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Krumkamp R, Struck NS, Lorenz E, Zimmermann M, Boahen KG, Sarpong N, Owusu-Dabo E, Pak GD, Jeon HJ, Marks F, Jacobs T, May J, Eibach D. Classification of invasive bloodstream infections and Plasmodium falciparum malaria using autoantibodies as biomarkers. Sci Rep 2020; 10:21168. [PMID: 33273605 PMCID: PMC7712777 DOI: 10.1038/s41598-020-78155-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/20/2020] [Indexed: 01/25/2023] Open
Abstract
A better understanding of disease-specific biomarker profiles during acute infections could guide the development of innovative diagnostic methods to differentiate between malaria and alternative causes of fever. We investigated autoantibody (AAb) profiles in febrile children (≤ 5 years) admitted to a hospital in rural Ghana. Serum samples from 30 children with a bacterial bloodstream infection and 35 children with Plasmodium falciparum malaria were analyzed using protein microarrays (Protoplex Immune Response Assay, ThermoFisher). A variable selection algorithm was applied to identify the smallest set of AAbs showing the best performance to classify malaria and bacteremia patients. The selection procedure identified 8 AAbs of which IFNGR2 and FBXW5 were selected in repeated model run. The classification error was 22%, which was mainly due to non-Typhi Salmonella (NTS) diagnoses being misclassified as malaria. Likewise, a cluster analysis grouped patients with NTS and malaria together, but separated malaria from non-NTS infections. Both current and recent malaria are a risk factor for NTS, therefore, a better understanding about the function of AAb in disease-specific immune responses is required in order to support their application for diagnostic purposes.
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Affiliation(s)
- Ralf Krumkamp
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Nicole Sunaina Struck
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany. .,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.
| | - Eva Lorenz
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Marlow Zimmermann
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
| | - Kennedy Gyau Boahen
- Department of Infectious Disease Epidemiology, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Nimako Sarpong
- Department of Infectious Disease Epidemiology, Kumasi Centre for Collaborative Research in Tropical Medicine (KCCR), Kumasi, Ghana
| | - Ellis Owusu-Dabo
- School of Public Health, Kwame Nkrumah University of Science and Technology (KNUST), Kumasi, Ghana
| | - Gi Deok Pak
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea
| | - Hyon Jin Jeon
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea
| | - Florian Marks
- Epidemiology Unit, International Vaccine Institute (IVI), Seoul, Republic of Korea.,The Department of Medicine, the University of Cambridge, Cambridge, UK
| | - Thomas Jacobs
- Research Group Protozoa Immunology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Jürgen May
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany.,First Medical Clinic and Polyclinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Daniel Eibach
- Department of Infectious Disease Epidemiology, Bernhard Nocht Institute for Tropical Medicine, Bernhard Nocht Str. 74, 20359, Hamburg, Germany.,German Centre for Infection Research (DZIF), Hamburg-Lübeck-Borstel-Riems, Hamburg, Germany
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Poulsen TBG, Damgaard D, Jørgensen MM, Senolt L, Blackburn JM, Nielsen CH, Stensballe A. Identification of Novel Native Autoantigens in Rheumatoid Arthritis. Biomedicines 2020; 8:biomedicines8060141. [PMID: 32486012 PMCID: PMC7345460 DOI: 10.3390/biomedicines8060141] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
The majority of patients diagnosed with rheumatoid arthritis (RA) have developed autoantibodies against neoepitopes in proteins that have undergone post-translational modification, e.g., citrullination or carbamylation. There is growing evidence of their molecular relevance and their potential utility to improve diagnosis, patient stratification, and prognosis for precision medicine. Autoantibodies reacting to native proteins may also have a role in RA pathogenesis, however, their reactivity patterns remain much less studied. We hypothesized that a high-density protein array technology could shed light onto the normal and disease-related autoantibodies produced in healthy and RA patient subgroups. In an exploratory study, we investigated the global reactivity of autoantibodies in plasma pools from 15 anti-cyclic citrullinated peptide (CCP)-positive and 10 anti-CCP-negative RA patients and 10 healthy donors against more than 1600 native and unmodified human proteins using a high-density protein array. A total of 102 proteins recognized by IgG autoantibodies were identified, hereof 86 were recognized by antibodies from CCP-positive RA patients and 76 from anti-CCP-negative RA patients, but not by antibodies from healthy donors. Twenty-four of the identified autoantigens have previously been identified in synovial fluid. Multiple human proteins in their native conformation are recognized by autoantibodies from anti-CCP-positive as well as anti-CCP-negative RA patients.
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Affiliation(s)
- Thomas B. G. Poulsen
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou district, Beijing 100049, China
- Correspondence: (T.B.G.P.); (A.S.); Tel.: +45-2615-9368 (T.B.G.P.); +45-6160-8786 (A.S.)
| | - Dres Damgaard
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark; (D.D.); (C.H.N.)
| | - Malene Møller Jørgensen
- Department of Clinical Immunology, Aalborg University Hospital, 9000 Aalborg, Denmark;
- Department of Clinical Medicine, Aalborg University, 9000 Aalborg, Denmark
| | - Ladislav Senolt
- Institute of Rheumatology and Department of Rheumatology, 1st Faculty of Medicine, Charles University, 121 08 Prague, Czech Republic;
| | - Jonathan M. Blackburn
- Department of Integrative Biomedical Sciences & Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7700, South Africa;
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore
| | - Claus H. Nielsen
- Institute for Inflammation Research, Center for Rheumatology and Spine Diseases, Copenhagen University Hospital Rigshospitalet, 2100 Copenhagen, Denmark; (D.D.); (C.H.N.)
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark
- Correspondence: (T.B.G.P.); (A.S.); Tel.: +45-2615-9368 (T.B.G.P.); +45-6160-8786 (A.S.)
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Sumera A, Anuar ND, Radhakrishnan AK, Ibrahim H, Rutt NH, Ismail NH, Tan TM, Baba AA. A Novel Method to Identify Autoantibodies against Putative Target Proteins in Serum from beta-Thalassemia Major: A Pilot Study. Biomedicines 2020; 8:E97. [PMID: 32357536 PMCID: PMC7277850 DOI: 10.3390/biomedicines8050097] [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: 03/23/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/31/2022] Open
Abstract
Abnormal immune reactivity in patients with beta-thalassemia (beta-thal) major can be associated with poor prognosis. Immunome protein-array analysis represents a powerful approach to identify novel biomarkers. The Sengenics Immunome Protein Array platform was used for high-throughput quantification of autoantibodies in 12 serum samples collected from nine beta-thal major patients and three non-thalassemia controls, which were run together with two pooled normal sera (Sengenics Internal QC samples). To obtain more accurate and reliable results, the evaluation of the biological relevance of the shortlisted biomarkers was analyzed using an Open Target Platform online database. Elevated autoantibodies directed against 23 autoantigens on the immunome array were identified and analyzed using a penetrance fold change-based bioinformatics method. Understanding the autoantibody profile of beta-thal major patients would help to further understand the pathogenesis of the disease. The identified autoantigens may serve as potential biomarkers for the prognosis of beta-thal major.
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Affiliation(s)
- Afshan Sumera
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia;
| | - Nur Diana Anuar
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore; (N.D.A.); (N.H.R.); (N.H.I.); (T.-M.T.)
| | - Ammu Kutty Radhakrishnan
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway 47500, Malaysia;
| | - Hishamshah Ibrahim
- Paediatrics Department, Kuala Lumpur General Hospital, Jalan Ipoh, Kuala Lumpur 50586, Malaysia;
| | - Nurul H. Rutt
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore; (N.D.A.); (N.H.R.); (N.H.I.); (T.-M.T.)
| | - Nur Hafiza Ismail
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore; (N.D.A.); (N.H.R.); (N.H.I.); (T.-M.T.)
| | - Ti-Myen Tan
- Sengenics Corporation Pte Ltd., Singapore 409051, Singapore; (N.D.A.); (N.H.R.); (N.H.I.); (T.-M.T.)
| | - Abdul Aziz Baba
- School of Medicine, International Medical University, Bukit Jalil, Kuala Lumpur 57000, Malaysia;
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Lawford HLS, Lee AC, Kumar S, Liley HG, Bora S. Establishing a conceptual framework of the impact of placental malaria on infant neurodevelopment. Int J Infect Dis 2019; 84:54-65. [PMID: 31028878 DOI: 10.1016/j.ijid.2019.04.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 04/12/2019] [Accepted: 04/18/2019] [Indexed: 01/11/2023] Open
Abstract
A novel conceptual framework to describe the relationship between placental malaria and adverse infant neurodevelopmental outcomes is proposed. This conceptual framework includes three distinct stages: (1) maternal and environmental risk factors for the development of placental malaria; (2) placental pathology and inflammation associated with placental malaria infection; and (3) postnatal impacts of placental malaria. The direct, indirect, and bidirectional effects of these risk factors on infant neurodevelopment across the three stages were critically examined. These factors ultimately culminate in an infant phenotype that not only leads to adverse birth outcomes, but also to increased risks of neurological, cognitive, and behavioural deficits that may impact the quality of life in this high-risk population. Multiple risk factors were identified in this conceptual framework; nonetheless, based on current evidence, a key knowledge gap is the uncertainty regarding which are the most important and how exactly they interact.
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Affiliation(s)
- Harriet L S Lawford
- Mothers, Babies and Women's Health Program, Mater Research Institute, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Anne Cc Lee
- Department of Pediatric Newborn Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sailesh Kumar
- Mothers, Babies and Women's Health Program, Mater Research Institute, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Helen G Liley
- Mothers, Babies and Women's Health Program, Mater Research Institute, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia
| | - Samudragupta Bora
- Mothers, Babies and Women's Health Program, Mater Research Institute, Faculty of Medicine, The University of Queensland, South Brisbane, QLD, Australia.
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Abstract
INTRODUCTION High-content protein microarrays in principle enable the functional interrogation of the human proteome in a broad range of applications, including biomarker discovery, profiling of immune responses, identification of enzyme substrates, and quantifying protein-small molecule, protein-protein and protein-DNA/RNA interactions. As with other microarrays, the underlying proteomic platforms are under active technological development and a range of different protein microarrays are now commercially available. However, deciphering the differences between these platforms to identify the most suitable protein microarray for the specific research question is not always straightforward. Areas covered: This review provides an overview of the technological basis, applications and limitations of some of the most commonly used full-length, recombinant protein and protein fragment microarray platforms, including ProtoArray Human Protein Microarrays, HuProt Human Proteome Microarrays, Human Protein Atlas Protein Fragment Arrays, Nucleic Acid Programmable Arrays and Immunome Protein Arrays. Expert commentary: The choice of appropriate protein microarray platform depends on the specific biological application in hand, with both more focused, lower density and higher density arrays having distinct advantages. Full-length protein arrays offer advantages in biomarker discovery profiling applications, although care is required in ensuring that the protein production and array fabrication methodology is compatible with the required downstream functionality.
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Affiliation(s)
- Jessica G Duarte
- a Cancer Immunobiology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine , La Trobe University , Heidelberg , Australia
| | - Jonathan M Blackburn
- b Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Faculty of Health Sciences , University of Cape Town , Observatory, South Africa
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