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Fu L, Li M, Lv J, Yang C, Zhang Z, Qin S, Li W, Wang X, Chen L. Deep neural network for discovering metabolism-related biomarkers for lung adenocarcinoma. Front Endocrinol (Lausanne) 2023; 14:1270772. [PMID: 37955007 PMCID: PMC10634586 DOI: 10.3389/fendo.2023.1270772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/03/2023] [Indexed: 11/14/2023] Open
Abstract
Introduction Lung cancer is a major cause of illness and death worldwide. Lung adenocarcinoma (LUAD) is its most common subtype. Metabolite-mRNA interactions play a crucial role in cancer metabolism. Thus, metabolism-related mRNAs are potential targets for cancer therapy. Methods This study constructed a network of metabolite-mRNA interactions (MMIs) using four databases. We retrieved mRNAs from the Tumor Genome Atlas (TCGA)-LUAD cohort showing significant expressional changes between tumor and non-tumor tissues and identified metabolism-related differential expression (DE) mRNAs among the MMIs. Candidate mRNAs showing significant contributions to the deep neural network (DNN) model were mined. Using MMIs and the results of function analysis, we created a subnetwork comprising candidate mRNAs and metabolites. Results Finally, 10 biomarkers were obtained after survival analysis and validation. Their good prognostic value in LUAD was validated in independent datasets. Their effectiveness was confirmed in the TCGA and an independent Clinical Proteomic Tumor Analysis Consortium (CPTAC) dataset by comparison with traditional machine-learning models. Conclusion To summarize, 10 metabolism-related biomarkers were identified, and their prognostic value was confirmed successfully through the MMI network and the DNN model. Our strategy bears implications to pave the way for investigating metabolic biomarkers in other cancers.
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Affiliation(s)
- Lei Fu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Manshi Li
- Department of Radiation Oncology, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Junjie Lv
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Chengcheng Yang
- Department of Respiratory, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zihan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shimei Qin
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wan Li
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xinyan Wang
- Department of Respiratory, Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Lina Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Yuce A, Keles M, Benli E, Cirakoglu A, Yazici I, Nalbant I. Comparison of Serum Gamma Glutamyl Transferase Levels between Prostate Cancer Patients and Their Healthy Peers. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:1487-1494. [PMID: 37593509 PMCID: PMC10430399 DOI: 10.18502/ijph.v52i7.13251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/18/2022] [Indexed: 08/19/2023]
Abstract
Background Prostate cancer (PCa) is the most common cancer affecting men, apart from cutaneous cancers. Serum prostate specific antigen (PSA) levels are frequently used to predict prostate cancer diagnosis. However, many causes (e.g., prostatitis, benign prostate obstruction, urethral catheterization) may cause elevated PSA, in addition to PCa. We aimed to investigate the gamma glutamyl transferase (GGT) levels, a serum biomarker not affected by situations other than cancer causing elevated PSA. Methods The study evaluated male patients with prostate biopsy due to high serum PSA levels and/or abnormal digital rectal examination (DRE) examined in Ordu University Education and Research Hospital, Ordu/Turkey urology clinic from April 2019 to April 2021. The patient group in the study included 261 men with PCa diagnosis and the control group included 245 healthy men with normal PSA levels, and no PCa and/or benign prostate obstruction (BPO). The two groups were compared in terms of serum GGT levels. Results GGT was significantly low in the PCa group and might be a predictor in terms of PCa (P=0.000). In the malignant (PCa) group, the GGT cut-off value was identified as 21.5 (sensitivity 68.6%, specificity 54.4%). Conclusion Serum GGT levels might assist in diagnosis of PCa. However, diagnostic power is weak due to low specificity. There is a need for studies investigating the efficacy of GGT levels for prediction of PCa diagnosis and assessing other parameters alongside GGT.
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Affiliation(s)
- Ahmet Yuce
- Department of Urology, Darende Hulusi Efendi State Hospital, Malatya, Turkey
| | - Mevlut Keles
- Department of Urology, Ordu University, Faculty of Medicine, Ordu, Turkey
| | - Erdal Benli
- Department of Urology, Ordu University, Faculty of Medicine, Ordu, Turkey
| | - Abdullah Cirakoglu
- Department of Urology, Ordu University, Faculty of Medicine, Ordu, Turkey
| | - Ibrahim Yazici
- Department of Urology, Ordu University, Faculty of Medicine, Ordu, Turkey
| | - Ismail Nalbant
- Department of Urology Lokman Hekim University, Ankara, Turkey
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MotieGhader H, Tabrizi-Nezhadi P, Deldar Abad Paskeh M, Baradaran B, Mokhtarzadeh A, Hashemi M, Lanjanian H, Jazayeri SM, Maleki M, Khodadadi E, Nematzadeh S, Kiani F, Maghsoudloo M, Masoudi-Nejad A. Drug repositioning in non-small cell lung cancer (NSCLC) using gene co-expression and drug–gene interaction networks analysis. Sci Rep 2022; 12:9417. [PMID: 35676421 PMCID: PMC9177601 DOI: 10.1038/s41598-022-13719-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Lung cancer is the most common cancer in men and women. This cancer is divided into two main types, namely non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). Around 85 to 90 percent of lung cancers are NSCLC. Repositioning potent candidate drugs in NSCLC treatment is one of the important topics in cancer studies. Drug repositioning (DR) or drug repurposing is a method for identifying new therapeutic uses of existing drugs. The current study applies a computational drug repositioning method to identify candidate drugs to treat NSCLC patients. To this end, at first, the transcriptomics profile of NSCLC and healthy (control) samples was obtained from the GEO database with the accession number GSE21933. Then, the gene co-expression network was reconstructed for NSCLC samples using the WGCNA, and two significant purple and magenta gene modules were extracted. Next, a list of transcription factor genes that regulate purple and magenta modules' genes was extracted from the TRRUST V2.0 online database, and the TF–TG (transcription factors–target genes) network was drawn. Afterward, a list of drugs targeting TF–TG genes was obtained from the DGIdb V4.0 database, and two drug–gene interaction networks, including drug-TG and drug-TF, were drawn. After analyzing gene co-expression TF–TG, and drug–gene interaction networks, 16 drugs were selected as potent candidates for NSCLC treatment. Out of 16 selected drugs, nine drugs, namely Methotrexate, Olanzapine, Haloperidol, Fluorouracil, Nifedipine, Paclitaxel, Verapamil, Dexamethasone, and Docetaxel, were chosen from the drug-TG sub-network. In addition, nine drugs, including Cisplatin, Daunorubicin, Dexamethasone, Methotrexate, Hydrocortisone, Doxorubicin, Azacitidine, Vorinostat, and Doxorubicin Hydrochloride, were selected from the drug-TF sub-network. Methotrexate and Dexamethasone are common in drug-TG and drug-TF sub-networks. In conclusion, this study proposed 16 drugs as potent candidates for NSCLC treatment through analyzing gene co-expression, TF–TG, and drug–gene interaction networks.
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Assessment of Glutathione Peroxidase-1 (GPX1) Gene Expression as a Specific Diagnostic and Prognostic Biomarker in Malignant Pleural Mesothelioma. Diagnostics (Basel) 2021; 11:diagnostics11122285. [PMID: 34943522 PMCID: PMC8700378 DOI: 10.3390/diagnostics11122285] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 12/01/2021] [Indexed: 12/29/2022] Open
Abstract
Malignant pleural mesothelioma (MPM) is a malignant tumor of the mesothelial lining of the thorax. It has been related to frequent exposure to asbestos. Diagnosis of malignant pleural mesothelioma is considered a criticizing problem for clinicians. Early diagnosis and sufficient surgical excision of MPM are considered the cornerstone success factors for the management of early MPM. Glutathione peroxidase-1 (GPX1) is an intracellular protein found to be extensively distributed in all cells, and it belongs to the GPX group. In the current study, we included ninety-eight patients with MPM that underwent surgery at the Zagazig University Hospital in Egypt. We assessed GPX1 gene expression level as it was thought to be related to pathogenicity of cancer in a variety of malignant tumors. We observed a significant elevation in GPX1-mRNA levels in MPM relative to the nearby normal pleural tissues. It was found to be of important diagnostic specificity in the differentiation of MPM from normal tissues. Moreover, we studied the survival of patients in correlation to the GPX1 expression levels and we reported that median overall survival was about 16 months in patients with high GPX1 expression levels, while it was found to be about 40 months in low GPX1 levels.
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García-Caparrós P, De Filippis L, Gul A, Hasanuzzaman M, Ozturk M, Altay V, Lao MT. Oxidative Stress and Antioxidant Metabolism under Adverse Environmental Conditions: a Review. THE BOTANICAL REVIEW 2021; 87:421-466. [PMID: 0 DOI: 10.1007/s12229-020-09231-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/01/2020] [Indexed: 05/25/2023]
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GSTM1 and GSTT1 double null genotypes determining cell fate and proliferation as potential risk factors of relapse in children with hematological malignancies after hematopoietic stem cell transplantation. J Cancer Res Clin Oncol 2021; 148:71-86. [PMID: 34499222 PMCID: PMC8752561 DOI: 10.1007/s00432-021-03769-2] [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: 07/06/2021] [Accepted: 08/14/2021] [Indexed: 10/29/2022]
Abstract
PURPOSE This study aimed to retrospectively evaluate the genetic association of null variants of glutathione S-transferases GSTM1 and GSTT1 with relapse incidence in children with hematological malignancies (HMs) undergoing busulfan (BU)- containing allogeneic hematopoietic stem cell transplantation (HSCT) and to assess the impact of these variants on BU-induced cytotoxicity on the immortalized lymphoblastoid cell lines (LCLs) and tumor THP1 GST gene-edited cell models. METHODS GSTM1- and GSTT1-null alleles were genotyped using germline DNA from whole blood prior to a conditioning BU-based regimen. Association of GSTM1- and GSTT1-null variants with relapse incidence was analyzed using multivariable competing risk analysis. BU-induced cell death studies were conducted in GSTs- null and non-null LCLs and CRISPR-Cas9 gene-edited THP1 leukemia cell lines. RESULTS Carrying GSTM1/GSTT1 double null genotype was found to be an independent risk factor for post-HSCT relapse in 86 children (adjusted HR: 6.52 [95% Cl, 2.76-15.42; p = 1.9 × 10-5]). BU-induced cell death preferentially in THP1GSTM1(non-null) and LCLsGSTM1(non-null) as shown by decreased viability, increased necrosis and levels of the oxidized form of glutathione compared to null cells, while GSTT1 non-null cells showed increased baseline proliferation. CONCLUSION The clinical association suggests that GSTM1/GSTT1 double null genotype could serve as genetic stratification biomarker for the high risk of post-HSCT relapse. Functional studies have indicated that GSTM1 status modulates BU-induced cell death. On the other hand, GSTT1 is proposed to be involved in baseline cell proliferation.
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Ghelli F, Bellisario V, Squillacioti G, Panizzolo M, Santovito A, Bono R. Formaldehyde in Hospitals Induces Oxidative Stress: The Role of GSTT1 and GSTM1 Polymorphisms. TOXICS 2021; 9:toxics9080178. [PMID: 34437496 PMCID: PMC8402352 DOI: 10.3390/toxics9080178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/19/2021] [Accepted: 07/28/2021] [Indexed: 12/03/2022]
Abstract
Despite the toxicity and health risk characteristics of formaldehyde (FA), it is currently used as a cytological fixative and the definition of safe exposure levels is still a matter of debate. Our aim was to investigate the alterations in both oxidative and inflammatory status in a hospital working population. The 68 workers recruited wore a personal air-FA passive sampler, provided a urine sample to measure 15-F2t-Isoprostane (15-F2t-IsoP) and malondialdehyde (MDA) and a blood specimen to measure tumour necrosis factor α (TNFα). Subjects were also genotyped for GSTT1 (Presence/Absence), GSTM1 (Presence/Absence), CYP1A1 exon 7 (A > G), and IL6 (−174, G > C). Workers were ex post split into formalin-employers (57.3 μg/m3) and non-employers (13.5 μg/m3). In the formalin-employers group we assessed significantly higher levels of 15-F2t-IsoP, MDA and TNFα (<0.001) in comparison to the non-employers group. The air-FA levels turned out to be positively correlated with 15-F2t-IsoP (p = 0.027) and MDA (p < 0.001). In the formalin-employers group the MDA level was significantly higher in GSTT1 Null (p = 0.038), GSTM1 Null (p = 0.031), and CYP1A1 exon 7 mutation carrier (p = 0.008) workers, compared to the wild type subjects. This study confirms the role of FA in biomolecular profiles alterations, highlighting how low occupational exposure can also result in measurable biological outcomes.
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Affiliation(s)
- Federica Ghelli
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy; (F.G.); (V.B.); (G.S.); (M.P.)
| | - Valeria Bellisario
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy; (F.G.); (V.B.); (G.S.); (M.P.)
| | - Giulia Squillacioti
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy; (F.G.); (V.B.); (G.S.); (M.P.)
| | - Marco Panizzolo
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy; (F.G.); (V.B.); (G.S.); (M.P.)
| | - Alfredo Santovito
- Department of Life Sciences and Systems Biology, University of Turin, 10123 Turin, Italy;
| | - Roberto Bono
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy; (F.G.); (V.B.); (G.S.); (M.P.)
- Correspondence: ; Tel.: +39-011-670-5818
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Ayuso P, García-Martín E, Agúndez JAG. Variability of the Genes Involved in the Cellular Redox Status and Their Implication in Drug Hypersensitivity Reactions. Antioxidants (Basel) 2021; 10:antiox10020294. [PMID: 33672092 PMCID: PMC7919686 DOI: 10.3390/antiox10020294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/13/2022] Open
Abstract
Adverse drug reactions are a major cause of morbidity and mortality. Of the great diversity of drugs involved in hypersensitivity drug reactions, the most frequent are non-steroidal anti-inflammatory drugs followed by β-lactam antibiotics. The redox status regulates the level of reactive oxygen and nitrogen species (RONS). RONS interplay and modulate the action of diverse biomolecules, such as inflammatory mediators and drugs. In this review, we address the role of the redox status in the initiation, as well as in the resolution of inflammatory processes involved in drug hypersensitivity reactions. We summarize the association findings between drug hypersensitivity reactions and variants in the genes that encode the enzymes related to the redox system such as enzymes related to glutathione: Glutathione S-transferase (GSTM1, GSTP, GSTT1) and glutathione peroxidase (GPX1), thioredoxin reductase (TXNRD1 and TXNRD2), superoxide dismutase (SOD1, SOD2, and SOD3), catalase (CAT), aldo-keto reductase (AKR), and the peroxiredoxin system (PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, PRDX6). Based on current evidence, the most relevant candidate redox genes related to hypersensitivity drug reactions are GSTM1, TXNRD1, SOD1, and SOD2. Increasing the understanding of pharmacogenetics in drug hypersensitivity reactions will contribute to the development of early diagnostic or prognosis tools, and will help to diminish the occurrence and/or the severity of these reactions.
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Affiliation(s)
- Pedro Ayuso
- Correspondence: ; Tel.: +34-927257000 (ext. 51038)
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Caramujo-Balseiro S, Faro C, Carvalho L. Metabolic pathways in sporadic colorectal carcinogenesis: A new proposal. Med Hypotheses 2021; 148:110512. [PMID: 33548761 DOI: 10.1016/j.mehy.2021.110512] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 01/09/2021] [Accepted: 01/22/2021] [Indexed: 02/07/2023]
Abstract
Given the reports made about geographical differences in Colorectal Cancer (CRC) occurrence, suggesting a link between dietary habits, genes and cancer risk, we hypothesise that there are four fundamental metabolic pathways involved in diet-genes interactions, directly implicated in colorectal carcinogenesis: folate metabolism; lipid metabolism; oxidative stress response; and inflammatory response. Supporting this hypothesis are the evidence given by the significant associations between several diet-genes polymorphisms and CRC, namely: MTHFR, MTR, MTRR and TS (involved in folate metabolism); NPY, APOA1, APOB, APOC3, APOE, CETP, LPL and PON1 (involved in lipid metabolism); MNSOD, SOD3, CAT, GSTP1, GSTT1 and GSTM1 (involved in oxidative stress response); and IL-1, IL-6, TNF-α, and TGF-β (involved in inflammatory response). We also highlight the association between some foods/nutrients/nutraceuticals that are important in CRC prevention or treatment and the four metabolic pathways proposed, and the recent results of genome-wide association studies, both assisting our hypothesis. Finally, we propose a new line of investigation with larger studies, using accurate dietary biomarkers and investigating the four metabolic pathways genes simultaneously. This line of investigation will be essential to understand the full complexity of the association between nature and nurture in CRC and perhaps in other types of cancers. Only with this in-depth knowledge will it be possible to make personalised nutrition recommendations for disease prevention and management.
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Affiliation(s)
- Sandra Caramujo-Balseiro
- Institute of Anatomical and Molecular Pathology, Faculty of Medicine - University of Coimbra, Coimbra, Portugal; Department of Life Sciences - University of Coimbra, Coimbra, Portugal.
| | - Carlos Faro
- Department of Life Sciences - University of Coimbra, Coimbra, Portugal; UC Biotech, Cantanhede, Portugal
| | - Lina Carvalho
- Institute of Anatomical and Molecular Pathology, Faculty of Medicine - University of Coimbra, Coimbra, Portugal
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The role of polymorphisms in glutathione-related genes in asbestos-related diseases. Radiol Oncol 2021; 55:179-186. [PMID: 33544514 PMCID: PMC8042823 DOI: 10.2478/raon-2021-0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/02/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND The study investigated the influence of GCLC, GCLM, GSTM1, GSTT1 and GSTP1 polymorphisms, as well as the influence of interactions between polymorphism and interactions between polymorphisms and asbestos exposure, on the risk of developing pleural plaques, asbestosis and malignant mesothelioma (MM). SUBJECTS AND METHODS The cross sectional study included 940 asbestos-exposed subjects, among them 390 subjects with pleural plaques, 147 subjects with asbestosis, 225 subjects with MM and 178 subjects with no asbestos-related disease. GCLC rs17883901, GCLM rs41303970, GSTM1 null, GSTT1 null, GSTP1 rs1695 and GSTP1 rs1138272 genotypes were determined using PCR based methods. In statistical analysis, logistic regression was used. RESULTS GSTT1 null genotype was associated with the decreased risk for pleural plaques (OR = 0.63; 95% CI = 0.40-0.98; p = 0.026) and asbestosis (OR = 0.51; 95% CI = 0.28-0.93; p = 0.028), but not for MM. A positive association was found between GSTP1 rs1695 AG + GG vs. AA genotypes for MM when compared to pleural plaques (OR = 1.39; 95% CI = 1.00-1.94; p = 0.049). The interactions between different polymorphisms showed no significant influence on the risk of investigated asbestos-related diseases. The interaction between GSTT1 null polymorphism and asbestos exposure decreased the MM risk (OR = 0.17; 95% CI = 0.03-0.85; p = 0.031). CONCLUSIONS Our findings suggest that GSTT1 null genotype may be associated with a decreased risk for pleural plaques and asbestosis, may modify the association between asbestos exposure and MM and may consequently act protectively on MM risk. This study also revealed a protective effect of the interaction between GSTP1 rs1695 polymorphism and asbestos exposure on MM risk.
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Nutrigenetics of antioxidant enzymes and micronutrient needs in the context of viral infections. Nutr Res Rev 2020; 34:174-184. [PMID: 33081856 DOI: 10.1017/s0954422420000244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Sustaining adequate nutritional needs of a population is a challenging task in normal times and a priority in times of crisis. There is no 'one-size-fits-all' solution that addresses nutrition. In relevance to the COVID-19 (coronavirus disease 2019) pandemic crisis, viral infections in general and RNA viruses in particular are known to induce and promote oxidative stress, consequently increasing the body's demand for micronutrients, especially those related to antioxidant enzymic systems, thus draining the body of micronutrients, and so hindering the human body's ability to cope optimally with oxidative stress. Common polymorphisms in major antioxidant enzymes, with world population minor allele frequencies ranging from 0·5 to 50 %, are related to altered enzymic function, with substantial potential effects on the body's ability to cope with viral infection-induced oxidative stress. In this review we highlight common SNP of the major antioxidant enzymes relevant to nutritional components in the context of viral infections, namely: superoxide dismutases, glutathione peroxidases and catalase. We delineate functional polymorphisms in several human antioxidant enzymes that require, especially during a viral crisis, adequate and potentially additional nutritional support to cope with the pathological consequences of disease. Thus, in face of the COVID-19 pandemic, nutrition should be tightly monitored and possibly supplemented, with special attention to those carrying common polymorphisms in antioxidant enzymes.
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Medjani S, Chellat-Rezgoune D, Kezai T, Chidekh M, Abadi N, Satta D. Association of CYP1A1, GSTM1 and GSTT1 gene polymorphisms with risk of prostate cancer in Algerian population. AFRICAN JOURNAL OF UROLOGY 2020. [DOI: 10.1186/s12301-020-00049-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
Background
Prostate cancer is the most common cancer in the world, and its etiology involves the interaction of genetic and environmental factors. Interindividual differences observed in the metabolism of xenobiotics may be due to polymorphisms of genes encoding the detoxification enzymes. This genetic variability seems to be associated with differences in susceptibility to certain types of cancers, including prostate cancer. Our study has been made in order to investigate a possible genetic predisposition to prostate cancer in an Algerian population, through the analysis of genetic polymorphisms of three enzymes metabolizing xenobiotics namely cytochrome P450 (CYP) 1A1, glutathione S-transferase mu 1 (GSTM1) and GST theta 1 (GSTT1).
Methods
The current case–control study included 101 prostate cancer patients and 101 healthy controls. Genotyping of CYP1A1 T3801C polymorphisms and GSTM1/GSTT-null was made, respectively, by PCR-RFLP and multiplex PCR.
Results
No significantly positive associations were found for the CYP1A1 T3801C [p = 0.71, OR = 1.23 (0.56–2.72)] and GSTM1-null [p = 0.26, OR = 1.37 (0.76–2.4)] polymorphisms and prostate cancer susceptibility. However, we detect a highly significant association between GSTT1-null genotype [p = 0.03, OR = 2.03 (1.06–3.99)], GSTM1/GSTT1-double null genotype [p = 0.027, OR = 2.6; CI (1.07–6.5)] and prostate cancer risk. Furthermore, no statistically significant differences between the studied polymorphisms and tumor parameters (the Gleason score and clinical stages of aggressiveness) at diagnosis of PCa.
Conclusions
The risk of developing prostate cancer in Algeria does not appear to be associated with CYP1A1 T3801C genotypes and GSTM1-null, but GSTT1-null and GSTM1/GSTT1-double null genotypes increased the risk of prostate cancer.
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Salimi S, Harati-Sadegh M, Eskandari M, Heidari Z. The effects of the genetic polymorphisms of antioxidant enzymes on susceptibility to papillary thyroid carcinoma. IUBMB Life 2020; 72:1045-1053. [PMID: 32031754 DOI: 10.1002/iub.2246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 01/24/2020] [Indexed: 12/14/2022]
Abstract
Several lines of evidences have indicated that inflammation play an important role in the carcinogenesis. During the inflammatory processes, free radical species are produced from oxidative stress. In normal conditions, enzymatic and nonenzymatic antioxidants remove these products. Manganese superoxide dismutase (MnSOD), glutathione peroxidase-1 (GPx-1), and catalase (CAT) are three important enzymes. Therefore, this study aimed to evaluate the effects of MnSOD (SOD2), GPX-1, and CAT genetic polymorphisms on papillary thyroid carcinoma (PTC) susceptibility. A total of 134 patients with PTC and 151 healthy controls were recruited to participate in this study. All samples were genotyped for SOD2 rs4880, GPX1 1050450, and CAT rs7943316 polymorphisms by polymerase chain reaction-restriction fragment length polymorphism method. The frequencies of the rs1050450, rs4880, and rs7943316 alleles and genotypes were not different between PTC patients and controls. However, the TC genotype of SOD2 rs4880 polymorphism was significantly higher in males compared to that in females in PTC patients (odds ratio [OR], 3.9 [95% CI, 1.5-11], p = .007). The rs4880 polymorphism was also associated with higher stages (III-IV) of PTC in dominant model. No significant correlation was found between GPX1-rs1050450 and CAT-rs7943316 polymorphisms and demographic, clinical, and pathological features of the disease. The SOD2 rs4880CT genotype was more frequent in males with PTC and patients with higher stages (III-IV) of disease (OR, 2.9 [95% CI, 1.1-7.7], p = .04). However, no significant association was found between GPX1-rs1050450 and CAT-rs7943316 variants and PTC or its demographic, clinical, and pathological features.
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Affiliation(s)
- Saeedeh Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.,Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Harati-Sadegh
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Moein Eskandari
- Department of Laboratory Sciences, School of Paramedical Sciences, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Zahra Heidari
- Department of Endocrinology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
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Song Y, Jin D, Ou N, Luo Z, Chen G, Chen J, Yang Y, Liu X. Gene Expression Profiles Identified Novel Urine Biomarkers for Diagnosis and Prognosis of High-Grade Bladder Urothelial Carcinoma. Front Oncol 2020; 10:394. [PMID: 32292720 PMCID: PMC7118735 DOI: 10.3389/fonc.2020.00394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 03/05/2020] [Indexed: 01/18/2023] Open
Abstract
Bladder urothelial carcinoma (BC) has been identified as one of the most common malignant neoplasm worldwide. High-grade bladder urothelial carcinoma (HGBC) is aggressive with a high risk of recurrence, progression, metastasis, and poor prognosis. Therefore, HGBC clinical management is still a challenge. We performed the present study to seek new urine biomarkers for HGBC and investigate how they promote HGBC progression and thus affect the prognosis based on large-scale sequencing data. We identified the overlapped differentially expressed genes (DEGs) by combining GSE68020 and The Cancer Genome Atlas (TCGA) datasets. Subsequent receiver operating characteristic (ROC) curves, Kaplan-Meier (KM) curves, and Cox regression were conducted to test the diagnostic and prognostic role of the hub genes. Chi-square test and logistic regression were carried out to analyze the associations between clinicopathologic characteristics and the hub genes. Ultimately, we performed gene set enrichment analysis (GSEA), protein-protein interaction (PPI) networks, and Bayesian networks (BNs) to explore the underlying mechanisms by which ECM1, CRYAB, CGNL1, and GPX3 are involved in tumor progression. Immunohistochemistry based on The Human Protein Atlas and quantitative real-time polymerase chain reaction based on urine samples confirmed the downregulation and diagnostic values of the hub genes in HGBC. In conclusion, our study indicated that CRYAB, CGNL1, ECM1, and GPX3 are potential urine biomarkers of HGBC. These four novel urine biomarkers will have attractive applications to provide new diagnostic methods, prognostic predictors and treatment targets for HGBC, which could improve the prognosis of HGBC patients, if validated by further experiments and larger prospective clinical trials.
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Affiliation(s)
- Yuxuan Song
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Donghui Jin
- Department of Cardiothoracic Surgery, Tianjin Medical University General Hospital, Tianjin, China
| | - Ningjing Ou
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhiwen Luo
- Department of Hepatobiliary Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guangyuan Chen
- The Second Clinical Medical School, Nanchang University, Nanchang, China
| | - Jingyi Chen
- Department of Gastroenterology and Institute of Clinical Molecular Biology, Peking University People's Hospital, Beijing, China
| | - Yongjiao Yang
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Xiaoqiang Liu
- Department of Urology, Tianjin Medical University General Hospital, Tianjin, China
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15
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Vallejos-Vidal E, Reyes-Cerpa S, Rivas-Pardo JA, Maisey K, Yáñez JM, Valenzuela H, Cea PA, Castro-Fernandez V, Tort L, Sandino AM, Imarai M, Reyes-López FE. Single-Nucleotide Polymorphisms (SNP) Mining and Their Effect on the Tridimensional Protein Structure Prediction in a Set of Immunity-Related Expressed Sequence Tags (EST) in Atlantic Salmon ( Salmo salar). Front Genet 2020; 10:1406. [PMID: 32174954 PMCID: PMC7056891 DOI: 10.3389/fgene.2019.01406] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are single genetic code variations considered one of the most common forms of nucleotide modifications. Such SNPs can be located in genes associated to immune response and, therefore, they may have direct implications over the phenotype of susceptibility to infections affecting the productive sector. In this study, a set of immune-related genes (cc motif chemokine 19 precursor [ccl19], integrin β2 (itβ2, also named cd18), glutathione transferase omega-1 [gsto-1], heat shock 70 KDa protein [hsp70], major histocompatibility complex class I [mhc-I]) were analyzed to identify SNPs by data mining. These genes were chosen based on their previously reported expression on infectious pancreatic necrosis virus (IPNV)-infected Atlantic salmon phenotype. The available EST sequences for these genes were obtained from the Unigene database. Twenty-eight SNPs were found in the genes evaluated and identified most of them as transition base changes. The effect of the SNPs located on the 5’-untranslated region (UTR) or 3’-UTR upon transcription factor binding sites and alternative splicing regulatory motifs was assessed and ranked with a low-medium predicted FASTSNP score risk. Synonymous SNPs were found on itβ2 (c.2275G > A), gsto-1 (c.558G > A), and hsp70 (c.1950C > T) with low FASTSNP predicted score risk. The difference in the relative synonymous codon usage (RSCU) value between the variant codons and the wild-type codon (ΔRSCU) showed one negative (hsp70 c.1950C > T) and two positive ΔRSCU values (itβ2 c.2275G > A; gsto-1 c.558G > A), suggesting that these synonymous SNPs (sSNPs) may be associated to differences in the local rate of elongation. Nonsynonymous SNPs (nsSNPs) in the gsto-1 translatable gene region were ranked, using SIFT and POLYPHEN web-tools, with the second highest (c.205A > G; c484T > C) and the highest (c.499T > C; c.769A > C) predicted score risk possible. Using homology modeling to predict the effect of these nonsynonymous SNPs, the most relevant nucleotide changes for gsto-1 were observed for the nsSNPs c.205A > G, c484T > C, and c.769A > C. Molecular dynamics was assessed to analyze if these GSTO-1 variants have significant differences in their conformational dynamics, suggesting these SNPs could have allosteric effects modulating its catalysis. Altogether, these results suggest that candidate SNPs identified may play a crucial potential role in the immune response of Atlantic salmon.
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Affiliation(s)
- Eva Vallejos-Vidal
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Sebastián Reyes-Cerpa
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Jaime Andrés Rivas-Pardo
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.,Escuela de Biotecnología, Facultad de Ciencias, Universidad Mayor, Santiago, Chile
| | - Kevin Maisey
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Hector Valenzuela
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Pablo A Cea
- Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Lluis Tort
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Ana M Sandino
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Mónica Imarai
- Centro de Biotecnología Acuícola, Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile
| | - Felipe E Reyes-López
- Department of Cell Biology, Physiology and Immunology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Barcelona, Spain
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16
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Borowczyk K, Olejarz P, Chwatko G, Szylberg M, Głowacki R. A Simplified Method for Simultaneous Determination of α-Lipoic Acid and Low-Molecular-Mass Thiols in Human Plasma. Int J Mol Sci 2020; 21:ijms21031049. [PMID: 32033303 PMCID: PMC7037620 DOI: 10.3390/ijms21031049] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/03/2020] [Accepted: 02/04/2020] [Indexed: 12/12/2022] Open
Abstract
α-Lipoic acid, glutathione, cysteine, and cysteinylglycine can be applied as therapeutic agents in civilization diseases such as diabetes mellitus, cardiovascular diseases, and cancers. On the other hand, a higher concentration of homocysteine can result in health problems and has been indicated as an independent risk factor for cardiovascular disease and accelerated atherosclerosis. Here, the first simplified HPLC-UV assay that enables simultaneous determination of α-lipoic acid and low-molecular-mass thiols in plasma, reduces the number of steps, shortens the total time of sample preparation, and limits the amount of single-use polypropylene laboratory materials is described. The assay is based on reversed-phase high performance liquid chromatography with UV detection and simultaneous reduction of disulfide bound with tris(2-carboxyethyl)phosphine and the selective pre-column derivatization of the thiol group with 1-benzyl-2-chloropyridinium bromide. Linearity in the detector responses for plasma samples were observed in ranges: 0.12-5.0 nmol mL-1 for α-lipoic acid; 2.0-20.0 nmol mL-1 for glutathione, cysteinylglycine, and homocysteine; and 40.0-400.0 for cysteine. The LODs for α-lipoic acid and low-molecular-mass thiols were 0.08 and 0.12 nmol mL-1, respectively, while LOQs were 0.12 and 0.16 nmol mL-1, respectively. The usefulness of the proposed method has been proven by its application to real samples.
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Affiliation(s)
- Kamila Borowczyk
- Department of Environmental Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163, 90-236 Łódź, Poland; (P.O.); (G.C.); (R.G.)
- Correspondence: ; Tel.: +48-426-3558-44; Fax: +48-4263-558-41
| | - Patrycja Olejarz
- Department of Environmental Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163, 90-236 Łódź, Poland; (P.O.); (G.C.); (R.G.)
| | - Grażyna Chwatko
- Department of Environmental Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163, 90-236 Łódź, Poland; (P.O.); (G.C.); (R.G.)
| | - Marcin Szylberg
- Rehabilitation Center “Kraszewski”, Kraszewskiego 7/9, 93-161 Łódź, Poland;
| | - Rafał Głowacki
- Department of Environmental Chemistry, Faculty of Chemistry, University of Lodz, Pomorska 163, 90-236 Łódź, Poland; (P.O.); (G.C.); (R.G.)
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17
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Teimoori B, Moradi-Shahrebabak M, Razavi M, Rezaei M, Harati-Sadegh M, Salimi S. The effect of GPx-1 rs1050450 and MnSOD rs4880 polymorphisms on PE susceptibility: a case- control study. Mol Biol Rep 2019; 46:6099-6104. [PMID: 31512047 DOI: 10.1007/s11033-019-05045-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 08/27/2019] [Indexed: 12/26/2022]
Abstract
Preeclampsia (PE) is a serious pregnancy complication whose etiology is not fully understood. However, previous reports have suggested that oxidative stress and genetic variants may contribute to the development of PE. This study aimed to examine the relationship between the Glutathione peroxidase-1(GPx-1) and Manganese Superoxide dismutase (MnSOD) polymorphisms and preeclampsia (PE) risk in Iranian women. Genotyping of the studied women, including 179 preeclamptic cases and 202 controls, for GPx-1 rs1050450 and MnSOD rs4880 polymorphisms was conducted using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Our results showed a 1.7- to 1.6-fold increased risk of PE in the rs1050450 CT and CT + TT (dominant model) genotypes compared to CC genotype (OR = 1.7, 95%CI 1.1-2.7; P = 0.01 and OR = 1.6, 95%CI 1.1-2.4; P = 0.02; respectively). We also found a marked correlation between TC and CC genotypes of MnSOD rs4880 polymorphism and a 1.9- to 2.3-fold increase risk of PE (OR = 1.9, 95%CI 1.2-2.9; P = 0.005 and OR = 2.3, 95%CI 1-5.1; P = 0.04, respectively). The rs4880 MnSOD polymorphism was correlated with increased risk of PE in the allelic and dominant models (OR = 1.8, 95% CI 1.2-2.5, P = 0.002; OR = 1.9, 95%CI 1.3-3, P = 0.002, respectively). High frequency of TC/CC genotype of MnSOD rs4880 and CT genotypes of rs1050450 polymorphism in PE patients compared to controls showed the contribution of these variants to PE susceptibility.
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Affiliation(s)
- Batool Teimoori
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Maryam Moradi-Shahrebabak
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Maryam Razavi
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahnaz Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Mahdiyeh Harati-Sadegh
- Genetic of Non-Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Saeedeh Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.
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18
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Zhuo C, Wang D, Zhou C, Chen C, Li J, Tian H, Li S, Ji F, Liu C, Chen M, Zhang L. Double-Edged Sword of Tumour Suppressor Genes in Schizophrenia. Front Mol Neurosci 2019; 12:1. [PMID: 30809121 PMCID: PMC6379290 DOI: 10.3389/fnmol.2019.00001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 01/07/2019] [Indexed: 12/18/2022] Open
Abstract
Schizophrenia (SCZ) is a common psychiatric disorder with polygenetic pathogenesis. Among the many identified candidate genes and loci, the group of tumour suppressor genes has drawn our interest. In this mini-review article, we describe evidence of a correlation between major tumour suppressor genes and SCZ development. Genetic mutations ranging from single nucleotide polymorphisms to large structural alterations have been found in tumour-related genes in patients with SCZ. Epigenetic mechanisms, including DNA methylation/acetylation and microRNA regulation of tumour suppressor genes, have also been implicated in SCZ. Beyond genetic correlations, we hope to establish causal relationships between tumour suppressor gene function and SCZ risk. Accumulating evidence shows that tumour suppressor genes may mediate cell survival and neural development, both of which contribute to SCZ aetiology. Moreover, converging intracellular signalling pathways indicate a role of tumour suppressor genes in SCZ pathogenesis. Tumour suppressor gene function may mediate a direct link between neural development and function and psychiatric disorders, including SCZ. A deeper understanding of how neural cell development is affected by tumour suppressors may lead to improved anti-psychotic drugs.
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Affiliation(s)
- Chuanjun Zhuo
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China.,Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China.,Department of Psychiatric Genetics, Tianjin Medical University, Tianjin, China.,Department of Psychiatry, Wenzhou Seventh People's Hospital, Wenzhou, China
| | - Dawei Wang
- Department of Neuroimaging Laboratory, Qilu Hospital of Shandong University, Jinan, China
| | - Chunhua Zhou
- Department of Pharmacy, The First Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ce Chen
- Department of Psychiatry, Wenzhou Seventh People's Hospital, Wenzhou, China
| | - Jie Li
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China
| | - Hongjun Tian
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China
| | - Shen Li
- Genetics Laboratory, Department of Neuroimaging, Department of Psychiatry, Nankai University Affiliated Anding Hospital, Tianjin Anding Hospital, Tianjin, China.,Department of Psychiatric Genetics, Tianjin Medical University, Tianjin, China
| | - Feng Ji
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Chuanxin Liu
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Min Chen
- Psychiatric Genetic Laboratory, Department of Psychiatry, Jining Medical University, Jining, China
| | - Li Zhang
- GHM Institute of CNS Regeneration, Jinan University, Guangzhou, China
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19
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Corso CR, Acco A. Glutathione system in animal model of solid tumors: From regulation to therapeutic target. Crit Rev Oncol Hematol 2018; 128:43-57. [DOI: 10.1016/j.critrevonc.2018.05.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 04/10/2018] [Accepted: 05/16/2018] [Indexed: 02/07/2023] Open
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20
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Senthil Kumar S, Muthuselvam P, Pugalenthi V, Subramanian N, Ramkumar KM, Suresh T, Suzuki T, Rajaguru P. Toxicoproteomic analysis of human lung epithelial cells exposed to steel industry ambient particulate matter (PM) reveals possible mechanism of PM related carcinogenesis. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2018; 239:483-492. [PMID: 29684875 DOI: 10.1016/j.envpol.2018.04.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/25/2018] [Accepted: 04/09/2018] [Indexed: 06/08/2023]
Abstract
Toxicoproteomic analysis of steel industry ambient particulate matter (PM) that contain high concentrations of PAHs and metals was done by treating human lung cancer cell-line, A549 and the cell lysates were analysed using quantitative label-free nano LC-MS/MS. A total of 18,562 peptides representing 1576 proteins were identified and quantified, with 196 proteins had significantly altered expression in the treated cells. Enrichment analyses revealed that proteins associated to redox homeostsis, metabolism, and cellular energy generation were inhibited while, proteins related to DNA damage and repair and other stresses were over expressed. Altered activities of several tumor associated proteins were observed. Protein-protein interaction network and biological pathway analysis of these differentially expressed proteins were carried out to obtain a systems level view of proteome changes. Together it could be inferred that PM exposure induced oxidative stress which could have lead into DNA damage and tumor related changes. However, lowering of cellular metabolism, and energy production could reduce its ability to overcome these stress. This kind of disequilibrium between the DNA damage and ability of the cells to repair the DNA damage may lead into genomic instability that is capable of acting as the driving force during PM induced carcinogenesis.
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Affiliation(s)
- S Senthil Kumar
- Bharathidasan Institute of Technology, Anna University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - P Muthuselvam
- Bharathidasan Institute of Technology, Anna University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - V Pugalenthi
- Bharathidasan Institute of Technology, Anna University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - N Subramanian
- Bharathidasan Institute of Technology, Anna University, Tiruchirappalli, 620024, Tamil Nadu, India
| | - K M Ramkumar
- SRM Research Institute, SRM University, Kattankulathur, 603203, Tamil Nadu, India
| | - T Suresh
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, 250-9501, Japan
| | - T Suzuki
- Division of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Tokyo, 250-9501, Japan
| | - P Rajaguru
- Bharathidasan Institute of Technology, Anna University, Tiruchirappalli, 620024, Tamil Nadu, India.
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21
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Genome-Wide Identification, Classification, and Expression Divergence of Glutathione-Transferase Family in Brassica rapa under Multiple Hormone Treatments. BIOMED RESEARCH INTERNATIONAL 2018; 2018:6023457. [PMID: 29992155 PMCID: PMC5994329 DOI: 10.1155/2018/6023457] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 04/03/2018] [Accepted: 04/16/2018] [Indexed: 12/26/2022]
Abstract
The GSTs is one of the most important multifunctional protein families which has been playing a crucial role in the different aspects of plant growth. This extensive study about GSTs may establish a solid foundation for the brief functional analysis of BraGSTs in future. In this study, a total of 75 genes were identified in B. rapa. Phylogenetic analysis characterized them into eight different subclasses, while Tau and Phi subclasses were the most numerous. The exon-intron structure and the motif composition of BraGSTs were exhibited accordingly to their subclasses. Notably, we also investigated 15 tandem paralogous pairs of genes, which highlighted that all the pairs were purifying in nature as their synonymous values were lower than 1.00. Duplication analysis indicated that about 45.33% of genes mainly occurred through tandem duplication in B. rapa. Predominately, the tandem cluster of genes in subclass Tau was greater than the other subclasses. Furthermore, among eight multiple hormonal treatments (ABA, GA, BR, ETH, IAA, IBA, NPA, and JA), most number of BraGSTs was activated by NPA, BR, and ABA treatments. This analysis has provided comprehensive information about GSTs family which may assist in elucidating their exact functions in B. rapa.
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22
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Makhtar SM, Husin A, Baba AA, Ankathil R. Association of GSTM1, GSTT1 and GSTP1 Ile105Val polymorphisms with clinical response to imatinib mesylate treatment among Malaysian chronic myeloid leukaemia patients. J Genet 2018; 96:633-639. [PMID: 28947711 DOI: 10.1007/s12041-017-0819-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The detoxifying activity of glutathione S-transferases (GST) enzymes not only protect cells from the adverse effects of xenobiotics, but also alters the effectiveness of drugs in cancer cells, resulting in toxicity or drug resistance. In this study, we aimed to evaluate the association of GSTM1, GSTT1 and GSTP1 Ile105Val polymorphisms with treatment response among Malaysian chronic myeloid leukaemia (CML) patients who everyday undergo 400 mg of imatinib mesylate (IM) therapy. Multiplex polymerase chain reaction (multiplex-PCR) was performed to detect GSTM1 and GSTT1 polymorphisms simultaneously and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was conducted to detect the GSTP1 Ile195Val polymorphism. On evaluating the association of the variant genotype with treatment outcome, heterozygous variant (AG) and homozygous variant (GG) of GSTP1 Ile105Val showed significantly a higher risk for the development of resistance to IM with OR: 1.951 (95% CI: 1.186-3.209, P = 0.009) and OR: 3.540 (95% CI: 1.305-9.606, P = 0.013), respectively. Likewise, GSTT1 null genotype was also associated with a significantly higher risk for the development of resistance to IM with OR = 1.664 (95% CI: 1.011-2.739, P = 0.045). Our results indicate the potential usefulness of GST polymorphism genotyping in predicting the IM treatment response among CML patients.
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Affiliation(s)
- Siti Maziras Makhtar
- Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia.
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23
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Dequanter D, Dok R, Koolen L, Vander Poorten V, Nuyts S. Prognostic Significance of Glutathione Peroxidase Levels (GPx1) in Head and Neck Cancers. Front Oncol 2017; 7:84. [PMID: 28536671 PMCID: PMC5423422 DOI: 10.3389/fonc.2017.00084] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/18/2017] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION To date, no reliable prognostic biological marker for all squamous cell carcinoma located in different subsites of the head and neck region has been identified and used in daily routine. In line with our previous studies, in which we showed a role of glutathione and associated enzymes as potential biological markers, we investigated the relationship between GPx1 and prognosis of head and neck squamous cell carcinoma. METHODS The association between GPx1 and patient and tumor related factors were investigated in 87 pretreatment biopsies from head and neck cancer patients treated by (chemo)radiation. Moreover, the influence of GPx1 expression on outcome parameters was assessed. RESULTS A significant difference was found in the T-stage between the low and high-expressing GPx1 groups. About 75% of the T3-T4 tumors were considered GPx1 low-expressing tumors, while low GPx1 expression was only seen in 25% of the T1-T2 tumors. There was also a significant difference found between the groups when looking at the different tumor sites. Local control, locoregional control, disease-free survival, and overall survival were the same in both groups. All these results indicate that GPx1 expression does not influence the radiotherapy response nor survival.
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Affiliation(s)
- Didier Dequanter
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, Belgium.,Department of Head and Neck Surgery, CHU Saint Pierre, Brussels, Belgium
| | - Ruveyda Dok
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, Belgium
| | - Louet Koolen
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, Belgium
| | - Vincent Vander Poorten
- Otorhinolaryngology, Head and Neck Surgery, Department of Oncology, Section Head and Neck Oncology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Sandra Nuyts
- Laboratory of Experimental Radiotherapy, Department of Oncology, KU Leuven, Belgium.,Department of Radiation Oncology, Leuven Cancer Institute, University Hospitals Leuven, Leuven, Belgium
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24
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Liu CJ, Yang JH, Huang FZ, Nie WP, Liu CP, Mao XH, Yin XM, Shen XB, Peng C, Chen MF, Jiang B, Liu XY, Wu JS. Glutathione-s-transferase A 4 (GSTA4) suppresses tumor growth and metastasis of human hepatocellular carcinoma by targeting AKT pathway. Am J Transl Res 2017; 9:301-315. [PMID: 28337261 PMCID: PMC5340668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/09/2016] [Indexed: 06/06/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most lethal malignancies of cancers and its prognosis remains dismal due to the paucity of effective therapeutic targets. Up-regulation of glutathione-s-transferase A 4 (GSTA4) is associated with poor prognosis of HCC, but its functional mechanism in HCC remains unclear. In this study, we investigated the roles of GSTA4 in tumor growth and metastasis of HCC and found that GSTA4 was frequently up-regulated in HCC tissues. Through gain- and loss-of-function studies, GSTA4 was demonstrated to significantly regulate cell proliferation, migration, and invasion in vitro. Furthermore, GSTA4 overexpressing significantly promoted the tumorigenicity and metastasis of HCC cells in nude mice models bearing human HCC, whereas silencing endogenous GSTA4 caused an opposite outcome. Moreover, we demonstrated that GSTA4 enhanced HCC aggressiveness by activating protein kinase B (AKT) signaling. In multivariate analysis, our results GSTA4 overexpression promotes the progression of hepatocellular carcinoma and might represent a novel therapeutic target for its treatment.
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Affiliation(s)
- Chang Jun Liu
- Department of General Surgery, The Third Xiangya Hospital of Central South University410013, Changsha, Hunan, China
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Jin Hui Yang
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Fei Zhou Huang
- Department of General Surgery, The Third Xiangya Hospital of Central South University410013, Changsha, Hunan, China
| | - Wan Pin Nie
- Department of General Surgery, The Third Xiangya Hospital of Central South University410013, Changsha, Hunan, China
| | - Chu Ping Liu
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Xian Hai Mao
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Xin Min Yin
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Xian Bo Shen
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Chuang Peng
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Mei Fu Chen
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Bo Jiang
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
| | - Xun Yang Liu
- Department of General Surgery, The Third Xiangya Hospital of Central South University410013, Changsha, Hunan, China
| | - Jin Shu Wu
- Department of Hepatobiliary Surgery Hunan People’s Hospital410005, Changsha, Hunan, China
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Falco M, Palma G, Rea D, De Biase D, Scala S, D'Aiuto M, Facchini G, Perdonà S, Barbieri A, Arra C. Tumour biomarkers: homeostasis as a novel prognostic indicator. Open Biol 2016; 6:160254. [PMID: 27927793 PMCID: PMC5204124 DOI: 10.1098/rsob.160254] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 11/10/2016] [Indexed: 12/15/2022] Open
Abstract
The term 'personalized medicine' refers to a medical procedure that consists in the grouping of patients based on their predicted individual response to therapy or risk of disease. In oncologic patients, a 'tailored' therapeutic approach may potentially improve their survival and well-being by not only reducing the tumour, but also enhancing therapeutic response and minimizing the adverse effects. Diagnostic tests are often used to select appropriate and optimal therapies that rely both on patient genome and other molecular/cellular analysis. Several studies have shown that lifestyle and environmental factors can influence the epigenome and that epigenetic events may be involved in carcinogenesis. Thus, in addition to traditional biomarkers, epigenetic factors are raising considerable interest, because they could potentially be used as an excellent tool for cancer diagnosis and prognosis. In this review, we summarize the role of conventional cancer genetic biomarkers and their association with epigenomics. Furthermore, we will focus on the so-called 'homeostatic biomarkers' that result from the physiological response to cancer, emphasizing the concept that an altered 'new' homeostasis influence not only tumour environment, but also the whole organism.
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Affiliation(s)
- Michela Falco
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
| | - Giuseppe Palma
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
| | - Domenica Rea
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
| | - Davide De Biase
- Department of Veterinary Medicine and Animal Production, University of Naples 'Federico II', Via Delpino 1, 80137 Naples, Italy
| | - Stefania Scala
- Molecular lmmunology and Immuneregulation, Istituto Nazionale per lo Studio e la Cura dei Tumori, IRCCS Naples 'Fondazione G. Pascale', Naples, italy, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
| | - Massimiliano D'Aiuto
- Division of Breast Surgery, Department of Breast Disease, National Cancer Institute, IRCCS, 'Fondazione Pascale', Naples, Italy
| | - Gaetano Facchini
- Division of Medical Oncology, Department of Uro-Gynaecological Oncology, , Istituto Nazionale per lo Studio e la Cura dei Tumori 'Fondazione G. Pascale', IRCCS, 80131 Naples, Italy
| | - Sisto Perdonà
- Department of Urology, Istituto Nazionale per lo Studio e la Cura dei Tumori 'Fondazione G. Pascale', IRCCS, 80131 Naples, Italy
| | - Antonio Barbieri
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
| | - Claudio Arra
- Struttura Semplice Dipartimentale Sperimentazione Animale, Istituto Nazionale Tumori 'Fondazione G. Pascale', IRCCS, Via Mariano Semmola, 80131 Naples, Italy
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De Martino M, Forzati F, Marfella M, Pellecchia S, Arra C, Terracciano L, Fusco A, Esposito F. HMGA1P7-pseudogene regulates H19 and Igf2 expression by a competitive endogenous RNA mechanism. Sci Rep 2016; 6:37622. [PMID: 27874091 PMCID: PMC5118720 DOI: 10.1038/srep37622] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 11/01/2016] [Indexed: 12/18/2022] Open
Abstract
Recent studies have revealed that pseudogene transcripts can function as competing endogenous RNAs, and thereby can also contribute to cancer when dysregulated. We have recently identified two pseudogenes, HMGA1P6 and HMGA1P7 for the HMGA1 gene whose overexpression has a critical role in cancer progression. These pseudogenes work as competitive endogenous RNA decoys for HMGA1 and other cancer related genes suggesting their role in carcinogenesis. Looking for new HMGA1 pseudogene ceRNAs, we performed RNA sequencing technology on mouse embryonic fibroblasts deriving from transgenic mice overexpressing HMGA1P7. Here, we report that HMGA1P7 mRNA sustains the H19 and Igf2 overexpression by acting as miRNA decoy. Lastly, the expression of HMGA1P7 was significantly correlated with H19 and IGF2 levels in human breast cancer thereby suggesting a role for HMGA1P7 deregulation in this neoplasia.
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Affiliation(s)
- Marco De Martino
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Floriana Forzati
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Marianna Marfella
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Simona Pellecchia
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Claudio Arra
- Istituto Nazionale dei Tumori, Fondazione Pascale, via Mariano Semmola, 80131 Naples, Italy
| | - Luigi Terracciano
- Institute of Pathology, Molecular Pathology Division, University of Basel, Schonbeinstrasse 40, 4003 Basel, Switzerland
| | - Alfredo Fusco
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
| | - Francesco Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale del CNR c/o Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Scuola di Medicina e Chirurgia di Napoli, Università degli Studi di Napoli "Federico II", via Pansini 5, 80131 Naples, Italy
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Roifman M, Choufani S, Turinsky AL, Drewlo S, Keating S, Brudno M, Kingdom J, Weksberg R. Genome-wide placental DNA methylation analysis of severely growth-discordant monochorionic twins reveals novel epigenetic targets for intrauterine growth restriction. Clin Epigenetics 2016; 8:70. [PMID: 27330572 PMCID: PMC4915063 DOI: 10.1186/s13148-016-0238-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/12/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Intrauterine growth restriction (IUGR), which refers to reduced fetal growth in the context of placental insufficiency, is etiologically heterogeneous. IUGR is associated not only with perinatal morbidity and mortality but also with adult-onset disorders, such as cardiovascular disease and diabetes, posing a major health burden. Placental epigenetic dysregulation has been proposed as one mechanism that causes IUGR; however, the spectrum of epigenetic pathophysiological mechanisms leading to IUGR remains to be elucidated. Monozygotic monochorionic twins are particularly affected by IUGR, in the setting of severe discordant growth. Because monozygotic twins have the same genotype at conception and a shared maternal environment, they provide an ideal model system for studying epigenetic dysregulation of the placenta. RESULTS We compared genome-wide placental DNA methylation patterns of severely growth-discordant twins to identify novel candidate genes for IUGR. Snap-frozen placental samples for eight severely growth-discordant monozygotic monochorionic twin pairs were obtained at delivery from each twin. A high-resolution DNA methylation array platform was used to identify methylation differences between IUGR and normal twins. Our analysis revealed differentially methylated regions in the promoters of eight genes: DECR1, ZNF300, DNAJA4, CCL28, LEPR, HSPA1A/L, GSTO1, and GNE. The largest methylation differences between the two groups were in the promoters of DECR1 and ZNF300. The significance of these group differences was independently validated by bisulfite pyrosequencing, implicating aberrations in fatty acid beta oxidation and transcriptional regulation, respectively. Further analysis of the array data identified methylation changes most prominently affecting the Wnt and cadherin pathways in the IUGR cohort. CONCLUSIONS Our results suggest that IUGR in monozygotic twins is associated with impairments in lipid metabolism and transcriptional regulation as well as cadherin and Wnt signaling. We show that monozygotic monochorionic twins discordant for growth provide a useful model to study one type of the epigenetic placental dysregulation that drives IUGR.
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Affiliation(s)
- Maian Roifman
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario Canada ; Department of Paediatrics, University of Toronto, Toronto, Ontario Canada ; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada ; The Prenatal and Medical Genetics Program, Department of Obstetrics and Gynaecology, Mount Sinai Hospital, Toronto, Ontario Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Andrei L Turinsky
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada ; Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada
| | - Sascha Drewlo
- C.S. Mott Center for Human Growth and Development, Wayne State School of Medicine, Wayne State University, Detroit, MI USA
| | - Sarah Keating
- Maternal-Fetal Medicine Division, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, Ontario Canada ; Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario Canada
| | - Michael Brudno
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada ; Centre for Computational Medicine, The Hospital for Sick Children, Toronto, Ontario Canada ; Department of Computer Science, University of Toronto, Toronto, Ontario Canada
| | - John Kingdom
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario Canada ; Department of Obstetrics and Gynecology, University of Toronto, Toronto, Ontario Canada
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario Canada ; Department of Paediatrics, University of Toronto, Toronto, Ontario Canada ; Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, Ontario Canada ; Institute of Medical Science, University of Toronto, Toronto, Ontario Canada
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