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Demenkov PS, Antropova EA, Adamovskaya AV, Mishchenko EL, Khlebodarova TM, Ivanisenko TV, Ivanisenko NV, Venzel AS, Lavrik IN, Ivanisenko VA. Prioritization of potential pharmacological targets for the development of anti-hepatocarcinoma drugs modulating the extrinsic apoptosis pathway: the reconstruction and analysis of associative gene networks help. Vavilovskii Zhurnal Genet Selektsii 2023; 27:784-793. [PMID: 38213696 PMCID: PMC10777304 DOI: 10.18699/vjgb-23-91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 01/13/2024] Open
Abstract
Hepatocellular carcinoma (HCC) is a common severe type of liver cancer characterized by an extremely aggressive course and low survival rates. It is known that disruptions in the regulation of apoptosis activation are some of the key features inherent in most cancer cells, which determines the pharmacological induction of apoptosis as an important strategy for cancer therapy. The computer design of chemical compounds capable of specifically regulating the external signaling pathway of apoptosis induction represents a promising approach for creating new effective ways of therapy for liver cancer and other oncological diseases. However, at present, most of the studies are devoted to pharmacological effects on the internal (mitochondrial) apoptosis pathway. In contrast, the external pathway induced via cell death receptors remains out of focus. Aberrant gene methylation, along with hepatitis C virus (HCV) infection, are important risk factors for the development of hepatocellular carcinoma. The reconstruction of gene networks describing the molecular mechanisms of interaction of aberrantly methylated genes with key participants of the extrinsic apoptosis pathway and their regulation by HCV proteins can provide important information when searching for pharmacological targets. In the present study, 13 criteria were proposed for prioritizing potential pharmacological targets for developing anti-hepatocarcinoma drugs modulating the extrinsic apoptosis pathway. The criteria are based on indicators of the structural and functional organization of reconstructed gene networks of hepatocarcinoma, the extrinsic apoptosis pathway, and regulatory pathways of virus-extrinsic apoptosis pathway interaction and aberrant gene methylation-extrinsic apoptosis pathway interaction using ANDSystem. The list of the top 100 gene targets ranked according to the prioritization rating was statistically significantly (p-value = 0.0002) enriched for known pharmacological targets approved by the FDA, indicating the correctness of the prioritization method. Among the promising potential pharmacological targets, six highly ranked genes (JUN, IL10, STAT3, MYC, TLR4, and KHDRBS1) are likely to deserve close attention.
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Affiliation(s)
- P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - E A Antropova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Adamovskaya
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - E L Mishchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - T M Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - T V Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - N V Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - I N Lavrik
- Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - V A Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Mishchenko EL, Makarova AA, Antropova EA, Venzel AS, Ivanisenko TV, Demenkov PS, Ivanisenko VA. Molecular-genetic pathways of hepatitis C virus regulation of the expression of cellular factors PREB and PLA2G4C, which play an important role in virus replication. Vavilovskii Zhurnal Genet Selektsii 2023; 27:776-783. [PMID: 38213698 PMCID: PMC10777288 DOI: 10.18699/vjgb-23-90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 01/13/2024] Open
Abstract
The participants of Hepatitis C virus (HCV) replication are both viral and host proteins. Therapeutic approaches based on activity inhibition of viral non-structural proteins NS3, NS5A, and NS5B are undergoing clinical trials. However, rapid mutation processes in the viral genome and acquisition of drug resistance to the existing drugs remain the main obstacles to fighting HCV. Identifying the host factors, exploring their role in HCV RNA replication, and studying viral effects on their expression is essential for understanding the mechanisms of viral replication and developing novel, effective curative approaches. It is known that the host factors PREB (prolactin regulatory element binding) and PLA2G4C (cytosolic phospholipase A2 gamma) are important for the functioning of the viral replicase complex and the formation of the platforms of HCV genome replication. The expression of PREB and PLA2G4C was significantly elevated in the presence of the HCV genome. However, the mechanisms of its regulation by HCV remain unknown. In this paper, using a text-mining technology provided by ANDSystem, we reconstructed and analyzed gene networks describing regulatory effects on the expression of PREB and PLA2G4C by HCV proteins. On the basis of the gene network analysis performed, we put forward hypotheses about the modulation of the host factors functions resulting from protein-protein interaction with HCV proteins. Among the viral proteins, NS3 showed the greatest number of regulatory linkages. We assumed that NS3 could inhibit the function of host transcription factor (TF) NOTCH1 by protein-protein interaction, leading to upregulation of PREB and PLA2G4C. Analysis of the gene networks and data on differential gene expression in HCV-infected cells allowed us to hypothesize further how HCV could regulate the expression of TFs, the binding sites of which are localized within PREB and PLA2G4C gene regions. The results obtained can be used for planning studies of the molecular-genetic mechanisms of viral-host interaction and searching for potential targets for anti-HCV therapy.
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Affiliation(s)
- E L Mishchenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A A Makarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E A Antropova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A S Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - T V Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - V A Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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Hongyao HE, Chun JI, Xiaoyan G, Fangfang L, Jing Z, Lin Z, Pengxiang Z, Zengchun L. Associative gene networks reveal novel candidates important for ADHD and dyslexia comorbidity. BMC Med Genomics 2023; 16:208. [PMID: 37667328 PMCID: PMC10478365 DOI: 10.1186/s12920-023-01502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 03/26/2023] [Indexed: 09/06/2023] Open
Abstract
BACKGROUND Attention deficit hyperactivity disorder (ADHD) is commonly associated with developmental dyslexia (DD), which are both prevalent and complicated pediatric neurodevelopmental disorders that have a significant influence on children's learning and development. Clinically, the comorbidity incidence of DD and ADHD is between 25 and 48%. Children with DD and ADHD may have more severe cognitive deficiencies, a poorer level of schooling, and a higher risk of social and emotional management disorders. Furthermore, patients with this comorbidity are frequently treated for a single condition in clinical settings, and the therapeutic outcome is poor. The development of effective treatment approaches against these diseases is complicated by their comorbidity features. This is often a major problem in diagnosis and treatment. In this study, we developed bioinformatical methodology for the analysis of the comorbidity of these two diseases. As such, the search for candidate genes related to the comorbid conditions of ADHD and DD can help in elucidating the molecular mechanisms underlying the comorbid condition, and can also be useful for genotyping and identifying new drug targets. RESULTS Using the ANDSystem tool, the reconstruction and analysis of gene networks associated with ADHD and dyslexia was carried out. The gene network of ADHD included 599 genes/proteins and 148,978 interactions, while that of dyslexia included 167 genes/proteins and 27,083 interactions. When the ANDSystem and GeneCards data were combined, a total of 213 genes/proteins for ADHD and dyslexia were found. An approach for ranking genes implicated in the comorbid condition of the two diseases was proposed. The approach is based on ten criteria for ranking genes by their importance, including relevance scores of association between disease and genes, standard methods of gene prioritization, as well as original criteria that take into account the characteristics of an associative gene network and the presence of known polymorphisms in the analyzed genes. Among the top 20 genes with the highest priority DRD2, DRD4, CNTNAP2 and GRIN2B are mentioned in the literature as directly linked with the comorbidity of ADHD and dyslexia. According to the proposed approach, the genes OPRM1, CHRNA4 and SNCA had the highest priority in the development of comorbidity of these two diseases. Additionally, it was revealed that the most relevant genes are involved in biological processes related to signal transduction, positive regulation of transcription from RNA polymerase II promoters, chemical synaptic transmission, response to drugs, ion transmembrane transport, nervous system development, cell adhesion, and neuron migration. CONCLUSIONS The application of methods of reconstruction and analysis of gene networks is a powerful tool for studying the molecular mechanisms of comorbid conditions. The method put forth to rank genes by their importance for the comorbid condition of ADHD and dyslexia was employed to predict genes that play key roles in the development of the comorbid condition. The results can be utilized to plan experiments for the identification of novel candidate genes and search for novel pharmacological targets.
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Affiliation(s)
- H E Hongyao
- Medical College of Shihezi University, Shihezi, China
| | - J I Chun
- Medical College of Shihezi University, Shihezi, China
| | - Gao Xiaoyan
- Medical College of Shihezi University, Shihezi, China
| | - Liu Fangfang
- Medical College of Shihezi University, Shihezi, China
| | - Zhang Jing
- Medical College of Shihezi University, Shihezi, China
| | - Zhong Lin
- Medical College of Shihezi University, Shihezi, China
| | - Zuo Pengxiang
- Medical College of Shihezi University, Shihezi, China.
| | - Li Zengchun
- Medical College of Shihezi University, Shihezi, China.
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Antropova EA, Khlebodarova TM, Demenkov PS, Volianskaia AR, Venzel AS, Ivanisenko NV, Gavrilenko AD, Ivanisenko TV, Adamovskaya AV, Revva PM, Kolchanov NA, Lavrik IN, Ivanisenko VA. Reconstruction of the regulatory hypermethylation network controlling hepatocellular carcinoma development during hepatitis C viral infection. J Integr Bioinform 2023; 20:jib-2023-0013. [PMID: 37978846 PMCID: PMC10757076 DOI: 10.1515/jib-2023-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/31/2023] [Indexed: 11/19/2023] Open
Abstract
Hepatocellular carcinoma (HCC) has been associated with hepatitis C viral (HCV) infection as a potential risk factor. Nonetheless, the precise genetic regulatory mechanisms triggered by the virus, leading to virus-induced hepatocarcinogenesis, remain unclear. We hypothesized that HCV proteins might modulate the activity of aberrantly methylated HCC genes through regulatory pathways. Virus-host regulatory pathways, interactions between proteins, gene expression, transport, and stability regulation, were reconstructed using the ANDSystem. Gene expression regulation was statistically significant. Gene network analysis identified four out of 70 HCC marker genes whose expression regulation by viral proteins may be associated with HCC: DNA-binding protein inhibitor ID - 1 (ID1), flap endonuclease 1 (FEN1), cyclin-dependent kinase inhibitor 2A (CDKN2A), and telomerase reverse transcriptase (TERT). It suggested the following viral protein effects in HCV/human protein heterocomplexes: HCV NS3(p70) protein activates human STAT3 and NOTC1; NS2-3(p23), NS5B(p68), NS1(E2), and core(p21) activate SETD2; NS5A inhibits SMYD3; and NS3 inhibits CCN2. Interestingly, NS3 and E1(gp32) activate c-Jun when it positively regulates CDKN2A and inhibit it when it represses TERT. The discovered regulatory mechanisms might be key areas of focus for creating medications and preventative therapies to decrease the likelihood of HCC development during HCV infection.
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Affiliation(s)
| | - Tamara M. Khlebodarova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Artur S. Venzel
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Nikita V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexandr D. Gavrilenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Timofey V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anna V. Adamovskaya
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Polina M. Revva
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Nikolay A. Kolchanov
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Inna N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106Magdeburg, Germany
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, Russia
- Kurchatov Genomic Center of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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Bragina EY, Gomboeva DE, Saik OV, Ivanisenko VA, Freidin MB, Nazarenko MS, Puzyrev VP. Apoptosis Genes as a Key to Identification of Inverse Comorbidity of Huntington's Disease and Cancer. Int J Mol Sci 2023; 24:ijms24119385. [PMID: 37298337 DOI: 10.3390/ijms24119385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
Cancer and neurodegenerative disorders present overwhelming challenges for healthcare worldwide. Epidemiological studies showed a decrease in cancer rates in patients with neurodegenerative disorders, including the Huntington disease (HD). Apoptosis is one of the most important processes for both cancer and neurodegeneration. We suggest that genes closely connected with apoptosis and associated with HD may affect carcinogenesis. We applied reconstruction and analysis of gene networks associated with HD and apoptosis and identified potentially important genes for inverse comorbidity of cancer and HD. The top 10 high-priority candidate genes included APOE, PSEN1, INS, IL6, SQSTM1, SP1, HTT, LEP, HSPA4, and BDNF. Functional analysis of these genes was carried out using gene ontology and KEGG pathways. By exploring genome-wide association study results, we identified genes associated with neurodegenerative and oncological disorders, as well as their endophenotypes and risk factors. We used publicly available datasets of HD and breast and prostate cancers to analyze the expression of the identified genes. Functional modules of these genes were characterized according to disease-specific tissues. This integrative approach revealed that these genes predominantly exert similar functions in different tissues. Apoptosis along with lipid metabolism dysregulation and cell homeostasis maintenance in the response to environmental stimulus and drugs are likely key processes in inverse comorbidity of cancer in patients with HD. Overall, the identified genes represent the promising targets for studying molecular relations of cancer and HD.
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Affiliation(s)
- Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Densema E Gomboeva
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, 634050 Tomsk, Russia
| | - Olga V Saik
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, 634050 Tomsk, Russia
- Department of Biology, School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
- Centre of Omics Technology, I.M. Sechenov First Moscow State Medical University, 119991 Moscow, Russia
| | - Maria S Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, 634050 Tomsk, Russia
- Department of Medical Genetics, Faculty of General Medicine, Siberian State Medical University, 634050 Tomsk, Russia
| | - Valery P Puzyrev
- Research Institute of Medical Genetics, Tomsk National Research Medical Centre, Russian Academy of Sciences, 634050 Tomsk, Russia
- Department of Medical Genetics, Faculty of General Medicine, Siberian State Medical University, 634050 Tomsk, Russia
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Seyedrezazadeh E, Ghoushouni S, Sharifi A, Zafari V, Zarredar H. Association of the Toll-like receptor 4 and NOX4 gene and protein levels in asthmatic patients with metabolic syndrome: A case–control study. JOURNAL OF RESEARCH IN MEDICAL SCIENCES 2023; 28:11. [PMID: 36974113 PMCID: PMC10039097 DOI: 10.4103/jrms.jrms_860_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 02/17/2022] [Accepted: 04/02/2022] [Indexed: 02/23/2023]
Abstract
Background Understanding the contributing of influence inflammatory biomarkers in asthmatic patients with metabolic syndrome is more important. Whereby, the present study considering the important association of NADPH oxidase4 (NOX4) and Toll- like receptor4 (TLR4) in the respiratory inflammatory responses in asthmatic patients with metabolic syndrome (AS-MetS) and asthmatic (AS) patients. Materials and Methods In this case-control study, 30 AS and 34 AS-MetS patients were enrolled. The Peripheral blood mononuclear cells (PBMCs) mRNA and protein levels of TLR4 and NOX4 were measured by qRT-PCR and western blot, respectively. Then their correlation was evaluated. Results The significant down-regulation of mRNA and protein PBMCs expression levels of TLR4 were observed in the AS-MetS group in comparison to AS one (P=0.03), but the NOX4 expression was non-significant. Additionally, the significant correlation was exhibited between mRNA expression levels of NOX4 and TLR4 in both AS-MetS (r= 0.440, P=0.009) and AS groups (r=0.909, P=0.0001). The association between TLR4 mRNA level and triglyceride in AS-MetS group (r=0.454, P=0.008,) and also white blood cells (WBC) in AS group (r= -0.507, P=0.006,) were significant. Conclusion The metabolic syndrome can significantly influence the expressions of TLR4 in AS-MetS. This study indicated that TLR4 and NOX4 altogether may provide valuable molecular knowledge of their relation with metabolic syndrome criteria for finding major pathways in different phenotype of asthma.
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Khlebodarova TM, Demenkov PS, Ivanisenko TV, Antropova EA, Lavrik IN, Ivanisenko VA. Primary and Secondary micro-RNA Modulation the Extrinsic Pathway of Apoptosis in Hepatocellular Carcinoma. Mol Biol 2023; 57:165-175. [PMID: 37128213 PMCID: PMC10131518 DOI: 10.1134/s0026893323020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 05/03/2023]
Abstract
Abstract-One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complicates the diagnosis, prognosis and response to treatment. In this regard, an individualized, patient-centered approach becomes important, in which the use of mimetics and hsa-miRNA inhibitors involved in the pathogenesis of the disease may be determinative. From this point of view hsa-miRNAs are of interest, their aberrant expression is associated with poor prognosis for patients and is associated with tumor progression due to dysregulation of programmed cell death (apoptosis). However, the effect of hsa-miRNA on tumor development depends not only on its direct effect on expression of genes, the primary targets, but also on secondary targets mediated by regulatory pathways. While the former are actively studied, the role of secondary targets of these hsa-miRNAs in modulating apoptosis is still unclear. The present work summarizes data on hsa-miRNAs whose primary targets are key genes of the extrinsic pathway of apoptosis. Their aberrant expression is associated with early disease relapse and poor patient outcome. For these hsa-miRNAs, using the software package ANDSystem, we reconstructed the regulation of the expression of secondary targets and analyzed their impact on the activity of the extrinsic pathway of apoptosis. The potential effect of hsa-miRNAs mediated by action on secondary targets is shown to negatively correlate with the number of primary targets. It is also shown that hsa-miR-373, hsa-miR-106b and hsa-miR-96 have the highest priority as markers of hepatocellular carcinoma, whose action on secondary targets enhances their anti-apoptotic effect.
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Affiliation(s)
- T. M. Khlebodarova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - P. S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - T. V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - E. A. Antropova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - I. N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - V. A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
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8
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Antropova E, Khlebodarova T, Demenkov P, Venzel A, Ivanisenko N, Gavrilenko A, Ivanisenko T, Adamovskaya A, Revva P, Lavrik I, Ivanisenko V. Computer analysis of regulation of hepatocarcinoma marker genes hypermethylated by HCV proteins. Vavilovskii Zhurnal Genet Selektsii 2022; 26:733-742. [PMID: 36714033 PMCID: PMC9840909 DOI: 10.18699/vjgb-22-89] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023] Open
Abstract
Hepatitis C virus (HCV) is a risk factor that leads to hepatocellular carcinoma (HCC) development. Epigenetic changes are known to play an important role in the molecular genetic mechanisms of virus-induced oncogenesis. Aberrant DNA methylation is a mediator of epigenetic changes that are closely associated with the HCC pathogenesis and considered a biomarker for its early diagnosis. The ANDSystem software package was used to reconstruct and evaluate the statistical significance of the pathways HCV could potentially use to regulate 32 hypermethylated genes in HCC, including both oncosuppressor and protumorigenic ones identified by genome-wide analysis of DNA methylation. The reconstructed pathways included those affecting protein-protein interactions (PPI), gene expression, protein activity, stability, and transport regulations, the expression regulation pathways being statistically significant. It has been shown that 8 out of 10 HCV proteins were involved in these pathways, the HCV NS3 protein being implicated in the largest number of regulatory pathways. NS3 was associated with the regulation of 5 tumor-suppressor genes, which may be the evidence of its central role in HCC pathogenesis. Analysis of the reconstructed pathways has demonstrated that following the transcription factor inhibition caused by binding to viral proteins, the expression of a number of oncosuppressors (WT1, MGMT, SOCS1, P53) was suppressed, while the expression of others (RASF1, RUNX3, WIF1, DAPK1) was activated. Thus, the performed gene-network reconstruction has shown that HCV proteins can influence not only the methylation status of oncosuppressor genes, but also their transcriptional regulation. The results obtained can be used in the search for pharmacological targets to develop new drugs against HCV-induced HCC.
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Affiliation(s)
- E.A. Antropova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, Russia
| | - T.M. Khlebodarova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - P.S. Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.S. Venzel
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - N.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.D. Gavrilenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - T.V. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - A.V. Adamovskaya
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
| | - P.M. Revva
- Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - I.N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, Magdeburg, Germany
| | - V.A. Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Scences, Novosibirsk, RussiaKurchatov Genomic Center of ICG SB RAS, Novosibirsk, RussiaNovosibirsk State University, Novosibirsk, Russia
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9
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Ivanisenko TV, Demenkov PS, Kolchanov NA, Ivanisenko VA. The New Version of the ANDDigest Tool with Improved AI-Based Short Names Recognition. Int J Mol Sci 2022; 23:ijms232314934. [PMID: 36499269 PMCID: PMC9738852 DOI: 10.3390/ijms232314934] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/19/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022] Open
Abstract
The body of scientific literature continues to grow annually. Over 1.5 million abstracts of biomedical publications were added to the PubMed database in 2021. Therefore, developing cognitive systems that provide a specialized search for information in scientific publications based on subject area ontology and modern artificial intelligence methods is urgently needed. We previously developed a web-based information retrieval system, ANDDigest, designed to search and analyze information in the PubMed database using a customized domain ontology. This paper presents an improved ANDDigest version that uses fine-tuned PubMedBERT classifiers to enhance the quality of short name recognition for molecular-genetics entities in PubMed abstracts on eight biological object types: cell components, diseases, side effects, genes, proteins, pathways, drugs, and metabolites. This approach increased average short name recognition accuracy by 13%.
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Affiliation(s)
- Timofey V. Ivanisenko
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Correspondence:
| | - Pavel S. Demenkov
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
| | - Nikolay A. Kolchanov
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, St. Pirogova 1, Novosibirsk 630090, Russia
| | - Vladimir A. Ivanisenko
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, St. Pirogova 1, Novosibirsk 630090, Russia
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10
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Plasma metabolomics and gene regulatory networks analysis reveal the role of nonstructural SARS-CoV-2 viral proteins in metabolic dysregulation in COVID-19 patients. Sci Rep 2022; 12:19977. [PMID: 36404352 PMCID: PMC9676188 DOI: 10.1038/s41598-022-24170-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/11/2022] [Indexed: 11/21/2022] Open
Abstract
Metabolomic analysis of blood plasma samples from COVID-19 patients is a promising approach allowing for the evaluation of disease progression. We performed the metabolomic analysis of plasma samples of 30 COVID-19 patients and the 19 controls using the high-performance liquid chromatography (HPLC) coupled with tandem mass spectrometric detection (LC-MS/MS). In our analysis, we identified 103 metabolites enriched in KEGG metabolic pathways such as amino acid metabolism and the biosynthesis of aminoacyl-tRNAs, which differed significantly between the COVID-19 patients and the controls. Using ANDSystem software, we performed the reconstruction of gene networks describing the potential genetic regulation of metabolic pathways perturbed in COVID-19 patients by SARS-CoV-2 proteins. The nonstructural proteins of SARS-CoV-2 (orf8 and nsp5) and structural protein E were involved in the greater number of regulatory pathways. The reconstructed gene networks suggest the hypotheses on the molecular mechanisms of virus-host interactions in COVID-19 pathology and provide a basis for the further experimental and computer studies of the regulation of metabolic pathways by SARS-CoV-2 proteins. Our metabolomic analysis suggests the need for nonstructural protein-based vaccines and the control strategy to reduce the disease progression of COVID-19.
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11
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Walid Al-Qerem, Jarab A, Abu Heshmeh SR, Ling J. Variables associated with asthma control among adult patients. J Asthma 2022; 60:1290-1298. [PMID: 36336819 DOI: 10.1080/02770903.2022.2144351] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Objective: Asthma is one of the most prevalent chronic diseases with a substantial impact on the health status of affected patients. Further research is necessary to identify factors contributing to poor asthma control. The current study aimed to investigate the factors associated with poor asthma control among adult asthmatic patients.Methods: In this case-control study, the Asthma Control Test (ACT) was translated into Arabic and distributed to adults with asthma attending two hospitals in Jordan to evaluate the degree of asthma control. The following variables were collected for each patient: sociodemographic information, comorbidities, appropriate use of inhaler technique, spirometric measurements, and medications use. Binary regression was used to evaluate factors associated with asthma control.Results: A total of 314 participants with a mean age of 51.47 years (±16.37) completed the study. ACT score had a mean of 16.68 (±4.86). The majority of asthmatic patients had insufficiently controlled asthma (64.6%). Binary regression results showed that previous respiratory infection history (p = 0.014, OR = 0.473 (95%CI 0.261-0.857)), higher exposure to irritants (p = 0.010, OR = 0.747 (95%CI 0.598-0.933)) decreased the odds of being in the controlled asthma group. Patients receiving inhaled corticosteroids (ICS) had higher odds of being in the controlled asthma group (p = 0.039, OR = 2.372 (95%CI 1.043-5.392)).Conclusions: The majority of asthma patients had insufficiently managed disease. The main factors that contributed to poor asthma control were respiratory infection history, increased exposure to asthma symptoms triggers, and ICS nonuse.
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Affiliation(s)
- Walid Al-Qerem
- Department of Pharmacy, Al-Zaytoonah University of Jordan, Amman 11733, Jordan
| | - Anan Jarab
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
- Collage of Pharmacy, Al Ain University, Abu Dhabi, UAE
| | - Shrouq R Abu Heshmeh
- Department of Clinical Pharmacy, Faculty of Pharmacy, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Jonathan Ling
- Faculty of Health Sciences and Wellbeing, University of Sunderland, Chester Road, Sunderland, SR1 3SD, United Kingdom
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12
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Gene Networks of Hyperglycemia, Diabetic Complications, and Human Proteins Targeted by SARS-CoV-2: What Is the Molecular Basis for Comorbidity? Int J Mol Sci 2022; 23:ijms23137247. [PMID: 35806251 PMCID: PMC9266766 DOI: 10.3390/ijms23137247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 06/25/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
People with diabetes are more likely to have severe COVID-19 compared to the general population. Moreover, diabetes and COVID-19 demonstrate a certain parallelism in the mechanisms and organ damage. In this work, we applied bioinformatics analysis of associative molecular networks to identify key molecules and pathophysiological processes that determine SARS-CoV-2-induced disorders in patients with diabetes. Using text-mining-based approaches and ANDSystem as a bioinformatics tool, we reconstructed and matched networks related to hyperglycemia, diabetic complications, insulin resistance, and beta cell dysfunction with networks of SARS-CoV-2-targeted proteins. The latter included SARS-CoV-2 entry receptors (ACE2 and DPP4), SARS-CoV-2 entry associated proteases (TMPRSS2, CTSB, and CTSL), and 332 human intracellular proteins interacting with SARS-CoV-2. A number of genes/proteins targeted by SARS-CoV-2 (ACE2, BRD2, COMT, CTSB, CTSL, DNMT1, DPP4, ERP44, F2RL1, GDF15, GPX1, HDAC2, HMOX1, HYOU1, IDE, LOX, NUTF2, PCNT, PLAT, RAB10, RHOA, SCARB1, and SELENOS) were found in the networks of vascular diabetic complications and insulin resistance. According to the Gene Ontology enrichment analysis, the defined molecules are involved in the response to hypoxia, reactive oxygen species metabolism, immune and inflammatory response, regulation of angiogenesis, platelet degranulation, and other processes. The results expand the understanding of the molecular basis of diabetes and COVID-19 comorbidity.
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Semaa A. Shaban, H. Salih M, Adnan F. AL-Azzawie. Association between GSTM1, GSTT1 gene polymorphisms and asthma in adult patients from Tikrit population of Iraq. Biomedicine (Taipei) 2022. [DOI: 10.51248/.v42i1.955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Introduction and Aim: Asthma is known as a polygenic and multifactorial disease. The underlying debate about the role of genetics in the development of asthma is still unclear. The objectives of this research are to examine whether the GSTM1 and GSTT1 gene polymorphisms are associated with asthma susceptibility.
Materials and Methods: A total of 70 patients with asthma and 20 healthy individuals were investigated in this study. Genotyping was carried out by using PCR protocol for analysis of GSTM1 and GSTT1 null/positive genotypes.
Results: Patients with asthma (34.285%) demonstrated a greater prevalence of the GSTM1, GSTT1 (-) genotype than the healthy subject (10%, P-value 0.012). A positive correlation was found between GSTT1, GSTM1 (+) genotype and healthy individuals (40%) compared with asthmatic patients (24.285%).
Conclusion: The results of this research support the idea that GSTM1, GSTT1 (-) genotype may play critical roles in asthmatic inflammatory response. Further experimental investigations are needed to estimate the role of GSTM1 and GSTT1 polymorphisms in asthma.
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Rathod A, Zhang H, Arshad SH, Ewart S, Relton CL, Karmaus W, Holloway JW. DNA Methylation and Asthma Acquisition during Adolescence and Post-Adolescence, an Epigenome-Wide Longitudinal Study. J Pers Med 2022; 12:202. [PMID: 35207690 PMCID: PMC8877984 DOI: 10.3390/jpm12020202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 02/01/2023] Open
Abstract
The role of epigenetics in the pathogenesis of asthma acquisition in adolescence and post-adolescence has been unknown. We carried out a longitudinal epigenome-wide association study, using data from the Isle of Wight Birth Cohort (IOWBC). To improve statistical power, we first screened CpGs based on associations of DNA methylation (DNAm) at an age of 10 years (pre-adolescence) with asthma acquisition at 10-18 years (during adolescence). A logistic regression with repeated measures was applied to CpGs that passed screening to examine the associations of pre-adolescence DNAm with asthma acquisition from 10-18 years and 18-26 years, with an interaction term to evaluate transition period specificity. Findings were further tested in an independent birth cohort, ALSPAC. In total, 205 CpGs (with 150 being females) showed associations with asthma acquisition (main or interaction effects) at FDR = 0.05 in IOWBC, of which 112 (90 being females) showed consistent associations in the ALSPAC. Genes that the identified CpGs were mapped to, e.g., AKAP1 and ENO1, have been shown to be associated with the risk of asthma. Our findings indicated that DNAm at specific CpGs was associated with asthma acquisition. CpGs showing such associations were likely to be different between males and females and, at certain CpGs, were unique to a specific transition period.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - Syed Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK;
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Newport, Isle of Wight PO30 5TG, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Susan Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI 48824, USA;
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 1QU, UK;
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
- National Institute for Health Research Bristol Biomedical Research Centre, University Hospitals Bristol and Weston NHS Foundation Trust, University of Bristol, Bristol BS8 2BN, UK
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38111, USA; (A.R.); (W.K.)
| | - John W. Holloway
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
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15
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Goncharova IA, Bragina EY, Zhalsanova IZ, Freidin MB, Nazarenko MS. Putative regulatory functions of SNPs associated with bronchial asthma, arterial hypertension and their comorbid phenotype. Vavilovskii Zhurnal Genet Selektsii 2022; 25:855-863. [PMID: 35088020 PMCID: PMC8761574 DOI: 10.18699/vj21.099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 11/19/2022] Open
Abstract
Linkage disequilibrium (LD) of single nucleotide polymorphisms (SNPs) of TLR4/AL160272.2 (rs1927914, rs1928298, rs7038716, rs7026297, rs7025144) was estimated in the Slavs of West Siberia. We further investigated an association of SNPs in TLR4/AL160272.2 (rs1927914, rs7038716, rs7025144), SERPINA1 (rs1980616), ATXN2/BRAP (rs11065987), IL2RB (rs2284033), NT5C2 (rs11191582), CARD8 (rs11669386), ANG/RNASE4 (rs1010461), and ABTB2/ САТ (rs2022318) genes with bronchial asthma (BA), arterial hypertension (AH) and their comorbidity. Then, the disease-associated SNPs were annotated in silico in relation to their potential regulatory functions. Strong LD was detected between rs1928298 and rs1927914, as well as rs7026297 and rs7038716 in the Slavs of West Siberia. It was found that the rs1927914 G allele of the TLR4 gene and the rs1980616 C allele of the SERPINA1 gene are associated with the predisposition to BA. These SNPs can affect binding affinity of transcription factors of the Pou and Klf4 families, as well as the expression levels of the TLR4 and SERPINA1 genes. The rs11065987 allele A of the ATXN2/BRAP genes, the rs11669386 A allele of the CARD8 gene, the rs2284033 allele G of the IL2RB gene, and the rs11191582 allele G of the NT5C2 gene were associated with the risk of AH. These variants can alter binding affinity of the Hoxa9, Irf, RORalpha1 and HMG-IY transcription factors, as well as the expression levels of the ALDH2, CARD8, NT5C2, ARL3, and SFXN2 genes in blood cells/vessels/heart, respectively. The risk of developing a comorbid phenotype of AD and AH is associated with the A allele of rs7038716 and the T allele of rs7025144 of the TLR4/AL160272.2 genes, the A allele of rs1010461 of the ANG gene and the C allele of rs2022318 of the ABTB2/CAT genes. Variants rs7038716 and rs7025144 can change the expression levels of the TLR4 gene in blood cells, while rs1010461 and rs2022318 influence the expression levels of the ANG and RNASE4 genes as well as the CAT and ABTB2 genes in blood cells, lungs/vessels/heart.
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Affiliation(s)
- I. A. Goncharova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - E. Yu. Bragina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - I. Zh. Zhalsanova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - M. B. Freidin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences
| | - M. S. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences
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16
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Hypoglycemia, Vascular Disease and Cognitive Dysfunction in Diabetes: Insights from Text Mining-Based Reconstruction and Bioinformatics Analysis of the Gene Networks. Int J Mol Sci 2021; 22:ijms222212419. [PMID: 34830301 PMCID: PMC8620086 DOI: 10.3390/ijms222212419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/16/2022] Open
Abstract
Hypoglycemia has been recognized as a risk factor for diabetic vascular complications and cognitive decline, but the molecular mechanisms of the effect of hypoglycemia on target organs are not fully understood. In this work, gene networks of hypoglycemia and cardiovascular disease, diabetic retinopathy, diabetic nephropathy, diabetic neuropathy, cognitive decline, and Alzheimer's disease were reconstructed using ANDSystem, a text-mining-based tool. The gene network of hypoglycemia included 141 genes and 2467 interactions. Enrichment analysis of Gene Ontology (GO) biological processes showed that the regulation of insulin secretion, glucose homeostasis, apoptosis, nitric oxide biosynthesis, and cell signaling are significantly enriched for hypoglycemia. Among the network hubs, INS, IL6, LEP, TNF, IL1B, EGFR, and FOS had the highest betweenness centrality, while GPR142, MBOAT4, SLC5A4, IGFBP6, PPY, G6PC1, SLC2A2, GYS2, GCGR, and AQP7 demonstrated the highest cross-talk specificity. Hypoglycemia-related genes were overrepresented in the gene networks of diabetic complications and comorbidity; moreover, 14 genes were mutual for all studied disorders. Eleven GO biological processes (glucose homeostasis, nitric oxide biosynthesis, smooth muscle cell proliferation, ERK1 and ERK2 cascade, etc.) were overrepresented in all reconstructed networks. The obtained results expand our understanding of the molecular mechanisms underlying the deteriorating effects of hypoglycemia in diabetes-associated vascular disease and cognitive dysfunction.
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17
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Demenkov PS, Oshchepkova ЕА, Demenkov PS, Ivanisenko TV, Ivanisenko VA. Prioritization of biological processes based on the reconstruction and analysis of associative gene networks describing the response of plants to adverse environmental factors. Vavilovskii Zhurnal Genet Selektsii 2021; 25:580-592. [PMID: 34723066 PMCID: PMC8543060 DOI: 10.18699/vj21.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 11/23/2022] Open
Abstract
Methods for prioritizing or ranking candidate genes according to their importance based on specif ic criteria
via the analysis of gene networks are widely used in biomedicine to search for genes associated with diseases and to
predict biomarkers, pharmacological targets and other clinically relevant molecules. These methods have also been
used in other f ields, particularly in crop production. This is largely due to the development of technologies to solve
problems in marker-oriented and genomic selection, which requires knowledge of the molecular genetic mechanisms
underlying the formation of agriculturally valuable traits. A new direction for the study of molecular genetic mechanisms
is the prioritization of biological processes based on the analysis of associative gene networks. Associative gene
networks are heterogeneous networks whose vertices can depict both molecular genetic objects (genes, proteins, metabolites,
etc.) and the higher-level factors (biological processes, diseases, external environmental factors, etc.) related
to regulatory, physicochemical or associative interactions. Using a previously developed method, biological processes
involved in plant responses to increased cadmium content, saline stress and drought conditions were prioritized according
to their degree of connection with the gene networks in the SOLANUM TUBEROSUM knowledge base. The
prioritization results indicate that fundamental processes, such as gene expression, post-translational modif ications,
protein degradation, programmed cell death, photosynthesis, signal transmission and stress response play important
roles in the common molecular genetic mechanisms for plant response to various adverse factors. On the other hand, a
group of processes related to the development of seeds (“seeding development”) was revealed to be drought specif ic,
while processes associated with ion transport (“ion transport”) were included in the list of responses specif ic to salt
stress and processes associated with the metabolism of lipids were found to be involved specif ically in the response to
cadmium.
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Affiliation(s)
- P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - Е А Oshchepkova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - P S Demenkov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
| | - T V Ivanisenko
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V A Ivanisenko
- Novosibirsk State University, Novosibirsk, Russiavosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
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18
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Cremades-Jimeno L, de Pedro MÁ, López-Ramos M, Sastre J, Mínguez P, Fernández IM, Baos S, Cárdaba B. Prioritizing Molecular Biomarkers in Asthma and Respiratory Allergy Using Systems Biology. Front Immunol 2021; 12:640791. [PMID: 33936056 PMCID: PMC8081895 DOI: 10.3389/fimmu.2021.640791] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/15/2021] [Indexed: 01/29/2023] Open
Abstract
Highly prevalent respiratory diseases such as asthma and allergy remain a pressing health challenge. Currently, there is an unmet need for precise diagnostic tools capable of predicting the great heterogeneity of these illnesses. In a previous study of 94 asthma/respiratory allergy biomarker candidates, we defined a group of potential biomarkers to distinguish clinical phenotypes (i.e. nonallergic asthma, allergic asthma, respiratory allergy without asthma) and disease severity. Here, we analyze our experimental results using complex algorithmic approaches that establish holistic disease models (systems biology), combining these insights with information available in specialized databases developed worldwide. With this approach, we aim to prioritize the most relevant biomarkers according to their specificity and mechanistic implication with molecular motifs of the diseases. The Therapeutic Performance Mapping System (Anaxomics’ TPMS technology) was used to generate one mathematical model per disease: allergic asthma (AA), non-allergic asthma (NA), and respiratory allergy (RA), defining specific molecular motifs for each. The relationship of our molecular biomarker candidates and each disease was analyzed by artificial neural networks (ANNs) scores. These analyses prioritized molecular biomarkers specific to the diseases and to particular molecular motifs. As a first step, molecular characterization of the pathophysiological processes of AA defined 16 molecular motifs: 2 specific for AA, 2 shared with RA, and 12 shared with NA. Mechanistic analysis showed 17 proteins that were strongly related to AA. Eleven proteins were associated with RA and 16 proteins with NA. Specificity analysis showed that 12 proteins were specific to AA, 7 were specific to RA, and 2 to NA. Finally, a triggering analysis revealed a relevant role for AKT1, STAT1, and MAPK13 in all three conditions and for TLR4 in asthmatic diseases (AA and NA). In conclusion, this study has enabled us to prioritize biomarkers depending on the functionality associated with each disease and with specific molecular motifs, which could improve the definition and usefulness of new molecular biomarkers.
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Affiliation(s)
- Lucía Cremades-Jimeno
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María Ángeles de Pedro
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - María López-Ramos
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Joaquín Sastre
- Allergy Department, Fundación Jiménez Díaz, Madrid, Spain.,Center for Biomedical Network of Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | | | - Selene Baos
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain
| | - Blanca Cárdaba
- Immunology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid (UAM), Madrid, Spain.,Center for Biomedical Network of Respiratory Diseases (CIBERES), ISCIII, Madrid, Spain
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19
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Saik OV, Klimontov VV. Bioinformatic Reconstruction and Analysis of Gene Networks Related to Glucose Variability in Diabetes and Its Complications. Int J Mol Sci 2020; 21:ijms21228691. [PMID: 33217980 PMCID: PMC7698756 DOI: 10.3390/ijms21228691] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 02/06/2023] Open
Abstract
Glucose variability (GV) has been recognized recently as a promoter of complications and therapeutic targets in diabetes. The aim of this study was to reconstruct and analyze gene networks related to GV in diabetes and its complications. For network analysis, we used the ANDSystem that provides automatic network reconstruction and analysis based on text mining. The network of GV consisted of 37 genes/proteins associated with both hyperglycemia and hypoglycemia. Cardiovascular system, pancreas, adipose and muscle tissues, gastrointestinal tract, and kidney were recognized as the loci with the highest expression of GV-related genes. According to Gene Ontology enrichment analysis, these genes are associated with insulin secretion, glucose metabolism, glycogen biosynthesis, gluconeogenesis, MAPK and JAK-STAT cascades, protein kinase B signaling, cell proliferation, nitric oxide biosynthesis, etc. GV-related genes were found to occupy central positions in the networks of diabetes complications (cardiovascular disease, diabetic nephropathy, retinopathy, and neuropathy) and were associated with response to hypoxia. Gene prioritization analysis identified new gene candidates (THBS1, FN1, HSP90AA1, EGFR, MAPK1, STAT3, TP53, EGF, GSK3B, and PTEN) potentially involved in GV. The results expand the understanding of the molecular mechanisms of the GV phenomenon in diabetes and provide molecular markers and therapeutic targets for future research.
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Affiliation(s)
- Olga V. Saik
- Laboratory of Endocrinology, Research Institute of Clinical and Experimental Lymphology—Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (RICEL—Branch of IC&G SB RAS), 630060 Novosibirsk, Russia;
- Laboratory of Computer Proteomics, Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (ICG SB RAS), 630090 Novosibirsk, Russia
- Correspondence:
| | - Vadim V. Klimontov
- Laboratory of Endocrinology, Research Institute of Clinical and Experimental Lymphology—Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (RICEL—Branch of IC&G SB RAS), 630060 Novosibirsk, Russia;
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Ivanisenko TV, Saik OV, Demenkov PS, Ivanisenko NV, Savostianov AN, Ivanisenko VA. ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. BMC Bioinformatics 2020; 21:228. [PMID: 32921303 PMCID: PMC7488989 DOI: 10.1186/s12859-020-03557-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The rapid growth of scientific literature has rendered the task of finding relevant information one of the critical problems in almost any research. Search engines, like Google Scholar, Web of Knowledge, PubMed, Scopus, and others, are highly effective in document search; however, they do not allow knowledge extraction. In contrast to the search engines, text-mining systems provide extraction of knowledge with representations in the form of semantic networks. Of particular interest are tools performing a full cycle of knowledge management and engineering, including automated retrieval, integration, and representation of knowledge in the form of semantic networks, their visualization, and analysis. STRING, Pathway Studio, MetaCore, and others are well-known examples of such products. Previously, we developed the Associative Network Discovery System (ANDSystem), which also implements such a cycle. However, the drawback of these systems is dependence on the employed ontologies describing the subject area, which limits their functionality in searching information based on user-specified queries. RESULTS The ANDDigest system is a new web-based module of the ANDSystem tool, permitting searching within PubMed by using dictionaries from the ANDSystem tool and sets of user-defined keywords. ANDDigest allows performing the search based on complex queries simultaneously, taking into account many types of objects from the ANDSystem's ontology. The system has a user-friendly interface, providing sorting, visualization, and filtering of the found information, including mapping of mentioned objects in text, linking to external databases, sorting of data by publication date, citations number, journal H-indices, etc. The system provides data on trends for identified entities based on dynamics of interest according to the frequency of their mentions in PubMed by years. CONCLUSIONS The main feature of ANDDigest is its functionality, serving as a specialized search for information about multiple associative relationships of objects from the ANDSystem's ontology vocabularies, taking into account user-specified keywords. The tool can be applied to the interpretation of experimental genetics data, the search for associations between molecular genetics objects, and the preparation of scientific and analytical reviews. It is presently available at https://anddigest.sysbio.ru/ .
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Affiliation(s)
- Timofey V Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
- Laboratory of Computer Genomics, Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia.
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia.
| | - Olga V Saik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Pavel S Demenkov
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia
| | - Nikita V Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | | | - Vladimir A Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Kurchatov Genomics Center, Institute of Cytology & Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090, Russia
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21
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Recent findings in the genetics and epigenetics of asthma and allergy. Semin Immunopathol 2020; 42:43-60. [PMID: 32060620 PMCID: PMC7066293 DOI: 10.1007/s00281-019-00777-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 12/22/2019] [Indexed: 12/16/2022]
Abstract
In asthma and allergy genetics, a trend towards a few main topics developed over the last 2 years. First, a number of studies have been published recently which focus on overlapping and/or very specific phenotypes: within the allergy spectrum but also reaching beyond, looking for common genetic traits shared between different diseases or disease entities. Secondly, an urgently needed focus has been put on asthma and allergy genetics in populations genetically different from European ancestry. This acknowledges that the majority of new asthma patients today are not white and asthma is a truly worldwide disease. In epigenetics, recent years have seen several large-scale epigenome-wide association studies (EWAS) being published and a further focus was on the interaction between the environment and epigenetic signatures. And finally, the major trends in current asthma and allergy genetics and epigenetics comes from the field of pharmacogenetics, where it is necessary to understand the susceptibility for and mechanisms of current asthma and allergy therapies while at the same time, we need to have scientific answers to the recent availability of novel drugs that hold the promise for a more individualized therapy.
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Zolotareva O, Saik OV, Königs C, Bragina EY, Goncharova IA, Freidin MB, Dosenko VE, Ivanisenko VA, Hofestädt R. Comorbidity of asthma and hypertension may be mediated by shared genetic dysregulation and drug side effects. Sci Rep 2019; 9:16302. [PMID: 31705029 PMCID: PMC6841742 DOI: 10.1038/s41598-019-52762-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023] Open
Abstract
Asthma and hypertension are complex diseases coinciding more frequently than expected by chance. Unraveling the mechanisms of comorbidity of asthma and hypertension is necessary for choosing the most appropriate treatment plan for patients with this comorbidity. Since both diseases have a strong genetic component in this article we aimed to find and study genes simultaneously associated with asthma and hypertension. We identified 330 shared genes and found that they form six modules on the interaction network. A strong overlap between genes associated with asthma and hypertension was found on the level of eQTL regulated genes and between targets of drugs relevant for asthma and hypertension. This suggests that the phenomenon of comorbidity of asthma and hypertension may be explained by altered genetic regulation or result from drug side effects. In this work we also demonstrate that not only drug indications but also contraindications provide an important source of molecular evidence helpful to uncover disease mechanisms. These findings give a clue to the possible mechanisms of comorbidity and highlight the direction for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld, Germany.
| | - Olga V Saik
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Cassandra Königs
- Bielefeld University, Bioinformatics and Medical Informatics Department, Bielefeld, Germany
| | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, Russia
| | - Ralf Hofestädt
- Bielefeld University, Bioinformatics and Medical Informatics Department, Bielefeld, Germany
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23
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Zolotareva O, Kleine M. A Survey of Gene Prioritization Tools for Mendelian and Complex Human Diseases. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2018-0069/jib-2018-0069.xml. [PMID: 31494632 PMCID: PMC7074139 DOI: 10.1515/jib-2018-0069] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 07/12/2019] [Indexed: 12/16/2022] Open
Abstract
Modern high-throughput experiments provide us with numerous potential associations between genes and diseases. Experimental validation of all the discovered associations, let alone all the possible interactions between them, is time-consuming and expensive. To facilitate the discovery of causative genes, various approaches for prioritization of genes according to their relevance for a given disease have been developed. In this article, we explain the gene prioritization problem and provide an overview of computational tools for gene prioritization. Among about a hundred of published gene prioritization tools, we select and briefly describe 14 most up-to-date and user-friendly. Also, we discuss the advantages and disadvantages of existing tools, challenges of their validation, and the directions for future research.
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Affiliation(s)
- Olga Zolotareva
- Bielefeld University, Faculty of Technology and Center for Biotechnology, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Universitätsstraße 25, Bielefeld, Germany
| | - Maren Kleine
- Bielefeld University, Faculty of Technology, Bioinformatics/Medical Informatics Department, Universitätsstraße 25, Bielefeld, Germany
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Zhao L, Chen C, Wang Y, Shen J, Ding Z. Conserved MicroRNA Act Boldly During Sprout Development and Quality Formation in Pingyang Tezaocha ( Camellia sinensis). Front Genet 2019; 10:237. [PMID: 31001312 PMCID: PMC6455055 DOI: 10.3389/fgene.2019.00237] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 03/04/2019] [Indexed: 01/20/2023] Open
Abstract
Tea tree [Camellia sinensis (L.) O. Kuntze] is an important leaf (sometimes tender stem)-using commercial plant with many medicinal uses. The development of newly sprouts would directly affect the yield and quality of tea product, especially significant for Pingyang Tezaocha (PYTZ) which takes up a large percent in the early spring tea market. MicroRNA (miRNA), particularly the conserved miRNAs, often position in the center of subtle and complex gene regulatory systems, precisely control the biological processes together with other factors in a spatio-temporal pattern. Here, quality-determined metabolites catechins, theanine and caffeine in PYTZ sprouts including buds (sBud), different development stages of leaves (sL1, sL2) and stems (sS1, sS2) were quantified. A total of 15 miRNA libraries of the same tissue with three repetitions for each were constructed to explore vital miRNAs during the biological processes of development and quality formation. We analyzed the whole miRNA profiles during the sprout development and defined conserved miRNA families in the tea plant. The differentially expressed miRNAs related to the expression profiles buds, leaves, and stems development stages were described. Twenty one miRNAs and eight miRNA-TF pairs that most likely to participate in regulating development, and at least two miRNA-TF-metabolite triplets that participate in both development and quality formation had been filtered. Our results indicated that conserved miRNA act boldly during important biological processes, they are (i) more likely to be linked with morphological function in primary metabolism during sprout development, and (ii) hold an important position in secondary metabolism during quality formation in tea plant, also (iii) coordinate with transcription factors in forming networks of complex multicellular organism regulation.
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Affiliation(s)
- Lei Zhao
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China.,Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Changsong Chen
- Tea Research Institute, Fujian Academy of Agricultural Sciences, Fu'an, China
| | - Yu Wang
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Jiazhi Shen
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhaotang Ding
- Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural Plants, College of Horticulture, Qingdao Agricultural University, Qingdao, China
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25
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Saik OV, Nimaev VV, Usmonov DB, Demenkov PS, Ivanisenko TV, Lavrik IN, Ivanisenko VA. Prioritization of genes involved in endothelial cell apoptosis by their implication in lymphedema using an analysis of associative gene networks with ANDSystem. BMC Med Genomics 2019; 12:47. [PMID: 30871556 PMCID: PMC6417156 DOI: 10.1186/s12920-019-0492-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Currently, more than 150 million people worldwide suffer from lymphedema. It is a chronic progressive disease characterized by high-protein edema of various parts of the body due to defects in lymphatic drainage. Molecular-genetic mechanisms of the disease are still poorly understood. Beginning of a clinical manifestation of primary lymphedema in middle age and the development of secondary lymphedema after treatment of breast cancer can be genetically determined. Disruption of endothelial cell apoptosis can be considered as one of the factors contributing to the development of lymphedema. However, a study of the relationship between genes associated with lymphedema and genes involved in endothelial apoptosis, in the associative gene network was not previously conducted. METHODS In the current work, we used well-known methods (ToppGene and Endeavour), as well as methods previously developed by us, to prioritize genes involved in endothelial apoptosis and to find potential participants of molecular-genetic mechanisms of lymphedema among them. Original methods of prioritization took into account the overrepresented Gene Ontology biological processes, the centrality of vertices in the associative gene network, describing the interactions of endothelial apoptosis genes with genes associated with lymphedema, and the association of the analyzed genes with diseases that are comorbid to lymphedema. RESULTS An assessment of the quality of prioritization was performed using criteria, which involved an analysis of the enrichment of the top-most priority genes by genes, which are known to have simultaneous interactions with lymphedema and endothelial cell apoptosis, as well as by genes differentially expressed in murine model of lymphedema. In particular, among genes involved in endothelial apoptosis, KDR, TNF, TEK, BMPR2, SERPINE1, IL10, CD40LG, CCL2, FASLG and ABL1 had the highest priority. The identified priority genes can be considered as candidates for genotyping in the studies involving the search for associations with lymphedema. CONCLUSIONS Analysis of interactions of these genes in the associative gene network of lymphedema can improve understanding of mechanisms of interaction between endothelial apoptosis and lymphangiogenesis, and shed light on the role of disturbance of these processes in the development of edema, chronic inflammation and connective tissue transformation during the progression of the disease.
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Affiliation(s)
- Olga V. Saik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Vadim V. Nimaev
- Laboratory of Surgical Lymphology and Lymphodetoxication, Research Institute of Clinical and Experimental Lymрhology – Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, st. Timakova 2, Novosibirsk, 630117 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Dilovarkhuja B. Usmonov
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
- Department of Neurosurgery, Ya. L. Tsivyan Novosibirsk Research Institute of Traumatology and Orthopedics, Ministry of Health of the Russian Federation, st. Frunze 17, Novosibirsk, 630091 Russia
| | - Pavel S. Demenkov
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Timofey V. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Inna N. Lavrik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Translational Inflammation Research, Institute of Experimental Internal Medicine, Otto von Guericke University Magdeburg, Medical Faculty, Pfalzer Platz 28, 39106 Magdeburg, Germany
| | - Vladimir A. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
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26
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Ivanisenko VA, Demenkov PS, Ivanisenko TV, Mishchenko EL, Saik OV. A new version of the ANDSystem tool for automatic extraction of knowledge from scientific publications with expanded functionality for reconstruction of associative gene networks by considering tissue-specific gene expression. BMC Bioinformatics 2019; 20:34. [PMID: 30717676 PMCID: PMC6362586 DOI: 10.1186/s12859-018-2567-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Consideration of tissue-specific gene expression in reconstruction and analysis of molecular genetic networks is necessary for a proper description of the processes occurring in a specified tissue. Currently, there are a number of computer systems that allow the user to reconstruct molecular-genetic networks using the data automatically extracted from the texts of scientific publications. Examples of such systems are STRING, Pathway Commons, MetaCore and Ingenuity. The MetaCore and Ingenuity systems permit taking into account tissue-specific gene expression during the reconstruction of gene networks. Previously, we developed the ANDSystem tool, which also provides an automated extraction of knowledge from scientific texts and allows the reconstruction of gene networks. The main difference between our system and other tools is in the different types of interactions between objects, which makes the ANDSystem complementary to existing well-known systems. However, previous versions of the ANDSystem did not contain any information on tissue-specific expression. RESULTS A new version of the ANDSystem has been developed. It offers the reconstruction of associative gene networks while taking into account the tissue-specific gene expression. The ANDSystem knowledge base features information on tissue-specific expression for 272 tissues. The system allows the reconstruction of combined gene networks, as well as performing the filtering of genes from such networks using the information on their tissue-specific expression. As an example of the application of such filtering, the gene network of the extrinsic apoptotic signaling pathway was analyzed. It was shown that considering different tissues can lead to changes in gene network structure, including changes in such indicators as betweenness centrality of vertices, clustering coefficient, network centralization, network density, etc. CONCLUSIONS: The consideration of tissue specificity can play an important role in the analysis of gene networks, in particular solving the problem of finding the most significant central genes. Thus, the new version of ANDSystem can be employed for a wide range of tasks related to biomedical studies of individual tissues. It is available at http://www-bionet.sscc.ru/and/cell /.
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Affiliation(s)
- Vladimir A. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Pavel S. Demenkov
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Timofey V. Ivanisenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
| | - Elena L. Mishchenko
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
| | - Olga V. Saik
- Laboratory of Computer-Assisted Proteomics, Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Prospekt Lavrentyeva 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, st. Pirogova 1, Novosibirsk, 630090 Russia
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27
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Affiliation(s)
- Tatiana V Tatarinova
- Department of Biology, University of La Verne, La Verne, CA, USA
- Department of Fundamental Biology and Biotechnology, Siberian Federal University, 660074, Krasnoyarsk, Russia
- Vavilov Institute of General Genetics RAS, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Ming Chen
- Zhejiang University, Hangzhou, 310058, China
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, 630090, Novosibirsk, Russia.
- Novosibirsk State University, 630090, Novosibirsk, Russia.
- A.O. Kovalevsky Institute of Marine Biological Research of RAS, 119334, Moscow, Russia.
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28
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Saik OV, Demenkov PS, Ivanisenko TV, Bragina EY, Freidin MB, Dosenko VE, Zolotareva OI, Choynzonov EL, Hofestaedt R, Ivanisenko VA. Search for New Candidate Genes Involved in the Comorbidity of Asthma and Hypertension Based on Automatic Analysis of Scientific Literature. J Integr Bioinform 2018; 15:/j/jib.2018.15.issue-4/jib-2018-0054/jib-2018-0054.xml. [PMID: 30864351 PMCID: PMC6348743 DOI: 10.1515/jib-2018-0054] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/31/2018] [Indexed: 12/20/2022] Open
Abstract
Comorbid states of diseases significantly complicate diagnosis and treatment. Molecular mechanisms of comorbid states of asthma and hypertension are still poorly understood. Prioritization is a way for identifying genes involved in complex phenotypic traits. Existing methods of prioritization consider genetic, expression and evolutionary data, molecular-genetic networks and other. In the case of molecular-genetic networks, as a rule, protein-protein interactions and KEGG networks are used. ANDSystem allows reconstructing associative gene networks, which include more than 20 types of interactions, including protein-protein interactions, expression regulation, transport, catalysis, etc. In this work, a set of genes has been prioritized to find genes potentially involved in asthma and hypertension comorbidity. The prioritization was carried out using well-known methods (ToppGene and Endeavor) and a cross-talk centrality criterion, calculated by analysis of associative gene networks from ANDSystem. The identified genes, including IL1A, CD40LG, STAT3, IL15, FAS, APP, TLR2, C3, IL13 and CXCL10, may be involved in the molecular mechanisms of comorbid asthma/hypertension. An analysis of the dynamics of the frequency of mentioning the most priority genes in scientific publications revealed that the top 100 priority genes are significantly enriched with genes with increased positive dynamics, which may be a positive sign for further studies of these genes.
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Affiliation(s)
- Olga V Saik
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Pavel S Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Timofey V Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Victor E Dosenko
- Bogomoletz Institute of Physiology, National Academy of Science, Kiev, Ukraine
| | - Olga I Zolotareva
- Bielefeld University, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld, Germany
| | - Evgeniy L Choynzonov
- Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Ralf Hofestaedt
- Bielefeld University, Technical Faculty, AG Bioinformatics and Medical Informatics, Bielefeld, Germany
| | - Vladimir A Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
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29
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Drevytska T, Morhachov R, Tumanovska L, Portnichenko G, Nagibin V, Boldyriev O, Lapikova-Bryhinska T, Gurianova V, Dons'koi B, Freidin M, Ivanisenko V, Bragina EY, Hofestädt R, Dosenko V. shRNA-Induced Knockdown of a Bioinformatically Predicted Target IL10 Influences Functional Parameters in Spontaneously Hypertensive Rats with Asthma. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0053/jib-2018-0053.xml. [PMID: 30530891 PMCID: PMC6348748 DOI: 10.1515/jib-2018-0053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022] Open
Abstract
One of the most common comorbid pathology is asthma and arterial hypertension. For experimental modeling of comorbidity we have used spontaneously hypertensive rats with ovalbumin (OVA)-induced asthma. Rats were randomly divided into three groups: control group, OVA-induced asthma group; OVA-induced asthma + IL10 shRNA interference group. Target gene (IL10) was predicted by ANDSystem. We have demonstrated that RNA-interference of IL10 affected cardiovascular (tested using Millar microcatheter system) as well as respiratory functions (tested using force-oscillation technique, Flexivent) in rats. We have shown that during RNA-interference of IL10 gene in vivo there were changes in both cardiac and lung function parameters. These changes in the cardiovascular parameters can be described as positive. But the more intensive heart workload can lead to exhaust and decompensation of the heart functions. Knockdown of IL10 gene in asthma modeling induces some positive changes in respiratory functions of asthmatic animals such as decreased elastance and increased compliance of the lungs, as well as less pronounced pathomorphological changes in the lung tissue. Thus, we provide the data about experimentally confirmed functionality changes of the target which was in silico predicted to be associated with both asthma and hypertension – in our new experimental model of comorbid pathology.
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Affiliation(s)
- Tatiana Drevytska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Roman Morhachov
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Lesya Tumanovska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Georgiy Portnichenko
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Vasyl Nagibin
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Oleksiy Boldyriev
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Tatiana Lapikova-Bryhinska
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Veronika Gurianova
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, Kyiv 01024, Ukraine
| | - Borys Dons'koi
- National Academy of Medical Sciences, State Institution "Institute of Pediatrics, Obstetrics and Gynecology", Kyiv, Ukraine
| | - Maxim Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Vladimir Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | - Ralf Hofestädt
- Bielefeld University, International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld, Germany.,Bielefeld University, Technical Faculty, AG Bioinformatics and Medical Informatics, Bielefeld, Germany
| | - Victor Dosenko
- Department of General and Molecular Pathophysiology, Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz str, Kyiv 01024, Ukraine
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Bragina EY, Goncharova IA, Garaeva AF, Nemerov EV, Babovskaya AA, Karpov AB, Semenova YV, Zhalsanova IZ, Gomboeva DE, Saik OV, Zolotareva OI, Ivanisenko VA, Dosenko VE, Hofestaedt R, Freidin MB. Molecular Relationships between Bronchial Asthma and Hypertension as Comorbid Diseases. J Integr Bioinform 2018; 15:/j/jib.ahead-of-print/jib-2018-0052/jib-2018-0052.xml. [PMID: 30530896 PMCID: PMC6348747 DOI: 10.1515/jib-2018-0052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/13/2018] [Indexed: 01/14/2023] Open
Abstract
Comorbidity, a co-incidence of several disorders in an individual, is a common phenomenon. Their development is governed by multiple factors, including genetic variation. The current study was set up to look at associations between isolated and comorbid diseases of bronchial asthma and hypertension, on one hand, and single nucleotide polymorphisms associated with regulation of gene expression (eQTL), on the other hand. A total of 96 eQTL SNPs were genotyped in 587 Russian individuals. Bronchial asthma alone was found to be associated with rs1927914 (TLR4), rs1928298 (intergenic variant), and rs1980616 (SERPINA1); hypertension alone was found to be associated with rs11065987 (intergenic variant); rs2284033 (IL2RB), rs11191582 (NT5C2), and rs11669386 (CARD8); comorbidity between asthma and hypertension was found to be associated with rs1010461 (ANG/RNASE4), rs7038716, rs7026297 (LOC105376244), rs7025144 (intergenic variant), and rs2022318 (intergenic variant). The results suggest that genetic background of comorbidity of asthma and hypertension is different from genetic backgrounds of both diseases manifesting isolated.
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Affiliation(s)
- Elena Yu Bragina
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
| | | | - Anna F Garaeva
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia.,Siberian State Medical University, Tomsk, Russia
| | | | | | - Andrey B Karpov
- Seversk Biophysical Research Centre of the Federal Medico-Biological Agency, Seversk, Russia
| | - Yulia V Semenova
- Seversk Clinical Hospital, Siberian Federal Research and Clinical Centre of the Federal Medico-Biological Agency, Seversk, Russia
| | | | | | - Olga V Saik
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Olga I Zolotareva
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany.,International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes" and Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Vladimir A Ivanisenko
- The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Victor E Dosenko
- Bogomoletz Institute of Physiology, National Academy of Science, Kiev, Ukraine
| | - Ralf Hofestaedt
- Bielefeld University, Bioinformatics/Medical Informatics Department, Bielefeld, Germany
| | - Maxim B Freidin
- Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russia
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31
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Yankina MA, Saik OV, Ivanisenko VA, Demenkov PS, Khusnutdinova EK. Evaluation of Prioritization Methods of Extrinsic Apoptotic Signaling Pathway Genes for Retrieval of the New Candidates Associated with Major Depressive Disorder. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418110170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Affiliation(s)
- Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.
- Novosibirsk State University, Novosibirsk, Russia.
| | | | - Ming Chen
- Zhejiang University, Hangzhou, China
| | - Ancha V Baranova
- Research Centre of Medical Genetics, Moscow, Russia
- George Mason University, Fairfax, VA, USA
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