1
|
Tavleeva MM, Rasova EE, Rybak AV, Belykh ES, Fefilova EA, Pnachina EM, Velegzhaninov IO. Dose-Dependent Effect of Mitochondrial Superoxide Dismutase Gene Overexpression on Radioresistance of HEK293T Cells. Int J Mol Sci 2023; 24:17315. [PMID: 38139144 PMCID: PMC10744337 DOI: 10.3390/ijms242417315] [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: 10/15/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Over the last two decades, a multitude of gain-of-function studies have been conducted on genes that encode antioxidative enzymes, including one of the key enzymes, manganese superoxide dismutase (SOD2). The results of such studies are often contradictory, as they strongly depend on many factors, such as the gene overexpression level. In this study, the effect of altering the ectopic expression level of major transcript variants of the SOD2 gene on the radioresistance of HEK293T cells was investigated using CRISPRa technology. A significant increase in cell viability in comparison with the transfection control was detected in cells with moderate SOD2 overexpression after irradiation at 2 Gy, but not at 3 or 5 Gy. A further increase in the level of SOD2 ectopic expression up to 22.5-fold resulted in increased cell viability detectable only after irradiation at 5 Gy. Furthermore, a 15-20-fold increase in SOD2 expression raised the clonogenic survival of cells after irradiation at 5 Gy. Simultaneous overexpression of genes encoding SOD2 and Catalase (CAT) enhanced clonogenic cell survival after irradiation more effectively than separate overexpression of both. In conjunction with the literature data on the suppression of the procarcinogenic effects of superoxide dismutase overexpression by ectopic expression of CAT, the data presented here suggest the potential efficacy of simultaneous overexpression of SOD2 and CAT to reduce oxidative stress occurring in various pathological processes. Moreover, these results illustrate the importance of selecting the degree of SOD2 overexpression to obtain a protective effect.
Collapse
Affiliation(s)
- Marina M. Tavleeva
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia; (M.M.T.); (E.E.R.); (A.V.R.); (E.S.B.)
| | - Elena E. Rasova
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia; (M.M.T.); (E.E.R.); (A.V.R.); (E.S.B.)
| | - Anna V. Rybak
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia; (M.M.T.); (E.E.R.); (A.V.R.); (E.S.B.)
| | - Elena S. Belykh
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia; (M.M.T.); (E.E.R.); (A.V.R.); (E.S.B.)
| | - Elizaveta A. Fefilova
- Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., St. Petersburg 194064, Russia;
| | - Elizaveta M. Pnachina
- Institute of Biology and Biomedicine, Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Ave., Nizhny Novgorod 603950, Russia;
| | - Ilya O. Velegzhaninov
- Institute of Biology of Komi Scientific Centre, Ural Branch of Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia; (M.M.T.); (E.E.R.); (A.V.R.); (E.S.B.)
| |
Collapse
|
2
|
Jenni R, Chikhaoui A, Nabouli I, Zaouak A, Khanchel F, Hammami-Ghorbel H, Yacoub-Youssef H. Differential Expression of ATM, NF-KB, PINK1 and Foxo3a in Radiation-Induced Basal Cell Carcinoma. Int J Mol Sci 2023; 24:ijms24087181. [PMID: 37108343 PMCID: PMC10138907 DOI: 10.3390/ijms24087181] [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: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
Research in normal tissue radiobiology is in continuous progress to assess cellular response following ionizing radiation exposure especially linked to carcinogenesis risk. This was observed among patients with a history of radiotherapy of the scalp for ringworm who developed basal cell carcinoma (BCC). However, the involved mechanisms remain largely undefined. We performed a gene expression analysis of tumor biopsies and blood of radiation-induced BCC and sporadic patients using reverse transcription-quantitative PCR. Differences across groups were assessed by statistical analysis. Bioinformatic analyses were conducted using miRNet. We showed a significant overexpression of the FOXO3a, ATM, P65, TNF-α and PINK1 genes among radiation-induced BCCs compared to BCCs in sporadic patients. ATM expression level was correlated with FOXO3a. Based on receiver-operating characteristic curves, the differentially expressed genes could significantly discriminate between the two groups. Nevertheless, TNF-α and PINK1 blood expression showed no statistical differences between BCC groups. Bioinformatic analysis revealed that the candidate genes may represent putative targets for microRNAs in the skin. Our findings may yield clues as to the molecular mechanism involved in radiation-induced BCC, suggesting that deregulation of ATM-NF-kB signaling and PINK1 gene expression may contribute to BCC radiation carcinogenesis and that the analyzed genes could represent candidate radiation biomarkers associated with radiation-induced BCC.
Collapse
Affiliation(s)
- Rim Jenni
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis1002, Tunisia
| | - Asma Chikhaoui
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis1002, Tunisia
| | - Imen Nabouli
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis1002, Tunisia
| | - Anissa Zaouak
- Department of Dermatology, Habib Thameur Hospital (LR12SP03), Medicine Faculty, University Tunis El Manar, Tunis 1008, Tunisia
| | - Fatma Khanchel
- Anatomopathology Department, Habib Thameur Hospital (LR12SP03), Medicine Faculty, University Tunis El Manar, Tunis 1008, Tunisia
| | - Houda Hammami-Ghorbel
- Department of Dermatology, Habib Thameur Hospital (LR12SP03), Medicine Faculty, University Tunis El Manar, Tunis 1008, Tunisia
| | - Houda Yacoub-Youssef
- Laboratory of Biomedical Genomics and Oncogenetics (LR16IPT05), Institut Pasteur de Tunis, University Tunis El Manar, Tunis1002, Tunisia
| |
Collapse
|
3
|
Längrich T, Bork K, Horstkorte R, Weber V, Hofmann B, Fuszard M, Olzscha H. Disturbance of Key Cellular Subproteomes upon Propofol Treatment Is Associated with Increased Permeability of the Blood-Brain Barrier. Proteomes 2022; 10:proteomes10030028. [PMID: 35997440 PMCID: PMC9397097 DOI: 10.3390/proteomes10030028] [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: 06/24/2022] [Revised: 08/02/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Background: Propofol is a short-acting anesthetic, which is often used for induction and maintenance of general anesthesia, sedation for mechanically ventilated adults and procedural sedation. Several side effects of propofol are known and a substantial number of patients suffer from post-operative delirium after propofol application. In this study, we analyzed the effect of propofol on the function and protein expression profile on a proteome-wide scale. Methods: We cultured human brain microvascular endothelial cells in absence and presence of propofol and analyzed the permeability of the blood-brain barrier (BBB) by fluorescein passage and protein abundance on a proteome-wide scale by mass spectrometry. Results: Propofol interfered with the function of the blood-brain barrier. This was not due to decreased adhesion of propofol-treated human brain microvascular endothelial cells. The proteomic analysis revealed that some key pathways in these cells were disturbed, such as oxygen metabolism, DNA damage recognition and response to stress. Conclusions: Propofol has strong effects on protein expression which could explain several side effects of propofol.
Collapse
Affiliation(s)
- Timo Längrich
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Kaya Bork
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Rüdiger Horstkorte
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Veronika Weber
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
| | - Britt Hofmann
- Klinik und Poliklinik für Herzchirurgie, Universitätsklinikum Halle (Saale), Ernst-Grube-Str. 20, 06120 Halle (Saale), Germany
| | - Matt Fuszard
- Core Facility—Proteomic Mass Spectrometry, Proteinzentrum Charles Tanford, Kurt-Mothes-Straße 3a, 06120 Halle (Saale), Germany
| | - Heidi Olzscha
- Institut für Physiologische Chemie, Martin-Luther-Universität Halle-Wittenberg, Hollystr. 1, 06114 Halle (Saale), Germany
- Medical School Hamburg MSH, University of Applied Sciences and Medical University, Institute of Molecular Medicine, Am Sandtorkai 76, 20457 Hamburg, Germany
- Correspondence:
| |
Collapse
|
4
|
Zhang QZ, Wen F, Yang HL, Cao YY, Peng RG, Wang YM, Nie L, Qin YK, Wu JJ, Zhao X, Zi D. GADD45α alleviates the CDDP resistance of SK-OV3/cddp cells via redox-mediated DNA damage. Oncol Lett 2021; 22:720. [PMID: 34429760 PMCID: PMC8371983 DOI: 10.3892/ol.2021.12981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 03/08/2021] [Indexed: 11/25/2022] Open
Abstract
Epithelial ovarian cancer has the highest mortality rate of all malignant ovarian cancer types. Great progress has been made in the treatment of ovarian cancer in recent years. However, drug resistance has led to a low level of 5-year survival rate of epithelial ovarian cancer, and the molecular mechanism of which remains unknown. The aim of the present study was to identify the role of redox status in the cisplatin (CDDP) resistance of ovarian cancer. CDDP-resistant SK-OV3 (SK-OV3/cddp) cells were prepared and their reactive oxygen species and glutathione levels were investigated. The effects of hydrogen peroxide on the CDDP sensitivity of the SK-OV3/cddp cells and their expression levels of the redox-associated protein growth arrest and DNA damage 45a (GADD45α) were also investigated. In addition, the impact of GADD45α overexpression on cell viability was evaluated in vitro and in vivo, and the levels of Ser-139 phosphorylated H2A histone family member X (γ-H2AX), which is associated with DNA damage, were detected. The results suggested that redox status affected the drug resistance of the ovarian cancer cells by increasing the expression of GADD45α. The overexpression of GADD45α reversed the CDDP resistance of the SK-OV3/cddp cells and increased the level of γ-H2AX. In conclusion, GADD45α alleviated the CDDP resistance of SK-OV3/cddp cells via the induction of redox-mediated DNA damage.
Collapse
Affiliation(s)
- Qi-Zhu Zhang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Fang Wen
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China.,Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550004, P.R. China
| | - Han-Lin Yang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yan-Yan Cao
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Ren Guo Peng
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan-Mei Wang
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Lei Nie
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Yuan-Kun Qin
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Jin-Jian Wu
- Department of Obstetrics and Gynecology, Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| | - Xing Zhao
- National and Guizhou Joint Engineering Laboratory for Cell Engineering and Biomedicine Technique, Center for Tissue Engineering and Stem Cell Research, Guizhou Province Key Laboratory of Regenerative Medicine, Guiyang, Guizhou 550004, P.R. China
| | - Dan Zi
- Department of Obstetrics and Gynecology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550004, P.R. China.,National and Guizhou Joint Engineering Laboratory for Cell Engineering and Biomedicine Technique, Center for Tissue Engineering and Stem Cell Research, Guizhou Province Key Laboratory of Regenerative Medicine, Guiyang, Guizhou 550004, P.R. China.,Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, Guizhou 550004, P.R. China
| |
Collapse
|
5
|
Ionizing Radiation and Translation Control: A Link to Radiation Hormesis? Int J Mol Sci 2020; 21:ijms21186650. [PMID: 32932812 PMCID: PMC7555331 DOI: 10.3390/ijms21186650] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 09/04/2020] [Indexed: 02/06/2023] Open
Abstract
Protein synthesis, or mRNA translation, is one of the most energy-consuming functions in cells. Translation of mRNA into proteins is thus highly regulated by and integrated with upstream and downstream signaling pathways, dependent on various transacting proteins and cis-acting elements within the substrate mRNAs. Under conditions of stress, such as exposure to ionizing radiation, regulatory mechanisms reprogram protein synthesis to translate mRNAs encoding proteins that ensure proper cellular responses. Interestingly, beneficial responses to low-dose radiation exposure, known as radiation hormesis, have been described in several models, but the molecular mechanisms behind this phenomenon are largely unknown. In this review, we explore how differences in cellular responses to high- vs. low-dose ionizing radiation are realized through the modulation of molecular pathways with a particular emphasis on the regulation of mRNA translation control.
Collapse
|
6
|
NoRC Recruitment by H2A.X Deposition at rRNA Gene Promoter Limits Embryonic Stem Cell Proliferation. Cell Rep 2019; 23:1853-1866. [PMID: 29742439 DOI: 10.1016/j.celrep.2018.04.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 01/16/2018] [Accepted: 04/04/2018] [Indexed: 01/22/2023] Open
Abstract
Embryonic stem cells (ESCs) display an abbreviated cell cycle, resulting in a short doubling time and rapid proliferation. The histone variant H2A.X is critical for proliferation of stem cells, although mechanistic insights have remained obscure. Here, we show that H2A.X defines the rate of mouse ESC proliferation independently of the DNA damage response pathway, and it associates with three major chromatin-modifying complexes. Our functional and biochemical analyses demonstrate that H2A.X-associated factors mediate the H2A.X-dependent effect on ESC proliferation and involve the nucleolar remodeling complex (NoRC). A specific H2A.X deposition at rDNA promoters determines the chromatin recruitment of the NoRC, histone modifications, the rRNA transcription, and the rate of proliferation. Collectively, our results suggest that NoRC assembly by H2A.X deposition at rRNA promoters silences transcription, and this represents an important regulatory component for ESC proliferation.
Collapse
|
7
|
Mura M, Jaksik R, Lalik A, Biernacki K, Kimmel M, Rzeszowska-Wolny J, Fujarewicz K. A mathematical model as a tool to identify microRNAs with highest impact on transcriptome changes. BMC Genomics 2019; 20:114. [PMID: 30727966 PMCID: PMC6366035 DOI: 10.1186/s12864-019-5464-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/21/2019] [Indexed: 01/06/2023] Open
Abstract
Background Rapid changes in the expression of many messenger RNA (mRNA) species follow exposure of cells to ionizing radiation. One of the hypothetical mechanisms of this response may include microRNA (miRNA) regulation, since the amounts of miRNAs in cells also vary upon irradiation. To address this possibility, we designed experiments using cancer-derived cell lines transfected with luciferase reporter gene containing sequences targeted by different miRNA species in its 3′- untranslated region. We focus on the early time-course response (1 h past irradiation) to eliminate secondary mRNA expression waves. Results Experiments revealed that the irradiation-induced changes in the mRNA expression depend on the miRNAs which interact with mRNA. To identify the strongest interactions, we propose a mathematical model which predicts the mRNA fold expression changes, caused by perturbation of microRNA-mRNA interactions. Model was applied to experimental data including various cell lines, irradiation doses and observation times, both ours and literature-based. Comparison of modelled and experimental mRNA expression levels given miRNA level changes allows estimating how many and which miRNAs play a significant role in transcriptome response to stress conditions in different cell types. As an example, in the human melanoma cell line the comparison suggests that, globally, a major part of the irradiation-induced changes of mRNA expression can be explained by perturbed miRNA-mRNA interactions. A subset of about 30 out of a few hundred miRNAs expressed in these cells appears to account for the changes. These miRNAs play crucial roles in regulatory mechanisms observed after irradiation. In addition, these miRNAs have a higher average content of GC and a higher number of targeted transcripts, and many have been reported to play a role in the development of cancer. Conclusions Our proposed mathematical modeling approach may be used to identify miRNAs which participate in responses of cells to ionizing radiation, and other stress factors such as extremes of temperature, exposure to toxins, and drugs. Electronic supplementary material The online version of this article (10.1186/s12864-019-5464-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Marzena Mura
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,, Ardigen S.A., ul. Bobrzyńskiego 14, 30-348, Cracow, Poland.
| | - Roman Jaksik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Anna Lalik
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland
| | - Krzysztof Biernacki
- Department of Medical and Molecular Biology, School of Medicine with the Division of Dentistry in Zabrze, Medical University of Silesia in Katowice, Katowice, USA
| | - Marek Kimmel
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland.,Departments of Statistics and Bioengineering, Rice University, MS 138, 6100 Main, Houston, TX, 77005, USA
| | - Joanna Rzeszowska-Wolny
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland. .,Centre of Biotechnology, Silesian University of Technology, ul. Bolesława Krzywoustego 8, 44-100, Gliwice, Poland.
| | - Krzysztof Fujarewicz
- Department of Systems Engineering, Institute of Automatic Control, Silesian University of Technology, ul. Akademicka 16, 44-100, Gliwice, Poland
| |
Collapse
|
8
|
Chen G, Yu L, Dong H, Liu Z, Sun Y. MiR-182 enhances radioresistance in non-small cell lung cancer cells by regulating FOXO3. Clin Exp Pharmacol Physiol 2019; 46:137-143. [PMID: 30307642 DOI: 10.1111/1440-1681.13041] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Gang Chen
- Department of Respiratory Medicine; People's Hospital of Haining; Haining China
| | - Lina Yu
- Department of Respiratory Medicine; People's Hospital of Haining; Haining China
| | - Hui Dong
- Department of Respiratory Medicine; People's Hospital of Haining; Haining China
| | - Zhihao Liu
- Department of Respiratory Medicine; People's Hospital of Haining; Haining China
| | - Yahong Sun
- Department of Respiratory Medicine; People's Hospital of Haining; Haining China
| |
Collapse
|
9
|
Zhao JZ, Mucaki EJ, Rogan PK. Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning. F1000Res 2018; 7:233. [PMID: 29904591 PMCID: PMC5981198 DOI: 10.12688/f1000research.14048.2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/11/2018] [Indexed: 12/20/2022] Open
Abstract
Background: Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. Methods: Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. Results: The best human signatures we derived exhibit k-fold validation accuracies of up to 98% ( DDB2, PRKDC, TPP2, PTPRE, and GADD45A) when validated over 209 samples and traditional validation accuracies of up to 92% ( DDB2, CD8A, TALDO1, PCNA, EIF4G2, LCN2, CDKN1A, PRKCH, ENO1, and PPM1D) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. Conclusions: Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.
Collapse
Affiliation(s)
- Jonathan Z.L. Zhao
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- Department of Computer Science, Faculty of Science, Western University, London, ON, N6A 2C1, Canada
| | - Eliseos J. Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Peter K. Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- Department of Computer Science, Faculty of Science, Western University, London, ON, N6A 2C1, Canada
- Department of Epidemiology & Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- CytoGnomix Inc., London, ON, N5X 3X5, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| |
Collapse
|
10
|
Zhao JZ, Mucaki EJ, Rogan PK. Predicting ionizing radiation exposure using biochemically-inspired genomic machine learning. F1000Res 2018; 7:233. [PMID: 29904591 PMCID: PMC5981198 DOI: 10.12688/f1000research.14048.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/19/2018] [Indexed: 09/27/2023] Open
Abstract
Background: Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. Methods: Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. Results: The best human signatures we derived exhibit k-fold validation accuracies of up to 98% ( DDB2, PRKDC, TPP2, PTPRE, and GADD45A) when validated over 209 samples and traditional validation accuracies of up to 92% ( DDB2, CD8A, TALDO1, PCNA, EIF4G2, LCN2, CDKN1A, PRKCH, ENO1, and PPM1D) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. Conclusions: Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.
Collapse
Affiliation(s)
- Jonathan Z.L. Zhao
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- Department of Computer Science, Faculty of Science, Western University, London, ON, N6A 2C1, Canada
| | - Eliseos J. Mucaki
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| | - Peter K. Rogan
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- Department of Computer Science, Faculty of Science, Western University, London, ON, N6A 2C1, Canada
- Department of Epidemiology & Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
- CytoGnomix Inc., London, ON, N5X 3X5, Canada
- Department of Oncology, Schulich School of Medicine and Dentistry, Western University, London, ON, N6A 2C1, Canada
| |
Collapse
|
11
|
Davy PMC, Allsopp RC, Donlon TA, Morris BJ, Willcox DC, Willcox BJ. FOXO3 and Exceptional Longevity: Insights From Hydra to Humans. Curr Top Dev Biol 2018; 127:193-212. [PMID: 29433738 DOI: 10.1016/bs.ctdb.2017.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Aging is a complex, multifactorial process with significant plasticity. While several biological pathways appear to influence aging, few genes have been identified that are both evolutionarily conserved and have a strong impact on aging and age-related phenotypes. The FoxO3 gene (FOXO3), and its homologs in model organisms, appears especially important, forming a key gene in the insulin/insulin-like growth factor-signaling pathway, and influencing life span across diverse species. We highlight some of the key findings that are associated with FoxO3 protein, its gene and homologs in relation to lifespan in different species, and the insights these findings might provide about the molecular, cellular, and physiological processes that modulate aging and longevity in humans.
Collapse
Affiliation(s)
- Philip M C Davy
- Institute for Biogenesis Research, University of Hawaii, Honolulu, HI, United States
| | - Richard C Allsopp
- Institute for Biogenesis Research, University of Hawaii, Honolulu, HI, United States
| | - Timothy A Donlon
- Honolulu Heart Program/Honolulu-Asia Aging Study, Kuakini Medical Center, Honolulu, HI, United States; Ohana Genetics, Honolulu, HI, United States
| | - Brian J Morris
- Honolulu Heart Program/Honolulu-Asia Aging Study, Kuakini Medical Center, Honolulu, HI, United States; John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States; School of Medical Sciences and Bosch Institute, University of Sydney, Sydney, NSW, Australia
| | - Donald Craig Willcox
- Honolulu Heart Program/Honolulu-Asia Aging Study, Kuakini Medical Center, Honolulu, HI, United States; John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States; Okinawa International University, Ginowan, Okinawa, Japan
| | - Bradley J Willcox
- Honolulu Heart Program/Honolulu-Asia Aging Study, Kuakini Medical Center, Honolulu, HI, United States; John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, United States.
| |
Collapse
|
12
|
Qian Z, Ren L, Wu D, Yang X, Zhou Z, Nie Q, Jiang G, Xue S, Weng W, Qiu Y, Lin Y. Overexpression of FoxO3a is associated with glioblastoma progression and predicts poor patient prognosis. Int J Cancer 2017; 140:2792-2804. [PMID: 28295288 DOI: 10.1002/ijc.30690] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022]
Abstract
Forkhead transcription factor FoxO3a has been reported to have ambiguous functions and distinct mechanisms in various solid tumors, including glioblastoma (GBM). Although a preliminary analysis of a small sample of patients indicated that FoxO3a aberrations in glioma might be related to aggressive clinical behavior, the clinical significance of FoxO3a in glioblastoma remains unclear. We investigated the expression of FoxO3a in a cohort of 91 glioblastoma specimens and analyzed the correlations of protein expression with patient prognosis. Furthermore, the functional impact of FoxO3a on GBM progression and the underlying mechanisms of FoxO3a regulation were explored in a series of in vitro and in vivo assays. FoxO3a expression was elevated in glioblastoma tissues, and high nuclear FoxO3a expression in human GBM tissues was associated with poor prognosis. Moreover, knockdown of FoxO3a significantly reduced the colony formation and invasion ability of GBM cells, whereas overexpression of FoxO3a promoted the colony formation and invasion ability. The results of in vivo GBM models further confirmed that FoxO3a knockdown inhibited GBM progression. More, the pro-oncogenic effects of FoxO3a in GBM were mediated by the activation of c-Myc, microtubule-associated protein 1 light chain 3 beta (LC3B) and Beclin1 in a mixed-lineage leukemia 2 (MLL2)-dependent manner. These findings suggest that high FoxO3a expression is associated with glioblastoma progression and that FoxO3a independently indicates poor prognosis in patients. FoxO3a might be a novel prognostic biomarker or a potential therapeutic target in glioblastoma.
Collapse
Affiliation(s)
- Zhongrun Qian
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Li Ren
- Department of Neurosurgery, Shanghai Pudong Hospital, Fudan University, Shanghai, China
| | - Dingchang Wu
- Department of Clinical Laboratory, Longyan First Hospital, Fujian Medical University, Longyan, China
| | - Xi Yang
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhiyi Zhou
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Quanmin Nie
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Gan Jiang
- Department of Pharmacology, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shuanglin Xue
- Department of Neurosurgery, Longyan First Hospital, Fujian Medical University, Longyan, China
| | - Weiji Weng
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yongming Qiu
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yingying Lin
- Department of Neurosurgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
13
|
Szatmári T, Kis D, Bogdándi EN, Benedek A, Bright S, Bowler D, Persa E, Kis E, Balogh A, Naszályi LN, Kadhim M, Sáfrány G, Lumniczky K. Extracellular Vesicles Mediate Radiation-Induced Systemic Bystander Signals in the Bone Marrow and Spleen. Front Immunol 2017; 8:347. [PMID: 28396668 PMCID: PMC5366932 DOI: 10.3389/fimmu.2017.00347] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 03/10/2017] [Indexed: 12/02/2022] Open
Abstract
Radiation-induced bystander effects refer to the induction of biological changes in cells not directly hit by radiation implying that the number of cells affected by radiation is larger than the actual number of irradiated cells. Recent in vitro studies suggest the role of extracellular vesicles (EVs) in mediating radiation-induced bystander signals, but in vivo investigations are still lacking. Here, we report an in vivo study investigating the role of EVs in mediating radiation effects. C57BL/6 mice were total-body irradiated with X-rays (0.1, 0.25, 2 Gy), and 24 h later, EVs were isolated from the bone marrow (BM) and were intravenously injected into unirradiated (so-called bystander) animals. EV-induced systemic effects were compared to radiation effects in the directly irradiated animals. Similar to direct radiation, EVs from irradiated mice induced complex DNA damage in EV-recipient animals, manifested in an increased level of chromosomal aberrations and the activation of the DNA damage response. However, while DNA damage after direct irradiation increased with the dose, EV-induced effects peaked at lower doses. A significantly reduced hematopoietic stem cell pool in the BM as well as CD4+ and CD8+ lymphocyte pool in the spleen was detected in mice injected with EVs isolated from animals irradiated with 2 Gy. These EV-induced alterations were comparable to changes present in the directly irradiated mice. The pool of TLR4-expressing dendritic cells was different in the directly irradiated mice, where it increased after 2 Gy and in the EV-recipient animals, where it strongly decreased in a dose-independent manner. A panel of eight differentially expressed microRNAs (miRNA) was identified in the EVs originating from both low- and high-dose-irradiated mice, with a predicted involvement in pathways related to DNA damage repair, hematopoietic, and immune system regulation, suggesting a direct involvement of these pathways in mediating radiation-induced systemic effects. In conclusion, we proved the role of EVs in transmitting certain radiation effects, identified miRNAs carried by EVs potentially responsible for these effects, and showed that the pattern of changes was often different in the directly irradiated and EV-recipient bystander mice, suggesting different mechanisms.
Collapse
Affiliation(s)
- Tünde Szatmári
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Dávid Kis
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Enikő Noémi Bogdándi
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Anett Benedek
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Scott Bright
- Genomic Instability Group, Department of Biological and Medical Sciences, Oxford Brookes University , Oxford , UK
| | - Deborah Bowler
- Genomic Instability Group, Department of Biological and Medical Sciences, Oxford Brookes University , Oxford , UK
| | - Eszter Persa
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Enikő Kis
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Andrea Balogh
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Lívia N Naszályi
- Research Group for Molecular Biophysics, Hungarian Academy of Sciences, Semmelweis University , Budapest , Hungary
| | - Munira Kadhim
- Genomic Instability Group, Department of Biological and Medical Sciences, Oxford Brookes University , Oxford , UK
| | - Géza Sáfrány
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| | - Katalin Lumniczky
- Division of Radiation Medicine, National Public Health Centre, National Research Directorate for Radiobiology and Radiohygiene , Budapest , Hungary
| |
Collapse
|
14
|
Hu L, Wang H, Huang L, Zhao Y, Wang J. Crosstalk between autophagy and intracellular radiation response (Review). Int J Oncol 2016; 49:2217-2226. [PMID: 27748893 DOI: 10.3892/ijo.2016.3719] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 09/27/2016] [Indexed: 11/06/2022] Open
Abstract
Autophagy induced by radiation is critical to cell fate decision. Evidence now sheds light on the importance of autophagy induced by cancer radiotherapy. Traditional view considers radiation can directly or indirectly damage DNA which can activate DNA damage the repair signaling pathway, a large number of proteins participating in DNA damage repair signaling pathway such as p53, ATM, PARP1, FOXO3a, mTOR and SIRT1 involved in autophagy regulation. However, emerging recent evidence suggests radiation can also cause injury to extranuclear targets such as plasma membrane, mitochondria and endoplasmic reticulum (ER) and induce accumulation of ceramide, ROS, and Ca2+ concentration which activate many signaling pathways to modulate autophagy. Herein we review the role of autophagy in radiation therapy and the potent intracellular autophagic triggers induced by radiation. We aim to provide a more theoretical basis of radiation-induced autophagy, and provide novel targets for developing cytotoxic drugs to increase radiosensitivity.
Collapse
Affiliation(s)
- Lelin Hu
- Department of Radiation Oncology, Peking University Third Hospital, Haidian, Beijing 100191, P.R. China
| | - Hao Wang
- Department of Radiation Oncology, Peking University Third Hospital, Haidian, Beijing 100191, P.R. China
| | - Li Huang
- Department of Radiation Oncology, Peking University Third Hospital, Haidian, Beijing 100191, P.R. China
| | - Yong Zhao
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China
| | - Junjie Wang
- Department of Radiation Oncology, Peking University Third Hospital, Haidian, Beijing 100191, P.R. China
| |
Collapse
|