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De Figueiredo I, Bartenlian B, Van der Rest G, Pallandre A, Halgand F. Proteomics Methodologies: The Search of Protein Biomarkers Using Microfluidic Systems Coupled to Mass Spectrometry. Proteomes 2023; 11:proteomes11020019. [PMID: 37218924 DOI: 10.3390/proteomes11020019] [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: 03/23/2023] [Revised: 04/29/2023] [Accepted: 05/07/2023] [Indexed: 05/24/2023] Open
Abstract
Protein biomarkers have been the subject of intensive studies as a target for disease diagnostics and monitoring. Indeed, biomarkers have been extensively used for personalized medicine. In biological samples, these biomarkers are most often present in low concentrations masked by a biologically complex proteome (e.g., blood) making their detection difficult. This complexity is further increased by the needs to detect proteoforms and proteome complexity such as the dynamic range of compound concentrations. The development of techniques that simultaneously pre-concentrate and identify low-abundance biomarkers in these proteomes constitutes an avant-garde approach to the early detection of pathologies. Chromatographic-based methods are widely used for protein separation, but these methods are not adapted for biomarker discovery, as they require complex sample handling due to the low biomarker concentration. Therefore, microfluidics devices have emerged as a technology to overcome these shortcomings. In terms of detection, mass spectrometry (MS) is the standard analytical tool given its high sensitivity and specificity. However, for MS, the biomarker must be introduced as pure as possible in order to avoid chemical noise and improve sensitivity. As a result, microfluidics coupled with MS has become increasingly popular in the field of biomarker discovery. This review will show the different approaches to protein enrichment using miniaturized devices and the importance of their coupling with MS.
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Affiliation(s)
- Isabel De Figueiredo
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Bernard Bartenlian
- Centre des Nanosciences et Nanotechnologies, Université Paris Saclay, 10 Boulevard Thomas Gobert, F91120 Palaiseau, France
| | - Guillaume Van der Rest
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Antoine Pallandre
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
| | - Frédéric Halgand
- Institut de Chimie Physique, Université Paris Saclay, Avenue Jean Perrin, F91400 Orsay, France
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Desire CT, Arrua RD, Strudwick XL, Kopecki Z, Cowin AJ, Hilder EF. The development of microfluidic-based western blotting: Technical advances and future perspectives. J Chromatogr A 2023; 1691:463813. [PMID: 36709548 DOI: 10.1016/j.chroma.2023.463813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/11/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Over the past two decades significant technical advancement in the field of western blotting has been made possible through the utilization of microfluidic technologies. In this review we provide a critical overview of these advancements, highlighting the advantages and disadvantages of each approach. Particular attention is paid to the development of now commercially available systems, including those for single cell analysis. This review also discusses more recent developments, including algorithms for automation and/or improved quantitation, the utilization of different materials/chemistries, use of projection electrophoresis, and the development of triBlots. Finally, the review includes commentary on future advances in the field based on current developments, and the potential of these systems for use as point-of-care devices in healthcare.
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Affiliation(s)
- Christopher T Desire
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - R Dario Arrua
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Xanthe L Strudwick
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Zlatko Kopecki
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Allison J Cowin
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia
| | - Emily F Hilder
- Future Industries Institute, University of South Australia, GPO Box 2471, Adelaide, SA 5001, Australia.
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Xie H, Ding X. The Intriguing Landscape of Single-Cell Protein Analysis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105932. [PMID: 35199955 PMCID: PMC9036017 DOI: 10.1002/advs.202105932] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Indexed: 05/15/2023]
Abstract
Profiling protein expression at single-cell resolution is essential for fundamental biological research (such as cell differentiation and tumor microenvironmental examination) and clinical precision medicine where only a limited number of primary cells are permitted. With the recent advances in engineering, chemistry, and biology, single-cell protein analysis methods are developed rapidly, which enable high-throughput and multiplexed protein measurements in thousands of individual cells. In combination with single cell RNA sequencing and mass spectrometry, single-cell multi-omics analysis can simultaneously measure multiple modalities including mRNAs, proteins, and metabolites in single cells, and obtain a more comprehensive exploration of cellular signaling processes, such as DNA modifications, chromatin accessibility, protein abundance, and gene perturbation. Here, the recent progress and applications of single-cell protein analysis technologies in the last decade are summarized. Current limitations, challenges, and possible future directions in this field are also discussed.
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Affiliation(s)
- Haiyang Xie
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
| | - Xianting Ding
- State Key Laboratory of Oncogenes and Related GenesInstitute for Personalized MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030China
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Kim JJ, Chan PPY, Vlassakis J, Geldert A, Herr AE. Microparticle Delivery of Protein Markers for Single-Cell Western Blotting from Microwells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1802865. [PMID: 30334351 PMCID: PMC6272123 DOI: 10.1002/smll.201802865] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Revised: 09/12/2018] [Indexed: 05/04/2023]
Abstract
Immunoblotting confers protein identification specificity beyond that of immunoassays by prepending protein electrophoresis (sizing) to immunoprobing. To accurately size protein targets, sample analysis includes concurrent analysis of protein markers with known molecular masses. To incorporate protein markers in single-cell western blotting, microwells are used to isolate individual cells and protein marker-coated microparticles. A magnetic field directs protein-coated microparticles to >75% of microwells, so as to 1) deliver a quantum of protein marker to each cell-laden microwell and 2) synchronize protein marker solubilization with cell lysis. Nickel-coated microparticles are designed, fabricated, and characterized, each conjugated with a mixture of histidine-tagged proteins (42.3-100 kDa). Imidazole in the cell lysis buffer solubilizes protein markers during a 30 s cell lysis step, with an observed protein marker release half-life of 4.46 s. Across hundreds of individual microwells and different microdevices, robust log-linear regression fits (R2 > 0.97) of protein molecular mass and electrophoretic mobility are observed. The protein marker and microparticle system is applied to determine the molecular masses of five endogenous proteins in breast cancer cells (GAPDH, β-TUB, CK8, STAT3, ER-α), with <20% mass error. Microparticle-delivered protein standards underpin robust, reproducible electrophoretic cytometry that complements single-cell genomics and transcriptomics.
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Affiliation(s)
- John J. Kim
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA; UCB-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Peggy P. Y. Chan
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA; Faculty of Science Engineering & Technology, Swinburne University of Technology, Melbourne, VIC 3122, Australia
| | - Julea Vlassakis
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA; UCB-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alisha Geldert
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA; UCB-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA
| | - Amy E. Herr
- Department of Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA, ; UCB-UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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Sanders BJ, Kim DC, Dunn RC. Recent Advances in Microscale Western Blotting. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2016; 8:7002-7013. [PMID: 28392839 PMCID: PMC5383213 DOI: 10.1039/c6ay01947a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Western blotting is a ubiquitous tool used extensively in the clinical and research settings to identify proteins and characterize their levels. It has rapidly become a mainstay in research laboratories due to its specificity, low cost, and ease of use. The specificity arises from the orthogonal processes used to identify proteins. Samples are first separated based on size and then probed with antibodies specific for the protein of interest. This confirmatory approach helps avoid pitfalls associated with antibody cross-reactivity and specificity issues. While the technique has evolved since its inception, the last decade has witnessed a paradigm shift in Western blotting technology. The introduction of capillary and microfluidic platforms has significantly decreased time and sample requirements while enabling high-throughput capabilities. These advances have enabled Western analysis down to the single cell level in highly parallel formats, opening vast new opportunities for studying cellular heterogeneity. Recent innovations in microscale Western blotting are surveyed, and the potential for enhancing detection using advances in label-free biosensing is briefly discussed.
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Affiliation(s)
- Brittany J Sanders
- Ralph Adams Institute of Bioanalytical Chemistry, Department of Chemistry, University of Kansas
| | - Daniel C Kim
- Ralph Adams Institute of Bioanalytical Chemistry, Department of Chemistry, University of Kansas
| | - Robert C Dunn
- Ralph Adams Institute of Bioanalytical Chemistry, Department of Chemistry, University of Kansas
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Pan Y, Karns K, Herr AE. Microfluidic electrophoretic mobility shift assays for quantitative biochemical analysis. Electrophoresis 2014; 35:2078-90. [PMID: 24591076 DOI: 10.1002/elps.201300500] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2013] [Revised: 01/31/2014] [Accepted: 02/09/2014] [Indexed: 02/02/2023]
Abstract
Electrophoretic mobility shift assays (EMSAs) play an important role in analytical chemistry, quantitative bioscience, and point-of-care diagnostics. Emerging microfluidic lab-on-a-chip technologies bring high throughput and multiplexed analysis to affinity-based electrophoretic separations, greatly advancing the performance of traditional EMSAs. This review elaborates on the relevant theoretical basis for EMSAs, surveys microfluidic-based EMSA applications in molecular conformation analyses, immunoassays, affinity assays and genomics, and outlines challenges and potential future improvements needed from this powerful assay.
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Affiliation(s)
- Yuchen Pan
- Graduate Program in Bioengineering, University of California San Francisco and University of California Berkeley, CA, USA
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Wang H, Shi Y, Yan J, Dong J, Li S, Xiao H, Xie H, Fan LY, Cao CX. Retardation Signal for Fluorescent Determination of Total Protein Content via Rapid and Sensitive Chip Moving Reaction Boundary Electrophoretic Titration. Anal Chem 2014; 86:2888-94. [DOI: 10.1021/ac403963f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Houyu Wang
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yongting Shi
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jian Yan
- Institute of Refrigeration
and Cryogenics, School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jingyu Dong
- School
of Chemistry and Molecule Engineering, East China University of Science and Technology, Shanghai 200234, China
| | - Si Li
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School
of Chemistry and Chemical Engieering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Haiyang Xie
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School
of Chemistry and Chemical Engieering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liu-Yin Fan
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School
of Chemistry and Chemical Engieering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Cheng-Xi Cao
- Laboratory of
Bioseparation and Analytical Biochemistry, State Key Laboratory of
Microbial Metabolism, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
- School
of Chemistry and Chemical Engieering, Shanghai Jiao Tong University, Shanghai 200240, China
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Chang HN, Leroueil PR, Selwa K, Gasper CJ, Tsuchida RE, Wang JJ, McHugh WM, Cornell TT, Baker JR, Goonewardena SN. Profiling inflammatory responses with microfluidic immunoblotting. PLoS One 2013; 8:e81889. [PMID: 24312374 PMCID: PMC3842271 DOI: 10.1371/journal.pone.0081889] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 10/17/2013] [Indexed: 11/18/2022] Open
Abstract
Rapid profiling of signaling pathways has been a long sought after goal in biological sciences and clinical medicine. To understand these signaling pathways, their protein components must be profiled. The protein components of signaling pathways are typically profiled with protein immunoblotting. Protein immunoblotting is a powerful technique but has several limitations including the large sample requirements, high amounts of antibody, and limitations in assay throughput. To overcome some of these limitations, we have designed a microfluidic protein immunoblotting device to profile multiple signaling pathways simultaneously. We show the utility of this approach by profiling inflammatory signaling pathways (NFκB, JAK-STAT, and MAPK) in cell models and human samples. The microfluidic immunoblotting device can profile proteins and protein modifications with 5380-fold less antibody compared to traditional protein immunoblotting. Additionally, this microfluidic device interfaces with commonly available immunoblotting equipment, has the ability to multiplex, and is compatible with several protein detection methodologies. We anticipate that this microfluidic device will complement existing techniques and is well suited for life science applications.
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Affiliation(s)
- Huai-Ning Chang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Pascale R. Leroueil
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Katherine Selwa
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - C. J. Gasper
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Ryan E. Tsuchida
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jason J. Wang
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Walker M. McHugh
- Division of Pediatric Critical Care Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Timothy T. Cornell
- Division of Pediatric Critical Care Medicine, Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, United States of America
| | - James R. Baker
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Sascha N. Goonewardena
- Michigan Nanotechnology Institute for Medicine and Biological Sciences, University of Michigan, Ann Arbor, Michigan, United States of America
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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Kim D, Herr AE. Protein immobilization techniques for microfluidic assays. BIOMICROFLUIDICS 2013; 7:41501. [PMID: 24003344 PMCID: PMC3747845 DOI: 10.1063/1.4816934] [Citation(s) in RCA: 218] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
Microfluidic systems have shown unequivocal performance improvements over conventional bench-top assays across a range of performance metrics. For example, specific advances have been made in reagent consumption, throughput, integration of multiple assay steps, assay automation, and multiplexing capability. For heterogeneous systems, controlled immobilization of reactants is essential for reliable, sensitive detection of analytes. In most cases, protein immobilization densities are maximized, while native activity and conformation are maintained. Immobilization methods and chemistries vary significantly depending on immobilization surface, protein properties, and specific assay goals. In this review, we present trade-offs considerations for common immobilization surface materials. We overview immobilization methods and chemistries, and discuss studies exemplar of key approaches-here with a specific emphasis on immunoassays and enzymatic reactors. Recent "smart immobilization" methods including the use of light, electrochemical, thermal, and chemical stimuli to attach and detach proteins on demand with precise spatial control are highlighted. Spatially encoded protein immobilization using DNA hybridization for multiplexed assays and reversible protein immobilization surfaces for repeatable assay are introduced as immobilization methods. We also describe multifunctional surface coatings that can perform tasks that were, until recently, relegated to multiple functional coatings. We consider the microfluidics literature from 1997 to present and close with a perspective on future approaches to protein immobilization.
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Affiliation(s)
- Dohyun Kim
- Department of Mechanical Engineering, Myongji University, 116 Myongji-ro, Cheoin-gu, Yongin-si, Gyeonggi-do 449-728, South Korea
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