2024},

date = {2024-12-00},

journal = {Nanotechnol Russia},

volume = {19},

number = {6},

pages = {1051--1060},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Vinogradova2024,

title = {Control of Conformational Integrity and Aggregation Stability of Monoclonal Antibodies and Their Conjugates by Nanodifferential Scanning Fluorimetry},

author = {D. S. Vinogradova and M. S. Bidzhieva and P. S. Kasatsky and V. S. Burdakov and A. A. Grachev and Zh. Yu. Sidorova and A. S. Spitsyna and A. Paleskava and N. A. Verlov and T. A. Shtam and A. L. Konevega},

doi = {10.1134/s2635167624602791},

issn = {2635-1684},

year  = {2024},

date = {2024-12-00},

journal = {Nanotechnol Russia},

volume = {19},

number = {S1},

pages = {S202--S209},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Verlov2024,

title = {Comparison of Pharmacokinetic Parameters and Biodistribution of Full-Size Antibodies and Nanoantibodies Specific to Human PD-L1},

author = {N. Verlov and O. Shashkova and I. Krutetskaya and L. Terekhina and S. Shatik and A. Pinevich and V. Burdakov and I. Kulakov and T. Shtam and A. Konevega and A. Stanzhevskii and M. Samoilovich},

doi = {10.1134/s2635167624602742},

issn = {2635-1684},

year  = {2024},

date = {2024-12-00},

journal = {Nanotechnol Russia},

volume = {19},

number = {S1},

pages = {S210--S217},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Demyanov2024,

title = {Development of New Monoclonal Antibodies against Cytotoxic T-Lymphocyte Antigen-4},

author = {A. V. Demyanov and L. A. Garaeva and E. V. Sergeeva and A. V. Nikitina and E. D. Putevich and S. S. Emelianova and A. S. Spitsyna and L. A. Solomina and A. S. Potyseva and A. V. Volnitskij and A. M. Solianik and Zh. Yu. Sidorova and A. V. Zhahov and V. S. Burdakov and N. A. Verlov and V. V. Kvanchiani and A. L. Konevega and T. A. Shtam},

doi = {10.1134/s1063774524602892},

issn = {1562-689X},

year  = {2024},

date = {2024-12-00},

journal = {Crystallogr. Rep.},

volume = {69},

number = {S1},

pages = {S38--S45},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pokrovsky2024,

title = {The influence of exogenous recombinant HSP 70 on the alteration of membrane stiffness in hippocampal neurons following the modeling of neonatal hypoxic-ischemic injury in mice},

author = {Vladimir M. Pokrovsky and Alexey V. Deikin and T Zhang and Nikolai A. Verlov and Andrey L. Konevega and Mikhail V. Korokin},

doi = {10.18413/rrpharmacology.10.547},

issn = {2658-381X},

year  = {2024},

date = {2024-11-11},

journal = {RRP},

volume = {10},

number = {4},

pages = {87--97},

publisher = {Belgorod National Research University},

abstract = {Introduction: The use of atomic force microscopy (AFM) to investigate membrane stiffness in neurons provides valuable insights into cellular mechanisms and their alterations in response to various pathophysiological conditions. Heat shock protein HSP 70, a component of the cellular stress response system, plays a role in stabilizing the protein structures of cellular organelles. However, studies examining changes in the stiffness of hippocampal neuronal membranes in its presence, particularly following cerebral circulation disturbances, have not been conducted yet.

Materials and Methods: The study was performed on a mixed culture of hippocampal neurons derived from 9-day-old male CD-1 mice, obtained 24 hours after modeling neonatal hypoxia-ischemia. The following groups were formed: Intact culture; HI culture; HI + rhHSP70 10-6 M; HI + rhHSP70 10-8 M; HI + rhHSP70 10-9 M; HI + rhHSP70 10-12 M, with the substance added in dilutions from an initial dose of 0.1 µg/g. The Young's modulus was measured using force spectroscopy, and maps of local stiffness of various surface areas were generated.

Results and Discussion: The neonatal hypoxia-ischemia model resulted in an 18% increase in the stiffness of the neuronal cell surface compared to the control group (p<0.001). The addition of rhHSP70 at concentrations of 10-6 M and 10-8 M to the HI culture led to an increase in membrane stiffness by 20% (p<0.001) and 3% (p<0.0034), respectively, while dilutions of rhHSP70 at 10-9 M and 10-12 M resulted in a decrease in membrane stiffness by 35% (p<0.001) and 22% (p<0.001) compared to the intact group, respectively. In comparison to such in the neuronal culture group after neonatal hypoxia-ischemia modeling, membrane stiffness with the addition of rhHSP70 at 10-8 M, 10-9 M, and 10^-12 M decreased by 17% (p<0.0004), 65% (p<0.001), and 49% (p<0.001), respectively.

Conclusion: Thus, the addition of rhHSP 70 results in a reduction in membrane stiffness in the mixed culture of hippocampal neurons in mice, compared to the intact culture obtained after neonatal hypoxia-ischemia. The AFM method allows for the assessment of how various molecules, such as heat shock proteins (e.g., rhHSP70), influence the mechanical properties of membranes, which may be critically important for the development of new therapeutic agents.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2024,

title = {Puzzle of Proteoform Variety—Where Is a Key?},

author = {Stanislav Naryzhny},

doi = {10.3390/proteomes12020015},

issn = {2227-7382},

year  = {2024},

date = {2024-06-00},

journal = {Proteomes},

volume = {12},

number = {2},

publisher = {MDPI AG},

abstract = {One of the human proteome puzzles is an imbalance between the theoretically calculated and experimentally measured amounts of proteoforms. Considering the possibility of combinations of different post-translational modifications (PTMs), the quantity of possible proteoforms is huge. An estimation gives more than a million different proteoforms in each cell type. But, it seems that there is strict control over the production and maintenance of PTMs. Although the potential complexity of proteoforms due to PTMs is tremendous, available information indicates that only a small part of it is being implemented. As a result, a protein could have many proteoforms according to the number of modification sites, but because of different systems of personal regulation, the profile of PTMs for a given protein in each organism is slightly different.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Borisenkova2024,

title = {Fullerene C60 Conjugate with Folic Acid and Polyvinylpyrrolidone for Targeted Delivery to Tumor Cells},

author = {Alina A. Borisenkova and Olga I. Bolshakova and Anna V. Titova and Irina S. Ryabokon and Maria A. Markova and Zhanna B. Lyutova and Victor P. Sedov and Elena Yu. Varfolomeeva and Vadim V. Bakhmetyev and Alexandr V. Arutyunyan and Vladimir S. Burdakov and Svetlana V. Sarantseva},

doi = {10.3390/ijms25105350},

issn = {1422-0067},

year  = {2024},

date = {2024-05-00},

journal = {IJMS},

volume = {25},

number = {10},

publisher = {MDPI AG},

abstract = {The use of targeted drug delivery systems, including those based on selective absorption by certain receptors on the surface of the target cell, can lead to a decrease in the minimum effective dose and the accompanying toxicity of the drug, as well as an increase in therapeutic efficacy. A fullerene C60 conjugate (FA-PVP-C60) with polyvinylpyrrolidone (PVP) as a biocompatible spacer and folic acid (FA) as a targeting ligand for tumor cells with increased expression of folate receptors (FR) was obtained. Using 13C NMR spectroscopy, FT-IR, UV-Vis spectrometry, fluorometry and thermal analysis, the formation of the conjugate was confirmed and the nature of the binding of its components was established. The average particle sizes of the conjugate in aqueous solutions and cell culture medium were determined using dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA). The FA-PVP-C60 showed antiradical activity against •DPPH, •OH and O2•−, but at the same time, it was shown to generate 1O2. It was found that the conjugate in the studied concentration range (up to 200 μg/mL) is non-toxic in vitro and does not affect the cell cycle. To confirm the ability of the conjugate to selectively accumulate through folate-mediated endocytosis, its uptake into cells was analyzed by flow cytometry and confocal microscopy. It was shown that the conjugate is less absorbed by A549 cells with low FR expression than by HeLa, which has a high level of expression of this receptor.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2024b,

title = {Proteomics and Its Applications in Cancers 2.0},

author = {Stanislav Naryzhny},

doi = {10.3390/ijms25084447},

issn = {1422-0067},

year  = {2024},

date = {2024-04-00},

journal = {IJMS},

volume = {25},

number = {8},

publisher = {MDPI AG},

abstract = {Considering the success of our previous Special Issue (SI) “Proteomics and Its Applications in Cancers”, we aimed to attract more publications where cancer proteomics is involved [...]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shtam2024,

title = {Assessment of Inhibition of the Growth of Breast and Colon Tumors when Blocking VEGFR-1 with Monoclonal Antibodies},

author = {T. A. Shtam and A. V. Demyanov and L. A. Garaeva and S. S. Emelianova and A. V. Nikitina and E. D. Putevich and A. S. Potyseva and M. S. Bidghieva and A. V. Volnitskiy and V. V. Kvanchiani and L. A. Solomina and K. A. Shabalin and E. V. Sergeeva and A. P. Trashkov and Zh. Yu. Sidorova and A. V. Zhahov and V. S. Burdakov and N. A. Verlov and A. L. Konevega},

doi = {10.1134/s263516762460086x},

issn = {2635-1684},

year  = {2024},

date = {2024-04-00},

journal = {Nanotechnol Russia},

volume = {19},

number = {2},

pages = {291--298},

publisher = {Pleiades Publishing Ltd},

abstract = {AbstractVascular endothelial growth factor receptor-1 (VEGFR-1) plays a critical role in tumor-associated angiogenesis. VEGFR-1 is found on the surface of tumor cells and cells in the tumor microenvironment. Blocking this receptor leads to the suppression of proliferation and increased apoptosis of tumor cells, reduction of tumor vascularization, inhibition of the production of immunosuppressive cytokines by tumor-associated macrophages, and the suppression of tumor invasion and metastasis. The creation of monoclonal antibody drugs that block VEGFR-1 is an urgent task in the development of potential antitumor therapeutic drugs. Target molecules created on the basis of antibodies that bind to VEGFR-1 are a promising basis for the creation of theranostic radiopharmaceuticals for the diagnosis and treatment of malignant neoplasms. To study the therapeutic potential of VEGFR-1 inhibition in breast and colon cancers using antibodies, monoclonal antibodies against recombinant human VEGFR-1 protein are developed. The resulting monoclonal antibodies bind to the VEGFR-1 receptor on the cell surface and effectively inhibit the proliferation of breast and colon cancer cells in vitro, reduce the growth rate of the tumor node in vivo, and prolong the survival of tumor-inoculated mice.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Emelianova2024,

title = {New Gliobastoma Cell Lines: Analysis of Genetic Changes, and Assessment of Sensitivity to Radiotherapy and Immunotherapy},

author = {S. S. Emelianova and A. V. Volnitskiy and A. M. Solianik and N. H. Tran and L. A. Garaeva and R. A. Pantina and M. N. Grunina and E. D. Putevich and A. S. Potyseva and A. M. Golubev and V. S. Burdakov and N. A. Verlov and S. N. Naryzhnyy and A. L. Konevega and T. A. Shtam},

doi = {10.1134/s2635167624600871},

issn = {2635-1684},

year  = {2024},

date = {2024-04-00},

journal = {Nanotechnol Russia},

volume = {19},

number = {2},

pages = {282--290},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kholkhoev2024,

title = {4D-printing of mechanically durable high-temperature shape memory polymer with good irradiation resistance},

author = {Bato Ch. Kholkhoev and Kseniia N. Bardakova and Alena N. Nikishina and Zakhar A. Matveev and Yuri M. Efremov and Anastasia A. Frolova and Anastasiya A. Akovantseva and Elena N. Gorenskaia and Nikolay A. Verlov and Peter S. Timashev and Vitalii F. Burdukovskii},

doi = {10.1016/j.apmt.2023.102022},

issn = {2352-9407},

year  = {2024},

date = {2024-02-00},

journal = {Applied Materials Today},

volume = {36},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Volnitskiy2024,

title = {OCT4 Expression in Gliomas Is Dependent on Cell Metabolism},

author = {Andrey Volnitskiy and Konstantin Shabalin and Rimma Pantina and Elena Varfolomeeva and Roman Kovalev and Vladimir Burdakov and Svetlana Emelianova and Luiza Garaeva and Alexander Yakimov and Marina Sogoyan and Michael Filatov and Andrey L. Konevega and Tatiana Shtam},

doi = {10.3390/cimb46020070},

issn = {1467-3045},

year  = {2024},

date = {2024-02-00},

journal = {CIMB},

volume = {46},

number = {2},

pages = {1107--1120},

publisher = {MDPI AG},

abstract = {The OCT4 transcription factor is necessary to maintain cell stemness in the early stages of embryogenesis and is involved in the formation of induced pluripotent stem cells, but its role in oncogenesis is not yet entirely clear. In this work, OCT4 expression was investigated in malignant gliomas. Twenty glioma cell lines and a sample of normal adult brain tissue were used. OCT4 expression was found in all studied glioma cell lines but was not detected in normal adult brain tissue. For one of these lines, OCT4 knockdown caused tumor cell death. By varying the culture conditions of these cells, we unexpectedly found that OCT4 expression increased when cells were incubated in serum-free medium, and this effect was significantly enhanced in serum-free and L-glutamine-free medium. L-glutamine and the Krebs cycle, which is slowed down in serum-free medium according to our NMR data, are sources of α-KG. Thus, our data indicate that OCT4 expression in gliomas may be regulated by the α-KG-dependent metabolic reprogramming of cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gorelov2024b,

title = {Determination of Hydrogen Bonds in GROMACS: A New Implementation to Overcome Memory Limitation},

author = {Sergey Gorelov and Anatoly Titov and Olga Tolicheva and Andrey Konevega and Alexey Shvetsov},

url = {https://doi.org/10.1021/acs.jcim.3c02087},

doi = {10.1021/acs.jcim.3c02087},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {64},

number = {16},

pages = {6241-6246},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Gorelov2024a,

title = {DSSP in GROMACS: Tool for Defining Secondary Structures of Proteins in Trajectories},

author = {Sergey Gorelov and Anatoly Titov and Olga Tolicheva and Andrey Konevega and Alexey Shvetsov},

url = {https://doi.org/10.1021/acs.jcim.3c01344},

doi = {10.1021/acs.jcim.3c01344},

year  = {2024},

date = {2024-01-01},

urldate = {2024-01-01},

journal = {Journal of Chemical Information and Modeling},

volume = {64},

number = {9},

pages = {3593-3598},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Ronzhina2024,

title = {Variability of haptoglobin beta-chain proteoforms},

author = {N.L. Ronzhina and E.S. Zorina and M.G. Zavialova and O.K. Legina and S.N. Naryzhny},

doi = {10.18097/pbmc20247002114},

issn = {2310-6905},

year  = {2024},

date = {2024-00-00},

journal = {BIOMED KHIM},

volume = {70},

number = {2},

pages = {114--124},

publisher = {Institute of Biochemistry},

abstract = {Existing knowledge on changes of the haptoglobin (Hp) molecule suggests that it may exist in multiple proteoforms, which obviously exhibit different functions. Using two-dimensional electrophoresis (2DE) in combination with mass spectrometry and immunodetection, we have analyzed blood plasma samples from both healthy donors and patients with primary grade IV glioblastoma (GBM), and obtained a detailed composite 2DE distribution map of β-chain proteoforms, as well as the full-length form of Hp (zonulin). Although the total level of plasma Hp exceeded normal values in cancer patients (especially patients with GBM), the presence of particuar proteoforms, detected by their position on the 2DE map, was very individual. Variability was found in both zonulin and the Hp β-chain. The presence of an alkaline form of zonulin in plasma can be considered a conditional, but insufficient, GBM biomarker. In other words, we found that at the level of minor proteoforms of Hp, even in normal conditions, there was a high individual variability. On the one hand, this raises questions about the reasons for such variability, if it is present not only in Hp, but also in other proteins. On the other hand, this may explain the discrepancy between the number of experimentally detected proteoforms and the theoretically possible ones not only in Hp, but also in other proteins.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Shtam2023,

title = {Experimental validation of proton boron capture therapy for glioma cells},

author = {Tatiana Shtam and Vladimir Burdakov and Alina Garina and Luiza Garaeva and Nhan Hau Tran and Andrey Volnitskiy and Eva Kuus and Dmitry Amerkanov and Fedor Pack and Georgy Andreev and Andrey Lubinskiy and Konstantin Shabalin and Nicolay Verlov and Evgeniy Ivanov and Victor Ezhov and Dmitry Lebedev and Andrey L. Konevega},

doi = {10.1038/s41598-023-28428-z},

issn = {2045-2322},

year  = {2023},

date = {2023-12-00},

journal = {Sci Rep},

volume = {13},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {AbstractProton boron capture therapy (PBCT) has emerged from particle acceleration research for enhancing the biological effectiveness of proton therapy. The mechanism responsible for the dose increase was supposed to be related to proton-boron fusion reactions (11B + p → 3α + 8.7 MeV). There has been some experimental evidence that the biological efficiency of protons is significantly higher for boron-11-containing prostate or breast cancer cells. The aim of this study was to evaluate the sensitizing potential of sodium borocaptate (BSH) under proton irradiation at the Bragg peak of cultured glioma cells. To address this problem, cells of two glioma lines were preincubated with 80 or 160 ppm boron-11, irradiated both at the middle of 200 MeV beam Spread-Out Bragg Peak (SOBP) and at the distal end of the 89.7 MeV beam SOBP and assessed for the viability, as well as their ability to form colonies. Our results clearly show that BSH provides for only a slight, if any, enhancement of the effect of proton radiation on the glioma cells in vitro. In addition, we repeated the experiments using the Du145 prostate cancer cell line, for which an increase in the biological efficiency of proton irradiation in the presence of sodium borocaptate was demonstrated previously. The data presented add new argument against the efficiency of proton boron capture therapy when based solely on direct dose-enhancement effect by the proton capture nuclear reaction, underlining the need to investigate the indirect effects of the secondary alpha irradiation depending on the state and treatment conditions of the irradiated tissue.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Tran2023,

title = {Radiosensitizing Effect of Dextran-Coated Iron Oxide Nanoparticles on Malignant Glioma Cells},

author = {Nhan Hau Tran and Vyacheslav Ryzhov and Andrey Volnitskiy and Dmitry Amerkanov and Fedor Pack and Aleksander M. Golubev and Alexandr Arutyunyan and Anastasiia Spitsyna and Vladimir Burdakov and Dmitry Lebedev and Andrey L. Konevega and Tatiana Shtam and Yaroslav Marchenko},

doi = {10.3390/ijms242015150},

issn = {1422-0067},

year  = {2023},

date = {2023-10-00},

journal = {IJMS},

volume = {24},

number = {20},

publisher = {MDPI AG},

abstract = {The potential of standard methods of radiation therapy is limited by the dose that can be safely delivered to the tumor, which could be too low for radical treatment. The dose efficiency can be increased by using radiosensitizers. In this study, we evaluated the sensitizing potential of biocompatible iron oxide nanoparticles coated with a dextran shell in A172 and Gl-Tr glioblastoma cells in vitro. The cells preincubated with nanoparticles for 24 h were exposed to ionizing radiation (X-ray, gamma, or proton) at doses of 0.5–6 Gy, and their viability was assessed by the Resazurin assay and by staining of the surviving cells with crystal violet. A statistically significant effect of radiosensitization by nanoparticles was observed in both cell lines when cells were exposed to 35 keV X-rays. A weak radiosensitizing effect was found only in the Gl-Tr line for the 1.2 MeV gamma irradiation and there was no radiosensitizing effect in both lines for the 200 MeV proton irradiation at the Bragg peak. A slight (ca. 10%) increase in the formation of additional reactive oxygen species after X-ray irradiation was found when nanoparticles were present. These results suggest that the nanoparticles absorbed by glioma cells can produce a significant radiosensitizing effect, probably due to the action of secondary electrons generated by the magnetite core, whereas the dextran shell of the nanoparticles used in these experiments appears to be rather stable under radiation exposure.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pushkin2023,

title = {Dynamics of biophysical characteristics of albumin in patients on programmed hemodialysis},

author = {A. S. Pushkin and A. V. Martynov and A. V. Arutyunyan and V. L. Emanuel and D. P. Piskunov and A. V. Iakovleva and V. S. Emanuel and A. A. Roshkovskaya},

doi = {10.36485/1561-6274-2023-27-3-32-43},

issn = {2541-9439},

year  = {2023},

date = {2023-09-12},

journal = {Nefrologiâ (St.-Peterbg.)},

volume = {27},

number = {3},

pages = {32--43},

publisher = {Non-profit organization Nephrology},

abstract = {Background. One of the components of the metabolome that performs multifaceted functions in homeostasis is blood albumin. The albumin molecule has a pronounced hydrophilicity, due to which it plays an important role in maintaining oncotic blood pressure. Thus, the expansion of knowledge about the interrelationships of traditional biochemical information about the concentration of albumin and the biophysical properties of its derivatives complements the idea of the pharmacological effect of albumin transfusions. THE AIM: to study of the biophysical properties of albumin in patients with chronic kidney disease on programmed hemodialysis.Patients and Methods. The study included 29 patients with chronic renal failure treated with programmed bicarbonate hemodialysis for an average of 110 months. To assess the condition of patients, a complex of laboratory studies was used, including hematological examination on Beckman Coulter analyzers; clinical assessment of nutritional status based on data from the analysis of medical histories; assessment of colloidal osmotic blood pressure by calculation, as well as by direct measurement on a BMT 923 oncometer; measurement of particle size in blood plasma by dynamic light scattering on a Photocor Compact spectrometer- Z. Statistical analysis of the material was performed using the Statistica for Windows v.6.0 software package. The null statistical hypothesis of the absence of differences and connections was rejected at p<0.05. RESULTS. The average correlation coefficient of oncotic pressure was 0.94 for total protein and 0.90 for albumin. Measurement of colloidal osmotic pressure showed a significant increase in pressure in each of the postdialysis samples. The hydrodynamic radius of the albumin peak for the predialysis sample is significantly higher, which may indicate a change in the sorption properties of the albumin surface. CONCLUSION. The calculation of oncotic pressure by the concentration of total protein, as a rule, provides clinical needs, however, with a significant concentration of toxins, clinical situations are possible in which a moderate decrease in the concentration of the "total protein" of the blood is detected, hence the main oncotic component – albumin is noted but there is a development pronounced edematous syndrome due to a significant decrease in oncotic pressure as a result of a conformational change in albumin molecules. In such situations, it is necessary to directly determine the oncotic pressure of the blood. Keywords: albumin, oncotic pressure, hydrodynamic radius, dialysis>˂0.05.Results. The average correlation coefficient of oncotic pressure was 0.94 for total protein and 0.90 for albumin. Measurement of colloidal osmotic pressure showed a significant increase in pressure in each of the postdialysis samples. The hydrodynamic radius of the albumin peak for the predialysis sample is significantly higher, which may indicate a change in the sorption properties of the albumin surface.Conclusion. The calculation of oncotic pressure by the concentration of total protein, as a rule, provides clinical needs, however, with a significant concentration of toxins, clinical situations are possible in which a moderate decrease in the concentration of the "total protein" of the blood is detected, hence the main oncotic component – albumin is noted but there is a development pronounced edematous syndrome due to a significant decrease in oncotic pressure as a result of a conformational change in albumin molecules. In such situations, it is necessary to directly determine the oncotic pressure of the blood.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bolshakova2023,

title = {Fullerenes on a Nanodiamond Platform Demonstrate Antibacterial Activity with Low Cytotoxicity},

author = {Olga Bolshakova and Vasily Lebedev and Elena Mikhailova and Olga Zherebyateva and Liliya Aznabaeva and Vladimir Burdakov and Yuri Kulvelis and Natalia Yevlampieva and Andrey Mironov and Igor Miroshnichenko and Svetlana Sarantseva},

doi = {10.3390/pharmaceutics15071984},

issn = {1999-4923},

year  = {2023},

date = {2023-07-00},

journal = {Pharmaceutics},

volume = {15},

number = {7},

publisher = {MDPI AG},

abstract = {Carbon nanoparticles with antimicrobial properties, such as fullerenes, can be distinguished among the promising means of combating pathogens characterized by resistance to commercial antibiotics. However, they have a number of limitations for their use in medicine. In particular, the insolubility of carbon nanoparticles in water leads to a low biocompatibility and especially strong aggregation when transferred to liquid media. To overcome the negative factors and enhance the action of fullerenes in an extended range of applications, for example, in antimicrobial photodynamic therapy, we created new water-soluble complexes containing, in addition to C60 fullerene, purified detonation nanodiamonds (AC960) and/or polyvinylpyrrolidone (PVP). The in vitro antibacterial activity and toxicity to human cells of the three-component complex C60+AC960+PVP were analyzed in comparison with binary C60+PVP and C60+AC960. All complexes showed a low toxicity to cultured human skin fibroblasts and ECV lines, as well as significant antimicrobial activity, which depend on the type of microorganisms exposed, the chemical composition of the complex, its dosage and exposure time. Complex C60+PVP+AC960 at a concentration of 175 µg/mL showed the most stable and pronounced inhibitory microbicidal/microbiostatic effect.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Iakovleva2023,

title = {Pathogenic Role of Posttranslational Isoforms of Uromodulin},

author = {A. V. Iakovleva and N. A. Verlov and M. G. Zaleskiy and S. B. Landa and V. V. Shapovalov and V. L. Emanuel},

doi = {10.1134/s0006350923030247},

issn = {1555-6654},

year  = {2023},

date = {2023-06-00},

journal = {BIOPHYSICS},

volume = {68},

number = {3},

pages = {489--494},

publisher = {Pleiades Publishing Ltd},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2023,

title = {Quantitative Aspects of the Human Cell Proteome},

author = {Stanislav Naryzhny},

doi = {10.3390/ijms24108524},

issn = {1422-0067},

year  = {2023},

date = {2023-05-00},

journal = {IJMS},

volume = {24},

number = {10},

publisher = {MDPI AG},

abstract = {The number and identity of proteins and proteoforms presented in a single human cell (a cellular proteome) are fundamental biological questions. The answers can be found with sophisticated and sensitive proteomics methods, including advanced mass spectrometry (MS) coupled with separation by gel electrophoresis and chromatography. So far, bioinformatics and experimental approaches have been applied to quantitate the complexity of the human proteome. This review analyzed the quantitative information obtained from several large-scale panoramic experiments in which high-resolution mass spectrometry-based proteomics in combination with liquid chromatography or two-dimensional gel electrophoresis (2DE) were used to evaluate the cellular proteome. It is important that even though all these experiments were performed in different labs using different equipment and calculation algorithms, the main conclusion about the distribution of proteome components (proteins or proteoforms) was basically the same for all human tissues or cells. It follows Zipf’s law and has a formula N = A/x, where N is the number of proteoforms, A is a coefficient, and x is the limit of proteoform detection in terms of abundance.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2023b,

title = {Proteomics and Its Applications in Cancers},

author = {Stanislav Naryzhny},

doi = {10.3390/ijms24054457},

issn = {1422-0067},

year  = {2023},

date = {2023-03-00},

journal = {IJMS},

volume = {24},

number = {5},

publisher = {MDPI AG},

abstract = {Cancer is a system malignant transformation that covers a wide group of diseases and can affect any organ of the human body [...]},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Miroshnikova2023,

title = {Cryo-electron microscopy of adipose tissue extracellular vesicles in obesity and type 2 diabetes mellitus},

author = {Valentina V. Miroshnikova and Kseniya V. Dracheva and Roman A. Kamyshinsky and Evgeny V. Yastremsky and Luiza A. Garaeva and Irina A. Pobozheva and Sergey B. Landa and Kristina A. Anisimova and Stanislav G. Balandov and Zarina M. Hamid and Dmitriy I. Vasilevsky and Sofya N. Pchelina and Andrey L. Konevega and Tatiana A. Shtam},

editor = {Takahiro Nemoto},

doi = {10.1371/journal.pone.0279652},

issn = {1932-6203},

year  = {2023},

date = {2023-02-24},

journal = {PLoS ONE},

volume = {18},

number = {2},

publisher = {Public Library of Science (PLoS)},

abstract = {Extracellular vesicles (EVs) are cell-derived membrane vesicles which play an important role in cell-to-cell communication and physiology. EVs deliver biological information from producing to recipient cells by transport of different cargo such as proteins, mRNAs, microRNAs, non-coding RNAs and lipids. Adipose tissue EVs could regulate metabolic and inflammatory interactions inside adipose tissue depots as well as distal tissues. Thus, adipose tissue EVs are assumed to be implicated in obesity-associated pathologies, notably in insulin resistance and type 2 diabetes mellitus (T2DM). In this study we for the first time characterize EVs secreted by visceral (VAT) and subcutaneous adipose tissue (SAT) of patients with obesity and T2DM with standard methods as well as analyze their morphology with cryo-electron microscopy. Cryo-electron microscopy allowed us to visualize heterogeneous population of EVs of various size and morphology including single EVs and EVs with internal membrane structures in samples from obese patients as well from the control group. Single vesicles prevailed (up to 85% for SAT, up to 75% for VAT) and higher proportion of EVs with internal membrane structures compared to SAT was typical for VAT. Decreased size of single and double SAT EVs compared to VAT EVs, large proportion of multilayered EVs and all EVs with internal membrane structures secreted by VAT distinguished obese patients with/without T2DM from the control group. These findings could support the idea of modified biogenesis of EVs during obesity and T2DM.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Usenko2023,

title = {Fraction of plasma exomeres and low-density lipoprotein cholesterol as a predictor of fatal outcome of COVID-19},

author = {Tatiana Usenko and Valentina Miroshnikova and Anastasia Bezrukova and Katerina Basharova and Sergey Landa and Zoia Korobova and Natalia Liubimova and Ivan Vlasov and Mikhael Nikolaev and Artem Izyumchenko and Elena Gavrilova and Irina Shlyk and Elena Chernitskaya and Yurii Kovalchuk and Petr Slominsky and Areg Totolian and Yurii Polushin and Sofya Pchelina},

editor = {Yi Cao},

doi = {10.1371/journal.pone.0278083},

issn = {1932-6203},

year  = {2023},

date = {2023-02-09},

journal = {PLoS ONE},

volume = {18},

number = {2},

publisher = {Public Library of Science (PLoS)},

abstract = {Transcriptomic analysis conducted by us previously revealed upregulation of genes involved in low-density lipoprotein particle receptor (LDLR) activity pathway in lethal COVID-19 caused by SARS-CoV-2 virus (severe acute respiratory syndrome coronavirus 2). Last data suggested the possible role of extracellular vesicles in COVID-19 pathogenesis. The aim of the present study was to retrospectively evaluate parameters of cholesterol metabolism and newly identified EVs, exomeres, as possible predictors of fatal outcome of COVID-19 patients infected by the Alpha and the Delta variants of SARS-CoV-2 virus. Blood from 67 patients with severe COVID-19 were collected at the time of admission to the intensive care unit (ICU) and 7 days after admission to the ICU. After 30 days patients were divided into two subgroups according to outcome—34 non-survivors and 33 survivors. This study demonstrated that plasma low- and high-density lipoprotein cholesterol levels (LDL-C and HDL-C) were decreased in non-survivors compared to controls at the time of admission to the ICU. The conjoint fraction of exomeres and LDL particles measured by dynamic light scattering (DLS) was decreased in non-survivors infected by the Alpha and the Delta variants compared to survivors at the time of admission to the ICU. We first showed that reduction of exomeres fraction may be critical in fatal outcome of COVID-19.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Zabrodskaya2022,

title = {Exosomes Released by Influenza-Virus-Infected Cells Carry Factors Capable of Suppressing Immune Defense Genes in Naïve Cells},

author = {Yana Zabrodskaya and Marina Plotnikova and Nina Gavrilova and Alexey Lozhkov and Sergey Klotchenko and Artem Kiselev and Vladimir Burdakov and Edward Ramsay and Lada Purvinsh and Marja Egorova and Vera Vysochinskaya and Irina Baranovskaya and Alexandra Brodskaya and Roman Povalikhin and Andrey Vasin},

doi = {10.3390/v14122690},

issn = {1999-4915},

year  = {2022},

date = {2022-12-00},

journal = {Viruses},

volume = {14},

number = {12},

publisher = {MDPI AG},

abstract = {Background: Exosomes are involved in intercellular communication and can transfer regulatory molecules between cells. Consequently, they can participate in host immune response regulation. For the influenza A virus (IAV), there is very limited information on changes in exosome composition during cell infection shedding light on the potential role of these extracellular membrane vesicles. Thus, the aim of our work was to study changes in exosomal composition following IAV infection of cells, as well as to evaluate their effect on uninfected cells. Methods: To characterize changes in the composition of cellular miRNAs and mRNAs of exosomes during IAV infection of A549 cells, NGS was used, as well as PCR to identify viral genes. Naïve A549 cells were stimulated with infected-cell-secreted exosomes for studying their activity. Changes in the expression of genes associated with the cell’s immune response were shown using PCR. The effect of exosomes on IAV replication was shown in MDCK cells using In-Cell ELISA and PCR of the supernatants. Results: A change in the miRNA composition (miR-21-3p, miR-26a-5p, miR-23a-5p, miR-548c-5p) and mRNA composition (RPL13A, MKNK2, TRIB3) of exosomes under the influence of the IAV was shown. Many RNAs were involved in the regulation of the immune response of the cell, mainly by suppressing it. After exosome stimulation of naïve cells, a significant decrease in the expression of genes involved in the immune response was shown (RIG1, IFIT1, MDA5, COX2, NFκB, AnxA1, PKR, IL6, IL18). When infecting MDCK cells, a significant decrease in nucleoprotein levels was observed in the presence of exosomes secreted by mock-infected cells. Viral levels in supernatants also decreased. Conclusions: Exosomes secreted by IAV-infected cells could reduce the immune response of neighboring intact cells, leading to more effective IAV replication. This may be associated both with regulatory functions of cellular miRNAs and mRNAs carried by exosomes, or with the presence of viral mRNAs encoding proteins with an immunosuppressive function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2022b,

title = {Construction of 2DE Patterns of Plasma Proteins: Aspect of Potential Tumor Markers},

author = {Stanislav Naryzhny and Natalia Ronzhina and Elena Zorina and Fedor Kabachenko and Nikolay Klopov and Victor Zgoda},

doi = {10.3390/ijms231911113},

issn = {1422-0067},

year  = {2022},

date = {2022-10-00},

journal = {IJMS},

volume = {23},

number = {19},

publisher = {MDPI AG},

abstract = {The use of tumor markers aids in the early detection of cancer recurrence and prognosis. There is a hope that they might also be useful in screening tests for the early detection of cancer. Here, the question of finding ideal tumor markers, which should be sensitive, specific, and reliable, is an acute issue. Human plasma is one of the most popular samples as it is commonly collected in the clinic and provides noninvasive, rapid analysis for any type of disease including cancer. Many efforts have been applied in searching for “ideal” tumor markers, digging very deep into plasma proteomes. The situation in this area can be improved in two ways—by attempting to find an ideal single tumor marker or by generating panels of different markers. In both cases, proteomics certainly plays a major role. There is a line of evidence that the most abundant, so-called “classical plasma proteins”, may be used to generate a tumor biomarker profile. To be comprehensive these profiles should have information not only about protein levels but also proteoform distribution for each protein. Initially, the profile of these proteins in norm should be generated. In our work, we collected bibliographic information about the connection of cancers with levels of “classical plasma proteins”. Additionally, we presented the proteoform profiles (2DE patterns) of these proteins in norm generated by two-dimensional electrophoresis with mass spectrometry and immunodetection. As a next step, similar profiles representing protein perturbations in plasma produced in the case of different cancers will be generated. Additionally, based on this information, different test systems can be developed.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Kropotova2022,

title = {Dipeptidylamino-tripeptidylcarboxypeptidase NEMP3 and DPP3 (DPP III) are the same protein},

author = {Ekaterina S. Kropotova and Ekaterina N. Pavlova and Stanislav N. Naryzhny and Mark I. Mosevitsky},

doi = {10.1016/j.bbrc.2022.05.078},

issn = {0006-291X},

year  = {2022},

date = {2022-08-00},

journal = {Biochemical and Biophysical Research Communications},

volume = {616},

pages = {110--114},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Bairamukov2022,

title = {Nanomechanical characterization of exosomes and concomitant nanoparticles from blood plasma by PeakForce AFM in liquid},

author = {Viktor Yu. Bairamukov and Anton S. Bukatin and Roman A. Kamyshinsky and Vladimir S. Burdakov and Evgeny B. Pichkur and Tatiana A. Shtam and Maria N. Starodubtseva},

doi = {10.1016/j.bbagen.2022.130139},

issn = {0304-4165},

year  = {2022},

date = {2022-07-00},

journal = {Biochimica et Biophysica Acta (BBA) - General Subjects},

volume = {1866},

number = {7},

publisher = {Elsevier BV},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Landa2022,

title = {Extracellular Particles as Carriers of Cholesterol Not Associated with Lipoproteins},

author = {Sergey Landa and Nicolay Verlov and Natalia Fedorova and Mikhail Filatov and Rimma Pantina and Vladimir Burdakov and Elena Varfolomeeva and Vladimir Emanuel},

doi = {10.3390/membranes12060618},

issn = {2077-0375},

year  = {2022},

date = {2022-06-00},

journal = {Membranes},

volume = {12},

number = {6},

publisher = {MDPI AG},

abstract = {Exosomes and exomeres are the smallest microparticles ranging from 20 to 130 nm in diameter. They are found in almost all biological fluids. Exosomes and exomeres are of considerable interest since they can be involved in intercellular signaling and are biological markers of the state of cells, which can be used for diagnostics. The nomenclature of exosomes remains poorly developed. Most researchers try to classify them based on the mode of formation, physicochemical characteristics, and the presence of tetrasporin markers CD9, CD63, and CD81. The data presented in this work show that although exomeres carry tetrasporin biomarkers, they differ from exosomes strongly in lipid composition, especially in cholesterol content. The production of exomeres by cells is associated with the synthesis of cholesterol in cells and is expressed or suppressed by regulators of the synthesis of mevalonate, an intermediate product of cholesterol metabolism. In addition, the work shows that the concentration of extracellular particles in the body correlates with the concentration of cholesterol in the plasma, but weakly correlates with the concentration of cholesterol in lipoproteins. This suggests that not all plasma cholesterol is associated with lipoproteins, as previously thought.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Konoplev2022,

title = {Label-Free Physical Techniques and Methodologies for Proteins Detection in Microfluidic Biosensor Structures},

author = {Georgii Konoplev and Darina Agafonova and Liubov Bakhchova and Nikolay Mukhin and Marharyta Kurachkina and Marc-Peter Schmidt and Nikolay Verlov and Alexander Sidorov and Aleksandr Oseev and Oksana Stepanova and Andrey Kozyrev and Alexander Dmitriev and Soeren Hirsch},

doi = {10.3390/biomedicines10020207},

issn = {2227-9059},

year  = {2022},

date = {2022-02-00},

journal = {Biomedicines},

volume = {10},

number = {2},

publisher = {MDPI AG},

abstract = {Proteins in biological fluids (blood, urine, cerebrospinal fluid) are important biomarkers of various pathological conditions. Protein biomarkers detection and quantification have been proven to be an indispensable diagnostic tool in clinical practice. There is a growing tendency towards using portable diagnostic biosensor devices for point-of-care (POC) analysis based on microfluidic technology as an alternative to conventional laboratory protein assays. In contrast to universally accepted analytical methods involving protein labeling, label-free approaches often allow the development of biosensors with minimal requirements for sample preparation by omitting expensive labelling reagents. The aim of the present work is to review the variety of physical label-free techniques of protein detection and characterization which are suitable for application in micro-fluidic structures and analyze the technological and material aspects of label-free biosensors that implement these methods. The most widely used optical and impedance spectroscopy techniques: absorption, fluorescence, surface plasmon resonance, Raman scattering, and interferometry, as well as new trends in photonics are reviewed. The challenges of materials selection, surfaces tailoring in microfluidic structures, and enhancement of the sensitivity and miniaturization of biosensor systems are discussed. The review provides an overview for current advances and future trends in microfluidics integrated technologies for label-free protein biomarkers detection and discusses existing challenges and a way towards novel solutions.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Naryzhny2022,

title = {Zonulin — regulation of tight contacts in the brain and intestine — facts and hypotheses},

author = {S.N. Naryzhny and O.K. Legina},

doi = {10.18097/pbmc20226805309},

issn = {2310-6905},

year  = {2022},

date = {2022-00-00},

journal = {BIOMED KHIM},

volume = {68},

number = {5},

pages = {309--320},

publisher = {Institute of Biochemistry},

abstract = {In recent years, the interrelationship between the brain and the gut has become an area of high scientific interest.  The intestine is responsible not only for digestion, as it contains millions of neurons, its own immune system,  and affects the emotional and cognitive processes. The relationship between the gut and the brain suggests that  the processes carried out by the gut microbiota play a significant role in the regulation of brain function, and vice versa.  A special role here is played by intercellular tight junctions (TJ), where the zonulin protein holds an important place.  Zonulin, an unprocessed precursor of mature haptoglobin, is the only physiological modulator of intercellular TJ  that can reversibly regulate the permeability of the intestinal (IB) and blood-brain (BBB) barriers in the human body.  BBB disruption and altered microbiota composition are associated with many diseases, including neurological disorders  and neuroinflammation. That is, there is a gut-brain axis (GBA) — a communication system through which the brain  modulates the functions of the gastrointestinal tract (GIT) and vice versa. GBA is based on neuronal, endocrine,  and immunological mechanisms that are interconnected at the organismal, organ, cellular, and molecular levels.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}