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Kraemer S, Schneider DJ, Paterson C, Perry D, Westacott MJ, Hagar Y, Katilius E, Lynch S, Russell TM, Johnson T, Astling DP, DeLisle RK, Cleveland J, Gold L, Drolet DW, Janjic N. Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome. J Proteome Res 2024. [PMID: 39038188 DOI: 10.1021/acs.jproteome.4c00411] [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: 07/24/2024]
Abstract
Measuring responses in the proteome to various perturbations improves our understanding of biological systems. The value of information gained from such studies is directly proportional to the number of proteins measured. To overcome technical challenges associated with highly multiplexed measurements, we developed an affinity reagent-based method that uses aptamers with protein-like side chains along with an assay that takes advantage of their unique properties. As hybrid affinity reagents, modified aptamers are fully comparable to antibodies in terms of binding characteristics toward proteins, including epitope size, shape complementarity, affinity and specificity. Our assay combines these intrinsic binding properties with serial kinetic proofreading steps to allow highly effective partitioning of stable specific complexes from unstable nonspecific complexes. The use of these orthogonal methods to enhance specificity effectively overcomes the severe limitation to multiplexing inherent to the use of sandwich-based methods. Our assay currently measures half of the unique proteins encoded in the human genome with femtomolar sensitivity, broad dynamic range and exceptionally high reproducibility. Using machine learning to identify patterns of change, we have developed tests based on measurement of multiple proteins predictive of current health states and future disease risk to guide a holistic approach to precision medicine.
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Affiliation(s)
- Stephan Kraemer
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel J Schneider
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Clare Paterson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Darryl Perry
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Matthew J Westacott
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Yolanda Hagar
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Evaldas Katilius
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Sean Lynch
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Theresa M Russell
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Ted Johnson
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - David P Astling
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Robert Kirk DeLisle
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Jason Cleveland
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Larry Gold
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Daniel W Drolet
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
| | - Nebojsa Janjic
- SomaLogic, 2495 Wilderness Place, Boulder, Colorado 80301, United States of America
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2
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Sun BB, Suhre K, Gibson BW. Promises and Challenges of populational Proteomics in Health and Disease. Mol Cell Proteomics 2024; 23:100786. [PMID: 38761890 PMCID: PMC11193116 DOI: 10.1016/j.mcpro.2024.100786] [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: 02/06/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/20/2024] Open
Abstract
Advances in proteomic assay technologies have significantly increased coverage and throughput, enabling recent increases in the number of large-scale population-based proteomic studies of human plasma and serum. Improvements in multiplexed protein assays have facilitated the quantification of thousands of proteins over a large dynamic range, a key requirement for detecting the lowest-ranging, and potentially the most disease-relevant, blood-circulating proteins. In this perspective, we examine how populational proteomic datasets in conjunction with other concurrent omic measures can be leveraged to better understand the genomic and non-genomic correlates of the soluble proteome, constructing biomarker panels for disease prediction, among others. Mass spectrometry workflows are discussed as they are becoming increasingly competitive with affinity-based array platforms in terms of speed, cost, and proteome coverage due to advances in both instrumentation and workflows. Despite much success, there remain considerable challenges such as orthogonal validation and absolute quantification. We also highlight emergent challenges associated with study design, analytical considerations, and data integration as population-scale studies are run in batches and may involve longitudinal samples collated over many years. Lastly, we take a look at the future of what the nascent next-generation proteomic technologies might provide to the analysis of large sets of blood samples, as well as the difficulties in designing large-scale studies that will likely require participation from multiple and complex funding sources and where data sharing, study designs, and financing must be solved.
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Affiliation(s)
- Benjamin B Sun
- Human Genetics, Informatics and Predictive Sciences, Bristol-Myers Squibb, Cambridge, Massachusetts, USA.
| | - Karsten Suhre
- Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Bradford W Gibson
- Pharmaceutical Chemistry, University of California, San Francisco, California, USA
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3
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Pathak AK, Shiau JC, Freitas RC, Kyle DE. Blood meals from 'dead-end' vertebrate hosts enhance transmission potential of malaria-infected mosquitoes. One Health 2023; 17:100582. [PMID: 38024285 PMCID: PMC10665158 DOI: 10.1016/j.onehlt.2023.100582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 06/08/2023] [Accepted: 06/08/2023] [Indexed: 12/01/2023] Open
Abstract
Ingestion of an additional blood meal(s) by a hematophagic insect can accelerate development of several vector-borne parasites and pathogens. Most studies, however, offer blood from the same vertebrate host species as the original challenge (for e.g., human for primary and additional blood meals). Here, we show a second blood meal from bovine and canine hosts can also enhance sporozoite migration in Anopheles stephensi mosquitoes infected with the human- and rodent-restricted Plasmodium falciparum and P. berghei, respectively. The extrinsic incubation period (time to sporozoite appearance in salivary glands) showed more consistent reductions with blood from human and bovine donors than canine blood, although the latter's effect may be confounded by the toxicity, albeit non-specific, associated with the anticoagulant used to collect whole blood from donors. The complex patterns of enhancement highlight the limitations of a laboratory system but are nonetheless reminiscent of parasite host-specificity and mosquito adaptations, and the genetic predisposition of An. stephensi for bovine blood. We suggest that in natural settings, a blood meal from any vertebrate host could accentuate the risk of human infections by P. falciparum: targeting vectors that also feed on animals, via endectocides for instance, may reduce the number of malaria-infected mosquitoes and thus directly lower residual transmission. Since endectocides also benefit animal health, our results underscore the utility of the One Health framework, which postulates that human health and well-being is interconnected with that of animals. We posit this framework will be further validated if our observations also apply to other vector-borne diseases which together are responsible for some of the highest rates of morbidity and mortality in socio-economically disadvantaged populations.
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Affiliation(s)
- Ashutosh K. Pathak
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, United States of America
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA 30602, United States of America
- Center for the Ecology of Infectious Diseases (CEID), University of Georgia, Athens, GA 30602, United States of America
- The SporoCore, CTEGD, University of Georgia, Athens, GA 30602, United States of America
| | - Justine C. Shiau
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, United States of America
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA 30602, United States of America
- Center for the Ecology of Infectious Diseases (CEID), University of Georgia, Athens, GA 30602, United States of America
- The SporoCore, CTEGD, University of Georgia, Athens, GA 30602, United States of America
| | - Rafael C.S. Freitas
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA 30602, United States of America
- The SporoCore, CTEGD, University of Georgia, Athens, GA 30602, United States of America
| | - Dennis E. Kyle
- Department of Infectious Diseases, University of Georgia, Athens, GA 30602, United States of America
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Athens, GA 30602, United States of America
- The SporoCore, CTEGD, University of Georgia, Athens, GA 30602, United States of America
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, United States of America
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4
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Billinger K, Okai CA, Russ M, Koy C, Röwer C, Opuni KFM, Illges H, Pecks U, Glocker MO. Dried serum spots on pre-punched filter paper discs are ready-to-use storage and shipping devices for blood-borne antigens and antibodies. J Immunol Methods 2023; 519:113519. [PMID: 37419022 DOI: 10.1016/j.jim.2023.113519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/09/2023]
Abstract
Dried serum spots that are well prepared can be attractive alternatives to frozen serum samples for shelving specimens in a medical or research center's biobank and mailing freshly prepared serum to specialized laboratories. During the pre-analytical phase, complications can arise which are often challenging to identify or are entirely overlooked. These complications can lead to reproducibility issues, which can be avoided in serum protein analysis by implementing optimized storage and transfer procedures. With a method that ensures accurate loading of filter paper discs with donor or patient serum, a gap in dried serum spot preparation and subsequent serum analysis shall be filled. Pre-punched filter paper discs with a 3 mm diameter are loaded within seconds in a highly reproducible fashion (approximately 10% standard deviation) when fully submerged in 10 μl of serum, named the "Submerge and Dry" protocol. Such prepared dried serum spots can store several hundred micrograms of proteins and other serum components. Serum-borne antigens and antibodies are reproducibly released in 20 μl elution buffer in high yields (approximately 90%). Dried serum spot-stored and eluted antigens kept their epitopes and antibodies their antigen binding abilities as was assessed by SDS-PAGE, 2D gel electrophoresis-based proteomics, and Western blot analysis, suggesting pre-punched filter paper discs as handy solution for serological tests.
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Affiliation(s)
- Kira Billinger
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Charles A Okai
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Manuela Russ
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Cornelia Koy
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Claudia Röwer
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany
| | - Kwabena F M Opuni
- Department of Pharmaceutical Chemistry, School of Pharmacy, College of Health Science, University of Ghana, P. O. Box LG43, Legon, Ghana
| | - Harald Illges
- Department of Applied Natural Sciences, Immunology and Cell Biology, Institute of Functional Gene Analytics, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Str. 20, 53359 Rheinbach, Germany
| | - Ulrich Pecks
- Department of Obstetrics and Gynecology, Medical Faculty, University of Schleswig-Holstein, Campus Kiel, Arnold-Heller-Straße 3, 24105 Kiel, Germany
| | - Michael O Glocker
- Proteome Center Rostock, Medical Faculty and Natural Science Faculty, University of Rostock, Schillingallee 69, 18057 Rostock, Germany.
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5
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Safari F, Kehelpannala C, Safarchi A, Batarseh AM, Vafaee F. Biomarker Reproducibility Challenge: A Review of Non-Nucleotide Biomarker Discovery Protocols from Body Fluids in Breast Cancer Diagnosis. Cancers (Basel) 2023; 15:2780. [PMID: 37345117 DOI: 10.3390/cancers15102780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 05/02/2023] [Accepted: 05/10/2023] [Indexed: 06/23/2023] Open
Abstract
Breast cancer has now become the most commonly diagnosed cancer, accounting for one in eight cancer diagnoses worldwide. Non-invasive diagnostic biomarkers and associated tests are superlative candidates to complement or improve current approaches for screening, early diagnosis, or prognosis of breast cancer. Biomarkers detected from body fluids such as blood (serum/plasma), urine, saliva, nipple aspiration fluid, and tears can detect breast cancer at its early stages in a minimally invasive way. The advancements in high-throughput molecular profiling (omics) technologies have opened an unprecedented opportunity for unbiased biomarker detection. However, the irreproducibility of biomarkers and discrepancies of reported markers have remained a major roadblock to clinical implementation, demanding the investigation of contributing factors and the development of standardised biomarker discovery pipelines. A typical biomarker discovery workflow includes pre-analytical, analytical, and post-analytical phases, from sample collection to model development. Variations introduced during these steps impact the data quality and the reproducibility of the findings. Here, we present a comprehensive review of methodological variations in biomarker discovery studies in breast cancer, with a focus on non-nucleotide biomarkers (i.e., proteins, lipids, and metabolites), highlighting the pre-analytical to post-analytical variables, which may affect the accurate identification of biomarkers from body fluids.
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Affiliation(s)
- Fatemeh Safari
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
| | - Cheka Kehelpannala
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Azadeh Safarchi
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- Microbiomes for One Systems Health, Health and Biosecurity, CSIRO, Westmead, NSW 2145, Australia
| | - Amani M Batarseh
- BCAL Diagnostics Ltd., Suite 506, 50 Clarence St, Sydney, NSW 2000, Australia
- BCAL Dx, The University of Sydney, Sydney Knowledge Hub, Merewether Building, Sydney, NSW 2006, Australia
| | - Fatemeh Vafaee
- School of Biotechnology and Biomolecular Sciences, University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- UNSW Data Science Hub (uDASH), University of New South Wales (UNSW Sydney), Sydney, NSW 2052, Australia
- OmniOmics.ai Pty Ltd., Sydney, NSW 2035, Australia
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6
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Challenges and Opportunities in Clinical Diagnostic Routine of Envenomation Using Blood Plasma Proteomics. Toxins (Basel) 2023; 15:toxins15030180. [PMID: 36977071 PMCID: PMC10056359 DOI: 10.3390/toxins15030180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Specific and sensitive tools for the diagnosis and monitoring of accidents by venomous animals are urgently needed. Several diagnostic and monitoring assays have been developed; however, they have not yet reached the clinic. This has resulted in late diagnoses, which represents one of the main causes of progression from mild to severe disease. Human blood is a protein-rich biological fluid that is routinely collected in hospital settings for diagnostic purposes, which can translate research progress from the laboratory to the clinic. Although it is a limited view, blood plasma proteins provide information about the clinical picture of envenomation. Proteome disturbances in response to envenomation by venomous animals have been identified, allowing mass spectrometry (MS)-based plasma proteomics to emerge as a tool in a range of clinical diagnostics and disease management that can be applied to cases of venomous animal envenomation. Here, we provide a review of the state of the art on routine laboratory diagnoses of envenomation by snakes, scorpions, bees, and spiders, as well as a review of the diagnostic methods and the challenges encountered. We present the state of the art on clinical proteomics as the standardization of procedures to be performed within and between research laboratories, favoring a more excellent peptide coverage of candidate proteins for biomarkers. Therefore, the selection of a sample type and method of preparation should be very specific and based on the discovery of biomarkers in specific approaches. However, the sample collection protocol (e.g., collection tube type) and the processing procedure of the sample (e.g., clotting temperature, time allowed for clotting, and anticoagulant used) are equally important to eliminate any bias.
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7
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Swanson DA, McGregor BL. Life History Metrics for Culex tarsalis (Diptera: Culicidae) and Culicoides sonorensis (Diptera: Ceratopogonidae) Are Not Impacted by Artificial Feeding on Defibrinated Versus EDTA-treated Blood. JOURNAL OF MEDICAL ENTOMOLOGY 2023; 60:224-227. [PMID: 36321536 DOI: 10.1093/jme/tjac171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 06/16/2023]
Abstract
Artificial blood feeding is a common practice for the study and maintenance of blood-feeding arthropod colonies. Commercially purchased blood is often treated to prevent clot-formation using either mechanical or chemical means. For many hematophagous insects, the effect that different anticoagulation methods may have on life history metrics is unclear. In the current study, Culex tarsalis Coquillett and Culicoides sonorensis Wirth & Jones were fed blood treated with either mechanical (defibrination) or chemical (K2 EDTA) anticoagulation methods. Several blood feeding and life history metrics were evaluated between treatment groups including proportion blood feeding, fecundity, fertility, and mortality. No significant differences were found for any of the measured life history metrics for either species. For experiments measuring aspects of these blood feeding and life history traits, blood treated using either defibrination or K2 EDTA anticoagulants should not impact experimental outcomes.
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Affiliation(s)
- Dustin A Swanson
- Arthropod-Borne Animal Diseases Research Unit, United States Department of Agriculture, 1515 College Avenue, Manhattan, KS 66502, USA
| | - Bethany L McGregor
- Arthropod-Borne Animal Diseases Research Unit, United States Department of Agriculture, 1515 College Avenue, Manhattan, KS 66502, USA
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8
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Waszczuk MA, Kuan PF, Yang X, Miao J, Kotov R, Luft BJ. Discovery and replication of blood-based proteomic signature of PTSD in 9/11 responders. Transl Psychiatry 2023; 13:8. [PMID: 36631443 PMCID: PMC9834302 DOI: 10.1038/s41398-022-02302-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 11/28/2022] [Accepted: 12/22/2022] [Indexed: 01/13/2023] Open
Abstract
Proteomics provides an opportunity to develop biomarkers for the early detection and monitoring of post-traumatic stress disorder (PTSD). However, research to date has been limited by small sample sizes and a lack of replication. This study performed Olink Proseek Multiplex Platform profiling of 81 proteins involved in neurological processes in 936 responders to the 9/11 disaster (mean age at blood draw = 55.41 years (SD = 7.93), 94.1% white, all men). Bivariate correlations and elastic net regressions were used in a discovery subsample to identify concurrent associations between PTSD symptom severity and the profiled proteins, and to create a multiprotein composite score. In hold-out subsamples, nine bivariate associations between PTSD symptoms and differentially expressed proteins were replicated: SKR3, NCAN, BCAN, MSR1, PVR, TNFRSF21, DRAXIN, CLM6, and SCARB2 (|r| = 0.08-0.17, p < 0.05). There were three replicated bivariate associations between lifetime PTSD diagnosis and differentially expressed proteins: SKR3, SIGLEC, and CPM (OR = 1.38-1.50, p < 0.05). The multiprotein composite score retained 38 proteins, including 10/11 proteins that replicated in bivariate tests. The composite score was significantly associated with PTSD symptom severity (β = 0.27, p < 0.001) and PTSD diagnosis (OR = 1.60, 95% CI: 1.17-2.19, p = 0.003) in the hold-out subsample. Overall, these findings suggest that PTSD is characterized by altered expression of several proteins implicated in neurological processes. Replicated associations with TNFRSF21, CLM6, and PVR support the neuroinflammatory signature of PTSD. The multiprotein composite score substantially increased associations with PTSD symptom severity over individual proteins. If generalizable to other populations, the current findings may inform the development of PTSD biomarkers.
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Affiliation(s)
- Monika A Waszczuk
- Department of Psychology, Rosalind Franklin University of Medicine and Science, North Chicago, IL, USA
| | - Pei-Fen Kuan
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Xiaohua Yang
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Jiaju Miao
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - Roman Kotov
- Department of Psychiatry, Stony Brook University, Stony Brook, NY, USA
| | - Benjamin J Luft
- Department of Medicine, Stony Brook University, Stony Brook, NY, USA.
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9
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Yunga ST, Gower AJ, Melrose AR, Fitzgerald MK, Rajendran A, Lusardi TA, Armstrong RJ, Minnier J, Jordan KR, McCarty OJT, David LL, Wilmarth PA, Reddy AP, Aslan JE. Effects of ex vivo blood anticoagulation and preanalytical processing time on the proteome content of platelets. J Thromb Haemost 2022; 20:1437-1450. [PMID: 35253976 PMCID: PMC9887642 DOI: 10.1111/jth.15694] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/03/2022] [Indexed: 02/03/2023]
Abstract
BACKGROUND Ex vivo assays of platelet function critically inform mechanistic and clinical hematology studies, where effects of divergent blood processing methods on platelet composition are apparent, but unspecified. OBJECTIVE Here, we evaluate how different blood anticoagulation options and processing times affect platelet function and protein content ex vivo. METHODS Parallel blood samples were collected from healthy human donors into sodium citrate, acid citrate dextrose, EDTA or heparin, and processed over an extended time course for functional and biochemical experiments, including platelet proteome quantification with multiplexed tandem mass tag (TMT) labeling and triple quadrupole mass spectrometry (MS). RESULTS Each anticoagulant had time-dependent effects on platelet function in whole blood. For instance, heparin enhanced platelet agonist reactivity, platelet-monocyte aggregate formation and platelet extracellular vesicle release, while EDTA increased platelet α-granule secretion. Following platelet isolation, TMT-MS quantified 3357 proteins amongst all prepared platelet samples. Altogether, >400 proteins were differentially abundant in platelets isolated from blood processed at 24 h versus 1 h post-phlebotomy, including proteins pertinent to membrane trafficking and exocytosis. Anticoagulant-specific effects on platelet proteomes included increased complement system and decreased α-granule proteins in platelets from EDTA-anticoagulated blood. Platelets prepared from heparinized blood had higher levels of histone and neutrophil-associated proteins in a manner related to neutrophil extracellular trap (NET) formation and platelet:NET interactions in whole blood ex vivo. CONCLUSION Our results demonstrate that different anticoagulants routinely used for blood collection have varying effects on platelets ex vivo, where methodology-associated alterations in platelet proteome may influence mechanistic, translational and biomarker studies.
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Affiliation(s)
- Samuel Tassi Yunga
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Austin J. Gower
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Alexander R. Melrose
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Meghan K. Fitzgerald
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashmitha Rajendran
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Theresa A. Lusardi
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Randall J. Armstrong
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Jessica Minnier
- Cancer Early Detection Advanced Research Center (CEDAR), Knight Cancer Institute, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Kelley R. Jordan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Owen J. T. McCarty
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Larry L. David
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Phillip A. Wilmarth
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Ashok P. Reddy
- Proteomics Shared Resource; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
| | - Joseph E. Aslan
- Department of Biomedical Engineering, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Knight Cardiovascular Institute, Division of Cardiology, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
- Department of Chemical Physiology & Biochemistry, School of Medicine; Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239; USA
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10
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Juurikka K, Åström P, Pekkala T, Öhman H, Sorsa T, Tervahartiala T, Salo T, Lehenkari P, Nyberg P. Insights into Preservation of Blood Biomarkers in Biobank Samples. Biopreserv Biobank 2022; 20:297-301. [PMID: 35020442 DOI: 10.1089/bio.2021.0096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Krista Juurikka
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Pirjo Åström
- The Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Tiina Pekkala
- Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
| | - Hanna Öhman
- Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland.,Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Timo Sorsa
- Department of Oral and Maxillofacial Diseases, Head and Neck Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Division of Periodontology, Department of Dental Medicine, Karolinska Institute, Stockholm, Sweden
| | - Taina Tervahartiala
- Department of Oral and Maxillofacial Diseases, Head and Neck Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Tuula Salo
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland.,Department of Oral and Maxillofacial Diseases, Head and Neck Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Translational Immunology Research Program (TRIMM), University of Helsinki, Helsinki, Finland
| | - Petri Lehenkari
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Pia Nyberg
- Cancer and Translational Medicine Research Unit, University of Oulu, Oulu, Finland.,Medical Research Center, Oulu University Hospital and University of Oulu, Oulu, Finland.,Biobank Borealis of Northern Finland, Oulu University Hospital, Oulu, Finland
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11
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Abstract
This protocol offers step-by-step instructions for preparation of raw blood plasma for liquid chromatography - tandem mass spectrometry (LC-MS/MS) analysis in clinical proteomics studies. The technique is simple, robust, and reproducible, and the entire transformation from plasma proteins to desalted tryptic peptides takes only 3-4 h. The protocol ensures efficient denaturation of native proteases that, in combination with the speediness of the procedure, prevents non-specific and irreproducible cleavage of digested peptides. The protocol can be adopted for large-scale studies and automation. For complete details on the use and execution of this protocol, please refer to Overmyer et al. (2020).
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Affiliation(s)
- Evgenia Shishkova
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
| | - Joshua J. Coon
- National Center for Quantitative Biology of Complex Systems, Madison, WI 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin - Madison, Madison, WI 53706, USA
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12
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Thompson AG, Oeckl P, Feneberg E, Bowser R, Otto M, Fischer R, Kessler B, Turner MR. Advancing mechanistic understanding and biomarker development in amyotrophic lateral sclerosis. Expert Rev Proteomics 2021; 18:977-994. [PMID: 34758687 DOI: 10.1080/14789450.2021.2004890] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Proteomic analysis has contributed significantly to the study of the neurodegenerative disease amyotrophic lateral sclerosis (ALS). It has helped to define the pathological change common to nearly all cases, namely intracellular aggregates of phosphorylated TDP-43, shifting the focus of pathogenesis in ALS toward RNA biology. Proteomics has also uniquely underpinned the delineation of disease mechanisms in model systems and has been central to recent advances in human ALS biomarker development. AREAS COVERED The contribution of proteomics to understanding the cellular pathological changes, disease mechanisms, and biomarker development in ALS are covered. EXPERT OPINION Proteomics has delivered unique insights into the pathogenesis of ALS and advanced the goal of objective measurements of disease activity to improve therapeutic trials. Further developments in sensitivity and quantification are expected, with application to the presymptomatic phase of human disease offering the hope of prevention strategies.
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Affiliation(s)
| | - Patrick Oeckl
- Department of Neurology, University of Ulm, Ulm, Germany.,German Center for Neurodegenerative Diseases (Dzne e.V.), Ulm, Germany
| | - Emily Feneberg
- Department of Neurology, Klinikum Rechts der Isar, Technical University Munich, Munich, Germany
| | - Robert Bowser
- Departments of Neurology and Translational Neuroscience, Barrow Neurological Institute, Phoenix, Arizona, USA
| | - Markus Otto
- Department of Neurology, University of Ulm, Ulm, Germany.,Department of Neurology, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Martin R Turner
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
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