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Hadpech S, Thongboonkerd V. Proteomic investigations of dengue virus infection: key discoveries over the last 10 years. Expert Rev Proteomics 2024; 21:281-295. [PMID: 39049185 DOI: 10.1080/14789450.2024.2383580] [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: 05/19/2023] [Accepted: 07/12/2024] [Indexed: 07/27/2024]
Abstract
INTRODUCTION Dengue virus (DENV) infection remains one of the most significant infectious diseases in humans. Several efforts have been made to address its molecular mechanisms. Over the last 10 years, proteomics has been widely applied to investigate various aspects of DENV infection. AREAS COVERED In this review, we briefly introduce common proteomics approaches using various mass spectrometric modalities followed by summarizing all the discoveries obtained from proteomic investigations of DENV infection over the last 10 years. These include the data on DENV-vector interactions and host responses to address the DENV biology and disease mechanisms. Moreover, applications of proteomics to disease prevention, diagnosis, vaccine design, development of anti-DENV agents and other new treatment strategies are discussed. EXPERT OPINION Despite efforts on disease prevention, DENV infection is still a significant global healthcare burden that affects the general population. As summarized herein, proteomic technologies with high-throughput capabilities have provided more in-depth details of protein dynamics during DENV infection. More extensive applications of proteomics and other powerful research tools would provide a promise to better cope and prevent this mosquito-borne infectious disease.
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Affiliation(s)
- Sudarat Hadpech
- Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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Sundling C, Yman V, Mousavian Z, Angenendt S, Foroogh F, von Horn E, Lautenbach MJ, Grunewald J, Färnert A, Sondén K. Disease-specific plasma protein profiles in patients with fever after traveling to tropical areas. Eur J Immunol 2024; 54:e2350784. [PMID: 38308504 DOI: 10.1002/eji.202350784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/16/2024] [Accepted: 01/17/2024] [Indexed: 02/04/2024]
Abstract
Fever is common among individuals seeking healthcare after traveling to tropical regions. Despite the association with potentially severe disease, the etiology is often not determined. Plasma protein patterns can be informative to understand the host response to infection and can potentially indicate the pathogen causing the disease. In this study, we measured 49 proteins in the plasma of 124 patients with fever after travel to tropical or subtropical regions. The patients had confirmed diagnoses of either malaria, dengue fever, influenza, bacterial respiratory tract infection, or bacterial gastroenteritis, representing the most common etiologies. We used multivariate and machine learning methods to identify combinations of proteins that contributed to distinguishing infected patients from healthy controls, and each other. Malaria displayed the most unique protein signature, indicating a strong immunoregulatory response with high levels of IL10, sTNFRI and II, and sCD25 but low levels of sCD40L. In contrast, bacterial gastroenteritis had high levels of sCD40L, APRIL, and IFN-γ, while dengue was the only infection with elevated IFN-α2. These results suggest that characterization of the inflammatory profile of individuals with fever can help to identify disease-specific host responses, which in turn can be used to guide future research on diagnostic strategies and therapeutic interventions.
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Affiliation(s)
- Christopher Sundling
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Victor Yman
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Stockholm South Hospital, Stockholm, Sweden
| | - Zaynab Mousavian
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sina Angenendt
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Fariba Foroogh
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Ellen von Horn
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
| | - Maximilian Julius Lautenbach
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Johan Grunewald
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Respiratory Medicine Unit, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm, Sweden
| | - Anna Färnert
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
- Department of Infectious Diseases, Karolinska University Hospital, Stockholm, Sweden
- Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Klara Sondén
- Division of Infectious Diseases, Department of Medicine Solna, Karolinska Institutet, Stockholm, Sweden
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Recker M, Fleischmann WA, Nghia TH, Truong NV, Nam LV, Duc Anh D, Song LH, The NT, Anh CX, Hoang NV, My Truong N, Toan NL, Kremsner PG, Velavan TP. Markers of prolonged hospitalisation in severe dengue. PLoS Negl Trop Dis 2024; 18:e0011922. [PMID: 38289968 PMCID: PMC10857710 DOI: 10.1371/journal.pntd.0011922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 02/09/2024] [Accepted: 01/15/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Dengue is one of the most common diseases in the tropics and subtropics. Whilst mortality is a rare event when adequate supportive care can be provided, a large number of patients get hospitalised with dengue every year that places a heavy burden on local health systems. A better understanding of the support required at the time of hospitalisation is therefore of critical importance for healthcare planning, especially when resources are limited during major outbreaks. METHODS Here we performed a retrospective analysis of clinical data from over 1500 individuals hospitalised with dengue in Vietnam between 2017 and 2019. Using a broad panel of potential biomarkers, we sought to evaluate robust predictors of prolonged hospitalisation periods. RESULTS Our analyses revealed a lead-time bias, whereby early admission to hospital correlates with longer hospital stays - irrespective of disease severity. Importantly, taking into account the symptom duration prior to hospitalisation significantly affects observed associations between hospitalisation length and previously reported risk markers of prolonged stays, which themselves showed marked inter-annual variations. Once corrected for symptom duration, age, temperature at admission and elevated neutrophil-to-lymphocyte ratio were found predictive of longer hospitalisation periods. CONCLUSION This study demonstrates that the time since dengue symptom onset is one of the most significant predictors for the length of hospital stays, independent of the assigned severity score. Pre-hospital symptom durations need to be accounted for to evaluate clinically relevant biomarkers of dengue hospitalisation trajectories.
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Affiliation(s)
- Mario Recker
- Institute for Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Centre for Ecology and Conservation, University of Exeter, Penryn Campus, Penryn, United Kingdom
| | - Wim A. Fleischmann
- Institute for Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
| | - Trinh Huu Nghia
- 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Nguyen Van Truong
- 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Le Van Nam
- 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Do Duc Anh
- Institute for Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Le Huu Song
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Nguyen Trong The
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | | | | | - Nhat My Truong
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
- 108 Military Central Hospital, Hanoi, Vietnam
| | - Nguyen Linh Toan
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Peter G. Kremsner
- Institute for Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Thirumalaisamy P. Velavan
- Institute for Tropical Medicine, University Hospital Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
- Faculty of Medicine, Duy Tan University, Da Nang, Vietnam
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Garishah FM, Boahen CK, Vadaq N, Pramudo SG, Tunjungputri RN, Riswari SF, van Rij RP, Alisjahbana B, Gasem MH, van der Ven AJAM, de Mast Q. Longitudinal proteomic profiling of the inflammatory response in dengue patients. PLoS Negl Trop Dis 2023; 17:e0011041. [PMID: 36595532 PMCID: PMC9838874 DOI: 10.1371/journal.pntd.0011041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 01/13/2023] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND The immunopathogenesis of dengue virus (DENV) infection remains incompletely understood. To increase our understanding of inflammatory response in non-severe dengue, we assessed longitudinal changes in the inflammatory proteome in patients with an acute DENV infection. METHODS Using a multiplex proximity extension assay (PEA), we measured relative levels of 368 inflammatory markers in plasma samples from hospitalized patients with non-severe DENV infection in the acute (n = 43) and convalescence (n = 35) phase of the infection and samples of healthy controls (n = 10). RESULTS We identified 203 upregulated and 39 downregulated proteins in acute versus convalescent plasma samples. The upregulated proteins had a strong representation of interferon (IFN) and IFN-inducible effector proteins, cytokines (e.g. IL-10, IL-33) and cytokine receptors, chemokines, pro-apoptotic proteins (e.g. granzymes) and endothelial markers. A number of differentially expressed proteins (DEPs) have not been reported in previous studies. Functional network analysis highlighted a central role for IFNγ, IL-10, IL-33 and chemokines. We identified different novel associations between inflammatory proteins and circulating concentrations of the endothelial glycocalyx disruption surrogate marker syndecan-1. Conclusion: This unbiased proteome analysis provides a comprehensive insight in the inflammatory response in DENV infection and its association with glycocalyx disruption.
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Affiliation(s)
- Fadel Muhammad Garishah
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Collins K. Boahen
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nadira Vadaq
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Setyo G. Pramudo
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
- Department of Internal Medicine, William Booth Hospital, Semarang, Indonesia
| | - Rahajeng N. Tunjungputri
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Silvita Fitri Riswari
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Biomedical Sciences, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Ronald P. van Rij
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bachti Alisjahbana
- Research Center for Care and Control of Infectious Disease (RC3ID), Universitas Padjadjaran, Bandung, Indonesia
- Department of Internal Medicine, Hasan Sadikin General Hospital, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Muhammad Hussein Gasem
- Center for Tropical and Infectious Diseases (CENTRID), Faculty of Medicine, Diponegoro University, Dr. Kariadi Hospital, Semarang, Indonesia
- Department of Internal Medicine, Diponegoro National University Hospital, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - André J. A. M. van der Ven
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine and the Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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Masoodi M, Peschka M, Schmiedel S, Haddad M, Frye M, Maas C, Lohse A, Huber S, Kirchhof P, Nofer JR, Renné T. Disturbed lipid and amino acid metabolisms in COVID-19 patients. J Mol Med (Berl) 2022; 100:555-568. [PMID: 35064792 PMCID: PMC8783191 DOI: 10.1007/s00109-022-02177-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 12/07/2021] [Accepted: 01/10/2022] [Indexed: 12/13/2022]
Abstract
The Coronavirus disease 2019 (COVID-19) pandemic is overwhelming the healthcare systems. Identification of systemic reactions underlying COVID-19 will lead to new biomarkers and therapeutic targets for monitoring and early intervention in this viral infection. We performed targeted metabolomics covering up to 630 metabolites within several key metabolic pathways in plasma samples of 20 hospitalized COVID-19 patients and 37 matched controls. Plasma metabolic signatures specifically differentiated severe COVID-19 from control patients. The identified metabolic signatures indicated distinct alterations in both lipid and amino acid metabolisms in COVID-19 compared to control patient plasma. Systems biology-based analyses identified sphingolipid, tryptophan, tyrosine, glutamine, arginine, and arachidonic acid metabolism as mostly impacted pathways in COVID-19 patients. Notably, gamma-aminobutyric acid (GABA) was significantly reduced in COVID-19 patients and GABA plasma levels allowed for stratification of COVID-19 patients with high sensitivity and specificity. The data reveal large metabolic disturbances in COVID-19 patients and suggest use of GABA as potential biomarker and therapeutic target for the infection.
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Affiliation(s)
- Mojgan Masoodi
- Institute of Clinical Chemistry, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Manuela Peschka
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Stefan Schmiedel
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Munif Haddad
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Maike Frye
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
| | - Coen Maas
- Department of Clinical Chemistry and Haematology, University Medical Center Utrecht, Utrecht, University, Utrecht, the Netherlands
| | - Ansgar Lohse
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Samuel Huber
- Center for Internal Medicine, Clinic of Gastroenterology, Infectiology and Tropical Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paulus Kirchhof
- Department of Cardiology, University Heart and Vascular Center UKE Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Cardiovascular Sciences, University of Birmingham, Birmingham, UK
- German Center for Cardiovascular Research (DZHK), Partner site Hamburg/Kiel/Lubeck, Hamburg, Germany
| | - Jerzy-Roch Nofer
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany
- Central Laboratory Facility, University Hospital Münster, Münster, Germany
| | - Thomas Renné
- Institute of Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg-Eppendorf, Martinistr. 52, D-20251, Hamburg, Germany.
- Irish Centre for Vascular Biology, School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland.
- Center for Thrombosis and Hemostasis (CTH), Johannes Gutenberg University Medical Center, Mainz, Germany.
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Islam MT, Quispe C, Herrera-Bravo J, Sarkar C, Sharma R, Garg N, Fredes LI, Martorell M, Alshehri MM, Sharifi-Rad J, Daştan SD, Calina D, Alsafi R, Alghamdi S, Batiha GES, Cruz-Martins N. Production, Transmission, Pathogenesis, and Control of Dengue Virus: A Literature-Based Undivided Perspective. BIOMED RESEARCH INTERNATIONAL 2021; 2021:4224816. [PMID: 34957305 PMCID: PMC8694986 DOI: 10.1155/2021/4224816] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 11/11/2021] [Accepted: 11/26/2021] [Indexed: 12/18/2022]
Abstract
Dengue remains one of the most serious and widespread mosquito-borne viral infections in human beings, with serious health problems or even death. About 50 to 100 million people are newly infected annually, with almost 2.5 billion people living at risk and resulting in 20,000 deaths. Dengue virus infection is especially transmitted through bites of Aedes mosquitos, hugely spread in tropical and subtropical environments, mostly found in urban and semiurban areas. Unfortunately, there is no particular therapeutic approach, but prevention, adequate consciousness, detection at earlier stage of viral infection, and appropriate medical care can lower the fatality rates. This review offers a comprehensive view of production, transmission, pathogenesis, and control measures of the dengue virus and its vectors.
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Affiliation(s)
- Muhammad Torequl Islam
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj (Dhaka)8100, Bangladesh
| | - Cristina Quispe
- Facultad de Ciencias de la Salud, Universidad Arturo Prat, Avda. Arturo Prat 2120, Iquique 1110939, Chile
| | - Jesús Herrera-Bravo
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomas, Chile
- Center of Molecular Biology and Pharmacogenetics, Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Chandan Sarkar
- Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj (Dhaka)8100, Bangladesh
| | - Rohit Sharma
- Department of Rasa Shastra & Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | - Neha Garg
- Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi-221005, Uttar Pradesh, India
| | | | - Miquel Martorell
- Department of Nutrition and Dietetics, Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, 4070386 Concepción, Chile
- Universidad de Concepción, Unidad de Desarrollo Tecnológico, UDT, Concepción 4070386, Chile
| | - Mohammed M. Alshehri
- Pharmaceutical Care Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | | | - Sevgi Durna Daştan
- Department of Biology, Faculty of Science, Sivas Cumhuriyet University, 58140 Sivas, Turkey
- Beekeeping Development Application and Research Center, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Radi Alsafi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Saad Alghamdi
- Laboratory Medicine Department, Faculty of Applied Medical Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Natália Cruz-Martins
- Faculty of Medicine, University of Porto, Porto, Portugal
- Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
- Institute of Research and Advanced Training in Health Sciences and Technologies (CESPU), Rua Central de Gandra, 1317, 4585-116 Gandra PRD, Portugal
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van Leur SW, Heunis T, Munnur D, Sanyal S. Pathogenesis and virulence of flavivirus infections. Virulence 2021; 12:2814-2838. [PMID: 34696709 PMCID: PMC8632085 DOI: 10.1080/21505594.2021.1996059] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/06/2021] [Accepted: 10/15/2021] [Indexed: 11/01/2022] Open
Abstract
The Flavivirus genus consists of >70 members including several that are considered significant human pathogens. Flaviviruses display a broad spectrum of diseases that can be roughly categorised into two phenotypes - systemic disease involving haemorrhage exemplified by dengue and yellow Fever virus, and neurological complications associated with the likes of West Nile and Zika viruses. Attempts to develop vaccines have been variably successful against some. Besides, mosquito-borne flaviviruses can be vertically transmitted in the arthropods, enabling long term persistence and the possibility of re-emergence. Therefore, developing strategies to combat disease is imperative even if vaccines become available. The cellular interactions of flaviviruses with their human hosts are key to establishing the viral lifecycle on the one hand, and activation of host immunity on the other. The latter should ideally eradicate infection, but often leads to immunopathological and neurological consequences. In this review, we use Dengue and Zika viruses to discuss what we have learned about the cellular and molecular determinants of the viral lifecycle and the accompanying immunopathology, while highlighting current knowledge gaps which need to be addressed in future studies.
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Affiliation(s)
| | - Tiaan Heunis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OxfordOX1 3RE, UK
| | - Deeksha Munnur
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OxfordOX1 3RE, UK
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OxfordOX1 3RE, UK
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Kumar V, Ray S, Ghantasala S, Srivastava S. An Integrated Quantitative Proteomics Workflow for Cancer Biomarker Discovery and Validation in Plasma. Front Oncol 2020; 10:543997. [PMID: 33072574 PMCID: PMC7538778 DOI: 10.3389/fonc.2020.543997] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 08/17/2020] [Indexed: 12/14/2022] Open
Abstract
Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well as clinical investigations for diagnostic and therapeutic purposes. However, the plasma proteome is extremely complex due to its wide dynamic range of protein concentrations and the presence of high-abundance proteins. Here we have described an optimized, integrated quantitative proteomics pipeline combining the label-free and multiplexed-labeling-based (iTRAQ and TMT) plasma proteome profiling methods for biomarker discovery, followed by the targeted approaches for validation of the identified potential marker proteins. In this workflow, the targeted quantitation of proteins is carried out by multiple-reaction monitoring (MRM) and parallel-reaction monitoring (PRM) mass spectrometry. Thus, our approach enables both unbiased screenings of biomarkers and their subsequent selective validation in human plasma. The overall procedure takes only ~2 days to complete, including the time for data acquisition (excluding database searching). This protocol is quick, flexible, and eliminates the need for a separate immunoassay-based validation workflow in blood cancer biomarker investigations. We anticipate that this plasma proteomics workflow will help to accelerate the cancer biomarker discovery program and provide a valuable resource to the cancer research community.
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Affiliation(s)
- Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Saicharan Ghantasala
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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Taunk K, Kalita B, Kale V, Chanukuppa V, Naiya T, Zingde SM, Rapole S. The development and clinical applications of proteomics: an Indian perspective. Expert Rev Proteomics 2020; 17:433-451. [PMID: 32576061 DOI: 10.1080/14789450.2020.1787157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION Proteomic research has been extensively used to identify potential biomarkers or targets for various diseases. Advances in mass spectrometry along with data analytics have led proteomics to become a powerful tool for exploring the critical molecular players associated with diseases, thereby, playing a significant role in the development of proteomic applications for the clinic. AREAS COVERED This review presents recent advances in the development and clinical applications of proteomics in India toward understanding various diseases including cancer, metabolic diseases, and reproductive diseases. Keywords combined with 'clinical proteomics in India' 'proteomic research in India' and 'mass spectrometry' were used to search PubMed. EXPERT OPINION The past decade has seen a significant increase in research in clinical proteomics in India. This approach has resulted in the development of proteomics-based marker technologies for disease management in the country. The majority of these investigations are still in the discovery phase and efforts have to be made to address the intended clinical use so that the identified potential biomarkers reach the clinic. To move toward this necessity, there is a pressing need to establish some key infrastructure requirements and meaningful collaborations between the clinicians and scientists which will enable more effective solutions to address health issues specific to India.
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Affiliation(s)
- Khushman Taunk
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India.,Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Bhargab Kalita
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | - Vaikhari Kale
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
| | | | - Tufan Naiya
- Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, West Bengal , Haringhata, West Bengal, India
| | - Surekha M Zingde
- CH3-53, Kendriya Vihar, Sector 11, Kharghar , Navi Mumbai, Maharashtra, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science , Pune, Maharashtra, India
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Jaiswal P, Ghosh M, Patra G, Saha B, Mukhopadhyay S. Clinical Proteomics Profiling for Biomarker Identification Among Patients Suffering With Indian Post Kala Azar Dermal Leishmaniasis. Front Cell Infect Microbiol 2020; 10:251. [PMID: 32528904 PMCID: PMC7266879 DOI: 10.3389/fcimb.2020.00251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 04/29/2020] [Indexed: 11/20/2022] Open
Abstract
Background: Post Kala Azar Dermal Leishmaniasis (PKDL) is a non-fatal dermal sequel of Visceral Leishmaniasis (VL), affecting individuals worldwide. Available diagnostic tools lack sensitivity and specificity toward identifying macular (MAC) PKDL patients, due to low parasite load in patients' sample. Confirmatory test like punch biopsy are invasive and painful. Considering the rural nature of this disease and the prevailing situation of diagnostic scenario, PKDL patients mostly remains unattended from receiving proper medical care. They in turn act as “mobile parasite reservoir,” responsible for VL transmission among healthy individuals (HI). This study aims to identify PKDL disease specific glycated protein biomarkers, utilizing the powerful LC-MS/MS technology, which is the tool of choice to efficiently identify and quantify disease specific protein biomarkers. These identified PKDL disease specific novel glycoproteins could be developed in future as immunochromatographic based assay for efficient case detection. Methodology: Previously our lab had identified importance of glycated (Circulating Immune Complexes) CICs, among PKDL patients. This study aims to further characterize disease specific glycated protein biomarkers, among MAC PKDL patients for both diagnostic and prognostic evaluation of the disease. LC-MS/MS based comparative spectral count analysis of MAC PKDL to polymorphic (POLY) PKDL, HI, and Cured (CR) individuals were performed. Proteins level alterations among all study groups were confirmed by Western blot and enzyme-linked immunosorbant Assay (ELISA). Results: Among MAC PKDL patients 43, 60, 90 proteins were altered compared to POLY PKDL, HI, and CR groups, respectively. Filtering for the most significant proteins, Plasminogen (PLG) and Vitronectin (VTN) were identified which promisingly identified MAC PKDL cases. Active surveillance results from endemic districts of West Bengal revealed drastic rise of MAC PKDL cases, alarming the urgency for field adaptive efficient biomarker. Conclusion: This current study aims to establish PLG and VTN as novel diagnostic and prognostic protein biomarker for MAC and POLY PKDL cases management.
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Affiliation(s)
- Priyank Jaiswal
- Department of Laboratory Medicine, School of Tropical Medicine, Kolkata, India
| | - Manab Ghosh
- Department of Tropical Medicine, School of Tropical Medicine, Department of Health & Family Welfare, Government of West Bengal, Kolkata, India
| | - Goutam Patra
- Department of Laboratory Medicine, School of Tropical Medicine, Kolkata, India
| | - Bibhuti Saha
- Department of Tropical Medicine, School of Tropical Medicine, Department of Health & Family Welfare, Government of West Bengal, Kolkata, India
| | - Sumi Mukhopadhyay
- Department of Laboratory Medicine, School of Tropical Medicine, Kolkata, India
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Balanza N, Erice C, Ngai M, Varo R, Kain KC, Bassat Q. Host-Based Prognostic Biomarkers to Improve Risk Stratification and Outcome of Febrile Children in Low- and Middle-Income Countries. Front Pediatr 2020; 8:552083. [PMID: 33072673 PMCID: PMC7530621 DOI: 10.3389/fped.2020.552083] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 08/12/2020] [Indexed: 12/15/2022] Open
Abstract
Fever is one of the leading causes for pediatric medical consultation and the most common symptom at clinical presentation in low- and middle-income countries (LMICs). Most febrile episodes are due to self-limited infections, but a small proportion of children will develop life-threatening infections. The early recognition of children who have or are progressing to a critical illness among all febrile cases is challenging, and there are currently no objective and quantitative tools to do so. This results in increased morbidity and mortality among children with impending life-threatening infections, whilst contributing to the unnecessary prescription of antibiotics, overwhelming health care facilities, and harm to patients receiving avoidable antimicrobial treatment. Specific fever origin is difficult to ascertain and co-infections in LMICs are common. However, many severe infections share common pathways of host injury irrespective of etiology, including immune and endothelial activation that contribute to the pathobiology of sepsis (i.e., pathogen "agnostic" mechanisms of disease). Importantly, mediators of these pathways are independent markers of disease severity and outcome. We propose that measuring circulating levels of these factors can provide quantitative and objective evidence to: enable early recognition of severe infection; guide patient triage and management; enhance post-discharge risk stratification and follow up; and mitigate potential gender bias in clinical decisions. Here, we review the clinical and biological evidence supporting the clinical utility of host immune and endothelial activation biomarkers as components of novel rapid triage tests, and discuss the challenges and needs for developing and implementing such tools.
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Affiliation(s)
- Núria Balanza
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain
| | - Clara Erice
- Sandra-Rotman Centre for Global Health, Toronto General Research Institute, University Health Network-Toronto General Hospital, Toronto, ON, Canada.,Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Michelle Ngai
- Sandra-Rotman Centre for Global Health, Toronto General Research Institute, University Health Network-Toronto General Hospital, Toronto, ON, Canada.,Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Rosauro Varo
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique
| | - Kevin C Kain
- Sandra-Rotman Centre for Global Health, Toronto General Research Institute, University Health Network-Toronto General Hospital, Toronto, ON, Canada.,Tropical Disease Unit, Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Quique Bassat
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça, Manhiça, Mozambique.,ICREA, Barcelona, Spain.,Pediatric Infectious Diseases Unit, Pediatrics Department, Hospital Sant Joan de Déu (University of Barcelona), Barcelona, Spain.,Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
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12
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Differential Pattern of Soluble Immune Markers in Asymptomatic Dengue, West Nile and Zika Virus Infections. Sci Rep 2019; 9:17172. [PMID: 31748599 PMCID: PMC6868147 DOI: 10.1038/s41598-019-53645-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/04/2019] [Indexed: 01/14/2023] Open
Abstract
Infections with dengue virus (DENV), West Nile virus (WNV) and Zika virus (ZIKV) usually present similar mild symptoms at early stages, and most infections (~80%) are asymptomatic. However, these infections may progress to severe disease with different clinical manifestations. In this study we attempted to identify unique characteristics for each infection at the presymptomatic/asymptomatic stage of infection and compared levels of soluble immune markers that have been shown to be altered during clinical course of these viral infections. Levels of soluble markers were determined by Luminex-based assays or by ELISA in plasma samples from asymptomatic blood donors who were reactive for RNA from DENV (n = 71), WNV (n = 52) or ZIKV (n = 44), and a control or non-infected (NI) group (n = 22). Results showed that even in the absence of symptoms, increased interleukin (IL) levels of IL-12, IL-17, IL-10, IL-5, CXCL9, E-Selectin and ST2/IL-1R4; and decreased levels of IL-13 and CD40 were found in all flavivirus group samples, compared to those from NI donors. DENV-infected donors demonstrated variation in expression of IL-1ra and IL-2; WNV-infected donors demonstrated variation in expression of IL-1ra, P-Selectin, IL-4 and IL-5; ZIKV-infected donors demonstrated variation in expression of IL-1ra, P-Selectin, IL-4, RANK-L, CD40L and C3a. The findings suggest that, even in the presymptomatic/asymptomatic phase of the infection, different immunomodulation profiles were associated with DENV, WNV and ZIKV infections.
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Dai YN, Tu YX, Meng D, Chen MJ, Zhang JJ, Gong YH, Tong YX, Wang MS, Pan HY, Huang HJ. Serum Proteomic Changes as Candidate Biomarkers of Intermediate Liver Fibrosis in Chronic Hepatitis B Infection. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2019; 23:167-179. [PMID: 30883302 DOI: 10.1089/omi.2018.0179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chronic hepatitis B (CHB) is a major global health burden. Liver fibrosis, an insidious process, is the main histopathological change in CHB that might lead to the end-stage liver disease if left untreated. The intermediate liver fibrosis (S2) is the optimal time to start antiviral therapy. The aim of the present study was to examine the proteomic changes in patients with CHB at different fibrotic stages, with a view to identify future serum biomarkers for S2. Ninety CHB patients were grouped into mild (S0-1), intermediate (S2), and severe liver fibrosis (S3-4) (61 men and 29 women; age 25-63 years). Isobaric tagging for relative and absolute quantitation was applied to screen proteins differentially expressed among the patient groups. Another 46 patients with CHB (age 25-59 years; 31 men and 15 women), and 16 healthy controls (age 26-61 years; 11 men and 5 women) were enrolled in a validation group. Enzyme-linked immunosorbent assay was used to verify the diagnostic value of the candidate biomarkers. We found 139 proteins that were differentially expressed between various fibrotic stage-paired comparisons. Five protein candidates were selected as potential biomarkers of S2 for further verification. Notably, ficolin-2 (FCN2) and carboxypeptidase B2 (CPB2) showed differential expression between patients and healthy controls. In conclusion, serum proteomic changes reported here offer new molecular leads for future research on biomarker candidates to identify liver fibrotic stages in CHB. In particular, FCN2 and CPB2 warrant further research on their possible mechanistic involvement in CHB pathogenesis.
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Affiliation(s)
- Yi-Ning Dai
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yue-Xing Tu
- 2 Department of Intensive Care Unit, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Di Meng
- 3 Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Mei-Juan Chen
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Jia-Jie Zhang
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yu-Han Gong
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yong-Xi Tong
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Ming-Shan Wang
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Hong-Ying Pan
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Hai-Jun Huang
- 1 Department of Infectious Diseases, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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Suttitheptumrong A, Rawarak N, Reamtong O, Boonnak K, Pattanakitsakul SN. Plectin is Required for Trans-Endothelial Permeability: A Model of Plectin Dysfunction in Human Endothelial Cells After TNF-α Treatment and Dengue Virus Infection. Proteomics 2018; 18:e1800215. [PMID: 30365215 DOI: 10.1002/pmic.201800215] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 10/15/2018] [Indexed: 12/11/2022]
Abstract
The clinical sign of dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS) in humans is increased vascular permeability. Virus-specific factors and host factors, including secreted cytokines and especially TNF-α, are suggested as having roles in the pathogenesis of these conditions. Proteomic analysis with MS is performed in membrane fraction isolated from human endothelial cells (EA.hy926) upon DENV infection and TNF-α treatment. In the 451 altered proteins that are identified, decreased plectin expression is revealed by Western blot analysis, while immunofluorescence staining (IFA) shows actin stress fiber rearrangement and decreased VE-cadherin in treated EA.hy926 cells. In vitro vascular permeability assay was used to determine transepithelial electrical resistance (TEER) in EA.hy926 cells seeded on collagen-coated Transwell inserts. The low level of TEER, the low expression of plectin and VE-cadherin, and the unusual organization of actin stress fiber are found to be correlated with increased membrane permeability in DENV2 and TNF-α-treated EA.hy926 cells. Similar results are observed when using siRNA knockdown plectin in mock EA.hy926 cells. This study provides better understanding of the role that disruption of cytoskeleton linker protein plays in increased vascular permeability, and suggests these factors as major contributors to vascular leakage in DHF/DSS patients.
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Affiliation(s)
- Aroonroong Suttitheptumrong
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nantapon Rawarak
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Onrapak Reamtong
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Kobporn Boonnak
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sa-Nga Pattanakitsakul
- Division of Molecular Medicine, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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