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Alam MJ, Rahman MH, Hossain MA, Hoque MR, Aktaruzzaman M. Bioinformatics and Systems Biology Approaches to Identify the Synergistic Effects of Alcohol Use Disorder on the Progression of Neurological Diseases. Neuroscience 2024; 543:65-82. [PMID: 38401711 DOI: 10.1016/j.neuroscience.2024.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Clinical investigations showed that individuals with Alcohol Use Disorder (AUD) have worse Neurological Disease (ND) development, pointing to possible pathogenic relationships between AUD and NDs. It remains difficult to identify risk factors that are predisposing between AUD and NDs. In order to fix these issues, we created the bioinformatics pipeline and network-based approaches for employing unbiased methods to discover genes abnormally stated in both AUD and NDs and to pinpoint some of the common molecular pathways that might underlie AUD and ND interaction. We found 100 differentially expressed genes (DEGs) in both the AUD and ND patient's tissue samples. The most important Gene Ontology (GO) terms and metabolic pathways, including positive control of cytotoxicity caused by T cells, proinflammatory responses, antigen processing and presentation, and platelet-triggered interactions with vascular and circulating cell pathways were then extracted using the overlapped DEGs. Protein-protein interaction analysis was used to identify hub proteins, including CCL2, IL1B, TH, MYCN, HLA-DRB1, SLC17A7, and HNF4A, in the pathways that have been reported as playing a function in these disorders. We determined several TFs (HNF4A, C4A, HLA-B, SNCA, HLA-DMB, SLC17A7, HLA-DRB1, HLA-C, HLA-A, and HLA-DPB1) and potential miRNAs (hsa-mir-34a-5p, hsa-mir-34c-5p, hsa-mir-449a, hsa-mir-155-5p, and hsa-mir-1-3p) were crucial for regulating the expression of AUD and ND which could serve as prospective targets for treatment. Our methodologies discovered unique putative biomarkers that point to the interaction between AUD and various neurological disorders, as well as pathways that could one day be the focus of therapeutic intervention.
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Affiliation(s)
- Md Jahangir Alam
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh; Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh
| | - Md Habibur Rahman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh; Center for Advanced Bioinformatics and Artificial Intelligence Research, Islamic University, Kushtia 7003, Bangladesh.
| | - Md Arju Hossain
- Department of Biotechnology and Genetic Engineering, Mawlana Bhashani Science and Technology University, Santosh, Tangail 1902, Bangladesh; Department of Microbiology, Primeasia University, Banani, Dhaka 1213, Bangladesh
| | - Md Robiul Hoque
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Md Aktaruzzaman
- Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
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Magoha L, Nyanza EC, Asori M, Thomas DSK. Informal welders' occupational safety and environmental health risks in northwestern Tanzania. PLOS GLOBAL PUBLIC HEALTH 2024; 4:e0002923. [PMID: 38416749 PMCID: PMC10901300 DOI: 10.1371/journal.pgph.0002923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 01/28/2024] [Indexed: 03/01/2024]
Abstract
Often with minimal formal training and protections, informal welders face significant occupational health and safety (OSH) risks. This cross-sectional study of 219 adult informal welders at 70 informal welding sites in Mwanza City, Tanzania aimed to: 1) capture knowledge and awareness of occupational risks and safety precautions, training, and self-reported work-related injuries and illness and 2) observe worker use of personal protective equipment and site safety. We hypothesized that knowledge, awareness, and site inspections would improve use of PPE and that improved safety and site inspections would reduce self-reported injuries and illness. A generalized linear model (GLM) was used to model all relationships. Robust standard error estimation was used to avoid overestimation of parameters. Having a post-secondary education (aβ = 1.01, 95% CI: 0.962, 1.061; p = 0. 0679), having training in OSH (aβ = 0.927, 95% CI: 0.872, 0.984, p = 0.014), increased knowledge of occupational risks (aβ = 1.305, 95% CI: 1.143, 1.491; p<0.001), and knowledge of safety measures (aβ = 1.112, 95% CI: 0.881, 1.404; p = 0.372) increased PPE use by 1%, 7.3%, 30.5%, and 11.2% respectively. Workers who used PPE were less likely to experience fire explosions (AOR = 0.149, 95% CI: 0.029, 0.751; p = 0.02), radiation exposure (AOR = 0.097, 95% CI: 0.016, 0.579, p = 0.01) or electric shocks (AOR = 0.012; 95% CI: 0.001, 0.11, p<0.001). Having increased knowledge of safety practices also decreased the odds of fire explosions (AOR = 0.075, 95% CI: 0.018, 0.314; p<0.001). Those with higher knowledge of occupational risk (aβ = 1.57, 95% CI: 1.404, 1.756; p<0.001) and safety measures (aβ = 1.628, 95% CI: 1.34, 1.978; p<0.001) were more likely to have more positive attitudes towards safety practices. Our findings suggest that comprehensive targeted interventions including increased knowledge of occupational risks, safety practices, and occupational health law through training, along with enforcement and inspection by government officials, would benefit the environmental and occupational health for informal welders.
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Affiliation(s)
- Leah Magoha
- Occupational Health and Safety Authority, Lake Zone Office, Mwanza, Tanzania
| | - Elias C Nyanza
- Department of Environmental, Occupational Health, and GIS, School of Public Health, Catholic University of Health and Allied Sciences, Bugando, Mwanza, Tanzania
| | - Moses Asori
- Department of Geography & Earth Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Deborah S K Thomas
- Department of Geography & Earth Sciences, The University of North Carolina at Charlotte, Charlotte, NC, United States of America
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Akhtar MR, Mondal MNI, Rana HK. Bioinformatics approach to identify the impacts of microgravity on the development of bone and joint diseases. INFORMATICS IN MEDICINE UNLOCKED 2023. [DOI: 10.1016/j.imu.2023.101211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023] Open
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Soltanpour Z, Rasoulzadeh Y, Ansarin K, Seyedrezazadeh E, Jafarpour M, Mohammadian Y, Khuniqi HN. Micronucleus assay of DNA damage among welders: effects of welding processes. MUTATION RESEARCH/GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 887:503598. [PMID: 37003654 DOI: 10.1016/j.mrgentox.2023.503598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/05/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023]
Abstract
Metal fumes, gases, noise, and radiation are hazardous occupational exposures that may be encountered by welders. We have evaluated DNA damage among welders; the buccal micronucleus cytome (BMCyt) assay was used. Thirty-four exposed welders (cases) and an equal number of non-welders (controls) participated in this study. Cell types including basal, early and late differentiated cells with micronucleus (MN), dense chromatin, karyorrhectic, pyknotic, karyolitic, and binucleated cells (NBUD) were measured. Damage levels among, arc, argon, and CO2 welders were statistically significantly higher, compared to the control group. Results showed that mean of MN and NBUDs as indicators of DNA damages among arc, argon and CO2 welding's were significantly higher compared to control group. Also, the mean of DNA damage levels were statistically higher among the arc welders than among the argon or CO2 welders; and levels were higher among the argon welders than the CO2 welders. Preventative measures need to be implemented to reduce exposure to harmful agents during welding.
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Affiliation(s)
- Zahra Soltanpour
- Department of Occupational Health Engineering, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yahya Rasoulzadeh
- Department of Occupational Health Engineering, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran; Road Traffic Injury Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Khalil Ansarin
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Jafarpour
- Department of Internal Medicine, School of Medicine, Imam Reza Medical Research & Training Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yousef Mohammadian
- Department of Occupational Health Engineering, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hakimeh Nazari Khuniqi
- Department of Occupational Health Engineering, Faculty of Health, Tabriz University of Medical Sciences, Tabriz, Iran
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Li G, Jiang J, Liao Y, Wan S, Yao Y, Luo Y, Chen X, Qian H, Dai X, Yin W, Min Z, Yi G, Tan X. Risk for lung-related diseases associated with welding fumes in an occupational population: Evidence from a Cox model. Front Public Health 2022; 10:990547. [PMID: 36091502 PMCID: PMC9455702 DOI: 10.3389/fpubh.2022.990547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 08/09/2022] [Indexed: 01/26/2023] Open
Abstract
Background Welding fumes are a risk factor for welder pneumoconiosis. However, there is a lack of population information on the occurrence of welding fume-induced lung cancer, and little is known about the welding fume pathogenesis. Methods Welding fume and metal ion concentrations were assessed in a vehicle factory in Wuhan. A Cox regression model estimated lung-related disease risk in workers by independent and combined factors. Results Workers' exposures were divided into four grades; the highest exposure was among the welders in the maintenance workshop, the highest Mn and Fe exposure was 4 grades, and the highest Cr exposure was 3 grades. Subgroup analysis found that the risk of lung-related disease was 2.17 (95% CI: 1.31-3.57, p < 0.05) in welders compared with non-welders, and the risk of pulmonary disease in male welders was 2.24 (95% CI: 1.34-3.73, p < 0.05) compared to non-welders. Smoking welders had a 2.44 (95% CI: 1.32-4.51, p < 0.01) higher incidence of lung-related diseases than non-welders. Total years of work as an independent protective factor for lung-related disease risk was 0.72 (95% CI: 0.66-0.78, p < 0.01). As an independent risk factor, high-high and high-low exposure had a 5.39 (95% CI: 2.52-11.52, p < 0.001) and 2.17 (95% CI: 1.07-4.41, p < 0.05) higher risk for lung-related diseases, respectively. Conclusions High welding fume exposure is a significant risk factor for lung-related disease in workers.
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Affiliation(s)
- Guangming Li
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan, China
| | - Jinfeng Jiang
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Yonggang Liao
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Siyu Wan
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Yong Yao
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Yongbin Luo
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Xuyu Chen
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan, China
| | - Huiling Qian
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan, China
| | - Xiayun Dai
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Wenjun Yin
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Zhiteng Min
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China
| | - Guilin Yi
- Wuhan Prevention and Treatment Center for Occupational Diseases, Wuhan, China,Guilin Yi
| | - Xiaodong Tan
- Department of Preventive Medicine, School of Public Health, Wuhan University, Wuhan, China,School of Health and Nurse, Wuchang University of Technology, Wuhan, China,*Correspondence: Xiaodong Tan
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Bioinformatics and System Biological Approaches for the Identification of Genetic Risk Factors in the Progression of Cardiovascular Disease. Cardiovasc Ther 2022; 2022:9034996. [PMID: 36035865 PMCID: PMC9381297 DOI: 10.1155/2022/9034996] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/17/2022] [Accepted: 07/23/2022] [Indexed: 11/17/2022] Open
Abstract
Background Cardiovascular disease (CVD) is the combination of coronary heart disease, myocardial infarction, rheumatic heart disease, and peripheral vascular disease of the heart and blood vessels. It is one of the leading deadly diseases that causes one-third of the deaths yearly in the globe. Additionally, the risk factors associated with it make the situation more complex for cardiovascular patients, which lead them towards mortality, but the genetic association between CVD and its risk factors is not clearly explored in the global literature. We addressed this issue and explored the linkage between CVD and its risk factors. Methods We developed an analytical approach to reveal the risk factors and their linkages with CVD. We used GEO microarray datasets for the CVD and other risk factors in this study. We performed several analyses including gene expression analysis, diseasome analysis, protein-protein interaction (PPI) analysis, and pathway analysis for discovering the relationship between CVD and its risk factors. We also examined the validation of our study using gold benchmark databases OMIM, dbGAP, and DisGeNET. Results We observed that the number of 32, 17, 53, 70, and 89 differentially expressed genes (DEGs) is overlapped between CVD and its risk factors of hypertension (HTN), type 2 diabetes (T2D), hypercholesterolemia (HCL), obesity, and aging, respectively. We identified 10 major hub proteins (FPR2, TNF, CXCL8, CXCL1, IL1B, VEGFA, CYBB, PTGS2, ITGAX, and CCR5), 12 significant functional pathways, and 11 gene ontological pathways that are associated with CVD. We also found the connection of CVD with its risk factors in the gold benchmark databases. Our experimental outcomes indicate a strong association of CVD with its risk factors of HTN, T2D, HCL, obesity, and aging. Conclusions Our computational approach explored the genetic association of CVD with its risk factors by identifying the significant DEGs, hub proteins, and signaling and ontological pathways. The outcomes of this study may be further used in the lab-based analysis for developing the effective treatment strategies of CVD.
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Kim S, Hollinger H, Radke EG. 'Omics in environmental epidemiological studies of chemical exposures: A systematic evidence map. ENVIRONMENT INTERNATIONAL 2022; 164:107243. [PMID: 35551006 DOI: 10.1016/j.envint.2022.107243] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 03/25/2022] [Accepted: 04/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study information to be used for various research objectives and applications. Environmental epidemiological studies that examine the impact of chemical exposures on various 'omic profiles in human populations provide relevant mechanistic information and can be used for benchmark dose modeling to derive potential human health reference values. OBJECTIVES To create a systematic evidence map of environmental epidemiological studies examining environmental contaminant exposures with 'omics in order to characterize the extent of available studies for future research needs. METHODS Systematic review methods were used to search and screen the literature and included the use of machine learning methods to facilitate screening studies. The Populations, Exposures, Comparators and Outcomes (PECO) criteria were developed to identify and screen relevant studies. Studies that met the PECO criteria after full-text review were summarized with information such as study population, study design, sample size, exposure measurement, and 'omics analysis. RESULTS Over 10,000 studies were identified from scientific databases. Screening processes were used to identify 84 studies considered PECO-relevant after full-text review. Various contaminants (e.g. phthalate, benzene, arsenic, etc.) were investigated in epidemiological studies that used one or more of the four 'omics of interest: epigenomics, transcriptomics, proteomics, and metabolomics . The epidemiological study designs that were used to explore single or integrated 'omic research questions with contaminant exposures were cohort studies, controlled trials, cross-sectional, and case-control studies. An interactive web-based systematic evidence map was created to display more study-related information. CONCLUSIONS This systematic evidence map is a novel tool to visually characterize the available environmental epidemiological studies investigating contaminants and biological effects using 'omics technology and serves as a resource for investigators and allows for a range of applications in chemical research and risk assessment needs.
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Affiliation(s)
- Stephanie Kim
- Superfund and Emergency Management Division, Region 2, U.S. Environmental Protection Agency, NY, USA.
| | - Hillary Hollinger
- Office of Pollution Prevention and Toxics, U.S. Environmental Protection Agency, NC, USA.
| | - Elizabeth G Radke
- Center for Public Health and Environmental Assessment, U.S. Environmental Protection Agency, D.C, USA.
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Rahman MH, Rana HK, Peng S, Kibria MG, Islam MZ, Mahmud SMH, Moni MA. Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. Comput Biol Med 2021; 138:104859. [PMID: 34601390 PMCID: PMC8483812 DOI: 10.1016/j.compbiomed.2021.104859] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/21/2021] [Accepted: 09/06/2021] [Indexed: 02/06/2023]
Abstract
The Coronavirus Disease 2019 (COVID-19) still tends to propagate and increase the occurrence of COVID-19 across the globe. The clinical and epidemiological analyses indicate the link between COVID-19 and Neurological Diseases (NDs) that drive the progression and severity of NDs. Elucidating why some patients with COVID-19 influence the progression of NDs and patients with NDs who are diagnosed with COVID-19 are becoming increasingly sick, although others are not is unclear. In this research, we investigated how COVID-19 and ND interact and the impact of COVID-19 on the severity of NDs by performing transcriptomic analyses of COVID-19 and NDs samples by developing the pipeline of bioinformatics and network-based approaches. The transcriptomic study identified the contributing genes which are then filtered with cell signaling pathway, gene ontology, protein-protein interactions, transcription factor, and microRNA analysis. Identifying hub-proteins using protein-protein interactions leads to the identification of a therapeutic strategy. Additionally, the incorporation of comorbidity interactions score enhances the identification beyond simply detecting novel biological mechanisms involved in the pathophysiology of COVID-19 and its NDs comorbidities. By computing the semantic similarity between COVID-19 and each of the ND, we have found gene-based maximum semantic score between COVID-19 and Parkinson's disease, the minimum semantic score between COVID-19 and Multiple sclerosis. Similarly, we have found gene ontology-based maximum semantic score between COVID-19 and Huntington disease, minimum semantic score between COVID-19 and Epilepsy disease. Finally, we validated our findings using gold-standard databases and literature searches to determine which genes and pathways had previously been associated with COVID-19 and NDs.
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Affiliation(s)
- Md Habibur Rahman
- Dept. of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Humayan Kabir Rana
- Dept. of Computer Science and Engineering, Green University of Bangladesh, Dhaka, Bangladesh
| | - Silong Peng
- Institute of Automation, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Beijing 100190, China
| | - Md Golam Kibria
- Dept. of Chemical and Petroleum Engineering, Schulich School of Engineering, University of Calgary, Canada
| | - Md Zahidul Islam
- Department of Electronics, Graduate School of Engineering, Nagoya University, Japan
| | - S M Hasan Mahmud
- Dept. of Computer Science, American International University Bangladesh, Dhaka, Bangladesh
| | - Mohammad Ali Moni
- School of Health and Rehabilitation Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, St Lucia, QLD 4072, Australia.
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Yousefsani BS, Mehri S, Pourahmad J, Hosseinzadeh H. Protective Effect of Crocin against Mitochondrial Damage and Memory Deficit Induced by Beta-amyloid in the Hippocampus of Rats. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2021; 20:79-94. [PMID: 34567148 PMCID: PMC8457717 DOI: 10.22037/ijpr.2020.112206.13604] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Alzheimer's disease is the most common form of dementia among the elderly. This progressive neurodegenerative disorder affects brain regions that control cognition, memory, language, speech, and awareness. As a potent antioxidant, crocin has been proposed to effectively manage the neurodegenerative disease. In this study, the recovery effects of crocin on the memory deficits caused by the intra-hippocampal injection of amyloid beta1-42 (Aβ1-42) were evaluated in rats. We also considered the protective effects of crocin on the mitochondrial damage caused by Aβ1-42. We examined the memory deficits of rats with the help of the Morris water maze. Then, we determined different mitochondrial toxicity endpoints caused by Aβ1-42, including mitochondrial ROS formation, lipid peroxidation, mitochondrial membrane potential collapse, mitochondrial outer membrane integrity, and cytochrome c release. Our results demonstrated that the behavioral signs of memory deficiency caused by Aβ1-42 significantly (P < 0.01) reduced by both pretreatment and post-treatment with crocin (30 mg/kg). Furthermore, crocin prevented all the Aβ1-42 induced above referenced mitochondrial upstream toxic events leading to neuronal apoptosis. These results demonstrated that crocin is a promising preventive candidate for the potential treatment of Alzheimer's disease. Furthermore, it seems that the antioxidant and neuroprotective effects of crocin are better seen when the compound is pretreated beforehand rather than introduced afterward in Aβ1-42 exposed mitochondria.
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Affiliation(s)
- Bahareh Sadat Yousefsani
- Research Institute for Islamic and Complementary Medicine, Iran University of Medical Sciences, Tehran, Iran.,Department of Traditional Pharmacy, School of Persian Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Soghra Mehri
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Jalal Pourahmad
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Hosseinzadeh
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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Quintana-Sosa M, León-Mejía G, Luna-Carrascal J, De Moya YS, Rodríguez IL, Acosta-Hoyos A, Anaya-Romero M, Trindade C, Narváez DM, Restrepo HGD, Dias J, Niekraszewicz L, Garcia ALH, Rohr P, da Silva J, Henriques JAP. Cytokinesis-block micronucleus cytome (CBMN-CYT) assay biomarkers and telomere length analysis in relation to inorganic elements in individuals exposed to welding fumes. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 212:111935. [PMID: 33578128 DOI: 10.1016/j.ecoenv.2021.111935] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/09/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
During the welding activities many compounds are released, several of these cause oxidative stress and inflammation and some are considered carcinogenic, in fact the International Agency for Research on Cancer established that welding fumes are carcinogenic to humans. The aim of the present study was to analyze the cytotoxic and genotoxic potential of exposure to welding fumes and to determine concentrations of metals in blood and urine of occupationally exposed workers. We included 98 welders and 100 non-exposed individuals. Our results show significant increase in the frequency of micronuclei (MN), nucleoplasmic bridges (NPB), nuclear buds (NBUD) and necrotic cells (NECR) in cytokinesis-block micronucleus cytome (CBMN-Cyt) assay, as well as in the telomere length (TL) of the exposed individuals with respect to the non-exposed group. In the analysis of the concentrations of inorganic elements using PIXE method, were found higher concentrations of Cr, Fe and Cu in the urine, and Cr, Fe, Mg, Al, S, and Mn in the blood in the exposed group compared to the non-exposed group. A significant correlation was observed between MN and age and between NPB and years of exposure. Additionally, we found a significant correlation for TL in relation to MN, NPB, age and years of exposure in the exposed group. Interestingly, a significant correlation between MN and the increase in the concentration of Mg, S, Fe and Cu in blood samples of the exposed group, and between MN and Cr, Fe, Ni and Cu in urine. Thus, our findings may be associated with oxidative and inflammatory damage processes generated by the components contained in welding fumes, suggesting a high occupational risk in welding workers.
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Affiliation(s)
- Milton Quintana-Sosa
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Grethel León-Mejía
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia.
| | - Jaime Luna-Carrascal
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Yurina Sh De Moya
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Ibeth Luna Rodríguez
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Antonio Acosta-Hoyos
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Marco Anaya-Romero
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | - Cristiano Trindade
- Universidad Simón Bolívar, Facultad de Ciencias Básicas y Biomédicas, Barranquilla, Colombia
| | | | | | - Johnny Dias
- Laboratório de Implantação Iônica, Instituto de Física, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Liana Niekraszewicz
- Laboratório de Implantação Iônica, Instituto de Física, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | | | - Paula Rohr
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil
| | - Juliana da Silva
- Laboratório de Genética Toxicológica, Universidade Luterana do Brasil (ULBRA), Canoas, RS, Brazil
| | - João Antonio Pêgas Henriques
- Departamento de Biofísica, Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Instituto de Biotecnologia, Universidade de Caxias do Sul (UCS), Caxias do Sul, RS, Brazil.
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Rahman MH, Rana HK, Peng S, Hu X, Chen C, Quinn JMW, Moni MA. Bioinformatics and machine learning methodologies to identify the effects of central nervous system disorders on glioblastoma progression. Brief Bioinform 2021; 22:6066369. [PMID: 33406529 DOI: 10.1093/bib/bbaa365] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 10/25/2020] [Accepted: 11/11/2020] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GBM) is a common malignant brain tumor which often presents as a comorbidity with central nervous system (CNS) disorders. Both CNS disorders and GBM cells release glutamate and show an abnormality, but differ in cellular behavior. So, their etiology is not well understood, nor is it clear how CNS disorders influence GBM behavior or growth. This led us to employ a quantitative analytical framework to unravel shared differentially expressed genes (DEGs) and cell signaling pathways that could link CNS disorders and GBM using datasets acquired from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA) datasets where normal tissue and disease-affected tissue were examined. After identifying DEGs, we identified disease-gene association networks and signaling pathways and performed gene ontology (GO) analyses as well as hub protein identifications to predict the roles of these DEGs. We expanded our study to determine the significant genes that may play a role in GBM progression and the survival of the GBM patients by exploiting clinical and genetic factors using the Cox Proportional Hazard Model and the Kaplan-Meier estimator. In this study, 177 DEGs with 129 upregulated and 48 downregulated genes were identified. Our findings indicate new ways that CNS disorders may influence the incidence of GBM progression, growth or establishment and may also function as biomarkers for GBM prognosis and potential targets for therapies. Our comparison with gold standard databases also provides further proof to support the connection of our identified biomarkers in the pathology underlying the GBM progression.
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Affiliation(s)
- Md Habibur Rahman
- Institute of Automation Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100190, China.,Department of Computer Science and Engineering, Islamic University, Kushtia 7003, Bangladesh
| | - Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Bangladesh
| | - Silong Peng
- Institute of Automation Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyuan Hu
- Institute of Automation Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100190, China
| | - Chen Chen
- Institute of Automation Chinese Academy of Sciences, Beijing 100190, China.,University of Chinese Academy of Sciences, Beijing 100190, China
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,The Surgical Education and Research Training Institute, Royal North Shore Hospital, Sydney, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,WHO Collaborating Centre on eHealth, School of Public Health and Community Medicine, Faculty of Medicine, The University of New South Wales, Sydney, Australia
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12
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Mesnil M, Defamie N, Naus C, Sarrouilhe D. Brain Disorders and Chemical Pollutants: A Gap Junction Link? Biomolecules 2020; 11:biom11010051. [PMID: 33396565 PMCID: PMC7824109 DOI: 10.3390/biom11010051] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/22/2020] [Accepted: 12/23/2020] [Indexed: 02/07/2023] Open
Abstract
The incidence of brain pathologies has increased during last decades. Better diagnosis (autism spectrum disorders) and longer life expectancy (Parkinson's disease, Alzheimer's disease) partly explain this increase, while emerging data suggest pollutant exposures as a possible but still underestimated cause of major brain disorders. Taking into account that the brain parenchyma is rich in gap junctions and that most pollutants inhibit their function; brain disorders might be the consequence of gap-junctional alterations due to long-term exposures to pollutants. In this article, this hypothesis is addressed through three complementary aspects: (1) the gap-junctional organization and connexin expression in brain parenchyma and their function; (2) the effect of major pollutants (pesticides, bisphenol A, phthalates, heavy metals, airborne particles, etc.) on gap-junctional and connexin functions; (3) a description of the major brain disorders categorized as neurodevelopmental (autism spectrum disorders, attention deficit hyperactivity disorders, epilepsy), neurobehavioral (migraines, major depressive disorders), neurodegenerative (Parkinson's and Alzheimer's diseases) and cancers (glioma), in which both connexin dysfunction and pollutant involvement have been described. Based on these different aspects, the possible involvement of pollutant-inhibited gap junctions in brain disorders is discussed for prenatal and postnatal exposures.
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Affiliation(s)
- Marc Mesnil
- Laboratoire STIM, ERL7003 CNRS-Université de Poitiers, 1 rue G. Bonnet–TSA 51 106, 86073 Poitiers, France; (M.M.); (N.D.)
| | - Norah Defamie
- Laboratoire STIM, ERL7003 CNRS-Université de Poitiers, 1 rue G. Bonnet–TSA 51 106, 86073 Poitiers, France; (M.M.); (N.D.)
| | - Christian Naus
- Faculty of Medicine, Department of Cellular & Physiological Sciences, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T1Z3, Canada;
| | - Denis Sarrouilhe
- Laboratoire de Physiologie Humaine, Faculté de Médecine et Pharmacie, 6 rue de La Milétrie, bât D1, TSA 51115, 86073 Poitiers, France
- Correspondence: ; Tel.: +33-5-49-45-43-58
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13
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A system biological approach to investigate the genetic profiling and comorbidities of type 2 diabetes. GENE REPORTS 2020. [DOI: 10.1016/j.genrep.2020.100830] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Haidar MN, Islam MB, Chowdhury UN, Rahman MR, Huq F, Quinn JMW, Moni MA. Network-based computational approach to identify genetic links between cardiomyopathy and its risk factors. IET Syst Biol 2020; 14:75-84. [PMID: 32196466 PMCID: PMC8687405 DOI: 10.1049/iet-syb.2019.0074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/23/2019] [Accepted: 10/21/2019] [Indexed: 12/11/2022] Open
Abstract
Cardiomyopathy (CMP) is a group of myocardial diseases that progressively impair cardiac function. The mechanisms underlying CMP development are poorly understood, but lifestyle factors are clearly implicated as risk factors. This study aimed to identify molecular biomarkers involved in inflammatory CMP development and progression using a systems biology approach. The authors analysed microarray gene expression datasets from CMP and tissues affected by risk factors including smoking, ageing factors, high body fat, clinical depression status, insulin resistance, high dietary red meat intake, chronic alcohol consumption, obesity, high-calorie diet and high-fat diet. The authors identified differentially expressed genes (DEGs) from each dataset and compared those from CMP and risk factor datasets to identify common DEGs. Gene set enrichment analyses identified metabolic and signalling pathways, including MAPK, RAS signalling and cardiomyopathy pathways. Protein-protein interaction (PPI) network analysis identified protein subnetworks and ten hub proteins (CDK2, ATM, CDT1, NCOR2, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E and HIST1H4L). Five transcription factors (FOXC1, GATA2, FOXL1, YY1, CREB1) and five miRNAs were also identified in CMP. Thus the authors' approach reveals candidate biomarkers that may enhance understanding of mechanisms underlying CMP and their link to risk factors. Such biomarkers may also be useful to develop new therapeutics for CMP.
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Affiliation(s)
- Md Nasim Haidar
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Utpala Nanda Chowdhury
- Department of Computer Science and Engineering, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Md Rezanur Rahman
- Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh
| | - Fazlul Huq
- School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, NSW 2006, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia.
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15
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Network-Based Genetic Profiling Reveals Cellular Pathway Differences Between Follicular Thyroid Carcinoma and Follicular Thyroid Adenoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17041373. [PMID: 32093341 PMCID: PMC7068514 DOI: 10.3390/ijerph17041373] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/05/2020] [Accepted: 02/12/2020] [Indexed: 12/11/2022]
Abstract
Molecular mechanisms underlying the pathogenesis and progression of malignant thyroid cancers, such as follicular thyroid carcinomas (FTCs), and how these differ from benign thyroid lesions, are poorly understood. In this study, we employed network-based integrative analyses of FTC and benign follicular thyroid adenoma (FTA) lesion transcriptomes to identify key genes and pathways that differ between them. We first analysed a microarray gene expression dataset (Gene Expression Omnibus GSE82208, n = 52) obtained from FTC and FTA tissues to identify differentially expressed genes (DEGs). Pathway analyses of these DEGs were then performed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) resources to identify potentially important pathways, and protein-protein interactions (PPIs) were examined to identify pathway hub genes. Our data analysis identified 598 DEGs, 133 genes with higher and 465 genes with lower expression in FTCs. We identified four significant pathways (one carbon pool by folate, p53 signalling, progesterone-mediated oocyte maturation signalling, and cell cycle pathways) connected to DEGs with high FTC expression; eight pathways were connected to DEGs with lower relative FTC expression. Ten GO groups were significantly connected with FTC-high expression DEGs and 80 with low-FTC expression DEGs. PPI analysis then identified 12 potential hub genes based on degree and betweenness centrality; namely, TOP2A, JUN, EGFR, CDK1, FOS, CDKN3, EZH2, TYMS, PBK, CDH1, UBE2C, and CCNB2. Moreover, transcription factors (TFs) were identified that may underlie gene expression differences observed between FTC and FTA, including FOXC1, GATA2, YY1, FOXL1, E2F1, NFIC, SRF, TFAP2A, HINFP, and CREB1. We also identified microRNA (miRNAs) that may also affect transcript levels of DEGs; these included hsa-mir-335-5p, -26b-5p, -124-3p, -16-5p, -192-5p, -1-3p, -17-5p, -92a-3p, -215-5p, and -20a-5p. Thus, our study identified DEGs, molecular pathways, TFs, and miRNAs that reflect molecular mechanisms that differ between FTC and benign FTA. Given the general similarities of these lesions and common tissue origin, some of these differences may reflect malignant progression potential, and include useful candidate biomarkers for FTC and identifying factors important for FTC pathogenesis.
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16
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Rana HK, Akhtar MR, Islam MB, Ahmed MB, Lió P, Huq F, Quinn JMW, Moni MA. Machine Learning and Bioinformatics Models to Identify Pathways that Mediate Influences of Welding Fumes on Cancer Progression. Sci Rep 2020; 10:2795. [PMID: 32066756 PMCID: PMC7026442 DOI: 10.1038/s41598-020-57916-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 12/21/2019] [Indexed: 12/13/2022] Open
Abstract
Welding generates and releases fumes that are hazardous to human health. Welding fumes (WFs) are a complex mix of metallic oxides, fluorides and silicates that can cause or exacerbate health problems in exposed individuals. In particular, WF inhalation over an extended period carries an increased risk of cancer, but how WFs may influence cancer behaviour or growth is unclear. To address this issue we employed a quantitative analytical framework to identify the gene expression effects of WFs that may affect the subsequent behaviour of the cancers. We examined datasets of transcript analyses made using microarray studies of WF-exposed tissues and of cancers, including datasets from colorectal cancer (CC), prostate cancer (PC), lung cancer (LC) and gastric cancer (GC). We constructed gene-disease association networks, identified signaling and ontological pathways, clustered protein-protein interaction network using multilayer network topology, and analyzed survival function of the significant genes using Cox proportional hazards (Cox PH) model and product-limit (PL) estimator. We observed that WF exposure causes altered expression of many genes (36, 13, 25 and 17 respectively) whose expression are also altered in CC, PC, LC and GC. Gene-disease association networks, signaling and ontological pathways, protein-protein interaction network, and survival functions of the significant genes suggest ways that WFs may influence the progression of CC, PC, LC and GC. This quantitative analytical framework has identified potentially novel mechanisms by which tissue WF exposure may lead to gene expression changes in tissue gene expression that affect cancer behaviour and, thus, cancer progression, growth or establishment.
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Affiliation(s)
- Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Dhaka, Bangladesh
| | - Mst Rashida Akhtar
- Department of Computer Science and Engineering, Varendra University, Rajshahi, Bangladesh
| | - M Babul Islam
- Department of Electrical and Electronic Engineering, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohammad Boshir Ahmed
- Bio-electronics Materials Laboratory, School of Materials Science and Engineering, Gwangju Institute of Science and Technology, 261 Cheomdan-gwagiro, Buk-gu, Gwangju, 500-712, Republic of Korea
| | - Pietro Lió
- Computer Laboratory, Department of Computer Science and Technology, University of Cambridge, 15 JJ Thomson Avenue, Cambridge, CB3 0FD, UK
| | - Fazlul Huq
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Mohammad Ali Moni
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia. .,Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.
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17
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Systems biology and bioinformatics approach to identify gene signatures, pathways and therapeutic targets of Alzheimer's disease. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100439] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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18
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A systems biology approach to identifying genetic factors affected by aging, lifestyle factors, and type 2 diabetes that influences Parkinson's disease progression. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100448] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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19
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Network-based identification of genetic factors in ageing, lifestyle and type 2 diabetes that influence to the progression of Alzheimer's disease. INFORMATICS IN MEDICINE UNLOCKED 2020. [DOI: 10.1016/j.imu.2020.100309] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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20
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A computational approach to identify blood cell-expressed Parkinson's disease biomarkers that are coordinately expressed in brain tissue. Comput Biol Med 2019; 113:103385. [PMID: 31437626 DOI: 10.1016/j.compbiomed.2019.103385] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 08/06/2019] [Accepted: 08/07/2019] [Indexed: 01/09/2023]
Abstract
Identification of genes whose regulation of expression is functionally similar in both brain tissue and blood cells could in principle enable monitoring of significant neurological traits and disorders by analysis of blood samples. We thus employed transcriptional analysis of pathologically affected tissues, using agnostic approaches to identify overlapping gene functions and integrating this transcriptomic information with expression quantitative trait loci (eQTL) data. Here, we estimate the correlation of gene expression in the top-associated cis-eQTLs of brain tissue and blood cells in Parkinson's Disease (PD). We introduced quantitative frameworks to reveal the complex relationship of various biasing genetic factors in PD, a neurodegenerative disease. We examined gene expression microarray and RNA-Seq datasets from human brain and blood tissues from PD-affected and control individuals. Differentially expressed genes (DEG) were identified for both brain and blood cells to determine common DEG overlaps. Based on neighborhood-based benchmarking and multilayer network topology approaches we then developed genetic associations of factors with PD. Overlapping DEG sets underwent gene enrichment using pathway analysis and gene ontology methods, which identified candidate common genes and pathways. We identified 12 significantly dysregulated genes shared by brain and blood cells, which were validated using dbGaP (gene SNP-disease linkage) database for gold-standard benchmarking of their significance in disease processes. Ontological and pathway analyses identified significant gene ontology and molecular pathways that indicate PD progression. In sum, we found possible novel links between pathological processes in brain tissue and blood cells by examining cell pathway commonalities, corroborating these associations using well validated datasets. This demonstrates that for brain-related pathologies combining gene expression analysis and blood cell cis-eQTL is a potentially powerful analytical approach. Thus, our methodologies facilitate data-driven approaches that can advance knowledge of disease mechanisms and may, with clinical validation, enable prediction of neurological dysfunction using blood cell transcript profiling.
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21
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Rana HK, Akhtar MR, Islam MB, Ahmed MB, Liò P, Quinn JMW, Huq F, Moni MA. Genetic effects of welding fumes on the development of respiratory system diseases. Comput Biol Med 2019; 108:142-149. [PMID: 31005006 DOI: 10.1016/j.compbiomed.2019.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/03/2019] [Accepted: 04/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND The welding process releases potentially hazardous gases and fumes, mainly composed of metallic oxides, fluorides and silicates. Long term welding fume (WF) inhalation is a recognized health issue that carries a risk of developing chronic health problems, particularly respiratory system diseases (RSDs). Aside from general airway irritation, WF exposure may drive direct cellular responses in the respiratory system which increase risk of RSD, but these are not well understood. METHODS We developed a quantitative framework to identify gene expression effects of WF exposure that may affect RSD development. We analyzed gene expression microarray data from WF-exposed tissues and RSD-affected tissues, including chronic bronchitis (CB), asthma (AS), pulmonary edema (PE), lung cancer (LC) datasets. We built disease-gene (diseasome) association networks and identified dysregulated signaling and ontological pathways, and protein-protein interaction sub-network using neighborhood-based benchmarking and multilayer network topology. RESULTS We observed many genes with altered expression in WF-exposed tissues were also among differentially expressed genes (DEGs) in RSD tissues; for CB, AS, PE and LC there were 34, 27, 50 and 26 genes respectively. DEG analysis, using disease association networks, pathways, ontological analysis and protein-protein interaction sub-network suggest significant links between WF exposure and the development of CB, AS, PE and LC. CONCLUSIONS Our network-based analysis and investigation of the genetic links of WFs and RSDs confirm a number of genes and gene products are plausible participants in RSD development. Our results are a significant resource to identify causal influences on the development of RSDs, particularly in the context of WF exposure.
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Affiliation(s)
- Humayan Kabir Rana
- Department of Computer Science and Engineering, Green University of Bangladesh, Bangladesh
| | - Mst Rashida Akhtar
- Department of Computer Science and Engineering, Varendra University, Rajshahi, Bangladesh
| | - M Babul Islam
- Department of Applied Physics and Electronic Engineering, University of Rajshahi, Bangladesh
| | - Mohammad Boshir Ahmed
- School of Civil and Environmental Engineering, University of Technology Sydney, NSW, 2007, Australia
| | - Pietro Liò
- Computer Laboratory, The University of Cambridge, 15 JJ Thomson Avenue, Cambridge, UK
| | - Julian M W Quinn
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Fazlul Huq
- Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia
| | - Mohammad Ali Moni
- Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia.
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