1
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Distinct patterns of serum and urine macrophage migration inhibitory factor kinetics predict death in sepsis: a prospective, observational clinical study. Sci Rep 2023; 13:588. [PMID: 36631486 PMCID: PMC9834307 DOI: 10.1038/s41598-023-27506-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023] Open
Abstract
Macrophage migration inhibitory factor (MIF) has been considered as a biomarker in sepsis, however the predictive value of the pattern of its kinetics in the serum and in the urine has remained unclarified. It is also unclear whether the kinetics of MIF are different between males and females. We conducted a single-center prospective, observational study with repeated measurements of MIF in serum and urine on days 0, 2, and 4 from admission to the intensive care unit (ICU) in 50 adult septic patients. We found that in patients who died within 90 days, there was an increase in serum MIF level from day 0 to 4, whereas in the survivors there was rather a decrease (p = 0.018). The kinetics were sex-dependent as the same difference in the pattern was present in males (p = 0.014), but not in females (p = 0.418). We also found that urine MIF was markedly lower in patients who died than in survivors of sepsis (p < 0.050). Urine MIF levels did not show temporal changes: there was no meaningful difference between day 0 and 4. These results suggest that kinetics of serum MIF during the initial days from ICU admission can predict death, especially in male patients. Additionally, lower urine MIF levels can also indicate death without showing meaningful temporal kinetics.
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2
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Hollas MAR, Robey M, Fellers R, LeDuc R, Thomas P, Kelleher N. The Human Proteoform Atlas: a FAIR community resource for experimentally derived proteoforms. Nucleic Acids Res 2022; 50:D526-D533. [PMID: 34986596 PMCID: PMC8728143 DOI: 10.1093/nar/gkab1086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/06/2021] [Accepted: 11/14/2021] [Indexed: 01/01/2023] Open
Abstract
The Human Proteoform Atlas (HPfA) is a web-based repository of experimentally verified human proteoforms on-line at http://human-proteoform-atlas.org and is a direct descendant of the Consortium of Top-Down Proteomics' (CTDP) Proteoform Atlas. Proteoforms are the specific forms of protein molecules expressed by our cells and include the unique combination of post-translational modifications (PTMs), alternative splicing and other sources of variation deriving from a specific gene. The HPfA uses a FAIR system to assign persistent identifiers to proteoforms which allows for redundancy calling and tracking from prior and future studies in the growing community of proteoform biology and measurement. The HPfA is organized around open ontologies and enables flexible classification of proteoforms. To achieve this, a public registry of experimentally verified proteoforms was also created. Submission of new proteoforms can be processed through email vianrtdphelp@northwestern.edu, and future iterations of these proteoform atlases will help to organize and assign function to proteoforms, their PTMs and their complexes in the years ahead.
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Affiliation(s)
- Michael A R Hollas
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Matthew T Robey
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Richard D LeDuc
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Paul M Thomas
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, and the Chemistry of Life Processes Institute, Northwestern University, Evanston, IL 60208, USA
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3
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Neagu AN, Whitham D, Buonanno E, Jenkins A, Alexa-Stratulat T, Tamba BI, Darie CC. Proteomics and its applications in breast cancer. Am J Cancer Res 2021; 11:4006-4049. [PMID: 34659875 PMCID: PMC8493401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023] Open
Abstract
Breast cancer is an individually unique, multi-faceted and chameleonic disease, an eternal challenge for the new era of high-integrated precision diagnostic and personalized oncomedicine. Besides traditional single-omics fields (such as genomics, epigenomics, transcriptomics and metabolomics) and multi-omics contributions (proteogenomics, proteotranscriptomics or reproductomics), several new "-omics" approaches and exciting proteomics subfields are contributing to basic and advanced understanding of these "multiple diseases termed breast cancer": phenomics/cellomics, connectomics and interactomics, secretomics, matrisomics, exosomics, angiomics, chaperomics and epichaperomics, phosphoproteomics, ubiquitinomics, metalloproteomics, terminomics, degradomics and metadegradomics, adhesomics, stressomics, microbiomics, immunomics, salivaomics, materiomics and other biomics. Throughout the extremely complex neoplastic process, a Breast Cancer Cell Continuum Concept (BCCCC) has been modeled in this review as a spatio-temporal and holistic approach, as long as the breast cancer represents a complex cascade comprising successively integrated populations of heterogeneous tumor and cancer-associated cells, that reflect the carcinoma's progression from a "driving mutation" and formation of the breast primary tumor, toward the distant secondary tumors in different tissues and organs, via circulating tumor cell populations. This BCCCC is widely sustained by a Breast Cancer Proteomic Continuum Concept (BCPCC), where each phenotype of neoplastic and tumor-associated cells is characterized by a changing and adaptive proteomic profile detected in solid and liquid minimal invasive biopsies by complex proteomics approaches. Such a profile is created, beginning with the proteomic landscape of different neoplastic cell populations and cancer-associated cells, followed by subsequent analysis of protein biomarkers involved in epithelial-mesenchymal transition and intravasation, circulating tumor cell proteomics, and, finally, by protein biomarkers that highlight the extravasation and distant metastatic invasion. Proteomics technologies are producing important data in breast cancer diagnostic, prognostic, and predictive biomarkers discovery and validation, are detecting genetic aberrations at the proteome level, describing functional and regulatory pathways and emphasizing specific protein and peptide profiles in human tissues, biological fluids, cell lines and animal models. Also, proteomics can identify different breast cancer subtypes and specific protein and proteoform expression, can assess the efficacy of cancer therapies at cellular and tissular level and can even identify new therapeutic target proteins in clinical studies.
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Affiliation(s)
- Anca-Narcisa Neagu
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
- Laboratory of Animal Histology, Faculty of Biology, “Alexandru Ioan Cuza” University of IașiCarol I bvd. No. 22, Iași 700505, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Emma Buonanno
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Avalon Jenkins
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
| | - Teodora Alexa-Stratulat
- Department of Medical Oncology-Radiotherapy, “Grigore T. Popa” University of Medicine and PharmacyIndependenței bvd. No. 16-18, Iași 700021, Romania
| | - Bogdan Ionel Tamba
- Advanced Center for Research and Development in Experimental Medicine (CEMEX), “Grigore T. Popa” University of Medicine and PharmacyMihail Kogălniceanu Street No. 9-13, Iași 700454, Romania
| | - Costel C Darie
- Biochemistry & Proteomics Group, Department of Chemistry and Biomolecular Science, Clarkson UniversityPotsdam, NY 13699-5810, USA
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4
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Neubert H, Shuford CM, Olah TV, Garofolo F, Schultz GA, Jones BR, Amaravadi L, Laterza OF, Xu K, Ackermann BL. Protein Biomarker Quantification by Immunoaffinity Liquid Chromatography–Tandem Mass Spectrometry: Current State and Future Vision. Clin Chem 2020; 66:282-301. [DOI: 10.1093/clinchem/hvz022] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Immunoaffinity–mass spectrometry (IA-MS) is an emerging analytical genre with several advantages for profiling and determination of protein biomarkers. Because IA-MS combines affinity capture, analogous to ligand binding assays (LBAs), with mass spectrometry (MS) detection, this platform is often described using the term hybrid methods. The purpose of this report is to provide an overview of the principles of IA-MS and to demonstrate, through application, the unique power and potential of this technology. By combining target immunoaffinity enrichment with the use of stable isotope-labeled internal standards and MS detection, IA-MS achieves high sensitivity while providing unparalleled specificity for the quantification of protein biomarkers in fluids and tissues. In recent years, significant uptake of IA-MS has occurred in the pharmaceutical industry, particularly in the early stages of clinical development, enabling biomarker measurement previously considered unattainable. By comparison, IA-MS adoption by CLIA laboratories has occurred more slowly. Current barriers to IA-MS use and opportunities for expanded adoption are discussed. The path forward involves identifying applications for which IA-MS is the best option compared with LBA or MS technologies alone. IA-MS will continue to benefit from advances in reagent generation, more sensitive and higher throughput MS technologies, and continued growth in use by the broader analytical community. Collectively, the pursuit of these opportunities will secure expanded long-term use of IA-MS for clinical applications.
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5
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Top-down mass spectrometric immunoassay for human insulin and its therapeutic analogs. J Proteomics 2018; 175:27-33. [DOI: 10.1016/j.jprot.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/08/2023]
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6
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Kupcova Skalnikova H, Cizkova J, Cervenka J, Vodicka P. Advances in Proteomic Techniques for Cytokine Analysis: Focus on Melanoma Research. Int J Mol Sci 2017; 18:E2697. [PMID: 29236046 PMCID: PMC5751298 DOI: 10.3390/ijms18122697] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 12/16/2022] Open
Abstract
Melanoma is a skin cancer with permanently increasing incidence and resistance to therapies in advanced stages. Reports of spontaneous regression and tumour infiltration with T-lymphocytes makes melanoma candidate for immunotherapies. Cytokines are key factors regulating immune response and intercellular communication in tumour microenvironment. Cytokines may be used in therapy of melanoma to modulate immune response. Cytokines also possess diagnostic and prognostic potential and cytokine production may reflect effects of immunotherapies. The purpose of this review is to give an overview of recent advances in proteomic techniques for the detection and quantification of cytokines in melanoma research. Approaches covered span from mass spectrometry to immunoassays for single molecule detection (ELISA, western blot), multiplex assays (chemiluminescent, bead-based (Luminex) and planar antibody arrays), ultrasensitive techniques (Singulex, Simoa, immuno-PCR, proximity ligation/extension assay, immunomagnetic reduction assay), to analyses of single cells producing cytokines (ELISpot, flow cytometry, mass cytometry and emerging techniques for single cell secretomics). Although this review is focused mainly on cancer and particularly melanoma, the discussed techniques are in general applicable to broad research field of biology and medicine, including stem cells, development, aging, immunology and intercellular communication.
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Affiliation(s)
- Helena Kupcova Skalnikova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
| | - Jana Cizkova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Veterinary Sciences, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences, Kamycka 129, 16500 Prague, Czech Republic.
| | - Jakub Cervenka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
- Department of Cell Biology, Faculty of Science, Charles University, Vinicna 7, 12843 Prague 4, Czech Republic.
| | - Petr Vodicka
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Rumburska 89, 27721 Libechov, Czech Republic.
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Nedelkov D. Mass Spectrometric Studies of Apolipoprotein Proteoforms and Their Role in Lipid Metabolism and Type 2 Diabetes. Proteomes 2017; 5:E27. [PMID: 29036931 PMCID: PMC5748562 DOI: 10.3390/proteomes5040027] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/10/2017] [Accepted: 10/11/2017] [Indexed: 12/14/2022] Open
Abstract
Apolipoproteins function as structural components of lipoprotein particles, cofactors for enzymes, and ligands for cell-surface receptors. Most of the apoliporoteins exhibit proteoforms, arising from single nucleotide polymorphisms (SNPs) and post-translational modifications such as glycosylation, oxidation, and sequence truncations. Reviewed here are recent studies correlating apolipoproteins proteoforms with the specific clinical measures of lipid metabolism and cardiometabolic risk. Targeted mass spectrometric immunoassays toward apolipoproteins A-I, A-II, and C-III were applied on large cross-sectional and longitudinal clinical cohorts. Several correlations were observed, including greater apolipoprotein A-I and A-II oxidation in patients with diabetes and cardiovascular disease, and a divergent apoC-III proteoforms association with plasma triglycerides, indicating significant differences in the metabolism of the individual apoC-III proteoforms. These are the first studies of their kind, correlating specific proteoforms with clinical measures in order to determine their utility as potential clinical biomarkers for disease diagnosis, risk stratification, and therapy decisions. Such studies provide the impetus for the further development and clinical translation of MS-based protein tests.
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8
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Nedelkov D. Human proteoforms as new targets for clinical mass spectrometry protein tests. Expert Rev Proteomics 2017; 14:691-699. [DOI: 10.1080/14789450.2017.1362337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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9
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Klont F, Ten Hacken NHT, Horvatovich P, Bakker SJL, Bischoff R. Assuring Consistent Performance of an Insulin-Like Growth Factor 1 MALDImmunoassay by Monitoring Measurement Quality Indicators. Anal Chem 2017; 89:6188-6195. [PMID: 28467045 PMCID: PMC5463271 DOI: 10.1021/acs.analchem.7b01125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Analytical
methods based on mass spectrometry (MS) have been successfully
applied in biomarker discovery studies, while the role of MS in translating
biomarker candidates to clinical diagnostics is less pronounced. MALDImmunoassays—methods
that combine immunoaffinity enrichment with matrix-assisted laser
desorption ionization time-of-flight (MALDI-TOF) mass spectrometric
detection—are attractive analytical approaches for large-scale
sample analysis by virtue of their ease of operation and high-throughput
capabilities. Despite this fact, MALDImmunoassays are not widely used
in clinical diagnostics, which is mainly due to the limited availability
of internal standards that can adequately correct for variability
in sample preparation and the MALDI process itself. Here we present
a novel MALDImmunoassay for quantification of insulin-like growth
factor 1 (IGF1) in human plasma. Reliable IGF1 quantification in the
range of 10–1000 ng/mL was achieved by employing 15N-IGF1 as internal standard, which proved to be an essential feature
of the IGF1 MALDImmunoassay. The method was validated according to
U.S. Food and Drug Administration (FDA) guidelines, which included
demonstrating the effectiveness of IGF1/IGF binding protein (IGF1/IGFBP)
complex dissociation using sodium dodecyl sulfate (SDS). Furthermore,
the MALDImmunoassay compared well with the IDS-iSYS IGF1 immunoassay
with high correlation (R2 = 0.99), although
substantially lower levels were reported by the MALDImmunoassay. The
method was tested on >1000 samples from a cohort of renal transplant
recipients to assess its performance in a clinical setting. On the
basis of this study, we identified readouts to monitor the quality
of the measurements. Our work shows that MALDI-TOF mass spectrometry
is suitable for quantitative biomarker analysis provided that an appropriate
internal standard is used and that readouts are monitored to assess
the quality of the measurements.
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Affiliation(s)
- Frank Klont
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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10
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Trenchevska O, Koska J, Sinari S, Yassine H, Reaven PD, Billheimer DD, Nelson RW, Nedelkov D. Association of Cystatin C Proteoforms with Estimated Glomerular Filtration Rate. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2016; 1:27-31. [PMID: 36778895 PMCID: PMC9913891 DOI: 10.1016/j.clinms.2016.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Background Cystatin C (CysC), a marker for chronic kidney disease, exists as three sequence proteoforms, in addition to the wild-type sequence: one contains hydroxyproline at position 3 (3Pro-OH), the two others have truncated sequences (des-S and des-SSP). Here, we examine correlations between each of these CysC proteoforms and estimated glomerular filtration rate (eGFR), a diagnostic criterion for chronic kidney disease (CKD). Methods CysC proteoform concentrations were determined from the plasma of 297 diabetes patients at a baseline time point and nine-months later, using a mass spectrometric immunoassay, and were correlated with eGFR calculations. Results In all samples, 3Pro-OH was the most abundant CysC proteoform, followed by the wild-type proteoform. Least abundant were the truncated CysC proteoforms, des-S and des-SSP, although they demonstrated stronger negative correlation with eGFR than the 3Pro-OH and wild-type proteoforms. The des-SSP truncated proteoform exhibited negative predictive value for eGFR. Conclusions The truncated CysC proteoforms show potential for clinical and prognostic utility in CKD staging. This could be useful in populations where current methods do not provide satisfactory solutions.
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Affiliation(s)
| | - Juraj Koska
- Department of Medicine, Phoenix Veteran Affairs Medical Center, Phoenix, AZ, USA
| | - Shripad Sinari
- Biostatics Consulting Lab, University of Arizona, Tucson, AZ, USA
| | - Hussein Yassine
- Department of Medicine, University of Southern California, Los Angeles, USA
| | - Peter D. Reaven
- Department of Medicine, Phoenix Veteran Affairs Medical Center, Phoenix, AZ, USA
| | | | | | - Dobrin Nedelkov
- The Biodesign Institute, Arizona State University, Tempe, AZ, USA,Corresponding author: , PO Box 876601, Tempe AZ 85287-6601, USA, Tel. 480-727-2280
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11
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Mass spectrometric immunoassays for discovery, screening and quantification of clinically relevant proteoforms. Bioanalysis 2016; 8:1623-1633. [PMID: 27396364 DOI: 10.4155/bio-2016-0060] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Human proteins can exist as multiple proteoforms with potential diagnostic or prognostic significance. MS top-down approaches are ideally suited for proteoforms identification because there is no prerequisite for a priori knowledge of the specific proteoform. One such top-down approach, termed mass spectrometric immunoassay utilizes antibody-derivatized microcolumns for rapid and contained proteoforms isolation and detection via MALDI-TOF MS. The mass spectrometric immunoassay can also provide quantitative measurement of the proteoforms through inclusion of an internal reference standard into the analytical sample, serving as normalizer for all sample processing and data acquisition steps. Reviewed here are recent developments and results from the application of mass spectrometric immunoassays for discovery of clinical correlations of specific proteoforms for the protein biomarkers RANTES, retinol binding protein, serum amyloid A and apolipoprotein C-III.
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12
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Quantitative analysis of hIgG1 in monkey serum by LC–MS/MS using mass spectrometric immunoassay. Bioanalysis 2016; 8:1035-49. [DOI: 10.4155/bio.16.32] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Aim: A sensitive generic LC–MS/MS method for hIgG1 quantification in cynomolgus monkey serum using mass spectrometric immunoassay disposable automation research tips (MSIA-D.A.R.T.'S™) is reported. Results: The hIgG1 was captured with a biotinylated mouse anti-hIgG antibody (50.0 µg/ml) targeting the fragment crystallizable (Fc) region. Elution from the streptavidin-coated MSIA-D.A.R.T.'s was conducted with 0.4% trifluoroacetic acid in water. The method was selective and linear from 10.0 to 1000 ng/ml using 100 µl of serum. The method was evaluated regarding accuracy, precision, carry-over, dilution, auto-sampler stability and applied for the determination of hIgG1 concentration in monkey serum after intravitreal administration. Conclusion: The present assay is suitable for quantitative analysis of hIgG1-based therapeutic proteins in monkey serum at low levels.
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Zaslavsky BY, Uversky VN, Chait A. Analytical applications of partitioning in aqueous two-phase systems: Exploring protein structural changes and protein–partner interactions in vitro and in vivo by solvent interaction analysis method. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:622-44. [DOI: 10.1016/j.bbapap.2016.02.017] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 02/16/2016] [Accepted: 02/21/2016] [Indexed: 12/29/2022]
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14
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Trenchevska O, Nelson RW, Nedelkov D. Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms. Proteomes 2016; 4:proteomes4010013. [PMID: 28248223 PMCID: PMC5217360 DOI: 10.3390/proteomes4010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins. MSIA enables protein profiling in a simple and high-throughput manner, by combining the selectivity of targeted immunoassays, with the specificity of mass spectrometric detection. MSIA has been used for qualitative and quantitative analysis of single and multiple proteoforms, distinguishing between normal fluctuations and changes related to clinical conditions. This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies. Provided are examples of some recent developments, and also discussed are the trends and challenges in mass spectrometry-based immunoassays for the next-phase of clinical applications.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Randall W Nelson
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Dobrin Nedelkov
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
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15
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Zhang X, Ding SN. General Strategy to Fabricate Electrochemiluminescence Sandwich-Type Nanoimmunosensors Using CdTe@ZnS Quantum Dots as Luminescent Labels and Fe3O4@SiO2 Nanoparticles as Magnetic Separable Scaffolds. ACS Sens 2016. [DOI: 10.1021/acssensors.5b00242] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Xin Zhang
- School of Chemistry and Chemical
Engineering, Southeast University, Nanjing 211189, China
| | - Shou-Nian Ding
- School of Chemistry and Chemical
Engineering, Southeast University, Nanjing 211189, China
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16
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Boström T, Takanen JO, Hober S. Antibodies as means for selective mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1021:3-13. [PMID: 26565067 DOI: 10.1016/j.jchromb.2015.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023]
Abstract
For protein analysis of biological samples, two major strategies are used today; mass spectrometry (MS) and antibody-based methods. Each strategy offers advantages and drawbacks. However, combining the two using an immunoenrichment step with MS analysis brings together the benefits of each method resulting in increased sensitivity, faster analysis and possibility of higher degrees of multiplexing. The immunoenrichment can be performed either on protein or peptide level and quantification standards can be added in order to enable determination of the absolute protein concentration in the sample. The combination of immunoenrichment and MS holds great promise for the future in both proteomics and clinical diagnostics. This review describes different setups of immunoenrichment coupled to mass spectrometry and how these can be utilized in various applications.
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Affiliation(s)
- Tove Boström
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Jenny Ottosson Takanen
- School of Biotechnology, Division of Proteomics and Nanobiotechnology, KTH-Royal Institute ofTechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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17
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Ménoret A, Crocker SJ, Rodriguez A, Rathinam VA, Clark RB, Vella AT. Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform. Proteomics Clin Appl 2015. [PMID: 26201056 DOI: 10.1002/prca.201500029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.
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Affiliation(s)
- Antoine Ménoret
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Stephen J Crocker
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, USA
| | - Annabelle Rodriguez
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Vijay A Rathinam
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Robert B Clark
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Anthony T Vella
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
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LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications. Bioanalysis 2015; 7:1943-58. [DOI: 10.4155/bio.15.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.
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Trenchevska O, Schaab MR, Nelson RW, Nedelkov D. Development of multiplex mass spectrometric immunoassay for detection and quantification of apolipoproteins C-I, C-II, C-III and their proteoforms. Methods 2015; 81:86-92. [PMID: 25752847 PMCID: PMC4574700 DOI: 10.1016/j.ymeth.2015.02.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/23/2015] [Accepted: 02/27/2015] [Indexed: 01/11/2023] Open
Abstract
The impetus for discovery and evaluation of protein biomarkers has been accelerated by recent development of advanced technologies for rapid and broad proteome analyses. Mass spectrometry (MS)-based protein assays hold great potential for in vitro biomarker studies. Described here is the development of a multiplex mass spectrometric immunoassay (MSIA) for quantification of apolipoprotein C-I (apoC-I), apolipoprotein C-II (apoC-II), apolipoprotein C-III (apoC-III) and their proteoforms. The multiplex MSIA assay was fast (∼ 40 min) and high-throughput (96 samples at a time). The assay was applied to a small cohort of human plasma samples, revealing the existence of multiple proteoforms for each apolipoprotein C. The quantitative aspect of the assay enabled determination of the concentration for each proteoform individually. Low-abundance proteoforms, such as fucosylated apoC-III, were detected in less than 20% of the samples. The distribution of apoC-III proteoforms varied among samples with similar total apoC-III concentrations. The multiplex analysis of the three apolipoproteins C and their proteoforms using quantitative MSIA represents a significant step forward toward better understanding of their physiological roles in health and disease.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Matthew R Schaab
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Randall W Nelson
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Dobrin Nedelkov
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States.
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A Microfluidic Love-Wave Biosensing Device for PSA Detection Based on an Aptamer Beacon Probe. SENSORS 2015; 15:13839-50. [PMID: 26110408 PMCID: PMC4507688 DOI: 10.3390/s150613839] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 05/29/2015] [Accepted: 06/09/2015] [Indexed: 11/30/2022]
Abstract
A label-free and selective aptamer beacon-based Love-wave biosensing device was developed for prostate specific antigen (PSA) detection. The device consists of the following parts: LiTaO3 substrate with SiO2 film as wave guide layer, two set of inter-digital transducers (IDT), gold film for immobilization of the biorecongniton layer and a polydimethylsiloxane (PDMS) microfluidic channels. DNA aptamer, or “artificial antibody”, was used as the specific biorecognition probe for PSA capture. Some nucleotides were added to the 3'-end of the aptamer to form a duplex with the 3'-end, turning the aptamer into an aptamer-beacon. Taking advantage of the selective target-induced assembly changes arising from the “aptamer beacon”, highly selective and specific detection of PSA was achieved. Furthermore, PDMS microfluidic channels were designed and fabricated to realize automated quantitative sample injection. After optimization of the experimental conditions, the established device showed good performance for PSA detection between 10 ng/mL to 1 μg/mL, with a detection limit of 10 ng/mL. The proposed sensor might be a promising alternative for point of care diagnostics.
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Gauthier MS, Pérusse JR, Awan Z, Bouchard A, Tessier S, Champagne J, Krastins B, Byram G, Chabot K, Garneau P, Rabasa-Lhoret R, Faubert D, Lopez MF, Seidah NG, Coulombe B. A semi-automated mass spectrometric immunoassay coupled to selected reaction monitoring (MSIA-SRM) reveals novel relationships between circulating PCSK9 and metabolic phenotypes in patient cohorts. Methods 2015; 81:66-73. [PMID: 25770357 DOI: 10.1016/j.ymeth.2015.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/25/2022] Open
Abstract
Proprotein convertase subtilisin/kexin type 9 (PCSK9) is a key regulator of circulating low density lipoprotein cholesterol (LDL-C) levels. Besides its full-length mature form, multiple variants of PCSK9 have been reported such as forms that are truncated, mutated and/or with posttranslational modifications (PTMs). Previous studies have demonstrated that most of these variants affect PCSK9's function and thereby LDL-C levels. Commercial ELISA kits are available for quantification of PCSK9, but do not allow discrimination between the various forms and PTMs of the protein. To address this issue and given the complexity and wide dynamic range of the plasma proteome, we have developed a mass spectrometric immunoassay coupled to selected reaction monitoring (MSIA-SRM) for the multiplexed quantification of several forms of circulating PCSK9 in human plasma. Our MSIA-SRM assay quantifies peptides spanning the various protein domains and the S688 phosphorylation site. The assay was applied in two distinct cohorts of obese patients and healthy pregnant women stratified by their circulating LDL-C levels. Seven PCSK9 peptides were monitored in plasma samples: one in the prodomain prior to the autocleavage site at Q152, one in the catalytic domain prior to the furin cleavage site at R218, two in the catalytic domain following R218, one in the cysteine and histidine rich domain (CHRD) and the C-terminal peptide phosphorylated at S688 and unmodified. The latter was not detectable in sufficient amounts to be quantified in human plasma. All peptides were measured with high reproducibility and with LLOQ and LOD below the clinical range. The abundance of 5 of the 6 detectable PCSK9 peptides was higher in obese patients stratified with high circulating LDL-C levels as compared to those with low LDL-C (p < 0.05). The same 5 peptides showed good and statistically significant correlations with LDL-C levels (0.55 < r < 0.65; 0.0002 ⩽ p ⩽ 0.002), but not the S688 phosphorylated peptide. However, this phosphopeptide was significantly correlated with insulin resistance (r = 0.48; p = 0.04). In the pregnant women cohort, none of the peptides were associated to LDL-C levels. However, the 6 detectable PCSK9 peptides, but not PCSK9 measured by ELISA, were significantly correlated with serum triglyceride levels in this cohort. Our results also suggest that PCSK9 circulates with S688 phosphorylated at high stoichiometry. In summary, we have developed and applied a robust and sensitive MSIA-SRM assay for the absolute quantification of all PCSK9 domains and a PTM in human plasma. This assay revealed novel relationships between PCSK9 and metabolic phenotypes, as compared to classical ELISA assays.
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Affiliation(s)
- Marie-Soleil Gauthier
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Joëlle R Pérusse
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Zuhier Awan
- King Abdulaziz University, Jeddah, Saudi Arabia; McGill University, Montréal, QC H3A 1A1, Canada
| | - Annie Bouchard
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Sylvain Tessier
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Josée Champagne
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Bryan Krastins
- Thermo Fisher Scientific, Biomarker Research Initiatives in Mass Spectrometry Center, 790 Memorial Drive, Cambridge, MA 02139, USA
| | - Gregory Byram
- Thermo Fisher Scientific, Biomarker Research Initiatives in Mass Spectrometry Center, 790 Memorial Drive, Cambridge, MA 02139, USA
| | - Katherine Chabot
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Pierre Garneau
- General Surgery Department, Hôpital du Sacré-Coeur de Montréal, Montréal, QC H4J 1C5, Canada
| | - Rémi Rabasa-Lhoret
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Denis Faubert
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Mary F Lopez
- Thermo Fisher Scientific, Biomarker Research Initiatives in Mass Spectrometry Center, 790 Memorial Drive, Cambridge, MA 02139, USA
| | - Nabil G Seidah
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Benoit Coulombe
- Institut de Recherches Cliniques de Montréal (affiliated to the Université de Montréal), 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada; Department of Biochemistry, Université de Montréal, Montréal, QC H3T 1J4, Canada.
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Scherl A. Clinical protein mass spectrometry. Methods 2015; 81:3-14. [PMID: 25752846 DOI: 10.1016/j.ymeth.2015.02.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/26/2022] Open
Abstract
Quantitative protein analysis is routinely performed in clinical chemistry laboratories for diagnosis, therapeutic monitoring, and prognosis. Today, protein assays are mostly performed either with non-specific detection methods or immunoassays. Mass spectrometry (MS) is a very specific analytical method potentially very well suited for clinical laboratories. Its unique advantage relies in the high specificity of the detection. Any protein sequence variant, the presence of a post-translational modification or degradation will differ in mass and structure, and these differences will appear in the mass spectrum of the protein. On the other hand, protein MS is a relatively young technique, demanding specialized personnel and expensive instrumentation. Many scientists and opinion leaders predict MS to replace immunoassays for routine protein analysis, but there are only few protein MS applications routinely used in clinical chemistry laboratories today. The present review consists of a didactical introduction summarizing the pros and cons of MS assays compared to immunoassays, the different instrumentations, and various MS protein assays that have been proposed and/or are used in clinical laboratories. An important distinction is made between full length protein analysis (top-down method) and peptide analysis after enzymatic digestion of the proteins (bottom-up method) and its implication for the protein assay. The document ends with an outlook on what type of analyses could be used in the future, and for what type of applications MS has a clear advantage compared to immunoassays.
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Affiliation(s)
- Alexander Scherl
- Department of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
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Platelet-derived MIF: A novel platelet chemokine with distinct recruitment properties. Atherosclerosis 2015; 239:1-10. [DOI: 10.1016/j.atherosclerosis.2014.12.039] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 11/06/2014] [Accepted: 12/18/2014] [Indexed: 11/21/2022]
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Trenchevska O, Sherma ND, Oran PE, Reaven PD, Nelson RW, Nedelkov D. Quantitative mass spectrometric immunoassay for the chemokine RANTES and its variants. J Proteomics 2014; 116:15-23. [PMID: 25549571 DOI: 10.1016/j.jprot.2014.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 12/12/2014] [Accepted: 12/19/2014] [Indexed: 01/27/2023]
Abstract
UNLABELLED The chemokine RANTES plays a key role in inflammation, cell recruitment and T cell activation. RANTES is heterogenic and exists as multiple variants in vivo. Herein we describe the development and characterization of a fully quantitative mass spectrometric immunoassay (MSIA) for analysis of intact RANTES and its proteoforms in human serum and plasma samples. The assay exhibits linearity over a wide concentration range (1.56-200ng/mL), intra- and inter-assay precision with CVs <10%, and good linearity and recovery correlations. The assay was tested in different biological matrices, and it was benchmarked against an existing RANTES ELISA. The new RANTES MSIA was used to analyze RANTES and its proteoforms in a small clinical cohort, revealing the quantitative distribution and frequency of the native and truncated RANTES proteoforms. BIOLOGICAL SIGNIFICANCE In the last two decades, RANTES has been studied extensively due to its association with numerous clinical conditions, including kidney-related, autoimmune, cardiovascular, viral and metabolic pathologies. Although a single gene product, RANTES is expressed in a range of cells and tissues presenting with different endogenously produced variants and PTMs. The structural variety and population diversity that has been identified for RANTES necessitate developing advanced methodologies that can provide insight into the protein heterogeneity and its function and regulation in disease. In this work we present a simple, efficient and high-throughput mass spectrometric immunoassay (MSIA) method for analysis of RANTES proteoforms. RANTES MSIA can detect and analyze RANTES proteoforms and provide an insight into the endogenous protein modifications.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States.
| | - Nisha D Sherma
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Paul E Oran
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | | | - Randall W Nelson
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Dobrin Nedelkov
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
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