Mariya Meschaninova - Academia.edu (original) (raw)

Papers by Mariya Meschaninova

Siberian Medical Review

Oligonucleotide aptamers seem to be promising delivery vehicles addressing boron compounds to tum... more Oligonucleotide aptamers seem to be promising delivery vehicles addressing boron compounds to tumour cells for boron neutron capture therapy (BNCT). Here, we report the first example of using 2'-F-RNA aptamer specific to human glioblastoma cells as a delivery agent for boron clusters, which provides cell internalisation sufficient for the BNCT model.

Acta naturae, Aug 3, 2023

Взаимодействие различных факторов роста и их рецепторов регулирует автономный рост раковых клеток... more Взаимодействие различных факторов роста и их рецепторов регулирует автономный рост раковых клеток [1]; так эпидермальный фактор роста (EGF) и его рецептор (EGFR) играют важную роль в патогенезе и прогрессировании различных типов злокачественных опухолей [2]. EGFR (или HER1) входит в семейство рецепторных тирозинкиназ ErbB, которое также включает HER2, HER3 и HER4. EGFR содержит внеклеточный домен, гидрофобный транс-мембранный домен, внутриклеточный каталитический тирозинкиназный домен и несколько внутриклеточных остатков тирозина [3]. В настоящее время в терапии опухолей используют два типа ингибиторов ErbB: моноклональные антитела против внеклеточного домена EGFR или HER2, такие, как цетуксимаб, матузумаб, панитумумаб, трастузумаб, пертузумаб, и ингибиторы тирозинкиназы, которые конкурируют за связывание в тирозинкиназном домене EGFR с молекулами РЕФЕРАТ Рецептор эпидермального фактора роста (EGFR)-онкогенная тирозинкиназа, которая участвует в возникновении и прогрессировании опухоли, поэтому ингибиторы EGFR и моноклональные антитела к этому рецептору имеют большое значение в терапии опухолей. Экспрессия трансгена EGFR в линии клеток MCF7 (MCF7-EGFR) аденокарциномы молочной железы человека, как показано нами ранее, стимулирует рост клеток в виде 3D-сфероидов. В представленной работе изучено, влияет ли ингибирование EGFR на сборку сфероидов или приводит к разрушению уже сформированных сфероидов. Сравнили действие анти-EGFR siРНК, моноклонального антитела цетуксимаб против EGFR и ингибитора тирозинкиназы AG1478 на диссоциированные и целые сфероиды клеток MCF7-EGFR. Чувствительность клеток MCF7-EGFR к цитотоксическому действию цетуксимаба и AG1478 была в 2.5 раза выше, чем у клеток родительской линии MCF7. Обнаружено, что подавление мРНК EGFR c помощью siРНК уменьшало образование сфер, тогда как обработка уже сформированных сфероидов не вызывала такого эффекта. Обработка диссоциированных сфероидов цетуксимабом и AG1478 также тормозила образование сфер MCF7-EGFR. Мы предполагаем, что экспрессия EGFR важна по крайней мере на стадии формирования сфероидов. Обнаружено значительное увеличение уровня белка адгезии N-кадгерина при переходе от адгезивной клеточной культуры MCF7wt к сфероидам MCF7-EGFR. При воздействии siРНК и цетуксимаба на клетки MCF7-EGFR уровень N-кадгерина снижался. Таким образом, показано участие N-кадгерина в EGFR-зависимом образовании сфероидов MCF7-EGFR. Сфероиды MCF7-EGFR являются релевантной моделью для изучения агрессивных гормон-положительных опухолей молочной железы. КЛЮЧЕВЫЕ СЛОВА 3D-культура клеток, сфероиды, MCF7, EGFR, siРНК, цетуксимаб, AG1478. СПИСОК СОКРАЩЕНИЙ EGFR-рецептор эпидермального фактора роста; siРНК-малая интерферирующая РНК; LF-Lipofectamine 3000; PI-йодид пропидия; wt-дикий тип; AG-ингибитор EGFR (AG1478); ДМСО-диметилсульфоксид; FDA-диацетат флуоресцеина; SD-стандартное отклонение; IC50-концентрация препарата, при которой гибель клеток достигает 50%.

Nucleic Acids Symposium Series, Sep 1, 2008

Biochimica et biophysica acta (N), May 1, 2003

Positioning of each nucleotide of the E site and the P site bound codons with respect to the 18S ... more Positioning of each nucleotide of the E site and the P site bound codons with respect to the 18S rRNA on the human ribosome was studied by cross-linking with mRNA analogs, derivatives of the hexaribonucleotide UUUGUU (comprising Phe and Val codons) that carried a perfluorophenylazide group on the second or the third uracil, and a derivative of the dodecaribonucleotide UUAGUAUUUAUU with a similar group on the guanine residue. The location of the modified nucleotides at any mRNA position from À 3 to + 3 (position + 1 corresponds to the 5Vnucleotide of the P site bound codon) was adjusted by the cognate tRNAs. A modified uridine at positions from À 1 to + 3 cross-linked to nucleotide G1207 of the 18S rRNA, and to nucleotide G961 when it was in position À 2. A modified guanosine crosslinked to nucleotide G1207 if it was in position À 3 of the mRNA. These data indicate that nucleotide G961 of the 18S rRNA is close only to mRNA positions À 3 and À 2, while G1207 is in the vicinity of positions from À 3 to + 3. The latter suggests that there is a sharp turn between the P and E site bound codons that brings nucleotide G1207 of the 18S rRNA close to each nucleotide of these codons. This correlates well with X-ray crystallographic data on bacterial ribosomes, indicating existence of a sharp turn between the P site and E site bound codons near a conserved nucleotide G926 of the 16S rRNA (corresponding to G1207 in 18S rRNA) close to helix 23b containing the conserved nucleotide 693 of the 16S rRNA (corresponding exactly to G961 of the 18S rRNA).

International Journal of Molecular Sciences, Dec 24, 2022

This article is an open access article distributed under the terms and conditions of the Creative... more This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY

Russian Journal of Bioorganic Chemistry, Sep 23, 2022

Growth hormone & IGF research, Nov 1, 2006

Biochemistry, Mar 8, 2012

Insulin-like growth factor I (IGF-I) and its cognate receptor (IGF-1R) contribute to normal cell ... more Insulin-like growth factor I (IGF-I) and its cognate receptor (IGF-1R) contribute to normal cell function and to tumorigenesis. The role of IGF-I signaling in tumor growth has been demonstrated in vivo using nucleic acid-based strategies. Here, we designed the first 10−23 DNAzymes directed against IGF-I mRNA. Unlike antisense approaches and RNA interference that require protein catalysis, DNAzymes catalyze protein-free RNA cleavage. We identified target sequences and measured catalytic properties of differently designed DNAzymes on short synthetic RNA targets and on in vitro transcribed IGF-I mRNA. The most efficient cleavers were then transfected into cells, and their inhibitory effect was analyzed using reporter gene assays. We found that increasing the size of DNAzyme flanking sequences and modifications of the termini with 2′-O-methyl residues improved cleavage rates of target RNAs. Modification of the catalytic loop with six 2′-O-methyl ribonucleotides at nonessential positions increased or decreased catalytic efficiency depending on the mRNA target site. In cells, DNAzymes with 2′-O-methyl-modified catalytic cores and flanking sequences were able to inhibit reporter gene activity because of specific recognition and cleavage of IGF-I mRNA sequences. Mutant DNAzymes with inactive catalytic cores were unable to block reporter gene expression, demonstrating that the RNA cleaving ability of 10−23 DNAzymes contributed to inhibitory mechanisms. Our results show that nuclease-resistant 2′-O-methyl-modified DNAzymes with high catalytic efficiencies are useful for inhibiting IGF-I gene function in cells.

Russian Journal of Bioorganic Chemistry, Mar 1, 2021

Delivery of siRNAs to blood cells is one of the most difficult tasks since there are no efficient... more Delivery of siRNAs to blood cells is one of the most difficult tasks since there are no efficient and nontoxic methods of delivering nucleic acids to these cells in vivo. Conjugation of siRNAs with targeting or lipophilic transport molecules is one of the most promising approaches to solving this problem, since it can provide efficient accumulation without toxic side effects. Therefore, in this work, we conjugated an siRNA molecule with lipophilic molecules for its delivery to PBMC (primary blood mononuclear cells) and whole blood cells. We showed that among the studied molecules, cholesterol is the most promising agent for this purpose. Further screening of conjugates with respect to the length of the linker connecting the siRNA and cholesterol showed that a linker containing six carbon atoms is optimal for the most efficient delivery of the siRNA into human cells in experiments in whole blood. The selected siRNA–cholesterol conjugate also efficiently accumulated in mouse blood cells and splenocytes upon intravenous injection.

Вавиловский журнал генетики и селекции, Oct 28, 2020

Аннотация. В работе охарактеризованы некоторые биологические особенности радиопротекторного дейст... more Аннотация. В работе охарактеризованы некоторые биологические особенности радиопротекторного действия пре парата двуцепочечной РНК. Обнаружено, что препарат дрожжевой РНК обладает пролонгированным радиопротекторным действием при облучении животных летальной дозой в 9.4 Гр. При облучении через 1 ч и на 4-е сутки после введения 7 мг препарата РНК выживает 100 % животных на 70-е сутки наблюдения, при облучении на 8-е и 12-е сутки-60 % животных. Были оценены временные параметры процесса репарации двуцепочечных разрывов, индуцированных γ-лучами. Выявлено, что введение препарата РНК в момент максимального количества двуцепочечных разрывов, через 1 ч после облучения, снижает эффективность радиопротекторного действия по сравнению с введением за 1 ч до облучения и через 4 ч после облучения. Проведено сравнение эффективности радиозащитного действия штатного радиопротектора Б-190 и препарата РНК в одном эксперименте. Установлено, что препарат суммарной РНК не уступает по эффективности препарату Б-190. Выживаемость на 40-е сутки после облучения для группы мышей, получавших препарат РНК, составила 78 %, для Б-190-67 % животных. В ходе аналитических исследований препарата суммарной РНК дрожжей обнаружилось, что препарат представляет собой смесь одноцепочечной и двуцепочечной РНК. Радиопротекторными свойствами обладает только двуцепочечная РНК. При введении 160 мкг препарата двуцепочечной РНК выживает 100 % подопытных животных после абсолютно летальной дозы гамма-радиации 9.4 Гр. Установлено, что радиозащитный эффект двуцепочечной РНК зависит не от последовательности, а от ее двуцепочечной формы, причем для осуществления радиопротекторного действия двуцепочечная РНК должна иметь «открытые» концы молекулы. Предполагается, что радиозащитное действие препарата двуцепочечной РНК связано с участием молекул РНК в корректном восстановлении поврежденного облучением хроматина в стволовых клетках крови. Сохранившие жизнеспособность стволовые гемопоэтические клетки мигрируют на периферию и достигают селезенки, где активно пролиферируют. Вновь образовавшаяся клеточная популяция восстанавливает кроветворную и иммунную системы, что определяет выживание летально облученных животных. Ключевые слова: двуцепочечная РНК; Б-190; селезеночные колонии; двуцепочечные разрывы.

Biochimie, May 1, 2021

The ribosomal protein eL38 is a component of the mammalian translation machine. The deletion of t... more The ribosomal protein eL38 is a component of the mammalian translation machine. The deletion of the Rpl38 locus in mice results in the Tail-short (Ts) mutant phenotype characterized by a shortened tail and other defects in the axial skeleton development. Here, using the next-generation sequencing of total RNA from HEK293 cells knocked down of eL38 mRNA by transfection with specific siRNAs, we examined the effect of reduced eL38 content on genomic transcription. An approximately 4-fold decrease in the level of eL38 was shown to cause changes in the expression of nearly 1500 genes. Among the down-regulated genes, there were those responsible for p53 activity, Ca2+ metabolism and several signaling processes, as well as genes involved in the organization and functioning of the cytoskeleton. The genes related to rRNA processing and translation, along with many others, including those whose dysregulation is associated with developmental disorders, turned out to be up-regulated. Thus, we demonstrated that the decreased RPL38 expression leads to a significant reorganization of genomic transcription. Our findings suggest a possible link between the balance of eL38 and genes implicated in osteogenesis, thereby contributing to the elucidation of the reasons for the appearance of the above Ts mutant phenotype in animals.

Journal of hematology and oncology research, Feb 15, 2016

Small interfering RNA (siRNA) based drugs for overcoming multiple drug resistance of hematologica... more Small interfering RNA (siRNA) based drugs for overcoming multiple drug resistance of hematological malignancies could solve the problem of poor response to the chemotherapy and hight relapse rate. The main factor that significantly limits biomedical application of siRNA is inefficient delivery to target cells and tissues. The attachment of siRNA to molecules, which enter into the cell by natural transport mechanisms, can improve cellular uptake of siRNA. In current study the carrier-free cellular uptake of siRNA containig cholesterol residues conjugated to the 5'-end of the sense strand via oligomethylene linker of various length (here and after Ch-siRNA) was explored. The data demonstrate that cholesterol residue increase the accumulation of siRNA in all tested cell lines and the primary cells. The efficiency of Ch-siRNA accumulation in K562 cells depends greatly on the leangth of the linker connecting cholesterol and siRNA: Ch-siRNAs with linker of 10-12 methylene units accumulate the most efficiently in this cells. It was found that Ch-siRNA effectively accumulates in MOLT-3 (acute lymphoblastic leukemia, ALL), HL-60 (acute myelogenous leukemia, AML), K562 (chronic myelogenous leukemia CML) and primary peripheral blood mononuclear cells (PBMC) from patient with non-Hodgkin lymphoma (NHL) or healthy donor resulting in near 100% of transfected cell when used at 1 mM concentration.

International Journal of Radiation Biology, Jul 28, 2020

Let [u, v] be a Bruhat interval and B(u, v) be its corresponding Bruhat graph. The combinatorial ... more Let [u, v] be a Bruhat interval and B(u, v) be its corresponding Bruhat graph. The combinatorial and topological structure of the longest u-v paths of B(u, v) has been extensively studied and is well-known. Nevertheless, not much is known of the remaining paths. Here we describe combinatorial properties of the shortest u-v paths of B(u, v). We also derive the non-negativity of some coefficients of the complete cd-index of [u, v]. Résumé. Soit [u, v] un intervalle de Bruhat et B(u, v) le graphe de Bruhat associé. La structure combinatoire et topologique des plus longs chemins de uà v dans B(u, v) est bien comprise, mais on sait peu de chose des autres chemins. Nous décrivons ici les propriétés combinatoires des plus courts de chemins de uà v. Nous prouvons aussi que certains coefficients du cd-indice complet de [u, v] sont positifs.

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2021

Abasic (AP) sites in mRNAs are lesions whose accumulation in cells is linked to various neurodege... more Abasic (AP) sites in mRNAs are lesions whose accumulation in cells is linked to various neurodegenerative diseases arising from the appearance of truncated peptides due to the premature cessation of translation of these mRNAs. It is believed that the translation of AP site-containing mRNAs is stopped when the damaged codon arrives to the A site, where it is not decoded. We propose an alternative translation arrest mechanism mediated by the 40S ribosomal subunit protein uS3. Recently, it has been shown that in human 80S ribosomal complexes assembled without translation factors, uS3 cross-links to the AP site at the 3'-terminus of the mRNA, whose undamaged part is bound at the 40S subunit channel, via its peptide 55-64 exposed near the mRNA entry pore. In this study, we examined whether such cross-linking occurs during the translation of mRNA with the AP site. To this end, we used a set of synthetic mRNAs bearing the AP site inserted in the desired location in their sequences. An analysis of 80S ribosomal complexes formed with these mRNAs in a mammalian cell-free protein-synthesizing system demonstrates that AP sites do indeed cross-link to uS3 in the course of the translation. We also show that the cross-linking occurs as soon as the AP site arrives to a common favorable position relative to uS3, which is independent on its location in the mRNA. Our findings suggest that the mechanism of stopping translation of damaged mRNAs involving uS3, along with the one mentioned above, could underlie ribosome-associated mRNA quality control.

Computational and Structural Biotechnology Journal, 2021

Graphical abstract

Russian Journal of Bioorganic Chemistry, 2019

The development of highly effective molecular and biological tools to facilitate the penetration ... more The development of highly effective molecular and biological tools to facilitate the penetration of therapeutic nucleic acids into cells opens a direct way to their successful application as drugs. It has been shown that the incorporation of single-stranded antisense oligonucleotides into concatemeric complexes enhances their binding to the membrane structures of eukaryotic cells, and the use of a cholesterol residue attached to one of the oligonucleotide strands considerably improves the delivery of concatemeric complexes of oligonucleotides to their intracellular target. In the present work, the efficiency of the formation of concatemeric structures from oligonucleotides carrying lipophilic fragments such as lithocholic acid, oleylamide of lithocholic acid, and cholesterol, attached to the 5′-end of the oligonucleotide through oligomethylene linkers of different length has been studied. It has been found that all modified oligonucleotides are capable of effectively "assembling" into concatemeric complexes; however, effective delivery into cells was observed only in the case of concatemeric complexes formed by oligonucleotides carrying a cholesterol residue attached through an aminohexanol linker. It has been shown that antisense oligonucleotides delivered to cells as part of these cholesterol-containing concatemeric complexes effectively inhibit the expression of the target gene.

Biochimie, 2018

The human ribosome can interact with the abasic site in mRNA via a specific peptide of the uS3 pr... more The human ribosome can interact with the abasic site in mRNA via a specific peptide of the uS3 protein located near the mRNA entry channel, Biochimie,

Nucleic acids research, Jan 25, 2018

The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-te... more The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two different types of ribosomal complexes with MR was observed. First, there were stable complexes where MR was fixed in the ribosomal mRNA-binding channel by the codon-anticodon interaction(s) with cognate tRNA(s). Second, we for the first time detected complexes assembled without tRNA due to the binding of MR most likely to an exposed peptide of ribosomal protein uS3 away from the mRNA channel. The analysis of interspin distances allowed the conclusion that 80S ribosomes facilitate dissociation of the duplex (MR)2: the equilibrium between the duplex and the single-stranded MR shifts to MR due to its efficient binding with ribosomes. Furthermore, we observed a significan...

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, 2016

In this work, we studied how the accessibility of structural elements of the mammalian 40S riboso... more In this work, we studied how the accessibility of structural elements of the mammalian 40S ribosomal mRNA entry channel, ribosomal protein (rp) uS3 and helix (h) 16 of the 18S rRNA, changes upon the translation initiation. In particular, we examined the accessibility of rp uS3 for binding of unstructured RNAs and of riboses in h16 towards attack with benzoyl cyanide (BzCN) in complexes assembled in rabbit reticulocyte lysate utilizing synthetic oligoribonucleotides as well as full-length and truncated up to the initiation AUG codon hepatitis C virus IRES as model mRNAs. With both mRNA types, the rp uS3 peptide recognizing single-stranded RNAs was shown to become shielded only in those 48S preinitiation complexes (PICs) that contained eIF3j bound to 40S subunit in the area between the decoding site and the mRNA entry channel. Chemical probing with BzCN revealed that h16 in the 48S PICs containing eIF3j or scanning factor DHX29 is strongly shielded; the effect was observed with all the mRNAs used, and h16 remained protected as well in 80S post-initiation complexes lacking these factors. Altogether, the obtained results allowed us to suggest that eIF3j bound at the 48S PICs makes the rp uS3 inaccessible for binding of RNAs and this factor subunit is responsible for the decrease of h16 conformational flexibility; the latter is manifested as reduced accessibility of h16 to BzCN. Thus, our findings provide new insights into how eIF3j is implicated in ensuring the proper conformation of the mRNA entry channel, thereby facilitating mRNA loading.

Biophysical Journal, 2015

mRNAs are involved in complicated supramolecular complexes with human 40S and 80S ribosomes respo... more mRNAs are involved in complicated supramolecular complexes with human 40S and 80S ribosomes responsible for the protein synthesis. In this work, a derivative of nonaribonucleotide pUUCGUAAAA with nitroxide spin labels attached to the 5 0-phosphate and to the C8 atom of the adenosine in sixth position (mRNA analog) was used for studying such complexes using double electron-electron resonance/pulsed electron-electron double resonance spectroscopy. The complexes were assembled with participation of tRNA Phe , which targeted triplet UUC of the derivative to the ribosomal peptidyl site and predetermined location of the adjacent GUA triplet coding for Val at the aminoacyl (A) site. The interspin distances were measured between the two labels of mRNA analog attached to the first nucleotide of the peptidyl site bound codon and to the third nucleotide of the A site bound codon, in the absence/presence of second tRNA bound at the A site. The values of the obtained interspin distances agree with those calculated for available near-atomic structures of similar complexes of 40S and 80S ribosomes, showing that neither 60S subunit nor tRNA at the A site have a noticeable effect on arrangement of mRNA at the codon-anticodon interaction area. In addition, the shapes of distance distributions in four studied ribosomal complexes allowed conclusions on conformational flexibility of mRNA in these complexes. Overall, the results of this study are the first, to our knowledge, demonstration of double electron-electron resonance/pulsed electron-electron double resonance application for measurements of intramolecular distances in multicomponent supramolecular complexes involving intricate cellular machineries and for evaluating dynamic properties of ligands bound to these machineries.