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Moreno E, Ciordia S, Fátima SM, Jiménez D, Martínez-Sanz J, Vizcarra P, Ron R, Sánchez-Conde M, Bargiela R, Sanchez-Carrillo S, Moreno S, Corrales F, Ferrer M, Serrano-Villar S. Proteomic snapshot of saliva samples predicts new pathways implicated in SARS-CoV-2 pathogenesis. Clin Proteomics 2024; 21:37. [PMID: 38778280 PMCID: PMC11112864 DOI: 10.1186/s12014-024-09482-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Information on the microbiome's human pathways and active members that can affect SARS-CoV-2 susceptibility and pathogenesis in the salivary proteome is very scarce. Here, we studied a unique collection of samples harvested from April to June 2020 from unvaccinated patients. METHODS We compared 10 infected and hospitalized patients with severe (n = 5) and moderate (n = 5) coronavirus disease (COVID-19) with 10 uninfected individuals, including non-COVID-19 but susceptible individuals (n = 5) and non-COVID-19 and nonsusceptible healthcare workers with repeated high-risk exposures (n = 5). RESULTS By performing high-throughput proteomic profiling in saliva samples, we detected 226 unique differentially expressed (DE) human proteins between groups (q-value ≤ 0.05) out of 3376 unambiguously identified proteins (false discovery rate ≤ 1%). Major differences were observed between the non-COVID-19 and nonsusceptible groups. Bioinformatics analysis of DE proteins revealed human proteomic signatures related to inflammatory responses, central cellular processes, and antiviral activity associated with the saliva of SARS-CoV-2-infected patients (p-value ≤ 0.0004). Discriminatory biomarker signatures from human saliva include cystatins, protective molecules present in the oral cavity, calprotectins, involved in cell cycle progression, and histones, related to nucleosome functions. The expression levels of two human proteins related to protein transport in the cytoplasm, DYNC1 (p-value, 0.0021) and MAPRE1 (p-value, 0.047), correlated with angiotensin-converting enzyme 2 (ACE2) plasma activity. Finally, the proteomes of microorganisms present in the saliva samples showed 4 main microbial functional features related to ribosome functioning that were overrepresented in the infected group. CONCLUSION Our study explores potential candidates involved in pathways implicated in SARS-CoV-2 susceptibility, although further studies in larger cohorts will be necessary.
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Affiliation(s)
- Elena Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain.
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain.
| | - Sergio Ciordia
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Santos Milhano Fátima
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Daniel Jiménez
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
| | - Javier Martínez-Sanz
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Pilar Vizcarra
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Raquel Ron
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Matilde Sánchez-Conde
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Rafael Bargiela
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, LL57 2UW, UK
| | - Sergio Sanchez-Carrillo
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
- Centro de Biologia Molecular Severo Ochoa (CBM), CSIC-UAM, 28049, Madrid, Spain
| | - Santiago Moreno
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
- Facultad de Medicina, Universidad de Alcalá de Henares, 28801, Alcalá de Henares, Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, Centro Nacional de Biotecnología (CNB), CSIC, 28049, Madrid, Spain
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049, Madrid, Spain
| | - Sergio Serrano-Villar
- Department of Infectious Diseases, Facultad de Medicina, Hospital Universitario Ramón y Cajal, IRYCIS, Carretera de Colmenar Viejo, Km 9.100, 28034, Madrid, Spain
- CIBERINFEC, Instituto de Salud Carlos III, 28029, Madrid, Spain
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Dongiovanni P, Meroni M, Aiello G, D’Amato A, Cenzato N, Casati S, Damiani G, Fenoglio C, Galimberti D, Grossi E, Prati D, Lamorte G, Bianco C, Valenti L, Soggiu A, Zapperi S, La Porta CAM, Del Fabbro M, Tartaglia GM. Salivary proteomic profile of young healthy subjects. Front Mol Biosci 2023; 10:1327233. [PMID: 38099196 PMCID: PMC10720708 DOI: 10.3389/fmolb.2023.1327233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Background: The incidence of noncommunicable diseases (NCDs) has been rapidly ramped up worldwide. Hence, there is an urgent need to non-invasively detect NCDs possibly by exploiting saliva as a 'liquid biopsy' to identify biomarkers of the health status. Since, the absence of standardized procedures of collection/analysis and the lack of normal ranges makes the use of saliva still tricky, our purpose was to outline a salivary proteomic profile which features healthy individuals. Methods: We collected saliva samples from 19 young blood donors as reference population and the proteomic profile was investigated through mass-spectrometry. Results: We identified 1,004 proteins of whose 243 proteins were shared by all subjects. By applying a data clustering approach, we found a set of six most representative proteins across all subjects including Coronin-1A, F-actin-capping protein subunit alpha, Immunoglobulin J chain, Prosaposin, 78 kDa glucose-regulated protein and Heat shock 70 kDa protein 1A and 1B. Conclusion: All of these proteins are involved in immune system activation, cellular stress responses, proliferation, and invasion thus suggesting their use as biomarkers in patients with NCDs.
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Affiliation(s)
- P. Dongiovanni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - M. Meroni
- Medicine and Metabolic Diseases, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Gilda Aiello
- Department of Human Science and Quality of Life Promotion, Telematic University San Raffaele, Rome, Italy
| | - A. D’Amato
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - N. Cenzato
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Casati
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - G. Damiani
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - C. Fenoglio
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - D. Galimberti
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- Neurodegenerative Diseases Unit, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - E. Grossi
- Villa Santa Maria Foundation, Tavernerio, Italy
| | - D. Prati
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. Lamorte
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - C. Bianco
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - L. Valenti
- Biological Resource Center, Department of Transfusion Medicine, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - A. Soggiu
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
| | - S. Zapperi
- Department of Physics, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - C. A. M. La Porta
- Department of Environmental Science and Policy, Center for Complexity and Biosystems, University of Milan, Milan, Italy
| | - M. Del Fabbro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - G. M. Tartaglia
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Milan, Italy
- SC Maxillo-Facial Surgery and Dentistry, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Milan, Italy
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Nimer RM, Alfaqih MA, Shehabat ER, Mujammami M, Abdel Rahman AM. Label-free quantitative proteomics analysis for type 2 diabetes mellitus early diagnostic marker discovery using data-independent acquisition mass spectrometry (DIA-MS). Sci Rep 2023; 13:20880. [PMID: 38012280 PMCID: PMC10682489 DOI: 10.1038/s41598-023-48185-3] [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: 03/24/2023] [Accepted: 11/23/2023] [Indexed: 11/29/2023] Open
Abstract
Type-2 diabetes mellitus (T2DM) therapy requires early diagnosis and complication avoidance. Unfortunately, current diagnostic markers do not meet these needs. Data-independent acquisition mass spectrometry (DIA-MS) offers a solution for clinical diagnosis, providing reliable and precise sample quantification. This study utilized DIA-MS to investigate proteomic differential expression in the serum of recently diagnosed T2DM patients. The study conducted a comparative protein expression analysis between healthy and recently diagnosed T2DM groups (discovery cohort). A candidate protein was then validated using enzyme-linked immune assay (ELISA) on serum samples collected from T2DM patients (n = 87) and healthy control (n = 60) (validation cohort). A total of 1074 proteins were identified, and 90 were significantly dysregulated between the two groups, including 32 newly associated with T2DM. Among these proteins, the expression of S100 calcium-binding protein A6 (S100A6) was validated by ELISA. It showed a significant increase in T2DM samples compared to the control group. It was evaluated as a biomarker using the receiver operating characteristic (ROC) curve, consistent with the DIA-MS results. Novel proteins are reported to be involved in the development and progression of T2DM. Further studies are required to investigate the differential expression of candidate marker proteins in a larger population of T2DM patients.
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Affiliation(s)
- Refat M Nimer
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan.
| | - Mahmoud A Alfaqih
- Department of Physiology and Biochemistry, Faculty of Medicine, Jordan University of Science and Technology, Irbid, 22110, Jordan
- Department of Biochemistry, College of Medicine and Medical Sciences, Arabian Gulf University, Manama, 15503, Bahrain
| | - Eman R Shehabat
- Department of Medical Laboratory Sciences, Jordan University of Science and Technology, Irbid, 22110, Jordan
| | - Muhammad Mujammami
- Department of Medicine, College of Medicine, King Saud University, 12372, Riyadh, Saudi Arabia
- University Diabetes Center, King Saud University Medical City, King Saud University, 12372, Riyadh, Saudi Arabia
| | - Anas M Abdel Rahman
- Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, A1B 3X7, Canada
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Huang B, Luo YL, Huang JL, Li GZ, Qiu SY, Huang CC. FAM3D inhibits gluconeogenesis in high glucose environment via DUSP1/ZFP36/SIK1 axis. Kaohsiung J Med Sci 2023; 39:254-265. [PMID: 36524461 DOI: 10.1002/kjm2.12633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/04/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Hyperglycemia is the most important factor leading to the complications of type 2 diabetes mellitus (T2DM). The primary condition for the treatment of T2DM is to change the glucose and lipid metabolism disorders in the liver and other insulin-sensitive tissues. The current study aims to unearth the potential molecular mechanism of inhibiting liver gluconeogenesis to provide a new theoretical basis for the treatment of T2DM. High glucose (HG) induction of HepG2 cells followed by treatment with sequence-similar family 3 member D (FAM3D). Dual specificity phosphatases 1 (DUSP1), zinc finger protein 36 (ZFP36), salt-induced kinase 1 (SIK1), p-SIK1, posphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) gene and protein expression level were detected by quantitative real-time polymerase chain reaction and western blot. The PEPCK and G6Pase activities were detected by enzyme linked immunosorbent assay. Glucose production assay to determine glucose content. The RNA binding protein immunoprecipitation assay was used to detect the binding of ZFP36 to SIK1. FAM3D facilitated the expression of DUSP1 but suppressed the expression of gluconeogenesis-related factors in an HG environment. The expression of ZFP36 was up-regulated in an HG environment. ZFP36 could reverse the inhibition of gluconeogenesis caused by FAM3D. HG-induced upregulation of ZFP36 was downregulated by overexpression of DUSP1. ZFP36 bound to SIK1, and downregulation of ZFP36 promoted SIK1 expression and inhibits gluconeogenesis. Our study demonstrated FAM3D inhibited gluconeogenesis through the DUSP1/ZFP36/SIK1 axis in an HG environment, which provided a new theoretical basis for exploring the pathogenesis and treatment strategy of T2DM.
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Affiliation(s)
- Bin Huang
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Yue-Ling Luo
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Jun-Ling Huang
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Guang-Zhi Li
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Shi-Yuan Qiu
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
| | - Chun-Chun Huang
- Department of General Medicine, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, People's Republic of China
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Simovska A, Hiljadnikova-Bajro M. Scientific potential of the salivary proteome in clinical management of Diabetes Mellitus. MAKEDONSKO FARMACEVTSKI BILTEN 2022. [DOI: 10.33320/maced.pharm.bull.2022.68.03.188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Angela Simovska
- Faculty of Pharmacy, Ss. Cyril and Methodius University in Skopje, Bul. Mother Teresa, no. 47, 1000 Skopje, Republic of North Macedonia
| | - Marija Hiljadnikova-Bajro
- Faculty of Pharmacy, Ss. Cyril and Methodius University in Skopje, Bul. Mother Teresa, no. 47, 1000 Skopje, Republic of North Macedonia
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Sohail MU, Mashood F, Oberbach A, Chennakkandathil S, Schmidt F. The role of pathogens in diabetes pathogenesis and the potential of immunoproteomics as a diagnostic and prognostic tool. Front Microbiol 2022; 13:1042362. [DOI: 10.3389/fmicb.2022.1042362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/26/2022] [Indexed: 11/15/2022] Open
Abstract
Diabetes mellitus (DM) is a group of metabolic diseases marked by hyperglycemia, which increases the risk of systemic infections. DM patients are at greater risk of hospitalization and mortality from bacterial, viral, and fungal infections. Poor glycemic control can result in skin, blood, bone, urinary, gastrointestinal, and respiratory tract infections and recurrent infections. Therefore, the evidence that infections play a critical role in DM progression and the hazard ratio for a person with DM dying from any infection is higher. Early diagnosis and better glycemic control can help prevent infections and improve treatment outcomes. Perhaps, half (49.7%) of the people living with DM are undiagnosed, resulting in a higher frequency of infections induced by the hyperglycemic milieu that favors immune dysfunction. Novel diagnostic and therapeutic markers for glycemic control and infection prevention are desirable. High-throughput blood-based immunoassays that screen infections and hyperglycemia are required to guide timely interventions and efficiently monitor treatment responses. The present review aims to collect information on the most common infections associated with DM, their origin, pathogenesis, and the potential of immunoproteomics assays in the early diagnosis of the infections. While infections are common in DM, their role in glycemic control and disease pathogenesis is poorly described. Nevertheless, more research is required to identify novel diagnostic and prognostic markers to understand DM pathogenesis and management of infections. Precise monitoring of diabetic infections by immunoproteomics may provide novel insights into disease pathogenesis and healthy prognosis.
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Olayanju OA, Mba IN, Awah NE, Akinmola OO, Ofagbor E, Okonkwo O, Olasehinde OE, Akintunde AAR, Abbiyesuku F. Oral innate immunity in patients with type 2 diabetes mellitus in a tertiary hospital in Ibadan Nigeria: a cross-sectional study. Pan Afr Med J 2022; 43:134. [PMID: 36762154 PMCID: PMC9898773 DOI: 10.11604/pamj.2022.43.134.34287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 09/01/2022] [Indexed: 11/16/2022] Open
Abstract
Introduction diabetes mellitus is associated with a high prevalence of oral infections. However, it is unclear how diabetes impacts oral innate antimicrobial proteins. This study evaluated salivary lysozyme and histatins, two major innate antimicrobial proteins, in patients with diabetes and non-diabetic controls. Methods a cross-sectional study where salivary lysozyme and histatins were measured alongside plasma glucose levels. Values of the salivary proteins were compared between the two groups; their association with glucose levels was also established using correlation and regression analysis. Results one hundred and fifty-one participants were recruited for this study, 85 (56.3%) of them had type 2 diabetes mellitus with a median fasting plasma glucose of 108.8 mg/dl (IQR 91.2-134.8) while the remaining 66 (43.7%) healthy non-diabetic controls had a median random plasma glucose of 101 mg/dl (IQR 89-112). The median salivary lysozyme was 32.5 ng/ml (IQR 25.0-39.6) in the group with diabetes and 36.4 ng/ml (IQR 31.4-42.1; p=0.01) in the non-diabetic control group. The median salivary histatins was 9.2 ng/ml (IQR 7.6 -10.2) in the group with diabetes and 14.7 ng/ml (IQR12.8-16.5; p<0.001) in the non-diabetic control group. Salivary lysozyme (r = -0.127; p =0.163) and histatins (r = -0.025; p = 0.424) were both negatively correlated with plasma glucose levels, and logistic regression showed that patients with diabetes are more likely to have lower levels of salivary lysozyme (0.957; p=0.013) and histatins (0.527; p<0.001). Conclusion patients with diabetes had reduced levels of salivary lysozyme and histatins, this could provide an insight into the associated high oral infection rates.
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Affiliation(s)
- Olatunde Ayodeji Olayanju
- Department of Chemical Pathology, Ben Carson (Snr) College of Health and Medical Sciences, Babcock University, Ilisan, Nigeria,,Corresponding author: Olatunde Ayodeji Olayanju, Department of Chemical Pathology, Ben Carson (Snr) College of Health and Medical Sciences, Babcock University, Ilisan, Nigeria.
| | | | - Nnaemeka Elvis Awah
- Department of Chemical Pathology, University College Hospital, Ibadan, Nigeria
| | | | - Ekitumi Ofagbor
- Royal Free London, National Health Service (NHS) Foundation Trust, London, England
| | - Onyiye Okonkwo
- Department of Anatomical Pathology, University College Hospital, Ibadan, Nigeria
| | - Olanrewaju Ezekiel Olasehinde
- Department of Chemical Pathology, Ben Carson (Snr) College of Health and Medical Sciences, Babcock University, Ilisan, Nigeria
| | - Akinbayo Abdul-Razaq Akintunde
- Department of Chemical Pathology, Ben Carson (Snr) College of Health and Medical Sciences, Babcock University, Ilisan, Nigeria
| | - Fayeofori Abbiyesuku
- Department of Chemical Pathology, Ben Carson (Snr) College of Health and Medical Sciences, Babcock University, Ilisan, Nigeria
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