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Shepelev MV, Kopantzev EP, Vinogradova TV, Sverdlov ED, Korobko IV. hTERT and BIRC5 gene promoters for cancer gene therapy: A comparative study. Oncol Lett 2016; 12:1204-1210. [PMID: 27446419 DOI: 10.3892/ol.2016.4718] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 06/02/2016] [Indexed: 12/11/2022] Open
Abstract
Human telomerase reverse transcriptase (hTERT) and survivin (BIRC5) gene promoters are frequently used for transcriptional targeting of tumor cells, yet there is no comprehensive comparative analysis allowing rational choice of a promoter for a particular therapy. In the current study, the transcriptional activity of hTERT, human BIRC5 and mouse Birc5 promoters and their modifications were compared in 10 human cancer cell lines using the luciferase reporter gene activity assay. The results revealed that BIRC5- and hTERT-based promoters had strikingly different cell specificities with comparable activities in only 40% of cell lines. Importantly, relative hTERT and BIRC5 transcript abundance cannot be used to predict the most potent promoter. Among the hTERT-based promoters that were assessed, modification with the minimal cytomegalovirus promoter generally resulted in the most potent activity. Mouse Birc5 and modified human BIRC5 promoters were superior to the unmodified human survivin promoter; however, their tumor specificities must be investigated further. In summary, the present results emphasize the desirability for construction of more universal tumor-specific promoters to efficiently target a wide spectrum of tumor cells.
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Affiliation(s)
- Mikhail V Shepelev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia
| | - Eugene P Kopantzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Tatiana V Vinogradova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Eugene D Sverdlov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow 123182, Russia
| | - Igor V Korobko
- Institute of Gene Biology, Russian Academy of Sciences, Moscow 119334, Russia; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
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Lezhnina K, Kovalchuk O, Zhavoronkov AA, Korzinkin MB, Zabolotneva AA, Shegay PV, Sokov DG, Gaifullin NM, Rusakov IG, Aliper AM, Roumiantsev SA, Alekseev BY, Borisov NM, Buzdin AA. Novel robust biomarkers for human bladder cancer based on activation of intracellular signaling pathways. Oncotarget 2015; 5:9022-32. [PMID: 25296972 PMCID: PMC4253415 DOI: 10.18632/oncotarget.2493] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We recently proposed a new bioinformatic algorithm called OncoFinder for quantifying the activation of intracellular signaling pathways. It was proved advantageous for minimizing errors of high-throughput gene expression analyses and showed strong potential for identifying new biomarkers. Here, for the first time, we applied OncoFinder for normal and cancerous tissues of the human bladder to identify biomarkers of bladder cancer. Using Illumina HT12v4 microarrays, we profiled gene expression in 17 cancer and seven non-cancerous bladder tissue samples. These experiments were done in two independent laboratories located in Russia and Canada. We calculated pathway activation strength values for the investigated transcriptomes and identified signaling pathways that were regulated differently in bladder cancer (BC) tissues compared with normal controls. We found, for both experimental datasets, 44 signaling pathways that serve as excellent new biomarkers of BC, supported by high area under the curve (AUC) values. We conclude that the OncoFinder approach is highly efficient in finding new biomarkers for cancer. These markers are mathematical functions involving multiple gene products, which distinguishes them from “traditional” expression biomarkers that only assess concentrations of single genes.
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Affiliation(s)
- Ksenia Lezhnina
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR. Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4. Canada Cancer and Aging Research Laboratories, Lethbridge, AB, Canada
| | - Alexander A Zhavoronkov
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia. Insilico Medicine, Inc, ETC, Johns Hopkins University, Baltimore, MD. Faculty of Biological and Medical Physics, Moscow Institute of Physics and Technology
| | | | - Anastasia A Zabolotneva
- Group for Genomic Regulation of Cell Signaling Systems, Shemyakn-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Peter V Shegay
- P.A. Herzen Moscow Oncological Research Institute, Moscow, Russia
| | | | - Nurshat M Gaifullin
- Lomonosov Moscow State University, Faculty of Fundamental Medicine, Moscow, Russia. Russian medical postgraduate academy,Moscow, Russia
| | - Igor G Rusakov
- P.A. Herzen Moscow Oncological Research Institute, Moscow, Russia
| | - Alexander M Aliper
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR. Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Sergey A Roumiantsev
- Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Boris Y Alekseev
- P.A. Herzen Moscow Oncological Research Institute, Moscow, Russia
| | - Nikolay M Borisov
- Laboratory of Systems Biology, A.I. Burnasyan Federal Medical Biophysical Center, Moscow, Russia
| | - Anton A Buzdin
- Pathway Pharmaceuticals, Wan Chai, Hong Kong, Hong Kong SAR. Laboratory of Bioinformatics, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia. Group for Genomic Regulation of Cell Signaling Systems, Shemyakn-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Abstract
Survivin is an anti-apoptotic protein belonging to the inhibitor of apoptosis protein (IAP) family. It is involved in the regulation of important physiological and pathological processes in cells and functions to inhibit cell apoptosis and promote cell proliferation. Normally and terminally differentiated tissues are nearly negative for survivin. In contrast, survivin is highly expressed in most human tumor tissues, including hepatocellular carcinoma (HCC). The abnormal overexpression of survivin is closely related to the malignant biological behaviors of tumors. During the development and progression of HCC, the high level of survivin expression promotes cancer cell proliferation, inhibits cancer cell apoptosis, induces tumor stromal angiogenesis, reduces the sensitivity of cancer cells to radiotherapy and chemotherapy, and ultimately affects the prognosis of patients with HCC. Survivin expression is regulated by a large number of factors. The latest discovery indicated that the transcription factor octamer-binding transcription factor 4 (OCT4) enhances the expression of survivin though cyclin D1 (CCND1), which, in part, accounts for tumor cell proliferation, recurrence and metastasis. Survivin plays key roles in HCC, which renders it an ideal target for the treatment of HCC. The present article reviews the research progress on the relationship between survivin and HCC and on the HCC treatment strategies targeting survivin.
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Jellen LC, Aliper A, Buzdin A, Zhavoronkov A. Screening and personalizing nootropic drugs and cognitive modulator regimens in silico. Front Syst Neurosci 2015; 9:4. [PMID: 25705179 PMCID: PMC4319391 DOI: 10.3389/fnsys.2015.00004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 01/10/2015] [Indexed: 12/16/2022] Open
Abstract
The go-to cognitive enhancers of today are those that are widely available rather than optimal for the user, including drugs typically prescribed for treatment of ADHD (e.g., methylphenidate) and sleep disturbances such as narcolepsy (modafinil). While highly effective in their intended therapeutic role, performance gains in healthy populations are modest at best and profoundly inconsistent across subgroups and individuals. We propose a method for in silico screening of possible novel cognitive enhancers followed by high-throughput in vivo and in vitro validation. The proposed method uses gene expression data to evaluate the the collection of activated or suppressed signaling pathways in tissues or neurons of the cognitively enhanced brain. An algorithm maps expression data onto signaling pathways and quantifies their individual activation strength. The collective pathways and their activation form what we term the signaling pathway cloud, a biological fingerprint of cognitive enhancement (or any other condition of interest). Drugs can then be screened and ranked based on their ability to minimize, mimic, or exaggerate pathway activation or suppression within that cloud. Using this approach, one may predict the efficacy of many drugs that may enhance various aspects of cognition before costly preclinical studies and clinical trials are undertaken.
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Affiliation(s)
- Leslie C Jellen
- Department of Genetics, Genomics, and Informatics, University of Tennessee Health Science Center Memphis, TN, USA
| | - Alexander Aliper
- Aging Research, Insilico Medicine, Emerging Technology Center, Johns Hopkins University Eastern Baltimore, MD, USA
| | - Anton Buzdin
- Personalized Medicine, Pathway Pharmaceuticals Ltd Wan Chai, Hong Kong
| | - Alex Zhavoronkov
- Aging Research, Insilico Medicine, Emerging Technology Center, Johns Hopkins University Eastern Baltimore, MD, USA ; Research, Biogerontology Research Foundation Truro, UK
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Kashkin K, Chernov I, Stukacheva E, Monastyrskaya G, Uspenskaya N, Kopantzev E, Sverdlov E. Cancer specificity of promoters of the genes controlling cell proliferation. J Cell Biochem 2015; 116:299-309. [PMID: 25187488 DOI: 10.1002/jcb.24968] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 08/29/2014] [Indexed: 12/20/2022]
Abstract
Violation of proliferation control is a common feature of cancer cells. We put forward the hypothesis that promoters of genes involved in the control of cell proliferation should possess intrinsic cancer specific activity. We cloned promoter regions of CDC6, POLD1, CKS1B, MCM2, and PLK1 genes into pGL3 reporter vector and studied their ability to drive heterologous gene expression in transfected cancer cells of different origin and in normal human fibroblasts. Each promoter was cloned in short (335-800 bp) and long (up to 2.3 kb) variants to cover probable location of core and whole promoter regulatory elements. Cloned promoters were significantly more active in cancer cells than in normal fibroblasts that may indicate their cancer specificity. Both versions of CDC6 promoters were shown to be most active while the activities of others were close to that of BIRC5 gene (survivin) gene promoter. Long and short variants of each cloned promoter demonstrated very similar cancer specificity with the exception of PLK1-long promoter that was substantially more specific than its short variant and other promoters under study. The data indicate that most of the important cis-regulatory transcription elements responsible for intrinsic cancer specificity are located in short variants of the promoters under study. CDC6 short promoter may serve as a promising candidate for transcription targeted cancer gene therapy.
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Affiliation(s)
- Kirill Kashkin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997, Russia
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Zhavoronkov A, Buzdin AA, Garazha AV, Borisov NM, Moskalev AA. Signaling pathway cloud regulation for in silico screening and ranking of the potential geroprotective drugs. Front Genet 2014; 5:49. [PMID: 24624136 PMCID: PMC3940060 DOI: 10.3389/fgene.2014.00049] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 02/16/2014] [Indexed: 12/24/2022] Open
Abstract
The major challenges of aging research include absence of the comprehensive set of aging biomarkers, the time it takes to evaluate the effects of various interventions on longevity in humans and the difficulty extrapolating the results from model organisms to humans. To address these challenges we propose the in silico method for screening and ranking the possible geroprotectors followed by the high-throughput in vivo and in vitro validation. The proposed method evaluates the changes in the collection of activated or suppressed signaling pathways involved in aging and longevity, termed signaling pathway cloud, constructed using the gene expression data and epigenetic profiles of young and old patients' tissues. The possible interventions are selected and rated according to their ability to regulate age-related changes and minimize differences in the signaling pathway cloud. While many algorithmic solutions to simulating the induction of the old into young metabolic profiles in silico are possible, this flexible and scalable approach may potentially be used to predict the efficacy of the many drugs that may extend human longevity before conducting pre-clinical work and expensive clinical trials.
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Affiliation(s)
- Alex Zhavoronkov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia ; First Oncology Research and Advisory Center Moscow, Russia ; The Biogerontology Research Foundation London, UK ; Department of Experimental and Molecular Medicine, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology Moscow, Russia
| | - Anton A Buzdin
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia ; First Oncology Research and Advisory Center Moscow, Russia ; Department of Experimental and Molecular Medicine, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology Moscow, Russia ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Moscow, Russia
| | - Andrey V Garazha
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia ; First Oncology Research and Advisory Center Moscow, Russia ; Department of Experimental and Molecular Medicine, D. Rogachyov Federal Research Center of Pediatric Hematology, Oncology and Immunology Moscow, Russia ; Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences Moscow, Russia
| | - Nikolay M Borisov
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia ; First Oncology Research and Advisory Center Moscow, Russia ; Burnasyan Federal Medical Biophysical Center Moscow, Russia
| | - Alexey A Moskalev
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology Dolgoprudny, Russia ; Department of Ecology, Syktyvkar State University Syktyvkar, Russia ; Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of Ural Branch of Russian Academy of Sciences Syktyvkar, Russia
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