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Schuster-Little N, Sokolovsky AD, Gentry A, Saraf A, Etzel MR, Patankar MS, Whelan RJ. Immunoaffinity-free chromatographic purification of ovarian cancer biomarker CA125 (MUC16) from blood serum enables mass spectrometry characterization. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 39177265 PMCID: PMC11342825 DOI: 10.1039/d4ay01172d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Accepted: 08/19/2024] [Indexed: 08/24/2024]
Abstract
The enrichment of trace proteins from human fluid samples is of great importance in diverse clinical and industrial applications. In clinical diagnostics, such enrichment may enable detection of trace proteins that serve as biomarkers of disease. Affinity-based approaches, such as immunoaffinity pulldown, are widely used to enrich trace proteins, but this strategy relies on the availability and performance of antibodies that act on all proteoforms in an unbiased manner. Our prior work to characterize MUC16 (the mucin protein that carries the ovarian cancer biomarker CA125) by mass spectrometry successfully overcame the reliance on affinity-based enrichment and was used to enrich this biomarker from ascites of individual ovarian cancer patients, however, this strategy was not demonstrated on clinically relevant volumes of serum, a biofluid that is more accessible than ascites. The present work developed a non-affinity-based chromatographic method to enrich MUC16 from serum. The enriched MUC16 sample was further processed using a Midi Top 14 abundant protein depletion column. Peptides identified using bottom-up proteomics yielded 1-8% coverage of MUC16. Additionally, MUC16 was detected in samples containing less than the clinical cut-off level of CA125 (35 U mL-1), suggesting that this strategy of enrichment and bottom-up proteomics can enable analysis of CA125 from the serum of individuals with early-stage ovarian cancer and those whose tumors express CA125 (MUC16) at low levels.
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Affiliation(s)
- Naviya Schuster-Little
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Andrew D Sokolovsky
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Ashten Gentry
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
| | - Anita Saraf
- Mass Spectrometry and Analytical Proteomics Laboratory, University of Kansas, Lawrence, KS, USA
| | - Mark R Etzel
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, USA
| | - Manish S Patankar
- Department of Obstetrics and Gynecology, University of Wisconsin-Madison, Madison, WI, USA
| | - Rebecca J Whelan
- Department of Chemistry, University of Kansas, Lawrence, KS, USA.
- Ralph N. Adams Institute for Bioanalytical Chemistry, University of Kansas, Lawrence, KS, USA
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Chao X, Zhang B, Yang S, Liu X, Zhang J, Zang X, Chen L, Qi L, Wang X, Hu H. Enrichment methods of N-linked glycopeptides from human serum or plasma: A mini-review. Carbohydr Res 2024; 538:109094. [PMID: 38564900 DOI: 10.1016/j.carres.2024.109094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/08/2024] [Accepted: 03/14/2024] [Indexed: 04/04/2024]
Abstract
Human diseases often correlate with changes in protein glycosylation, which can be observed in serum or plasma samples. N-glycosylation, the most common form, can provide potential biomarkers for disease prognosis and diagnosis. However, glycoproteins constitute a relatively small proportion of the total proteins in human serum and plasma compared to the non-glycosylated protein albumin, which constitutes the majority. The detection of microheterogeneity and low glycan abundance presents a challenge. Mass spectrometry facilitates glycoproteomics research, yet it faces challenges due to interference from abundant plasma proteins. Therefore, methods have emerged to enrich N-glycans and N-linked glycopeptides using glycan affinity, chemical properties, stationary phase chemical coupling, bioorthogonal techniques, and other alternatives. This review focuses on N-glycans and N-glycopeptides enrichment in human serum or plasma, emphasizing methods and applications. Although not exhaustive, it aims to elucidate principles and showcase the utility and limitations of glycoproteome characterization.
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Affiliation(s)
- Xuyuan Chao
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Baoying Zhang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Shengjie Yang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xizi Liu
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, People's Republic of China
| | - Jingyi Zhang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xin Zang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Lu Chen
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, People's Republic of China.
| | - Han Hu
- Institute of Apicultural Research/Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Chinese Academy of Agricultural Sciences, No. 1 Beigou Xiangshan, Beijing, 100093, People's Republic of China.
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Ubaida-Mohien C, Tanaka T, Tian Q, Moore Z, Moaddel R, Basisty N, Simonsick EM, Ferrucci L. Blood Biomarkers for Healthy Aging. Gerontology 2023; 69:1167-1174. [PMID: 37166337 PMCID: PMC11137618 DOI: 10.1159/000530795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/22/2023] [Indexed: 05/12/2023] Open
Abstract
Measuring the abundance of biological molecules and their chemical modifications in blood and tissues has been the cornerstone of research and medical diagnoses for decades. Although the number and variety of molecules that can be measured have expanded exponentially, the blood biomarkers routinely assessed in medical practice remain limited to a few dozen, which have not substantially changed over the last 30-40 years. The discovery of novel biomarkers would allow, for example, risk stratification or monitoring of disease progression or the effectiveness of treatments and interventions, improving clinical practice in myriad ways. In this review, we combine the biomarker discovery concept with geroscience. Geroscience bridges aging research and translation to clinical applications by combining the framework of medical gerontology with high-technology medical research. With the development of geroscience and the rise of blood biomarkers, there has been a paradigm shift from disease prevention and cure to promoting health and healthy aging. New -omic technologies have played a role in the development of blood biomarkers, including epigenetic, proteomic, metabolomic, and lipidomic markers, which have emerged as correlates or predictors of health status, from disease to exceptional health.
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Affiliation(s)
- Ceereena Ubaida-Mohien
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Qu Tian
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Zenobia Moore
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Ruin Moaddel
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Nathan Basisty
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Eleanor M Simonsick
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, USA
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King CD, Kapp KL, Arul AB, Choi MJ, Robinson RAS. Advancements in automation for plasma proteomics sample preparation. Mol Omics 2022; 18:828-839. [PMID: 36048090 PMCID: PMC9879274 DOI: 10.1039/d2mo00122e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Automation is necessary to increase sample processing throughput for large-scale clinical analyses. Replacement of manual pipettes with robotic liquid handler systems is especially helpful in processing blood-based samples, such as plasma and serum. These samples are very heterogenous, and protein expression can vary greatly from sample-to-sample, even for healthy controls. Detection of true biological changes requires that variation from sample preparation steps and downstream analytical detection methods, such as mass spectrometry, remains low. In this mini-review, we discuss plasma proteomics protocols and the benefits of automation towards enabling detection of low abundant proteins and providing low sample error and increased sample throughput. This discussion includes considerations for automation of major sample depletion and/or enrichment strategies for plasma toward mass spectrometry detection.
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Affiliation(s)
- Christina D King
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Kathryn L Kapp
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
| | - Albert B Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Min Ji Choi
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, USA
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, USA
- Vanderbilt Memory & Alzheimer's Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, USA
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, Tennessee 37232, USA
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Artan M, Hartl M, Chen W, de Bono M. Depletion of endogenously biotinylated carboxylases enhances the sensitivity of TurboID-mediated proximity labeling in Caenorhabditis elegans. J Biol Chem 2022; 298:102343. [PMID: 35933017 PMCID: PMC9437848 DOI: 10.1016/j.jbc.2022.102343] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/25/2022] Open
Abstract
Proximity-dependent protein labeling provides a powerful in vivo strategy to characterize the interactomes of specific proteins. We previously optimized a proximity labeling protocol for Caenorhabditis elegans using the highly active biotin ligase TurboID. A significant constraint on the sensitivity of TurboID is the presence of abundant endogenously biotinylated proteins that take up bandwidth in the mass spectrometer, notably carboxylases that use biotin as a cofactor. In C. elegans, these comprise POD-2/acetyl-CoA carboxylase alpha, PCCA-1/propionyl-CoA carboxylase alpha, PYC-1/pyruvate carboxylase, and MCCC-1/methylcrotonyl-CoA carboxylase alpha. Here, we developed ways to remove these carboxylases prior to streptavidin purification and mass spectrometry by engineering their corresponding genes to add a C-terminal His10 tag. This allows us to deplete them from C. elegans lysates using immobilized metal affinity chromatography. To demonstrate the method's efficacy, we use it to expand the interactome map of the presynaptic active zone protein ELKS-1. We identify many known active zone proteins, including UNC-10/RIM, SYD-2/liprin-alpha, SAD-1/BRSK1, CLA-1/CLArinet, C16E9.2/Sentryn, as well as previously uncharacterized potentially synaptic proteins such as the ortholog of human angiomotin, F59C12.3 and the uncharacterized protein R148.3. Our approach provides a quick and inexpensive solution to a common contaminant problem in biotin-dependent proximity labeling. The approach may be applicable to other model organisms and will enable deeper and more complete analysis of interactors for proteins of interest.
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Affiliation(s)
- Murat Artan
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
| | - Markus Hartl
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Weiqiang Chen
- Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter (VBC), Vienna, Austria
| | - Mario de Bono
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria.
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Mirlashari MR, Vetlesen A, Nissen-Meyer LSH, Stensland ME, Singh SK, Nyman TA, Hetland G. Proteomic study of apheresis platelets made HLA class I deficient for transfusion of refractory patients. Proteomics Clin Appl 2021; 15:e2100022. [PMID: 34510746 DOI: 10.1002/prca.202100022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 11/06/2022]
Abstract
PURPOSE Refractoriness can occur after repeated platelet (PLT) transfusions because of alloimmunization to HLA class I antigens on transfused PLTs and generation of anti-HLA antibodies that bind to the foreign PLTs and initiate their destruction. Such refractoriness can be overcome by provision of HLA-matched PLTs from HLA typed donors. However, since the procedure is both expensive and time-consuming, an alternative approach is to deplete PLTs of HLA class I molecules by a brief treatment with citric acid, on ice. This is shown to be feasible without damaging PLT function. We used label free quantitative mass spectrometry (MS)-based proteomics to investigate the effect of acid treatment on apheresis PLTs for combatting immunologic PLT refractoriness. EXPERIMENTAL DESIGN Proteomic analyses are undertaken using PLTs from seven apheresis concentrates, which were split in two with or without acid treatment. RESULTS In total 1717 proteins in apheresis PLTs were quantified using proteomics. Data are available via ProteomeXchange with identifier PXD027893 . Of these, the amount of 80 proteins changed significantly after acid treatment, but overall there were not any major differences in proteomes between samples with and without acid treatment. CONCLUSIONS AND CLINICAL RELEVANCE In general, the changes of PLT proteins after treatment with citric acid were quite small and functionally safe. Hence, this result taken together with our previously published data indicates that acid treated PLTs can be used for treatment of patients with PLT refractoriness and opens up for a clinical trial.
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Affiliation(s)
| | - Annette Vetlesen
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | | | - Maria Ekman Stensland
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Sachin Kumar Singh
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - Tuula Anneli Nyman
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Geir Hetland
- Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
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Masaki T, Kodera Y, Terasaki M, Fujimoto K, Hirano T, Shichiri M. GIP_HUMAN[22-51] is a new proatherogenic peptide identified by native plasma peptidomics. Sci Rep 2021; 11:14470. [PMID: 34262109 PMCID: PMC8280211 DOI: 10.1038/s41598-021-93862-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022] Open
Abstract
We recently established a new plasma peptidomic technique and comprehensively identified a large number of low-molecular weight and low-abundance native peptides using a single drop of human plasma. To discover a novel polypeptide that potently modulates the cardiovascular system, we performed a bioinformatics analysis of the large-scale identification results, sequentially synthesized the selected peptide sequences, tested their biological activities, and identified a 30-amino-acid proatherogenic peptide, GIP_HUMAN[22-51], as a potent proatherosclerotic peptide hormone. GIP_HUMAN[22-51] has a common precursor with the glucose-dependent insulinotropic polypeptide (GIP) and is located immediately N-terminal to GIP. Chronic infusion of GIP_HUMAN[22-51] into ApoE-/- mice accelerated the development of aortic atherosclerotic lesions, which were inhibited by co-infusions with an anti-GIP_HUMAN[22-51] antibody. GIP_HUMAN[22-51] increased the serum concentrations of many inflammatory and proatherogenic proteins, whereas neutralising antibodies reduced their levels. GIP_HUMAN[22-51] induced IκB-α degradation and nuclear translocation of NF-κB in human vascular endothelial cells and macrophages. Immunoreactive GIP_HUMAN[22-51] was detected in human tissues but there was no colocalization with the GIP. The plasma GIP_HUMAN[22-51] concentration in healthy humans determined using a stable-isotope tagged peptide was approximately 0.6 nM. This study discovered a novel endogenous proatherogenic peptide by using a human plasma native peptidomic resource.
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Affiliation(s)
- Tsuguto Masaki
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
| | - Yoshio Kodera
- Department of Physics, Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Michishige Terasaki
- Division of Diabetes, Metabolism and Endocrinology, Department of Medicine, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Kazumi Fujimoto
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan
- Department of Physics, Center for Disease Proteomics, Kitasato University School of Science, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tsutomu Hirano
- Division of Diabetes, Metabolism and Endocrinology, Department of Medicine, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Masayoshi Shichiri
- Department of Endocrinology, Diabetes and Metabolism, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa, 252-0374, Japan.
- Tokyo Kyosai Hospital, 2-3-8 Nakameguro, Meguro-ku, Tokyo, 153-8934, Japan.
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Using Omics Approaches in the Discovery of Biomarkers for Early Diagnosis of Johne's Disease in Sheep and Goats. Animals (Basel) 2021; 11:ani11071912. [PMID: 34199073 PMCID: PMC8300312 DOI: 10.3390/ani11071912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/23/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. Abstract Johne’s disease (JD) is caused by Mycobacterium avium subsp. paratuberculosis (MAP) and is an important and emerging problem in livestock; therefore, its control and prevention is a priority to reduce economic losses and health risks. Most JD research has been carried out on cattle, but interest in the pathogenesis and diagnosis of this disease in sheep and goats is greatest in developing countries. Sheep and goats are also a relevant part of livestock production in Europe and Australia, and these species provide an excellent resource to study and better understand the mechanism of survival of MAP and gain insights into possible approaches to control this disease. This review gives an overview of the literature on paratuberculosis in sheep and goats, highlighting the immunological aspects and the potential for “omics” approaches to identify effective biomarkers for the early detection of infection. As JD has a long incubation period before the disease becomes evident, early diagnosis is important to control the spread of the disease.
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Wang X, Chen M, Dai L, Tan C, Hu L, Zhang Y, Xiao Y, Li F, Zeng C, Xiang Z, Wang Y, Zhang W, Zhang X, Ran Q, Li Z, Chen L. Potential biomarkers for inherited thrombocytopenia 2 identified by plasma proteomics. Platelets 2021; 33:443-450. [PMID: 34101524 DOI: 10.1080/09537104.2021.1937594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Inherited thrombocytopenia 2 (THC2) is difficult to diagnose due to the lack of specific clinical characteristics and diagnostic methods. To identify potential plasma protein biomarkers for THC2, we collected the plasma samples from a THC2 family (9 THC2 and 15 non-THC2 members), enriched the medium and low abundant proteins using Proteominer and analyzed the protein profiles using the liquid chromatography-mass spectrometry in data independent acquisition mode. Initially, we detected 784 proteins in the plasma samples of this family and identified 27 up-regulated and 36 down-regulated in the THC2 group compared to the non-THC2 group (|log2 ratio| >1 and p-value <0.05). To improve the predictive power, top eight dysregulated proteins (B7Z2B4, LTF, HP, ERN1, IGHV1-8, A0A0X9V9C4, VH6DJ, and D3JV41) were selected by an area under the curve-based random forest process to construct a clinical model. Multivariate analysis with random forest and support vector machine showed that the prediction model provided high discrimination ability for THC2 diagnosis (AUC: 1.000 and 0.967, respectively). The potential plasma protein biomarkers will be tested in more THC2 patients and other thrombocytopenia patients to further validate their specificity and sensitivity.
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Affiliation(s)
- Xiaojie Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Maoshan Chen
- Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne, Australia
| | - Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Chengning Tan
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Lanyue Hu
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yichi Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yanni Xiao
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Fengjie Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Cheng Zeng
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zheng Xiang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Yali Wang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Weiwei Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Xiaomei Zhang
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Qian Ran
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zhongjun Li
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
| | - Li Chen
- Laboratory of Radiation Biology, Department of Blood Transfusion, Laboratory Medicine Center, The Second Affiliated Hospital, Army Medical University, Chongqing, China
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Hossen MN, Elechalawar CK, Sjoelund V, Moore K, Mannel R, Bhattacharya R, Mukherjee P. Experimental conditions influence the formation and composition of the corona around gold nanoparticles. Cancer Nanotechnol 2021; 12:1. [PMID: 33456622 PMCID: PMC7788026 DOI: 10.1186/s12645-020-00071-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Ovarian cancer is one of the deadliest gynecological malignancies. While the overall survival of ovarian cancer patients has slightly improved in recent years in the developed world, it remains clinically challenging due to its frequent late diagnosis and the lack of reliable diagnostic and/or prognostic markers. The aim of this study was to identify potential new molecular target proteins (NMTPs) responsible for the poor outcomes. When nanoparticles (NP) are exposed to biological fluids, a protein coat, termed the protein corona (PC), forms around the NP, and the PC represents a tool to identify NMTPs. This study investigates the influence of pre-processing conditions, such as lysis conditions and serum/plasma treatment, on the PC composition and the resulting identification of NMTPs. RESULTS Using gel electrophoresis, pre-processing conditions, including cell-lysis techniques and enrichment of low-abundance proteins (LAPs) by immunocentrifugation of serum/plasma, were shown to alter the relative amounts and compositions of proteins. PCs formed when 20 nm gold-NPs (GNPs) were incubated with lysate proteins from either RIPA- or urea lysis. Proteomic analysis of these PCs showed 2-22-fold enrichment of NMTPs in PCs from urea lysates as compared to RIPA lysates. Enriched NMTPs were then classified as cellular components, biological and molecular functions-associated proteins. The impact of enriched LAPs (eLAPs) on both PC composition and NMTP identification was shown by comparative proteomic analysis of original plasma, eLAPs, and PCs derived from eLAPs; eLAPs-PCs enhanced the abundance of NMTPs approximately 13%. Several NMTPs, including gasdermin-B, dermcidin, and kallistatin, were identified by this method demonstrating the potential use of this PC approach for molecular target discovery. CONCLUSION The current study showed that the pre-processing conditions modulate PC composition and can be used to enhance identification of NMTPs.
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Affiliation(s)
- Md. Nazir Hossen
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Chandra Kumar Elechalawar
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Virginie Sjoelund
- Department of Cell Biology, Mass Spectroscopy/Proteomic Core, University of Oklahoma Health Science Center, Oklahoma City, OK 73104 USA
| | - Kathleen Moore
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Robert Mannel
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Resham Bhattacharya
- Department of Obstetrics and Gynecology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
| | - Priyabrata Mukherjee
- Peggy and Charles Stephenson Cancer Laboratory Research, Oklahoma Stanton L. Young Biomedical Research Center, University of Oklahoma Health Sciences Center, 975 N.E., Suite # 1409 10th Street, Oklahoma City, OK 73104 USA
- Department of Pathology, University of Oklahoma Health Science Center, Oklahoma City, OK USA
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11
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Wu X, Guo J, Chen Y, Liu X, Yang G, Wu Y, Tian Y, Liu N, Yang L, Wei S, Deng H, Chen W. The 60-kDa heat shock protein regulates energy rearrangement and protein synthesis to promote proliferation of multiple myeloma cells. Br J Haematol 2020; 190:741-752. [PMID: 32155663 DOI: 10.1111/bjh.16569] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
To investigate the cellular mechanisms of multiple myeloma (MM), we used liquid chromatography-tandem mass spectrometry for proteomics analysis of CD138+ plasma cells from patients with MM and healthy controls. We found that the 60-kDa heat shock protein (HSP60, also known as HSPD1) was significantly upregulated in myeloma cells. HSP60 is an important chaperone protein that regulates the homeostasis of mitochondrial proteins and maintains mitochondrial function. Knockdown (KD) of HSP60 in myeloma cells resulted in inhibition of proliferation and reduced the quality of the mitochondria. Mitochondrial stress tests showed that HSP60 KD inhibited glycolysis and mitochondrial activity. Metabolomics showed a decrease in glycolysis and tricarboxylic acid cycle metabolites, and inhibited the formation of creatine and phosphocreatine by the reaction of S-adenosylmethionine (SAM) with amino acids mediated by demethyladenosine transferase 1, mitochondrial (TFB1M) and reduced energy storage substances. Moreover, HSP60 silencing influenced the synthesis of ribonucleotides and nicotinamide adenine dinucleotide phosphate (NADPH) by the pentose phosphate pathway to inhibit cell proliferation. HSP60 KD inhibited 5' adenosine monophosphate-activated protein kinase (AMPK), which inhibited the key enzyme 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), effecting the metabolism of fatty acids by inhibiting malonyl-coenzyme A. Our data suggest that reduced HSP60 expression alters metabolic reprogramming in MM, inhibits tumour progression and reduces mitochondrial-dependent biosynthesis, suggesting that HSP60 is a potential therapeutic target for MM treatment.
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Affiliation(s)
- Xiaoxiao Wu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Jianying Guo
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Yuling Chen
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiaohui Liu
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Guangzhong Yang
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yin Wu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Ying Tian
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Nian Liu
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Lin Yang
- Department of Hematology, The Second Hospital of Hebei medical University, Shi Jia Zhuang, China
| | - Songren Wei
- Department of Pharmacy, Foshan Maternal and Child Healthy Research Institute, Affiliated Hospital of Southern Medical University, Foshan, China
| | - Haiteng Deng
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenming Chen
- Department of Hematology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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12
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Morro B, Doherty MK, Balseiro P, Handeland SO, MacKenzie S, Sveier H, Albalat A. Plasma proteome profiling of freshwater and seawater life stages of rainbow trout (Oncorhynchus mykiss). PLoS One 2020; 15:e0227003. [PMID: 31899766 PMCID: PMC6941806 DOI: 10.1371/journal.pone.0227003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/09/2019] [Indexed: 01/18/2023] Open
Abstract
The sea-run phenotype of rainbow trout (Oncorhynchus mykiss), like other anadromous salmonids, present a juvenile stage fully adapted to life in freshwater known as parr. Development in freshwater is followed by the smolt stage, where preadaptations needed for seawater life are developed making fish ready to migrate to the ocean, after which event they become post-smolts. While these three life stages have been studied using a variety of approaches, proteomics has never been used for such purpose. The present study characterised the blood plasma proteome of parr, smolt and post-smolt rainbow trout using a gel electrophoresis liquid chromatography tandem mass spectrometry approach alone or in combination with low-abundant protein enrichment technology (combinatorial peptide ligand library). In total, 1,822 proteins were quantified, 17.95% of them being detected only in plasma post enrichment. Across all life stages, the most abundant proteins were ankyrin-2, DNA primase large subunit, actin, serum albumin, apolipoproteins, hemoglobin subunits, hemopexin-like proteins and complement C3. When comparing the different life stages, 17 proteins involved in mechanisms to cope with hyperosmotic stress and retinal changes, as well as the downregulation of nonessential processes in smolts, were significantly different between parr and smolt samples. On the other hand, 11 proteins related to increased growth in post-smolts, and also related to coping with hyperosmotic stress and to retinal changes, were significantly different between smolt and post-smolt samples. Overall, this study presents a series of proteins with the potential to complement current seawater-readiness assessment tests in rainbow trout, which can be measured non-lethally in an easily accessible biofluid. Furthermore, this study represents a first in-depth characterisation of the rainbow trout blood plasma proteome, having considered three life stages of the fish and used both fractionation alone or in combination with enrichment methods to increase protein detection.
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Affiliation(s)
- Bernat Morro
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
| | - Mary K. Doherty
- Institute of Health Research and Innovation, Centre for Health Science, University of the Highlands and Islands, Inverness, Scotland, United Kingdom
| | | | | | - Simon MacKenzie
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
- NORCE AS, Universitetet i Bergen, Bergen, Norway
| | - Harald Sveier
- Lerøy Seafood Group ASA, Universitetet i Bergen, Bergen, Norway
| | - Amaya Albalat
- Institute of Aquaculture, University of Stirling, Stirling, Scotland, United Kingdom
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13
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Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
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14
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Toby TK, Fornelli L, Srzentić K, DeHart CJ, Levitsky J, Friedewald J, Kelleher NL. A comprehensive pipeline for translational top-down proteomics from a single blood draw. Nat Protoc 2019; 14:119-152. [PMID: 30518910 DOI: 10.1038/s41596-018-0085-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics (TDP) by mass spectrometry (MS) is a technique by which intact proteins are analyzed. It has become increasingly popDesalting and concentrating GELFrEEular in translational research because of the value of characterizing distinct proteoforms of intact proteins. Compared to bottom-up proteomics (BUP) strategies, which measure digested peptide mixtures, TDP provides highly specific molecular information that avoids the bioinformatic challenge of protein inference. However, the technique has been difficult to implement widely because of inherent limitations of existing sample preparation methods and instrumentation. Recent improvements in proteoform pre-fractionation and the availability of high-resolution benchtop mass spectrometers have made it possible to use high-throughput TDP for the analysis of complex clinical samples. Here, we provide a comprehensive protocol for analysis of a common sample type in translational research: human peripheral blood mononuclear cells (PBMCs). The pipeline comprises multiple workflows that can be treated as modular by the reader and used for various applications. First, sample collection and cell preservation are described for two clinical biorepository storage schemes. Cell lysis and proteoform pre-fractionation by gel-eluted liquid fractionation entrapment electrophoresis are then described. Importantly, instrument setup and liquid chromatography-tandem MS are described for TDP analyses, which rely on high-resolution Fourier-transform MS. Finally, data processing and analysis are described using two different, application-dependent software tools: ProSight Lite for targeted analyses of one or a few proteoforms and TDPortal for high-throughput TDP in discovery mode. For a single sample, the minimum completion time of the entire experiment is 72 h.
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Affiliation(s)
- Timothy K Toby
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Luca Fornelli
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Kristina Srzentić
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA
| | - Josh Levitsky
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - John Friedewald
- Comprehensive Transplant Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Neil L Kelleher
- Departments of Chemistry and of Molecular Biosciences, Northwestern University, Evanston, IL, USA. .,National Resource for Translational and Developmental Proteomics, Northwestern University, Evanston, IL, USA.
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15
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Cole LM, Clench MR, Francese S. Sample Treatment for Tissue Proteomics in Cancer, Toxicology, and Forensics. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:77-123. [PMID: 31236840 DOI: 10.1007/978-3-030-12298-0_4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Since the birth of proteomics science in the 1990, the number of applications and of sample preparation methods has grown exponentially, making a huge contribution to the knowledge in life science disciplines. Continuous improvements in the sample treatment strategies unlock and reveal the fine details of disease mechanisms, drug potency, and toxicity as well as enable new disciplines to be investigated such as forensic science.This chapter will cover the most recent developments in sample preparation strategies for tissue proteomics in three areas, namely, cancer, toxicology, and forensics, thus also demonstrating breath of application within the domain of health and well-being, pharmaceuticals, and secure societies.In particular, in the area of cancer (human tumor biomarkers), the most efficient and multi-informative proteomic strategies will be covered in relation to the subsequent application of matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and liquid extraction surface analysis (LESA), due to their ability to provide molecular localization of tumor biomarkers albeit with different spatial resolution.With respect to toxicology, methodologies applied in toxicoproteomics will be illustrated with examples from its use in two important areas: the study of drug-induced liver injury (DILI) and studies of effects of chemical and environmental insults on skin, i.e., the effects of irritants, sensitizers, and ionizing radiation. Within this chapter, mainly tissue proteomics sample preparation methods for LC-MS/MS analysis will be discussed as (i) the use of LC-MS/MS is majorly represented in the research efforts of the bioanalytical community in this area and (ii) LC-MS/MS still is the gold standard for quantification studies.Finally, the use of proteomics will also be discussed in forensic science with respect to the information that can be recovered from blood and fingerprint evidence which are commonly encountered at the scene of the crime. The application of proteomic strategies for the analysis of blood and fingerprints is novel and proteomic preparation methods will be reported in relation to the subsequent use of mass spectrometry without any hyphenation. While generally yielding more information, hyphenated methods are often more laborious and time-consuming; since forensic investigations need quick turnaround, without compromising validity of the information, the prospect to develop methods for the application of quick forensic mass spectrometry techniques such as MALDI-MS (in imaging or profiling mode) is of great interest.
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Affiliation(s)
- L M Cole
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - M R Clench
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK
| | - S Francese
- Biomolecular Science Research Centre, Centre for Mass Spectrometry Imaging, Sheffield Hallam University, Sheffield, UK.
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16
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Haslene-Hox H. Measuring gradients in body fluids - A tool for elucidating physiological processes, diagnosis and treatment of disease. Clin Chim Acta 2018; 489:233-241. [PMID: 30145208 DOI: 10.1016/j.cca.2018.08.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 01/03/2023]
Affiliation(s)
- Hanne Haslene-Hox
- SINTEF Industry, Department of biotechnology and nanomedicine, Sem Sælands vei 2A, 7034 Trondheim, Norway.
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17
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Pisanu S, Biosa G, Carcangiu L, Uzzau S, Pagnozzi D. Comparative evaluation of seven commercial products for human serum enrichment/depletion by shotgun proteomics. Talanta 2018; 185:213-220. [DOI: 10.1016/j.talanta.2018.03.086] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 12/14/2022]
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18
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Red blood cell storage and clinical outcomes: new insights. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2018; 15:101-103. [PMID: 28263164 DOI: 10.2450/2017.0018-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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19
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Reisz JA, Tzounakas VL, Nemkov T, Voulgaridou AI, Papassideri IS, Kriebardis AG, D'Alessandro A, Antonelou MH. Metabolic Linkage and Correlations to Storage Capacity in Erythrocytes from Glucose 6-Phosphate Dehydrogenase-Deficient Donors. Front Med (Lausanne) 2018; 4:248. [PMID: 29376053 PMCID: PMC5768619 DOI: 10.3389/fmed.2017.00248] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 12/19/2017] [Indexed: 12/16/2022] Open
Abstract
Objective In glucose 6-phosphate dehydrogenase (G6PD) deficiency, decreased NADPH regeneration in the pentose phosphate pathway and subnormal levels of reduced glutathione result in insufficient antioxidant defense, increased susceptibility of red blood cells (RBCs) to oxidative stress, and acute hemolysis following exposure to pro-oxidant drugs and infections. Despite the fact that redox disequilibrium is a prominent feature of RBC storage lesion, it has been reported that the G6PD-deficient RBCs store well, at least in respect to energy metabolism, but their overall metabolic phenotypes and molecular linkages to the storability profile are scarcely investigated. Methods We performed UHPLC-MS metabolomics analyses of weekly sampled RBC concentrates from G6PD sufficient and deficient donors, stored in citrate phosphate dextrose/saline adenine glucose mannitol from day 0 to storage day 42, followed by statistical and bioinformatics integration of the data. Results Other than previously reported alterations in glycolysis, metabolomics analyses revealed bioactive lipids, free fatty acids, bile acids, amino acids, and purines as top variables discriminating RBC concentrates for G6PD-deficient donors. Two-way ANOVA showed significant changes in the storage-dependent variation in fumarate, one-carbon, and sulfur metabolism, glutathione homeostasis, and antioxidant defense (including urate) components in G6PD-deficient vs. sufficient donors. The levels of free fatty acids and their oxidized derivatives, as well as those of membrane-associated plasticizers were significantly lower in G6PD-deficient units in comparison to controls. By using the strongest correlations between in vivo and ex vivo metabolic and physiological parameters, consecutively present throughout the storage period, several interactomes were produced that revealed an interesting interplay between redox, energy, and hemolysis variables, which may be further associated with donor-specific differences in the post-transfusion performance of G6PD-deficient RBCs. Conclusion The metabolic phenotypes of G6PD-deficient donors recapitulate the basic storage lesion profile that leads to loss of metabolic linkage and rewiring. Donor-related issues affect the storability of RBCs even in the narrow context of this donor subgroup in a way likely relevant to transfusion medicine.
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Affiliation(s)
- Julie A Reisz
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Vassilis L Tzounakas
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, United States
| | | | - Issidora S Papassideri
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Anastasios G Kriebardis
- Department of Medical Laboratories, Faculty of Health and Caring Professions, Technological and Educational Institute of Athens, Athens, Greece
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado, Aurora, CO, United States
| | - Marianna H Antonelou
- Department of Biology, School of Science, National and Kapodistrian University of Athens, Athens, Greece
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20
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Al-Daghri NM, Torretta E, Capitanio D, Fania C, Guerini FR, Sabico SB, Clerici M, Gelfi C. Intermediate and low abundant protein analysis of vitamin D deficient obese and non-obese subjects by MALDI-profiling. Sci Rep 2017; 7:12633. [PMID: 28974732 PMCID: PMC5626753 DOI: 10.1038/s41598-017-13020-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/12/2017] [Indexed: 12/16/2022] Open
Abstract
Obesity is a pathological condition caused by genetic and environmental factors, including vitamin D deficiency, which increases the risk of developing cardiovascular disorders and diabetes. This case-control study was designed to verify whether serum profiles could be identified differentiating obese and non-obese Saudis characterized by vitamin D deficiency and pathological levels of triglycerides, high-density lipoprotein cholesterol and high total cholesterol levels. The serum protein profiles of 64 vitamin D deficient (serum 25(OH)D < 50nmol/L) individuals with metabolic syndrome and with (n = 31; BMI ≥ 30) or without (n = 33; BMI < 30) obesity were analyzed by a quantitative label-free mass spectrometry approach (MALDI-profiling), combined with different serum immunodepletion strategies (Human7 and Human14 immuno-chromatographies), to analyze the intermediate- and low-abundant protein components. The analysis of intermediate-abundant proteins (Human7) in obese vs. non-obese subjects identified 14 changed peaks (p < 0.05) in the m/z range 1500–35000. Furthermore, the Human14 depletion provided new profiles related to obesity (121 changed peaks). Among changed peaks, 11 were identified in the m/z range 1500–4000 Da by high-resolution tandem mass spectrometry, belonging to apolipoprotein CIII, apolipoprotein B100, alpha-1-antichymotrypsin and complement C3. Data herein show that distinct protein profiles identify specific peptides belonging to lipid metabolism and inflammation processes that are associated with obesity and vitamin D deficiency.
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Affiliation(s)
- Nasser M Al-Daghri
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Enrica Torretta
- Department of Biomedical Sciences for Health, University of Milan, Segrate (Milan), Italy
| | - Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Segrate (Milan), Italy
| | - Chiara Fania
- Clinical Proteomics Unit, Scientific Institute for Research, Hospitalization and Health Care (IRCCS) Policlinico San Donato, San Donato Milanese (Milan), Italy
| | | | - Shaun B Sabico
- Prince Mutaib Chair for Biomarkers of Osteoporosis, Biochemistry Department, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Mario Clerici
- Don C. Gnocchi Foundation, IRCCS, Milan, Italy.,Department of Physiopathology and Transplants, University of Milan, Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Segrate (Milan), Italy. .,Clinical Proteomics Unit, Scientific Institute for Research, Hospitalization and Health Care (IRCCS) Policlinico San Donato, San Donato Milanese (Milan), Italy.
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21
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D'Alessandro A, Seghatchian J. Hitchhiker's guide to the red cell storage galaxy: Omics technologies and the quality issue. Transfus Apher Sci 2017; 56:248-253. [PMID: 28343934 DOI: 10.1016/j.transci.2017.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Red blood cell storage in the blood bank makes millions of units of available for transfusion to civilian and military recipients every year. From glass bottles to plastic bags, from anticoagulants to complex additives, from whole blood to leukocyte filtered packed red blood cells: huge strides have been made in the field of blood component processing and storage in the blood bank during the last century. Still, refrigerated preservation of packed red blood cells under blood bank conditions results in the progressive accumulation of a wide series of biochemical and morphological changes to the stored erythrocytes, collectively referred to as the storage lesion(s). Approximately ten years ago, retrospective clinical evidence had suggested that such lesion(s) may be clinically relevant and mediate some of the untoward transfusion-related effects observed especially in some categories of recipients at risk (e.g. massively or chronically transfused recipients). Since then, randomized clinical trials have failed to prospectively detect any signal related to red cell storage duration and increased morbidity and mortality in several categories of recipients, at the limits of the statistical power of these studies. While a good part of the transfusion community has immediately adopted the take-home message "if it isn't broken, don't fix it" (i.e. no change to the standard of practice should be pursued), decision makers have been further questioning whether there may be room for further improvements in this field. Provocatively, we argue that consensus has yet to be unanimously reached on what makes a good quality marker of the red cell storage lesion and transfusion safety/efficacy. In other words, if it is true that "you can't manage what you can't measure", then future advancements in the field of transfusion medicine will necessarily rely on state of the art analytical omics technologies of well-defined quality parameters. Heavily borrowing from Douglas Adam's imaginary repertoire from the world famous "Hitchhiker's guide to the galaxy", we briefly summarize how some of the principles for intergalactic hitchhikers may indeed apply to inform navigation through the complex universe of red cell storage quality, safety and efficacy.
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Affiliation(s)
- Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.
| | - Jerard Seghatchian
- International Consultancy in Blood Component Quality/Safety Improvement, Audit/Inspection and DDR Strategies, London, UK.
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22
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D’Alessandro A, Nemkov T, Reisz J, Dzieciatkowska M, Wither MJ, Hansen KC. Omics markers of the red cell storage lesion and metabolic linkage. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2017; 15:137-144. [PMID: 28263171 PMCID: PMC5336335 DOI: 10.2450/2017.0341-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 12/28/2016] [Indexed: 01/28/2023]
Abstract
The introduction of omics technologies in the field of Transfusion Medicine has significantly advanced our understanding of the red cell storage lesion. While the clinical relevance of such a lesion is still a matter of debate, quantitative and redox proteomics approaches, as well quantitative metabolic flux analysis and metabolic tracing experiments promise to revolutionise our understanding of the role of blood processing strategies, inform the design and testing of novel additives or technologies (such as pathogen reduction), and evaluate the clinical relevance of donor and recipient biological variability with respect to red cell storability and transfusion outcomes. By reviewing existing literature in this rapidly expanding research endeavour, we highlight for the first time a correlation between metabolic markers of the red cell storage age and protein markers of haemolysis. Finally, we introduce the concept of metabolic linkage, i.e. the appreciation of a network of highly correlated small molecule metabolites which results from biochemical constraints of erythrocyte metabolic enzyme activities. For the foreseeable future, red cell studies will advance Transfusion Medicine and haematology by addressing the alteration of metabolic linkage phenotypes in response to stimuli, including, but not limited to, storage additives, enzymopathies (e.g. glucose 6-phosphate dehydrogenase deficiency), hypoxia, sepsis or haemorrhage.
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Affiliation(s)
- Angelo D’Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
| | - Travis Nemkov
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
| | - Julie Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
| | - Matthew J. Wither
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
| | - Kirk C. Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver - Anschutz Medical Campus, Aurora, CO, United States of America
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23
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D'Alessandro A, Zolla L. Proteomic analysis of red blood cells and the potential for the clinic: what have we learned so far? Expert Rev Proteomics 2017; 14:243-252. [PMID: 28162022 DOI: 10.1080/14789450.2017.1291347] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
INTRODUCTION Red blood cells (RBC) are the most abundant host cells in the human body. Mature erythrocytes are devoid of nuclei and organelles and have always been regarded as circulating 'bags of hemoglobin'. The advent of proteomics has challenged this assumption, revealing unanticipated complexity and novel roles for RBCs not just in gas transport, but also in systemic metabolic homeostasis in health and disease. Areas covered: In this review we will summarize the main advancements in the field of discovery mode and redox/quantitative proteomics with respect to RBC biology. We thus focus on translational/clinical applications, such as transfusion medicine, hematology (e.g. hemoglobinopathies) and personalized medicine. Synergy of omics technologies - especially proteomics and metabolomics - are highlighted as a hallmark of clinical metabolomics applications for the foreseeable future. Expert commentary: The introduction of advanced proteomics technologies, especially quantitative and redox proteomics, and the integration of proteomics data with omics information gathered through orthogonal technologies (especially metabolomics) promise to revolutionize many biomedical areas, from hematology and transfusion medicine to personalized medicine and clinical biochemistry.
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Affiliation(s)
- Angelo D'Alessandro
- a Department of Biochemistry and Molecular Genetics , University of Colorado Denver - Anschutz Medical Campus , Aurora , CO , USA
| | - Lello Zolla
- b Department of Ecological and Biological Sciences , Universita' degli Studi della Tuscia , Viterbo , Italy
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24
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Reisz JA, Chessler KM, Dzieciatkowska M, D'Alessandro A, Hansen KC. Blood and Plasma Proteomics: Targeted Quantitation and Posttranslational Redox Modifications. Methods Mol Biol 2017; 1619:353-371. [PMID: 28674896 DOI: 10.1007/978-1-4939-7057-5_24] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Proteome profiling using mass spectrometry is extensively utilized to understand the physiological characteristics of cells, tissues, fluids, and many other biological matrices. From the earliest days of the proteomics era, exploratory analyses of the blood protein complement have attracted a great deal of interest, owing to the pivotal importance of blood cells and biofluids (serum, plasma) for research and biomedical purposes. Once challenged by the high dynamic range of protein concentrations, low sensitivity of mass spectrometers, and poor annotation of proteomics databases, the techniques in this field have quickly evolved in recent years, particularly in the areas of absolute quantification of proteins and in mapping of posttranslational modifications. Here we describe (a) the design and production of heavy isotope-labeled peptides used as reporter internal standards for absolute protein quantification and (b) a redox proteomics approach to optimize sample preparation and database searching to elucidate oxidative modifications to protein amino acids. The two methods achieve complimentary goals in the field of blood research and pave the way for future translation of next-generation proteomics technologies into clinical practice.
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Affiliation(s)
- Julie A Reisz
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Katelyn M Chessler
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA.
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, Anschutz Medical Campus, 12801 E. 17th Ave., Aurora, CO, 80045, USA
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Chang AL, Kim Y, Seitz AP, Schuster RM, Pritts TA. pH modulation ameliorates the red blood cell storage lesion in a murine model of transfusion. J Surg Res 2016; 212:54-59. [PMID: 28550922 DOI: 10.1016/j.jss.2016.12.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 12/12/2016] [Accepted: 12/21/2016] [Indexed: 11/18/2022]
Abstract
BACKGROUND Prolonged storage of packed red blood cells (pRBCs) induces a series of harmful biochemical and metabolic changes known as the RBC storage lesion. RBCs are currently stored in an acidic storage solution, but the effect of pH on the RBC storage lesion is unknown. We investigated the effect of modulation of storage pH on the RBC storage lesion and on erythrocyte survival after transfusion. METHODS Murine pRBCs were stored in Additive Solution-3 (AS3) under standard conditions (pH, 5.8), acidic AS3 (pH, 4.5), or alkalinized AS3 (pH, 8.5). pRBC units were analyzed at the end of the storage period. Several components of the storage lesion were measured, including cell-free hemoglobin, microparticle production, phosphatidylserine externalization, lactate accumulation, and byproducts of lipid peroxidation. Carboxyfluorescein-labeled erythrocytes were transfused into healthy mice to determine cell survival. RESULTS Compared with pRBCs stored in standard AS3, those stored in alkaline solution exhibited decreased hemolysis, phosphatidylserine externalization, microparticle production, and lipid peroxidation. Lactate levels were greater after storage in alkaline conditions, suggesting that these pRBCs remained more metabolically viable. Storage in acidic AS3 accelerated erythrocyte deterioration. Compared with standard AS3 storage, circulating half-life of cells was increased by alkaline storage but decreased in acidic conditions. CONCLUSIONS Storage pH significantly affects the quality of stored RBCs and cell survival after transfusion. Current erythrocyte storage solutions may benefit from refinements in pH levels.
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Affiliation(s)
- Alex L Chang
- Department of Surgery, Institute of Military Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Young Kim
- Department of Surgery, Institute of Military Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Aaron P Seitz
- Department of Surgery, Institute of Military Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Rebecca M Schuster
- Department of Surgery, Institute of Military Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Timothy A Pritts
- Department of Surgery, Institute of Military Medicine, University of Cincinnati, Cincinnati, Ohio.
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Schubert P, Culibrk B, Karwal S, Goodrich RP, Devine DV. Protein translation occurs in platelet concentrates despite riboflavin/UV light pathogen inactivation treatment. Proteomics Clin Appl 2016; 10:839-50. [DOI: 10.1002/prca.201500139] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 05/15/2016] [Accepted: 05/22/2016] [Indexed: 12/21/2022]
Affiliation(s)
- Peter Schubert
- Centre for Innovation; Canadian Blood Services, University of British Columbia; Vancouver BC Canada
- Centre for Blood Research, University of British Columbia; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
| | - Brankica Culibrk
- Centre for Innovation; Canadian Blood Services, University of British Columbia; Vancouver BC Canada
- Centre for Blood Research, University of British Columbia; Vancouver BC Canada
| | - Simrath Karwal
- Centre for Innovation; Canadian Blood Services, University of British Columbia; Vancouver BC Canada
- Centre for Blood Research, University of British Columbia; Vancouver BC Canada
| | | | - Dana V. Devine
- Centre for Innovation; Canadian Blood Services, University of British Columbia; Vancouver BC Canada
- Centre for Blood Research, University of British Columbia; Vancouver BC Canada
- Department of Pathology and Laboratory Medicine; University of British Columbia; Vancouver BC Canada
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Deininger L, Patel E, Clench MR, Sears V, Sammon C, Francese S. Proteomics goes forensic: Detection and mapping of blood signatures in fingermarks. Proteomics 2016; 16:1707-17. [DOI: 10.1002/pmic.201500544] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/13/2016] [Accepted: 04/22/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Lisa Deininger
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Ekta Patel
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Malcolm R. Clench
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
| | - Vaughn Sears
- Centre for Applied Science and Technology; Home Office; St Albans UK
| | - Chris Sammon
- Materials and Engineering Research Institute; Sheffield Hallam University; Sheffield UK
| | - Simona Francese
- Centre for Mass Spectrometry Imaging; Biomolecular Research Centre; Sheffield Hallam University; Sheffield UK
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Goodman SR, Pace BS, Hansen KC, D'alessandro A, Xia Y, Daescu O, Glatt SJ. Minireview: Multiomic candidate biomarkers for clinical manifestations of sickle cell severity: Early steps to precision medicine. Exp Biol Med (Maywood) 2016; 241:772-81. [PMID: 27022133 DOI: 10.1177/1535370216640150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In this review, we provide a description of those candidate biomarkers which have been demonstrated by multiple-omics approaches to vary in correlation with specific clinical manifestations of sickle cell severity. We believe that future clinical analyses of severity phenotype will require a multiomic analysis, or an omics stack approach, which includes integrated interactomics. It will also require the analysis of big data sets. These candidate biomarkers, whether they are individual or panels of functionally linked markers, will require future validation in large prospective and retrospective clinical studies. Once validated, the hope is that informative biomarkers will be used for the identification of individuals most likely to experience severe complications, and thereby be applied for the design of patient-specific therapeutic approaches and response to treatment. This would be the beginning of precision medicine for sickle cell disease.
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Affiliation(s)
- Steven R Goodman
- Department of Pediatrics and Department of Physiology, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Betty S Pace
- Department of Pediatrics, Augusta University, Augusta, GA 30912, USA
| | - Kirk C Hansen
- Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80202, USA
| | - Angelo D'alessandro
- Biochemistry and Molecular Genetics, University of Colorado Denver, Aurora, CO 80202, USA
| | - Yang Xia
- Biochemistry and Molecular Biology Department, University of Texas at Houston, TX 77030, USA
| | - Ovidiu Daescu
- University of Texas at Dallas, Richardson, TX 75080, USA
| | - Stephen J Glatt
- Department of Psychiatry and Behavioral Sciences, SUNY Upstate Medical University, Syracuse, NY 13210, USA
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Derazshamshir A, Baydemir G, Yılmaz F, Bereli N, Denizli A. Preparation of cryogel columns for depletion of hemoglobin from human blood. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2016; 44:792-9. [DOI: 10.3109/21691401.2015.1129623] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Patel E, Cicatiello P, Deininger L, Clench MR, Marino G, Giardina P, Langenburg G, West A, Marshall P, Sears V, Francese S. A proteomic approach for the rapid, multi-informative and reliable identification of blood. Analyst 2016; 141:191-8. [DOI: 10.1039/c5an02016f] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Blood evidence is frequently encountered at the scene of violent crimes and can provide valuable intelligence in the forensic investigation of serious offences.
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Affiliation(s)
- E. Patel
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
| | - P. Cicatiello
- Dipartimento di Scienze Chimiche
- Universita’ di Napoli Federico II
- via Cinthia I-80126 Naples
- Italy
| | - L. Deininger
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
| | - M. R. Clench
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
| | - G. Marino
- Dipartimento di Scienze Chimiche
- Universita’ di Napoli Federico II
- via Cinthia I-80126 Naples
- Italy
| | - P. Giardina
- Dipartimento di Scienze Chimiche
- Universita’ di Napoli Federico II
- via Cinthia I-80126 Naples
- Italy
| | | | | | | | - V. Sears
- Centre for Applied Science and Technology
- St Albans
- UK
| | - S. Francese
- Biomolecular Research Centre
- Sheffield Hallam University
- Sheffield
- UK
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Deterioration of red blood cell mechanical properties is reduced in anaerobic storage. BLOOD TRANSFUSION = TRASFUSIONE DEL SANGUE 2015; 14:80-8. [PMID: 26674833 DOI: 10.2450/2015.0241-15] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 10/15/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Hypothermic storage of red blood cells (RBCs) results in progressive deterioration of the rheological properties of the cells, which may reduce the efficacy of RBC transfusions. Recent studies have suggested that storing RBC units under anaerobic conditions may reduce this storage-induced deterioration. MATERIALS AND METHODS The aim of this study was to compare the rheological properties of conventionally and anaerobically stored RBC and provide a measure of the relationship between oxidative damage to stored RBC and their ability to perfuse microvascular networks. Three different microfluidic devices were used to measure the ability of both types of stored RBC to perfuse artificial microvascular networks. Flow rates of the RBC passing through the entire network (bulk perfusion) and the individual capillaries (capillary perfusion) of the devices were measured on days 2, 21, 42, and 63 of storage. RESULTS The bulk perfusion rates for anaerobically stored RBC were significantly higher than for conventionally stored RBCs over the entire duration of storage for all devices (up to 10% on day 42; up to 14% on day 63). Capillary perfusion rates suggested that anaerobically stored RBC units contained significantly fewer non-deformable RBC capable of transiently plugging microfluidic device capillaries. The number of plugging events caused by these non-deformable RBC increased over the 63 days of hypothermic storage by nearly 16- to 21-fold for conventionally stored units, and by only about 3- to 6-fold for anaerobically stored units. DISCUSSION The perfusion measurements suggest that anaerobically stored RBC retain a greater ability to perfuse networks of artificial capillaries compared to conventionally (aerobically) stored RBC. It is likely that anaerobic storage confers this positive effect on the bulk mechanical properties of stored RBC by significantly reducing the number of non-deformable cells present in the overall population of relatively well-preserved RBC.
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Abstract
Studies on animal models have documented a role for the water-soluble protein fraction of mesenteric lymph as a conduit from hemorrhagic shock to acute lung injury and postinjury multiple organ failure. We hypothesize that mesenteric lymph is not an ultrafiltrate of plasma and contains specific protein mediators that may predispose patients to acute lung injury/multiple organ failure. Mesenteric lymph and plasma were collected from critically ill or injured patients and from nine patients with lymphatic injuries, during semielective spine reconstruction, or immediately before organ donation. Proteomic analyses were performed through immunoaffinity depletion of the 14 most abundant plasma proteins and 1D gel electrophoresis followed by liquid chromatography coupled online with mass spectrometry analyses. Overall, 548 proteins were identified in the patients undergoing semielective surgery, of which 155 were uniquely present in the lymph. In addition, the postshock plasma proteome was characterized by peculiar features, suggesting that only a partial overlap exists between the plasma and mesenteric lymph from trauma patients. Differential proteins between the matched plasma and mesenteric lymph from trauma patients could be related to coagulopathy and hypercoagulability, cell lysis, proinflammatory responses and immune system activation, extracellular matrix remodeling, lymph-specific immunomodulation and vascular hypoactivity/neoangiogenesis, and energy/redox metabolic adaptation to trauma. In conclusion, the proteome of mesenteric lymph is biologically different (in qualitative and quantitative terms) than that of a mere plasma ultrafiltrate.
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Wei W, Huang XH, Liang D, Zeng YY, Ma C, Wu YB, Li YT, Zhang X, Zeng JH, Liu JF. A proteomic analysis of transplanted liver in a rat model of chronic rejection. Clin Res Hepatol Gastroenterol 2015; 39:340-50. [PMID: 25468549 DOI: 10.1016/j.clinre.2014.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 07/29/2014] [Accepted: 10/03/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND Chronic rejection (CR) is an important cause of liver allograft failure. In the latter condition, re-transplantation of the liver (ReLT) is the only option for survival. Unfortunately, with the current state of knowledge, it is difficult to diagnose and treat early CR. OBJECTIVE To explore the biomarkers of the chronic rejection in orthotopic liver transplantation (OLT). METHODS A rat model of chronic liver allograft rejection was established, and the differential protein expression in chronic allograft rejection (CR) was analyzed by iTRAQ-MALDI-TOF/TOF. RESULTS Expression of sixty-two proteins was found to be significantly changed in CR rats. In the present study, CLU, Lcn2 and Krt19 were identified and quantified as early and reliable biomarkers for chronic rejection. CONCLUSION Analysis of differential protein expression by iTRAQ-MALDI-TOF/TOF is a potentially effective method to help understand the mechanism of CR in orthotopic liver transplantation. The proteins CLU, Lcn2 and Krt19 might be potential prognostic markers for predicting chronic rejection after liver transplantation.
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Affiliation(s)
- Wei Wei
- The First Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
| | - Xin-Hui Huang
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Dong Liang
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yong-Yi Zeng
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Chuang Ma
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yan-Bin Wu
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Yun-Tong Li
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Xiang Zhang
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jin-Hua Zeng
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Jing-Feng Liu
- Liver Disease Center, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China.
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Yin HR, Xie LQ, Xu Y, Cai SJ, Yao J, Yang PY, Lu HJ. Direct-S: a directed mass spectrometry method for biomarker verification in native serum. Analyst 2015; 140:3654-62. [PMID: 25873488 DOI: 10.1039/c5an00165j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Serum has been the logical choice and most-used bio-specimen for monitoring biomarkers. However, direct analysis of low-abundance biomarkers in serum is still a problem. Here, we have established a directed mass spectrometry (inclusion list driven MS) method, Direct-S, for direct quantification of protein biomarkers in native serum samples without high-abundance protein depletion or pre-fractionation. In Direct-S, an (18)O-labeling technique was used to produce internal standards of the targeted peptides, and only targeted peptides were selected for tandem mass spectrometry (MS/MS) fragmentation to increase sensitivity and efficiency. The (16)O/(18)O ion pairs of target peptides and the elution time/fragmental pattern of the internal standards were used to facilitate the identification of the low-abundance peptides. Using Direct-S, three candidate biomarkers, α1-antitrypsin (A1AT), galectin-3 binding protein (LG3BP) and cathepsin D (CTSD), which represent different abundance levels, were quantified in serum samples of colorectal cancer (CRC) patients and healthy candidates. Direct-S exhibited good linearity of response from 20 fmol to 0.5 nmol (r > 0.9845). Reliable quantification across five orders of magnitude and as low as 71 pg μL(-1) was achieved in serum samples. In conclusion, Direct-S is a low cost, convenient and accurate method for verifying serum biomarkers.
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Affiliation(s)
- Hong-Rui Yin
- Shanghai Cancer Centre and Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China.
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Proteomics of apheresis platelet supernatants during routine storage: Gender-related differences. J Proteomics 2014; 112:190-209. [PMID: 25201077 DOI: 10.1016/j.jprot.2014.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 08/28/2014] [Accepted: 08/31/2014] [Indexed: 12/30/2022]
Abstract
UNLABELLED Proteomics has identified potential pathways involved in platelet storage lesions, which correlate with untoward effects in the recipient, including febrile non-haemolytic reactions. We hypothesize that an additional pathway involves protein mediators that accumulate in the platelet supernatants during routine storage in a donor gender-specific fashion. Apheresis platelet concentrates were collected from 5 healthy males and 5 females and routinely stored. The 14 most abundant plasma proteins were removed and the supernatant proteins from days 1 and 5 were analyzed via 1D-SDS-PAGE/nanoLC-MS/MS, before label-free quantitative proteomics analyses. Findings from a subset of 18 proteins were validated via LC-SRM analyses against stable isotope labeled standards. A total of 503 distinct proteins were detected in the platelet supernatants from the 4 sample groups: female or male donor platelets, either at storage day 1 or 5. Proteomics suggested a storage and gender-dependent impairment of blood coagulation mediators, pro-inflammatory complement components and cytokines, energy and redox metabolic enzymes. The supernatants from female donors demonstrated increased deregulation of structural proteins, extracellular matrix proteins and focal adhesion proteins, possibly indicating storage-dependent platelet activation. Routine storage of platelet concentrates induces changes in the supernatant proteome, which may have effects on the transfused patient, some of which are related to donor gender. BIOLOGICAL SIGNIFICANCE The rationale behind this study is that protein components in platelet releasates have been increasingly observed to play a key role in adverse events and impaired homeostasis in transfused recipients. In this view, proteomics has recently emerged as a functional tool to address the issue of protein composition of platelet releasates from buffy coat-derived platelet concentrates in the blood bank. Despite early encouraging studies on buffy coat-derived platelet concentrates, platelet releasates from apheresis platelets have not been hitherto addressed by means of extensive proteomics technologies. Indeed, apheresis platelets are resuspended in donors' plasma, which hampers detection of less abundant proteins, owing to the overwhelming abundance of albumin (and a handful of other proteins), and the dynamic range of protein concentrations of plasma proteins. In order to cope with these issues, we hereby performed an immuno-affinity column-based depletion of the 14 most abundant plasma proteins. Samples were thus assayed via GeLC-MS, a workflow that allowed us to cover an unprecedented portion of the platelet supernatant proteome, in comparison to previous transfusion medicine-oriented studies in the literature. Finally, we hereby address the issue of biological variability, by considering the donor gender as a key factor influencing the composition of apheresis platelet supernatants. As a result, we could conclude that platelet supernatants from male and female donors are not only different in the first place, but they also store differently. This conclusion has been so far only suggested by classic transfusion medicine studies, but has been hitherto unsupported by actual biochemistry/proteomics investigations. In our opinion, the main strengths of this study are related to the analytical workflow (immunodepletion and GeLC-MS) and proteome coverage, the translational validity of the results (from a transfusion medicine standpoint) and the biological conclusion about the intrinsic (and storage-dependent) gender-related differences of platelet supernatants.
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Reumer A, Maes E, Mertens I, Cho WCS, Landuyt B, Valkenborg D, Schoofs L, Baggerman G. Colorectal cancer biomarker discovery and validation using LC-MS/MS-based proteomics in blood: truth or dare? Expert Rev Proteomics 2014; 11:449-463. [PMID: 24702250 DOI: 10.1586/14789450.2014.905743] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Globally, colorectal cancer (CRC) is the third most common malignant neoplasm. However, highly sensitive, specific, noninvasive tests that allow CRC diagnosis at an early stage are still needed. As circulatory blood reflects the physiological status of an individual and/or the disease status for several disorders, efforts have been undertaken to identify candidate diagnostic CRC markers in plasma and serum. In this review, the challenges, bottlenecks and promising properties of mass spectrometry (MS)-based proteomics in blood are discussed. More specifically, important aspects in clinical design, sample retrieval, sample preparation, and MS analysis are presented. The recent developments in targeted MS approaches in plasma or serum are highlighted as well.
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Affiliation(s)
- Ank Reumer
- KU Leuven, Animal Physiology and Neurobiology Section, Naamsestraat 59, BE-3000 Leuven, Belgium
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Identification of plasma biomarker candidates in glioblastoma using an antibody-array-based proteomic approach. Radiol Oncol 2014; 48:257-66. [PMID: 25177240 PMCID: PMC4110082 DOI: 10.2478/raon-2014-0014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/10/2014] [Indexed: 12/30/2022] Open
Abstract
Background Glioblastoma multiforme (GBM) is a brain tumour with a very high patient mortality rate, with a median survival of 47 weeks. This might be improved by the identification of novel diagnostic, prognostic and predictive therapy-response biomarkers, preferentially through the monitoring of the patient blood. The aim of this study was to define the impact of GBM in terms of alterations of the plasma protein levels in these patients. Materials and methods. We used a commercially available antibody array that includes 656 antibodies to analyse blood plasma samples from 17 healthy volunteers in comparison with 17 blood plasma samples from patients with GBM. Results We identified 11 plasma proteins that are statistically most strongly associated with the presence of GBM. These proteins belong to three functional signalling pathways: T-cell signalling and immune responses; cell adhesion and migration; and cell-cycle control and apoptosis. Thus, we can consider this identified set of proteins as potential diagnostic biomarker candidates for GBM. In addition, a set of 16 plasma proteins were significantly associated with the overall survival of these patients with GBM. Guanine nucleotide binding protein alpha (GNAO1) was associated with both GBM presence and survival of patients with GBM. Conclusions Antibody array analysis represents a useful tool for the screening of plasma samples for potential cancer biomarker candidates in small-scale exploratory experiments; however, clinical validation of these candidates requires their further evaluation in a larger study on an independent cohort of patients.
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Prudent M, D’Alessandro A, Cazenave JP, Devine DV, Gachet C, Greinacher A, Lion N, Schubert P, Steil L, Thiele T, Tissot JD, Völker U, Zolla L. Proteome Changes in Platelets After Pathogen Inactivation—An Interlaboratory Consensus. Transfus Med Rev 2014; 28:72-83. [DOI: 10.1016/j.tmrv.2014.02.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 01/31/2014] [Accepted: 02/07/2014] [Indexed: 12/21/2022]
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Prudent M, Tissot JD, Lion N. Proteomics of blood and derived products: what’s next? Expert Rev Proteomics 2014; 8:717-37. [DOI: 10.1586/epr.11.58] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Alexandre BM. Proteomic mining of the red blood cell: focus on the membrane proteome. Expert Rev Proteomics 2014; 7:165-8. [DOI: 10.1586/epr.09.96] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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42
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Di Michele M, Van Geet C, Freson K. Recent advances in platelet proteomics. Expert Rev Proteomics 2014; 9:451-66. [DOI: 10.1586/epr.12.31] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Kemptner J, Witzeneder K, Hennerbichler S, Gabriel C. Proteomic analysis of human-derived cell culture supplements. ACTA ACUST UNITED AC 2013; 40:413-5. [PMID: 24474891 DOI: 10.1159/000356241] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Accepted: 06/21/2013] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Development of cell therapy and advanced therapy medicinal products depends on in vitro expansion of human cells in fetal bovine serum (FBS) supplemented media. Human-derived supplements, such as human serum (huS) and human platelet lysate (hPL), represent suitable alternatives to FBS. Various studies demonstrated that the use of these human alternatives result in comparable or even improved proliferation and expansion ratios. METHODS Within this study three human supplement alternatives, huS, hPLP (plasma containing hPL) and hPLN (plasma replaced by saline), were compared by 2D gel electrophoresis, an important tool in proteomic analysis. 2D gel electrophoresis allows the determination of the protein number and the detection of protein changes (decreasing/increasing concentration). RESULTS AND CONCLUSION The comparison of huS, hPLP, and hPLN gels resulted in clearly visible differences in protein pattern, protein number and concentration, particularly when comparing huS with hPL and hPLP with hPLN.
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Affiliation(s)
- Jasmin Kemptner
- Red Cross Blood Transfusion Service of Upper Austria ; Austrian Cluster for Tissue Regeneration, Linz, Austria
| | - Karin Witzeneder
- Red Cross Blood Transfusion Service of Upper Austria ; Austrian Cluster for Tissue Regeneration, Linz, Austria
| | - Simone Hennerbichler
- Red Cross Blood Transfusion Service of Upper Austria ; Austrian Cluster for Tissue Regeneration, Linz, Austria
| | - Christian Gabriel
- Red Cross Blood Transfusion Service of Upper Austria ; Austrian Cluster for Tissue Regeneration, Linz, Austria
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Boichenko AP, Govorukhina N, van der Zee AGJ, Bischoff R. Multidimensional separation of tryptic peptides from human serum proteins using reversed-phase, strong cation exchange, weak anion exchange, and fused-core fluorinated stationary phases. J Sep Sci 2013; 36:3463-70. [PMID: 24039020 DOI: 10.1002/jssc.201300750] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 12/19/2022]
Abstract
Proteome profiling of crude serum is a challenging task due to the wide dynamic range of protein concentrations and the presence of high-abundance proteins, which cover >90% of the total protein mass in serum. Peptide fractionation on strong cation exchange, weak anion exchange in the electrostatic repulsion hydrophilic interaction chromatography (ERLIC) mode, RP C18 at pH 2.5 (low pH), fused-core fluorinated at pH 2.5, and RP C18 at pH 9.7 (high pH) stationary phases resulted in two to three times more identified proteins and three to four times more identified peptides in comparison with 1D nanoChip-LC-MS/MS quadrupole TOF analysis (45 proteins, 185 peptides). The largest number of peptides and proteins was identified after prefractionation in the ERLIC mode due to the more uniform distribution of peptides among the collected fractions and on the RP column at high pH due to the high efficiency of RP separations and the complementary selectivity of both techniques to low-pH RP chromatography. A 3D separation scheme combining ERLIC, high-pH RP, and low-pH nanoChip-LC-MS/MS for crude serum proteome profiling resulted in the identification of 208 proteins and 1088 peptides with the lowest reported concentration of 11 ng/mL for heat shock protein 74.
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Affiliation(s)
- Alexander P Boichenko
- Department of Analytical Biochemistry, University of Groningen, Groningen, The Netherlands
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Rembach A, Ryan TM, Roberts BR, Doecke JD, Wilson WJ, Watt AD, Barnham KJ, Masters CL. Progress towards a consensus on biomarkers for Alzheimer’s disease: a review of peripheral analytes. Biomark Med 2013; 7:641-62. [DOI: 10.2217/bmm.13.59] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of dementia in the elderly population and attempts to develop therapies have been unsuccessful because there is no means to target an effective therapeutic window. CNS biomarkers are insightful but impractical for high-throughput population-based screening. Therefore, a peripheral, blood-based biomarker for AD would significantly improve early diagnosis, potentially enable presymptomatic detection and facilitate effective targeting of disease-modifying treatments. The various constituents of blood, including plasma, platelets and cellular fractions, are now being systematically explored as a pool of putative peripheral biomarkers for AD. In this review we cover some less known peripheral biomarkers and highlight the latest developments for their clinical application.
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Affiliation(s)
- Alan Rembach
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia.
| | - Tim M Ryan
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Blaine R Roberts
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - James D Doecke
- The Australian e-Health Research Centre, Herston, Queensland, 4029, Australia
- CSIRO Preventative Health National Research Flagship, North Ryde, New South Wales, 2113, Australia
| | - William J Wilson
- CSIRO Preventative Health National Research Flagship, North Ryde, New South Wales, 2113, Australia
| | - Andrew D Watt
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Kevin J Barnham
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
| | - Colin L Masters
- The Mental Health Research Institute, The University of Melbourne, Kenneth Myer Building, 30 Royal Parade, Parkville, Victoria, 3010, Australia
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Uzun L, Armutcu C, Biçen Ö, Ersöz A, Say R, Denizli A. Simultaneous depletion of immunoglobulin G and albumin from human plasma using novel monolithic cryogel columns. Colloids Surf B Biointerfaces 2013; 112:1-8. [PMID: 23928053 DOI: 10.1016/j.colsurfb.2013.07.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 07/01/2013] [Accepted: 07/03/2013] [Indexed: 10/26/2022]
Abstract
In this study, we aimed to develop an alternative matrix able to deplete the albumin (Alb) and immunoglobulin G (IgG) from blood plasma simultaneously to prepare plasma samples for large-scale applications of blood-related proteomics. As a first step, nano-protein A nanoparticles (nanoProA) were prepared and characterized. Subsequently, cibacron blue F3GA (CB) was immobilized onto the nanoProA's to enhance their specific affinity for Alb molecules. Finally, both nanoparticles, specifically, nanoProA and CB-nanoProA, were separately embedded into cryogel structures to combine advantages of the nanoparticles with those of the cryogels. The protein adsorption was optimized using aqueous Alb and IgG solutions separately. Subsequently, competitive protein adsorption was performed using a protein mixture prepared with Alb and IgG adhering to their plasma protein ratios. Because of the CB-immobilization, the Alb depletion performance of the cryogels increased whereas the IgG depleting performance decreased. Using the nanoProA, embedded cryogel removed 99.3% of the IgG, while using the CB-nanoProA embedded cryogel removed 97.5% of the Alb content. The simultaneous depletion performances of the cryogels for Alb and IgG were characterized using sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In this study, the monolithic cryogel-based adsorbents were classified as an alternative matrix to prepare plasma samples for proteomics applications at the preparative scale.
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Affiliation(s)
- Lokman Uzun
- Hacettepe University, Department of Chemistry, Beytepe, Ankara, Turkey.
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Pallotta V, D’Alessandro A, Rinalducci S, Zolla L. Native Protein Complexes in the Cytoplasm of Red Blood Cells. J Proteome Res 2013; 12:3529-46. [DOI: 10.1021/pr400431b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Valeria Pallotta
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Angelo D’Alessandro
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Sara Rinalducci
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
| | - Lello Zolla
- Department of Ecological
and Biological Sciences, University of Tuscia, Largo dell’Università,
snc, 01100 Viterbo, Italy
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48
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Goodman SR, Daescu O, Kakhniashvili DG, Zivanic M. The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 2013; 238:509-18. [DOI: 10.1177/1535370213488474] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
In this minireview, we focus on advances in our knowledge of the human erythrocyte proteome and interactome that have occurred since our seminal review on the topic published in 2007. As will be explained, the number of unique proteins has grown from 751 in 2007 to 2289 as of today. We describe how proteomics and interactomics tools have been used to probe critical protein changes in disorders impacting the blood. The primary example used is the work done on sickle cell disease where biomarkers of severity have been identified, protein changes in the erythrocyte membranes identified, pharmacoproteomic impact of hydroxyurea studied and interactomics used to identify erythrocyte protein changes that are predicted to have the greatest impact on protein interaction networks.
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Affiliation(s)
- Steven R Goodman
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Ovidiu Daescu
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
| | - David G Kakhniashvili
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Marko Zivanic
- Department of Computer Science, University of Texas at Dallas, Richardson, TX 75080, USA
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Ortiz A, Richa L, Defer C, Dernis D, Huart JJ, Tokarski C, Rolando C. Proteomics applied to transfusion plasma: the beginning of the story. Vox Sang 2013; 104:275-91. [PMID: 23438183 DOI: 10.1111/j.1423-0410.2012.01663.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
'Safe blood' is and has always been the major concern in transfusion medicine. Plasma can undergo virus inactivation treatments based on physicochemical, photochemical or thermal methodologies for pathogen inactivation. The validation of these treatments is essentially based on clottability assays and clotting factors' titration; however, their impact on plasma proteins at the molecular level has not yet been evaluated. Proteomics appears as particularly adapted to identify, to localize and, consequently, to correlate these modifications to the biological activity change. At the crossroads of biology and analytical sciences, proteomics is the large-scale study of proteins in tissues, physiological fluids or cells at a given moment and in a precise environment. The proteomic strategy is based on a set of methodologies involving separative techniques like mono- and bidimensional gel electrophoresis and chromatography, analytical techniques, especially mass spectrometry, and bioinformatics. Even if plasma has been extensively studied since the very beginning of proteomics, its application to transfusion medicine has just begun. In the first part of this review, we present the principles of proteomics analysis. Then, we propose a state of the art of proteomics applied to plasma analysis. Finally, the use of proteomics for the evaluation of the impact of storage conditions and pathogen inactivation treatments applied to transfusion plasma and for the evaluation of therapeutic protein fractionated is discussed.
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Affiliation(s)
- A Ortiz
- USR CNRS 3290, Miniaturisation pour la Synthèse, l'Analyse et la Protéomique (MSAP), Université de Lille 1, Sciences et Technologie, Villeneuve d'Ascq, France
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Marrocco C, D'Alessandro A, Girelli G, Zolla L. Proteomic analysis of platelets treated with gamma irradiation versus a commercial photochemical pathogen reduction technology. Transfusion 2013; 53:1808-20. [DOI: 10.1111/trf.12060] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 09/20/2012] [Accepted: 10/12/2012] [Indexed: 12/18/2022]
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