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Rankawat S, Kundal K, Chakraborty S, Kumar R, Ray S. A comprehensive rhythmicity analysis of host proteins and immune factors involved in malaria pathogenesis to decipher the importance of host circadian clock in malaria. Front Immunol 2023; 14:1210299. [PMID: 37638001 PMCID: PMC10449258 DOI: 10.3389/fimmu.2023.1210299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/17/2023] [Indexed: 08/29/2023] Open
Abstract
Background Circadian rhythms broadly impact human health by regulating our daily physiological and metabolic processes. The circadian clocks substantially regulate our immune responses and susceptibility to infections. Malaria parasites have intrinsic molecular oscillations and coordinate their infection cycle with host rhythms. Considering the cyclical nature of malaria, a clear understanding of the circadian regulations in malaria pathogenesis and host responses is of immense importance. Methods We have thoroughly investigated the transcript level rhythmic patterns in blood proteins altered in falciparum and vivax malaria and malaria-related immune factors in mice, baboons, and humans by analyzing datasets from published literature and comprehensive databases. Using the Metascape and DAVID platforms, we analyzed Gene Ontology terms and physiological pathways associated with the rhythmic malaria-associated host immune factors. Results We observed that almost 50% of the malaria-associated host immune factors are rhythmic in mice and humans. Overlapping rhythmic genes identified in mice, baboons, and humans, exhibited enrichment (Q < 0.05, fold-enrichment > 5) of multiple physiological pathways essential for host immune and defense response, including cytokine production, leukocyte activation, cellular defense, and response, regulation of kinase activity, B-cell receptor signaling pathway, and cellular response to cytokine stimulus. Conclusions Our analysis indicates a robust circadian regulation on multiple interconnected host response pathways and immunological networks in malaria, evident from numerous rhythmic genes involved in those pathways. Host immune rhythms play a vital role in the temporal regulation of host-parasite interactions and defense machinery in malaria.
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Affiliation(s)
| | | | | | | | - Sandipan Ray
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
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2
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Aggarwal S, Peng WK, Srivastava S. Multi-Omics Advancements towards Plasmodium vivax Malaria Diagnosis. Diagnostics (Basel) 2021; 11:2222. [PMID: 34943459 PMCID: PMC8700291 DOI: 10.3390/diagnostics11122222] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/21/2021] [Accepted: 11/22/2021] [Indexed: 11/16/2022] Open
Abstract
Plasmodium vivax malaria is one of the most lethal infectious diseases, with 7 million infections annually. One of the roadblocks to global malaria elimination is the lack of highly sensitive, specific, and accurate diagnostic tools. The absence of diagnostic tools in particular has led to poor differentiation among parasite species, poor prognosis, and delayed treatment. The improvement necessary in diagnostic tools can be broadly grouped into two categories: technologies-driven and omics-driven progress over time. This article discusses the recent advancement in omics-based malaria for identifying the next generation biomarkers for a highly sensitive and specific assay with a rapid and antecedent prognosis of the disease. We summarize the state-of-the-art diagnostic technologies, the key challenges, opportunities, and emerging prospects of multi-omics-based sensors.
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Affiliation(s)
- Shalini Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India;
| | - Weng Kung Peng
- Songshan Lake Materials Laboratory, Building A1, University Innovation Park, Dongguan 523808, China
- Precision Medicine-Engineering Group, International Iberian Nanotechnology Laboratory, 4715-330 Braga, Portugal
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India;
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Kumar V, Ray S, Aggarwal S, Biswas D, Jadhav M, Yadav R, Sabnis SV, Banerjee S, Talukdar A, Kochar SK, Shetty S, Sehgal K, Patankar S, Srivastava S. Multiplexed quantitative proteomics provides mechanistic cues for malaria severity and complexity. Commun Biol 2020; 3:683. [PMID: 33204009 PMCID: PMC7672109 DOI: 10.1038/s42003-020-01384-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/14/2020] [Indexed: 12/11/2022] Open
Abstract
Management of severe malaria remains a critical global challenge. In this study, using a multiplexed quantitative proteomics pipeline we systematically investigated the plasma proteome alterations in non-severe and severe malaria patients. We identified a few parasite proteins in severe malaria patients, which could be promising from a diagnostic perspective. Further, from host proteome analysis we observed substantial modulations in many crucial physiological pathways, including lipid metabolism, cytokine signaling, complement, and coagulation cascades in severe malaria. We propose that severe manifestations of malaria are possibly underpinned by modulations of the host physiology and defense machinery, which is evidently reflected in the plasma proteome alterations. Importantly, we identified multiple blood markers that can effectively define different complications of severe falciparum malaria, including cerebral syndromes and severe anemia. The ability of our identified blood markers to distinguish different severe complications of malaria may aid in developing new clinical tests for monitoring malaria severity.
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Affiliation(s)
- Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Shalini Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Deeptarup Biswas
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Manali Jadhav
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Radha Yadav
- Department of Mathematics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sanjeev V Sabnis
- Department of Mathematics, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Soumaditya Banerjee
- Medicine Department, Medical College Hospital Kolkata, 88, College Street, Kolkata, 700073, India
| | - Arunansu Talukdar
- Medicine Department, Medical College Hospital Kolkata, 88, College Street, Kolkata, 700073, India
| | - Sanjay K Kochar
- Department of Medicine, Malaria Research Centre, S.P. Medical College, Bikaner, 334003, India
| | - Suvin Shetty
- Dr. L H Hiranandani Hospital, Mumbai, 400076, India
| | | | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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4
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di Masi A, De Simone G, Ciaccio C, D'Orso S, Coletta M, Ascenzi P. Haptoglobin: From hemoglobin scavenging to human health. Mol Aspects Med 2020; 73:100851. [PMID: 32660714 DOI: 10.1016/j.mam.2020.100851] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 02/07/2023]
Abstract
Haptoglobin (Hp) belongs to the family of acute-phase plasma proteins and represents the most important plasma detoxifier of hemoglobin (Hb). The basic Hp molecule is a tetrameric protein built by two α/β dimers. Each Hp α/β dimer is encoded by a single gene and is synthesized as a single polypeptide. Following post-translational protease-dependent cleavage of the Hp polypeptide, the α and β chains are linked by disulfide bridge(s) to generate the mature Hp protein. As human Hp gene is characterized by two common Hp1 and Hp2 alleles, three major genotypes can result (i.e., Hp1-1, Hp2-1, and Hp2-2). Hp regulates Hb clearance from circulation by the macrophage-specific receptor CD163, thus preventing Hb-mediated severe consequences for health. Indeed, the antioxidant and Hb binding properties of Hp as well as its ability to stimulate cells of the monocyte/macrophage lineage and to modulate the helper T-cell type 1 and type 2 balance significantly associate with a variety of pathogenic disorders (e.g., infectious diseases, diabetes, cardiovascular diseases, and cancer). Alternative functions of the variants Hp1 and Hp2 have been reported, particularly in the susceptibility and protection against infectious (e.g., pulmonary tuberculosis, HIV, and malaria) and non-infectious (e.g., diabetes, cardiovascular diseases and obesity) diseases. Both high and low levels of Hp are indicative of clinical conditions: Hp plasma levels increase during infections, inflammation, and various malignant diseases, and decrease during malnutrition, hemolysis, hepatic disease, allergic reactions, and seizure disorders. Of note, the Hp:Hb complexes display heme-based reactivity; in fact, they bind several ferrous and ferric ligands, including O2, CO, and NO, and display (pseudo-)enzymatic properties (e.g., NO and peroxynitrite detoxification). Here, genetic, biochemical, biomedical, and biotechnological aspects of Hp are reviewed.
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Affiliation(s)
- Alessandra di Masi
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Giovanna De Simone
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Chiara Ciaccio
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Silvia D'Orso
- Department of Sciences, Roma Tre University, Viale Guglielmo Marconi 446, I-00146 Roma, Italy
| | - Massimo Coletta
- Department of Clinical Sciences and Translational Medicine, University of Roma "Tor Vergata", Via Montpellier 1, I-00133, Roma, Italy; Interuniversity Consortium for the Research on the Chemistry of Metals in Biological Systems, Via Celso Ulpiani 27, I-70126, Bari, Italy
| | - Paolo Ascenzi
- Interdepartmental Laboratory for Electron Microscopy, Roma Tre University, Via della Vasca Navale 79, I-00146, Roma, Italy.
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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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6
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The use of proteomics for the identification of promising vaccine and diagnostic biomarkers in Plasmodium falciparum. Parasitology 2020; 147:1255-1262. [PMID: 32618524 DOI: 10.1017/s003118202000102x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plasmodium falciparum is the main cause of severe malaria in humans that can lead to death. There is growing evidence of drug-resistance in P. falciparum treatment, and the design of effective vaccines remains an ongoing strategy to control the disease. On the other hand, the recognition of specific diagnostic markers for P. falciparum can accelerate the diagnosis of this parasite in the early stages of infection. Therefore, the identification of novel antigenic proteins especially by proteomic tools is urgent for vaccination and diagnosis of P. falciparum. The proteome diversity of the life cycle stages of P. falciparum, the altered proteome of P. falciparum-infected human sera and altered proteins in P. falciparum-infected erythrocytes could be proposed as appropriate proteins for the aforementioned aims. Accordingly, this review highlights and proposes different proteins identified using proteomic approaches as promising markers in the diagnosis and vaccination of P. falciparum. It seems that most of the candidates identified in this study were able to elicit immune responses in the P. falciparum-infected hosts and they also played major roles in the life cycle, pathogenicity and key pathways of this parasite.
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7
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Babele P, Kumar RB, Rajoria S, Rashid F, Malakar D, Bhagyawant SS, Kamboj DV, Alam SI. Putative serum protein biomarkers for epsilon toxin exposure in mouse model using LC-MS/MS analysis. Anaerobe 2020; 63:102209. [PMID: 32387808 DOI: 10.1016/j.anaerobe.2020.102209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/21/2020] [Accepted: 05/01/2020] [Indexed: 11/17/2022]
Abstract
Epsilon toxin (ETX), produced by Clostridium perfringens Type B or type D strains, is a potential biological and toxin warfare (BTW) agent, largely for its very high toxicity. The toxin is implicated in several animal diseases. Using LC-MS/MS analysis, we report here elucidation of putative serum maker proteins for ETX exposure with an objective of the early diagnosis of intoxication. Of 166 consensus proteins (488 peptides), showing ETX-induced alterations, 119 proteins exhibited increase and 47 proteins showed decreased abundance in serum, as revealed by SWATH (DIA) acquisition on LC-MS/MS and label free quantitative analysis of control and test samples. Complement and coagulation cascade, nitrogen metabolism, negative regulation of peptidase activity, and response to ROS were among the biological processes and pathways perturbed by the ETX exposure. Interaction network indicated enzyme inhibitor activity, detoxification of ROS, and steroid binding functions were the major interaction networks for the proteins with increased abundance, while, hemostasis and structural molecule activity were the prominent networks for the down-regulated proteins. Validation studies were carried out by immunoprecipitation, ELISA, and Western blot analysis of selected proteins to demonstrate diagnostic potential of the putative marker proteins of ETX exposure.
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Affiliation(s)
- Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Sakshi Rajoria
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Faraz Rashid
- Sciex, 121 DHR, Udyog Vihar, Gurugram, Haryana, India
| | - Dipankar Malakar
- School of Studies in Biotechnology, Jiwaji University, Gwalior, India
| | | | - Dev Vrat Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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8
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Abah SE, Burté F, Howell SA, Lagunju I, Shokunbi WA, Wahlgren M, Sodeinde O, Brown BJ, Holder AA, Fernandez-Reyes D. Depleted circulatory complement-lysis inhibitor (CLI) in childhood cerebral malaria returns to normal with convalescence. Malar J 2020; 19:167. [PMID: 32336276 PMCID: PMC7184698 DOI: 10.1186/s12936-020-03241-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 04/17/2020] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Cerebral malaria (CM), is a life-threatening childhood malaria syndrome with high mortality. CM is associated with impaired consciousness and neurological damage. It is not fully understood, as yet, why some children develop CM. Presented here is an observation from longitudinal studies on CM in a paediatric cohort of children from a large, densely-populated and malaria holoendemic, sub-Saharan, West African metropolis. METHODS Plasma samples were collected from a cohort of children with CM, severe malarial anaemia (SMA), uncomplicated malaria (UM), non-malaria positive healthy community controls (CC), and coma and anemic patients without malaria, as disease controls (DC). Proteomic two-dimensional difference gel electrophoresis (2D-DIGE) and mass spectrometry were used in a discovery cohort to identify plasma proteins that might be discriminatory among these clinical groups. The circulatory levels of identified proteins of interest were quantified by ELISA in a prospective validation cohort. RESULTS The proteome analysis revealed differential abundance of circulatory complement-lysis inhibitor (CLI), also known as Clusterin (CLU). CLI circulatory level was low at hospital admission in all children presenting with CM and recovered to normal level during convalescence (p < 0.0001). At acute onset, circulatory level of CLI in the CM group significantly discriminates CM from the UM, SMA, DC and CC groups. CONCLUSIONS The CLI circulatory level is low in all patients in the CM group at admission, but recovers through convalescence. The level of CLI at acute onset may be a specific discriminatory marker of CM. This work suggests that CLI may play a role in the pathophysiology of CM and may be useful in the diagnosis and follow-up of children presenting with CM.
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Affiliation(s)
| | - Florence Burté
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Steven A Howell
- Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ikeoluwa Lagunju
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Wuraola A Shokunbi
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Mats Wahlgren
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Olugbemiro Sodeinde
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Computer Science, Faculty of Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - Biobele J Brown
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | | | - Delmiro Fernandez-Reyes
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.
- Childhood Malaria Research Group, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria.
- Department of Computer Science, Faculty of Engineering, University College London, Gower Street, London, WC1E 6BT, UK.
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9
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Venkatesh A, Aggarwal S, Kumar S, Rajyaguru S, Kumar V, Bankar S, Shastri J, Patankar S, Srivastava S. Comprehensive proteomics investigation of P. vivax-infected human plasma and parasite isolates. BMC Infect Dis 2020; 20:188. [PMID: 32122317 PMCID: PMC7053139 DOI: 10.1186/s12879-020-4885-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 02/13/2020] [Indexed: 02/06/2023] Open
Abstract
Background In recent times, Plasmodium vivax (P. vivax) has become a serious threat to public health due to its ability to cause severe infection with fatal outcomes. Its unique biology makes it resilient to control measures that are otherwise effective against P. falciparum. A deeper understanding of P. vivax biology and pathogenesis is, therefore, essential for developing the right control strategies. Proteomics of P. falciparum has been helpful in studying disease biology and elucidating molecular mechanisms involved in the development of disease. However, unlike P. falciparum, proteomics data for P. vivax infection is minimal due to the absence of a continuous culture system. The dependence on clinical samples and animal models has drastically limited P. vivax research, creating critical knowledge gaps in our understanding of the disease. This study describes an in-depth proteomics analysis of P. vivax-infected human plasma and parasite isolates, to understand parasite biology, pathogenesis, and to identify new diagnostic targets for P. vivax malaria. Methods A mass-spectrometry- (MS) based proteomics approach (Q Exactive) was applied to analyze human plasma and parasite isolates from vivax malaria patients visiting a primary health centre in India. Additionally, a targeted proteomics assay was standardized for validating unique peptides of most recurring parasite proteins. Results Thirty-eight P. vivax proteins were detected in human plasma with high confidence. Several glycolytic enzymes were found along with hypothetical, cytoskeletal, ribosomal, and nuclear proteins. Additionally, 103 highly abundant P. vivax proteins were detected in parasite isolates. This represents the highest number of parasite proteins to be reported from clinical samples so far. Interestingly, five of these; three Plasmodium exported proteins (PVX_003545, PVX_003555 and PVX_121935), a hypothetical protein (PVX_083555) and Pvstp1 (subtelomeric transmembrane protein 1, PVX_094303) were found in both plasma and parasite isolates. Conclusions A parasite proteomics investigation is essential to understand disease pathobiology and design novel interventions. Control strategies against P. vivax also depend on early diagnosis. This work provides deeper insights into the biology of P. vivax by identifying proteins expressed by the parasite during its complex life-cycle within the human host. The study also reports antigens that may be explored as diagnostic candidates.
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Affiliation(s)
- Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Shalini Aggarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Swati Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Srushti Rajyaguru
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sheetal Bankar
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.
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10
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Tran TM, Crompton PD. Decoding the complexities of human malaria through systems immunology. Immunol Rev 2019; 293:144-162. [PMID: 31680289 DOI: 10.1111/imr.12817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022]
Abstract
The complexity of the Plasmodium parasite and its life cycle poses a challenge to our understanding of the host immune response against malaria. Studying human immune responses during natural and experimental Plasmodium infections can enhance our understanding of malaria-protective immunity and inform the design of disease-modifying adjunctive therapies and next-generation malaria vaccines. Systems immunology can complement conventional approaches to facilitate our understanding of the complex immune response to the highly dynamic malaria parasite. In this review, recent studies that used systems-based approaches to evaluate human immune responses during natural and experimental Plasmodium falciparum and Plasmodium vivax infections as well as during immunization with candidate malaria vaccines are summarized and related to each other. The potential for next-generation technologies to address the current limitations of systems-based studies of human malaria are discussed.
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Affiliation(s)
- Tuan M Tran
- Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.,Ryan White Center for Pediatric Infectious Disease and Global Health, Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
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11
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Babele P, Verma S, Kumar RB, Bhagyawant SS, Kamboj DV, Alam SI. Elucidation of protein biomarkers in plasma and urine for epsilon toxin exposure in mouse model. Anaerobe 2019; 59:76-91. [PMID: 31145997 DOI: 10.1016/j.anaerobe.2019.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 05/02/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023]
Abstract
Epsilon toxin (ETX) is the major virulence determinant of C. perfringens type B or type D strains, causing diseases in animals, besides being a listed biological and toxin warfare (BTW) agent. Keeping in mind the high lethality and the rapid onset of clinical manifestations, early diagnosis of epsilon toxin exposure is of paramount importance for implementation of appropriate medical countermeasures. Using a 2DE-MS approach, the present study is the first comprehensive proteomic elucidation of ETX-induced protein markers in the mouse model, providing putative targets for early diagnosis of ETX exposure. A total of 52 unique proteins showing ETX-induced modulations were identified in plasma and urine samples. Fibrinogen, apolipoprotein, serum amyloid protein, plasminogen, serum albumin, glutathione peroxidase, transferrin, major urinary protein 2, haptoglobin, transthyretin, and vitamin D-binding protein were among the proteins observed in more than one dataset with altered abundance after the ETX-intoxication. The predicted localization, function, and interaction of the ETX-modulated proteins in the plasma and urine indicated involvement of multiple pathways; extracellular proteins, followed by macromolecular complexes associated with blood coagulation and plasminogen activating cascade, being the most prominent among others. The putative markers elucidated here warrants further validation and can be of immense value for the early diagnosis of ETX exposure.
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Affiliation(s)
- Prabhakar Babele
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Smarti Verma
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Ravi Bhushan Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | | | - Dev Vrat Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India
| | - Syed Imteyaz Alam
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, 474002, India.
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12
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Patel SK, Rajora N, Kumar S, Sahu A, Kochar SK, Krishna CM, Srivastava S. Rapid Discrimination of Malaria- and Dengue-Infected Patients Sera Using Raman Spectroscopy. Anal Chem 2019; 91:7054-7062. [PMID: 31033270 DOI: 10.1021/acs.analchem.8b05907] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Malaria and dengue have overlapping clinical symptoms and are prevalent in the same geographic region (tropical and subtropical), hence precise diagnosis is challenging. The high mortality rate associated with both malaria and dengue could be attributed to "false", "delayed", or "missed" diagnosis. The present study thus aims to stratify malaria and dengue using Raman spectroscopy (RS). In total, 130 human sera were analyzed for model development and double-blinded testing. Principal components linear discriminant analysis (PC-LDA) of acquired RS-spectra could classify malaria and dengue with a minor overlap of 16.7%. Receiver operating characteristic (ROC) analysis of test samples showed sensitivity/specificity of 0.9529 for malaria vs healthy controls (HC) and 0.9584 for dengue vs HC. The Raman findings were complemented by mass spectroscopy (MS)-based metabolite analysis of 8 individuals, each from malaria, dengue, and HC. Several of the metabolites, including amino acids, cell-free DNA, creatinine, and bilirubin, assigned for the predominant RS-bands were also identified by MS and showed similar trends. Our data clearly indicates that RS-based serum analysis using a microprobe has immense potential for early, accurate, and automated detection and discrimination of malaria and dengue, and in the future, it could be extrapolated in field-settings combined with hand-held RS. Further, this approach might be extended to diagnose other closely related infections with similar clinical manifestations.
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Affiliation(s)
- Sandip K Patel
- Department of Biosciences and Bioengineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Nishant Rajora
- Department of Biosciences and Bioengineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Saurabh Kumar
- Department of Biosciences and Bioengineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
| | - Aditi Sahu
- Chilakapati Lab, ACTREC , Tata Memorial Center , Kharghar, Navi Mumbai 410210 , India
| | - Sanjay K Kochar
- Department of Medicine, Malaria Research Center , S.P. Medical College , Bikaner 334003 , India
| | - C Murali Krishna
- Chilakapati Lab, ACTREC , Tata Memorial Center , Kharghar, Navi Mumbai 410210 , India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , India
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13
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Bourgard C, Albrecht L, Kayano ACAV, Sunnerhagen P, Costa FTM. Plasmodium vivax Biology: Insights Provided by Genomics, Transcriptomics and Proteomics. Front Cell Infect Microbiol 2018; 8:34. [PMID: 29473024 PMCID: PMC5809496 DOI: 10.3389/fcimb.2018.00034] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 01/25/2018] [Indexed: 12/17/2022] Open
Abstract
During the last decade, the vast omics field has revolutionized biological research, especially the genomics, transcriptomics and proteomics branches, as technological tools become available to the field researcher and allow difficult question-driven studies to be addressed. Parasitology has greatly benefited from next generation sequencing (NGS) projects, which have resulted in a broadened comprehension of basic parasite molecular biology, ecology and epidemiology. Malariology is one example where application of this technology has greatly contributed to a better understanding of Plasmodium spp. biology and host-parasite interactions. Among the several parasite species that cause human malaria, the neglected Plasmodium vivax presents great research challenges, as in vitro culturing is not yet feasible and functional assays are heavily limited. Therefore, there are gaps in our P. vivax biology knowledge that affect decisions for control policies aiming to eradicate vivax malaria in the near future. In this review, we provide a snapshot of key discoveries already achieved in P. vivax sequencing projects, focusing on developments, hurdles, and limitations currently faced by the research community, as well as perspectives on future vivax malaria research.
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Affiliation(s)
- Catarina Bourgard
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Letusa Albrecht
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil.,Laboratory of Regulation of Gene Expression, Instituto Carlos Chagas, Curitiba, Brazil
| | - Ana C A V Kayano
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
| | - Per Sunnerhagen
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Fabio T M Costa
- Laboratory of Tropical Diseases, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas - UNICAMP, Campinas, Brazil
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Patankar S, Sharma S, Rathod PK, Duraisingh MT. Malaria in India: The Need for New Targets for Diagnosis and Detection of Plasmodium vivax. Proteomics Clin Appl 2018; 12:e1700024. [PMID: 29193853 DOI: 10.1002/prca.201700024] [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: 03/31/2017] [Revised: 08/28/2017] [Indexed: 11/08/2022]
Abstract
Plasmodium vivax is a protozoan parasite that is one of the causative agents of human malaria. Due to several occult features of its life cycle, P. vivax threatens to be a problem for the recent efforts toward elimination of malaria globally. With an emphasis on malaria elimination goals, the authors summarize the major gaps in P. vivax diagnosis and describe how proteomics technologies have begun to contribute toward the discovery of antigens that could be used for various technology platforms and applications. The authors suggest areas where, in the future, proteomics technologies could fill in gaps in P. vivax diagnosis that have proved difficult. The discovery of new parasite antigens, host responses, and immune signatures using proteomics technologies will be a key part of the global malaria elimination efforts.
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Affiliation(s)
- Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Shobhona Sharma
- Department of Biological Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | | | - Manoj T Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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15
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Awasthi G, Tyagi S, Kumar V, Patel SK, Rojh D, Sakrappanavar V, Kochar SK, Talukdar A, Samanta B, Das A, Srivastava S, Patankar S. A Proteogenomic Analysis of Haptoglobin in Malaria. Proteomics Clin Appl 2017; 12:e1700077. [PMID: 28960920 DOI: 10.1002/prca.201700077] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 08/08/2017] [Indexed: 12/29/2022]
Affiliation(s)
- Gauri Awasthi
- Molecular Parasitology Lab; Department of Biosciences and Bioengineering; IIT Bombay; Mumbai Maharashtra India
| | - Suchi Tyagi
- National Institute of Malaria Research; Field Unit, Civil Hospital; Nadiad Gujarat India
| | - Vipin Kumar
- Proteomics Lab; Department of Biosciences and Bioengineering; IIT Bombay; Mumbai Maharashtra India
| | - Sandip Kumar Patel
- Proteomics Lab; Department of Biosciences and Bioengineering; IIT Bombay; Mumbai Maharashtra India
| | | | - Vijeth Sakrappanavar
- Department of Medicine; Basaveshwara Medical College and Hospital; Chitradurga Karnataka India
| | | | - Arunansu Talukdar
- Medicine Department; Medical College Hospital Kolkata; Kolkata West Bengal India
| | - Biaus Samanta
- Medicine Department; Medical College Hospital Kolkata; Kolkata West Bengal India
| | - Aparup Das
- ICMR-National Institute for research in Tribal Health; Jabalpur Madhya Pradesh India
| | - Sanjeeva Srivastava
- Proteomics Lab; Department of Biosciences and Bioengineering; IIT Bombay; Mumbai Maharashtra India
| | - Swati Patankar
- Molecular Parasitology Lab; Department of Biosciences and Bioengineering; IIT Bombay; Mumbai Maharashtra India
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16
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Venkatesh A, Lahiri A, Reddy PJ, Shastri J, Bankar S, Patankar S, Srivastava S. Identification of Highly Expressed Plasmodium Vivax Proteins from Clinical Isolates Using Proteomics. Proteomics Clin Appl 2017; 12:e1700046. [PMID: 28841253 DOI: 10.1002/prca.201700046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 07/08/2017] [Indexed: 12/11/2022]
Abstract
Plasmodium vivax is the most geographically widespread species responsible for malaria in humans. Our study focused on identifying highly expressed parasite proteins using a shotgun proteomics approach. Parasites (P. vivax) are isolated from seven patient samples using saponin lysis. Protein extracts from these parasites are processed and subjected to LC-MS/MS analysis. An overall proteome coverage of 605 P. vivax proteins along with 1670 human host proteins are obtained upon combining the data from LC-MS/MS runs. While a major proportion of the P. vivax proteins are either hypothetical or involved in basic cellular activities, few proteins such as tryptophan-rich antigen (Pv-fam-a; PVX_090265), Pv-fam-d protein (PVX_101520), Plasmodium exported protein (PVX_003545), Pvstp1 (PVX_094303) and hypothetical protein (PVX_083555) are detected in more than 80% of the clinical isolates and found to be unique to P. vivax without orthologs in P. falciparum. Our proteomics study on individual parasite isolates reveals highly expressed P. vivax proteins, few of which may be good candidates for vivax malaria diagnosis due to their abundance and absence in P. falciparum. This study represents the first step towards the identification of biomarkers for P. vivax malaria. In future, their clinical diagnostic values must be explored and validated on large patient cohorts.
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Affiliation(s)
- Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Anwesha Lahiri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Jayanthi Shastri
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai
| | - Sheetal Bankar
- Department of Microbiology, T. N. Medical College and BYL Nair Hospital, Mumbai
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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17
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Ray S, Patel SK, Venkatesh A, Chatterjee G, Ansari NN, Gogtay NJ, Thatte UM, Gandhe P, Varma SG, Patankar S, Srivastava S. Quantitative Proteomics Analysis of Plasmodium vivax Induced Alterations in Human Serum during the Acute and Convalescent Phases of Infection. Sci Rep 2017; 7:4400. [PMID: 28667326 PMCID: PMC5493610 DOI: 10.1038/s41598-017-04447-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 05/15/2017] [Indexed: 12/23/2022] Open
Abstract
The radial distribution of Plasmodium vivax malaria burden has evoked enormous concern among the global research community. In this study, we have investigated the serum proteome alterations in non-severe vivax malaria patients before and during patient recuperation starting from the early febrile to the defervescence and convalescent stages of the infection. We have also performed an extensive quantitative proteomics analysis to compare the serum proteome profiles of vivax malaria patients with low (LPVM) and moderately-high (MPVM) parasitemia with healthy community controls. Interestingly, some of the serum proteins such as Serum amyloid A, Apolipoprotein A1, C-reactive protein, Titin and Haptoglobin, were found to be sequentially altered with respect to increased parasite counts. Analysis of a longitudinal cohort of malaria patients indicated reversible alterations in serum levels of some proteins such as Haptoglobin, Apolipoprotein E, Apolipoprotein A1, Carbonic anhydrase 1, and Hemoglobin subunit alpha upon treatment; however, the levels of a few other proteins did not return to the baseline even during the convalescent phase of the infection. Here we present the first comprehensive serum proteomics analysis of vivax malaria patients with different levels of parasitemia and during the acute and convalescent phases of the infection.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Department of Clinical Biochemistry, Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, United Kingdom
| | - Sandip K Patel
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Apoorva Venkatesh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Gangadhar Chatterjee
- Dept of Biochemistry, Grant Govt Medical College and Sir JJ Group of Hospitals, Byculla, Mumbai, 400008, India
| | - Naziya N Ansari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Nithya J Gogtay
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Urmila M Thatte
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Prajakta Gandhe
- Departments of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai, 400012, India
| | - Santosh G Varma
- Dept of Biochemistry, Grant Govt Medical College and Sir JJ Group of Hospitals, Byculla, Mumbai, 400008, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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18
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Rai V, Muthuraj M, Gandhi MN, Das D, Srivastava S. Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae. Sci Rep 2017; 7:45732. [PMID: 28378827 PMCID: PMC5381106 DOI: 10.1038/srep45732] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
To understand the post-transcriptional molecular mechanisms attributing to oleaginousness in microalgae challenged with nitrogen starvation (N-starvation), the longitudinal proteome dynamics of Chlorella sp. FC2 IITG was investigated using multipronged quantitative proteomics and multiple reaction monitoring assays. Physiological data suggested a remarkably enhanced lipid accumulation with concomitant reduction in carbon flux towards carbohydrate, protein and chlorophyll biosynthesis. The proteomics-based investigations identified the down-regulation of enzymes involved in chlorophyll biosynthesis (porphobilinogen deaminase) and photosynthetic carbon fixation (sedoheptulose-1,7 bisphosphate and phosphoribulokinase). Profound up-regulation of hydroxyacyl-ACP dehydrogenase and enoyl-ACP reductase ascertained lipid accumulation. The carbon skeletons to be integrated into lipid precursors were regenerated by glycolysis, β-oxidation and TCA cycle. The enhanced expression of glycolysis and pentose phosphate pathway enzymes indicates heightened energy needs of FC2 cells for the sustenance of N-starvation. FC2 cells strategically reserved nitrogen by incorporating it into the TCA-cycle intermediates to form amino acids; particularly the enzymes involved in the biosynthesis of glutamate, aspartate and arginine were up-regulated. Regulation of arginine, superoxide dismutase, thioredoxin-peroxiredoxin, lipocalin, serine-hydroxymethyltransferase, cysteine synthase, and octanoyltransferase play a critical role in maintaining cellular homeostasis during N-starvation. These findings may provide a rationale for genetic engineering of microalgae, which may enable synchronized biomass and lipid synthesis.
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Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Wadhwani Research Center for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Muthusivaramapandian Muthuraj
- Department of Biosciences and Bioengineering, Centre for Energy, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Mayuri N. Gandhi
- Centre for Research in Nanotechnology & Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debasish Das
- Department of Biosciences and Bioengineering, Centre for Energy, Indian Institute of Technology Guwahati, Assam 781039, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, Powai - 400067, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Wadhwani Research Center for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, Powai - 400067, India
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19
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Mukherjee S, Bandyopadhyay A. Proteomics in India: the clinical aspect. Clin Proteomics 2016; 13:21. [PMID: 27822170 PMCID: PMC5097398 DOI: 10.1186/s12014-016-9122-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 08/12/2016] [Indexed: 02/07/2023] Open
Abstract
Proteomics has emerged as a highly promising bioanalytical technique in various aspects of applied biological research. In Indian academia, proteomics research has grown remarkably over the last decade. It is being extensively used for both basic as well as translation research in the areas of infectious and immune disorders, reproductive disorders, cardiovascular diseases, diabetes, eye disorders, human cancers and hematological disorders. Recently, some seminal works on clinical proteomics have been reported from several laboratories across India. This review aims to shed light on the increasing use of proteomics in India in a variety of biological conditions. It also highlights that India has the expertise and infrastructure needed for pursuing proteomics research in the country and to participate in global initiatives. Research in clinical proteomics is gradually picking up pace in India and its future seems very bright.
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Affiliation(s)
- Somaditya Mukherjee
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
| | - Arun Bandyopadhyay
- Cell Biology and Physiology Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata, 700032 India
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20
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Venkatesh A, Patel SK, Ray S, Shastri J, Chatterjee G, Kochar SK, Patankar S, Srivastava S. Proteomics ofPlasmodium vivaxmalaria: new insights, progress and potential. Expert Rev Proteomics 2016; 13:771-82. [DOI: 10.1080/14789450.2016.1210515] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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21
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Clinicopathological Analysis and Multipronged Quantitative Proteomics Reveal Oxidative Stress and Cytoskeletal Proteins as Possible Markers for Severe Vivax Malaria. Sci Rep 2016; 6:24557. [PMID: 27090372 PMCID: PMC4835765 DOI: 10.1038/srep24557] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 03/30/2016] [Indexed: 02/04/2023] Open
Abstract
In Plasmodium vivax malaria, mechanisms that trigger transition from uncomplicated to fatal severe infections are obscure. In this multi-disciplinary study we have performed a comprehensive analysis of clinicopathological parameters and serum proteome profiles of vivax malaria patients with different severity levels of infection to investigate pathogenesis of severe malaria and identify surrogate markers of severity. Clinicopathological analysis and proteomics profiling has provided evidences for the modulation of diverse physiological pathways including oxidative stress, cytoskeletal regulation, lipid metabolism and complement cascades in severe malaria. Strikingly, unlike severe falciparum malaria the blood coagulation cascade was not found to be affected adversely in acute P. vivax infection. To the best of our knowledge, this is the first comprehensive proteomics study, which identified some possible cues for severe P. vivax infection. Our results suggest that Superoxide dismutase, Vitronectin, Titin, Apolipoprotein E, Serum amyloid A, and Haptoglobin are potential predictive markers for malaria severity.
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22
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Elphinstone RE, Riley F, Lin T, Higgins S, Dhabangi A, Musoke C, Cserti-Gazdewich C, Regan RF, Warren HS, Kain KC. Dysregulation of the haem-haemopexin axis is associated with severe malaria in a case-control study of Ugandan children. Malar J 2015; 14:511. [PMID: 26691827 PMCID: PMC4687388 DOI: 10.1186/s12936-015-1028-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/02/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Malaria is associated with haemolysis and the release of plasma haem. Plasma haem can cause endothelial injury and organ dysfunction, and is normally scavenged by haemopexin to limit toxicity. It was hypothesized that dysregulation of the haem-haemopexin pathway contributes to severe and fatal malaria infections. METHODS Plasma levels of haemin (oxidized haem), haemopexin, haptoglobin, and haemoglobin were quantified in a case-control study of Ugandan children with Plasmodium falciparum malaria. Levels at presentation were compared in children with uncomplicated malaria (UM; n = 29), severe malarial anaemia (SMA; n = 27) or cerebral malaria (CM; n = 31), and evaluated for utility in predicting fatal (n = 19) vs non-fatal (n = 39) outcomes in severe disease. A causal role for haemopexin was assessed in a pre-clinical model of experimental cerebral malaria (ECM), following disruption of mouse haemopexin gene (hpx). Analysis was done using Kruskall Wallis tests, Mann-Whitney tests, log-rank tests for survival, and repeated measures ANOVA. RESULTS In Ugandan children presenting with P. falciparum malaria, haemin levels were higher and haemopexin levels were lower in SMA and CM compared to children with UM (haemin, p < 0.01; haemopexin, p < 0.0001). Among all cases of severe malaria, elevated levels of haemin and cell-free haemoglobin at presentation were associated with subsequent mortality (p < 0.05). Compared to ECM-resistant BALB/c mice, susceptible C57BL/6 mice had lower circulating levels of haemopexin (p < 0.01), and targeted deletion of the haemopexin gene, hpx, resulted in increased mortality compared to their wild type littermates (p < 0.05). CONCLUSIONS These data indicate that plasma levels of haemin and haemopexin measured at presentation correlate with malaria severity and levels of haemin and cell-free haemoglobin predict outcome in paediatric severe malaria. Mechanistic studies in the ECM model support a causal role for the haem-haemopexin axis in ECM pathobiology.
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Affiliation(s)
- Robyn E Elphinstone
- Sandra Rotman Centre for Global Health, University Health Network-Toronto General Hospital, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Tropical Disease Unit, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Frank Riley
- Infectious Disease Unit, Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA.
| | - Tian Lin
- Infectious Disease Unit, Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA.
| | - Sarah Higgins
- Sandra Rotman Centre for Global Health, University Health Network-Toronto General Hospital, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Tropical Disease Unit, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Aggrey Dhabangi
- Makerere University College of Health Sciences, Kampala, Uganda.
| | - Charles Musoke
- Makerere University College of Health Sciences, Kampala, Uganda.
| | - Christine Cserti-Gazdewich
- Laboratory Medicine Program (Transfusion Medicine), University Health Network/University of Toronto, Toronto, ON, Canada.
| | - Raymond F Regan
- Department of Emergency Medicine, Thomas Jefferson University, Philadelphia, PA, USA.
| | - H Shaw Warren
- Infectious Disease Unit, Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA.
| | - Kevin C Kain
- Sandra Rotman Centre for Global Health, University Health Network-Toronto General Hospital, Toronto, ON, Canada. .,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada. .,Tropical Disease Unit, Department of Medicine, University of Toronto, Toronto, ON, Canada.
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Sharma S, Ray S, Mukherjee S, Moiyadi A, Sridhar E, Srivastava S. Multipronged quantitative proteomic analyses indicate modulation of various signal transduction pathways in human meningiomas. Proteomics 2015; 15:394-407. [PMID: 25413884 DOI: 10.1002/pmic.201400328] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/23/2014] [Accepted: 11/12/2014] [Indexed: 12/17/2022]
Abstract
Meningiomas (MGs) are frequent tumors of the CNS originating from the meningeal layers of the spinal cord and the brain. In this study, comparative tissue proteomic analysis of low and high grades of MGs was performed by using iTRAQ-based quantitative proteomics in combination with ESI-quadrupole-TOF and Q-Exactive MS, and results were validated by employing ELISA. Combining the results obtained from two MS platforms, we were able to identify overall 4308 proteins (1% false discover rate), among which 2367 exhibited differential expression (more than and equal to 2 peptide and ≥ 1.5-fold in at least one grade) in MGs. Several differentially expressed proteins were found to be associated with diverse signaling pathways, including integrin, Wnt, Ras, epidermal growth factor receptor, and FGR signaling. Proteins, such as vinculin or histones, which act as the signaling activators to initiate multiple signaling pathways, were found to be upregulated in MGs. Quite a few candidates, such as protein S-100A6, aldehyde dehydrogenase mitochondrial, AHNAK, cytoskeleton-associated protein 4, and caveolin, showed sequential increase in low- and high-grade MGs, whereas differential expressions of collagen alpha-1 (VI), protein S100-A9, 14 kDa phosphohistidine phosphatase, or transgelin-2 were found to be grade specific. Our findings provide new insights regarding the association of various signal transduction pathways in MG pathogenesis and may introduce new opportunities for the early detection and prognosis of MGs.
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Affiliation(s)
- Samridhi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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24
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Multifaceted Role of Heme during Severe Plasmodium falciparum Infections in India. Infect Immun 2015; 83:3793-9. [PMID: 26169278 DOI: 10.1128/iai.00531-15] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 07/03/2015] [Indexed: 12/20/2022] Open
Abstract
Several immunomodulatory factors are involved in malaria pathogenesis. Among them, heme has been shown to play a role in the pathophysiology of severe malaria in rodents, but its role in human severe malaria remains unclear. Circulating levels of total heme and its main scavenger, hemopexin, along with cytokine/chemokine levels and biological parameters, including hemoglobin and creatinine levels, as well as transaminase activities, were measured in the plasma of 237 Plasmodium falciparum-infected patients living in the state of Odisha, India, where malaria is endemic. All patients were categorized into well-defined groups of mild malaria, cerebral malaria (CM), or severe noncerebral malaria, which included acute renal failure (ARF) and hepatopathy. Our results show a significant increase in total plasma heme levels with malaria severity, especially for CM and malarial ARF. Spearman rank correlation and canonical correlation analyses have shown a correlation between total heme, hemopexin, interleukin-10, tumor necrosis factor alpha, gamma interferon-induced protein 10 (IP-10), and monocyte chemotactic protein 1 (MCP-1) levels. In addition, canonical correlations revealed that heme, along with IP-10, was associated with the CM pathophysiology, whereas both IP-10 and MCP-1 together with heme discriminated ARF. Altogether, our data indicate that heme, in association with cytokines and chemokines, is involved in the pathophysiology of both CM and ARF but through different mechanisms.
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Grover Shah V, Ray S, Karlsson R, Srivastava S. Calibration-free concentration analysis of protein biomarkers in human serum using surface plasmon resonance. Talanta 2015; 144:801-8. [PMID: 26452893 DOI: 10.1016/j.talanta.2015.06.074] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Revised: 06/24/2015] [Accepted: 06/25/2015] [Indexed: 10/23/2022]
Abstract
In complex biological samples such as serum, determination of specific and active concentration of target proteins, independent of a calibration curve, will be valuable in many applications. Calibration-free concentration analysis (CFCA) is a surface plasmon resonance (SPR)-based label-free approach, which calculates active concentration of proteins using their known diffusion coefficient and observed changes in binding rates at different flow rates under diffusion-limited conditions. Here, for the first time we demonstrate the application of CFCA for determining protein biomarker abundance, specifically serum amyloid A (SAA), directly in the serum samples of patients suffering from different infectious and non-infectious diseases. The assay involves preparation of appropriate reaction surfaces by immobilizing antibodies on CM5 chips via amine coupling followed by serum sample preparation and injection over activated and reference surfaces at flow-rates of 5 and 100 μL/min. The system was validated in healthy and diseased (infectious and non-infectious) serum samples by quantifying two different proteins: β2-microglobulin (β2M) and SAA. All concentration assays were performed for nearly 100 serum samples, which showed reliable quantification in unattended runs with high accuracy and sensitivity. The method could detect the serum β2M to as low as 13 ng/mL in 1000-fold serum dilution, indicating the possible utility of this approach to detect low abundance protein biomarkers in body fluids. Applying the CFCA approach, significant difference in serum abundance of SAA was identified in diseased subjects as compared to the healthy controls, which correlated well with our previous proteomic investigations. Estimation of SAA concentration for a subset of healthy and diseased sera was also performed using ELISA, and the trend was observed to be similar in both SPR assay and ELISA. The reproducibility of CFCA in various serum samples made the interpretation of assay simple and reliable. This study illustrates a significant step forward in rapid monitoring of several protein markers in serum samples, with utility in biomarker validation and other therapeutic applications.
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Affiliation(s)
- Veenita Grover Shah
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India; Wipro GE Healthcare, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | | | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Autoantibody profile of patients infected with knowlesi malaria. Clin Chim Acta 2015; 448:33-8. [PMID: 26086445 DOI: 10.1016/j.cca.2015.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 05/05/2015] [Accepted: 06/03/2015] [Indexed: 01/13/2023]
Abstract
BACKGROUND Autoantibodies or antibodies against self-antigens are produced either during physiological processes to maintain homeostasis or pathological process such as trauma and infection. Infection with parasites including Plasmodium has been shown to generally induce elevated self-antibody (autoantibody) levels. Plasmodium knowlesi is increasingly recognized as one of the most important emerging human malaria in Southeast Asia that can cause severe infection leading to mortality. Autoimmune-like phenomena have been hypothesized to play a role in the protective immune responses in malaria infection. METHODS We studied the autoantibody profile from serum of eleven patients diagnosed with P. knowlesi. Autoantigen arrays were used to elucidate the autoantibody repertoire of P. knowlesi infected patients. The patented OGT Discovery Array with 1636 correctly folded antigen was employed. RESULTS Analysis of the patient versus control sera gave us 24 antigens with high reactivity with serum antibodies. CONCLUSIONS Understanding the autoantibody profile of malarious patients infected with P. knowlesi would help to further understand the host-parasite interaction, host immune response and disease pathogenesis. These reactive antigens may serve as potential biomarkers for cases of asymptomatic malaria and mild malaria or predictive markers for severe malaria.
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Ray S, Kumar V, Bhave A, Singh V, Gogtay NJ, Thatte UM, Talukdar A, Kochar SK, Patankar S, Srivastava S. Proteomic analysis of Plasmodium falciparum induced alterations in humans from different endemic regions of India to decipher malaria pathogenesis and identify surrogate markers of severity. J Proteomics 2015; 127:103-13. [PMID: 25982387 DOI: 10.1016/j.jprot.2015.04.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 04/21/2015] [Accepted: 04/29/2015] [Indexed: 11/17/2022]
Abstract
India significantly contributes to the global malaria burden and has the largest population in the world at risk of malaria. This study aims to analyze alterations in the human serum proteome as a consequence of non-severe and severe infections by the malaria parasite Plasmodium falciparum to identify markers related to disease severity and to obtain mechanistic insights about disease pathogenesis and host immune responses. In discovery phase of the study, a comprehensive quantitative proteomic analysis was performed using gel-based (2D-DIGE) and gel-free (iTRAQ) techniques on two independent mass spectrometry platforms (ESI-Q-TOF and Q-Exactive mass spectrometry), and selected targets were validated by ELISA. Proteins showing altered serum abundance in falciparum malaria patients revealed the modulation of different physiological pathways including chemokine and cytokine signaling, IL-12 signaling and production in macrophages, complement cascades, blood coagulation, and protein ubiquitination pathways. Some muscle related and cytoskeletal proteins such as titin and galectin-3-binding protein were found to be up-regulated in severe malaria patients. Hemoglobin levels and platelet counts were also found to be drastically lower in severe malaria patients. Identified proteins including serum amyloid A, C-reactive protein, apolipoprotein E and haptoglobin, which exhibited sequential alterations in their serum abundance in different severity levels of malaria, could serve as potential predictive markers for disease severity. To the best of our information, we report here the first comprehensive analysis describing the serum proteomic alterations observed in severe P. falciparum infected patients from different malaria endemic regions of India. This article is part of a Special Issue entitled: Proteomics in India.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vipin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Amruta Bhave
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Vaidhvi Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nithya J Gogtay
- Department of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai 400012, India
| | - Urmila M Thatte
- Department of Clinical Pharmacology, Seth GS Medical College & KEM Hospital, Parel, Mumbai 400012, India
| | - Arunansu Talukdar
- Department of Medicine, Medical College and Hospital Kolkata, 88, College Street, Kolkata 700073, India
| | - Sanjay K Kochar
- Department of Medicine, Malaria Research Center, S.P. Medical College, Bikaner 334003, India
| | - Swati Patankar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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Reddy PJ, Sinha S, Ray S, Sathe GJ, Chatterjee A, Prasad TSK, Dhali S, Srikanth R, Panda D, Srivastava S. Comprehensive analysis of temporal alterations in cellular proteome of Bacillus subtilis under curcumin treatment. PLoS One 2015; 10:e0120620. [PMID: 25874956 PMCID: PMC4397091 DOI: 10.1371/journal.pone.0120620] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Accepted: 02/05/2015] [Indexed: 11/18/2022] Open
Abstract
Curcumin is a natural dietary compound with antimicrobial activity against various gram positive and negative bacteria. This study aims to investigate the proteome level alterations in Bacillus subtilis due to curcumin treatment and identification of its molecular/cellular targets to understand the mechanism of action. We have performed a comprehensive proteomic analysis of B. subtilis AH75 strain at different time intervals of curcumin treatment (20, 60 and 120 min after the drug exposure, three replicates) to compare the protein expression profiles using two complementary quantitative proteomic techniques, 2D-DIGE and iTRAQ. To the best of our knowledge, this is the first comprehensive longitudinal investigation describing the effect of curcumin treatment on B. subtilis proteome. The proteomics analysis revealed several interesting targets such UDP-N-acetylglucosamine 1-carboxyvinyltransferase 1, putative septation protein SpoVG and ATP-dependent Clp protease proteolytic subunit. Further, in silico pathway analysis using DAVID and KOBAS has revealed modulation of pathways related to the fatty acid metabolism and cell wall synthesis, which are crucial for cell viability. Our findings revealed that curcumin treatment lead to inhibition of the cell wall and fatty acid synthesis in addition to differential expression of many crucial proteins involved in modulation of bacterial metabolism. Findings obtained from proteomics analysis were further validated using 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) assay for respiratory activity, resazurin assay for metabolic activity and membrane integrity assay by potassium and inorganic phosphate leakage measurement. The gene expression analysis of selected cell wall biosynthesis enzymes has strengthened the proteomics findings and indicated the major effect of curcumin on cell division.
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Affiliation(s)
- Panga Jaipal Reddy
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sneha Sinha
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Gajanan J. Sathe
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
- Manipal University, Madhav Nagar,Manipal, India
| | - T. S. Keshava Prasad
- Institute of Bioinformatics, International Tech Park, Whitefield, Bangalore, India
| | - Snigdha Dhali
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Rapole Srikanth
- Proteomics Laboratory, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- * E-mail:
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Zingde SM. Has Proteomics come of age in India? J Proteomics 2015; 127:3-6. [PMID: 25748142 DOI: 10.1016/j.jprot.2015.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 02/25/2015] [Indexed: 12/24/2022]
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Chen Y, Chan CK, Kerishnan JP, Lau YL, Wong YL, Gopinath SC. Identification of circulating biomarkers in sera of Plasmodium knowlesi-infected malaria patients--comparison against Plasmodium vivax infection. BMC Infect Dis 2015; 15:49. [PMID: 25656928 PMCID: PMC4336705 DOI: 10.1186/s12879-015-0786-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Accepted: 01/27/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Plasmodium knowlesi was identified as the fifth major malaria parasite in humans. It presents severe clinical symptoms and leads to mortality as a result of hyperparasitemia in a short period of time. This study aimed to improve the current understanding of P. knowlesi and identify potential biomarkers for knowlesi malaria. METHODS In the present study, we have employed two-dimensional gel electrophoresis-coupled immunoblotting techniques and mass spectrometry to identify novel circulating markers in sera from P. knowlesi-infected patients. Specifically, we have compared serum protein profiles from P. knowlesi-infected patients against those of healthy or P. vivax-infected individuals. RESULTS We identified several immunoreactive proteins in malarial-infected subjects, including alpha-2-HS glycoprotein (AHSG), serotransferrin (TF), complement C3c (C3), hemopexin (HPX), zinc-2-alpha glycoprotein (ZAG1), apolipoprotein A1 (Apo-A1), haptoglobin (HAP), and alpha-1-B-glycoprotein (A1BG). However, only TF and HPX displayed enhanced antigenicity and specificity, suggesting that they might represent valid markers for detecting P. knowlesi infection. Additionally, six P. knowlesi-specific antigens were identified (K15, K16, K28, K29, K30, and K38). Moreover, although HAP antigenicity was observed during P. vivax infection, it was undetectable in P. knowlesi-infected subjects. CONCLUSIONS We have demonstrated the application of immunoproteomics approach to identify potential candidate biomarkers for knowlesi malaria infection.
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Affiliation(s)
- Yeng Chen
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Oral Cancer Research and Coordinating Center, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia.
| | - Choon K Chan
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Gelugor, Penang, Malaysia.
| | - Jesinda P Kerishnan
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yee L Lau
- Department of Parasitology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yin-Ling Wong
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Subash Cb Gopinath
- Department of Oral Biology & Biomedical Sciences, Faculty of Dentistry, University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Institute of Nano Electronic Engineering (INEE), & School of Bioprocess Engineering, Universiti Malaysia Perlis, Kangar, Perlis, Malaysia.
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A comprehensive proteomic analysis of totarol induced alterations in Bacillus subtilis by multipronged quantitative proteomics. J Proteomics 2015; 114:247-62. [DOI: 10.1016/j.jprot.2014.10.025] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 09/28/2014] [Accepted: 10/20/2014] [Indexed: 12/25/2022]
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32
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Yang WE, Woods CW, Tsalik EL. Host-Based Diagnostics for Detection and Prognosis of Infectious Diseases. J Microbiol Methods 2015. [DOI: 10.1016/bs.mim.2015.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Orimadegun AE, Orimadegun BE. Serum Apolipoprotein-A1 and Cholesterol Levels in Nigerian Children with Plasmodium falciparum Infection. Med Princ Pract 2015; 24:318-24. [PMID: 26021459 PMCID: PMC5588239 DOI: 10.1159/000430812] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2014] [Accepted: 04/20/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE This study was carried out to determine whether or not Plasmodium falciparum malaria infection significantly affected apolipoprotein-A1 and cholesterol levels and if apolipoprotein-A1 correlated with the malaria severity in children younger than 5 years old. SUBJECTS AND METHODS Two hundred and fifty-five children, 170 of whom had microscopically confirmed P. falciparum infection, i.e. 85 cases of uncomplicated malaria (UM) and 85 of complicated malaria (CM), and 85 healthy controls were enrolled in this study. Serum levels of apolipoprotein-A1, total cholesterol, high-density lipoprotein (HDL), low-density lipoprotein (LDL) and triglycerides were determined. These levels were compared among the malaria and control groups, using ANOVA and post hoc analyses at p = 0.05. RESULTS There were significant differences in the mean serum levels of apolipoprotein-A1 (UM: 104.5 ± 38.1 mg/dl, CM: 90.9 ± 33.3 mg/dl and controls: 129.7 ± 48.3 mg/dl; p < 0.001), total cholesterol (UM: 138.8 ± 62.9 mg/dl, CM: 121.2 ± 55.2 mg/dl and controls: 155.1 ± 69.8 mg/dl; p = 0.002) and LDL (UM: 98.2 ± 55.5 mg/dl, CM: 84.3 ± 47.4 mg/dl and controls: 122.7 ± 69.4 mg/dl; p < 0.001). Post hoc analyses revealed that children with UM and CM had significantly lower levels of apolipoprotein-A1, cholesterol, HDL and LDL than controls but that there was no difference between the 2 malaria groups. Reductions in levels of lipids and apolipoprotein-A1 were worse in CM than in UM. CONCLUSION Altered levels of serum lipids with CM were associated with a reduction in apolipoprotein-A1. These findings have potential diagnostic utility for the management of malaria.
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Affiliation(s)
- Adebola Emmanuel Orimadegun
- Institute of Child Health, University of Ibadan, Nigeria
- *Adebola E. Orimadegun, Institute of Child Health, College of Medicine, University of Ibadan, Ibadan (Nigeria), E-Mail
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Plasmodium vivax trophozoite-stage proteomes. J Proteomics 2014; 115:157-76. [PMID: 25545414 DOI: 10.1016/j.jprot.2014.12.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 11/17/2014] [Accepted: 12/21/2014] [Indexed: 02/06/2023]
Abstract
UNLABELLED Plasmodium vivax is the causative infectious agent of 80-300 million annual cases of malaria. Many aspects of this parasite's biology remain unknown. To further elucidate the interaction of P. vivax with its Saimiri boliviensis host, we obtained detailed proteomes of infected red blood cells, representing the trophozoite-enriched stage of development. Data from two of three biological replicate proteomes, emphasized here, were analyzed using five search engines, which enhanced identifications and resulted in the most comprehensive P. vivax proteomes to date, with 1375 P. vivax and 3209 S. boliviensis identified proteins. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with P. vivax's known reticulocyte host-cell specificity. A majority of the host and pathogen proteins identified belong to specific functional categories, and several parasite gene families, while 33% of the P. vivax proteins have no reported function. Hemoglobin was significantly oxidized in both proteomes, and additional protein oxidation and nitration was detected in one of the two proteomes. Detailed analyses of these post-translational modifications are presented. The proteins identified here significantly expand the known P. vivax proteome and complexity of available host protein functionality underlying the host-parasite interactive biology, and reveal unsuspected oxidative modifications that may impact protein function. BIOLOGICAL SIGNIFICANCE Plasmodium vivax malaria is a serious neglected disease, causing an estimated 80 to 300 million cases annually in 95 countries. Infection can result in significant morbidity and possible death. P. vivax, unlike the much better-studied Plasmodium falciparum species, cannot be grown in long-term culture, has a dormant form in the liver called the hypnozoite stage, has a reticulocyte host-cell preference in the blood, and creates caveolae vesicle complexes at the surface of the infected reticulocyte membranes. Studies of stage-specific P. vivax expressed proteomes have been limited in scope and focused mainly on pathogen proteins, thus limiting understanding of the biology of this pathogen and its host interactions. Here three P. vivax proteomes are reported from biological replicates based on purified trophozoite-infected reticulocytes from different Saimiri boliviensis infections (the main non-human primate experimental model for P. vivax biology and pathogenesis). An in-depth analysis of two of the proteomes using 2D LC/MS/MS and multiple search engines identified 1375 pathogen proteins and 3209 host proteins. Numerous functional categories of both host and pathogen proteins were identified, including several known P. vivax protein family members (e.g., PHIST, eTRAMP and VIR), and 33% of protein identifications were classified as hypothetical. Ribosome subunit proteins were noted for both P. vivax and S. boliviensis, consistent with this parasite species' known reticulocyte host-cell specificity. In two biological replicates analyzed for post-translational modifications, hemoglobin was extensively oxidized, and various other proteins were also oxidized or nitrated in one of the two replicates. The cause of such protein modification remains to be determined but could include oxidized heme and oxygen radicals released from the infected red blood cell's parasite-induced acidic digestive vacuoles. In any case, the data suggests the presence of distinct infection-specific conditions whereby both the pathogen and host infected red blood cell proteins may be subject to significant oxidative stress.
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Sharma S, Ray S, Moiyadi A, Sridhar E, Srivastava S. Quantitative proteomic analysis of meningiomas for the identification of surrogate protein markers. Sci Rep 2014; 4:7140. [PMID: 25413266 PMCID: PMC5382771 DOI: 10.1038/srep07140] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 09/15/2014] [Indexed: 12/11/2022] Open
Abstract
Meningiomas are the most common non-glial tumors of the brain and spine. Pathophysiology and definite histological grading of meningiomas are frequently found to be deceptive due to their unusual morphological features and locations. Here for the first time we report a comprehensive serum proteomic analysis of different grades of meningiomas by using multiple quantitative proteomic and immunoassay-based approaches to obtain mechanistic insights about disease pathogenesis and identify grade specific protein signatures. In silico functional analysis revealed modulation of different vital physiological pathways including complement and coagulation cascades, metabolism of lipids and lipoproteins, immune signaling, cell growth and apoptosis and integrin signaling in meningiomas. ROC curve analysis demonstrated apolipoprotein E and A-I and hemopexin as efficient predictors for meningiomas. Identified proteins like vimentin, alpha-2-macroglobulin, apolipoprotein B and A-I and antithrombin-III, which exhibited a sequential increase in different malignancy grades of meningiomas, could serve as potential predictive markers.
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Affiliation(s)
- Samridhi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Aliasgar Moiyadi
- Department of Neurosurgery, Advanced Center for Treatment Research and Education in Cancer, Tata Memorial Center, Kharghar, Navi Mumbai 410210, India
| | - Epari Sridhar
- Department of Pathology, Tata Memorial Hospital, Mumbai 400012, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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Dutta M, Subramani E, Taunk K, Gajbhiye A, Seal S, Pendharkar N, Dhali S, Ray CD, Lodh I, Chakravarty B, Dasgupta S, Rapole S, Chaudhury K. Mass spectrometry and bioinformatics analysis data. Data Brief 2014. [PMID: 26217699 PMCID: PMC4459760 DOI: 10.1016/j.dib.2014.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
2DE and 2D-DIGE based proteomics analysis of serum from women with endometriosis revealed several proteins to be dysregulated. A complete list of these proteins along with their mass spectrometry data and subsequent bioinformatics analysis are presented here. The data is related to “Investigation of serum proteome alterations in human endometriosis” by Dutta et al. [1].
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Affiliation(s)
- Mainak Dutta
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Elavarasan Subramani
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | | | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Chaitali Datta Ray
- Institute of Post Graduate Medical Education & Research, Obstetrics & Gynecology, Kolkata, West Bengal, India
| | - Indrani Lodh
- Institute of Reproductive Medicine, Sector-III, Kolkata, West Bengal, India
| | | | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
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Dutta M, Subramani E, Taunk K, Gajbhiye A, Seal S, Pendharkar N, Dhali S, Ray CD, Lodh I, Chakravarty B, Dasgupta S, Rapole S, Chaudhury K. Investigation of serum proteome alterations in human endometriosis. J Proteomics 2014; 114:182-96. [PMID: 25449831 DOI: 10.1016/j.jprot.2014.10.021] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 10/23/2014] [Accepted: 10/29/2014] [Indexed: 12/26/2022]
Abstract
UNLABELLED Endometriosis is a common benign gynecological disease, characterized by proliferation of functional endometrial glands and stroma outside the uterine cavity. The present study involves investigation of alterations in the serum proteome of endometriosis patients compared to healthy controls using 2DE and 2D-DIGE combined with MALDI TOF/TOF-MS. Comparison of serum proteome of endometriosis patients and healthy subjects revealed 25 significant differentially expressed proteins. Gene ontology and network analysis, performed using PANTHER, DAVID, WebGestalt and STRING, revealed that the differentially expressed proteins are majorly involved in response to stimulus, immune system, metabolic, localization and cellular processes. For serum diagnostic marker identification, several robust statistical screening procedures were applied to identify the set of the most significant proteins responsible for successful diagnosis of different endometriosis stages. Partial least squares (PLS) based marker selection tool and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to identify the most significant proteins for disease prediction. Western blotting validation in a separate cohort of patients revealed that haptoglobin (HP), Ig kappa chain C region (IGKC), alpha-1B-glycoprotein (A1BG) can be considered effective serum protein markers for the diagnosis of Stage II, III and IV endometriosis. For diagnosis of Stage I, only IGKC and HP seemed promising. BIOLOGICAL SIGNIFICANCE Globally, about 12 in 100 women of reproductive age are diagnosed with endometriosis. The pathogenesis of the disease still remains unclear, leading to non-specific therapeutic approaches for disease management. Moreover, there is a delay of 8-12years in correct diagnosis after the initial onset of symptoms leading to a considerable impact on the woman's lifestyle. Also, the gold standard for diagnosis of endometriosis, laparoscopy, is an invasive procedure. The value of a noninvasive or semi-invasive diagnostic test for endometriosis with easily accessible fluids such as plasma, serum, urine, and saliva is, therefore, rightfully recognized. The present study is expected to considerably improve the understanding of the disease pathogenesis along with improved diagnostics and therapeutic approaches leading to better management of the disease.
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Affiliation(s)
- Mainak Dutta
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Elavarasan Subramani
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Akshada Gajbhiye
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | | | - Namita Pendharkar
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Snigdha Dhali
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Chaitali Datta Ray
- Institute of Post Graduate Medical Education & Research, Obstetrics & Gynecology, Kolkata, West Bengal, India
| | - Indrani Lodh
- Institute of Reproductive Medicine, Sector-III, Kolkata, West Bengal, India
| | | | - Swagata Dasgupta
- Department of Chemistry, Indian Institute of Technology, Kharagpur, West Bengal, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune, Maharashtra, India
| | - Koel Chaudhury
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, West Bengal, India.
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Identification of protein markers in patients infected with Plasmodium knowlesi, Plasmodium falciparum and Plasmodium vivax. Int J Mol Sci 2014; 15:19952-61. [PMID: 25372941 PMCID: PMC4264148 DOI: 10.3390/ijms151119952] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/08/2014] [Accepted: 10/22/2014] [Indexed: 11/17/2022] Open
Abstract
Malaria is caused by parasitic protozoans of the genus Plasmodium and is one of the most prevalent infectious diseases in tropical and subtropical regions. For this reason, effective and practical diagnostic methods are urgently needed to control the spread of malaria. The aim of the current study was to identify a panel of new malarial markers, which could be used to diagnose patients infected with various Plasmodium species, including P. knowlesi, P. vivax and P. falciparum. Sera from malaria-infected patients were pooled and compared to control sera obtained from healthy individuals using the isobaric tags for relative and absolute quantitation (iTRAQ) technique. Mass spectrometry was used to identify serum proteins and quantify their relative abundance. We found that the levels of several proteins were increased in pooled serum from infected patients, including cell adhesion molecule-4 and C-reactive protein. In contrast, the serum concentration of haptoglobin was reduced in malaria-infected individuals, which we verified by western blot assay. Therefore, these proteins might represent infectious markers of malaria, which could be used to develop novel diagnostic tools for detecting P. knowlesi, P. vivax and P. falciparum. However, these potential malarial markers will need to be validated in a larger population of infected individuals.
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Moreno-Pérez DA, Dégano R, Ibarrola N, Muro A, Patarroyo MA. Determining the Plasmodium vivax VCG-1 strain blood stage proteome. J Proteomics 2014; 113:268-280. [PMID: 25316051 DOI: 10.1016/j.jprot.2014.10.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/17/2014] [Accepted: 10/02/2014] [Indexed: 01/31/2023]
Abstract
Plasmodium vivax is the second most prevalent parasite species causing malaria in humans living in tropical and subtropical areas throughout the world. There have been few P. vivax proteomic studies to date and they have focused on using clinical isolates, given the technical difficulties concerning how to maintain an in vitro culture of this species. This study was thus focused on identifying the P. vivax VCG-1 strain proteome during its blood lifecycle through LC-MS/MS; this led to identifying 734 proteins, thus increasing the overall number reported for P. vivax to date. Some of them have previously been related to reticulocyte invasion, parasite virulence and growth and others are new molecules possibly playing a functional role during metabolic processes, as predicted by Database for Annotation, Visualization and Integrated Discovery (DAVID) functional analysis. This is the first large-scale proteomic analysis of a P. vivax strain adapted to a non-human primate model showing the parasite protein repertoire during the blood lifecycle. Database searches facilitated the in silico prediction of proteins proposed for evaluation in further experimental assays regarding their potential as pharmacologic targets or as component of a totally efficient vaccine against malaria caused by P. vivax. BIOLOGICAL SIGNIFICANCE P. vivax malaria continues being a public health problem around world. Although considerable progress has been made in understanding genome- and transcriptome-related P. vivax biology, there are few proteome studies, currently representing only 8.5% of the predicted in silico proteome reported in public databases. A high-throughput proteomic assay was used for discovering new P. vivax intra-reticulocyte asexual stage molecules taken from parasites maintained in vivo in a primate model. The methodology avoided the main problem related to standardising an in vitro culture system to obtain enough samples for protein identification and annotation. This study provides a source of potential information contributing towards a basic understanding of P. vivax biology related to parasite proteins which are of significant importance for the malaria research community.
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Affiliation(s)
- D A Moreno-Pérez
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, Colombia; Universidad del Rosario, Calle 63D No. 24-31, Bogotá, Colombia; IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.
| | - R Dégano
- Unidad de Proteómica, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.
| | - N Ibarrola
- Unidad de Proteómica, Centro de Investigación del Cáncer, CSIC-Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, Spain.
| | - A Muro
- IBSAL-CIETUS (Instituto de Investigación Biomédica de Salamanca-Centro de Investigación en Enfermedades Tropicales de la Universidad de Salamanca), Facultad de Farmacia, Universidad de Salamanca, Salamanca, Spain.
| | - M A Patarroyo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Carrera 50 No. 26-20, Bogotá, Colombia; Universidad del Rosario, Calle 63D No. 24-31, Bogotá, Colombia.
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40
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Comparative proteomics of mitosis and meiosis in Saccharomyces cerevisiae. J Proteomics 2014; 109:1-15. [DOI: 10.1016/j.jprot.2014.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 05/21/2014] [Accepted: 06/08/2014] [Indexed: 12/18/2022]
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Song SH, Han M, Choi YS, Dan KS, Yang MG, Song J, Park SS, Lee JH. Proteomic profiling of serum from patients with tuberculosis. Ann Lab Med 2014; 34:345-53. [PMID: 25187886 PMCID: PMC4151002 DOI: 10.3343/alm.2014.34.5.345] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Revised: 12/31/2013] [Accepted: 05/29/2014] [Indexed: 11/19/2022] Open
Abstract
Background Effective treatment and monitoring of tuberculosis (TB) requires biomarkers that can be easily evaluated in blood samples. The aim of this study was to analyze the serum proteome of patients with TB and to identify protein biomarkers for TB. Methods Serum samples from 26 TB patients and 31 controls were analyzed by using nano-flow ultra-performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry in data-independent mode, and protein and peptide amounts were calculated by using a label-free quantitative approach. The generated data were analyzed by using principal component analysis and partial least squares discriminant analysis, a multivariate statistical method. Results Of more than 500 proteins identified, alpha-1-antitrypsin was the most discriminative, which was 4.4 times higher in TB patients than in controls. Peptides from alpha-1-antitrypsin and antithrombin III increased in TB patients and showed a high variable importance in the projection scores and coefficient in partial least square discriminant analysis. Conclusions Sera from patients with TB had higher alpha-1-antitrypsin levels than sera from control participants. Alpha-1-antitrypsin levels may aid in the diagnosis of TB.
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Affiliation(s)
- Sang Hoon Song
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Minje Han
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Yang Seon Choi
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Ki Soon Dan
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Man Gil Yang
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea
| | - Junghan Song
- Department of Laboratory Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
| | - Sung Sup Park
- Clinical Proteomics Laboratory, Seoul National University Hospital, Seoul, Korea. ; Biomedical Research Institute and Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Jae Ho Lee
- Department of Internal Medicine, Seoul National University Bundang Hospital, Seongnam, Korea
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Bachmann J, Burté F, Pramana S, Conte I, Brown BJ, Orimadegun AE, Ajetunmobi WA, Afolabi NK, Akinkunmi F, Omokhodion S, Akinbami FO, Shokunbi WA, Kampf C, Pawitan Y, Uhlén M, Sodeinde O, Schwenk JM, Wahlgren M, Fernandez-Reyes D, Nilsson P. Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria. PLoS Pathog 2014; 10:e1004038. [PMID: 24743550 PMCID: PMC3990714 DOI: 10.1371/journal.ppat.1004038] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2013] [Accepted: 02/06/2014] [Indexed: 01/21/2023] Open
Abstract
Systemic inflammation and sequestration of parasitized erythrocytes are central processes in the pathophysiology of severe Plasmodium falciparum childhood malaria. However, it is still not understood why some children are more at risks to develop malaria complications than others. To identify human proteins in plasma related to childhood malaria syndromes, multiplex antibody suspension bead arrays were employed. Out of the 1,015 proteins analyzed in plasma from more than 700 children, 41 differed between malaria infected children and community controls, whereas 13 discriminated uncomplicated malaria from severe malaria syndromes. Markers of oxidative stress were found related to severe malaria anemia while markers of endothelial activation, platelet adhesion and muscular damage were identified in relation to children with cerebral malaria. These findings suggest the presence of generalized vascular inflammation, vascular wall modulations, activation of endothelium and unbalanced glucose metabolism in severe malaria. The increased levels of specific muscle proteins in plasma implicate potential muscle damage and microvasculature lesions during the course of cerebral malaria. Why do some malaria-infected children develop severe and lethal forms of the disease, while others only have mild forms? In order to try to find potential answers or clues to this question, we have here analyzed more than 1,000 different human proteins in the blood of more than 500 malaria-infected children from Ibadan in Nigeria, a holoendemic malaria region. We identified several proteins that were present at higher levels in the blood from the children that developed severe malaria in comparison to those that did not. Some of the most interesting identified proteins were muscle specific proteins, which indicate that damaged muscles could be a discriminatory pathologic event in cerebral malaria compared to other malaria cases. These findings will hopefully lead to an increased understanding of the disease and may contribute to the development of clinical algorithms that could predict which children are more at risks to severe malaria. This in turn will be of high value in the management of these children in already overloaded tertiary-care health facilities in urban large densely-populated sub-Saharan cities with holoendemic malaria such as in the case of Ibadan and Lagos.
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Affiliation(s)
- Julie Bachmann
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Florence Burté
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Setia Pramana
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Ianina Conte
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
| | - Biobele J. Brown
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Adebola E. Orimadegun
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Wasiu A. Ajetunmobi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Nathaniel K. Afolabi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Francis Akinkunmi
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
| | - Samuel Omokhodion
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Felix O. Akinbami
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Wuraola A. Shokunbi
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Caroline Kampf
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Yudi Pawitan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Mathias Uhlén
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Olugbemiro Sodeinde
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
| | - Jochen M. Schwenk
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Mats Wahlgren
- Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail: (MW); (DFR); (PN)
| | - Delmiro Fernandez-Reyes
- Division of Parasitology, Medical Research Council National Institute for Medical Research, London, United Kingdom
- Department of Paediatrics, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Department of Haematology, College of Medicine, University of Ibadan, University College Hospital, Ibadan, Nigeria
- Childhood Malaria Research Group, University College Hospital, Ibadan, Nigeria
- Brighton & Sussex Medical School, Sussex University, Brighton, United Kingdom
- * E-mail: (MW); (DFR); (PN)
| | - Peter Nilsson
- SciLifeLab Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (MW); (DFR); (PN)
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Ray S, Patel SK, Kumar V, Damahe J, Srivastava S. Differential expression of serum/plasma proteins in various infectious diseases: specific or nonspecific signatures. Proteomics Clin Appl 2013; 8:53-72. [PMID: 24293340 PMCID: PMC7168033 DOI: 10.1002/prca.201300074] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 11/04/2013] [Accepted: 11/06/2013] [Indexed: 01/26/2023]
Abstract
Apart from direct detection of the infecting organisms or biomarker of the pathogen itself, surrogate host markers are also useful for sensitive and early diagnosis of pathogenic infections. Early detection of pathogenic infections, discrimination among closely related diseases with overlapping clinical manifestations, and monitoring of disease progression can be achieved by analyzing blood biomarkers. Therefore, over the last decade large numbers of proteomics studies have been conducted to identify differentially expressed human serum/plasma proteins in different infectious diseases with the intent of discovering novel potential diagnostic/prognostic biomarkers. However, in-depth review of the literature indicates that many reported biomarkers are altered in the same way in multiple infectious diseases, regardless of the type of infection. This might be a consequence of generic acute phase reactions, while the uniquely modulated candidates in different pathogenic infections could be indicators of some specific responses. In this review article, we will provide a comprehensive analysis of differentially expressed serum/plasma proteins in various infectious diseases and categorize the protein markers associated with generic or specific responses. The challenges associated with the discovery, validation, and translational phases of serum/plasma biomarker establishment are also discussed.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Wadhwani Research Centre for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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Malaria proteomics: insights into the parasite-host interactions in the pathogenic space. J Proteomics 2013; 97:107-25. [PMID: 24140976 DOI: 10.1016/j.jprot.2013.10.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 06/23/2013] [Accepted: 10/08/2013] [Indexed: 11/23/2022]
Abstract
Proteomics is improving malaria research by providing global information on relevant protein sets from the parasite and the host in connection with its cellular structures and specific functions. In the last decade, reports have described biologically significant elements in the proteome of Plasmodium, which are selectively targeted and quantified, allowing for sensitive and high-throughput comparisons. The identification of molecules by which the parasite and the host react during the malaria infection is crucial to the understanding of the underlying pathogenic mechanisms. Hence, proteomics is playing a major role by defining the elements within the pathogenic space between both organisms that change across the parasite life cycle in association with the host transformation and response. Proteomics has identified post-translational modifications in the parasite and the host that are discussed in terms of functional interactions in malaria parasitism. Furthermore, the contribution of proteomics to the investigation of immunogens for potential vaccine candidates is summarized. The malaria-specific technological advances in proteomics are particularly suited now for identifying host-parasite interactions that could lead to promising targets for therapy, diagnosis or prevention. In this review, we examine the knowledge gained on the biology, pathogenesis, immunity and diagnosis of Plasmodium infection from recent proteomic studies. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Puttamallesh VN, Sreenivasamurthy SK, Singh PK, Harsha HC, Ganjiwale A, Broor S, Pandey A, Narayana J, Prasad TSK. Proteomic profiling of serum samples from chikungunya-infected patients provides insights into host response. Clin Proteomics 2013; 10:14. [PMID: 24124767 PMCID: PMC3879382 DOI: 10.1186/1559-0275-10-14] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/17/2013] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chikungunya is a highly debilitating febrile illness caused by Chikungunya virus, a single-stranded RNA virus, which is transmitted by Aedes aegypti or Aedes albopictus mosquito species. The pathogenesis and host responses in individuals infected with the chikungunya virus are not well understood at the molecular level. We carried out proteomic profiling of serum samples from chikungunya patients in order to identify molecules associated with the host response to infection by this virus. RESULTS Proteomic profiling of serum obtained from the infected individuals resulted in identification of 569 proteins. Of these, 63 proteins were found to be differentially expressed (≥ 2-fold) in patient as compared to control sera. These differentially expressed proteins were involved in various processes such as lipid metabolism, immune response, transport, signal transduction and apoptosis. CONCLUSIONS This is the first report providing a global proteomic profile of serum samples from individuals infected with the chikungunya virus. Our data provide an insight into the proteins that are involved as host response factors during an infection. These proteins include clusterin, apolipoproteins and S100A family of proteins.
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Affiliation(s)
- Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | | | - Pradeep Kumar Singh
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - H C Harsha
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
| | - Anjali Ganjiwale
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - Shobha Broor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi 110 029, India
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
- McKusick-Nathans Institute of Genetic Medicine and Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore 21205 MD, USA
| | - Jayasuryan Narayana
- Microtest Innovations Pvt. Limited, International Technology Park, Bangalore 560 066, India
| | - T S Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore 560 066, India
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Ray S, Srivastava R, Tripathi K, Vaibhav V, Patankar S, Srivastava S. Serum proteome changes in dengue virus-infected patients from a dengue-endemic area of India: towards new molecular targets? OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:527-36. [PMID: 22917478 DOI: 10.1089/omi.2012.0037] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The global burden of dengue continues to worsen, specifically in tropical and subtropical countries, and has evolved as a major public health problem. We investigated the changes in serum proteome in dengue fever (DF) patients from a dengue-endemic area of India to obtain mechanistic insights about the disease pathogenesis, the host immune response, and identification of potential serum protein biomarkers of this infectious disease. In this study, serum samples from DF patients, healthy subjects, and patients with falciparum malaria (an infectious disease control) were investigated by 2D-DIGE in combination with MALDI-TOF/TOF MS. The findings were validated with Western blotting. Functional clustering of the identified proteins was performed using PANTHER and DAVID tools. Compared to the healthy controls, we found significant changes in the expression levels of 48 protein spots corresponding to 18 unique proteins (7 downregulated and 11 upregulated) in DF patients (p<0.05). Among these differentially-expressed proteins, 11 candidates exhibited different trends in dengue fever compared to falciparum malaria. Importantly, our results suggest that dengue virus infection leads to alterations in expression levels of multiple serum proteins involved in diverse and vital physiological pathways, including acute phase response signaling, complement cascades, hemostasis, and blood coagulation. For the first time we report here that the serum levels of hemopexin, haptoglobin, serum amyloid P, and kininogen precursor, are altered in DF. This study informs the pathogenesis and host immune response to dengue virus infection, as well as the current search for new diagnostic and molecular drug targets.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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