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Staroverov V, Galatenko A, Knyazev E, Tonevitsky A. Mathematical model explains differences in Omicron and Delta SARS-CoV-2 dynamics in Caco-2 and Calu-3 cells. PeerJ 2024; 12:e16964. [PMID: 38560455 PMCID: PMC10981414 DOI: 10.7717/peerj.16964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/26/2024] [Indexed: 04/04/2024] Open
Abstract
Within-host infection dynamics of Omicron dramatically differs from previous variants of SARS-CoV-2. However, little is still known about which parameters of virus-cell interplay contribute to the observed attenuated replication and pathogenicity of Omicron. Mathematical models, often expressed as systems of differential equations, are frequently employed to study the infection dynamics of various viruses. Adopting such models for results of in vitro experiments can be beneficial in a number of aspects, such as model simplification (e.g., the absence of adaptive immune response and innate immunity cells), better measurement accuracy, and the possibility to measure additional data types in comparison with in vivo case. In this study, we consider a refinement of our previously developed and validated model based on a system of integro-differential equations. We fit the model to the experimental data of Omicron and Delta infections in Caco-2 (human intestinal epithelium model) and Calu-3 (lung epithelium model) cell lines. The data include known information on initial conditions, infectious virus titers, and intracellular viral RNA measurements at several time points post-infection. The model accurately explains the experimental data for both variants in both cell lines using only three variant- and cell-line-specific parameters. Namely, the cell entry rate is significantly lower for Omicron, and Omicron triggers a stronger cytokine production rate (i.e., innate immune response) in infected cells, ultimately making uninfected cells resistant to the virus. Notably, differences in only a single parameter (e.g., cell entry rate) are insufficient to obtain a reliable model fit for the experimental data.
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Affiliation(s)
- Vladimir Staroverov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Evgeny Knyazev
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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2
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Driedonks TAP, Nyberg LH, Conte A, Ma Z, Pekosz A, Duban E, Tonevitsky A, Sültmann H, Turchinovich A, Witwer KW. Viral and host small RNA transcriptome analysis of SARS-CoV-1 and SARS-CoV-2-infected human cells reveals novel viral short RNAs. Heliyon 2024; 10:e24570. [PMID: 38314306 PMCID: PMC10837498 DOI: 10.1016/j.heliyon.2024.e24570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 12/18/2023] [Accepted: 01/10/2024] [Indexed: 02/06/2024] Open
Abstract
RNA viruses have been shown to express various short RNAs, some of which have regulatory roles during replication, transcription, and translation of viral genomes. However, short viral RNAs generated from SARS-CoV-1 and SARS-CoV-2 genomic RNAs remained largely unexplored, possibly due limitations of the widely used library preparation methods for small RNA deep sequencing and corresponding data processing. By analyzing publicly available small RNA sequencing datasets, we observed that human Calu-3 cells infected by SARS-CoV-1 or SARS-CoV-2 accumulate multiple previously unreported short viral RNAs. In addition, we verified the presence of the five most abundant SARS-CoV-2 short viral RNAs in SARS-CoV-2-infected human lung adenocarcinoma cells by quantitative PCR. Interestingly, the copy number of the observed SARS-CoV-2 short viral RNAs dramatically exceeded the expression of previously reported viral microRNAs in the same cells. We hypothesize that the reported SARS-CoV-2 short viral RNAs could serve as biomarkers for early infection stages due to their high abundance. Furthermore, unlike SARS-CoV-1, the SARS-CoV-2 infection induced significant (Benjamini-Hochberg-corrected p-value <0.05) deregulation of Y-RNA, transfer RNA, vault RNA, as well as more than 300 endogenous short RNAs that aligned predominantly to human protein-coding and long noncoding RNA transcripts. In particular, more than 20-fold upregulation of reads derived from Y-RNA (and several transfer RNAs) have been documented in RNA-seq datasets from SARS-CoV-2 infected cells. Finally, a significant proportion of short RNAs derived from full-length viral genomes also aligned to various human genome (hg38) sequences, suggesting opportunities to investigate regulatory roles of short viral RNAs during infection. Further characterization of the small RNA landscape of both viral and host genomes is clearly warranted to improve our understanding of molecular events related to infection and to design more efficient strategies for therapeutic interventions as well as early diagnosis.
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Affiliation(s)
- Tom A P Driedonks
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lyle H Nyberg
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Abigail Conte
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Zexu Ma
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Andrey Turchinovich
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), Heidelberg, Germany
- Heidelberg Biolabs GmbH, Heidelberg, Germany
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Heidelberg University, Heidelberg/Mannheim, Germany
| | - Kenneth W Witwer
- Department of Molecular and Comparative Pathobiology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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3
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Everest‐Dass A, Nersisyan S, Maar H, Novosad V, Schröder‐Schwarz J, Freytag V, Stuke JL, Beine MC, Schiecke A, Haider M, Kriegs M, Elakad O, Bohnenberger H, Conradi L, Raygorodskaya M, Krause L, von Itzstein M, Tonevitsky A, Schumacher U, Maltseva D, Wicklein D, Lange T. Spontaneous metastasis xenograft models link CD44 isoform 4 to angiogenesis, hypoxia, EMT and mitochondria-related pathways in colorectal cancer. Mol Oncol 2024; 18:62-90. [PMID: 37849446 PMCID: PMC10766209 DOI: 10.1002/1878-0261.13535] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 08/10/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023] Open
Abstract
Hematogenous metastasis limits the survival of colorectal cancer (CRC) patients. Here, we illuminated the roles of CD44 isoforms in this process. Isoforms 3 and 4 were predominantly expressed in CRC patients. CD44 isoform 4 indicated poor outcome and correlated with epithelial-mesenchymal transition (EMT) and decreased oxidative phosphorylation (OxPhos) in patients; opposite associations were found for isoform 3. Pan-CD44 knockdown (kd) independently impaired primary tumor formation and abrogated distant metastasis in CRC xenografts. The xenograft tumors mainly expressed the clinically relevant CD44 isoforms 3 and 4. Both isoforms were enhanced in the paranecrotic, hypoxic tumor regions but were generally absent in lung metastases. Upon CD44 kd, tumor angiogenesis was increased in the paranecrotic areas, accompanied by reduced hypoxia-inducible factor-1α and CEACAM5 but increased E-cadherin expression. Mitochondrial genes and proteins were induced upon pan-CD44 kd, as were OxPhos genes. Hypoxia increased VEGF release from tumor spheres, particularly upon CD44 kd. Genes affected upon CD44 kd in xenografts specifically overlapped concordantly with genes correlating with CD44 isoform 4 (but not isoform 3) in patients, validating the clinical relevance of the used model and highlighting the metastasis-promoting role of CD44 isoform 4.
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Affiliation(s)
- Arun Everest‐Dass
- Institute for GlycomicsGriffith University, Gold Coast CampusAustralia
| | - Stepan Nersisyan
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Institute of Molecular BiologyThe National Academy of Sciences of the Republic of ArmeniaYerevanArmenia
- Armenian Bioinformatics Institute (ABI)YerevanArmenia
- Present address:
Computational Medicine CenterThomas Jefferson UniversityPhiladelphiaPAUSA
| | - Hanna Maar
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Victor Novosad
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
| | | | - Vera Freytag
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Johanna L. Stuke
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Mia C. Beine
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Alina Schiecke
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Marie‐Therese Haider
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Malte Kriegs
- Department of Radiobiology and Radiation OncologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Omar Elakad
- Institute of PathologyUniversity Medical Center GöttingenGermany
| | | | - Lena‐Christin Conradi
- Clinic for General, Visceral and Pediatric SurgeryUniversity Medical Center GöttingenGermany
| | | | - Linda Krause
- Institute of Medical Biometry and EpidemiologyUniversity Medical Center Hamburg‐EppendorfGermany
| | - Mark von Itzstein
- Institute for GlycomicsGriffith University, Gold Coast CampusAustralia
| | - Alexander Tonevitsky
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
- Shemyakin‐Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
- Art Photonics GmbHBerlinGermany
| | - Udo Schumacher
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Medical School BerlinGermany
| | - Diana Maltseva
- Faculty of Biology and BiotechnologyHSE UniversityMoscowRussia
| | - Daniel Wicklein
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Department of Anatomy and Cell BiologyUniversity of MarburgGermany
| | - Tobias Lange
- Institute of Anatomy and Experimental MorphologyUniversity Medical Center Hamburg‐EppendorfGermany
- Institute of Anatomy IJena University HospitalGermany
- Comprehensive Cancer Center Central Germany (CCCG)Jena and LeipzigGermany
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4
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Makarova J, Maltseva D, Tonevitsky A. Challenges in characterization of transcriptomes of extracellular vesicles and non-vesicular extracellular RNA carriers. Front Mol Biosci 2023; 10:1327985. [PMID: 38116380 PMCID: PMC10729812 DOI: 10.3389/fmolb.2023.1327985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Abstract
Since its original discovery over a decade ago, extracellular RNA (exRNA) has been found in all biological fluids. Furthermore, extracellular microRNA has been shown to be involved in communication between various cell types. Importantly, the exRNA is protected from RNases degradation by certain carriers including membrane vesicles and non-vesicular protein nanoparticles. Each type of carrier has its unique exRNA profile, which may vary depending on cell type and physiological conditions. To clarify putative mechanisms of intercellular communication mediated by exRNA, the RNA profile of each carrier has to be characterized. While current methods of biofluids fractionation are continuously improving, they fail to completely separate exRNA carriers. Likewise, most popular library preparation approaches for RNA sequencing do not allow obtaining exhaustive and unbiased data on exRNA transcriptome. In this mini review we discuss ongoing progress in the field of exRNA, with the focus on exRNA carriers, analyze the key methodological challenges and provide recommendations on how the latter could be overcome.
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Affiliation(s)
- Julia Makarova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Hertsen Moscow Oncology Research Center, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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5
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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6
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Lebedeva S, Margaryan A, Smolyarchuk E, Nedorubov A, Materenchuk M, Tonevitsky A, Mutig K. Metabolic effects of vasopressin in pathophysiology of diabetic kidney disease. Front Endocrinol (Lausanne) 2023; 14:1176199. [PMID: 37790608 PMCID: PMC10545091 DOI: 10.3389/fendo.2023.1176199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023] Open
Abstract
The diabetic kidney disease (DKD) is the major cause of the chronic kidney disease (CKD). Enhanced plasma vasopressin (VP) levels have been associated with the pathophysiology of DKD and CKD. Stimulation of VP release in DKD is caused by glucose-dependent reset of the osmostat leading to secondary pathophysiologic effects mediated by distinct VP receptor types. VP is a stress hormone exhibiting the antidiuretic action in the kidney along with broad adaptive effects in other organs. Excessive activation of the vasopressin type 2 (V2) receptor in the kidney leads to glomerular hyperfiltration and nephron loss, whereas stimulation of vasopressin V1a or V1b receptors in the liver, pancreas, and adrenal glands promotes catabolic metabolism for energy mobilization, enhancing glucose production and aggravating DKD. Increasing availability of selective VP receptor antagonists opens new therapeutic windows separating the renal and extra-renal VP effects for the concrete applications. Improved understanding of these paradigms is mandatory for further drug design and translational implementation. The present concise review focuses on metabolic effects of VP affecting DKD pathophysiology.
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Affiliation(s)
- Svetlana Lebedeva
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Arus Margaryan
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Elena Smolyarchuk
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Andrey Nedorubov
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Maria Materenchuk
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Kerim Mutig
- Department of Pharmacology, Institute of Pharmacy, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Translational Physiology, Charité-Universitätsmedizin, Berlin, Germany
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7
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Zhiyanov A, Shkurnikov M, Nersisyan A, Hui C, Baranova A, Tonevitsky A. The signature of SARS-CoV-2 evolution reflects selective pressures within human guts. J Med Virol 2023; 95:e28996. [PMID: 37515485 DOI: 10.1002/jmv.28996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/09/2023] [Accepted: 07/16/2023] [Indexed: 07/31/2023]
Abstract
In somatic cells, microRNAs (miRNAs) bind to the genomes of RNA viruses and influence their translation and replication. In London and Berlin samples represented in GISAID database, we traced severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages and divided these sequenced in two groups, "Ancestral variants" and "Omicrons," and analyzed them through the prism of the tissue-specific binding between host miRNAs and viral messenger RNAs. We demonstrate a significant number of miRNA-binding sites in the NSP4 region of the SARS-CoV-2 genome, with evidence of evolutionary pressure within this region exerted by human intestinal miRNAs. Notably, in infected cells, NSP4 promotes the formation of double-membrane vesicles, which serve as the scaffolds for replication-transcriptional complexes and protect viral RNA from intracellular destruction. In 3 years of selection, the loss of many miRNA-binding sites in general and those within the NSP4 in particular has shaped the SARS-CoV-2 genomes. With that, the descendants of the BA.2 variants were promoted as dominant strains, which define current momentum of the pandemics.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Ashot Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Cai Hui
- Department of Nanoengineering, Sun Yat-Sen University, Shenzhen, China
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, Virginia, USA
- Research Centre for Medical Genetics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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Zhiyanov A, Engibaryan N, Nersisyan S, Shkurnikov M, Tonevitsky A. Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer. Bioinformatics 2023; 39:6998206. [PMID: 36688696 PMCID: PMC9901399 DOI: 10.1093/bioinformatics/btad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 01/10/2023] [Accepted: 01/22/2023] [Indexed: 01/24/2023] Open
Abstract
MOTIVATION One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential expression analysis, differential co-expression one aims to detect pairs or clusters whose mutual expression changes between two conditions. RESULTS We developed Differential Co-expression Network Analysis (DCoNA)-an open-source statistical tool that allows one to identify pair interactions, which correlation significantly changes between two conditions. Comparing DCoNA with the state-of-the-art analog, we showed that DCoNA is a faster, more accurate and less memory-consuming tool. We applied DCoNA to prostate mRNA/miRNA-seq data collected from The Cancer Genome Atlas (TCGA) and compared predicted regulatory interactions of miRNA isoforms (isomiRs) and their target mRNAs between normal and cancer samples. As a result, almost all highly expressed isomiRs lost negative correlation with their targets in prostate cancer samples compared to ones without the pathology. One exception to this trend was the canonical isomiR of hsa-miR-93-5p acquiring cancer-specific targets. Further analysis showed that cancer aggressiveness simultaneously increased with the expression level of this isomiR in both TCGA primary tumor samples and 153 blood plasma samples of P. Hertsen Moscow Oncology Research Institute patients' cohort analyzed by miRNA microarrays. AVAILABILITY AND IMPLEMENTATION Source code and documentation of DCoNA are available at https://github.com/zhiyanov/DCoNA. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia
| | - Stepan Nersisyan
- Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia.,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.,P. Hertsen Moscow Oncology Research Institute, National Center of Medical Radiological Research, Moscow 125284, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow 101000, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia.,Art Photonics GmbH, Berlin 12489, Germany
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9
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Staroverov V, Nersisyan S, Galatenko A, Alekseev D, Lukashevich S, Polyakov F, Anisimov N, Tonevitsky A. Development of a novel mathematical model that explains SARS-CoV-2 infection dynamics in Caco-2 cells. PeerJ 2023; 11:e14828. [PMID: 36748087 PMCID: PMC9899056 DOI: 10.7717/peerj.14828] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 01/09/2023] [Indexed: 02/04/2023] Open
Abstract
Mathematical modeling is widely used to study within-host viral dynamics. However, to the best of our knowledge, for the case of SARS-CoV-2 such analyses were mainly conducted with the use of viral load data and for the wild type (WT) variant of the virus. In addition, only few studies analyzed models for in vitro data, which are less noisy and more reproducible. In this work we collected multiple data types for SARS-CoV-2-infected Caco-2 cell lines, including infectious virus titers, measurements of intracellular viral RNA, cell viability data and percentage of infected cells for the WT and Delta variants. We showed that standard models cannot explain some key observations given the absence of cytopathic effect in human cell lines. We propose a novel mathematical model for in vitro SARS-CoV-2 dynamics, which included explicit modeling of intracellular events such as exhaustion of cellular resources required for virus production. The model also explicitly considers innate immune response. The proposed model accurately explained experimental data. Attenuated replication of the Delta variant in Caco-2 cells could be explained by our model on the basis of just two parameters: decreased cell entry rate and increased cytokine production rate.
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Affiliation(s)
- Vladimir Staroverov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Current Affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy Alekseev
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Sofya Lukashevich
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Fedor Polyakov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Nikita Anisimov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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10
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Shkurnikov M, Nersisyan S, Averinskaya D, Chekova M, Polyakov F, Titov A, Doroshenko D, Vechorko V, Tonevitsky A. HLA-A*01:01 allele diminishing in COVID-19 patients population associated with non-structural epitope abundance in CD8+ T-cell repertoire. PeerJ 2023; 11:e14707. [PMID: 36691482 PMCID: PMC9864130 DOI: 10.7717/peerj.14707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/15/2022] [Indexed: 01/19/2023] Open
Abstract
In mid-2021, the SARS-CoV-2 Delta variant caused the third wave of the COVID-19 pandemic in several countries worldwide. The pivotal studies were aimed at studying changes in the efficiency of neutralizing antibodies to the spike protein. However, much less attention was paid to the T-cell response and the presentation of virus peptides by MHC-I molecules. In this study, we compared the features of the HLA-I genotype in symptomatic patients with COVID-19 in the first and third waves of the pandemic. As a result, we could identify the diminishing of carriers of the HLA-A*01:01 allele in the third wave and demonstrate the unique properties of this allele. Thus, HLA-A*01:01-binding immunoprevalent epitopes are mostly derived from ORF1ab. A set of epitopes from ORF1ab was tested, and their high immunogenicity was confirmed. Moreover, analysis of the results of single-cell phenotyping of T-cells in recovered patients showed that the predominant phenotype in HLA-A*01:01 carriers is central memory T-cells. The predominance of T-lymphocytes of this phenotype may contribute to forming long-term T-cell immunity in carriers of this allele. Our results can be the basis for highly effective vaccines based on ORF1ab peptides.
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Affiliation(s)
- Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Darya Averinskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Milena Chekova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Fedor Polyakov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Aleksei Titov
- National Research Center for Hematology, Moscow, Russia
| | | | | | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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Nikulin S, Razumovskaya A, Poloznikov A, Zakharova G, Alekseev B, Tonevitsky A. ELOVL5 and IGFBP6 genes modulate sensitivity of breast cancer cells to ferroptosis. Front Mol Biosci 2023; 10:1075704. [PMID: 36714261 PMCID: PMC9880435 DOI: 10.3389/fmolb.2023.1075704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 01/03/2023] [Indexed: 01/14/2023] Open
Abstract
Introduction: Relapse of breast cancer is one of the key obstacles to successful treatment. Previously we have shown that low expression of ELOVL5 and IGFBP6 genes in breast cancer tissue corresponded to poor prognosis. ELOVL5 participates directly in the elongation of polyunsaturated fatty acids (PUFAs) that are considered to play an important role in cancer cell metabolism. Thus, in this work we studied the changes in lipid metabolism in breast cancer cells with reduced expression of either ELOVL5 or IGFBP6 gene. Methods: MDA-MB-231 cells with a stable knockdown of either ELOVL5 or IGFBP6 gene were used in this study. Transcriptomic and proteomic analysis as well as RT-PCR were utilized to assess gene expression. Content of individual fatty acids in the cells was measured with HPLC-MS. HPLC was used for analysis of the kinetics of PUFAs uptake. Cell viability was measured with MTS assay. Flow cytometry was used to measure activation of apoptosis. Fluorescent microscopy was utilized to assess accumulation of ROS and formation of lipid droplets. Glutathione peroxidase activity was measured with a colorimetric assay. Results: We found that the knockdown of IGFBP6 gene led to significant changes in the profile of fatty acids in the cells and in the expression of many genes associated with lipid metabolism. As some PUFAs are known to inhibit proliferation and cause death of cancer cells, we also tested the response of the cells to single PUFAs and to combinations of docosahexaenoic acid (DHA, a n-3 PUFA) with standard chemotherapeutic drugs. Our data suggest that external PUFAs cause cell death by activation of ferroptosis, an iron-dependent mechanism of cell death with excessive lipid peroxidation. Moreover, both knockdowns increased cells' sensitivity to ferroptosis, probably due to a significant decrease in the activity of the antioxidant enzyme GPX4. Addition of DHA to commonly used chemotherapeutic drugs enhanced their effect significantly, especially for the cells with low expression of IGFBP6 gene. Discussion: The results of this study suggest that addition of PUFAs to the treatment regimen for the patients with low expression of IGFBP6 and ELOVL5 genes can be potentially beneficial and is worth testing in a clinically relevant setting.
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Affiliation(s)
- Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia,*Correspondence: Sergey Nikulin,
| | | | - Andrey Poloznikov
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Galina Zakharova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Boris Alekseev
- P. A. Hertsen Moscow Oncology Research Center, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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12
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Nersisyan S, Zhiyanov A, Engibaryan N, Maltseva D, Tonevitsky A. A novel approach for a joint analysis of isomiR and mRNA expression data reveals features of isomiR targeting in breast cancer. Front Genet 2022; 13:1070528. [PMID: 36531236 PMCID: PMC9751988 DOI: 10.3389/fgene.2022.1070528] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 11/21/2022] [Indexed: 07/31/2023] Open
Abstract
A widely used procedure for selecting significant miRNA-mRNA or isomiR-mRNA pairs out of predicted interactions involves calculating the correlation between expression levels of miRNAs/isomiRs and mRNAs in a series of samples. In this manuscript, we aimed to assess the validity of this procedure by comparing isomiR-mRNA correlation profiles in sets of sequence-based predicted target mRNAs and non-target mRNAs (negative controls). Target prediction was carried out using RNA22 and TargetScan algorithms. Spearman's correlation analysis was conducted using miRNA and mRNA sequencing data of The Cancer Genome Atlas Breast Invasive Carcinoma (TCGA-BRCA) project. Luminal A, luminal B, basal-like breast cancer subtypes, and adjacent normal tissue samples were analyzed separately. Using the sets of putative targets and non-targets, we introduced adjusted isomiR targeting activity (ITA)-the number of negatively correlated potential isomiR targets adjusted by the background (estimated using non-target mRNAs). We found that for most isomiRs a significant negative correlation between isomiR-mRNA expression levels appeared more often in a set of predicted targets compared to the non-targets. This trend was detected for both classical seed region binding types (8mer, 7mer-m8, 7mer-A1, 6mer) predicted by TargetScan and the non-classical ones (G:U wobbles and up to one mismatch or unpaired nucleotide within seed sequence) predicted by RNA22. Adjusted ITA distributions were similar for target sites located in 3'-UTRs and coding mRNA sequences, while 5'-UTRs had much lower scores. Finally, we observed strong cancer subtype-specific patterns of isomiR activity, highlighting the differences between breast cancer molecular subtypes and normal tissues. Surprisingly, our target prediction- and correlation-based estimates of isomiR activities were practically non-correlated with the average isomiR expression levels neither in cancerous nor in normal samples.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Art Photonics GmbH, Berlin, Germany
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13
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Chen LC, Nersisyan S, Wu CJ, Chang CM, Tonevitsky A, Guo CL, Chang WC. On the peptide binding affinity changes in population-specific HLA repertoires to the SARS-CoV-2 variants Delta and Omicron. J Autoimmun 2022; 133:102952. [PMID: 36427410 PMCID: PMC9650568 DOI: 10.1016/j.jaut.2022.102952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 11/05/2022] [Accepted: 11/06/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE To investigate the changes of Spike protein-HLA binding affinity profiles between the Wuhan strain and two dominant variants, the Delta and the Omicron strains, among the Taiwanese, the British and the Russian populations. METHODS The HLA frequencies and the HLA-peptide binding affinity profiles in the T-CoV database were combined to conduct the study. We focused on the public alleles in the three populations (HLA-A, HLA-B, HLA-C, HLA-DRB1, and/or HLA-DPA1/DPB1 alleles) and the altered peptides of the spike protein (compared to the Wuhan strain) in the Delta G/478K·V1 (B.1.617.2 + AY.1 + AY.2) and the Omicron (BA.1) strains. RESULTS For the Delta strain, tight bindings of the altered peptides to the HLA alleles decrease in all three populations and almost vanish in the Taiwanese population. For the Omicron strain, tight bindings are mostly preserved for both HLA classes and in the Taiwanese and the British populations, with a slight reduction in HLA class II in the Taiwanese (1.4%), while the Russian population preserves a relatively high fraction of tight bindings for both HLA classes. CONCLUSION We comprehensively reported the changes in the HLA-associated SARS-CoV-2 Spike protein peptide binding profiles among the Taiwanese, the British, and the Russian populations. Further studies are needed to understand the immunological mechanisms and the clinical value of our findings.
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Affiliation(s)
- Lu-Chun Chen
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Chang-Jiun Wu
- Department of Genomic Medicine, University of Texas, MD Anderson Cancer Center. Houston Texas, USA
| | - Che-Mai Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Chin-Lin Guo
- Institute of Physics, Academia Sinica, Taipei, Taiwan,Corresponding author. Institute of Physics, Academia Sinica, No. 128, Sec. 2, Academia Rd., Nangang Dist., Taipei City 115201, Taiwan. Tel.: (886) 988545414
| | - Wei-Chiao Chang
- Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Medical Education and Research, Integrative Research Center for Critical Care, Wan fang Hospital, Taipei Medical University, Taipei, Taiwan,Master Program in Clinical Genomics and Proteomics, School of Pharmacy, Taipei Medical University, Taipei, Taiwan,Department of Pharmacy, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan,Corresponding author. Department of Clinical Pharmacy, School of Pharmacy, Taipei Medical University, No. 250 Wuxing St., Xinyi Dist., Taipei City 110, Taiwan. Tel.: (886) 928121979
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14
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Nersisyan S, Gorbonos A, Makhonin A, Zhiyanov A, Shkurnikov M, Tonevitsky A. isomiRTar: a comprehensive portal of pan-cancer 5'-isomiR targeting. PeerJ 2022; 10:e14205. [PMID: 36275459 PMCID: PMC9583861 DOI: 10.7717/peerj.14205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 09/19/2022] [Indexed: 01/24/2023] Open
Abstract
Inaccurate cleavage of pri- and pre-miRNA hairpins by Drosha and Dicer results in the generation of miRNA isoforms known as isomiRs. isomiRs with 5'-end variations (5'-isomiRs) create a new dimension in miRNA research since they have different seed regions and distinct targetomes. We developed isomiRTar (https://isomirtar.hse.ru)-a comprehensive portal that allows one to analyze expression profiles and targeting activity of 5'-isomiRs in cancer. Using the Cancer Genome Atlas sequencing data, we compiled the list of 1022 5'-isomiRs expressed in 9282 tumor samples across 31 cancer types. Sequences of these isomiRs were used to predict target genes with miRDB and TargetScan. The putative interactions were then subjected to the co-expression analysis in each cancer type to identify isomiR-target pairs supported by significant negative correlations. Downstream analysis of the data deposited in isomiRTar revealed both cancer-specific and cancer-conserved 5'-isomiR expression landscapes. Pairs of isomiRs differing in one nucleotide shift from 5'-end had poorly overlapping targetomes with the median Jaccard index of 0.06. The analysis of colorectal cancer 5'-isomiR-mediated regulatory networks revealed promising candidate tumor suppressor isomiRs: hsa-miR-203a-3p-+1, hsa-miR-192-5p-+1 and hsa-miR-148a-3p-0. In summary, we believe that isomiRTar will help researchers find novel mechanisms of isomiR-mediated gene silencing in different types of cancer.
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Affiliation(s)
- Stepan Nersisyan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | | | - Alexey Makhonin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Art Photonics GmbH, Berlin, Germany
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15
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Nersisyan S, Zhiyanov A, Zakharova M, Ishina I, Kurbatskaia I, Mamedov A, Galatenko A, Shkurnikov M, Gabibov A, Tonevitsky A. Alterations in SARS-CoV-2 Omicron and Delta peptides presentation by HLA molecules. PeerJ 2022; 10:e13354. [PMID: 35502206 PMCID: PMC9055995 DOI: 10.7717/peerj.13354] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/08/2022] [Indexed: 01/15/2023] Open
Abstract
The T-cell immune response is a major determinant of effective SARS-CoV-2 clearance. Here, using the recently developed T-CoV bioinformatics pipeline (https://t-cov.hse.ru) we analyzed the peculiarities of the viral peptide presentation for the Omicron, Delta and Wuhan variants of SARS-CoV-2. First, we showed the absence of significant differences in the presentation of SARS-CoV-2-derived peptides by the most frequent HLA class I/II alleles and the corresponding HLA haplotypes. Then, the analysis was limited to the set of peptides originating from the Spike proteins of the considered SARS-CoV-2 variants. The major finding was the destructive effect of the Omicron mutations on PINLVRDLPQGFSAL peptide, which was the only tight binder from the Spike protein for HLA-DRB1*03:01 allele and some associated haplotypes. Specifically, we predicted a dramatical decline in binding affinity of HLA-DRB1*03:01 and this peptide both because of the Omicron BA.1 mutations (N211 deletion, L212I substitution and EPE 212-214 insertion) and the Omicron BA.2 mutations (V213G substitution). The computational prediction was experimentally validated by ELISA with the use of corresponding thioredoxin-fused peptides and recombinant HLA-DR molecules. Another finding was the significant reduction in the number of tightly binding Spike peptides for HLA-B*07:02 HLA class I allele (both for Omicron and Delta variants). Overall, the majority of HLA alleles and haplotypes was not significantly affected by the mutations, suggesting the maintenance of effective T-cell immunity against the Omicron and Delta variants. Finally, we introduced the Omicron variant to T-CoV portal and added the functionality of haplotype-level analysis to it.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Institute of Molecular Biology, The National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia,Armenian Bioinformatics Institute (ABI), Yerevan, Armenia
| | - Anton Zhiyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maria Zakharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Ishina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Inna Kurbatskaia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Azad Mamedov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Gabibov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia,Art Photonics GmbH, Berlin, Germany
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16
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Titov A, Shaykhutdinova R, Shcherbakova OV, Serdyuk YV, Sheetikov SA, Zornikova KV, Maleeva AV, Khmelevskaya A, Dianov DV, Shakirova NT, Malko DB, Shkurnikov M, Nersisyan S, Tonevitsky A, Khamaganova E, Ershov AV, Osipova EY, Nikolaev RV, Pershin DE, Vedmedskia VA, Maschan M, Ginanova VR, Efimov GA. Immunogenic epitope panel for accurate detection of non-cross-reactive T cell response to SARS-CoV-2. JCI Insight 2022; 7:157699. [PMID: 35389886 PMCID: PMC9090254 DOI: 10.1172/jci.insight.157699] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/30/2022] [Indexed: 11/17/2022] Open
Abstract
The ongoing COVID-19 pandemic calls for more effective diagnostic tools. T cell response assessment serves as an independent indicator of prior COVID-19 exposure while also contributing to a more comprehensive characterization of SARS-CoV-2 immunity. In this study, we systematically assessed the immunogenicity of 118 epitopes with immune cells collected from multiple cohorts of vaccinated, convalescent, healthy unexposed, and SARS-CoV-2–exposed donors. We identified 75 immunogenic epitopes, 24 of which were immunodominant. We further confirmed HLA restriction for 49 epitopes and described association with more than 1 HLA allele for 14 of these. Exclusion of 2 cross-reactive epitopes that generated a response in prepandemic samples left us with a 73-epitope set that offered excellent diagnostic specificity without losing sensitivity compared with full-length antigens, and this evoked a robust cross-reactive response. We subsequently incorporated this set of epitopes into an in vitro diagnostic Corona-T-test, which achieved a diagnostic accuracy of 95% in a clinical trial. In a cohort of asymptomatic seronegative individuals with a history of prolonged SARS-CoV-2 exposure, we observed a complete absence of T cell response to our epitope panel. In combination with strong reactivity to full-length antigens, this suggests that a cross-reactive response might protect these individuals.
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Affiliation(s)
- Aleksei Titov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Regina Shaykhutdinova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Olga V Shcherbakova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Yana V Serdyuk
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Savely A Sheetikov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Ksenia V Zornikova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Alexandra V Maleeva
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Alexandra Khmelevskaya
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Dmitry V Dianov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Naina T Shakirova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Dmitry B Malko
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russian Federation
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russian Federation
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russian Federation
| | - Ekaterina Khamaganova
- Laboratory of HLA Genotyping, National Research Center for Hematology, Moscow, Russian Federation
| | | | - Elena Y Osipova
- Stem Cell Physiology Laboratory, Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Ruslan V Nikolaev
- Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Dmitry E Pershin
- Transplantation Immunology and Immunotherapy Laboratory, Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Viktoria A Vedmedskia
- Transplantation Immunology and Immunotherapy Laboratory, Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Mikhail Maschan
- Dmitry Rogachev National Medical Research Center Of Pediatric Hematology, Oncology and Immunology, Moscow, Russian Federation
| | - Victoria R Ginanova
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
| | - Grigory A Efimov
- Laboratory of Transplantation Immunology, National Research Center for Hematology, Moscow, Russian Federation
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17
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Nersisyan S, Novosad V, Galatenko A, Sokolov A, Bokov G, Konovalov A, Alekseev D, Tonevitsky A. ExhauFS: exhaustive search-based feature selection for classification and survival regression. PeerJ 2022; 10:e13200. [PMID: 35378930 PMCID: PMC8976470 DOI: 10.7717/peerj.13200] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 01/12/2023] Open
Abstract
Feature selection is one of the main techniques used to prevent overfitting in machine learning applications. The most straightforward approach for feature selection is an exhaustive search: one can go over all possible feature combinations and pick up the model with the highest accuracy. This method together with its optimizations were actively used in biomedical research, however, publicly available implementation is missing. We present ExhauFS-the user-friendly command-line implementation of the exhaustive search approach for classification and survival regression. Aside from tool description, we included three application examples in the manuscript to comprehensively review the implemented functionality. First, we executed ExhauFS on a toy cervical cancer dataset to illustrate basic concepts. Then, multi-cohort microarray breast cancer datasets were used to construct gene signatures for 5-year recurrence classification. The vast majority of signatures constructed by ExhauFS passed 0.65 threshold of sensitivity and specificity on all datasets, including the validation one. Moreover, a number of gene signatures demonstrated reliable performance on independent RNA-seq dataset without any coefficient re-tuning, i.e., turned out to be cross-platform. Finally, Cox survival regression models were used to fit isomiR signatures for overall survival prediction for patients with colorectal cancer. Similarly to the previous example, the major part of models passed the pre-defined concordance index threshold 0.65 on all datasets. In both real-world scenarios (breast and colorectal cancer datasets), ExhauFS was benchmarked against state-of-the-art feature selection models, including L1-regularized sparse models. In case of breast cancer, we were unable to construct reliable cross-platform classifiers using alternative feature selection approaches. In case of colorectal cancer not a single model passed the same 0.65 threshold. Source codes and documentation of ExhauFS are available on GitHub: https://github.com/s-a-nersisyan/ExhauFS.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Victor Novosad
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Andrey Sokolov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Grigoriy Bokov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Konovalov
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Dmitry Alekseev
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia,Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia,Institute of Nanotechnologies of Microelectronics RAS, Moscow, Russia
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18
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Poloznikov A, Nikulin S, Bolotina L, Kachmazov A, Raigorodskaya M, Kudryavtseva A, Bakhtogarimov I, Rodin S, Gaisina I, Topchiy M, Asachenko A, Novosad V, Tonevitsky A, Alekseev B. 9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. Front Pharmacol 2021; 12:777114. [PMID: 34955846 PMCID: PMC8696016 DOI: 10.3389/fphar.2021.777114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/08/2021] [Indexed: 11/13/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and lethal types of cancer. Although researchers have made significant efforts to study the mechanisms underlying CRC drug resistance, our knowledge of this disease is still limited, and novel therapies are in high demand. It is urgent to find new targeted therapy considering limited chemotherapy options. KRAS mutations are the most frequent molecular alterations in CRC. However, there are no approved K-Ras targeted therapies for these tumors yet. GSK-3β is demonstrated to be a critically important kinase for the survival and proliferation of K-Ras–dependent pancreatic cancer cells. In this study, we tested combinations of standard-of-care therapy and 9-ING-41, a small molecule inhibitor of GSK-3β, in CRC cell lines and patient-derived tumor organoid models of CRC. We demonstrate that 9-ING-41 inhibits the growth of CRC cells via a distinct from chemotherapy mechanism of action. Although molecular biomarkers of 9-ING-41 efficacy are yet to be identified, the addition of 9-ING-41 to the standard-of-care drugs 5-FU and oxaliplatin could significantly enhance growth inhibition in certain CRC cells. The results of the transcriptomic analysis support our findings of cell cycle arrest and DNA repair deficiency in 9-ING-41–treated CRC cells. Notably, we find substantial similarity in the changes of the transcriptomic profile after inhibition of GSK-3β and suppression of STK33, another critically important kinase for K-Ras–dependent cells, which could be an interesting point for future research. Overall, the results of this study provide a rationale for the further investigation of GSK-3 inhibitors in combination with standard-of-care treatment of CRC.
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Affiliation(s)
- Andrey Poloznikov
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Sergey Nikulin
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Larisa Bolotina
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | - Andrei Kachmazov
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
| | | | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Ildar Bakhtogarimov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergey Rodin
- Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Irina Gaisina
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois, Chicago, IL, United States
| | - Maxim Topchiy
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Andrey Asachenko
- A. V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russia
| | - Victor Novosad
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,Scientific Research Centre Bioclinicum, Moscow, Russia.,Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Boris Alekseev
- P. Hertsen Moscow Oncology Research Institute-Branch of the National Medical Research Radiological Centre of the Ministry of Health of Russian Federation, Moscow, Russia
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19
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Nersisyan S, Novosad V, Engibaryan N, Ushkaryov Y, Nikulin S, Tonevitsky A. ECM-Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer. Front Genet 2021; 12:782699. [PMID: 34938324 PMCID: PMC8685507 DOI: 10.3389/fgene.2021.782699] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/05/2021] [Indexed: 12/12/2022] Open
Abstract
Interactions of the extracellular matrix (ECM) and cellular receptors constitute one of the crucial pathways involved in colorectal cancer progression and metastasis. With the use of bioinformatics analysis, we comprehensively evaluated the prognostic information concentrated in the genes from this pathway. First, we constructed a ECM-receptor regulatory network by integrating the transcription factor (TF) and 5'-isomiR interaction databases with mRNA/miRNA-seq data from The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD). Notably, one-third of interactions mediated by 5'-isomiRs was represented by noncanonical isomiRs (isomiRs, whose 5'-end sequence did not match with the canonical miRBase version). Then, exhaustive search-based feature selection was used to fit prognostic signatures composed of nodes from the network for overall survival prediction. Two reliable prognostic signatures were identified and validated on the independent The Cancer Genome Atlas Rectum Adenocarcinoma (TCGA-READ) cohort. The first signature was made up by six genes, directly involved in ECM-receptor interaction: AGRN, DAG1, FN1, ITGA5, THBS3, and TNC (concordance index 0.61, logrank test p = 0.0164, 3-years ROC AUC = 0.68). The second hybrid signature was composed of three regulators: hsa-miR-32-5p, NR1H2, and SNAI1 (concordance index 0.64, logrank test p = 0.0229, 3-years ROC AUC = 0.71). While hsa-miR-32-5p exclusively regulated ECM-related genes (COL1A2 and ITGA5), NR1H2 and SNAI1 also targeted other pathways (adhesion, cell cycle, and cell division). Concordant distributions of the respective risk scores across four stages of colorectal cancer and adjacent normal mucosa additionally confirmed reliability of the models.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Victor Novosad
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Yuri Ushkaryov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Medway School of Pharmacy, University of Kent, Chatham, United Kingdom
| | - Sergey Nikulin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- P. Hertsen Moscow Oncology Research Institute—Branch, National Medical Research Radiological Centre, Ministry of Health of Russian Federation, Moscow, Russia
- School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
- SRC Bioclinicum, Moscow, Russia
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20
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Nersisyan S, Ahlers AK, Lange T, Wicklein D, Galatenko A, Bohnenberger H, Elakad O, Conradi LC, Genduso S, Maar H, Schiecke A, Maltseva D, Raygorodskaya M, Makarova J, Schumacher U, Tonevitsky A. Low expression of CD24 is associated with poor survival in colorectal cancer. Biochimie 2021; 192:91-101. [PMID: 34637894 DOI: 10.1016/j.biochi.2021.10.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/24/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022]
Abstract
In this study we analyzed expression of CD24 in a cohort of colorectal cancer patients using immunohistochemistry staining of CD24. We found a significant association between absence or low expression of CD24 (10% of membranous and 55% of cytoplasmic staining) and shortened patient survival. Protein localization played a crucial role in the prognosis: membranous form was the major and prognostic one in primary tumors, while cytoplasmic expression was elevated in liver metastases compared to the primary tumors and contained prognostic information. Then, using The Cancer Genome Atlas Colon Adenocarcinoma (TCGA-COAD) RNA-seq data, we showed that CD24 mRNA level was two-fold decreased in primary colorectal cancers compared to adjacent normal mucosa. Like the protein staining data, ten percent of patients with the lowest mRNA expression levels of CD24 in primary tumors had reduced survival compared to the ones with higher expression. To explain these findings mechanistically, shRNA-mediated CD24 knockdown was performed in HT-29 colorectal cancer cells. It resulted in the increase of cell migration in vitro, no changes in proliferation and apoptosis, and a slight decrease in cell invasion. As increased cell migration is a hallmark of metastasis formation, this finding corroborates the association of a decreased CD24 expression with poor prognosis. Differential gene expression analysis revealed upregulation of genes involved in cell migration in the group of patients with low CD24 expression, including integrin subunit α3 and α3, β3 subunits of laminin 332. Further co-expression analysis identified SPI1, STAT1 and IRF1 transcription factors as putative master-regulators in this group.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Ann-Kristin Ahlers
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia; Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | | | - Omar Elakad
- Institute of Pathology, University Medical Center, Göttingen, Germany
| | - Lena-Christin Conradi
- Clinic for General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Sandra Genduso
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Hanna Maar
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alina Schiecke
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Maria Raygorodskaya
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia
| | - Julia Makarova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Medical Center, Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia; SRC Bioclinicum, Moscow, Russia.
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21
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Knyazev E, Nersisyan S, Tonevitsky A. Endocytosis and Transcytosis of SARS-CoV-2 Across the Intestinal Epithelium and Other Tissue Barriers. Front Immunol 2021; 12:636966. [PMID: 34557180 PMCID: PMC8452982 DOI: 10.3389/fimmu.2021.636966] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
Since 2003, the world has been confronted with three new betacoronaviruses that cause human respiratory infections: SARS-CoV, which causes severe acute respiratory syndrome (SARS), MERS-CoV, which causes Middle East respiratory syndrome (MERS), and SARS-CoV-2, which causes Coronavirus Disease 2019 (COVID-19). The mechanisms of coronavirus transmission and dissemination in the human body determine the diagnostic and therapeutic strategies. An important problem is the possibility that viral particles overcome tissue barriers such as the intestine, respiratory tract, blood-brain barrier, and placenta. In this work, we will 1) consider the issue of endocytosis and the possibility of transcytosis and paracellular trafficking of coronaviruses across tissue barriers with an emphasis on the intestinal epithelium; 2) discuss the possibility of antibody-mediated transcytosis of opsonized viruses due to complexes of immunoglobulins with their receptors; 3) assess the possibility of the virus transfer into extracellular vesicles during intracellular transport; and 4) describe the clinical significance of these processes. Models of the intestinal epithelium and other barrier tissues for in vitro transcytosis studies will also be briefly characterized.
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Affiliation(s)
- Evgeny Knyazev
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), Moscow, Russia
| | - Alexander Tonevitsky
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,Faculty of Biology and Biotechnology, National Research University Higher School of Economics (HSE), Moscow, Russia
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22
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Nersisyan S, Zhiyanov A, Shkurnikov M, Tonevitsky A. T-CoV: a comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations. Nucleic Acids Res 2021; 50:D883-D887. [PMID: 34396391 PMCID: PMC8385993 DOI: 10.1093/nar/gkab701] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
Rapidly appearing SARS-CoV-2 mutations can affect T cell epitopes, which can help the virus to evade either CD8 or CD4 T-cell responses. We developed T-cell COVID-19 Atlas (T-CoV, https://t-cov.hse.ru) – the comprehensive web portal, which allows one to analyze how SARS-CoV-2 mutations alter the presentation of viral peptides by HLA molecules. The data are presented for common virus variants and the most frequent HLA class I and class II alleles. Binding affinities of HLA molecules and viral peptides were assessed with accurate in silico methods. The obtained results highlight the importance of taking HLA alleles diversity into account: mutation-mediated alterations in HLA-peptide interactions were highly dependent on HLA alleles. For example, we found that the essential number of peptides tightly bound to HLA-B*07:02 in the reference Wuhan variant ceased to be tight binders for the Indian (Delta) and the UK (Alpha) variants. In summary, we believe that T-CoV will help researchers and clinicians to predict the susceptibility of individuals with different HLA genotypes to infection with variants of SARS-CoV-2 and/or forecast its severity.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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23
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Abstract
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5'-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. In this manuscript, we analysed the distribution of miRNA cleavage positions across 31 different cancers using miRNA sequencing data of TCGA project. As a result, we found that the processing positions are not tissue specific and that all miRNAs could be correctly classified as ones exhibiting homogeneous or heterogeneous cleavage at one of the four cleavage sites. In 42% of cases (42 out of 100 miRNAs), we observed imprecise 5'-end Dicer cleavage, while this fraction was only 14% for Drosha (14 out of 99). To the contrary, almost all cleavage sites of 3'-ends (either Drosha or Dicer) were heterogeneous. With the use of only four nucleotides surrounding a 5'-end Dicer cleavage position we built a model which allowed us to distinguish between homogeneous and heterogeneous cleavage with the reliable quality (ROC AUC = 0.68). Finally, we showed the possible applications of the study by the analysis of two 5'-end isoforms originating from the same exogeneous shRNA hairpin. It turned out that the less expressed shRNA variant was functionally active, which led to the increased off-targeting. Thus, the obtained results could be applied to the design of shRNAs whose processing will result in a single 5'-variant.
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Affiliation(s)
- Anton Zhiyanov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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24
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Kemper M, Schiecke A, Maar H, Nikulin S, Poloznikov A, Galatenko V, Tachezy M, Gebauer F, Lange T, Riecken K, Tonevitsky A, Aigner A, Izbicki J, Schumacher U, Wicklein D. Integrin alpha-V is an important driver in pancreatic adenocarcinoma progression. J Exp Clin Cancer Res 2021; 40:214. [PMID: 34174926 PMCID: PMC8235815 DOI: 10.1186/s13046-021-01946-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 04/13/2021] [Indexed: 01/10/2023]
Abstract
Background Mesothelial E- and P-selectins substantially mediate the intraperitoneal spread of Pancreatic ductal adenocarcinoma (PDA) cells in xenograft models. In the absence of selectins in the host, the integrin subunit alpha-V (ITGAV, CD51) was upregulated in the remaining metastatic deposits. Here we present the first experimental study to investigate if ITGAV plays a functional role in PDA tumor growth and progression with a particular focus on intraperitoneal carcinomatosis. Methods Knockdown of ITGAV was generated using an RNA interference-mediated approach in two PDA cell lines. Tumor growth, intraperitoneal and distant metastasis were analyzed in a xenograft model. Cell lines were characterized in vitro. Gene expression of the xenograft tumors was analyzed. Patient samples were histologically classified and associations to survival were evaluated. Results The knockdown of ITGAV in PDA cells strongly reduces primary tumor growth, peritoneal carcinomatosis and spontaneous pulmonary metastasis. ITGAV activates latent TGF-β and thereby drives epithelial-mesenchymal transition. Combined depletion of ITGAV on the tumor cells and E- and P-selectins in the tumor-host synergistically almost abolishes intraperitoneal spread. Accordingly, high expression of ITGAV in PDA cells was associated with reduced survival in patients. Conclusion Combined depletion of ITGAV in PDA cells and E- and P-selectins in host mice massively suppresses intraperitoneal carcinomatosis of PDA cells xenografted into immunodeficient mice, confirming the hypothesis of a partly redundant adhesion cascade of metastasizing cancer cells. Our data strongly encourage developing novel therapeutic approaches for the combined targeting of E- and P-selectins and ITGAV in PDA. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01946-2.
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Affiliation(s)
- Marius Kemper
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany. .,Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Alina Schiecke
- Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hanna Maar
- Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sergey Nikulin
- Dmitry Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Andrey Poloznikov
- Dmitry Rogachev Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Vladimir Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Michael Tachezy
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Florian Gebauer
- Department of General, Visceral and Tumor Surgery, University Hospital Cologne, Köln, Germany
| | - Tobias Lange
- Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, Higher School of Economics University, Moscow, Russia
| | - Achim Aigner
- Rudolf-Boehm-Institute for Pharmacology and Toxicology, Clinical Pharmacology, Medical Faculty, University of Leipzig, Leipzig, Germany
| | - Jakob Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
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25
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Nikulin S, Zakharova G, Poloznikov A, Raigorodskaya M, Wicklein D, Schumacher U, Nersisyan S, Bergquist J, Bakalkin G, Astakhova L, Tonevitsky A. Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. Front Genet 2021; 12:662843. [PMID: 34149804 PMCID: PMC8206645 DOI: 10.3389/fgene.2021.662843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/20/2021] [Indexed: 12/09/2022] Open
Abstract
Breast cancer (BC) is the leading cause of death from malignant neoplasms among women worldwide, and metastatic BC presents the biggest problems for treatment. Previously, it was shown that lower expression of ELOVL5 and IGFBP6 genes is associated with a higher risk of the formation of distant metastases in BC. In this work, we studied the change in phenotypical traits, as well as in the transcriptomic and proteomic profiles of BC cells as a result of the stable knockdown of ELOVL5 and IGFBP6 genes. The knockdown of ELOVL5 and IGFBP6 genes was found to lead to a strong increase in the expression of the matrix metalloproteinase (MMP) MMP1. These results were in good agreement with the correlation analysis of gene expression in tumor samples from patients and were additionally confirmed by zymography. The knockdown of ELOVL5 and IGFBP6 genes was also discovered to change the expression of a group of genes involved in the formation of intercellular contacts. In particular, the expression of the CDH11 gene was markedly reduced, which also complies with the correlation analysis. The spheroid formation assay showed that intercellular adhesion decreased as a result of the knockdown of the ELOVL5 and IGFBP6 genes. Thus, the obtained data indicate that malignant breast tumors with reduced expression of the ELOVL5 and IGFBP6 genes can metastasize with a higher probability due to a more efficient invasion of tumor cells.
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Affiliation(s)
- Sergey Nikulin
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | | | - Andrey Poloznikov
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia.,School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Maria Raigorodskaya
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia.,Scientific Research Centre Bioclinicum, Moscow, Russia
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia
| | - Jonas Bergquist
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Georgy Bakalkin
- Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Lidiia Astakhova
- Scientific Research Centre Bioclinicum, Moscow, Russia.,School of Life Sciences, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics, Moscow, Russia.,Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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26
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Nersisyan S, Galatenko A, Chekova M, Tonevitsky A. Hypoxia-Induced miR-148a Downregulation Contributes to Poor Survival in Colorectal Cancer. Front Genet 2021; 12:662468. [PMID: 34135940 PMCID: PMC8202010 DOI: 10.3389/fgene.2021.662468] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 04/21/2021] [Indexed: 11/25/2022] Open
Abstract
Hypoxia is an extensively investigated condition due to its contribution to various pathophysiological processes including cancer progression and metastasis formation. MicroRNAs (miRNAs) are well-known post-transcriptional gene expression regulators. However, their contribution to molecular response to hypoxia is highly dependent on cell/tissue types and causes of hypoxia. One of the most important examples is colorectal cancer, where no consensus on hypoxia-regulated miRNAs has been reached so far. In this work, we applied integrated mRNA and small RNA sequencing, followed by bioinformatics analysis, to study the landscape of hypoxia-induced miRNA and mRNA expression alterations in human colorectal cancer cell lines (HT-29 and Caco-2). A hypoxic microenvironment was chemically modeled using two different treatments: cobalt(II) chloride and oxyquinoline. Only one miRNA, hsa-miR-210-3p, was upregulated in all experimental conditions, while there were nine differentially expressed miRNAs under both treatments within the same cell line. Further bioinformatics analysis revealed a complex hypoxia-induced regulatory network: hypoxic downregulation of hsa-miR-148a-3p led to the upregulation of its two target genes, ITGA5 and PRNP, which was shown to be a factor contributing to tumor progression and poor survival in colorectal cancer patients.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia.,Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Milena Chekova
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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27
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Nersisyan S, Galatenko A, Galatenko V, Shkurnikov M, Tonevitsky A. miRGTF-net: Integrative miRNA-gene-TF network analysis reveals key drivers of breast cancer recurrence. PLoS One 2021; 16:e0249424. [PMID: 33852600 PMCID: PMC8046230 DOI: 10.1371/journal.pone.0249424] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 03/17/2021] [Indexed: 12/14/2022] Open
Abstract
Analysis of regulatory networks is a powerful framework for identification and quantification of intracellular interactions. We introduce miRGTF-net, a novel tool for construction of miRNA-gene-TF networks. We consider multiple transcriptional and post-transcriptional interaction types, including regulation of gene and miRNA expression by transcription factors, gene silencing by miRNAs, and co-expression of host genes with their intronic miRNAs. The underlying algorithm uses information on experimentally validated interactions as well as integrative miRNA/mRNA expression profiles in a given set of samples. The latter ensures simultaneous tissue-specificity and biological validity of interactions. We applied miRGTF-net to paired miRNA/mRNA-sequencing data of breast cancer samples from The Cancer Genome Atlas (TCGA). Together with topological analysis of the constructed network we showed that considered players can form reliable prognostic gene signatures for ER-positive breast cancer. A number of signatures demonstrated remarkably high accuracy on transcriptomic data obtained by both microarrays and RNA sequencing from several independent patient cohorts. Furthermore, an essential part of prognostic genes were identified as direct targets of transcription factor E2F1. The putative interplay between estrogen receptor alpha and E2F1 was suggested as a potential recurrence factor in patients treated with tamoxifen. Source codes of miRGTF-net are available at GitHub (https://github.com/s-a-nersisyan/miRGTF-net).
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- * E-mail:
| | - Alexei Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
- Moscow Center for Fundamental and Applied Mathematics, Moscow, Russia
| | - Vladimir Galatenko
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Shkurnikov
- P.A. Hertsen Moscow Oncology Research Center, Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
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28
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Shkurnikov M, Nersisyan S, Jankevic T, Galatenko A, Gordeev I, Vechorko V, Tonevitsky A. Association of HLA Class I Genotypes With Severity of Coronavirus Disease-19. Front Immunol 2021; 12:641900. [PMID: 33732261 PMCID: PMC7959787 DOI: 10.3389/fimmu.2021.641900] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
Human leukocyte antigen (HLA) class I molecules play a crucial role in the development of a specific immune response to viral infections by presenting viral peptides at the cell surface where they will be further recognized by T cells. In the present manuscript, we explored whether HLA class I genotypes can be associated with the critical course of Coronavirus Disease-19 by searching possible connections between genotypes of deceased patients and their age at death. HLA-A, HLA-B, and HLA-C genotypes of n = 111 deceased patients with COVID-19 (Moscow, Russia) and n = 428 volunteers were identified with next-generation sequencing. Deceased patients were split into two groups according to age at the time of death: n = 26 adult patients aged below 60 and n = 85 elderly patients over 60. With the use of HLA class I genotypes, we developed a risk score (RS) which was associated with the ability to present severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) peptides by the HLA class I molecule set of an individual. The resulting RS was significantly higher in the group of deceased adults compared to elderly adults [p = 0.00348, area under the receiver operating characteristic curve (AUC ROC = 0.68)]. In particular, presence of HLA-A*01:01 allele was associated with high risk, while HLA-A*02:01 and HLA-A*03:01 mainly contributed to low risk. The analysis of patients with homozygosity strongly highlighted these results: homozygosity by HLA-A*01:01 accompanied early deaths, while only one HLA-A*02:01 homozygote died before 60 years of age. Application of the constructed RS model to an independent Spanish patients cohort (n = 45) revealed that the score was also associated with the severity of the disease. The obtained results suggest the important role of HLA class I peptide presentation in the development of a specific immune response to COVID-19.
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Affiliation(s)
- Maxim Shkurnikov
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Tatjana Jankevic
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Alexei Galatenko
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Ivan Gordeev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
- O.M. Filatov City Clinical Hospital, Moscow, Russia
| | | | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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29
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Nersisyan S, Engibaryan N, Gorbonos A, Kirdey K, Makhonin A, Tonevitsky A. Potential role of cellular miRNAs in coronavirus-host interplay. PeerJ 2020; 8:e9994. [PMID: 32983652 PMCID: PMC7497610 DOI: 10.7717/peerj.9994] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/28/2020] [Indexed: 12/25/2022] Open
Abstract
Host miRNAs are known as important regulators of virus replication and pathogenesis. They can interact with various viruses through several possible mechanisms including direct binding of viral RNA. Identification of human miRNAs involved in coronavirus-host interplay becomes important due to the ongoing COVID-19 pandemic. In this article we performed computational prediction of high-confidence direct interactions between miRNAs and seven human coronavirus RNAs. As a result, we identified six miRNAs (miR-21-3p, miR-195-5p, miR-16-5p, miR-3065-5p, miR-424-5p and miR-421) with high binding probability across all analyzed viruses. Further bioinformatic analysis of binding sites revealed high conservativity of miRNA binding regions within RNAs of human coronaviruses and their strains. In order to discover the entire miRNA-virus interplay we further analyzed lungs miRNome of SARS-CoV infected mice using publicly available miRNA sequencing data. We found that miRNA miR-21-3p has the largest probability of binding the human coronavirus RNAs and being dramatically up-regulated in mouse lungs during infection induced by SARS-CoV.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Narek Engibaryan
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | | | - Ksenia Kirdey
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexey Makhonin
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
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30
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Nersisyan S, Shkurnikov M, Turchinovich A, Knyazev E, Tonevitsky A. Integrative analysis of miRNA and mRNA sequencing data reveals potential regulatory mechanisms of ACE2 and TMPRSS2. PLoS One 2020; 15:e0235987. [PMID: 32726325 PMCID: PMC7390267 DOI: 10.1371/journal.pone.0235987] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 06/25/2020] [Indexed: 12/17/2022] Open
Abstract
Development of novel approaches for regulating the expression of angiotensin-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) is becoming increasingly important within the context of the ongoing COVID-19 pandemic since these enzymes play a crucial role in cell infection. In this work we searched for putative ACE2 and TMPRSS2 expression regulation networks mediated by various miRNA isoforms (isomiR) across different human organs using publicly available paired miRNA/mRNA-sequencing data from The Cancer Genome Atlas (TCGA) project. As a result, we identified several miRNA families targeting ACE2 and TMPRSS2 genes in multiple tissues. In particular, we found that lysine-specific demethylase 5B (JARID1B), encoded by the KDM5B gene, can indirectly affect ACE2 / TMPRSS2 expression by repressing transcription of hsa-let-7e / hsa-mir-125a and hsa-mir-141 / hsa-miR-200 miRNA families which are targeting these genes.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Shkurnikov
- P.A. Hertsen Moscow Oncology Research Center, Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Evgeny Knyazev
- Faculty of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, Higher School of Economics, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
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31
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Maltseva D, Raygorodskaya M, Knyazev E, Zgoda V, Tikhonova O, Zaidi S, Nikulin S, Baranova A, Turchinovich A, Rodin S, Tonevitsky A. Knockdown of the α5 laminin chain affects differentiation of colorectal cancer cells and their sensitivity to chemotherapy. Biochimie 2020; 174:107-116. [PMID: 32334043 DOI: 10.1016/j.biochi.2020.04.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 04/13/2020] [Accepted: 04/14/2020] [Indexed: 02/07/2023]
Abstract
The interaction of tumor cells with the extracellular matrix (ECM) may affect the rate of cancer progression and metastasis. One of the major components of ECM are laminins, the heterotrimeric glycoproteins consisting of α-, β-, and γ-chains (αβγ). Laminins interact with their cell surface receptors and, thus, regulate multiple cellular processes. In this work, we demonstrate that shRNA-mediated knockdown of the α5 laminin chain results in Wnt- and mTORC1-dependent partial dedifferentiation of colorectal cancer cells. Furthermore, we showed that this dedifferentiation involved activation of ER-stress signaling, pathway promoting the sensitivity of cells to 5-fluorouracil.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya str. 13/4, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, 117997, Moscow, Russia; Scientific Research Center Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia.
| | - Maria Raygorodskaya
- Scientific Research Center Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia
| | - Evgeny Knyazev
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya str. 13/4, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, 117997, Moscow, Russia
| | - Victor Zgoda
- Institute of Biomedical Chemistry, Pogodinskaya str. 10, 119121, Moscow, Russia
| | - Olga Tikhonova
- Institute of Biomedical Chemistry, Pogodinskaya str. 10, 119121, Moscow, Russia
| | - Shan Zaidi
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA
| | - Sergey Nikulin
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya str. 13/4, 117997, Moscow, Russia; Moscow Institute of Physics and Technology, Institutskiy per. 9, 141700, Dolgoprudny, Russia
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, 22030, USA; Moscow Institute of Physics and Technology, Institutskiy per. 9, 141700, Dolgoprudny, Russia; Research Center of Medical Genetics, Moskvorechye str. 1, 115522, Moscow, Russia
| | | | - Sergey Rodin
- Department of Surgical Sciences, Ångström Laboratory, Uppsala University, 752 37, Uppsala, Sweden
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, National Research University Higher School of Economics, Myasnitskaya str. 13/4, 117997, Moscow, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Miklukho-Maklaya str. 16/10, 117997, Moscow, Russia; Scientific Research Center Bioclinicum, Ugreshskaya str. 2/85, 115088, Moscow, Russia.
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32
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Marx U, Akabane T, Andersson TB, Baker E, Beilmann M, Beken S, Brendler-Schwaab S, Cirit M, David R, Dehne EM, Durieux I, Ewart L, Fitzpatrick SC, Frey O, Fuchs F, Griffith LG, Hamilton GA, Hartung T, Hoeng J, Hogberg H, Hughes DJ, Ingber DE, Iskandar A, Kanamori T, Kojima H, Kuehnl J, Leist M, Li B, Loskill P, Mendrick DL, Neumann T, Pallocca G, Rusyn I, Smirnova L, Steger-Hartmann T, Tagle DA, Tonevitsky A, Tsyb S, Trapecar M, Van de Water B, Van den Eijnden-van Raaij J, Vulto P, Watanabe K, Wolf A, Zhou X, Roth A. Biology-inspired microphysiological systems to advance patient benefit and animal welfare in drug development. ALTEX 2020; 37:365-394. [PMID: 32113184 PMCID: PMC7863570 DOI: 10.14573/altex.2001241] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 02/27/2020] [Indexed: 12/24/2022]
Abstract
The first microfluidic microphysiological systems (MPS) entered the academic scene more than 15 years ago and were considered an enabling technology to human (patho)biology in vitro and, therefore, provide alternative approaches to laboratory animals in pharmaceutical drug development and academic research. Nowadays, the field generates more than a thousand scientific publications per year. Despite the MPS hype in academia and by platform providers, which says this technology is about to reshape the entire in vitro culture landscape in basic and applied research, MPS approaches have neither been widely adopted by the pharmaceutical industry yet nor reached regulated drug authorization processes at all. Here, 46 leading experts from all stakeholders - academia, MPS supplier industry, pharmaceutical and consumer products industries, and leading regulatory agencies - worldwide have analyzed existing challenges and hurdles along the MPS-based assay life cycle in a second workshop of this kind in June 2019. They identified that the level of qualification of MPS-based assays for a given context of use and a communication gap between stakeholders are the major challenges for industrial adoption by end-users. Finally, a regulatory acceptance dilemma exists against that background. This t4 report elaborates on these findings in detail and summarizes solutions how to overcome the roadblocks. It provides recommendations and a roadmap towards regulatory accepted MPS-based models and assays for patients' benefit and further laboratory animal reduction in drug development. Finally, experts highlighted the potential of MPS-based human disease models to feedback into laboratory animal replacement in basic life science research.
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Affiliation(s)
- Uwe Marx
- TissUse GmbH, Berlin, Germany.,Technische Universitaet Berlin, Germany
| | - Takafumi Akabane
- Stem Cell Evaluation Technology Research Association, Tokyo, Japan
| | - Tommy B Andersson
- DMPK, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Elizabeth Baker
- Physicians Committee for Responsible Medicine, Washington DC, USA
| | - Mario Beilmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Non-clinical Drug Safety, Biberach, Germany
| | - Sonja Beken
- Federal Agency for Medicines and Health Products, Brussels, Belgium
| | | | | | - Rhiannon David
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Lorna Ewart
- Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Suzanne C Fitzpatrick
- US Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD, USA
| | | | - Florian Fuchs
- Novartis Institutes for BioMedical Research Chemical Biology & Therapeutics, Basel, Switzerland
| | | | | | - Thomas Hartung
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA.,Center for Alternatives to Animal Testing-Europe, University of Konstanz, Konstanz, Germany.,AxoSim, Inc., New Orleans, LA, USA
| | - Julia Hoeng
- Philip Morris International R&D, Neuchâtel, Switzerland
| | - Helena Hogberg
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Donald E Ingber
- Wyss Institute for Biology Inspired Engineering, Harvard University, Boston, USA
| | | | - Toshiyuki Kanamori
- National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Hajime Kojima
- Japanese Center for Validation of Animal Methods, Tokyo, Japan
| | | | - Marcel Leist
- Center for Alternatives to Animal Testing-Europe, University of Konstanz, Konstanz, Germany
| | - Bo Li
- National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, Beijing, P.R. China
| | - Peter Loskill
- Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB, Stuttgart, Germany.,Faculty of Medicine, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Donna L Mendrick
- National Center for Toxicological Research, FDA, Silver Spring, MD, USA
| | | | - Giorgia Pallocca
- Center for Alternatives to Animal Testing-Europe, University of Konstanz, Konstanz, Germany
| | - Ivan Rusyn
- Texas A&M University, College Station, TX, USA
| | - Lena Smirnova
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | | | - Danilo A Tagle
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Tonevitsky
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Russia.,National Research University Higher School of Economics, Russia
| | - Sergej Tsyb
- Russian Ministry of Production and Trade, Moscow, Russia
| | | | | | | | | | | | | | - Xiaobing Zhou
- National Center for Safety Evaluation of Drugs, National Institutes for Food and Drug Control, Beijing, P.R. China
| | - Adrian Roth
- F. Hoffmann-La Roche Ltd, Roche Innovation Center Basel, Switzerland
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33
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Nersisyan S, Shkurnikov M, Poloznikov A, Turchinovich A, Burwinkel B, Anisimov N, Tonevitsky A. A Post-Processing Algorithm for miRNA Microarray Data. Int J Mol Sci 2020; 21:ijms21041228. [PMID: 32059403 PMCID: PMC7072892 DOI: 10.3390/ijms21041228] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 02/04/2020] [Accepted: 02/10/2020] [Indexed: 11/16/2022] Open
Abstract
One of the main disadvantages of using DNA microarrays for miRNA expression profiling is the inability of adequate comparison of expression values across different miRNAs. This leads to a large amount of miRNAs with high scores which are actually not expressed in examined samples, i.e., false positives. We propose a post-processing algorithm which performs scoring of miRNAs in the results of microarray analysis based on expression values, time of discovery of miRNA, and correlation level between the expressions of miRNA and corresponding pre-miRNA in considered samples. The algorithm was successfully validated by the comparison of the results of its application to miRNA microarray breast tumor samples with publicly available miRNA-seq breast tumor data. Additionally, we obtained possible reasons why miRNA can appear as a false positive in microarray study using paired miRNA sequencing and array data. The use of DNA microarrays for estimating miRNA expression profile is limited by several factors. One of them consists of problems with comparing expression values of different miRNAs. In this work, we show that situation can be significantly improved if some additional information is taken into consideration in a comparison.
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Affiliation(s)
- Stepan Nersisyan
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Leninskie Gory 1, 119991 Moscow, Russia
- Correspondence:
| | - Maxim Shkurnikov
- P.A. Hertsen Moscow Oncology Research Center, Branch of National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Second Botkinsky lane 3, 125284 Moscow, Russia;
| | - Andrey Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, 249036 Obninks, Russia;
- School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia;
| | - Andrey Turchinovich
- Molecular Epidemiology C080, German Cancer Research Center, 69120 Heidelberg, Germany; (A.T.); (B.B.)
- SciBerg e.Kfm, 68309 Mannheim, Germany
| | - Barbara Burwinkel
- Molecular Epidemiology C080, German Cancer Research Center, 69120 Heidelberg, Germany; (A.T.); (B.B.)
- University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Nikita Anisimov
- School of Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia;
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, 117312 Moscow, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, 117997 Moscow, Russia
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34
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Gerasimenko T, Nikulin S, Zakharova G, Poloznikov A, Petrov V, Baranova A, Tonevitsky A. Impedance Spectroscopy as a Tool for Monitoring Performance in 3D Models of Epithelial Tissues. Front Bioeng Biotechnol 2020; 7:474. [PMID: 32039179 PMCID: PMC6992543 DOI: 10.3389/fbioe.2019.00474] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/23/2019] [Indexed: 12/29/2022] Open
Abstract
In contrast to traditional 2D cell cultures, both 3D models and organ-on-a-chip devices allow the study of the physiological responses of human cells. These models reconstruct human tissues in conditions closely resembling the body. Translation of these techniques into practice is hindered by associated labor costs, a need which may be remedied by automation. Impedance spectroscopy (IS) is a promising, automation-compatible label-free technology allowing to carry out a wide range of measurements both in real-time and as endpoints. IS has been applied to both the barrier cultures and the 3D constructs. Here we provide an overview of the impedance-based analysis in different setups and discuss its utility for organ-on-a-chip devices. Most attractive features of impedance-based assays are their compatibility with high-throughput format and supports for the measurements in real time with high temporal resolution, which allow tracing of the kinetics. As of now, IS-based techniques are not free of limitations, including imperfect understanding of the parameters that have their effects on the impedance, especially in 3D cell models, and relatively high cost of the consumables. Moreover, as the theory of IS stems from electromagnetic theory and is quite complex, work on popularization and explanation of the method for experimental biologists is required. It is expected that overcoming these limitations will lead to eventual establishing IS based systems as a standard for automated management of cell-based experiments in both academic and industry environments.
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Affiliation(s)
| | - Sergey Nikulin
- Scientific Research Centre Bioclinicum, Moscow, Russia
- Laboratory of Microphysiological Systems, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Galina Zakharova
- Laboratory of Molecular Oncoendocrinology, Endocrinology Research Centre, Moscow, Russia
| | - Andrey Poloznikov
- Laboratory of Microphysiological Systems, School of Biomedicine, Far Eastern Federal University, Vladivostok, Russia
- Department of Translational Oncology, National Medical Research Radiological Center of the Ministry of Health of the Russian Federation, Obninsk, Russia
| | - Vladimir Petrov
- Scientific Research Centre Bioclinicum, Moscow, Russia
- Department of Development and Research of Micro- and Nanosystems, Institute of Nanotechnologies of Microelectronics RAS, Moscow, Russia
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
- Laboratory of Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Laboratory of Functional Genomics, “Research Centre for Medical Genetics”, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia
- Laboratory of Microfluidic Technologies for Biomedicine, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia
- art photonics GmbH, Berlin, Germany
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35
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Shkurnikov M, Nikulin S, Nersisyan S, Poloznikov A, Zaidi S, Baranova A, Schumacher U, Wicklein D, Tonevitsky A. LAMA4-Regulating miR-4274 and Its Host Gene SORCS2 Play a Role in IGFBP6-Dependent Effects on Phenotype of Basal-Like Breast Cancer. Front Mol Biosci 2019; 6:122. [PMID: 31781574 PMCID: PMC6857517 DOI: 10.3389/fmolb.2019.00122] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 10/22/2019] [Indexed: 12/12/2022] Open
Abstract
Specificity of RNAi to selected target is challenged by off-target effects, both canonical and non-canonical. Notably, more than half of all human microRNAs are co-expressed with hosting them proteincoding genes. Here we dissect regulatory subnetwork centered on IGFBP6 gene, which is associated with low proliferative state and high migratory activity of basal-like breast cancer. We inhibited expression of IGFBP6 gene in a model cell line for basal-like breast carcinoma MDA-MB-231, then traced secondary and tertiary effects of this knockdown to LAMA4, a laminin encoding gene that contributes to the phenotype of triple-negative breast cancer. LAMA4-regulating miRNA miR-4274 and its host gene SORCS2 were highlighted as intermediate regulators of the expression levels of LAMA4, which correlated in a basal-like breast carcinoma sample subset of TCGA to the levels of SORCS2 negatively. Overall, our study points that the secondary and tertiary layers of regulatory interactions are certainly underappreciated. As these types of molecular event may significantly contribute to the formation of the cell phenotypes after RNA interference based knockdowns, further studies of multilayered molecular networks affected by RNAi are warranted.
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Affiliation(s)
- Maxim Shkurnikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninks, Russia
| | | | - Stepan Nersisyan
- Faculty of Mechanics and Mathematics, Lomonosov Moscow State University, Moscow, Russia
| | - Andrey Poloznikov
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Obninks, Russia.,Far Eastern Federal University, Vladivostok, Russia
| | - Shan Zaidi
- School of Systems Biology, George Mason University, Fairfax, VA, United States
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States.,Research Center of Medical Genetics, Moscow, Russia
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Cancer Center, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Cancer Center, University Medical-Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnologies, Higher School of Economics, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,Art Photonics GmbH, Berlin, Germany
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36
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Marx U, Walles H, Hoffmann S, Lindner G, Horland R, Sonntag F, Klotzbach U, Sakharov D, Tonevitsky A, Lauster R. ‘Human-on-a-chip’ Developments: A Translational Cutting-edge Alternative to Systemic Safety Assessment and Efficiency Evaluation of Substances in Laboratory Animals and Man? Altern Lab Anim 2019; 40:235-57. [DOI: 10.1177/026119291204000504] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Uwe Marx
- Technische Universität Berlin, Department of Biotechnology, Berlin, Germany
| | | | - Silke Hoffmann
- Technische Universität Berlin, Department of Biotechnology, Berlin, Germany
| | - Gerd Lindner
- Technische Universität Berlin, Department of Biotechnology, Berlin, Germany
| | - Reyk Horland
- Technische Universität Berlin, Department of Biotechnology, Berlin, Germany
| | - Frank Sonntag
- Fraunhofer-Institut für Werkstoff- und Strahltechnik IWS, Dresden, Germany
| | - Udo Klotzbach
- Fraunhofer-Institut für Werkstoff- und Strahltechnik IWS, Dresden, Germany
| | | | | | - Roland Lauster
- Technische Universität Berlin, Department of Biotechnology, Berlin, Germany
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37
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Sakharov D, Maltseva D, Knyazev E, Nikulin S, Poloznikov A, Shilin S, Baranova A, Tsypina I, Tonevitsky A. Towards embedding Caco-2 model of gut interface in a microfluidic device to enable multi-organ models for systems biology. BMC Syst Biol 2019; 13:19. [PMID: 30836980 PMCID: PMC6399809 DOI: 10.1186/s12918-019-0686-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Background A cancer cell line originating from human epithelial colorectal adenocarcinoma (Caco-2 cells) serves as a high capacity model for a preclinical screening of drugs. Recent need for incorporating barrier tissue into multi-organ chips calls for inclusion of Caco-2 cells into microperfused environment. Results This article describes a series of systems biology insights obtained from comparing Caco-2 models cells grown as conventional 2D layer and in a microfluidic chip. When basic electrical parameters of Caco-2 monolayers were evaluated using impedance spectrometry and MTT assays, no differences were noted. On the other hand, the microarray profiling of mRNAs and miRNAs revealed that grows on a microfluidic chip leads to the change in the production of specific miRNA, which regulate a set of genes for cell adhesion molecules (CAMs), and provide for more complete differentiation of Caco-2 monolayer. Moreover, the sets of miRNAs secreted at the apical surface of Caco-2 monolayers grown in conventional 2D culture and in microfluidic device differ. Conclusions When integrated into a multi-tissue platform, Caco-2 cells may aid in generating insights into complex pathophysiological processes, not possible to dissect in conventional cultures.
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Affiliation(s)
| | | | | | | | | | | | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax VA, USA.,Research Center of Medical Genetics, Moscow, Russia
| | - Irina Tsypina
- SRC BioClinicum, Moscow, Russia.,Department of Cell Biology, Higher School of Economics, Moscow, Russia
| | - Alexander Tonevitsky
- SRC BioClinicum, Moscow, Russia.,Department of Cell Biology, Higher School of Economics, Moscow, Russia.,Art photonics GmbH, Berlin, Germany
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38
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Abstract
Exosomes and microvesicles are two major categories of extracellular vesicles (EVs) released by almost all cell types and are highly abundant in biological fluids. Both the molecular composition of EVs and their release are thought to be strictly regulated by external stimuli. Multiple studies have consistently demonstrated that EVs transfer proteins, lipids and RNA between various cell types, thus mediating intercellular communication, and signaling. Importantly, small non-coding RNAs within EVs are thought to be major contributors to the molecular events occurring in the recipient cell. Furthermore, RNA cargo in exosomes and microvesicles could hold tremendous potential as non-invasive biomarkers for multiple disorders, including pathologies of the immune system. This mini-review is aimed to provide the state-of-the-art in the EVs-associated RNA transcriptome field, as well as the comprehensive analysis of previous studies characterizing RNA content within EVs released by various cells using next-generation sequencing. Finally, we highlight the technical challenges associated with obtaining pure EVs and deep sequencing of the EV-associated RNAs.
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Affiliation(s)
- Andrey Turchinovich
- SciBerg e.Kfm, Mannheim, Germany.,Molecular Epidemiology C080, German Cancer Research Center, Heidelberg, Germany
| | - Oxana Drapkina
- National Medical Research Center for Preventive Medicine, Moscow, Russia
| | - Alexander Tonevitsky
- Department of Cell Biology, Higher School of Economics, Moscow, Russia.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Moscow, Russia.,SRC BioClinicum, Moscow, Russia
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Baranova A, Maltseva D, Tonevitsky A. Adipose may actively delay progression of NAFLD by releasing tumor-suppressing, anti-fibrotic miR-122 into circulation. Obes Rev 2019; 20:108-118. [PMID: 30248223 DOI: 10.1111/obr.12765] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/07/2018] [Accepted: 08/09/2018] [Indexed: 12/12/2022]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is the most common liver pathology. Here we propose tissue-cooperative, homeostatic model of NAFLD. During early stages of NAFLD the intrahepatic production of miR-122 falls, while the secretion of miRNA-containing exosomes by adipose increases. Bloodstream carries exosome to the liver, where their miRNA cargo is released to regulate their intrahepatic targets. When the deterioration of adipose catches up with the failing hepatic parenchyma, the external supply of liver-supporting miRNAs gradually tapers off, leading to the fibrotic decompensation of the liver and an increase in hepatic carcinogenesis. This model may explain paradoxical observations of the disease-associated decrease in intrahepatic production of certain miRNAs with an increase in their levels in serum. Infusions of miR-122 and, possibly, some other miRNAs may be efficient for preventing NAFLD-associated hepatocellular carcinoma. The best candidates for exosome-wrapped miRNA producer are adipose tissue-derived mesenchymal stem cells (MSCs), known for their capacity to shed large amounts of exosomes into the media. Notably, MSC-derived exosomes with no specific loading are already tested in patients with liver fibrosis. Carrier exosomes may be co-manufactured along with their cargo. Exosome-delivered miRNA cocktails may augment functioning of human organs suffering from a variety of chronic diseases.
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Affiliation(s)
- A Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, USA.,Research Center for Medical Genetics, Moscow, Russia
| | - D Maltseva
- Department of Fundamental Medicine, School of Biomedicine, Far Eastern Federal University (FEFU), Vladivostok, Russia.,Scientific Research Center Bioclinicum (SRC Bioclinicum), Moscow, Russia
| | - A Tonevitsky
- Scientific Research Center Bioclinicum (SRC Bioclinicum), Moscow, Russia.,Higher School of Economics, Moscow, Russia
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Turchinovich A, Baranova A, Drapkina O, Tonevitsky A. Cell-Free Circulating Nucleic Acids as Early Biomarkers for NAFLD and NAFLD-Associated Disorders. Front Physiol 2018; 9:1256. [PMID: 30294278 PMCID: PMC6158334 DOI: 10.3389/fphys.2018.01256] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 08/20/2018] [Indexed: 12/16/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the worldwide most common cause of chronic liver pathology, which prevalence strongly correlates with the increasing incidence of diabetes, obesity and metabolic syndrome in the general population. Simple steatosis, the earliest NAFLD stage, usually remains asymptomatic, and appropriate changes in the lifestyle, as well as the diet, can reverse the affected liver into the healthy state. The potential of simple steatosis to progress into severe fibrotic stages and to facilitate carcinogenesis necessitates timely NAFLD detection and risk stratification in community-based healthcare settings. Since their initial discovery a decade ago, extracellular circulating miRNAs have been found in all human biological fluids including blood and shown to hold great promises as non-invasive biomarkers. Normally, intracellular miRNAs participate in the regulation of gene expression, but once released by dying/dead cells they remain highly stable in the extracellular environment for prolonged periods. Therefore, circulating miRNA profiles can reflect the ongoing pathogenic processes in body's tissues and organs, and enable highly sensitive non-invasive diagnosis of multiple disorders. A non-urgent character of the NAFLD-related decision-making justifies the use of chronic liver diseases as an excellent test case for examining the practical utility of circulating miRNAs as biomarkers for longitudinal monitoring of human health. In this review, we summarize the state-of-the-art in the field of early diagnosis of NAFLD using circulating blood miRNAs, and stress the necessity of additional experimental validation of their diagnostic potential. We further emphasize on the potential diagnostics promises of other cell-free RNA species found in human biological fluids.
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Affiliation(s)
- Andrey Turchinovich
- SciBerg e.Kfm, Mannheim, Germany
- Molecular Epidemiology C080, German Cancer Research Center, Heidelberg, Germany
| | - Ancha Baranova
- School of Systems Biology, George Mason University, Fairfax, VA, United States
- Research Center for Medical Genetics, Moscow, Russia
- Atlas Biomed Group, Moscow, Russia
| | - Oksana Drapkina
- Federal State Institution National Research Center for Preventive Medicine, Moscow, Russia
| | - Alexander Tonevitsky
- Department of Cell Biology, Higher School of Economics, Moscow, Russia
- art photonics GmbH, Berlin, Germany
- SRC Bioclinicum, Moscow, Russia
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Poloznikov A, Gazaryan I, Shkurnikov M, Nikulin S, Drapkina O, Baranova A, Tonevitsky A. In vitro and in silico liver models: Current trends, challenges and opportunities. ALTEX 2018; 35:397-412. [PMID: 29813171 DOI: 10.14573/altex.1803221] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/22/2018] [Indexed: 11/23/2022]
Abstract
Most common drug development failures originate from either bioavailability problems, or unexpected toxic effects. The culprit is often the liver, which is responsible for biotransformation of a majority of xenobiotics. Liver may be modeled using "liver on a chip" devices, which may include established cell lines, primary human cells, and stem cell-derived hepatocyte-like cells. The choice of biological material along with its processing and maintenance greatly influence both the device performance and the resultant toxicity predictions. Impediments to the development of "liver on a chip" technology include the problems with standardization of cells, limitations imposed by culturing and the necessity to develop more complicated fluidic contours. Fortunately, recent breakthroughs in the development of cell-based reporters, including ones with fluorescent label, permits monitoring of the behavior of the cells embed into the "liver on a chip" devices. Finally, a set of computational approaches has been developed to model both particular toxic response and the homeostasis of human liver as a whole; these approaches pave a way to enhance the in silico stage of assessment for a potential toxicity.
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Affiliation(s)
- Andrey Poloznikov
- Hertsen Moscow Oncology Research Institute, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia.,Far Eastern Federal University, Vladivostok, Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Irina Gazaryan
- Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia.,Department of Cell Biology and Anatomy, School of Medicine, New York Medical College, Valhalla, NY, USA.,Department of Chemistry and Physical Sciences, Dyson College, Pace University, Pleasantville, NY, USA
| | - Maxim Shkurnikov
- Hertsen Moscow Oncology Research Institute, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Sergey Nikulin
- Hertsen Moscow Oncology Research Institute, Branch of the National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia.,Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia
| | - Oxana Drapkina
- National Research Center for Preventive Medicine of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Ancha Baranova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow, Russia.,School of Systems Biology, George Mason University (GMU), Fairfax, VA, USA.,Federal State Budgetary Institution "Research Centre for Medical Genetics", Moscow, Russia
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Sakharov D, Shilin S, Gazizov I, Nikulin S, Poloznikov A, Tonevitsky A. Online TEER measurements for barrier model systems in microfluidic chips. Toxicol Lett 2017. [DOI: 10.1016/j.toxlet.2017.07.953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Mutsenko VV, Bazhenov VV, Rogulska O, Tarusin DN, Schütz K, Brüggemeier S, Gossla E, Akkineni AR, Meißner H, Lode A, Meschke S, Ehrlich A, Petović S, Martinović R, Djurović M, Stelling AL, Nikulin S, Rodin S, Tonevitsky A, Gelinsky M, Petrenko AY, Glasmacher B, Ehrlich H. 3D chitinous scaffolds derived from cultivated marine demosponge Aplysina aerophoba for tissue engineering approaches based on human mesenchymal stromal cells. Int J Biol Macromol 2017; 104:1966-1974. [PMID: 28347785 DOI: 10.1016/j.ijbiomac.2017.03.116] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 03/21/2017] [Indexed: 01/21/2023]
Abstract
The recently discovered chitin-based scaffolds derived from poriferans have the necessary prosperities for potential use in tissue engineering. Among the various demosponges of the Verongida order, Aplysina aerophoba is an attractive target for more in-depth investigations, as it is a renewable source of unique 3D microporous chitinous scaffolds. We found these chitinous scaffolds were cytocompatible and supported attachment, growth and proliferation of human mesenchymal stromal cells (hMSCs) in vitro. Cultivation of hMSCs on the scaffolds for 7days resulted in a two-fold increase in their metabolic activity, indicating increased cell numbers. Cells cultured onto chitin scaffolds in differentiation media were able to differentiate into the chondrogenic, adipogenic and osteogenic lineages, respectively. These results indicate A. aerophoba is a novel source of chitin scaffolds to futher hMSCs-based tissue engineering strategies.
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Affiliation(s)
- Vitalii V Mutsenko
- Institute for Problems of Cryobiology and Cryomedicine of the NAS Ukraine, Pereyaslavskaya Str. 23, 61015 Kharkov, Ukraine; Institute for Multiphase Processes, Leibniz Universität Hannover, Callinstraße 36, 30167 Hannover, Germany.
| | - Vasilii V Bazhenov
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger Straße 23, 09599 Freiberg, Germany
| | - Olena Rogulska
- Institute for Problems of Cryobiology and Cryomedicine of the NAS Ukraine, Pereyaslavskaya Str. 23, 61015 Kharkov, Ukraine
| | - Dmitriy N Tarusin
- Institute for Problems of Cryobiology and Cryomedicine of the NAS Ukraine, Pereyaslavskaya Str. 23, 61015 Kharkov, Ukraine
| | - Kathleen Schütz
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Sophie Brüggemeier
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Elke Gossla
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Ashwini R Akkineni
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Heike Meißner
- Department of Prosthetic Dentistry, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Anja Lode
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | | | - Andre Ehrlich
- BromMarin GmbH, Wernerstraße 1, 09599 Freiberg, Germany
| | - Slavica Petović
- Institute of Marine Biology, Institute of marine biology, University of Montenegro, 85330 Kotor, Montenegro
| | - Rajko Martinović
- Institute of Marine Biology, Institute of marine biology, University of Montenegro, 85330 Kotor, Montenegro
| | - Mirko Djurović
- Institute of Marine Biology, Institute of marine biology, University of Montenegro, 85330 Kotor, Montenegro
| | - Allison L Stelling
- Department of Biochemistry, Duke University School of Medicine, 27710 Durham, North Carolina, USA
| | - Sergey Nikulin
- Moscow Institute of Physics and Technology, Institutskii Per. 9, 141700, Dolgoprudny, Moscow Region, Russia
| | - Sergey Rodin
- P.A. Hertsen Moscow Research Oncology Institute, Botkinskii p. 3, 125284 Moscow, Russia
| | - Alexander Tonevitsky
- P.A. Hertsen Moscow Research Oncology Institute, Botkinskii p. 3, 125284 Moscow, Russia
| | - Michael Gelinsky
- Centre for Translational Bone, Joint and Soft Tissue Research, Faculty of Medicine and University Hospital Carl Gustav Carus of Technische Universität Dresden, Fetscherstraße 74, 01307 Dresden, Germany
| | - Alexander Y Petrenko
- Institute for Problems of Cryobiology and Cryomedicine of the NAS Ukraine, Pereyaslavskaya Str. 23, 61015 Kharkov, Ukraine
| | - Birgit Glasmacher
- Institute for Multiphase Processes, Leibniz Universität Hannover, Callinstraße 36, 30167 Hannover, Germany
| | - Hermann Ehrlich
- Institute of Experimental Physics, TU Bergakademie Freiberg, Leipziger Straße 23, 09599 Freiberg, Germany.
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Marx U, Andersson TB, Bahinski A, Beilmann M, Beken S, Cassee FR, Cirit M, Daneshian M, Fitzpatrick S, Frey O, Gaertner C, Giese C, Griffith L, Hartung T, Heringa MB, Hoeng J, de Jong WH, Kojima H, Kuehnl J, Luch A, Maschmeyer I, Sakharov D, Sips AJAM, Steger-Hartmann T, Tagle DA, Tonevitsky A, Tralau T, Tsyb S, van de Stolpe A, Vandebriel R, Vulto P, Wang J, Wiest J, Rodenburg M, Roth A. Biology-inspired microphysiological system approaches to solve the prediction dilemma of substance testing. ALTEX 2016; 33:272-321. [PMID: 27180100 PMCID: PMC5396467 DOI: 10.14573/altex.1603161] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/11/2016] [Indexed: 01/09/2023]
Abstract
The recent advent of microphysiological systems - microfluidic biomimetic devices that aspire to emulate the biology of human tissues, organs and circulation in vitro - is envisaged to enable a global paradigm shift in drug development. An extraordinary US governmental initiative and various dedicated research programs in Europe and Asia have led recently to the first cutting-edge achievements of human single-organ and multi-organ engineering based on microphysiological systems. The expectation is that test systems established on this basis would model various disease stages, and predict toxicity, immunogenicity, ADME profiles and treatment efficacy prior to clinical testing. Consequently, this technology could significantly affect the way drug substances are developed in the future. Furthermore, microphysiological system-based assays may revolutionize our current global programs of prioritization of hazard characterization for any new substances to be used, for example, in agriculture, food, ecosystems or cosmetics, thus, replacing laboratory animal models used currently. Thirty-six experts from academia, industry and regulatory bodies present here the results of an intensive workshop (held in June 2015, Berlin, Germany). They review the status quo of microphysiological systems available today against industry needs, and assess the broad variety of approaches with fit-for-purpose potential in the drug development cycle. Feasible technical solutions to reach the next levels of human biology in vitro are proposed. Furthermore, key organ-on-a-chip case studies, as well as various national and international programs are highlighted. Finally, a roadmap into the future is outlined, to allow for more predictive and regulatory-accepted substance testing on a global scale.
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45
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Stepanov A, Belyy A, Kasheverov I, Rybinets A, Dronina M, Dyachenko I, Murashev A, Knorre V, Sakharov D, Ponomarenko N, Tsetlin V, Tonevitsky A, Deyev S, Belogurov A, Gabibov A. Development of a recombinant immunotoxin for the immunotherapy of autoreactive lymphocytes expressing MOG-specific BCRs. Biotechnol Lett 2016; 38:1173-80. [PMID: 27099070 DOI: 10.1007/s10529-016-2092-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 03/17/2016] [Indexed: 11/24/2022]
Abstract
OBJECTIVE Myelin oligodendrocyte glycoprotein (MOG) is one of the major autoantigens in multiple sclerosis (MS), therefore selective depletion of autoreactive lymphocytes exposing MOG-specific B cell receptors (BCRs) would be beneficial in terms of MS treatment. RESULTS Using E. coli we generated an efficient protocol for the purification of the recombinant immunotoxin DT-MOG composed of the extracellular Ig-like domain of MOG fused in frame with the catalytic and translocation subunits of diphtheria toxin (DT, Corynebacterium diphtheriae) under native conditions with a final yield of 1.5 mg per liter of culture medium. Recombinant DT-MOG was recognized in vitro by MOG-reactive antibodies and has catalytic activity comparable with wild-type DT. CONCLUSION Enhanced pharmacokinetics (mean residence time in the bloodstream of 61 min) and minimized diminished nonspecific toxicity (LD50 = 1.76 mg/kg) of the DT-MOG makes it a potential candidate for the immunotherapy of MS.
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Affiliation(s)
- Alexey Stepanov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan, Russia
| | - Alexander Belyy
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997.,Department of Bacterial Infections, Gamaleya Research Institute, Gamaleya Str., 18, Moscow, Russia, 123098
| | - Igor Kasheverov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Alexandra Rybinets
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Maria Dronina
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Igor Dyachenko
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Arkady Murashev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Vera Knorre
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Dmitry Sakharov
- SRC Bioclinicum, Ugreshskaya str 2/85, Moscow, Russia, 115088
| | - Natalya Ponomarenko
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Victor Tsetlin
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | | | - Sergey Deyev
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997
| | - Alexey Belogurov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan, Russia
| | - Alexander Gabibov
- M.M. Shemyakin and Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, Moscow, Russia, 117997. .,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Tatarstan, Russia.
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Langley G, Austin CP, Balapure AK, Birnbaum LS, Bucher JR, Fentem J, Fitzpatrick SC, Fowle JR, Kavlock RJ, Kitano H, Lidbury BA, Muotri AR, Peng SQ, Sakharov D, Seidle T, Trez T, Tonevitsky A, van de Stolpe A, Whelan M, Willett C. Lessons from Toxicology: Developing a 21st-Century Paradigm for Medical Research. Environ Health Perspect 2015; 123:A268-72. [PMID: 26523530 PMCID: PMC4629751 DOI: 10.1289/ehp.1510345] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Biomedical developments in the 21st century provide an unprecedented opportunity to gain a dynamic systems-level and human-specific understanding of the causes and pathophysiologies of disease. This understanding is a vital need, in view of continuing failures in health research, drug discovery, and clinical translation. The full potential of advanced approaches may not be achieved within a 20th-century conceptual framework dominated by animal models. Novel technologies are being integrated into environmental health research and are also applicable to disease research, but these advances need a new medical research and drug discovery paradigm to gain maximal benefits. We suggest a new conceptual framework that repurposes the 21st-century transition underway in toxicology. Human disease should be conceived as resulting from integrated extrinsic and intrinsic causes, with research focused on modern human-specific models to understand disease pathways at multiple biological levels that are analogous to adverse outcome pathways in toxicology. Systems biology tools should be used to integrate and interpret data about disease causation and pathophysiology. Such an approach promises progress in overcoming the current roadblocks to understanding human disease and successful drug discovery and translation. A discourse should begin now to identify and consider the many challenges and questions that need to be solved.
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Affiliation(s)
- Gill Langley
- Research and Toxicology Department, Humane Society International, London, United Kingdom
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Oliveira-Ferrer L, Rößler K, Haustein V, Schröder C, Wicklein D, Maltseva D, Khaustova N, Samatov T, Tonevitsky A, Mahner S, Jänicke F, Schumacher U, Milde-Langosch K. c-FOS suppresses ovarian cancer progression by changing adhesion. Br J Cancer 2013; 110:753-63. [PMID: 24322891 PMCID: PMC3915133 DOI: 10.1038/bjc.2013.774] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 11/07/2013] [Accepted: 11/13/2013] [Indexed: 01/11/2023] Open
Abstract
Background: C-Fos was initially described as oncogene, but was associated with favourable prognosis in ovarian cancer (OvCa) patients. The molecular and functional aspects underlying this effect are still unknown. Methods: Using stable transfectants of SKOV3 and OVCAR8 cells, proliferation, migration, invasion and apoptotic potential of c-FOS-overexpressing clones and controls were compared. Adherence to components of the extracellular matrix was analysed in static assays, and adhesion to E-selectin, endothelial and mesothelial cells in dynamic flow assays. The effect of c-FOS in vivo was studied after intraperitoneal injection of SKOV3 clones into SCID mice, and changes in gene expression were determined by microarray analysis. Results: Tumour growth after injection into SCID mice was strongly delayed by c-FOS overexpression, with reduction of lung metastases and circulating tumour cells. In vitro, c-FOS had only weak influence on proliferation and migration, but was strongly pro-apoptotic. Adhesion to components of the extracellular matrix (collagen I, IV) and to E-selectin, endothelial and mesothelial cells was significantly reduced in c-FOS-overexpressing OvCa cells. This corresponds to deregulation of adhesion proteins and glycosylation enzymes in microarray analysis. Conclusion: In addition to its known pro-apoptotic effect, c-FOS might influence OvCa progression by changing the adhesion of OvCa cells to peritoneal surfaces.
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Affiliation(s)
- L Oliveira-Ferrer
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - K Rößler
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - V Haustein
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - C Schröder
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - D Wicklein
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - D Maltseva
- SRC Bioclinicum, Ugreshskaya Street 2/85, Moscow 115088, Russia
| | - N Khaustova
- SRC Bioclinicum, Ugreshskaya Street 2/85, Moscow 115088, Russia
| | - T Samatov
- SRC Bioclinicum, Ugreshskaya Street 2/85, Moscow 115088, Russia
| | - A Tonevitsky
- Institute of General Pathology and Pathophysiology, Baltijskaya Street 8, Moscow 125315, Russia
| | - S Mahner
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - F Jänicke
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - U Schumacher
- Department of Anatomy and Experimental Morphology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
| | - K Milde-Langosch
- Department of Gynecology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20246, Hamburg, Germany
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Abstract
A new simple method for non-invasive cell culture viability monitoring based on vital fluorescent stains is introduced, and its efficiency for long-term experiments on cells is demonstrated. In contrast to common methods for cell viability control, which are usually either destructive (like flow-type counters or dead cells coloring and counting), or hardly quantitative like fluorescent microscopy, the method described is automated, does not require the removal of cells from their growth area and is sensitive enough to deal with as low as tens of cells.
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Affiliation(s)
- Ilia Sergachev
- SRC Bioclinicum, Ugreshskaya 2-85, Moscow, 115088, Russia
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Sysoeva OV, Wittmann M, Mierau A, Polikanova I, Strüder HK, Tonevitsky A. Physical exercise speeds up motor timing. Front Psychol 2013; 4:612. [PMID: 24062707 PMCID: PMC3769678 DOI: 10.3389/fpsyg.2013.00612] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 08/21/2013] [Indexed: 11/18/2022] Open
Abstract
This study aimed to examine effect of physical exercise on motor timing: personal, maximum and “once per second” tapping. The acute effect was examined by comparing the baseline tapping with that after acute exercise in 9 amateur athletes, 8 elite synchronous swimmers and 9 elite biathletes. Then the baseline tapping was compared among athletes of different sports and professional levels (15 elite biathletes, 27 elite cross-country skiers, 15 elite synchronous swimmers and 9 amateur wrestlers) with a control group (44 non-athletes) not involved in regular exercise to examine the sport-specific or long-term effects. Maximum and “once per second” tapping speed increased after acute physical exercise and were also faster in elite athletes compared to controls during the baseline condition. However, personal tapping tempo was not affected by exercise. In addition, physical exercise had no effects on the variability of the intertap interval. The accuracy of “once per second” tapping differentiates controls and amateur wrestlers from elite synchronous swimmers and skiers suggesting sport-specific adaptations to play a role. It is concluded that acute physical exercise selectively speeds up motor timing but does not affect its variability and accuracy, and this speeding-up is suggested to transfer into a long-term effect in elite athletes.
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Affiliation(s)
- Olga V Sysoeva
- The Center for Neurocognitive Research (MEG-Center), Moscow State University of Psychology and Education Moscow, Russia ; Laboratory of Human Higher Nervous Activity, Institute for Higher Nervous Activity and Neurophysiology, Russian Academy of Sciences Moscow, Russia
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Smirnov K, Sysoeva O, Tonevitsky A, Ivanitsky A, Polikanova I. P4-5 Molecular genetic and EEG correlates of aggressiveness. Clin Neurophysiol 2010. [DOI: 10.1016/s1388-2457(10)60500-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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