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Sendic S, Mansouri L, Hong MG, Schwenk JM, Eriksson MJ, Hylander B, Lundahl J, Jacobson SH. Soluble CD14 and Osteoprotegerin Associate with Ankle-Brachial Index as a Measure of Arterial Stiffness in Patients with Mild-to-Moderate Chronic Kidney Disease in a Five-Year Prospective Study. Cardiorenal Med 2023; 13:189-201. [PMID: 37231818 DOI: 10.1159/000530985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 03/28/2023] [Indexed: 05/27/2023] Open
Abstract
INTRODUCTION Vascular lesions and arterial stiffness appear at early stages of chronic kidney disease (CKD) and follow an accelerated course with disease progression, contributing to high cardiovascular mortality. There are limited prospective data on mechanisms contributing to progression of arterial stiffness in mild-to-moderate CKD (stages 2-3). METHODS We applied an affinity proteomics approach to identify candidates of circulating biomarkers with potential impact on vascular lesions in CKD and selected soluble cluster of differentiation 14 (sCD14), angiogenin (ANG), and osteoprotegerin (OPG) for further analysis. We studied their association with ankle-brachial index (ABI) and carotid intima-media thickness, as measures of arteriosclerosis and atherosclerosis, respectively, in 48 patients with CKD stages 2-3, who were prospectively followed and intensively treated for 5 years, and 44 healthy controls. RESULTS Concentrations of sCD14 (p < 0.001), ANG (p < 0.001), and OPG (p < 0.05) were higher in patients with CKD 2-3 at baseline, and sCD14 (p < 0.001) and ANG (p < 0.001) remained elevated in CKD patients at follow-up. There were positive correlations between ABI and sCD14 levels (r = 0.36, p = 0.01) and between ABI and OPG (r = 0.31, p = 0.03) at 5 years. The changes in sCD14 during follow-up correlated to changes in ABI from baseline to 5 years (r = 0.41, p = 0.004). CONCLUSION Elevated levels of circulating sCD14 and OPG in patients with CKD 2-3 were significantly associated with ABI, a measure of arterial stiffness. An increase in sCD14 over time in CKD 2-3 patients was associated with a corresponding increase in ABI. Further studies are needed to examine if early intensive multifactorial medication to align with international treatment targets may influence cardiovascular outcomes.
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Affiliation(s)
- Senka Sendic
- Division of Nephrology, Department of Clinical Sciences, Karolinska Institutet, Danderyd University Hospital, Stockholm, Sweden
| | - Ladan Mansouri
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Maria J Eriksson
- Department of Clinical Physiology, Karolinska University Hospital, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Britta Hylander
- Division of Nephrology, Department of Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Joachim Lundahl
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Stockholm, Sweden
| | - Stefan H Jacobson
- Division of Nephrology, Department of Clinical Sciences, Karolinska Institutet, Danderyd University Hospital, Stockholm, Sweden
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Grgurevic L, Novak R, Salai G, Hrkac S, Mocibob M, Vojtusek IK, Laganovic M. Stage II of Chronic Kidney Disease-A Tipping Point in Disease Progression? Biomedicines 2022; 10:1522. [PMID: 35884827 PMCID: PMC9313233 DOI: 10.3390/biomedicines10071522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/20/2022] [Accepted: 06/25/2022] [Indexed: 11/17/2022] Open
Abstract
Chronic kidney disease (CKD) is the progressive loss of renal function. Although advances have been made in understanding the progression of CKD, key molecular events in complex pathophysiological mechanisms that mark each stage of renal failure remain largely unknown. Changes in plasma protein profiles in different disease stages are important for identification of early diagnostic markers and potential therapeutic targets. The goal of this study was to determine the molecular profile of each CKD stage (from 1 to 5), aiming to specifically point out markedly expressed or downregulated proteins. We performed a cross-sectional shotgun-proteomic study of pooled plasma across CKD stages and compared them to healthy controls. After sample pooling and heparin-column purification we analysed proteomes from healthy to CKD stage 1 through 5 participants' plasma by liquid-chromatography/mass-spectrometry. We identified 453 proteins across all study groups. Our results indicate that key events, which may later affect the course of disease progression and the overall pathophysiological background, are most pronounced in CKD stage 2, with an emphasis on inflammation, lipoprotein metabolism, angiogenesis and tissue regeneration. We hypothesize that CKD stage 2 is the tipping point in disease progression and a suitable point in disease course for the development of therapeutic solutions.
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Affiliation(s)
- Lovorka Grgurevic
- Department of Anatomy, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (R.N.); (G.S.); (S.H.)
| | - Rudjer Novak
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (R.N.); (G.S.); (S.H.)
| | - Grgur Salai
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (R.N.); (G.S.); (S.H.)
- Department of Pulmonology, University Hospital Dubrava, 10000 Zagreb, Croatia
| | - Stela Hrkac
- Center for Translational and Clinical Research, Department of Proteomics, School of Medicine, University of Zagreb, 10000 Zagreb, Croatia; (R.N.); (G.S.); (S.H.)
- Department of Emergency Medicine, University Hospital Centre Zagreb, 10000 Zagreb, Croatia
| | - Marko Mocibob
- Department of Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia;
| | - Ivana Kovacevic Vojtusek
- Department of Nephrology, Arterial Hypertension, Dialysis and Transplantation, University Hospital Center Zagreb, 10000 Zagreb, Croatia;
| | - Mario Laganovic
- Department of Nephrology, University Hospital Merkur, 10000 Zagreb, Croatia;
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Lourenço BN, Schmiedt CW, Alabady MS, Stanton JB, Coleman AE, Brown CA, Rissi DR, Brown SA, Tarigo JL. Analysis of genes associated with proinflammatory and profibrotic pathways upregulated in ischemia-induced chronic kidney disease in cats. Am J Vet Res 2021; 82:589-597. [PMID: 34166083 DOI: 10.2460/ajvr.82.7.589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To use RNA sequencing (RNAseq) to characterize renal transcriptional activities of genes associated with proinflammatory and profibrotic pathways in ischemia-induced chronic kidney disease (CKD) in cats. SAMPLES Banked renal tissues from 6 cats with experimentally induced CKD (renal ischemia [RI] group) and 9 healthy cats (control group). PROCEDURES Transcriptome analysis with RNAseq, followed by gene ontology and cluster analyses, were performed on banked tissue samples of the right kidneys (control kidneys) from cats in the control group and of both kidneys from cats in the RI group, in which unilateral (right) RI had been induced 6 months before the cats were euthanized and the ischemic kidneys (IKs) and contralateral nonischemic kidneys (CNIKs) were harvested. Results for the IKs, CNIKs, and control kidneys were compared to identify potential differentially expressed genes and overrepresented proinflammatory and profibrotic pathways. RESULTS Genes from the gene ontology pathways of collagen binding (eg, transforming growth factor-β1), metalloendopeptidase activity (eg, metalloproteinase [MMP]-7, MMP-9, MMP-11, MMP-13, MMP-16, MMP-23B, and MMP-28), chemokine activity, and T-cell migration were overrepresented as upregulated in tissue samples of the IKs versus control kidneys. Genes associated with the extracellular matrix (eg, TIMP-1, fibulin-1, secreted phosphoprotein-1, matrix Gla protein, and connective tissue growth factor) were upregulated in tissue samples from both the IKs and CNIKs, compared with tissues from the control kidneys. CONCLUSIONS AND CLINICAL RELEVANCE Unilateral ischemic injury differentially altered gene expression in both kidneys, compared with control kidneys. Fibulin-1, secreted phosphoprotein-1, and matrix Gla protein may be candidate biomarkers of active kidney injury in cats.
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Affiliation(s)
- Bianca N Lourenço
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Chad W Schmiedt
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Magdy S Alabady
- From the Department of Plant Biology, Franklin College of Arts and Sciences, and Georgia Genomics and Bioinformatics Core, University of Georgia, Athens, GA 30602
| | - James B Stanton
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Amanda E Coleman
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Cathy A Brown
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Daniel R Rissi
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Scott A Brown
- From the Department of Small Animal Medicine and Surgery, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
- From the Department of Physiology and Pharmacology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
| | - Jaime L Tarigo
- From the Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA 30602
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Mikus M, Järnbert-Pettersson H, Johansson C, Nilsson P, Scheynius A, Alm J. Protein profiles in plasma: Development from infancy to 5 years of age. Proteomics Clin Appl 2021; 15:e2000038. [PMID: 33830667 DOI: 10.1002/prca.202000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 11/10/2022]
Abstract
PURPOSE Little is known about the longitudinal development of different plasma protein levels during early childhood and particularly in relation to lifestyle factors. This study aimed to monitor the plasma proteome early in life and the influence of different lifestyles. EXPERIMENTAL DESIGN A multiplex bead-based immunoassay was used to analyze plasma levels of 97 proteins in 280 blood samples longitudinally collected in children at 6, 12, 24, and 60 months of age living in families with an anthroposophic (n = 15), partly anthroposophic (n = 27), or non-anthroposophic (n = 28) lifestyle. RESULTS A total of 68 proteins (70%) showed significantly altered plasma levels between 6 months and 5 years of age. In lifestyle stratified analysis, 59 of 97 (61%) proteins were altered over time within one or more of the three lifestyle groups. Nearly half of these proteins (28 out of 59) changed irrespective of lifestyle. The temporal changes represented four longitudinal trends of the plasma proteins during development, also following stratification of lifestyle. CONCLUSIONS AND CLINICAL RELEVANCE Our findings contribute to understand the development of the plasma proteome under the influence of lifestyle exposures in early childhood.
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Affiliation(s)
- Maria Mikus
- Department of Protein Science, Division of Affinity Proteomics, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hans Järnbert-Pettersson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Catharina Johansson
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Peter Nilsson
- Department of Protein Science, Division of Affinity Proteomics, SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Annika Scheynius
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,SciLifeLab, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Johan Alm
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
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Feng S, Gao Y, Yin D, Lv L, Wen Y, Li Z, Wang B, Wu M, Liu B. Identification of Lumican and Fibromodulin as Hub Genes Associated with Accumulation of Extracellular Matrix in Diabetic Nephropathy. Kidney Blood Press Res 2021; 46:275-285. [PMID: 33887734 DOI: 10.1159/000514013] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/22/2020] [Indexed: 01/27/2023] Open
Abstract
INTRODUCTION Diabetic nephropathy (DN) remains a major cause of end-stage renal disease. The development of novel biomarkers and early diagnosis of DN are of great clinical importance. The goal of this study was to identify hub genes with diagnostic potential for DN by weighted gene co-expression network analysis (WGCNA). METHODS Gene Expression Omnibus database was searched for microarray data including distinct types of CKD. Gene co-expression network was constructed, and modules specific for DN were identified by WGCNA. Gene ontology (GO) analysis was performed, and the hub genes were screened out within the selected gene modules. In addition, cross-validation was performed in an independent dataset and in samples of renal biopsies with DN and other types of glomerular diseases. RESULTS Dataset GSE99339 was selected, and a total of 179 microdissected glomeruli samples were analyzed, including DN, normal control, and 7 groups of other glomerular diseases. Twenty-three modules of the total 10,947 genes were grouped by WGCNA, and a module was specifically correlated with DN (r = 0.54, p = 9e-15). GO analysis showed that module genes were mainly enriched in the accumulation of extracellular matrix (ECM). LUM, ELN, FBLN1, MMP2, FBLN5, and FMOD were identified as hub genes. Cross verification showed LUM and FMOD were higher in the DN group and were negatively correlated with estimated glomerular filtration rate (eGFR). In renal biopsies, expression levels of LUM and FMOD were higher in DN than IgA nephropathy, membranous nephropathy, and normal controls. CONCLUSION By using WGCNA approach, we identified LUM and FMOD related to ECM accumulation and were specific for DN. These 2 genes may represent potential candidate diagnostic biomarkers of DN.
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Affiliation(s)
- Songtao Feng
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Yueming Gao
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Di Yin
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Linli Lv
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Yi Wen
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Zuolin Li
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Bin Wang
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Min Wu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
| | - Bicheng Liu
- Institute of Nephrology, Zhong Da Hospital, Southeast University School of Medicine, Nanjing, China
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Li Y, Chen Z, Zhang J, Zhang Q, He L, Xu M, Xu G, Geng H, Fang X. Quantitative Proteome of Infant Stenotic Ureters Reveals Extracellular Matrix Organization and Oxidative Stress Dysregulation Underlying Ureteropelvic Junction Obstruction. Proteomics Clin Appl 2020; 14:e2000030. [PMID: 32969194 DOI: 10.1002/prca.202000030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/21/2020] [Indexed: 11/09/2022]
Abstract
PURPOSE Ureteropelvic junction obstruction (UPJO) is the most frequent cause of congenital hydronephrosis in child. To better investigate the molecular mechanisms of this pathological process, the stenotic ureter proteome of UPJO in infants is compared with their own normal pre-stenotic segments. EXPERIMENTAL DESIGN Data independent acquisition-based proteomics are performed to compare proteome between pre-stenotic and stenotic ureter from nine UPJO infants. Gene ontology analysis, hierarchical cluster analysis, and network interaction are performed to characterize biological functions of significantly altered proteins. Selected significantly altered proteins are validated by western blot on another three UPJO infants. RESULTS 15 proteins are up-regulated and 33 proteins are down-regulated during stenotic pathology. Significantly altered proteins are involved in decreased extracellular matrix and cytoskeleton organization, increased regulation of oxidative activity, and altered inflammatory associated exocytosis. Significant expression of biglycan, fibulin-1, myosin-10, cytochrome b5 are validated providing possible mechanism in UPJO which could be associated impaired smooth muscle cell, epithelial integrity, and increased oxidative stress. CONCLUSIONS AND CLINICAL RELEVANCE: This study provides molecular evidence of dysregulated extracellular matrix organization, impaired smooth muscle cell, and oxidative stress during UPJO pathology, indicating that biglycan, fibulin-1, myosin-10, cytochrome b5 might reflect the pathology of UPJO.
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Affiliation(s)
- Yueyan Li
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Zhoutong Chen
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Junqi Zhang
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Qimin Zhang
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Lei He
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Maosheng Xu
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Guofeng Xu
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Hongquan Geng
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Xiaoliang Fang
- Department of Pediatric Urology, Xin hua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
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Dos Reis Monteiro MLG, Custódio FB, de Menezes Neves PDM, Ferreira FM, Watanabe EH, Lerário AM, de Araújo LS, Balbo BEP, Pinto VCD, Barbosa LMG, de Paiva Marques V, Machado JR, Reis MA, Onuchic LF. A novel single amino acid deletion impairs fibronectin function and causes familial glomerulopathy with fibronectin deposits: case report of a family. BMC Nephrol 2019; 20:322. [PMID: 31419955 PMCID: PMC6697944 DOI: 10.1186/s12882-019-1507-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/31/2019] [Indexed: 11/23/2022] Open
Abstract
Background Glomerulopathy with fibronectin deposits is an autosomal dominant disease associated with proteinuria, hematuria, hypertension and renal function decline. Forty percent of the cases are caused by mutations in FN1, the gene that encodes fibronectin. Case presentation This report describes two cases of Glomerulopathy with fibronectin deposits, involving a 47-year-old father and a 14-year-old son. The renal biopsies showed glomeruli with endocapillary hypercellularity and large amounts of mesangial and subendothelial eosinophilic deposits. Immunohistochemistry for fibronectin was markedly positive. Whole exome sequencing identified a novel FN1 mutation that leads to an amino-acid deletion in both patients (Ile1988del), a variant that required primary amino-acid sequence analysis for assessment of pathogenicity. Our primary sequence analyses revealed that Ile1988 is very highly conserved among relative sequences and is positioned in a C-terminal FN3 domain containing heparin- and fibulin-1-binding sites. This mutation was predicted as deleterious and molecular mechanics simulations support that it can change the tertiary structure and affect the complex folding and its molecular functionality. Conclusion The current report not only documents the occurrence of two GFND cases in an affected family and deeply characterizes its anatomopathological features but also identifies a novel pathogenic mutation in FN1, analyzes its structural and functional implications, and supports its pathogenicity.
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Affiliation(s)
| | | | | | | | - Elieser Hitoshi Watanabe
- Divisions of Nephrology and Molecular Medicine, University of São Paulo School of Medicine, São Paulo, SP, Brazil
| | | | - Liliane Silvano de Araújo
- Nephropathology Service, Federal University of Triângulo Mineiro, Praça Manoel Terra, 330 - Bairro Abadia, Uberaba, MG, 38015-050, Brazil
| | - Bruno Eduardo Pedroso Balbo
- Divisions of Nephrology and Molecular Medicine, University of São Paulo School of Medicine, São Paulo, SP, Brazil
| | | | - Lívia Maria Gruli Barbosa
- Divisions of Nephrology and Molecular Medicine, University of São Paulo School of Medicine, São Paulo, SP, Brazil
| | | | - Juliana Reis Machado
- Nephropathology Service, Federal University of Triângulo Mineiro, Praça Manoel Terra, 330 - Bairro Abadia, Uberaba, MG, 38015-050, Brazil
| | - Marlene Antônia Reis
- Nephropathology Service, Federal University of Triângulo Mineiro, Praça Manoel Terra, 330 - Bairro Abadia, Uberaba, MG, 38015-050, Brazil.
| | - Luiz Fernando Onuchic
- Divisions of Nephrology and Molecular Medicine, University of São Paulo School of Medicine, São Paulo, SP, Brazil
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Fredolini C, Byström S, Sanchez-Rivera L, Ioannou M, Tamburro D, Pontén F, Branca RM, Nilsson P, Lehtiö J, Schwenk JM. Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles. Sci Rep 2019; 9:8324. [PMID: 31171813 PMCID: PMC6554399 DOI: 10.1038/s41598-019-43552-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 04/27/2019] [Indexed: 11/16/2022] Open
Abstract
There is a strong need for procedures that enable context and application dependent validation of antibodies. Here, we applied a magnetic bead assisted workflow and immunoprecipitation mass spectrometry (IP-MS/MS) to assess antibody selectivity for the detection of proteins in human plasma. A resource was built on 414 IP experiments using 157 antibodies (targeting 120 unique proteins) in assays with heat-treated or untreated EDTA plasma. For each protein we determined their antibody related degrees of enrichment using z-scores and their frequencies of identification across all IP assays. Out of 1,313 unique endogenous proteins, 426 proteins (33%) were detected in >20% of IPs, and these background components were mainly comprised of proteins from the complement system. For 45% (70/157) of the tested antibodies, the expected target proteins were enriched (z-score ≥ 3). Among these 70 antibodies, 59 (84%) co-enriched other proteins beside the intended target and mainly due to sequence homology or protein abundance. We also detected protein interactions in plasma, and for IGFBP2 confirmed these using several antibodies and sandwich immunoassays. The protein enrichment data with plasma provide a very useful and yet lacking resource for the assessment of antibody selectivity. Our insights will contribute to a more informed use of affinity reagents for plasma proteomics assays.
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Affiliation(s)
- Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Laura Sanchez-Rivera
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Marina Ioannou
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Davide Tamburro
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, 751 85, Uppsala, Sweden
| | - Rui M Branca
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Peter Nilsson
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden
| | - Janne Lehtiö
- Cancer Proteomics, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, 171 21, Solna, Sweden
| | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH - Royal Institute of Technology, 171 21, Solna, Sweden.
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Bedri SK, Nilsson OB, Fink K, Månberg A, Hamsten C, Ayoglu B, Manouchehrinia A, Nilsson P, Olsson T, Hillert J, Grönlund H, Glaser A. Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment. PLoS One 2019; 14:e0217208. [PMID: 31141529 PMCID: PMC6541274 DOI: 10.1371/journal.pone.0217208] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 05/07/2019] [Indexed: 12/14/2022] Open
Abstract
Multiple sclerosis (MS) treatment options have improved significantly over the past decades, but the consequences of MS can still be devastating and the needs for monitoring treatment surveillance are considerable. In the current study we used affinity proteomics technology to identify potential biomarkers which could ultimately be used to as facilitate treatment decisions. We profiled the intra-individual changes in the levels of 59 target proteins using an antibody suspension bead array in serial plasma samples from 44 MS patients during treatment with natalizumab followed by fingolimod. Nine proteins showed decreasing plasma levels during natalizumab treatment, with PEBP1 and RTN3 displaying the most significant changes. Protein levels remained stable during fingolimod treatment for both proteins. The decreasing PEBP1 levels during natalizumab treatment could be validated using ELISA and replicated in an independent cohort. These results support the use of this technology as a high throughput method of identifying potentially useful biomarkers of MS treatment.
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Affiliation(s)
- Sahl Khalid Bedri
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
- * E-mail:
| | - Ola B. Nilsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
- TCER AB, c/o Advice Företagsassistans i Stockholm AB, Stockholm, Sweden
| | - Katharina Fink
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
- Department of Neurology, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Månberg
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Carl Hamsten
- Immunology and Allergy unit, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Burcu Ayoglu
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Ali Manouchehrinia
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Tomas Olsson
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
| | - Jan Hillert
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
| | - Hans Grönlund
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
| | - Anna Glaser
- Department of Clinical Neuroscience and Centrum for Molecular Medicine at Karolinska, Institutet, Stockholm, Sweden
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Chen L, Su W, Chen H, Chen DQ, Wang M, Guo Y, Zhao YY. Proteomics for Biomarker Identification and Clinical Application in Kidney Disease. Adv Clin Chem 2018; 85:91-113. [PMID: 29655463 DOI: 10.1016/bs.acc.2018.02.005] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Treatment effectiveness for kidney disease is limited by lack of accuracy, sensitivity, specificity of diagnostic, prognostic, and therapeutic biomarkers. The gold standard test renal biopsy along with serum creatinine and proteinuria is often necessary to establish a diagnosis, particularly in glomerular disease. Proteomics has become a powerful tool for novel biomarker discovery in kidney disease. Novel proteomics offer earlier and more accurate diagnosis of renal pathology than possible with traditional biomarkers such as serum creatinine and urine protein. In addition, proteomic biomarkers could also be useful to choose the most suitable therapeutic targets. This review focuses on the current status of proteomic biomarkers from animal models (5/6 nephrectomy, unilateral ureteral obstruction, and diabetic nephropathy) and human studies (chronic kidney disease, glomerular diseases, transplantation, dialysis, acute and drug-induced kidney injury) to assess relevant findings and clinical usefulness. Current issues and problems related to the discovery, validation, and clinical application of proteomic biomarkers are discussed. We also describe several proteomic strategies highlighting technologic advancements, specimen selection, data processing and analysis. This review might provide help in future proteomic studies to improve the diagnosis and management of kidney disease.
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Affiliation(s)
- Lin Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Wei Su
- Baoji Central Hospital, Baoji, China
| | - Hua Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Dan-Qian Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Ming Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China
| | - Yan Guo
- University of New Mexico, Comprehensive Cancer Center, Albuquerque, NM, United States
| | - Ying-Yong Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, School of Life Science, Northwest University, Xi'an, China.
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11
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Abstract
Protein profiling through affinity proteomic approaches represents a powerful strategy for the analysis of human body fluids. Cerebrospinal fluid (CSF), being the fluid proximal to the central nervous system, is commonly analyzed in the context of neurological diseases, and can offer novel insights into the physiological state of the brain. Ultimately, and by analyzing the presence of brain-derived proteins in larger sets of samples that represent different phenotypes, profiling of CSF may serve as an important source to discover and verify disease-associated markers. Here, we describe a multiplexed and flexible protein profiling approach using antibody-based assays on suspension bead arrays. Through streamlined sample processing, protein biotinylation, and single-binder assay readout, this method enables high-throughput neuroproteomic analysis of up to 384 proteins in 384 samples.
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12
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Papadopoulos T, Krochmal M, Cisek K, Fernandes M, Husi H, Stevens R, Bascands JL, Schanstra JP, Klein J. Omics databases on kidney disease: where they can be found and how to benefit from them. Clin Kidney J 2016; 9:343-52. [PMID: 27274817 PMCID: PMC4886900 DOI: 10.1093/ckj/sfv155] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/21/2015] [Indexed: 02/07/2023] Open
Abstract
In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.
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Affiliation(s)
- Theofilos Papadopoulos
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Magdalena Krochmal
- Biotechnology Division, Biomedical Research Foundation Academy of Athens, Athens, Greece; Institute for Molecular Cardiovascular Research, Universitätsklinikum RWTH Aachen, Aachen, Germany
| | | | - Marco Fernandes
- BHF Glasgow Cardiovascular Research Centre , University of Glasgow , Glasgow , UK
| | - Holger Husi
- BHF Glasgow Cardiovascular Research Centre , University of Glasgow , Glasgow , UK
| | - Robert Stevens
- School of Computer Science , University of Manchester , Manchester , UK
| | - Jean-Loup Bascands
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Joost P Schanstra
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
| | - Julie Klein
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1048, Institut of Cardiovascular and Metabolic Disease, Toulouse, France; Université Toulouse III Paul-Sabatier, Toulouse, France
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13
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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14
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Mischak H, Critselis E, Hanash S, Gallagher WM, Vlahou A, Ioannidis JPA. Epidemiologic design and analysis for proteomic studies: a primer on -omic technologies. Am J Epidemiol 2015; 181:635-47. [PMID: 25792606 DOI: 10.1093/aje/kwu462] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 12/15/2014] [Indexed: 12/13/2022] Open
Abstract
Proteome analysis is increasingly being used in investigations elucidating the molecular basis of disease, identifying diagnostic and prognostic markers, and ultimately improving patient care. We appraised the current status of proteomic investigations using human samples, including the state of the art in proteomic technologies, from sample preparation to data evaluation approaches, as well as key epidemiologic, statistical, and translational issues. We systematically reviewed the most highly cited clinical proteomic studies published between January 2009 and March 2014 that included a minimum of 100 samples, as well as strategies that have been successfully implemented to enhance the translational relevance of proteomic investigations. Limited comparability between studies and lack of specification of biomarker context of use are frequently observed. Nevertheless, there are initial examples of successful biomarker discovery in cross-sectional studies followed by validation in high-risk longitudinal cohorts. Translational potential is currently hindered, as limitations in proteomic investigations are not accounted for. Interdisciplinary communication between proteomics experts, basic researchers, epidemiologists, and clinicians, an orchestrated assimilation of required resources, and a more systematic translational outlook for accumulation of evidence may augment the public health impact of proteomic investigations.
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15
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Abstract
All of life is regulated by complex and organized chemical reactions that help dictate when to grow, to move, to reproduce, and to die. When these processes go awry, or are interrupted by pathological agents, diseases such as cancer, autoimmunity, or infections can result. Cytokines, chemokines, growth factors, adipokines, and other chemical moieties make up a vast subset of these chemical reactions that are altered in disease states, and monitoring changes in these molecules could provide for the identification of disease biomarkers. From the first identification of carcinoembryonic antigen, to the discovery of prostate-specific antigen, to numerous others described within, biomarkers of disease are detectable in a plethora of sample types. The growing number of biomarkers for infection, autoimmunity, and cancer allow for increasingly early detection, to identification of novel drug targets, to prognostic indicators of disease outcome. However, more and more studies are finding that a single cytokine or growth factor is insufficient as a true disease biomarker and that a more global perspective is needed to understand true disease biology. Such a broad view requires a multiplexed platform for chemical detection, and antibody arrays meet and exceed this need by performing this detection in a high-throughput fashion. Herein, we will discuss how antibody arrays have evolved, and how they have helped direct new drug target design, helped identify therapeutic disease markers, and helped in earlier disease detection. From asthma to renal disease, and neurological dysfunction to immunologic disorders, antibody arrays afford a bright future for new biomarkers discovery.
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16
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Abstract
Proteomic biomarkers offer the hope of improving the management of patients with kidney diseases by enabling more accurate and earlier detection of renal pathology than is possible with currently available biomarkers, serum creatinine and urinary albumin. In addition, proteomic biomarkers could also be useful to define the most suitable therapeutic targets in a given patient or disease setting. This Review describes the current status of proteomic and protein biomarkers in the context of kidney diseases. The valuable lessons learned from early clinical studies of potential proteomic biomarkers in kidney disease are presented to give context to the newly identified biomarkers, which have potential for actual clinical implementation. This article also includes an overview of protein-based biomarker candidates that are undergoing development for use in nephrology, focusing on those with the greatest potential for clinical implementation. Relevant issues and problems associated with the discovery, validation and clinical application of proteomic biomarkers are discussed, along with suggestions for solutions that might help to guide the design of future proteomic studies. These improvements might remove some of the current obstacles to the utilization of proteomic biomarkers, with potentially beneficial results.
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17
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Overgaard M, Cangemi C, Jensen ML, Argraves WS, Rasmussen LM. Total and isoform-specific quantitative assessment of circulating fibulin-1 using selected reaction monitoring MS and time-resolved immunofluorometry. Proteomics Clin Appl 2015; 9:767-75. [PMID: 25331251 DOI: 10.1002/prca.201400070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 09/25/2014] [Accepted: 10/15/2014] [Indexed: 01/17/2023]
Abstract
PURPOSE Targeted proteomics using SRM-MS combined with stable-isotope dilution has emerged as a promising quantitative technique for the study of circulating protein biomarkers. The purpose of this study was to develop and characterize robust quantitative assays for the emerging cardiovascular biomarker fibulin-1 and its circulating isoforms in human plasma. EXPERIMENTAL DESIGN We used bioinformatics analysis to predict total and isoform-specific tryptic peptides for absolute quantitation using SRM-MS. Fibulin-1 was quantitated in plasma by nanoflow-LC-SRM-MS in undepleted plasma and time-resolved immunofluorometric assay (TRIFMA). Both methods were validated and compared to a commercial ELISA (CircuLex). Molecular size determination was performed under native conditions by SEC analysis coupled to SRM-MS and TRIFMA. RESULTS Absolute quantitation of total fibulin-1, isoforms -1C, and -1D was performed by SRM-MS. Fibulin-1C was the most abundant isoform in plasma. Circulating fibulin-1 isoforms were homo -or hetero multimeric complexes (range 318-364 kDa). Good correlation was obtained between SRM-MS and TRIFMA but not CircuLex. CONCLUSIONS AND CLINICAL RELEVANCE For biomarker studies using smaller cohorts, SRM-MS provides an alternative measure of total and specific fibulin-1 isoforms in undepleted plasma. For larger cohorts TRIFMA provides a faster platform for fibulin-1 quantitation in plasma. While the correlation between these methods was acceptable, low correlation was obtained between the commercial CircuLex assay and SRM-MS or TRIFMA.
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Affiliation(s)
- Martin Overgaard
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Claudia Cangemi
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - Martin L Jensen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - William S Argraves
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Lars M Rasmussen
- Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark.,Centre for Individualized Medicine in Arterial Diseases, Odense University Hospital, Odense, Denmark.,Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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18
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Jaffar J, Unger S, Corte TJ, Keller M, Wolters PJ, Richeldi L, Cerri S, Prêle CM, Hansbro PM, Argraves WS, Oliver RA, Oliver BG, Black JL, Burgess JK. Fibulin-1 predicts disease progression in patients with idiopathic pulmonary fibrosis. Chest 2014; 146:1055-1063. [PMID: 24832167 PMCID: PMC4188142 DOI: 10.1378/chest.13-2688] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/16/2014] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The underlying mechanisms of idiopathic pulmonary fibrosis (IPF) are unknown. This progressive disease has high mortality rates, and current models for prediction of mortality have limited value in identifying which patients will progress. We previously showed that the glycoprotein fibulin-1 is involved in enhanced proliferation and wound repair by mesenchymal cells and, thus, may contribute to lung fibrosis in IPF. METHODS Serum, lung tissue, and lung function values were obtained from four independent locations (Sydney, NSW, and Perth, WA, Australia; San Francisco, CA; and Modena, Italy). Patients with IPF were followed for a minimum of 1 year and progression was defined as a significant decline in lung function or death. Primary parenchymal lung fibroblasts of 15 patients with and without IPF were cultured under nonstimulatory conditions. Fibulin-1 levels in serum, and secreted or deposited by fibroblasts, were measured by western blot and in lung tissue by immunohistochemistry. RESULTS Serum fibulin-1 levels were increased in patients with IPF compared with subjects without lung disease (P = .006). Furthermore, tissue fibulin-1 levels were increased in patients with IPF (P = .02) and correlated negatively with lung function (r = -0.9, P < .05). Primary parenchymal fibroblasts from patients with IPF produced more fibulin-1 than those from subjects without IPF (P < .05). Finally, serum fibulin-1 levels at first blood draw predicted disease progression in IPF within 1 year (area under the curve , 0.71; 95% CI, 0.57-0.86; P = .012). CONCLUSIONS Fibulin-1 is a novel potential biomarker for disease progression in IPF and raises the possibility that it could be used as a target for the development of new treatments.
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Affiliation(s)
- Jade Jaffar
- The Woolcock Institute of Medical Research, The University of Sydney, Glebe, NSW, Australia; Discipline of Pharmacology, The University of Sydney, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, and Royal Prince Alfred Hospital (Sydney Local Health District), Sydney, NSW, Australia.
| | - Sofia Unger
- The Woolcock Institute of Medical Research, The University of Sydney, Glebe, NSW, Australia
| | - Tamera J Corte
- Sydney Medical School, The University of Sydney, and Royal Prince Alfred Hospital (Sydney Local Health District), Sydney, NSW, Australia
| | - Michael Keller
- Sydney Medical School, The University of Sydney, and Royal Prince Alfred Hospital (Sydney Local Health District), Sydney, NSW, Australia
| | - Paul J Wolters
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA
| | - Luca Richeldi
- Department of Respiratory Diseases, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy; Department of Interstitial Lung Disease, University of Southampton, Southampton, England
| | - Stefania Cerri
- Department of Respiratory Diseases, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Cecilia M Prêle
- Lung Institute of Western Australia, Centre for Asthma Allergy and Respiratory Research, The University of Western Australia, Perth, WA, Australia; Centre for Cell Therapy and Regenerative Medicine, School of Medicine and Pharmacology, The University of Western Australia and Western Australian Institute for Medical Research, Perth, WA, Australia
| | - Philip M Hansbro
- Priority Research Centre for Asthma and Respiratory Disease, The University of Newcastle and Hunter Medical Research Institute (HMRI), New Lambton Heights, NSW, Australia
| | - William Scott Argraves
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC
| | - Rema A Oliver
- Surgical and Orthopaedic Research Laboratories, Prince of Wales Clinical School, University of New South Wales, Randwick, NSW, Australia
| | - Brian G Oliver
- The Woolcock Institute of Medical Research, The University of Sydney, Glebe, NSW, Australia; School of Medical and Molecular Biosciences, The University of Technology Sydney, Sydney, NSW, Australia
| | - Judith L Black
- The Woolcock Institute of Medical Research, The University of Sydney, Glebe, NSW, Australia; Discipline of Pharmacology, The University of Sydney, Sydney, NSW, Australia
| | - Janette K Burgess
- The Woolcock Institute of Medical Research, The University of Sydney, Glebe, NSW, Australia; Discipline of Pharmacology, The University of Sydney, Sydney, NSW, Australia; Sydney Medical School, The University of Sydney, and Royal Prince Alfred Hospital (Sydney Local Health District), Sydney, NSW, Australia
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19
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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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20
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Drobin K, Nilsson P, Schwenk JM. Highly multiplexed antibody suspension bead arrays for plasma protein profiling. Methods Mol Biol 2014; 1023:137-45. [PMID: 23765623 DOI: 10.1007/978-1-4614-7209-4_8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Alongside the increasing availability of affinity reagents, antibody microarrays have become a powerful tool to screen for target proteins in complex samples. Applying directly labeled samples onto arrays instead of using sandwich assays offers an approach to facilitate a systematic, high-throughput, and flexible exploration of protein profiles in body fluids such as serum or plasma. As an alternative to planar arrays, a system based on color-coded beads for the creation of antibody arrays in suspension has become available to offer a microtiter plate-based option for screening larger number of samples with variable sets of capture reagents. A procedure was established for analyzing biotinylated samples without the necessity to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher pg/ml levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 samples for up to 384 proteins per assay.
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Affiliation(s)
- Kimi Drobin
- Science for Life Laboratory Stockholm, School of Biotechnology, KTH-Royal Institute of Technology, Stockholm, Sweden
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21
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Darmanis S, Cui T, Drobin K, Li SC, Öberg K, Nilsson P, Schwenk JM, Giandomenico V. Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors. PLoS One 2013; 8:e81712. [PMID: 24282616 PMCID: PMC3839889 DOI: 10.1371/journal.pone.0081712] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Accepted: 10/23/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Patients with well-differentiated small intestine neuroendocrine tumors (WD-SI-NETs) are most often diagnosed at a metastatic stage of disease, which reduces possibilities for a curative treatment. Thus new approaches for earlier detection and improved monitoring of the disease are required. MATERIALS AND METHODS Suspension bead arrays targeting 124 unique proteins with antibodies from the Human Protein Atlas were used to profile biotinylated serum samples. Discoveries from a cohort of 77 individuals were followed up in a cohort of 132 individuals both including healthy controls as well as patients with untreated primary WD-SI-NETs, lymph node metastases and liver metastases. RESULTS A set of 20 antibodies suggested promising proteins for further verification based on technically verified statistical significance. Proceeding, we assessed the classification performance in an independent cohort of patient serum, achieving, classification accuracy of up to 85% with different subsets of antibodies in respective pairwise group comparisons. The protein profiles of nine targets, namely IGFBP2, IGF1, SHKBP1, ETS1, IL1α, STX2, MAML3, EGR3 and XIAP were verified as significant contributors to tumor classification. CONCLUSIONS We propose new potential protein biomarker candidates for classifying WD-SI-NETs at different stage of disease. Further evaluation of these proteins in larger sample sets and with alternative approaches is needed in order to further improve our understanding of their functional relation to WD-SI-NETs and their eventual use in diagnostics.
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Affiliation(s)
- Spyros Darmanis
- Department of Immunology, Genetics, and Pathology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Tao Cui
- Department of Medical Sciences, Endocrine Oncology, Uppsala University, Uppsala, Sweden
| | - Kimi Drobin
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Su-Chen Li
- Department of Medical Sciences, Endocrine Oncology, Uppsala University, Uppsala, Sweden
| | - Kjell Öberg
- Department of Medical Sciences, Endocrine Oncology, Uppsala University, Uppsala, Sweden
- Clinic of Endocrine Oncology, Uppsala University Hospital, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
| | - Peter Nilsson
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
- * E-mail: (VG); (JMS)
| | - Valeria Giandomenico
- Department of Medical Sciences, Endocrine Oncology, Uppsala University, Uppsala, Sweden
- Science for Life Laboratory, Uppsala, Sweden
- * E-mail: (VG); (JMS)
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22
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Neiman M, Fredolini C, Johansson H, Lehtiö J, Nygren PÅ, Uhlén M, Nilsson P, Schwenk JM. Selectivity analysis of single binder assays used in plasma protein profiling. Proteomics 2013; 13:3406-10. [PMID: 24151238 PMCID: PMC4265267 DOI: 10.1002/pmic.201300030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2013] [Revised: 09/24/2013] [Accepted: 10/04/2013] [Indexed: 11/29/2022]
Abstract
The increasing availability of antibodies toward human proteins enables broad explorations of the proteomic landscape in cells, tissues, and body fluids. This includes assays with antibody suspension bead arrays that generate protein profiles of plasma samples by flow cytometer analysis. However, antibody selectivity is context dependent so it is necessary to corroborate on-target detection over off-target binding. To address this, we describe a concept to directly verify interactions from antibody-coupled beads by analysis of their eluates by Western blots and MS. We demonstrate selective antibody binding in complex samples with antibodies toward a set of chosen proteins with different abundance in plasma and serum, and illustrate the need to adjust sample and bead concentrations accordingly. The presented approach will serve as an important tool for resolving differential protein profiles from antibody arrays within plasma biomarker discoveries.
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Affiliation(s)
- Maja Neiman
- Science for Life Laboratory, School of Biotechnology, KTH-Royal Institute of Technology, Solna, Sweden
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23
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Scholze A, Bladbjerg EM, Sidelmann JJ, Diederichsen ACP, Mickley H, Nybo M, Argraves WS, Marckmann P, Rasmussen LM. Plasma concentrations of extracellular matrix protein fibulin-1 are related to cardiovascular risk markers in chronic kidney disease and diabetes. Cardiovasc Diabetol 2013; 12:6. [PMID: 23294625 PMCID: PMC3570481 DOI: 10.1186/1475-2840-12-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 01/03/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Fibulin-1 is one of a few extracellular matrix proteins present in blood in high concentrations. We aimed to define the relationship between plasma fibulin-1 levels and risk markers of cardiovascular disease. METHODS Plasma fibulin-1 was determined in subjects with chronic kidney disease (n = 32; median age 62.5, inter-quartile range 51 - 73 years) and 60 age-matched control subjects. Among kidney disease patients serological biomarkers related to cardiovascular disease (fibrinogen, interleukin 6, C-reactive protein) were measured. Arterial applanation tonometry was used to determine central hemodynamic and arterial stiffness indices. RESULTS We observed a positive correlation of fibulin-1 levels with age (r = 0.38; p = 0.033), glycated hemoglobin (r = 0.80; p = 0.003), creatinine (r = 0.35; p = 0.045), and fibrinogen (r = 0.39; p = 0.027). Glomerular filtration rate and fibulin-1 were inversely correlated (r = -0.57; p = 0.022). There was a positive correlation between fibulin-1 and central pulse pressure (r = 0.44; p = 0.011) and central augmentation pressure (r = 0.55; p = 0.001). In a multivariable regression model, diabetes, creatinine, fibrinogen and central augmentation pressure were independent predictors of plasma fibulin-1. CONCLUSION Increased plasma fibulin-1 levels were associated with diabetes and impaired kidney function. Furthermore, fibulin-1 levels were associated with hemodynamic cardiovascular risk markers. Fibulin-1 is a candidate in the pathogenesis of cardiovascular disease observed in chronic kidney disease and diabetes.
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Affiliation(s)
- Alexandra Scholze
- Clinical Research Unit, Department of Nephrology, Odense University Hospital, Odense, Denmark.
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24
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Kruger R, Schutte R, Huisman HW, Argraves WS, Rasmussen LM, Olsen MH, Schutte AE. NT-proBNP is associated with fibulin-1 in Africans: the SAfrEIC study. Atherosclerosis 2012; 222:216-21. [PMID: 22349089 DOI: 10.1016/j.atherosclerosis.2012.01.045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Revised: 01/18/2012] [Accepted: 01/28/2012] [Indexed: 11/17/2022]
Abstract
OBJECTIVES The N-terminal prohormone B-type natriuretic peptide (NT-proBNP) is involved in the regulation of volume load and secreted when systemic cardiac overload occurs. Fibulin-1 on the other hand is a component of many extracellular matrix proteins including those present in atherosclerotic lesions, expressed in elastin-containing fibres of blood vessels, and also in the heart. Due to an alarming prevalence of hypertensive heart disease in black South Africans, we investigated the associations of NT-proBNP with fibulin-1 and markers of arterial stiffness in Africans and Caucasians. METHODS We included 231 Africans and 238 Caucasians from South Africa aged 22-77 years. Serum NT-proBNP and fibulin-1 levels were determined, and arterial compliance and pulse wave velocity were measured. RESULTS Africans had significantly higher blood pressure and NT-proBNP levels than Caucasians and African men had higher fibulin-1 levels than Caucasian men. In single regression analysis, NT-proBNP was significantly associated with fibulin-1 in African men and Caucasian women. NT-proBNP correlated negatively with arterial compliance in all groups except Caucasian women. After partial adjustments, the association between NT-proBNP and fibulin-1 strengthened in African men only. After full adjustment in multiple regression analysis, the association of NT-proBNP with fibulin-1 was confirmed in African men (R(2)=0.41; β=0.26; p<0.01) and also in younger women (R(2)=0.34; β=0.251; p=0.012). CONCLUSIONS Only Africans indicated a significant independent association between NT-proBNP and fibulin-1, suggesting that cardiovascular alterations are already present in this relatively young African population as opposed to Caucasians.
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Affiliation(s)
- R Kruger
- Hypertension in Africa Research Team (HART), North-West University, Potchefstroom, South Africa.
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25
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Häggmark A, Neiman M, Drobin K, Zwahlen M, Uhlén M, Nilsson P, Schwenk JM. Classification of protein profiles from antibody microarrays using heat and detergent treatment. N Biotechnol 2011; 29:564-70. [PMID: 22023822 DOI: 10.1016/j.nbt.2011.10.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Revised: 10/09/2011] [Accepted: 10/09/2011] [Indexed: 01/16/2023]
Abstract
Antibody microarrays offer new opportunities for exploring the proteome and to identify biomarker candidates in human serum and plasma. Here, we have investigated the effect of heat and detergents on an antibody-based suspension bead array (SBA) assay using polyclonal antibodies and biotinylated plasma samples. With protein profiles from more than 2300 antibodies generated in 384-plex antibody SBAs, three major classes of heat and detergent susceptibility could be described. The results show that washing of the beads with SDS (rather than Tween) after target binding lowered intensity levels of basically all profiles and that about 50% of the profiles appeared to be lowered to a similar extent by heating of the sample. About 33% of the profiles appeared to be insensitive to heat treatment while another 17% showed a positive influence of heat to yield elevated profiles. The results suggest that the classification of antibodies is driven by the molecular properties of the antibody-antigen interaction and can generally not be predicted based on protein class or Western blot data. The experimental scheme presented here can be used to systematically categorize antibodies and thereby combine antibodies with similar properties into targeted arrays for analysis of plasma and serum.
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Affiliation(s)
- Anna Häggmark
- Science for Life Laboratory Stockholm, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, SE-171 21 Solna, Sweden
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