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Chen ZZ, Dufresne J, Bowden P, Miao M, Marshall JG. Extraction of naturally occurring peptides versus the tryptic digestion of proteins from fetal versus adult bovine serum for LC-ESI-MS/MS. Anal Biochem 2024; 689:115497. [PMID: 38461948 DOI: 10.1016/j.ab.2024.115497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 02/23/2024] [Accepted: 02/25/2024] [Indexed: 03/12/2024]
Abstract
The naturally occurring peptides and digested proteins of fetal versus adult bovine serum were compared by LC-ESI-MS/MS after correction against noise from blank injections and random MS/MS spectra as statistical controls. Serum peptides were extracted by differential precipitation with mixtures of acetonitrile and water. Serum proteins were separated by partition chromatography over quaternary amine resin followed by tryptic digestion. The rigorous X!TANDEM goodness of fit algorithm that has a low error rate as demonstrated by low FDR q-values (q ≤ 0.01) showed qualitative and quantitative agreement with the SEQUEST cross correlation algorithm on 12,052 protein gene symbols. Tryptic digestion provided a quantitative identification of the serum proteins where observation frequency reflected known high abundance. In contrast, the naturally occurring peptides reflected the cleavage of common serum proteins such as C4A, C3, FGB, HPX, A2M but also proteins in lower concentration such as F13A1, IK, collagens and protocadherins. Proteins associated with cellular growth and development such as actins (ACT), ribosomal proteins like Ribosomal protein S6 (RPS6), synthetic enzymes and extracellular matrix factors were enriched in fetal calf serum. In contrast to the large literature from cord blood, IgG light chains were absent from fetal serum as observed by LC-ESI-MS/MS and confirmed by ELISA.
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Affiliation(s)
- Zhuo Zhen Chen
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Jaimie Dufresne
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Peter Bowden
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - Ming Miao
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
| | - John G Marshall
- Research Analytical Biochemistry Laboratory (RABL), Department of Chemistry and Biology, Toronto Metropolitan University, Canada.
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2
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Schmitz T, Freuer D, Goßlau Y, Warm TD, Hyhlik-Dürr A, Linseisen J, Meisinger C, Kirchberger I. Can inflammatory plasma proteins predict Long COVID or Fatigue severity after SARS-CoV-2 infection? Virus Res 2024; 344:199363. [PMID: 38508399 PMCID: PMC10979265 DOI: 10.1016/j.virusres.2024.199363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/11/2024] [Accepted: 03/18/2024] [Indexed: 03/22/2024]
Abstract
OBJECTIVE To investigate whether specific immune response plasma proteins can predict an elevated risk of developing Long COVID symptoms or fatigue severity after SARS-CoV-2 infection. METHODS This study was based on 257 outpatients with test-confirmed SARS-CoV-2 infection between February 2020 and January 2021. At least 12 weeks after the acute infection, 92 plasma proteins were measured using the Olink Target 96 immune response panel (median time between acute infection and venous blood sampling was 38.8 [IQR: 24.0-48.0] weeks). The presence of Long COVID symptoms and fatigue severity was assessed 115.8 [92.5-118.6] weeks after the acute infection by a follow-up postal survey. Long COVID (yes/no) was defined as having one or more of the following symptoms: fatigue, shortness of breath, concentration or memory problems. The severity of fatigue was assessed using the Fatigue Assessment Scale (FAS). In multivariable-adjusted logistic and linear regression models the associations between each plasma protein (exposure) and Long COVID (yes/no) or severity of fatigue were investigated. RESULTS Nine plasma proteins were significantly associated with Long COVID before, but not after adjusting for multiple testing (FDR-adjustment): DFFA, TRIM5, TRIM21, HEXIM1, SRPK2, PRDX5, PIK3AP1, IFNLR1 and HCLS1. Moreover, a total of 10 proteins were significantly associated with severity of fatigue before FDR-adjustment: SRPK2, ITGA6, CLEC4G, HEXIM1, PPP1R9B, PLXNA4, PRDX5, DAPP1, STC1 and HCLS1. Only SRPK2 and ITGA6 remained significantly associated after FDR-adjustment. CONCLUSIONS This study demonstrates that certain immune response plasma proteins might play an important role in the pathophysiology of Long COVID and severity of fatigue after SARS-CoV-2 infection.
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Affiliation(s)
- Timo Schmitz
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany.
| | - Dennis Freuer
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Yvonne Goßlau
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Tobias Dominik Warm
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Alexander Hyhlik-Dürr
- Vascular Surgery, Faculty of Medicine, University of Augsburg, Stenglinstr. 2, 86156, Augsburg, Germany
| | - Jakob Linseisen
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Christa Meisinger
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Inge Kirchberger
- Epidemiology, Medical Faculty, University of Augsburg, Augsburg, Germany
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Ademhan Tural D, Emiralioglu N, Akin S, Alboga D, Ozsezen B, Nayir Buyuksahin H, Guzelkas I, Kasikci M, Sunman B, Gungor I, Yalcin E, Dogru D, Kiper N, Demirel AH, Ozcelik U. Galectin-3 levels in children with cystic fibrosis. Eur J Pediatr 2024; 183:2333-2342. [PMID: 38430280 DOI: 10.1007/s00431-024-05479-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/15/2024] [Accepted: 02/10/2024] [Indexed: 03/03/2024]
Abstract
Cystic fibrosis (CF) is a multisystemic disease in which airway obstruction, infection, and inflammation play a critical role in the pathogenesis and progression of CF lung disease. The carbohydrate-binding protein Galectin-3 is increased in several inflammatory and fibrotic diseases and has recently been forwarded as a biomarker in these diseases. We aimed to define the role of serum Galectin-3 in children with CF by comparison with healthy subjects. This is a cross-sectional, case-control study. 143 CF and 30 healthy subjects were enrolled in the study. Peripheral blood and sputum concentrations of Galectins-3, interleukin (IL)-17A, IL-8, and neutrophil elastase (NE) were determined with commercial ELISA kits. There was no significant difference between the groups in age and gender (p = 0.592, p = 0.613, respectively). Serum Galectin-3 and NE concentrations were higher in the patient group than in healthy controls (p = 0.002, p < 0.001, respectively). There were no significant differences between groups according to IL-17A and IL-8 concentrations. Serum Galectin-3 was correlated with age (r = 0.289, p < 0.001) and body mass index (BMI) (r = 0.493, p < 0.001) in children with CF. Sputum Galectin-3 levels are negatively correlated with percent predictive forced expiratory volume in 1 s (FEV1) (r = - 0.297, p = 0.029), FEV1 z-score, (r = - 0.316, p = 0.020), percent predictive forced vital capacity (FVC) (r = - 0.347, p = 0.010), and FVC z-score (r = - 0.373, p = 0.006). Conclusion: The study shows that serum Galectin-3 levels increased in clinically stable CF patients, and serum Galectin-3 response may depend on age, gender, and BMI. The sputum Galectin-3 was found to be negatively correlated with patients' lung functions. What is known: • Galectin-3 is a key regulator of chronic inflammation in the lung, liver, kidney, and tumor microenvironment. What is new: • Children with cystic fibrosis (CF) have higher serum Galectin-3 concentrations than healthy children. • Serum Galectin-3 expression influenced by age, BMI, and gender in children with CF.
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Affiliation(s)
- Dilber Ademhan Tural
- Department of Pediatric Pulmonology, Ankara Bilkent City Hospital, Ankara, Turkey.
| | - Nagehan Emiralioglu
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Senay Akin
- Department of Sport Medicine, Hacettepe University, Ankara, Turkey
| | - Didem Alboga
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Beste Ozsezen
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Halime Nayir Buyuksahin
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Ismail Guzelkas
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Merve Kasikci
- Department of Biostatistics, Hacettepe University, Ankara, Turkey
| | - Birce Sunman
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Irem Gungor
- Department of Sport Medicine, Hacettepe University, Ankara, Turkey
| | - Ebru Yalcin
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Deniz Dogru
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | - Nural Kiper
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
| | | | - Ugur Ozcelik
- Department of Pediatric Pulmonology, School of Medicine, Hacettepe University, Ihsan Dogramaci Children's Hospital, Ankara, Turkey
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Royer P, Björnson E, Adiels M, Álvez MB, Fagerberg L, Bäckhed F, Uhlén M, Gummesson A, Bergström G. Plasma proteomics for prediction of subclinical coronary artery calcifications in primary prevention. Am Heart J 2024; 271:55-67. [PMID: 38325523 DOI: 10.1016/j.ahj.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/09/2024]
Abstract
BACKGROUND AND AIMS Recent developments in high-throughput proteomic technologies enable the discovery of novel biomarkers of coronary atherosclerosis. The aims of this study were to test if plasma protein subsets could detect coronary artery calcifications (CAC) in asymptomatic individuals and if they add predictive value beyond traditional risk factors. METHODS Using proximity extension assays, 1,342 plasma proteins were measured in 1,827 individuals from the Impaired Glucose Tolerance and Microbiota (IGTM) study and 883 individuals from the Swedish Cardiopulmonary BioImage Study (SCAPIS) aged 50-64 years without history of ischaemic heart disease and with CAC assessed by computed tomography. After data-driven feature selection, extreme gradient boosting machine learning models were trained on the IGTM cohort to predict the presence of CAC using combinations of proteins and traditional risk factors. The trained models were validated in SCAPIS. RESULTS The best plasma protein subset (44 proteins) predicted CAC with an area under the curve (AUC) of 0.691 in the validation cohort. However, this was not better than prediction by traditional risk factors alone (AUC = 0.710, P = .17). Adding proteins to traditional risk factors did not improve the predictions (AUC = 0.705, P = .6). Most of these 44 proteins were highly correlated with traditional risk factors. CONCLUSIONS A plasma protein subset that could predict the presence of subclinical CAC was identified but it did not outperform nor improve a model based on traditional risk factors. Thus, support for this targeted proteomics platform to predict subclinical CAC beyond traditional risk factors was not found.
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Affiliation(s)
- Patrick Royer
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden; Department of Critical Care, University Hospital of Martinique, Fort-de-France, France
| | - Elias Björnson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden
| | - Martin Adiels
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden; School of Public Health and Community Medicine, Institute of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - María Bueno Álvez
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Bäckhed
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Anders Gummesson
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Genetics and Genomics, Gothenburg, Sweden
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, Gothenburg University, Gothenburg, Sweden; Region Västra Götaland, Sahlgrenska University Hospital, Department of Clinical Physiology, Gothenburg, Sweden.
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Kimura Y, Nakai Y, Ino Y, Akiyama T, Moriyama K, Ohira T, Saito T, Inaba Y, Kumagai K, Ryo A, Hirano H. Identification of gravity-responsive serum proteins in spaceflight mice using a quantitative proteomic approach with data-independent acquisition mass spectrometry. Proteomics 2024; 24:e2300214. [PMID: 38475964 DOI: 10.1002/pmic.202300214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 03/05/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Physical inactivity associated with gravity unloading, such as microgravity during spaceflight and hindlimb unloading (HU), can cause various physiological changes. In this study, we attempted to identify serum proteins whose levels fluctuated in response to gravity unloading. First, we quantitatively assessed changes in the serum proteome profiles of spaceflight mice using mass spectrometry with data-independent acquisition. The serum levels of several proteins involved in the responses to estrogen and glucocorticoid, blood vessel maturation, osteoblast differentiation, and ossification were changed by microgravity exposure. Furthermore, a collective evaluation of serum proteomic data from spaceflight and HU mice identified 30 serum proteins, including Mmp2, Igfbp2, Tnc, Cdh5, and Pmel, whose levels varied to a similar extent in both gravity unloading models. These changes in serum levels could be involved in the physiological changes induced by gravity unloading. A collective evaluation of serum, femur, and soleus muscle proteome data of spaceflight mice also showed 24 serum proteins, including Igfbp5, Igfbp3, and Postn, whose levels could be associated with biological changes induced by microgravity. This study examined serum proteome profiles in response to gravity unloading, and may help deepen our understanding of microgravity adaptation mechanisms during prolonged spaceflight missions.
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Affiliation(s)
- Yayoi Kimura
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Yusuke Nakai
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Yoko Ino
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Tomoko Akiyama
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Kayano Moriyama
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Takashi Ohira
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
- Department of Physiology and Regenerative Medicine, Kindai University Faculty of Medicine, Osaka, Japan
| | | | - Yutaka Inaba
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Ken Kumagai
- Department of Orthopaedic Surgery, Yokohama City University School of Medicine, Yokohama, Japan
| | - Akihide Ryo
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
| | - Hisashi Hirano
- Advanced Medical Research Center, Yokohama City University, Yokohama, Japan
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6
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He H, Wang L, Wang X, Zhang M. Artificial intelligence in serum protein electrophoresis: history, state of the art, and perspective. Crit Rev Clin Lab Sci 2024; 61:226-240. [PMID: 37909425 DOI: 10.1080/10408363.2023.2274325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
Serum protein electrophoresis (SPEP) is a valuable laboratory test that separates proteins from the blood based on their electrical charge and size. The test can detect and analyze various protein abnormalities, and the interpretation of graphic SPEP features plays a crucial role in the diagnosis and monitoring of conditions, such as myeloma. Furthermore, the advancement of artificial intelligence (AI) technology presents an opportunity to enhance the organization and optimization of analytical procedures by streamlining the process and reducing the potential for human error in SPEP analysis, thereby making the process more efficient and reliable. For instance, AI can assist in the identification of protein peaks, the calculation of their relative proportions, and the detection of abnormalities or inconsistencies. This review explores the characteristics and limitations of AI in SPEP, and the role of standardization in improving its clinical utility. It also offers guidance on the rational ordering and interpreting of SPEP results in conjunction with AI. Such integration can effectively reduce the time and resources required for manual analysis while improving the accuracy and consistency of the results.
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Affiliation(s)
- He He
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Lingfeng Wang
- College of Computer Science, Sichuan University, Chengdu, China
| | - Xia Wang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
| | - Mei Zhang
- Department of Laboratory Medicine, West China Hospital of Sichuan University, Chengdu, China
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7
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Sathyan S, Milman S, Ayers E, Gao T, Verghese J, Barzilai N. Plasma proteomic profile of abdominal obesity in older adults. Obesity (Silver Spring) 2024; 32:938-948. [PMID: 38439214 PMCID: PMC11039368 DOI: 10.1002/oby.24000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 12/30/2023] [Accepted: 01/07/2024] [Indexed: 03/06/2024]
Abstract
OBJECTIVE This study examines the plasma proteomic profile of abdominal obesity in older adults. METHODS The association of abdominal obesity (waist circumference [WC]) with 4265 plasma proteins identified using the SomaScan Assay was examined in 969 Ashkenazi Jewish participants (LonGenity cohort), aged 65 years and older (mean [SD] age 75.7 [6.7] years, 55.4% women), using regression models. Pathway analysis, as well as weighted correlation network analysis, was performed. WC was determined from the proteome using elastic net regression. RESULTS A total of 480 out of 4265 proteins were associated with WC in the linear regression model. Leptin (β [SE] = 12.363 [0.490]), inhibin β C chain (INHBC; β [SE] = 24.324 [1.448]), insulin-like growth factor-binding protein 2 (IGFBP-2; β [SE] = -12.782 [0.841]), heparan-sulfate 6-O-sulfotransferase 3 (H6ST3; β [SE] = -39.995 [2.729]), and matrix-remodeling-associated protein 8 (MXRA8; β [SE] = -27.101 [1.850]) were the top proteins associated with WC. Cell adhesion, extracellular matrix remodeling, and IGF transport pathways were the top enriched pathways associated with WC. WC signature determined from plasma proteins was highly correlated with measured WC (r = 0.80) and was associated with various metabolic and physical traits. CONCLUSIONS The study unveiled a multifaceted plasma proteomic profile of abdominal obesity in older adults, offering insights into its wide-ranging impact on the proteome. It also elucidated novel proteins, clusters of correlated proteins, and pathways that are intricately associated with abdominal obesity.
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Affiliation(s)
- Sanish Sathyan
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sofiya Milman
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emmeline Ayers
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tina Gao
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joe Verghese
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY, USA
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Nir Barzilai
- Institute for Aging Research, Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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8
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Nygren D, Torisson G, Happonen L, Mellhammar L, Linder A, Elf J, Yan H, Welinder C, Holm K. Proteomic Characterization of Plasma in Lemierre's Syndrome. Thromb Haemost 2024; 124:432-440. [PMID: 37857346 PMCID: PMC11038868 DOI: 10.1055/a-2195-3927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 10/18/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND The underlying mechanisms of thrombosis in Lemierre's syndrome and other septic thrombophlebitis are incompletely understood. Therefore, in this case control study we aimed to generate hypotheses on its pathogenesis by studying the plasma proteome in patients with these conditions. METHODS All patients with Lemierre's syndrome in the Skåne Region, Sweden, were enrolled prospectively during 2017 to 2021 as cases. Age-matched patients with other severe infections were enrolled as controls. Patient plasma samples were analyzed using label-free data-independent acquisition liquid chromatography tandem mass spectrometry. Differentially expressed proteins in Lemierre's syndrome versus other severe infections were highlighted. Functions of differentially expressed proteins were defined based on a literature search focused on previous associations with thrombosis. RESULTS Eight patients with Lemierre's syndrome and 15 with other severe infections were compared. Here, 20/449 identified proteins were differentially expressed between the groups. Of these, 14/20 had functions previously associated with thrombosis. Twelve of 14 had a suggested prothrombotic effect in Lemierre's syndrome, whereas 2/14 had a suggested antithrombotic effect. CONCLUSION Proteins involved in several thrombogenic pathways were differentially expressed in Lemierre's syndrome compared to other severe infections. Among identified proteins, several were associated with endothelial damage, platelet activation, and degranulation, and warrant further targeted studies.
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Affiliation(s)
- David Nygren
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Gustav Torisson
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
- Department of Translational Medicine, Clinical Infection Medicine, Lund University, Malmö, Sweden
| | - Lotta Happonen
- Division of Infection Medicine, Lund University, Lund, Sweden
| | - Lisa Mellhammar
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Adam Linder
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
| | - Johan Elf
- Center of Thrombosis and Haemostasis, Skåne University Hospital, Malmö, Sweden
| | - Hong Yan
- The Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Charlotte Welinder
- The Swedish National Infrastructure for Biological Mass Spectrometry (BioMS), Lund University, Lund, Sweden
| | - Karin Holm
- Division of Infection Medicine, Lund University, Lund, Sweden
- Department of Infectious Diseases, Skåne University Hospital, Lund/Malmö, Sweden
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9
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Li N, Huang J, He S, Zheng Q, Ye F, Qin Z, Wang D, Xiao T, Mao M, Zhou Z, Tang T, Zhang L, Wang X, Wang Y, Lyu Y, Liu L, Dai L, Wang J, Guan J. The development of a novel zeolite-based assay for efficient and deep plasma proteomic profiling. J Nanobiotechnology 2024; 22:164. [PMID: 38600601 PMCID: PMC11007927 DOI: 10.1186/s12951-024-02404-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Plasma proteins are considered the most informative source of biomarkers for disease diagnosis and monitoring. Mass spectrometry (MS)-based proteomics has been applied to identify biomarkers in plasma, but the complexity of the plasma proteome and the extremely large dynamic range of protein abundances in plasma make the clinical application of plasma proteomics highly challenging. We designed and synthesized zeolite-based nanoparticles to deplete high-abundance plasma proteins. The resulting novel plasma proteomic assay can measure approximately 3000 plasma proteins in a 45 min chromatographic gradient. Compared to those in neat and depleted plasma, the plasma proteins identified by our assay exhibited distinct biological profiles, as validated in several public datasets. A pilot investigation of the proteomic profile of a hepatocellular carcinoma (HCC) cohort identified 15 promising protein features, highlighting the diagnostic value of the plasma proteome in distinguishing individuals with and without HCC. Furthermore, this assay can be easily integrated with all current downstream protein profiling methods and potentially extended to other biofluids. In conclusion, we established a robust and efficient plasma proteomic assay with unprecedented identification depth, paving the way for the translation of plasma proteomics into clinical applications.
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Affiliation(s)
- Nan Li
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jingnan Huang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Shangwen He
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Qiaocong Zheng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Department of Oncology, People's Hospital of YangJiang, Yangjiang, 529500, Guangdong, China
| | - Feng Ye
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhengxing Qin
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Dong Wang
- College of Chemistry and Chemical Engineering, China University of Petroleum (East China), Qingdao, 266580, Shandong, China
| | - Ting Xiao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Mengyuan Mao
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhenhua Zhou
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Tingxi Tang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Longshan Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Xiaoqing Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yingqiao Wang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ying Lyu
- Department of Traditional Chinese Medicine, Nanfang Hospital,, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Laiyu Liu
- Chronic Airways Diseases Laboratory, Department of Respiratory and Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Lingyun Dai
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Jigang Wang
- Department of Nephrology, Shenzhen Key Laboratory of Kidney Diseases, Shenzhen People's Hospital, (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, China.
- School of Medicine, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
| | - Jian Guan
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China.
- Guangdong Province Key Laboratory of Molecular Tumor Pathology, Guangzhou, 510515, Guangdong, China.
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10
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Zaza Q, Ousguine A, Biaz A, Idrissi SEM, Dami A, Abilkassem R, Bouhsain S. Anodic Peak on Capillary Serum Protein Electrophoresis. Clin Lab 2024; 70. [PMID: 38469781 DOI: 10.7754/clin.lab.2023.230945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
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11
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Naddaf M. Long-COVID signatures identified in huge analysis of blood proteins. Nature 2024; 626:19-20. [PMID: 38238626 DOI: 10.1038/d41586-024-00158-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
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12
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Santiago VF, Rosa-Fernandes L, Macedo-da-Silva J, Angeli CB, Mule SN, Marinho CRF, Torrecilhas AC, Marie SNK, Palmisano G. Isolation of Extracellular Vesicles Using Titanium Dioxide Microspheres. Adv Exp Med Biol 2024; 1443:1-22. [PMID: 38409413 DOI: 10.1007/978-3-031-50624-6_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Extracellular vesicles (EVs) are bilayer membrane particles released from several cell types to the extracellular environment. EVs have a crucial role in cell-cell communication, involving different biological processes in health and diseases. Due to the potential of biomarkers for several diseases as diagnostic and therapeutic tools, it is relevant to understand the biology of the EVs and their content. One of the current challenges involving EVs is regarding the purification method, which is a critical step for EV's functional and characterization studies. Ultracentrifugation is the most used method for EV isolation, where the nanoparticles are separated in sequential centrifugation to isolate the EVs based on their size. However, for viscous biofluids such as plasma, there is a co-isolation of the most abundant proteins, which can impair the EV's protein identification due to the low abundance of these proteins and signal suppression by the most abundant plasma proteins. Emerging techniques have gained attention in recent years. Titanium dioxide (TiO2) is one of the most promising techniques due to its property for selective isolation based on the interaction with phospholipids in the EV membrane. Using a small amount of TiO2 beads and a low volume of plasma, it is possible to isolate EVs with reduced plasma protein co-isolation. This study describes a comprehensive workflow for the isolation and characterization of plasma extracellular vesicles (EVs) using mass spectrometry-based proteomics techniques. The aim of this chapter is describe the EV isolation using TiO2 beads enrichment and high-throughput mass spectrometry techniques to efficiently identify the protein composition of EVs in a fast and straightforward manner.
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Affiliation(s)
- Veronica Feijoli Santiago
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, Australia
| | - Janaina Macedo-da-Silva
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudia B Angeli
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Simon Ngao Mule
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Claudio R F Marinho
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Claudia Torrecilhas
- Instituto de Ciências Ambientais, Químicas e Farmacêuticas; Departamento de Ciências Farmacêuticas; Laboratório de Imunologia Celular e Bioquímica de Fungos e Protozoários. Departamento de Ciências Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Suely N K Marie
- Laboratory of Molecular and Cellular Biology (LIM15), Department of Neurology, Fac-uldade de Medicina FMUSP, University of São Paulo, São Paulo, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia.
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13
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Li Y, Li H, Ma W, Maegele M, Tang Y, Gu Z. Proteomic profiling of serum exosomes reveals acute phase response and promotion of inflammatory and platelet activation pathways in patients with heat stroke. PeerJ 2023; 11:e16590. [PMID: 38107577 PMCID: PMC10725172 DOI: 10.7717/peerj.16590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 11/14/2023] [Indexed: 12/19/2023] Open
Abstract
Background: The pathological mechanism of heat stroke (HS) involves the acute phase response, unbalanced immunological/inflammatory reactions, and coagulation initiation, especially platelet activation. Although exosomes contain proteins involved in these biological processes, their protein cargo levels and potential roles in HS remain unknown. This study explored the serum exosome protein expression patterns after HS and their potential roles in the pathogenesis of HS. Methods: Blood samples were collected from ten patients diagnosed with HS upon admission to the intensive care unit (six with severe HS and four with mild HS). Samples from six healthy volunteers were included as control. Using ultracentrifugation, exosomes were prudently isolated, and their protein contents were profiled using liquid chromatography-tandem mass spectrometry analysis with isobaric tags for relative and absolute quantification-based proteomics. Results: Compared with healthy volunteers, patients with HS showed significant changes in the levels of 33 exosomal proteins (23 upregulated and 10 downregulated). The most upregulated proteins included serum amyloid A-1 (SAA-1), von Willebrand factor (vWF), S100A8, and histone H3. In addition, SAA-1, vWF, platelet membrane glycoprotein, S100A8, and histone H3 were more enriched in the exosomes from patients with severe HS than from those with mild HS. Gene ontology analysis revealed that the HS-modulated exosomal proteins were mostly related to inflammatory response, including the acute-phase response, platelet activation/degranulation, and innate immune response. Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed significant enrichment of proteins in the IL-17 signaling pathway, platelet activation, neutrophil extracellular trap formation, Fc epsilon RI signaling pathway, chemokine signaling pathway, and NOD-like receptor signaling pathway, among others. Several serum exosomal proteins, including SAA-1, vWF, and S100A8, which are related to the acute phase, inflammatory response, and platelet activation, were confirmed to be elevated in patients with HS, and were significantly correlated with disease severity, organ dysfunction, and death. Conclusion: Overall, this study explores the potential role of the serum exosomal proteome in the inflammatory response and platelet activation in HS, suggests the pathological mechanisms underlying HS-induced injuries, and recommends reliable exosomal biomarkers for predicting HS prognosis.
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Affiliation(s)
- Yue Li
- Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, China
- Department of Treatment, Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- Department of Intensive Care Unit, General Hospital of Southern Theatre Command of PLA, Guangzhou, China
- Department of Emergency Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Huan Li
- Department of ICU, Sun Yat-sen University Cancer Center, Guangzhou, China
- Sate Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wenjuan Ma
- Department of ICU, Sun Yat-sen University Cancer Center, Guangzhou, China
- Sate Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Marc Maegele
- University Witten/Herdecke (UW/H), Köln, German
- Department for Trauma and Orthopedic Surgery, Cologne-Merheim Medical Center (CMMC), University Witten/Herdecke (UW/H), Campus Cologne-Merheim, Ostmerheimerstr, Köln, Germany
| | - Youqing Tang
- Department of Emergency Medicine, Guangdong Second Provincial General Hospital, Guangzhou, China
| | - Zhengtao Gu
- Academy of Orthopedics, Guangdong Province, Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Guangzhou, China
- Department of Treatment, Center for Traumatic Injuries, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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14
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Kazimierska K, Biel W. Comparative Analysis of Spray-Dried Porcine Plasma and Hydrolyzed Porcine Protein as Animal-Blood-Derived Protein Ingredients for Pet Nutrition. Molecules 2023; 28:7917. [PMID: 38067646 PMCID: PMC10707792 DOI: 10.3390/molecules28237917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/28/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023] Open
Abstract
Spray-dried porcine plasma (SDPP) and hydrolyzed porcine protein (HPP) are promising animal protein ingredients sourced from healthy animal blood that are rich in biomolecules, including immunoglobulins, and can be an appropriate and valuable animal protein ingredient to supply the growing need for ingredients that meet the natural needs of carnivorous pets. The aim of this preliminary study was to analyze the chemical composition and mineral profile of a novel HPP compared with results for SDPP. The basic composition analysis followed AOAC guidelines, and the elemental analysis utilized atomic absorption spectrometry. Statistical comparisons employed an independent Student's t-test (p < 0.05). Both SDPP and HPP are low in moisture (<4.3%) and rich in protein, with SDPP significantly exceeding HPP (75.4% vs. 71.4%). They boast mineral richness indicated by crude ash content (12.7% and 12.5%), featuring Na, K, P, and the trace elements Mo, Fe, and Zn. Notably, SDPP contains elevated molybdenum levels (51.39 mg/100 g vs. 10.93 mg/100 g in HPP), an essential element for diverse animal functions. Quantifying these elements in raw materials aids in achieving optimal nutrient levels in the final product. The study underscores SDPP as an excellent protein source, confirming that its nutritional value is similar to or better than other protein components in pet food.
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Affiliation(s)
- Katarzyna Kazimierska
- Department of Monogastric Animal Sciences, Division of Animal Nutrition and Food, West Pomeranian University of Technology in Szczecin, 29 Klemensa Janickiego, 71270 Szczecin, Poland;
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15
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Pranata J, Dunn M, Drake M, Barbano DM. Effect of temperature and protein concentration on the protein types within the ultracentrifugation supernatant of liquid micellar casein concentrate. J Dairy Sci 2023; 106:8331-8340. [PMID: 37641294 DOI: 10.3168/jds.2023-23595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/05/2023] [Indexed: 08/31/2023]
Abstract
Liquid micellar casein concentrate (MCC) is an ideal milk-based protein ingredient for neutral-pH ready-to-drink beverages. The texture and mouthfeel of liquid MCC-based beverages depend on the beverage protein content, as well as the composition of soluble proteins in the aqueous phase around the casein micelle. The objective of this study was to determine the composition of soluble proteins in the aqueous phase around the casein micelles in skim milk and liquid MCC containing 7.0% and 11.6% protein content. Skim milk was pasteurized and concentrated to 7% protein content by microfiltration and then to 18% protein content by ultrafiltration. The 18% MCC was then serially diluted with distilled water to produce 11.6% and 7.0% protein MCC. Skim milk, 7.0% MCC, and 11.6% MCC representing starting materials with different protein concentrations were each ultracentrifuged at 100,605 × g for 2 h. The ultracentrifugation for each of the starting materials was performed at 3 different temperatures: 4°C, 20°C, and 37°C. The ultracentrifugation supernatants were collected to represent the aqueous phase around the casein micelle in MCC solutions. The supernatants were analyzed by Kjeldahl to determine the crude protein, casein, and casein as a percentage of crude protein content, and by sodium dodecyl sulfate PAGE to determine the composition of the individual proteins. Most of the proteins in MCC supernatant (about 45%) were casein proteolysis products. The remaining proteins in the MCC supernatant consisted of a combination of intact αS-, β-, and κ-caseins (about 40%) and serum proteins (14-18%). Concentrations of αS-casein and β-casein in the supernatant increased with decreasing temperature, especially at higher protein concentrations. Temperature and interaction between temperature and protein explained about 80% of the variation in concentration of supernatant αS- and β-caseins. Concentration of supernatant κ-casein, casein proteolysis products, and serum protein increased with increasing MCC protein concentration, and MCC protein concentration explained most of the variation in supernatant κ-casein, casein proteolysis products, and serum protein concentrations. Predicted MCC apparent viscosity was positively associated with the dissociation of αS- and β-caseins. Optimal beverage viscosity could be achieved by controlling the dissociation of these proteins in MCC.
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Affiliation(s)
- Joice Pranata
- Northeast Dairy Food Research Center, Department of Food Science, Cornell University, Ithaca, NY 14853
| | - Marshall Dunn
- Southeast Dairy Foods Research Center, Department of Food, Bioprocessing and Nutritional Sciences, North Carolina State University, Raleigh, NC 27695
| | - MaryAnne Drake
- Southeast Dairy Foods Research Center, Department of Food, Bioprocessing and Nutritional Sciences, North Carolina State University, Raleigh, NC 27695
| | - David M Barbano
- Northeast Dairy Food Research Center, Department of Food Science, Cornell University, Ithaca, NY 14853.
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16
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Bai HH, Wang XF, Zhang BY, Liu W. A comparison of size exclusion chromatography-based tandem strategies for plasma exosome enrichment and proteomic analysis. Anal Methods 2023; 15:6245-6251. [PMID: 37955202 DOI: 10.1039/d3ay01704d] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2023]
Abstract
Proteomic analysis of exosomes from human plasma faces a tremendous challenge mainly due to the low abundance of the exosome itself and the complexity of the plasma matrix. Therefore, enrichment of exosomes from human plasma is an essential and indispensable step for large scale and in depth proteomic analysis. Size exclusion chromatography (SEC) is one of the most extensively used methods for exosome isolation from human plasma and many SEC-based tandem methods were established in order to increase the purity of the enriched exosomes and thus the accuracy of the proteomic analysis. To compare the advantages and disadvantages of the different isolation methods and subsequently to promote the establishment of a standardized method for plasma proteomic research, the capacities of the direct SEC method, the combination of SEC with ultracentrifugation (SEC-UC), ultrafiltration (SEC-UF), and titanium dioxide microspheres (SEC-TiO2) were systematically evaluated for exosome isolation from human plasma and thus proteomic analysis. The results demonstrated that the SEC-based tandem methods were superior to the direct SEC method in the purity of exosomes isolated from human plasma. Additionally, the SEC-UC method possessed the highest number of the total identified proteins and the overlapped proteins with the top 100 exosome markers in comparison with the other methods. The SEC-TiO2 method displayed the biggest capacity for plasma protein deleting. We expect that the research will have more beneficial values in the field of exosome research.
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Affiliation(s)
- H H Bai
- Department of Pharmacy, Beijing YouAn Hospital, Capital Medical University, Beijing 100069, PR China.
| | - X F Wang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - B Y Zhang
- Beijing Shijitan Hospital, Capital Medical University, Beijing 100038, PR China
| | - W Liu
- Department of Pharmacy, Beijing YouAn Hospital, Capital Medical University, Beijing 100069, PR China.
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17
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Koeppel L, Denkinger CM, Wyss R, Broger T, Chegou NN, Dunty JM, Scott K, Cáceres T, Dutoit E, Ugarte-Gil C, Nicol M, Gotuzzo E, Corstjens PLAM, Geluk A, Sutherland J, Sigal GB, Moreau E, Albertini A, Mantsoki A, Ongarello S, Walzl G, Fernandez Suarez M. Diagnostic performance of host protein signatures as a triage test for active pulmonary TB. J Clin Microbiol 2023; 61:e0026423. [PMID: 37724874 PMCID: PMC10654108 DOI: 10.1128/jcm.00264-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 07/14/2023] [Indexed: 09/21/2023] Open
Abstract
The current four-symptom screen recommended by the World Health Organization (WHO) is widely used as screen to initiate diagnostic testing for active pulmonary tuberculosis (TB), yet the performance is poor especially when TB prevalence is low. In contrast, more sensitive molecular tests are less suitable for placement at primary care level in low-resource settings. In order to meet the WHO End TB targets, new diagnostic approaches are urgently needed to find the missing undiagnosed cases. Proteomics-derived blood host biomarkers have been explored because protein detection technologies are suitable for the point-of-care setting and could meet cost targets. This study aimed to find a biomarker signature that fulfills WHO's target product profile (TPP) for a TB screening. Twelve blood-based protein biomarkers from three sample populations (Vietnam, Peru, and South Africa) were analyzed individually and in combinations via advanced statistical methods and machine learning algorithms. The combination of I-309, SYWC and kallistatin showed the most promising results to discern active TB throughout the data sets meeting the TPP for a triage test in adults from two countries (Peru and South Africa). The top-performing individual markers identified at the global level (I-309 and SYWC) were also among the best-performing markers at country level in South Africa and Vietnam. This analysis clearly shows that a host protein biomarker assay is feasible in adults for certain geographical regions based on one or two biomarkers with a performance that meets minimal WHO TPP criteria.
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Affiliation(s)
- Lisa Koeppel
- Division of Infectious Disease and Tropical Medicine, University of Heidelberg, Heidelberg, Germany
| | - Claudia M. Denkinger
- Division of Infectious Disease and Tropical Medicine, University of Heidelberg, Heidelberg, Germany
- FIND, Geneva, Switzerland
- German Center for Infection Research (DZIF), Heidelberg University Hospital Partner Site, Heidelberg, Germany
| | | | - Tobias Broger
- Division of Infectious Disease and Tropical Medicine, University of Heidelberg, Heidelberg, Germany
- FIND, Geneva, Switzerland
| | - Novel N. Chegou
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jill M. Dunty
- Meso Scale Diagnostics, LLC, Rockville, Maryland, USA
| | - Kerry Scott
- Meso Scale Diagnostics, LLC, Rockville, Maryland, USA
| | - Tatiana Cáceres
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Elloise Dutoit
- Division of Medical Microbiology at the University of Cape Town (UCT), Cape Town, South Africa
| | - Cesar Ugarte-Gil
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- School of Medicine, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Mark Nicol
- Division of Medical Microbiology at the University of Cape Town (UCT), Cape Town, South Africa
- Division of Infection and Immunity, School of Biomedical Sciences, University of Western Australia, Perth, Australia
| | - Eduardo Gotuzzo
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- School of Medicine, Universidad Peruana Cayetano Heredia (UPCH), Lima, Peru
| | - Paul L. A. M. Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Jayne Sutherland
- TB Research Group, Vaccines and Immunity Theme, MRC Unit The Gambia at LSHTM, Banjul, Gambia
| | | | | | | | | | | | - Gerhard Walzl
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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18
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Sheley WC, Cray C, Wilber MQ, Carter ED, Kumar R, Hardman RH, Towe AE, Gray MJ, Miller DL. A Pilot Study Investigating Plasma Protein Electrophoresis in One Anuran and Six Urodelan Species. J Wildl Dis 2023; 59:796-803. [PMID: 37846919 DOI: 10.7589/jwd-d-23-00004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/02/2023] [Indexed: 10/18/2023]
Abstract
As threats to amphibian health increase, there is a growing need for diagnostic tools to assess and monitor their health status. Plasma protein electrophoresis has proven to be useful in other nonmammalian species. It enables quantification of protein fractions in plasma that may be altered in various disease processes, and is therefore useful in narrowing down differential diagnoses and detecting inflammation, in combination with other modalities such as biochemical and hematologic testing. The amphibian electrophoretogram must be defined before baseline reference intervals are obtained across species. Agarose gel electrophoresis was performed on plasma samples collected from presumed clinically normal individuals of one anuran and six urodelans: Osteopilus septentrionalis (n=2), Gyrinophilus porphyriticus (n=1), Notophthalmus viridescens (n=1), Eurycea guttolineata (n=2), Amphiuma tridactylum (n=2), Cryptobranchus alleganiensis (n=5), and Siren lacertina (n=6). The electrophoretograms varied in number of fractions between each species; however, the number of fractions was consistent within a species. An albumin migrating fraction was consistently observed in all species. A prealbumin migrating fraction was identified in species that primarily use organs other than skin for respiration. This study provides preliminary examples of a normal plasma protein electrophoretogram for seven amphibian species. Further studies quantifying reference intervals and identification of protein fractions will help establish protein electrophoresis as a useful tool in amphibian health investigations.
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Affiliation(s)
- Wesley C Sheley
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, Tennessee 37996, USA
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Carolyn Cray
- Division of Comparative Pathology, University of Miami Miller School of Medicine, 1600 NW 10th Avenue, Miami, Florida 33136, USA
| | - Mark Q Wilber
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Edward D Carter
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Rajeev Kumar
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Rebecca H Hardman
- One Health Initiative, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Anastasia E Towe
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, Tennessee 37996, USA
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Matthew J Gray
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
| | - Debra L Miller
- Department of Biomedical and Diagnostic Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, Tennessee 37996, USA
- Center for Wildlife Health, University of Tennessee Institute of Agriculture, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
- One Health Initiative, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, Tennessee 37996, USA
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19
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Eldjarn GH, Ferkingstad E, Lund SH, Helgason H, Magnusson OT, Gunnarsdottir K, Olafsdottir TA, Halldorsson BV, Olason PI, Zink F, Gudjonsson SA, Sveinbjornsson G, Magnusson MI, Helgason A, Oddsson A, Halldorsson GH, Magnusson MK, Saevarsdottir S, Eiriksdottir T, Masson G, Stefansson H, Jonsdottir I, Holm H, Rafnar T, Melsted P, Saemundsdottir J, Norddahl GL, Thorleifsson G, Ulfarsson MO, Gudbjartsson DF, Thorsteinsdottir U, Sulem P, Stefansson K. Large-scale plasma proteomics comparisons through genetics and disease associations. Nature 2023; 622:348-358. [PMID: 37794188 PMCID: PMC10567571 DOI: 10.1038/s41586-023-06563-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 08/22/2023] [Indexed: 10/06/2023]
Abstract
High-throughput proteomics platforms measuring thousands of proteins in plasma combined with genomic and phenotypic information have the power to bridge the gap between the genome and diseases. Here we performed association studies of Olink Explore 3072 data generated by the UK Biobank Pharma Proteomics Project1 on plasma samples from more than 50,000 UK Biobank participants with phenotypic and genotypic data, stratifying on British or Irish, African and South Asian ancestries. We compared the results with those of a SomaScan v4 study on plasma from 36,000 Icelandic people2, for 1,514 of whom Olink data were also available. We found modest correlation between the two platforms. Although cis protein quantitative trait loci were detected for a similar absolute number of assays on the two platforms (2,101 on Olink versus 2,120 on SomaScan), the proportion of assays with such supporting evidence for assay performance was higher on the Olink platform (72% versus 43%). A considerable number of proteins had genomic associations that differed between the platforms. We provide examples where differences between platforms may influence conclusions drawn from the integration of protein levels with the study of diseases. We demonstrate how leveraging the diverse ancestries of participants in the UK Biobank helps to detect novel associations and refine genomic location. Our results show the value of the information provided by the two most commonly used high-throughput proteomics platforms and demonstrate the differences between them that at times provides useful complementarity.
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Affiliation(s)
| | | | - Sigrun H Lund
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Hannes Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Bjarni V Halldorsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | - Agnar Helgason
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | | | - Magnus K Magnusson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Saedis Saevarsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Ingileif Jonsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Hilma Holm
- deCODE Genetics/Amgen, Reykjavik, Iceland
| | | | - Pall Melsted
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | | | - Magnus O Ulfarsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Electrical and Computer Engineering, University of Iceland, Reykjavik, Iceland
| | - Daniel F Gudbjartsson
- deCODE Genetics/Amgen, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Unnur Thorsteinsdottir
- deCODE Genetics/Amgen, Reykjavik, Iceland
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Kari Stefansson
- deCODE Genetics/Amgen, Reykjavik, Iceland.
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland.
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20
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Dhindsa RS, Burren OS, Sun BB, Prins BP, Matelska D, Wheeler E, Mitchell J, Oerton E, Hristova VA, Smith KR, Carss K, Wasilewski S, Harper AR, Paul DS, Fabre MA, Runz H, Viollet C, Challis B, Platt A, Vitsios D, Ashley EA, Whelan CD, Pangalos MN, Wang Q, Petrovski S. Rare variant associations with plasma protein levels in the UK Biobank. Nature 2023; 622:339-347. [PMID: 37794183 PMCID: PMC10567546 DOI: 10.1038/s41586-023-06547-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 08/15/2023] [Indexed: 10/06/2023]
Abstract
Integrating human genomics and proteomics can help elucidate disease mechanisms, identify clinical biomarkers and discover drug targets1-4. Because previous proteogenomic studies have focused on common variation via genome-wide association studies, the contribution of rare variants to the plasma proteome remains largely unknown. Here we identify associations between rare protein-coding variants and 2,923 plasma protein abundances measured in 49,736 UK Biobank individuals. Our variant-level exome-wide association study identified 5,433 rare genotype-protein associations, of which 81% were undetected in a previous genome-wide association study of the same cohort5. We then looked at aggregate signals using gene-level collapsing analysis, which revealed 1,962 gene-protein associations. Of the 691 gene-level signals from protein-truncating variants, 99.4% were associated with decreased protein levels. STAB1 and STAB2, encoding scavenger receptors involved in plasma protein clearance, emerged as pleiotropic loci, with 77 and 41 protein associations, respectively. We demonstrate the utility of our publicly accessible resource through several applications. These include detailing an allelic series in NLRC4, identifying potential biomarkers for a fatty liver disease-associated variant in HSD17B13 and bolstering phenome-wide association studies by integrating protein quantitative trait loci with protein-truncating variants in collapsing analyses. Finally, we uncover distinct proteomic consequences of clonal haematopoiesis (CH), including an association between TET2-CH and increased FLT3 levels. Our results highlight a considerable role for rare variation in plasma protein abundance and the value of proteogenomics in therapeutic discovery.
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Affiliation(s)
- Ryan S Dhindsa
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US.
| | - Oliver S Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benjamin B Sun
- Translational Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Bram P Prins
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dorota Matelska
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Eleanor Wheeler
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Jonathan Mitchell
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Erin Oerton
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ventzislava A Hristova
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US
| | - Katherine R Smith
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Keren Carss
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Sebastian Wasilewski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Andrew R Harper
- Clinical Development, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dirk S Paul
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Margarete A Fabre
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Heiko Runz
- Translational Sciences, Research & Development, Biogen Inc., Cambridge, MA, US
| | - Coralie Viollet
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Benjamin Challis
- Translational Science and Experimental Medicine, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Adam Platt
- Translational Science and Experimental Medicine, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Dimitrios Vitsios
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Euan A Ashley
- Division of Cardiology, Department of Medicine, Stanford University, Palo Alto, CA, USA
| | | | | | - Quanli Wang
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, MD, US
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK.
- Department of Medicine, Austin Health, University of Melbourne, Melbourne, Victoria, Australia.
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21
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Sun BB, Chiou J, Traylor M, Benner C, Hsu YH, Richardson TG, Surendran P, Mahajan A, Robins C, Vasquez-Grinnell SG, Hou L, Kvikstad EM, Burren OS, Davitte J, Ferber KL, Gillies CE, Hedman ÅK, Hu S, Lin T, Mikkilineni R, Pendergrass RK, Pickering C, Prins B, Baird D, Chen CY, Ward LD, Deaton AM, Welsh S, Willis CM, Lehner N, Arnold M, Wörheide MA, Suhre K, Kastenmüller G, Sethi A, Cule M, Raj A, Burkitt-Gray L, Melamud E, Black MH, Fauman EB, Howson JMM, Kang HM, McCarthy MI, Nioi P, Petrovski S, Scott RA, Smith EN, Szalma S, Waterworth DM, Mitnaul LJ, Szustakowski JD, Gibson BW, Miller MR, Whelan CD. Plasma proteomic associations with genetics and health in the UK Biobank. Nature 2023; 622:329-338. [PMID: 37794186 PMCID: PMC10567551 DOI: 10.1038/s41586-023-06592-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
The Pharma Proteomics Project is a precompetitive biopharmaceutical consortium characterizing the plasma proteomic profiles of 54,219 UK Biobank participants. Here we provide a detailed summary of this initiative, including technical and biological validations, insights into proteomic disease signatures, and prediction modelling for various demographic and health indicators. We present comprehensive protein quantitative trait locus (pQTL) mapping of 2,923 proteins that identifies 14,287 primary genetic associations, of which 81% are previously undescribed, alongside ancestry-specific pQTL mapping in non-European individuals. The study provides an updated characterization of the genetic architecture of the plasma proteome, contextualized with projected pQTL discovery rates as sample sizes and proteomic assay coverages increase over time. We offer extensive insights into trans pQTLs across multiple biological domains, highlight genetic influences on ligand-receptor interactions and pathway perturbations across a diverse collection of cytokines and complement networks, and illustrate long-range epistatic effects of ABO blood group and FUT2 secretor status on proteins with gastrointestinal tissue-enriched expression. We demonstrate the utility of these data for drug discovery by extending the genetic proxied effects of protein targets, such as PCSK9, on additional endpoints, and disentangle specific genes and proteins perturbed at loci associated with COVID-19 susceptibility. This public-private partnership provides the scientific community with an open-access proteomics resource of considerable breadth and depth to help to elucidate the biological mechanisms underlying proteo-genomic discoveries and accelerate the development of biomarkers, predictive models and therapeutics1.
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Affiliation(s)
- Benjamin B Sun
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
| | - Joshua Chiou
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Matthew Traylor
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Tom G Richardson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
- Genomic Sciences, GlaxoSmithKline, Stevenage, UK
| | | | | | - Chloe Robins
- Genomic Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | | | - Liping Hou
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | | | - Oliver S Burren
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | - Kyle L Ferber
- Biostatistics, Research and Development, Biogen, Cambridge, MA, USA
| | | | - Åsa K Hedman
- External Science and Innovation Target Sciences, Worldwide Research, Development and Medical, Pfizer, Stockholm, Sweden
| | - Sile Hu
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Tinchi Lin
- Analytics and Data Sciences, Biogen, Cambridge, MA, USA
| | - Rajesh Mikkilineni
- Data Science Institute, Takeda Development Center Americas, Cambridge, MA, USA
| | | | | | - Bram Prins
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Denis Baird
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Chia-Yen Chen
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA
| | - Lucas D Ward
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Aimee M Deaton
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | | | - Carissa M Willis
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Nick Lehner
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Maria A Wörheide
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Anil Raj
- Calico Life Sciences, San Francisco, CA, USA
| | | | | | - Mary Helen Black
- Population Analytics, Janssen Research & Development, Spring House, PA, USA
| | - Eric B Fauman
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Joanna M M Howson
- Human Genetics Centre of Excellence, Novo Nordisk Research Centre Oxford, Oxford, UK
| | | | | | - Paul Nioi
- Alnylam Human Genetics, Discovery & Translational Research, Alnylam Pharmaceuticals, Cambridge, MA, USA
| | - Slavé Petrovski
- Centre for Genomics Research, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | | | - Erin N Smith
- Takeda Development Center Americas, San Diego, CA, USA
| | - Sándor Szalma
- Takeda Development Center Americas, San Diego, CA, USA
| | | | | | | | | | - Melissa R Miller
- Internal Medicine Research Unit, Worldwide Research, Development and Medical, Pfizer, Cambridge, MA, USA
| | - Christopher D Whelan
- Translational Sciences, Research & Development, Biogen, Cambridge, MA, USA.
- Neuroscience Data Science, Janssen Research & Development, Cambridge, MA, USA.
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22
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da Fonseca LA, Montiani-Ferreira F, Soto J, Jones MP, Zagaya N, Cray C. Comparison of agarose gel and capillary zone electrophoresis methods with preliminary reference interval generation using capillary zone electrophoresis in bald eagles (Haliaeetus leucocephalus). Vet Clin Pathol 2023; 52:452-460. [PMID: 36973576 DOI: 10.1111/vcp.13210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/27/2022] [Accepted: 10/22/2022] [Indexed: 03/29/2023]
Abstract
BACKGROUND Electrophoresis can be used to aid in the diagnosis of different diseases in avian species. Capillary zone electrophoresis (CZE) is an automated method that is proposed to be superior to the dye methods used in agarose gel electrophoresis (AGE). However, reference intervals (RIs) for CZE in avian species and comparison studies between electrophoretic methods are lacking. OBJECTIVES The goals of the current study were to compare AGE and CZE methods and determine reference intervals for CZE using plasma from bald eagles (Haliaeetus leucocephalus). METHODS Heparinized plasma samples from 44 bald eagles (mean age 18.7 years) under managed care were examined by AGE and CZE. Method comparison analyses were completed, as well as the generation of preliminary RIs using the CZE method and ASVCP guidelines. RESULTS Passing-Bablok regression and Bland-Altman plots demonstrate that these methods are not equivalent. All fractions were significantly correlated between the methods except for alpha 1 globulin. Inter-assay and intra-assay CVs for CZE were lower or comparable to AGE and ranged from 2.4% to 15.4%, and 0.8% to 8.3%, respectively. CZE resolved more fractions than AGE with two fractions observed in the beta and gamma region vs one for AGE in each region. CONCLUSIONS CZE provided improved resolution and reproducibility for the quantitation of protein fractions in the bald eagle. Although most fraction results correlated with AGE, these methods were judged as not equivalent, necessitating method-specific Rls. Reference intervals generated from a limited number of mostly aged individuals under managed care should be considered preliminary; additional studies will aid in the production of more robust intervals.
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Affiliation(s)
- Leandro Abreu da Fonseca
- Departamento de Veterinária, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Division of Comparative Pathology, Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Fabiano Montiani-Ferreira
- Division of Comparative Pathology, Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
- Departamento de Medicina Veterinária, Universidade Federal do Paraná, Curitiba, Puerto Rico, Brazil
| | - Jeny Soto
- Division of Comparative Pathology, Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | | | - Nancy Zagaya
- The American Eagle Foundation, Pigeon Forge, Tennessee, USA
| | - Carolyn Cray
- Division of Comparative Pathology, Department of Pathology & Laboratory Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
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23
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Manthei DM, Li SH. A Beta Region Peak on Serum Protein Electrophoresis. Clin Chem 2023; 69:1092-1093. [PMID: 38518296 DOI: 10.1093/clinchem/hvad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/27/2023] [Indexed: 03/24/2024]
Affiliation(s)
- David M Manthei
- University of Michigan, Department of Pathology, Ann Arbor, United States
| | - Shih-Hon Li
- University of Michigan, Department of Pathology, Ann Arbor, United States
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24
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Meng Z, Zhang S, Li W, Wang Y, Wang M, Liu X, Liu CL, Liao S, Liu T, Yang C, Lindholt JS, Rasmussen LM, Obel LM, Stubbe J, Diederichsen AC, Sun Y, Chen Y, Yu PB, Libby P, Shi GP, Guo J. Cationic proteins from eosinophils bind bone morphogenetic protein receptors promoting vascular calcification and atherogenesis. Eur Heart J 2023; 44:2763-2783. [PMID: 37279475 PMCID: PMC10393071 DOI: 10.1093/eurheartj/ehad262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 02/28/2023] [Accepted: 04/17/2023] [Indexed: 06/08/2023] Open
Abstract
AIMS Blood eosinophil count and eosinophil cationic protein (ECP) concentration are risk factors of cardiovascular diseases. This study tested whether and how eosinophils and ECP contribute to vascular calcification and atherogenesis. METHODS AND RESULTS Immunostaining revealed eosinophil accumulation in human and mouse atherosclerotic lesions. Eosinophil deficiency in ΔdblGATA mice slowed atherogenesis with increased lesion smooth muscle cell (SMC) content and reduced calcification. This protection in ΔdblGATA mice was muted when mice received donor eosinophils from wild-type (WT), Il4-/-, and Il13-/- mice or mouse eosinophil-associated-ribonuclease-1 (mEar1), a murine homologue of ECP. Eosinophils or mEar1 but not interleukin (IL) 4 or IL13 increased the calcification of SMC from WT mice but not those from Runt-related transcription factor-2 (Runx2) knockout mice. Immunoblot analyses showed that eosinophils and mEar1 activated Smad-1/5/8 but did not affect Smad-2/3 activation or expression of bone morphogenetic protein receptors (BMPR-1A/1B/2) or transforming growth factor (TGF)-β receptors (TGFBR1/2) in SMC from WT and Runx2 knockout mice. Immunoprecipitation showed that mEar1 formed immune complexes with BMPR-1A/1B but not TGFBR1/2. Immunofluorescence double-staining, ligand binding, and Scatchard plot analysis demonstrated that mEar1 bound to BMPR-1A and BMPR-1B with similar affinity. Likewise, human ECP and eosinophil-derived neurotoxin (EDN) also bound to BMPR-1A/1B on human vascular SMC and promoted SMC osteogenic differentiation. In a cohort of 5864 men from the Danish Cardiovascular Screening trial and its subpopulation of 394 participants, blood eosinophil counts and ECP levels correlated with the calcification scores of different arterial segments from coronary arteries to iliac arteries. CONCLUSION Eosinophils release cationic proteins that can promote SMC calcification and atherogenesis using the BMPR-1A/1B-Smad-1/5/8-Runx2 signalling pathway.
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Affiliation(s)
- Zhaojie Meng
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Shuya Zhang
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
- Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research & Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of the First Affiliated Hospital, Hainan Medical University, Haikou 571199, Hainan, China
| | - Wei Li
- College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Yunzhe Wang
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Minjie Wang
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Xin Liu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Cong-Lin Liu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
- Department of Cardiology, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Sha Liao
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Tianxiao Liu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Chongzhe Yang
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
- Department of Geriatrics, National Key Clinical Specialty, Guangzhou First People's Hospital, Guangzhou Medical University, Guangzhou 510000, Guangdong, China
| | - Jes S Lindholt
- Department of Cardiothoracic and Vascular Surgery, Odense University Hospital, Odense, Denmark
- Elite Research Centre of Individualized Treatment for Arterial Disease, University Hospital, Odense, Denmark
| | - Lars M Rasmussen
- Elite Research Centre of Individualized Treatment for Arterial Disease, University Hospital, Odense, Denmark
- Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
| | - Lasse M Obel
- Elite Research Centre of Individualized Treatment for Arterial Disease, University Hospital, Odense, Denmark
- Department of Clinical Biochemistry, Odense University Hospital, Odense, Denmark
| | - Jane Stubbe
- Cardiovascular and Renal Research unit, Institute for Molecular Medicine, University of Southern Denmark, Odense, Denmark
| | - Axel C Diederichsen
- Elite Research Centre of Individualized Treatment for Arterial Disease, University Hospital, Odense, Denmark
- Department of Cardiology, Odense University Hospital, Odense, Denmark
| | - Yong Sun
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Birmingham VA Medical Center, Research Department, Birmingham, AL 35294, USA
| | - Yabing Chen
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Birmingham VA Medical Center, Research Department, Birmingham, AL 35294, USA
| | - Paul B Yu
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Peter Libby
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Guo-Ping Shi
- Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, NRB-7, Boston, MA 02115, USA
| | - Junli Guo
- Hainan Provincial Key Laboratory for Tropical Cardiovascular Diseases Research & Key Laboratory of Emergency and Trauma of Ministry of Education, Institute of Cardiovascular Research of the First Affiliated Hospital, Hainan Medical University, Haikou 571199, Hainan, China
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25
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Arfuso F, Piccione G, Guttadauro A, Monteverde V, Giudice E, Giannetto C. Serum C-reactive Protein and Protein Electrophoretic Pattern Correlated With Age in Horses. J Equine Vet Sci 2023; 126:104561. [PMID: 37160186 DOI: 10.1016/j.jevs.2023.104561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/22/2023] [Accepted: 05/06/2023] [Indexed: 05/11/2023]
Abstract
Inflammaging or chronic, low-grade inflammation is a phenomenon characterizing age-related pathologies and natural processes in aging tissues. This study aimed to investigate the effect of age on the serum levels of C-reactive protein and protein electrophoretic pattern in horses. Thirty Italian Saddle horses from the same horse training center, were enrolled and divided in three equal groups according to their age: Group A (2-4 years), Group B (7-10 years), Group C (15-20 years). Blood samples were collected from each horse to evaluate hematological parameters and the serum concentration of C-reactive protein (CRP), total proteins, albumin, α1-, α-2, β1-, β2- and γ-globulins. One-way analysis of variance showed an age-related difference in the concentration of CRP, α1- and α2-globulins (P < 0.001) which increased with aging. Albumin and albumin:globulin ratio showed lower values in Groups B and C than Group A (P < 0.001). Age of horses showed a negative correlation with the values of albumin, and a positive correlation with CRP, α1- and α2-globulins concentration. The results of the current study suggest an increased acute phase response in adult and old horses compared to young ones. As α-globulin fractions include many other acute phase proteins (APPs) in addition to CRP, further studies to assess what other APPs could be involved in chronic inflammation or "inflammaging" are recommended in horse in order to improve knowledge on the key inflammatory biomarkers during aging in this species.
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Affiliation(s)
- Francesca Arfuso
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Giuseppe Piccione
- Department of Veterinary Sciences, University of Messina, Messina, Italy..
| | | | - Vincenzo Monteverde
- Experimental Zooprophylactic Institute of Sicily, A. Mirri, Via Gino Marinuzzi, Palermo, Italy
| | - Elisabetta Giudice
- Department of Veterinary Sciences, University of Messina, Messina, Italy
| | - Claudia Giannetto
- Department of Veterinary Sciences, University of Messina, Messina, Italy
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26
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Burton JB, Carruthers NJ, Stemmer PM. Enriching extracellular vesicles for mass spectrometry. Mass Spectrom Rev 2023; 42:779-795. [PMID: 34632607 DOI: 10.1002/mas.21738] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
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Affiliation(s)
- Jordan B Burton
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
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Dowling P, Ohlendieck K. DIGE Analysis of Immunodepleted Plasma. Methods Mol Biol 2023; 2596:363-375. [PMID: 36378451 DOI: 10.1007/978-1-0716-2831-7_25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
This chapter focuses on upstream immunodepletion of high-abundance proteins from plasma samples and subsequent analysis by fluorescence two-dimensional difference gel electrophoresis (2D-DIGE). The abundances of proteins in biofluid proteomes, such as serum, plasma, saliva, and bronchoalveolar lavage fluid (BALF), can exceed ten orders of magnitude. This substantial dynamic range is problematic for the detection of medium and low-abundance proteins by 2D-DIGE analysis. To increase the detection, quantification, and identification of medium-low-abundance proteins, the targeted depletion of known abundant proteins with antibody columns has been successfully employed. From the literature, it is clear that the performance of abundant protein depletion with immunodepletion columns has been successful in broadening the coverage of the biofluid proteome and facilitating the identification of disease-specific biomarkers. The task for a successful biomarker strategy involves the combination of a reproducible and robust fractionation method, coupled with a highly accurate quantitative method, a task that is exemplified by combining both immunodepletion and 2D-DIGE together to discover significant proteins associated with the disease phenotype.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland
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Abstract
The discovery of clinically relevant biomarkers using gel-based proteomics has proven extremely challenging, principally because of the large dynamic range of protein abundances in biofluids such as blood and the fact that only a small number of proteins constitute the vast majority of total blood protein mass. Various separation, depletion, enrichment, and quantitative developments coupled with improvements in gel-based protein quantification technologies, specifically fluorescence two-dimensional difference gel electrophoresis (2D-DIGE), have contributed to significant improvements in the detection and identification of lower abundance proteins. One of these enrichment technologies, ProteoMiner, is the focus of this chapter. The ProteoMiner technology utilizes hexapeptide bead library with huge diversity to bind and enrich low-abundance proteins but at the same time suppresses the concentration of high-abundance proteins in subsequent analysis.
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Affiliation(s)
- Sandra Murphy
- Charles River Laboratories, Saffron Walden, Essex, United Kingdom
| | - Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, Co. Kildare, Ireland.
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Daves M, Piccin A, Vicidomini C, De Luisi A, Mega A. Utility of serum indices in a particular case of serum protein electrophoresis. Biochem Med (Zagreb) 2022; 32:030802. [PMID: 35966258 PMCID: PMC9344864 DOI: 10.11613/bm.2022.030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/06/2022] [Indexed: 11/03/2022] Open
Abstract
Screening and measurement of monoclonal (M) proteins are commonly performed using capillary zone electrophoresis (CZE). The identification of M-protein or monoclonal component (CM) is an essential requirement for diagnosis and monitoring of monoclonal gammopathies. The detection of CM has been largely improved by CZE. Capillary electrophoresis estimates CM more accurately, because absence of variation due to different dye binding affinities of proteins as instead seen with agarose gel electrophoresis. However, interferences can be present in CZE. This occurs because all substances absorbing at 200 nm can be identified. Recognition and handling of specimens exhibiting such interferences is essential to ensure accurate diagnostic and patient safety. We herein report on an unusual case of serum protein electrophoresis, to highlight that laboratory staff must be aware of and familiarise with the information provided by laboratory instruments. For example, in the case of serum indices, about specimen quality.
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Affiliation(s)
- Massimo Daves
- Clinical Biochemical Laboratory, Hospital of Bolzano, Bolzano, Italy
- Corresponding author:
| | - Andrea Piccin
- Northern Ireland Blood Transfusion Service, Belfast, UK
- Department of Internal Medicine V, Medical University of Innsbruck, Innsbruck, Austria
- Department of Industrial Engineering, University of Trento, Trento, Italy
| | | | - Antonia De Luisi
- Clinical Biochemical Laboratory, Hospital of Bolzano, Bolzano, Italy
| | - Andrea Mega
- Division of Gastroenterology, Hospital of Bolzano, Bolzano, Italy
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Triebel J, Markl-Hahn H, Harris D, Bertsch T. High Resolution Continuous Elution Electrophoresis for the Evaluation of Low Abundance Serum Proteins. Clin Lab 2022; 68. [PMID: 35443591 DOI: 10.7754/clin.lab.2021.210827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND The evaluation of low abundance biomarkers in the circulating low molecular weight serum proteome is an important source of information. Techniques for sample preparation to remove high abundant proteins and to enrich the low molecular weight fraction are usually required prior to novel biomarker detection. METHODS A continuous elution electrophoresis was used to separate the low molecular weight serum proteins from the high abundance serum proteins, such as albumin and immunoglobulins. Centrifugal concentration, SDS-PAGE, and total protein staining were performed to analyze eluted protein fractions. RESULTS Consecutive concentrated serum protein fractions demonstrate separation at a high resolution of 1 - 2 kDa below 20 kDa. CONCLUSIONS Continuous elution electrophoresis is an adequate method to eliminate high abundance proteins which interfere with the detection of low abundance biomarkers in the low molecular weight proteome and to enrich its proteins for subsequent detection and clinical evaluation.
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Rumer KK, Hedou J, Tsai A, Einhaus J, Verdonk F, Stanley N, Choisy B, Ganio E, Bonham A, Jacobsen D, Warrington B, Gao X, Tingle M, McAllister TN, Fallahzadeh R, Feyaerts D, Stelzer I, Gaudilliere D, Ando K, Shelton A, Morris A, Kebebew E, Aghaeepour N, Kin C, Angst MS, Gaudilliere B. Integrated Single-cell and Plasma Proteomic Modeling to Predict Surgical Site Complications: A Prospective Cohort Study. Ann Surg 2022; 275:582-590. [PMID: 34954754 PMCID: PMC8816871 DOI: 10.1097/sla.0000000000005348] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE The aim of this study was to determine whether single-cell and plasma proteomic elements of the host's immune response to surgery accurately identify patients who develop a surgical site complication (SSC) after major abdominal surgery. SUMMARY BACKGROUND DATA SSCs may occur in up to 25% of patients undergoing bowel resection, resulting in significant morbidity and economic burden. However, the accurate prediction of SSCs remains clinically challenging. Leveraging high-content proteomic technologies to comprehensively profile patients' immune response to surgery is a promising approach to identify predictive biological factors of SSCs. METHODS Forty-one patients undergoing non-cancer bowel resection were prospectively enrolled. Blood samples collected before surgery and on postoperative day one (POD1) were analyzed using a combination of single-cell mass cytometry and plasma proteomics. The primary outcome was the occurrence of an SSC, including surgical site infection, anastomotic leak, or wound dehiscence within 30 days of surgery. RESULTS A multiomic model integrating the single-cell and plasma proteomic data collected on POD1 accurately differentiated patients with (n = 11) and without (n = 30) an SSC [area under the curve (AUC) = 0.86]. Model features included coregulated proinflammatory (eg, IL-6- and MyD88- signaling responses in myeloid cells) and immunosuppressive (eg, JAK/STAT signaling responses in M-MDSCs and Tregs) events preceding an SSC. Importantly, analysis of the immunological data obtained before surgery also yielded a model accurately predicting SSCs (AUC = 0.82). CONCLUSIONS The multiomic analysis of patients' immune response after surgery and immune state before surgery revealed systemic immune signatures preceding the development of SSCs. Our results suggest that integrating immunological data in perioperative risk assessment paradigms is a plausible strategy to guide individualized clinical care.
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Affiliation(s)
- Kristen K. Rumer
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Julien Hedou
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Amy Tsai
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Jakob Einhaus
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Hematology, Oncology, Clinical Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
| | - Franck Verdonk
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Sorbonne University, GRC 29, DMU DREAM, Assistance Publique-Hôpitaux de Paris, France
| | - Natalie Stanley
- Department of Computer Science and Computational Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Benjamin Choisy
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Edward Ganio
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Adam Bonham
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Danielle Jacobsen
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Beata Warrington
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Xiaoxiao Gao
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Martha Tingle
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Tiffany N. McAllister
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Ramin Fallahzadeh
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Dorien Feyaerts
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Ina Stelzer
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Dyani Gaudilliere
- Division of Plastic and Reconstructive Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Kazuo Ando
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Andrew Shelton
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Arden Morris
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Electron Kebebew
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Nima Aghaeepour
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Biomedical Data Sciences, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
| | - Cindy Kin
- Division of General Surgery, Department of Surgery, School of Medicine, Stanford University, Stanford, CA
| | - Martin S. Angst
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
| | - Brice Gaudilliere
- Department of Anesthesiology, Perioperative and Pain Medicine, School of Medicine, Stanford University, Stanford, CA
- Department of Pediatrics, Stanford University, Stanford, CA
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Gaither C, Popp R, Zahedi RP, Borchers CH. Multiple reaction monitoring-mass spectrometry enables robust quantitation of plasma proteins regardless of whole blood processing delays that may occur in the clinic. Mol Cell Proteomics 2022; 21:100212. [PMID: 35182769 PMCID: PMC9062485 DOI: 10.1016/j.mcpro.2022.100212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 01/24/2022] [Accepted: 02/13/2022] [Indexed: 12/23/2022] Open
Abstract
Plasma is an important biofluid for clinical research and diagnostics. In the clinic, unpredictable delays—from minutes to hours—between blood collection and plasma generation are often unavoidable. These delays can potentially lead to protein degradation and modification and might considerably affect intact protein measurement methods such as sandwich enzyme-linked immunosorbent assays that bind proteins on two epitopes to increase specificity, thus requiring largely intact protein structures. Here, we investigated, using multiple reaction monitoring mass spectrometry (MRM-MS), how delays in plasma processing affect peptide-centric “bottom-up” proteomics. We used validated assays for proteotypic peptide surrogates of 270 human proteins to analyze plasma generated after whole blood had been kept at room temperature from 0 to 40 h to mimic delays that occur in the clinic. Moreover, we evaluated the impact of different plasma-thawing conditions on MRM-based plasma protein quantitation. We demonstrate that >90% of protein concentration measurements were unaffected by the thawing procedure and by up to 40-h delayed plasma generation, reflected by relative standard deviations (RSDs) of <30%. Of the 159 MRM assays that yielded quantitative results in 60% of the measured time points, 139 enabled a stable protein quantitation (RSD <20%), 14 showed a slight variation (RSD 20–30%), and 6 appeared unstable/irreproducible (RSD > 30%). These results demonstrate the high robustness and thus the potential for MRM-based plasma-protein quantitation to be used in a clinical setting. In contrast to enzyme-linked immunosorbent assay, peptide-based MRM assays do not require intact three-dimensional protein structures for an accurate and precise quantitation of protein concentrations in the original sample. Delays in whole blood processing often cannot be avoided in the clinic. These delays might affect measurements by intact protein assays such as ELISA. The impact on LC/MRM was evaluated using validated assays to quantify 270 proteins. >95% of the measured concentrations had RSDs <30% between delays of 0 to 40 h. Protein quantitation by LC/MRM-MS is robust against pitfalls in the clinical setting.
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Affiliation(s)
| | - Robert Popp
- MRM Proteomics Inc, Montreal, Quebec, Canada
| | - René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.
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Yang M, Huang Y, Wu H, Li C, Ling S, Sun J, Shen H, Yue B, Zhang X. Blood transcriptome analysis revealed the immune changes and immunological adaptation of wildness training giant pandas. Mol Genet Genomics 2022; 297:227-239. [PMID: 34985592 DOI: 10.1007/s00438-021-01841-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 11/23/2021] [Indexed: 01/06/2023]
Abstract
The giant panda (Ailuropoda melanoleuca) is a global flagship species for biodiversity conservation. As the time for captive giant pandas to be released into the wild matures, wildness training is provided to allow adaptation to their natural environment. It is assumed that changes in the immune system would be integral in this adaptation from captive to wild, where many more pathogens would be encountered in their natural habitats. Therefore, this study aims to determine the expression changes of immune-related genes and their potential as immunoassay markers for adaptation monitoring in wildness training giant pandas, and then to understand the adaptation strategy of wildness training giant pandas to the wild environment, thereby improving the success rate of panda reintroduction. We obtained 300 differentially expressed genes (DEGs) by RNA-seq, with 239 up-regulated and 61 down-regulated DEGs in wildness training giant pandas compared to captive pandas. Functional enrichment analysis indicated that up-regulated DEGs were enriched in several immune-related terms and pathways. There were 21 immune-related DEGs, in which most of them were up-regulated in wildness training giant pandas, including several critical innate and cellular immune genes. IL1R2 was the most significantly up-regulated gene and is a signature of homeostasis within the immune system. In the protein-protein interaction (PPI) analysis, CXCL8, CXCL10, and CCL5 were identified as the hub immune genes. Our results suggested that wildness training giant pandas have stronger innate and cellular immunity than captive giant pandas, and we proposed that a gene set of CXCL8, CXCL10, CCL5, CD3D, NFKBIA, TBX21, IL12RB2, and IL1R2 may serve as potential immunoassay markers to monitor and assess the immune status of wildness training giant pandas. Our study offers the first insight into immune alterations of wildness training giant pandas, paving the way for monitoring and evaluating the immune status of giant pandas when reintroducing them into the wild.
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Affiliation(s)
- Miao Yang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Yan Huang
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Honglin Wu
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Caiwu Li
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Shanshan Ling
- Key Laboratory of State Forestry and Grassland Administration on Conservation Biology of Rare Animals in The Giant Panda National Park, China Conservation and Research Center for the Giant Panda, Dujiangyan, 623006, Sichuan, People's Republic of China
| | - Jie Sun
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Haibo Shen
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Bisong Yue
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife, College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, 610064, People's Republic of China.
- Sichuan University, No. 24 South Section 1, Yihuan Road, Chengdu, 610065, Sichuan, China.
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Bayrakci N, Ozkan G, Mutlu LC, Erdem L, Yildirim I, Gulen D, Celikkol A. Relationship between serum soluble endothelial protein C receptor level and COVID-19 findings. Blood Coagul Fibrinolysis 2021; 32:550-555. [PMID: 34321403 PMCID: PMC8630928 DOI: 10.1097/mbc.0000000000001070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 07/01/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022]
Abstract
Coronavirus-related disease-2019 (COVID-19)-associated coagulopathy presents predominantly with thrombosis and leads to complications in close association with inflammatory process. Soluble endothelial protein C receptor (sEPCR), which is the soluble form of EPCR, reduces the anticoagulant and anti-inflammatory activity of activated protein C. The purpose of this study is to investigate the relationship between sEPCR and the laboratory parameters and thorax computed tomography (CT) findings in the course of COVID-19. Twenty-five laboratory-confirmed [reverse transcription-quantitative polimerase chain reaction (RT-qPCR) positive] and 24 clinically diagnosed (RT-qPCR negative) COVID-19 patients were enrolled in the study. Blood specimens were collected for sEPCR and haematological and biochemical parameter measurement. Thorax CT was performed to detect COVID-19 findings. These parameters from RT-qPCR positive and negative patients were then compared. Although there was no difference between the groups in terms of symptoms, the time between the onset of symptoms and the admission time was shorter in RT-qPCR positive group (P = 0.000). sEPCR levels were significantly higher in the RT-qPCR positive group (P = 0.011). Patients with ground-glass opacity and bilateral involvement on thorax CT have higher serum sEPCR levels (P = 0.012 and 0.043, respectively). This study has shown for the first time that serum sEPCR levels, which is a member of coagulation cascade and has also been reported to be associated with inflammation, is higher in patients with positive RT-qPCR test and patients with GGO or bilateral involvement on thorax CT regardless of the PCR result.
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Affiliation(s)
| | | | | | | | | | | | - Aliye Celikkol
- Department of Clinical Biochemistry, Tekirdag Namik Kemal University, School of Medicine, Tekirdag, Turkey
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Costa JZ, Del Pozo J, McLean K, Inglis N, Sourd P, Bordeianu A, Thompson KD. Proteomic characterization of serum proteins from Atlantic salmon (Salmo salar L.) from an outbreak with cardiomyopathy syndrome. J Fish Dis 2021; 44:1697-1709. [PMID: 34224170 DOI: 10.1111/jfd.13488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Cardiomyopathy syndrome (CMS), caused by piscine myocarditis virus (PMCV), is a serious challenge to Atlantic salmon (Salmo salar L.) aquaculture. Regrettably, husbandry techniques are the only tool to manage CMS outbreaks, and no prophylactic measures are available at present. Early diagnosis of CMS is therefore desirable, preferably with non-lethal diagnostic methods, such as serum biomarkers. To identify candidate biomarkers for CMS, the protein content of pools of sera (4 fish/pool) from salmon with a CMS outbreak (3 pools) and from clinically healthy salmon (3 pools) was compared using liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS). Overall, seven proteins were uniquely identified in the sera of clinically healthy fish, while 27 proteins were unique to the sera of CMS fish. Of the latter, 24 have been associated with cardiac disease in humans. These were grouped as leakage enzymes (creatine kinase, lactate dehydrogenase, glycogen phosphorylase and carbonic anhydrase); host reaction proteins (acute-phase response proteins-haptoglobin, fibrinogen, α2-macroglobulin and ceruloplasmin; and complement-related proteins); and regeneration/remodelling proteins (fibronectin, lumican and retinol). Clinical evaluation of the suitability of these proteins as biomarkers of CMS, either individually or as part of a panel, is a logical next step for the development of early diagnostic tools for CMS.
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Affiliation(s)
- Janina Z Costa
- Aquaculture Research Group, Moredun Research Institute, Pentlands Science Park, Penicuik (Edinburgh), UK
| | - Jorge Del Pozo
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
| | - Kevin McLean
- Proteomics Facilities, Moredun Research Institute, Pentlands Science Park, Penicuik (Edinburgh), UK
| | - Neil Inglis
- Proteomics Facilities, Moredun Research Institute, Pentlands Science Park, Penicuik (Edinburgh), UK
| | - Philippe Sourd
- Cooke Aquaculture Scotland, Willow House, Strathclyde Business Park, Bellshill, UK
| | - Andrei Bordeianu
- Cooke Aquaculture Scotland, Willow House, Strathclyde Business Park, Bellshill, UK
| | - Kim D Thompson
- Aquaculture Research Group, Moredun Research Institute, Pentlands Science Park, Penicuik (Edinburgh), UK
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Andersson KE, Adamovicz L, Mumm LE, Bradley SE, Winter JM, Glowacki G, Cray C, Allender MC. Plasma electrophoresis profiles of Blanding's turtles (Emydoidea blandingii) and influences of month, age, sex, health status, and location. PLoS One 2021; 16:e0258397. [PMID: 34648539 PMCID: PMC8516212 DOI: 10.1371/journal.pone.0258397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 09/24/2021] [Indexed: 11/29/2022] Open
Abstract
Baseline plasma electrophoresis profiles (EPH) are important components of overall health and may aid in the conservation and captive management of species. The aim of this study was to establish plasma protein fractions for free-ranging Blanding’s turtles (Emydoidea blandingii) and evaluate differences due to age class (adult vs. sub-adult vs. juvenile), sex (male, female, or unknown), year (2018 vs. 2019), month (May vs. June vs. July), health status, and geographical location (managed vs. unmanaged sites). Blood samples were obtained from 156 Blanding’s turtles in the summer of 2018 and 129 in 2019 at two adjacent sites in Illinois. Results of the multivariate analysis demonstrated that age class, sex, year, month, health status, and geographical location all contributed to the variation observed in free-ranging populations. Adult females had the highest concentration of many protein fractions, likely associated with reproductive activity. Juveniles had lower protein concentrations. Temperature and rainfall differences between years impacted concentrations between 2018 and 2019, while May and June of both years saw higher levels in some protein fractions likely due to peak breeding and nesting season. Individuals with evidence of trauma or disease also showed increased plasma protein fractions when compared to those that were considered healthy. The two sites showed a wide/large variation over the two years. All of these factors emphasize the importance of considering multiple demographic or environmental factors when interpreting the EPH fractions. Establishing ranges for these analytes will allow investigation into disease prevalence and other environmental factors impacting this endangered species.
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Affiliation(s)
- Kirsten E. Andersson
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
- * E-mail: (KEA); (MCA)
| | - Laura Adamovicz
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
| | - Lauren E. Mumm
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
| | - Samantha E. Bradley
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
| | - John M. Winter
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
| | - Gary Glowacki
- Lake County Forest Preserve District, Libertyville, IL, United States of America
| | - Carolyn Cray
- Department of Pathology & Laboratory Medicine, School of Medicine, University of Miami, Miami, FL, United States of America
| | - Matthew C. Allender
- Wildlife Epidemiology Laboratory, College of Veterinary Medicine, University of Illinois, Urbana, IL, United States of America
- * E-mail: (KEA); (MCA)
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Azkargorta M, Iloro I, Escobes I, Cabrera D, Falcon-Perez JM, Elortza F, Royo F. Human Serum Extracellular Vesicle Proteomic Profile Depends on the Enrichment Method Employed. Int J Mol Sci 2021; 22:ijms222011144. [PMID: 34681804 PMCID: PMC8540106 DOI: 10.3390/ijms222011144] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/10/2021] [Accepted: 10/13/2021] [Indexed: 12/16/2022] Open
Abstract
The proteomic profiling of serum samples supposes a challenge due to the large abundance of a few blood proteins in comparison with other circulating proteins coming from different tissues and cells. Although the sensitivity of protein detection has increased enormously in the last years, specific strategies are still required to enrich less abundant proteins and get rid of abundant proteins such as albumin, lipoproteins, and immunoglobulins. One of the alternatives that has become more promising is to characterize circulating extracellular vesicles from serum samples that have great interest in biomedicine. In the present work, we enriched the extracellular vesicles fraction from human serum by applying different techniques, including ultracentrifugation, size-exclusion chromatography, and two commercial precipitation methods based on different mechanisms of action. To improve the performance and efficacy of the techniques to promote purity of the preparations, we have employed a small volume of serum samples (<100 mL). The comparative proteomic profiling of the enriched preparations shows that ultracentrifugation procedure yielded a larger and completely different set of proteins than other techniques, including mitochondrial and ribosome related proteins. The results showed that size exclusion chromatography carries over lipoprotein associated proteins, while a polymer-based precipitation kit has more affinity for proteins associated with granules of platelets. The precipitation kit that targets glycosylation molecules enriches differentially protein harboring glycosylation sites, including immunoglobulins and proteins of the membrane attack complex.
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Affiliation(s)
- Mikel Azkargorta
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Ibon Iloro
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Iraide Escobes
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Diana Cabrera
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
| | - Juan M. Falcon-Perez
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
| | - Felix Elortza
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
| | - Felix Royo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), 48160 Derio, Spain; (M.A.); (I.I.); (I.E.); (D.C.); (J.M.F.-P.)
- Network Center of Cooperative Research in Biomedicine of Hepatic and Digestive Diseases (CIBERehd), 28029 Madrid, Spain
- Correspondence: (F.E.); (F.R.)
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Greco F, Anastasi F, Pardini LF, Dilillo M, Vannini E, Baroncelli L, Caleo M, McDonnell LA. Longitudinal Bottom-Up Proteomics of Serum, Serum Extracellular Vesicles, and Cerebrospinal Fluid Reveals Candidate Biomarkers for Early Detection of Glioblastoma in a Murine Model. Molecules 2021; 26:5992. [PMID: 34641541 PMCID: PMC8512455 DOI: 10.3390/molecules26195992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/04/2022] Open
Abstract
Glioblastoma Multiforme (GBM) is a brain tumor with a poor prognosis and low survival rates. GBM is diagnosed at an advanced stage, so little information is available on the early stage of the disease and few improvements have been made for earlier diagnosis. Longitudinal murine models are a promising platform for biomarker discovery as they allow access to the early stages of the disease. Nevertheless, their use in proteomics has been limited owing to the low sample amount that can be collected at each longitudinal time point. Here we used optimized microproteomics workflows to investigate longitudinal changes in the protein profile of serum, serum small extracellular vesicles (sEVs), and cerebrospinal fluid (CSF) in a GBM murine model. Baseline, pre-symptomatic, and symptomatic tumor stages were determined using non-invasive motor tests. Forty-four proteins displayed significant differences in signal intensities during GBM progression. Dysregulated proteins are involved in cell motility, cell growth, and angiogenesis. Most of the dysregulated proteins already exhibited a difference from baseline at the pre-symptomatic stage of the disease, suggesting that early effects of GBM might be detectable before symptom onset.
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Affiliation(s)
- Francesco Greco
- Institute of Life Sciences, Sant’Anna School of Advanced Studies, 56127 Pisa, Italy;
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Federica Anastasi
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- NEST Laboratories, Scuola Normale Superiore, 56127 Pisa, Italy
| | - Luca Fidia Pardini
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
- Department of Chemistry and Industrial Chemistry, University of Pisa, 56124 Pisa, Italy
| | - Marialaura Dilillo
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
| | - Eleonora Vannini
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Fondazione Umberto Veronesi, 20122 Milano, Italy
| | - Laura Baroncelli
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- IRCCS Fondazione Stella Maris, 56018 Calambrone, Italy
| | - Matteo Caleo
- CNR, Neuroscience Institute, 56124 Pisa, Italy; (E.V.); (L.B.); (M.C.)
- Dipartimento di Scienze Biomediche, Università di Padova, 35131 Padova, Italy
| | - Liam A. McDonnell
- Fondazione Pisana per la Scienza ONLUS, 56017 San Giuliano Terme, Italy; (F.A.); (L.F.P.); (M.D.)
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Droma D, Kumar S, Paul T, Pal P, Saharan N, Kumar K, Poojary N. Biomarkers for assessing chronic toxicity of carbamazepine, an anticonvulsants drug on Pangasianodon hypophthalmus (Sauvage, 1878). Environ Toxicol Pharmacol 2021; 87:103691. [PMID: 34153508 DOI: 10.1016/j.etap.2021.103691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 06/03/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
In recent times, carbamazepine (CBZ) as an anticonvulsants drug has raised attention because of its safety concern in the aquatic environment. The present study aimed to evaluate the sub-lethal effects of CBZ (1%, 0.1 % and 0.01 % of 96 h LC50) on P. hypophthalmus for 60 days based on haematological, biochemical, and genotoxicity biomarkers. Chronic exposure of CBZ altered blood profiles (total erythrocyte count, packed cell volume, haemoglobin) and serum biomarkers such as alkaline phosphates, cholesterol, lactate dehydrogenase and transaminase enzymes. Oxidative stress biomarkers such as superoxide dismutase (SOD) and catalase (CAT) activity were also substantially affected in all treatments. Genotoxicity study revealed the formation of micronucleus in erythrocytes of exposed fish. Integrated Biomarker Response (IBR) study showed cholesterol, serum glutamic oxaloacetic transaminase (SGOT) in serum and SOD, CAT in liver tissue are the best organ-based enzyme biomarkers. The present report concludes that an environmentally realistic concentration of CBZ can pose a serious threat to aquatic organisms.
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Affiliation(s)
- Dawa Droma
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India
| | - Saurav Kumar
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India.
| | - Tapas Paul
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India
| | - Prasenjit Pal
- College of Fisheries, Central Agricultural University (I), Lembucherra, Tripura, 799210, India
| | - Neelam Saharan
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India
| | - Kundan Kumar
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India
| | - Nalini Poojary
- Aquatic Environment and Health Management Division, ICAR- Central Institute of Fisheries Education, Mumbai, 400 061, India
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Kivimäki M, Walker KA, Pentti J, Nyberg ST, Mars N, Vahtera J, Suominen SB, Lallukka T, Rahkonen O, Pietiläinen O, Koskinen A, Väänänen A, Kalsi JK, Goldberg M, Zins M, Alfredsson L, Westerholm PJM, Knutsson A, Theorell T, Ervasti J, Oksanen T, Sipilä PN, Tabak AG, Ferrie JE, Williams SA, Livingston G, Gottesman RF, Singh-Manoux A, Zetterberg H, Lindbohm JV. Cognitive stimulation in the workplace, plasma proteins, and risk of dementia: three analyses of population cohort studies. BMJ 2021; 374:n1804. [PMID: 34407988 PMCID: PMC8372196 DOI: 10.1136/bmj.n1804] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVES To examine the association between cognitively stimulating work and subsequent risk of dementia and to identify protein pathways for this association. DESIGN Multicohort study with three sets of analyses. SETTING United Kingdom, Europe, and the United States. PARTICIPANTS Three associations were examined: cognitive stimulation and dementia risk in 107 896 participants from seven population based prospective cohort studies from the IPD-Work consortium (individual participant data meta-analysis in working populations); cognitive stimulation and proteins in a random sample of 2261 participants from one cohort study; and proteins and dementia risk in 13 656 participants from two cohort studies. MAIN OUTCOME MEASURES Cognitive stimulation was measured at baseline using standard questionnaire instruments on active versus passive jobs and at baseline and over time using a job exposure matrix indicator. 4953 proteins in plasma samples were scanned. Follow-up of incident dementia varied between 13.7 to 30.1 years depending on the cohort. People with dementia were identified through linked electronic health records and repeated clinical examinations. RESULTS During 1.8 million person years at risk, 1143 people with dementia were recorded. The risk of dementia was found to be lower for participants with high compared with low cognitive stimulation at work (crude incidence of dementia per 10 000 person years 4.8 in the high stimulation group and 7.3 in the low stimulation group, age and sex adjusted hazard ratio 0.77, 95% confidence interval 0.65 to 0.92, heterogeneity in cohort specific estimates I2=0%, P=0.99). This association was robust to additional adjustment for education, risk factors for dementia in adulthood (smoking, heavy alcohol consumption, physical inactivity, job strain, obesity, hypertension, and prevalent diabetes at baseline), and cardiometabolic diseases (diabetes, coronary heart disease, stroke) before dementia diagnosis (fully adjusted hazard ratio 0.82, 95% confidence interval 0.68 to 0.98). The risk of dementia was also observed during the first 10 years of follow-up (hazard ratio 0.60, 95% confidence interval 0.37 to 0.95) and from year 10 onwards (0.79, 0.66 to 0.95) and replicated using a repeated job exposure matrix indicator of cognitive stimulation (hazard ratio per 1 standard deviation increase 0.77, 95% confidence interval 0.69 to 0.86). In analysis controlling for multiple testing, higher cognitive stimulation at work was associated with lower levels of proteins that inhibit central nervous system axonogenesis and synaptogenesis: slit homologue 2 (SLIT2, fully adjusted β -0.34, P<0.001), carbohydrate sulfotransferase 12 (CHSTC, fully adjusted β -0.33, P<0.001), and peptidyl-glycine α-amidating monooxygenase (AMD, fully adjusted β -0.32, P<0.001). These proteins were associated with increased dementia risk, with the fully adjusted hazard ratio per 1 SD being 1.16 (95% confidence interval 1.05 to 1.28) for SLIT2, 1.13 (1.00 to 1.27) for CHSTC, and 1.04 (0.97 to 1.13) for AMD. CONCLUSIONS The risk of dementia in old age was found to be lower in people with cognitively stimulating jobs than in those with non-stimulating jobs. The findings that cognitive stimulation is associated with lower levels of plasma proteins that potentially inhibit axonogenesis and synaptogenesis and increase the risk of dementia might provide clues to underlying biological mechanisms.
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Affiliation(s)
- Mika Kivimäki
- Department of Epidemiology and Public Health, University College London, London, UK
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Keenan A Walker
- Department of Neurology, The Johns Hopkins University, Baltimore, MD, USA
- Laboratory of Behavioral Neuroscience, National Institute on Aging, Intramural Research Program, Baltimore, MD, USA
| | - Jaana Pentti
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Finnish Institute of Occupational Health, Helsinki, Finland
- Department of Public Health, University of Turku, Turku, Finland
| | - Solja T Nyberg
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Nina Mars
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jussi Vahtera
- Department of Public Health, University of Turku, Turku, Finland
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
| | - Sakari B Suominen
- Department of Public Health, University of Turku, Turku, Finland
- School of Health Science, University of Skövde, Skövde, Sweden
| | - Tea Lallukka
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ossi Rahkonen
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Pietiläinen
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Aki Koskinen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Ari Väänänen
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Jatinderpal K Kalsi
- Department of Epidemiology and Public Health, University College London, London, UK
| | - Marcel Goldberg
- Inserm UMS 011, Population-Based Epidemiological Cohorts Unit, Villejuif, France
- Université de Paris, INSERM U1153, Epidemiology of Ageing and Neurodegenerative Diseases, Paris, France
| | - Marie Zins
- Inserm UMS 011, Population-Based Epidemiological Cohorts Unit, Villejuif, France
- Université de Paris, INSERM U1153, Epidemiology of Ageing and Neurodegenerative Diseases, Paris, France
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| | | | - Anders Knutsson
- Department of Health Sciences, Mid Sweden University, Sundsvall, Sweden
| | - Töres Theorell
- Stress Research Institute, Stockholm University, Stockholm, Sweden
| | - Jenni Ervasti
- Finnish Institute of Occupational Health, Helsinki, Finland
| | - Tuula Oksanen
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, Kuopio, Finland
| | - Pyry N Sipilä
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Adam G Tabak
- Department of Epidemiology and Public Health, University College London, London, UK
- Department of Internal Medicine and Oncology and Department of Public Health, Semmelweis University, Budapest, Hungary
| | - Jane E Ferrie
- Department of Epidemiology and Public Health, University College London, London, UK
- Bristol Medical School, University of Bristol, Bristol, UK
| | | | - Gill Livingston
- Division of Psychiatry, University College London, London, UK
- Camden and Islington NHS Foundation Trust, London, UK
| | | | - Archana Singh-Manoux
- Department of Epidemiology and Public Health, University College London, London, UK
- Université de Paris, INSERM U1153, Epidemiology of Ageing and Neurodegenerative Diseases, Paris, France
| | - Henrik Zetterberg
- Department of Neurodegenerative Disease and UK Dementia Research Institute, University College London, London, UK
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, and Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
| | - Joni V Lindbohm
- Department of Epidemiology and Public Health, University College London, London, UK
- Clinicum, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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Bai B, Vanderwall D, Li Y, Wang X, Poudel S, Wang H, Dey KK, Chen PC, Yang K, Peng J. Proteomic landscape of Alzheimer's Disease: novel insights into pathogenesis and biomarker discovery. Mol Neurodegener 2021; 16:55. [PMID: 34384464 PMCID: PMC8359598 DOI: 10.1186/s13024-021-00474-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 07/18/2021] [Indexed: 12/15/2022] Open
Abstract
Mass spectrometry-based proteomics empowers deep profiling of proteome and protein posttranslational modifications (PTMs) in Alzheimer's disease (AD). Here we review the advances and limitations in historic and recent AD proteomic research. Complementary to genetic mapping, proteomic studies not only validate canonical amyloid and tau pathways, but also uncover novel components in broad protein networks, such as RNA splicing, development, immunity, membrane transport, lipid metabolism, synaptic function, and mitochondrial activity. Meta-analysis of seven deep datasets reveals 2,698 differentially expressed (DE) proteins in the landscape of AD brain proteome (n = 12,017 proteins/genes), covering 35 reported AD genes and risk loci. The DE proteins contain cellular markers enriched in neurons, microglia, astrocytes, oligodendrocytes, and epithelial cells, supporting the involvement of diverse cell types in AD pathology. We discuss the hypothesized protective or detrimental roles of selected DE proteins, emphasizing top proteins in "amyloidome" (all biomolecules in amyloid plaques) and disease progression. Comprehensive PTM analysis represents another layer of molecular events in AD. In particular, tau PTMs are correlated with disease stages and indicate the heterogeneity of individual AD patients. Moreover, the unprecedented proteomic coverage of biofluids, such as cerebrospinal fluid and serum, procures novel putative AD biomarkers through meta-analysis. Thus, proteomics-driven systems biology presents a new frontier to link genotype, proteotype, and phenotype, accelerating the development of improved AD models and treatment strategies.
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Affiliation(s)
- Bing Bai
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Center for Precision Medicine, Department of Laboratory Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Jiangsu 210008 Nanjing, China
| | - David Vanderwall
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Yuxin Li
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Current address: Department of Biology, University of North Dakota, ND 58202 Grand Forks, USA
| | - Suresh Poudel
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Hong Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ping-Chung Chen
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Ka Yang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
- Center for Proteomics and Metabolomics, St. Jude Children’s Research Hospital, 38105 Memphis, TN USA
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Martini WZ, Yu YM, Chung KK, Dubick MA. Muscle deteriorations become prominent within 24 hours after admission in severely burned adults. J Trauma Acute Care Surg 2021; 91:S176-S181. [PMID: 34117171 DOI: 10.1097/ta.0000000000003285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Severe burn injury results in profound catabolic deterioration. Although burn-related catabolism has been well stated, it is unclear when the catabolic response begins. This study characterized acute changes of muscle protein breakdown at the admission and the day after in severely burned adults. METHODS Twelve patients (43 ± 19 years old) with 40% ± 21% total body surface area burns were prospectively enrolled into an observational study approved by institutional review board. Urinary samples were collected on admission day and the day after (day 1). Patient demographic and clinical data of vital signs, blood gas and chemistry, and coagulation status were collected. Catabolic changes of muscle breakdown were quantified by urinary excretion of 3-methylhisitidine, determined by gas chromatography and mass spectrometry analysis. RESULTS Compared with admission day, burned patients had elevated mean ± SD arterial pressure (from 90 ± 5 mm Hg to 108 ± 7 mm Hg) and heart rate (from 102 ± 7 beats per minute to 119 ± 4 beats per minute both p < 0.05) after 24 hours. Their 24-hour urinary output was 1,586 ± 813 mL at admission day to 1,911 ± 1,048 mL on day 1. The 24-hour urea excretion was elevated from 172 ± 101 mg/kg per day at admission day to 302 ± 183 mg/kg per day on day 1 (both p < 0.05), with no change in creatinine excretion. Urinary 3-methylhisitidine excretion increased from 0.75 ± 0.74 mg/kg per day at admission to 1.14 ± 0.86 mg/kg per day on day 1 (p < 0.05). The estimated skeletal muscle protein breakdown was increased from 1.1 ± 1.0 g/kg per day at admission day to 1.6 ± 1.2 g/kg per day on day 1 (p < 0.05). There were no changes in prothrombin time, activated partial thromboplastin time, or platelets. CONCLUSION In severely burned patients, catabolic muscle protein breakdown is elevated within 24 hours after admission and before changes in coagulation. These findings suggest that early interventions may be needed to effectively attenuate the catabolic responses in burn patients. LEVEL OF EVIDENCE Prospective and observational study, level II.
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Affiliation(s)
- Wenjun Z Martini
- From the Department of Damage Control Resuscitation (W.Z.M.,M.A.D.), US Army Institute of Surgical Research, Fort Sam Houston,Texas; Department of Surgery (Y.-M.Y.), Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts; and Department of Medicine (K.K.C.), School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland
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Okai CA, Wölter M, Russ M, Koy C, Petre BA, Rath W, Pecks U, Glocker MO. Profiling of intact blood proteins by matrix-assisted laser desorption/ionization mass spectrometry without the need for freezing - Dried serum spots as future clinical tools for patient screening. Rapid Commun Mass Spectrom 2021; 35:e9121. [PMID: 33955049 DOI: 10.1002/rcm.9121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/30/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
RATIONALE To open up new ways for matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS)-based patient screening, blood serum is the most preferred specimen because of its richness in patho-physiological information and due to ease of collection. To overcome deleterious freeze/thaw cycles and to reduce high costs for shipping and storage, we sought to develop a procedure which enables MALDI-MS protein profiling of blood serum proteins without the need for serum freezing. METHODS Blood sera from patients/donors were divided into portions which after pre-incubation were fast frozen. Thawed aliquots were deposited on filter paper discs and air-dried at room temperature. Intact serum proteins were eluted with acid-labile detergent-containing solutions and were desalted by employing a reversed-phase bead system. Purified protein solutions were screened by MALDI-MS using standardized instrument settings. RESULTS MALDI mass spectra from protein solutions which were eluted from filter paper discs and desalted showed on average 25 strong ion signals (mass range m/z 6000 to 10,000) from intact serum proteins (apolipoproteins, complement proteins, transthyretin and hemoglobin) and from proteolytic processing products. Semi-quantitative analysis of three ion pairs: m/z 6433 and 6631, m/z 8205 and 8916, as well as m/z 9275 and 9422, indicated that the mass spectra from either pre-incubated fast-frozen serum or pre-incubated dried serum spot eluted serum contained the same information on protein composition. CONCLUSIONS A workflow that avoids the conventional cold-chain and yet enables the investigation of intact serum proteins and/or serum proteolysis products by MALDI-MS profiling was developed. The presented protocol tremendously broadens the clinical application of MALDI-MS and simultaneously allows a reduction in the costs for storage and shipping of serum samples. This will pave the way for clinical screening of patients also in areas with limited access to health care systems, and/or specialized laboratories.
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Affiliation(s)
- Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Manja Wölter
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
- Department of Obstetrics and Gynecology, Medical Faculty, University of Rostock, Clinic Südstadt, Rostock, 18059, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
| | - Brindusa A Petre
- Department of Chemistry, Alexandru Ioan Cuza University, Bd. Carol I, No.11, Iasi, 700506, Romania
- Transcend Research Center, Regional Institute of Oncology, General Henri Mathias, No.2-4, Iasi, 700483, Romania
| | - Werner Rath
- Department of Obstetrics and Gynecology, Medical Faculty, RWTH Aachen University, Aachen, 52062, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, Kiel, 24105, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, Rostock, 18057, Germany
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Majewski M, Jurgoński A. The Effect of Hemp ( Cannabis sativa L.) Seeds and Hemp Seed Oil on Vascular Dysfunction in Obese Male Zucker Rats. Nutrients 2021; 13:nu13082575. [PMID: 34444734 PMCID: PMC8398088 DOI: 10.3390/nu13082575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/17/2021] [Accepted: 07/26/2021] [Indexed: 12/25/2022] Open
Abstract
Seeds of industrial hemp (Cannabis sativa L.) contain a large amount of protein (26.3%), dietary fiber (27.5%), and fatty acids (33.2%), including linoleic, α-linolenic, and some amount of γ-linolenic acid. In our study, obese male Zucker rats (n = 6) at 8 weeks of age were supplemented for a further 4 weeks with either ground hemp seeds (12% diet) or lipid fractions in the form of hemp seed oil (4% diet). Hemp oil decreased blood plasma HDL-cholesterol (x0.76, p ≤ 0.0001), triglycerides (x0.55, p = 0.01), and calculated atherogenic parameters. Meanwhile, hemp seeds decreased HDL-cholesterol (x0.71, p ≤ 0.0001) and total cholesterol (x0.81, p = 0.006) but not the atherogenic index. The plasma antioxidant capacity of water-soluble compounds was decreased by the seeds (x0.30, p = 0.0015), which in turn was associated with a decrease in plasma uric acid (x0.18, p = 0.03). Dietary hemp seeds also decreased plasma urea (x0.80, p = 0.02), while the oil decreased the plasma total protein (x0.90, p = 0.05). Hemp seeds and the oil decreased lipid peroxidation in the blood plasma and in the heart (reflected as malondialdehyde content), improved contraction to noradrenaline, and up-regulated the sensitivity of potassium channels dependent on ATP and Ca2+. Meanwhile, acetylcholine-induced vasodilation was improved by hemp seeds exclusively. Dietary supplementation with ground hemp seeds was much more beneficial than the oil, which suggests that the lipid fractions are only partially responsible for this effect.
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Affiliation(s)
- Michał Majewski
- Department of Pharmacology and Toxicology, Faculty of Medicine, UWM, 10-082 Olsztyn, Poland
- Correspondence: (M.M.); (A.J.); Tel.: +48-89-524-56-68 (M.M.); +48-89-523-46-01 (A.J.)
| | - Adam Jurgoński
- Division of Food Science, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland
- Correspondence: (M.M.); (A.J.); Tel.: +48-89-524-56-68 (M.M.); +48-89-523-46-01 (A.J.)
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Delannoy-Bruno O, Desai C, Raman AS, Chen RY, Hibberd MC, Cheng J, Han N, Castillo JJ, Couture G, Lebrilla CB, Barve RA, Lombard V, Henrissat B, Leyn SA, Rodionov DA, Osterman AL, Hayashi DK, Meynier A, Vinoy S, Kirbach K, Wilmot T, Heath AC, Klein S, Barratt MJ, Gordon JI. Evaluating microbiome-directed fibre snacks in gnotobiotic mice and humans. Nature 2021; 595:91-95. [PMID: 34163075 PMCID: PMC8324079 DOI: 10.1038/s41586-021-03671-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023]
Abstract
Changing food preferences brought about by westernization that have deleterious health effects1,2-combined with myriad forces that are contributing to increased food insecurity-are catalysing efforts to identify more nutritious and affordable foods3. Consumption of dietary fibre can help to prevent cardiovascular disease, type 2 diabetes and obesity4-6. A substantial number of reports have explored the effects of dietary fibre on the gut microbial community7-9. However, the microbiome is complex, dynamic and exhibits considerable intra- and interpersonal variation in its composition and functions. The large number of potential interactions between the components of the microbiome makes it challenging to define the mechanisms by which food ingredients affect community properties. Here we address the question of how foods containing different fibre preparations can be designed to alter functions associated with specific components of the microbiome. Because a marked increase in snack consumption is associated with westernization, we formulated snack prototypes using plant fibres from different sustainable sources that targeted distinct features of the gut microbiomes of individuals with obesity when transplanted into gnotobiotic mice. We used these snacks to supplement controlled diets that were consumed by adult individuals with obesity or who were overweight. Fibre-specific changes in their microbiomes were linked to changes in their plasma proteomes indicative of an altered physiological state.
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Affiliation(s)
- Omar Delannoy-Bruno
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Chandani Desai
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Arjun S Raman
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Robert Y Chen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Matthew C Hibberd
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jiye Cheng
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Nathan Han
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
| | - Juan J Castillo
- Department of Chemistry, University of California, Davis, CA, USA
| | - Garret Couture
- Department of Chemistry, University of California, Davis, CA, USA
| | | | - Ruteja A Barve
- Department of Genetics, Washington University School of Medicine, St Louis, MO, USA
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique and Aix-Marseille Université, Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Semen A Leyn
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Dmitry A Rodionov
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- A. A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russia
| | - Andrei L Osterman
- Infectious and Inflammatory Disease Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | | | | | - Kyleigh Kirbach
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Tara Wilmot
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, USA
| | - Samuel Klein
- Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
| | - Michael J Barratt
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA
| | - Jeffrey I Gordon
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO, USA.
- Center for Gut Microbiome and Nutrition Research, Washington University School of Medicine, St Louis, MO, USA.
- Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO, USA.
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Zhuo Y, Zhang Y, Li M, Wu H, Gong S, Hu X, Fu Y, Shen X, Sun B, Wu JL, Li N. Hepatotoxic evaluation of toosendanin via biomarker quantification and pathway mapping of large-scale chemical proteomics. Food Chem Toxicol 2021; 153:112257. [PMID: 34000341 DOI: 10.1016/j.fct.2021.112257] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/15/2021] [Accepted: 05/07/2021] [Indexed: 01/15/2023]
Abstract
Drug-induced liver injury (DILI) is a major side effect, sometimes can't be exactly evaluated by current approaches partly as the covalent modification of drug or its reactive metabolites (RMs) with proteins is a possible reason. In this study, we developed a rapid, sensitive, and specific analytical method to assess the hepatotoxicity induced by drug covalently modified proteins based on the quantification of the modified amino acids using toosendanin (TSN), a hepatotoxic chemical, as an example. TSN RM-protein adducts both in rat liver and blood showed good correlation with the severity of hepatotoxicity. Thus, TSN RM-protein adducts in serum can potentially serve as minimally invasive biomarkers of hepatotoxicity. Meanwhile, large-scale chemical proteomics analysis showed that at least 84 proteins were modified by TSN RMs in rat liver, and the bioinformatics analysis revealed that TSN might induce hepatotoxicity through multi-target protein-protein interaction especially involved in energy metabolism. These findings suggest that our approach may serve as a valuable tool to evaluate DILI and investigate the possible mechanism, especially for complex compounds.
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Affiliation(s)
- Yue Zhuo
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China; Science and Technology Innovation Center, Guangzhou University of Chinese Medicine, Guangzhou, 510405, China
| | - Yida Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China; State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Meng Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China
| | - Haiying Wu
- Department of Emergency, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China
| | - Xiaolan Hu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China
| | - Yu Fu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China
| | - Xinzi Shen
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China
| | - Baoqing Sun
- State Key Laboratory of Respiratory Disease, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, PR China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China.
| | - Na Li
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Avenida Wai Long, Taipa, Macau SAR, 999078, PR China.
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Schranner D, Schönfelder M, Römisch‐Margl W, Scherr J, Schlegel J, Zelger O, Riermeier A, Kaps S, Prehn C, Adamski J, Söhnlein Q, Stöcker F, Kreuzpointner F, Halle M, Kastenmüller G, Wackerhage H. Physiological extremes of the human blood metabolome: A metabolomics analysis of highly glycolytic, oxidative, and anabolic athletes. Physiol Rep 2021; 9:e14885. [PMID: 34152092 PMCID: PMC8215680 DOI: 10.14814/phy2.14885] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022] Open
Abstract
Human metabolism is highly variable. At one end of the spectrum, defects of enzymes, transporters, and metabolic regulation result in metabolic diseases such as diabetes mellitus or inborn errors of metabolism. At the other end of the spectrum, favorable genetics and years of training combine to result in physiologically extreme forms of metabolism in athletes. Here, we investigated how the highly glycolytic metabolism of sprinters, highly oxidative metabolism of endurance athletes, and highly anabolic metabolism of natural bodybuilders affect their serum metabolome at rest and after a bout of exercise to exhaustion. We used targeted mass spectrometry-based metabolomics to measure the serum concentrations of 151 metabolites and 43 metabolite ratios or sums in 15 competitive male athletes (6 endurance athletes, 5 sprinters, and 4 natural bodybuilders) and 4 untrained control subjects at fasted rest and 5 minutes after a maximum graded bicycle test to exhaustion. The analysis of all 194 metabolite concentrations, ratios and sums revealed that natural bodybuilders and endurance athletes had overall different metabolite profiles, whereas sprinters and untrained controls were more similar. Specifically, natural bodybuilders had 1.5 to 1.8-fold higher concentrations of specific phosphatidylcholines and lower levels of branched chain amino acids than all other subjects. Endurance athletes had 1.4-fold higher levels of a metabolite ratio showing the activity of carnitine-palmitoyl-transferase I and 1.4-fold lower levels of various alkyl-acyl-phosphatidylcholines. When we compared the effect of exercise between groups, endurance athletes showed 1.3-fold higher increases of hexose and of tetradecenoylcarnitine (C14:1). In summary, physiologically extreme metabolic capacities of endurance athletes and natural bodybuilders are associated with unique blood metabolite concentrations, ratios, and sums at rest and after exercise. Our results suggest that long-term specific training, along with genetics and other athlete-specific factors systematically change metabolite concentrations at rest and after exercise.
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Affiliation(s)
- Daniela Schranner
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Martin Schönfelder
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | | | - Johannes Scherr
- University Center for Prevention and Sports MedicineUniversity Hospital BalgristUniversität ZürichZurichSwitzerland
| | - Jürgen Schlegel
- Department of NeuropathologyInstitute of PathologyTechnische Universität MünchenMunichGermany
| | - Otto Zelger
- Department of Prevention and Sports MedicineTechnische Universität MünchenMunichGermany
| | - Annett Riermeier
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Stephanie Kaps
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Cornelia Prehn
- Research Unit Molecular Endocrinology and MetabolismHelmholtz Zentrum MünchenNeuherbergGermany
| | - Jerzy Adamski
- Research Unit Molecular Endocrinology and MetabolismHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes ResearchNeuherbergGermany
- Chair of Experimental GeneticsTechnische Universität MünchenFreising‐WeihenstephanGermany
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingapore
| | - Quirin Söhnlein
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Fabian Stöcker
- Teaching and Educational LabDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Florian Kreuzpointner
- Prevention CenterDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
| | - Martin Halle
- Department of Prevention and Sports MedicineTechnische Universität MünchenMunichGermany
| | - Gabi Kastenmüller
- Institute of Computational BiologyHelmholtz Zentrum MünchenNeuherbergGermany
- German Center for Diabetes ResearchNeuherbergGermany
| | - Henning Wackerhage
- Exercise BiologyDepartment of Sport and Health SciencesTechnische Universität MünchenMunichGermany
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Kalla R, Adams AT, Bergemalm D, Vatn S, Kennedy NA, Ricanek P, Lindstrom J, Ocklind A, Hjelm F, Ventham NT, Ho GT, Petren C, Repsilber D, Söderholm J, Pierik M, D’Amato M, Gomollón F, Olbjorn C, Jahnsen J, Vatn MH, Halfvarson J, Satsangi J. Serum proteomic profiling at diagnosis predicts clinical course, and need for intensification of treatment in inflammatory bowel disease. J Crohns Colitis 2021; 15:699-708. [PMID: 33201212 PMCID: PMC8095384 DOI: 10.1093/ecco-jcc/jjaa230] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND Success in personalized medicine in complex disease is critically dependent on biomarker discovery. We profiled serum proteins using a novel proximity extension assay [PEA] to identify diagnostic and prognostic biomarkers in inflammatory bowel disease [IBD]. METHODS We conducted a prospective case-control study in an inception cohort of 552 patients [328 IBD, 224 non-IBD], profiling proteins recruited across six centres. Treatment escalation was characterized by the need for biological agents or surgery after initial disease remission. Nested leave-one-out cross-validation was used to examine the performance of diagnostic and prognostic proteins. RESULTS A total of 66 serum proteins differentiated IBD from symptomatic non-IBD controls, including matrix metallopeptidase-12 [MMP-12; Holm-adjusted p = 4.1 × 10-23] and oncostatin-M [OSM; p = 3.7 × 10-16]. Nine of these proteins are associated with cis-germline variation [59 independent single nucleotide polymorphisms]. Fifteen proteins, all members of tumour necrosis factor-independent pathways including interleukin-1 (IL-1) and OSM, predicted escalation, over a median follow-up of 518 [interquartile range 224-756] days. Nested cross-validation of the entire data set allowed characterization of five-protein models [96% comprising five core proteins ITGAV, EpCAM, IL18, SLAMF7 and IL8], which define a high-risk subgroup in IBD [hazard ratio 3.90, confidence interval: 2.43-6.26], or allowed distinct two- and three-protein models for ulcerative colitis and Crohn's disease respectively. CONCLUSION We have characterized a simple oligo-protein panel that has the potential to identify IBD from symptomatic controls and to predict future disease course. Further prospective work is required to validate our findings.
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Affiliation(s)
- R Kalla
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - A T Adams
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - D Bergemalm
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - S Vatn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
| | - N A Kennedy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Exeter IBD and Pharmacogenetics group, University of Exeter, UK
| | - P Ricanek
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Lindstrom
- Health Services Research Unit, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | | | - F Hjelm
- Olink Proteomics, Uppsala, Sweden
| | - N T Ventham
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
| | - G T Ho
- MRC Centre for Inflammation Research, Queens Medical Research Institute, University of Edinburgh, UK
| | - C Petren
- Olink Proteomics, Uppsala, Sweden
| | - D Repsilber
- School of Medical Sciences, Örebro University, Örebro, Sweden
| | - J Söderholm
- Department of Surgery and Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - M Pierik
- Maastricht University Medical Centre (MUMC), Department of Gastroenterology and Hepatology, Maastricht, Netherlands
| | - M D’Amato
- BioCruces Health Research Institute and Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- School of Biological Sciences, Monash University, Victoria, Australia
| | - F Gomollón
- HCU ‘Lozano Blesa’, IIS Aragón, Zaragoza, Spain
| | - C Olbjorn
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Jahnsen
- Department of Gastroenterology, Akershus University Hospital, Lørenskog, Norway
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - M H Vatn
- Institute of Clinical Medicine, Campus Ahus, University of Oslo, Oslo, Norway
| | - J Halfvarson
- Department of Gastroenterology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - J Satsangi
- Institute of Genetics and Molecular Medicine, University of Edinburgh, UK
- Translational Gastroenterology Unit, Nuffield Department of Medicine, Experimental Medicine Division, University of Oxford, John Radcliffe Hospital, Oxford, UK
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Cao F, Zhang R, Xu L, Liu M, Yuan Y. Application of Capillary Electrophoresis in Monoclonal Gammopathies and the Cutoff Value of Monoclonal Protein in Differential Diagnosis of Multiple Myeloma and Other Monoclonal Gammopathies. Ann Clin Lab Sci 2021; 51:400-407. [PMID: 34162571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
OBJECTIVE Monoclonal protein (MP) exists in various diseases, and capillary electrophoresis (CE) has been widely used to detect MP. However, there is not much research on the application value of MP in the differential diagnosis of monoclonal gammopathies. This study aimed to explore MP's cutoff value for the differential diagnosis of multiple myeloma (MM) and other monoclonal gammopathies (MGs). METHODS A retrospective analysis of 8167 cases was conducted. Serum MP was detected by CE, and the patients' clinical information was collected from the clinical database of our hospital. RESULTS 985 cases had MP with high peaks, and 91.1% were diagnosed with malignant diseases. The MP showed small peaks in 471 cases, and only 24.4% were diagnosed with malignant diseases. Among the MPs, the IgG-κ type was the most common type, followed by the IgG-λ, IgA-κ, IgA-λ, free λ light chain, IgM-κ, free κ light chain, double clone, and IgM-λ types. Differences in the MP of the IgG, IgA, IgM, and FLC types between the MM group and MGUS group were statistically different (P<0.01). The MP of the IgG, IgA, and FLC types showed clear specificity and sensitivity in discriminating MM from other monoclonal gammopathies in ROC curve analysis. Serum IgM had statistical significance in the differential diagnosis between WM and other MGs (P<0.01). However, there was no statistical significance in the differential diagnosis between MM and other MGs (P=0.140). The cutoff values of the MP of the IgG, IgA, and FLC types were >18.67g/L, >13.86g/L, and >10.15g/L, respectively, for the differential diagnosis of MM and other MGs. The cutoff value of the MP of IgM for the WM diagnosis was >37.75 g/L. CONCLUSION CE has good clinical application value in the diagnosis of monoclonal gammopathies, and MP can be used in the differential diagnosis of MM and other monoclonal gammopathies.
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Affiliation(s)
- Fangfang Cao
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Rui Zhang
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Longqiang Xu
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengyang Liu
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yuan Yuan
- Department of Clinical Laboratory, the Affiliated Hospital of Qingdao University, Qingdao, China
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50
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Manyelo CM, Chegou NN, Seddon JA, Snyders CI, Mutavhatsindi H, Manngo PM, Walzl G, Stanley K, Solomons RS. Serum and cerebrospinal fluid host proteins indicate stroke in children with tuberculous meningitis. PLoS One 2021; 16:e0250944. [PMID: 33930055 PMCID: PMC8087017 DOI: 10.1371/journal.pone.0250944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Stroke is a common complication in children with tuberculous meningitis (TBM). Host proteins may give us insight into the mechanisms of stroke in TBM and serve as biomarkers for detection of stroke, however, they have not been widely explored. In this study, we compared the concentrations of cerebrospinal fluid (CSF) and serum proteins between children who had TBM-related stroke and children with TBM without stroke. Methods We collected CSF and serum from 47 children consecutively admitted to the Tygerberg Academic Hospital in Cape Town, South Africa between November 2016, and November 2017, on suspicion of having TBM. A multiplex platform was used to measure the concentrations of 69 host proteins in CSF and serum from all study participants. Results After classification of study participants, 23 (48.9%) out of the 47 study participants were diagnosed with TBM, of which 14 (60.9%) demonstrated radiological arterial ischemic infarction. The levels of lipocalin-2, sRAGE, IP-10/ CXCL10, sVCAM-1, MMP-1, and PDGF-AA in CSF samples and the levels of D-dimer, ADAMTS13, SAA, ferritin, MCP-1/ CCL2, GDF-15 and IL-13 in serum samples were statistically different between children who had TBM-related stroke and children with TBM without stroke. After correcting for multiple testing, only the levels of sVCAM-1, MMP-1, sRAGE, and IP-10/ CXCL10 in CSF were statistically different between the two groups. CSF and serum protein biosignatures indicated stroke in children diagnosed with TBM with up to 100% sensitivity and 88.9% specificity. Conclusion Serum and CSF proteins may serve as biomarkers for identifying individuals with stroke amongst children diagnosed with TBM at admission and may guide us to understand the biology of stroke in TBM. This was a pilot study, and thus further investigations in larger studies are needed.
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Affiliation(s)
- Charles M. Manyelo
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Novel N. Chegou
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - James A. Seddon
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
| | - Candice I. Snyders
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Hygon Mutavhatsindi
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Portia M. Manngo
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Gerhard Walzl
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kim Stanley
- Division of Molecular Biology and Human Genetics, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Regan S. Solomons
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- * E-mail:
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