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Alibekova Long M, Benman WKJ, Petrikas N, Bugaj LJ, Hughes AJ. Enhancing Single-Cell Western Blotting Sensitivity Using Diffusive Analyte Blotting and Antibody Conjugate Amplification. Anal Chem 2023; 95:17894-17902. [PMID: 37974303 DOI: 10.1021/acs.analchem.3c04130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
While there are many techniques to achieve highly sensitive, multiplex detection of RNA and DNA from single cells, detecting protein content often suffers from low limits of detection and throughput. Miniaturized, high-sensitivity Western blots on single cells (scWesterns) are attractive because they do not require advanced instrumentation. By physically separating analytes, scWesterns also uniquely mitigate limitations to target protein multiplexing posed by the affinity reagent performance. However, a fundamental limitation of scWesterns is their limited sensitivity for detecting low-abundance proteins, which arises from transport barriers posed by the separation gel against detection species. Here we address the sensitivity by decoupling the electrophoretic separation medium from the detection medium. We transfer scWestern separations to a nitrocellulose blotting medium with distinct mass transfer advantages over traditional in-gel probing, yielding a 5.9-fold improvement in the limit of detection. We next amplify probing of blotted proteins with enzyme-antibody conjugates, which are incompatible with traditional in-gel probing to achieve further improvement in the limit of detection to 1000 molecules, a 120-fold improvement. This enables us to detect 100% of cells in an EGFP-expressing population using fluorescently tagged and enzyme-conjugated antibodies compared to 84.5% of cells using in-gel detection. These results suggest the compatibility of nitrocellulose-immobilized scWesterns with a variety of affinity reagents─not previously accessible for in-gel use─for further signal amplification and detection of low-abundance targets.
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Affiliation(s)
- Mariia Alibekova Long
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - William K J Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
| | - Nathan Petrikas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukasz J Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Alex J Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, Pennsylvania, 19104, United States
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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Long MA, Benman W, Petrikas N, Bugaj LJ, Hughes AJ. Enhancing single-cell western blotting sensitivity using diffusive analyte blotting and antibody conjugate amplification. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544857. [PMID: 37398364 PMCID: PMC10312704 DOI: 10.1101/2023.06.13.544857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
While there are many techniques to achieve highly sensitive, multiplex detection of RNA and DNA from single cells, detecting protein contents often suffers from low limits of detection and throughput. Miniaturized, high-sensitivity western blots on single cells (scWesterns) are attractive since they do not require advanced instrumentation. By physically separating analytes, scWesterns also uniquely mitigate limitations to target protein multiplexing posed by affinity reagent performance. However, a fundamental limitation of scWesterns is their limited sensitivity for detecting low-abundance proteins, which arises from transport barriers posed by the separation gel against detection species. Here we address sensitivity by decoupling the electrophoretic separation medium from the detection medium. We transfer scWestern separations to a nitrocellulose blotting medium with distinct mass transfer advantages over traditional in-gel probing, yielding a 5.9-fold improvement in limit of detection. We next amplify probing of blotted proteins with enzyme-antibody conjugates which are incompatible with traditional in-gel probing to achieve further improvement in the limit of detection to 103 molecules, a 520-fold improvement. This enables us to detect 85% and 100% of cells in an EGFP-expressing population using fluorescently tagged and enzyme-conjugated antibodies respectively, compared to 47% of cells using in-gel detection. These results suggest compatibility of nitrocellulose-immobilized scWesterns with a variety of affinity reagents - not previously accessible for in-gel use - for further signal amplification and detection of low abundance targets.
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Affiliation(s)
- Mariia Alibekova Long
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - William Benman
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
| | - Nathan Petrikas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Currently at Tempus Labs Inc., Chicago, IL, USA
| | - Lukasz J. Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Alex J. Hughes
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Bioengineering Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, PA, USA
- Institute for Regenerative Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Cell and Developmental Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Center for Soft and Living Matter, University of Pennsylvania, Philadelphia, PA, 19104, USA
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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: 0] [Impact Index Per Article: 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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