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Kobelyatskaya A, Pudova E, Fedorova M, Nyushko K, Alekseev B, Kaprin A, Trofimov D, Sukhikh G, Snezhkina A, Krasnov G, Razin S, Kudryavtseva A. Differentially methylated CpG sites associated with the high-risk group of prostate cancer. J Integr Bioinform 2020. [PMCID: PMC7790183 DOI: 10.1515/jib-2020-0031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Prostate cancer (PC) is one of the most common and socially significant oncological diseases among men. Bioinformatic analysis of omics data allows identifying molecular genetic changes associated with the disease development, as well as markers of prognosis and response to therapy. Alterations in DNA methylation and histone modification profiles widely occur in malignant tumors. In this study, we analyzed changes in DNA methylation in three groups of PC patients based on data from The Cancer Genome Atlas project (TCGA, https://portal.gdc.cancer.gov): (1) high- and intermediate-risk of the tumor progression, (2) favorable and unfavorable prognoses within the high-risk group, and (3) TMPRSS2-ERG-positive (tumors with TMPRSS2-ERG fusion transcript) and TMPRSS2-ERG-free cases within the high-risk group. We found eight CpG sites (cg07548607, cg13533340, cg16643088, cg18467168, cg23324953, cg23753247, cg25773620, and cg27148952) hypermethylated in the high-risk group compared with the intermediate-risk group of PC. Seven differentially methylated CpG sites (cg00063748, cg06834698, cg18607127, cg25273707, cg01704198, cg02067712, and cg02157224) were associated with unfavorable prognosis within the high-risk group. Six CpG sites (cg01138171, cg14060519, cg19570244, cg24492886, cg25605277, and cg26228280) were hypomethylated in TMPRSS2-ERG-positive PC compared to TMPRSS2-ERG-negative tumors within the high-risk group. The CpG sites were localized, predominantly, in regulatory genome regions belonging to promoters of the following genes: ARHGEF4, C6orf141, C8orf86, CLASP2, CSRNP1, GDA, GSX1, IQSEC1, MYOF, OR10A3, PLCD1, PLEC1, PRDM16, PTAFR, RP11-844P9.2, SCYL3, VPS13D, WT1, and ZSWIM2. For these genes, analysis of differential expression and its correlation with CpG site methylation (β-value level) was also performed. In addition, STK33 and PLCD1 had similar changes in colorectal cancer. As for the CSRNP1, the ARHGEF4, and the WT1 genes, misregulated expression levels were mentioned in lung, liver, pancreatic and androgen-independent prostate cancer. The potential impact of changed methylation on the mRNA level was determined for the CSRNP1, STK33, PLCD1, ARHGEF4, WT1, SCYL3, and VPS13D genes. The above CpG sites could be considered as potential prognostic markers of the high-risk group of PC.
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Affiliation(s)
- Anastasiya Kobelyatskaya
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, http://www.genebiology.ru/
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Kirill Nyushko
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Boris Alekseev
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Andrey Kaprin
- National Medical Research Radiological Center, Ministry of Health of the Russian Federation, Moscow, Russia, https://nmicr.ru/
| | - Dmitry Trofimov
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov, Ministry of Health of the Russian Federation, Moscow, Russia, https://en.ncagp.ru/
| | - Gennady Sukhikh
- National Medical Research Center for Obstetrics, Gynecology and Perinatology named after Academician V.I. Kulakov, Ministry of Health of the Russian Federation, Moscow, Russia, https://en.ncagp.ru/
| | - Anastasia Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
| | - Sergey Razin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia, http://www.genebiology.ru/
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia, http://www.eimb.ru/
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Moskalev A, Shaposhnikov M, Proshkina E, Belyi A, Fedintsev A, Zhikrivetskaya S, Guvatova Z, Sadritdinova A, Snezhkina A, Krasnov G, Kudryavtseva A. The influence of pro-longevity gene Gclc overexpression on the age-dependent changes in Drosophila transcriptome and biological functions. BMC Genomics 2016; 17:1046. [PMID: 28105938 PMCID: PMC5249042 DOI: 10.1186/s12864-016-3356-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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] [Indexed: 12/21/2022] Open
Abstract
Background Transcriptional changes that contribute to the organism’s longevity and prevent the age-dependent decline of biological functions are not well understood. Here, we overexpressed pro-longevity gene encoding glutamate-cysteine ligase catalytic subunit (Gclc) and analyzed age-dependent changes in transcriptome that associated with the longevity, stress resistance, locomotor activity, circadian rhythmicity, and fertility. Results Here we reproduced the life extension effect of neuronal overexpression of the Gclc gene and investigated its influence on the age-depended dynamics of transcriptome and biological functions such as fecundity, spontaneous locomotor activity and circadian rhythmicity, as well as on the resistance to oxidative, proteotoxic and osmotic stresses. It was shown that Gclc overexpression reduces locomotor activity in the young and middle ages compared to control flies. Gclc overexpression slowed down the age-dependent decline of locomotor activity and circadian rhythmicity, and resistance to stress treatments. Gclc level demonstrated associations with the expression of genes involved in a variety of cellular processes including Jak-STAT, MAPK, FOXO, Notch, mTOR, TGF-beta signaling pathways, translation, protein processing in endoplasmic reticulum, proteasomal degradation, glycolysis, oxidative phosphorylation, apoptosis, regulation of circadian rhythms, differentiation of neurons, synaptic plasticity and transmission. Conclusions Our study revealed that Gclc overexpression induces transcriptional changes associated with the lifespan extension and uncovered pathways that may be associated with the age-dependent decline of biological functions. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3356-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexey Moskalev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. .,Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia. .,Moscow Institute of Physics and Technology, Dolgoprudny, Russia. .,Syktyvkar State University, Syktyvkar, Russia.
| | - Mikhail Shaposhnikov
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | - Ekaterina Proshkina
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | - Alexey Belyi
- Institute of Biology of Komi Science Center of Ural Branch of RAS, Syktyvkar, Russia.,Syktyvkar State University, Syktyvkar, Russia
| | | | | | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Asiya Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anastasia Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
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Moskalev A, Zhikrivetskaya S, Krasnov G, Shaposhnikov M, Proshkina E, Borisoglebsky D, Danilov A, Peregudova D, Sharapova I, Dobrovolskaya E, Solovev I, Zemskaya N, Shilova L, Snezhkina A, Kudryavtseva A. A comparison of the transcriptome of Drosophila melanogaster in response to entomopathogenic fungus, ionizing radiation, starvation and cold shock. BMC Genomics 2015; 16 Suppl 13:S8. [PMID: 26694630 PMCID: PMC4686790 DOI: 10.1186/1471-2164-16-s13-s8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background The molecular mechanisms that determine the organism's response to a variety of doses and modalities of stress factors are not well understood. Results We studied effects of ionizing radiation (144, 360 and 864 Gy), entomopathogenic fungus (10 and 100 CFU), starvation (16 h), and cold shock (+4, 0 and -4°C) on an organism's viability indicators (survival and locomotor activity) and transcriptome changes in the Drosophila melanogaster model. All stress factors but cold shock resulted in a decrease of lifespan proportional to the dose of treatment. However, stress-factors affected locomotor activity without correlation with lifespan. Our data revealed both significant similarities and differences in differential gene expression and the activity of biological processes under the influence of stress factors. Conclusions Studied doses of stress treatments deleteriously affect the organism's viability and lead to different changes of both general and specific cellular stress response mechanisms.
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Moskalev A, Shaposhnikov M, Snezhkina A, Kogan V, Plyusnina E, Peregudova D, Melnikova N, Uroshlev L, Mylnikov S, Dmitriev A, Plusnin S, Fedichev P, Kudryavtseva A. Mining gene expression data for pollutants (dioxin, toluene, formaldehyde) and low dose of gamma-irradiation. PLoS One 2014; 9:e86051. [PMID: 24475070 PMCID: PMC3901678 DOI: 10.1371/journal.pone.0086051] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 12/04/2013] [Indexed: 12/28/2022] Open
Abstract
General and specific effects of molecular genetic responses to adverse environmental factors are not well understood. This study examines genome-wide gene expression profiles of Drosophila melanogaster in response to ionizing radiation, formaldehyde, toluene, and 2,3,7,8-tetrachlorodibenzo-p-dioxin. We performed RNA-seq analysis on 25,415 transcripts to measure the change in gene expression in males and females separately. An analysis of the genes unique to each treatment yielded a list of genes as a gene expression signature. In the case of radiation exposure, both sexes exhibited a reproducible increase in their expression of the transcription factors sugarbabe and tramtrack. The influence of dioxin up-regulated metabolic genes, such as anachronism, CG16727, and several genes with unknown function. Toluene activated a gene involved in the response to the toxins, Cyp12d1-p; the transcription factor Fer3's gene; the metabolic genes CG2065, CG30427, and CG34447; and the genes Spn28Da and Spn3, which are responsible for reproduction and immunity. All significantly differentially expressed genes, including those shared among the stressors, can be divided into gene groups using Gene Ontology Biological Process identifiers. These gene groups are related to defense response, biological regulation, the cell cycle, metabolic process, and circadian rhythms. KEGG molecular pathway analysis revealed alteration of the Notch signaling pathway, TGF-beta signaling pathway, proteasome, basal transcription factors, nucleotide excision repair, Jak-STAT signaling pathway, circadian rhythm, Hippo signaling pathway, mTOR signaling pathway, ribosome, mismatch repair, RNA polymerase, mRNA surveillance pathway, Hedgehog signaling pathway, and DNA replication genes. Females and, to a lesser extent, males actively metabolize xenobiotics by the action of cytochrome P450 when under the influence of dioxin and toluene. Finally, in this work we obtained gene expression signatures pollutants (dioxin, toluene), low dose of gamma-irradiation and common molecular pathways for different kind of stressors.
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Affiliation(s)
- Alexey Moskalev
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mikhail Shaposhnikov
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Anastasia Snezhkina
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Valeria Kogan
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Quantum Pharmaceuticals, Moscow, Russia
| | - Ekaterina Plyusnina
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Darya Peregudova
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
| | - Nataliya Melnikova
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Leonid Uroshlev
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
- Department of Computational Systems Biology, Vavilov Institute of General Genetics, Moscow, Russia
| | - Sergey Mylnikov
- Department of Genetics, St. Petersburg State University, St. Petersburg, Russia
| | - Alexey Dmitriev
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
| | - Sergey Plusnin
- Laboratory of Molecular Radiobiology and Gerontology, Institute of Biology of Komi Science Center of RAS, Syktyvkar, Russia
- Ecological Department, Syktyvkar State University, Syktyvkar, Russia
| | - Peter Fedichev
- Laboratory of Genetics of Aging and Longevity, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- Quantum Pharmaceuticals, Moscow, Russia
| | - Anna Kudryavtseva
- Group of Postgenomic Studies, Engelhardt Institute of Molecular Biology of RAS, Moscow, Russia
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