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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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2
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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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3
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Abstract
Hydrogels are important structural and operative components of microfluidic systems, finding diverse utility in biological sample preparation and interrogation. One inherent challenge for integrating hydrogels into microfluidic tools is thermodynamic molecular partitioning, which reduces the in-gel concentration of molecular solutes (e.g., biomolecular regents), as compared to the solute concentration in an applied solution. Consequently, biomolecular reagent access to in-gel scaffolded biological samples (e.g., encapsulated cells, microbial cultures, target analytes) is adversely impacted in hydrogels. Further, biomolecular reagents are typically introduced to the hydrogel via diffusion. This passive process requires long incubation periods compared to active biomolecular delivery techniques. Electrotransfer is an active technique used in Western blots and other gel-based immunoassays that overcomes limitations of size exclusion (increasing the total probe mass delivered into gel) and expedites probe delivery, even in millimeter-thick slab gels. While compatible with conventional slab gels, electrotransfer has not been adapted to thin gels (50-250 μm thick), which are of great interest as components of open microfluidic devices (vs enclosed microchannel-based devices). Mechanically delicate, thin gels are often mounted on rigid support substrates (glass, plastic) that are electrically insulating. Consequently, to adapt electrotransfer to thin-gel devices, we replace rigid insulating support substrates with novel, mechanically robust, yet electrically conductive nanoporous membranes. We describe grafting nanoporous membranes to thin-polyacrylamide-gel layers via silanization, characterize the electrical conductivity of silane-treated nanoporous membranes, and report the dependence of in-gel immunoprobe concentration on transfer duration for passive diffusion and active electrotransfer. Alternative microdevice component layers─including the mechanically robust, electrically conductive nanoporous membranes reported here─provide new functionality for integration into an increasing array of open microfluidic systems.
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Affiliation(s)
- Andoni P Mourdoukoutas
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, California 94720, United States
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
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4
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Hennig S, Shu Z, Gutzweiler L, Koltay P, von Stetten F, Zengerle R, Früh SM. Paper-based open microfluidic platform for protein electrophoresis and immunoprobing. Electrophoresis 2021; 43:621-631. [PMID: 34902175 DOI: 10.1002/elps.202100327] [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: 10/07/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 11/10/2022]
Abstract
Protein electrophoresis and immunoblotting are indispensable analytical tools for the characterization of proteins and posttranslational modifications in complex sample matrices. Owing to the lack of automation, commonly employed slab-gel systems suffer from high time demand, significant sample/antibody consumption, and limited reproducibility. To overcome these limitations, we developed a paper-based open microfluidic platform for electrophoretic protein separation and subsequent transfer to protein-binding membranes for immunoprobing. Electrophoresis microstructures were digitally printed into cellulose acetate membranes that provide mechanical stability while maintaining full accessibility of the microstructures for consecutive immunological analysis. As a proof-of-concept, we demonstrate separation of fluorescently labeled marker proteins in a wide molecular weight range (15-120 kDa) within only 15 min, reducing the time demand for the entire workflow (from sample preparation to immunoassay) to approximately one hour. Sample consumption was reduced 10- to 150-fold compared to slab-gel systems, owing to system miniaturization. Moreover, we successfully applied the paper-based approach to complex samples such as crude bacterial cell extracts. We envisage that this platform will find its use in protein analysis workflows for scarce and precious samples, providing a unique opportunity to extract profound immunological information from limited sample amounts in a fast fashion with minimal hands-on time.
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Affiliation(s)
| | - Zhe Shu
- Hahn-Schickard, Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | | | - Peter Koltay
- Hahn-Schickard, Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Felix von Stetten
- Hahn-Schickard, Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Roland Zengerle
- Hahn-Schickard, Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
| | - Susanna M Früh
- Hahn-Schickard, Freiburg, Germany.,Laboratory for MEMS Applications, IMTEK - Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany
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5
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Gopal A, Herr AE. Segmentation-based analysis of single-cell immunoblots. Electrophoresis 2021; 42:2070-2080. [PMID: 34357587 PMCID: PMC8526408 DOI: 10.1002/elps.202100144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/06/2021] [Accepted: 07/27/2021] [Indexed: 11/11/2022]
Abstract
From genomics to transcriptomics to proteomics, microfluidic tools underpin recent advances in single-cell biology. Detection of specific proteoforms-with single-cell resolution-presents challenges in detection specificity and sensitivity. Miniaturization of protein immunoblots to single-cell resolution mitigates these challenges. For example, in microfluidic western blotting, protein targets are separated by electrophoresis and subsequently detected using fluorescently labeled antibody probes. To quantify the expression level of each protein target, the fluorescent protein bands are fit to Gaussians; yet, this method is difficult to use with noisy, low-abundance, or low-SNR protein bands, and with significant band skew or dispersion. In this study, we investigate segmentation-based approaches to robustly quantify protein bands from single-cell protein immunoblots. As compared to a Gaussian fitting pipeline, the segmentation pipeline detects >1.5× more protein bands for downstream quantification as well as more of the low-abundance protein bands (i.e., with SNR ∼3). Utilizing deep learning-based segmentation approaches increases the recovery of low-SNR protein bands by an additional 50%. However, we find that segmentation-based approaches are less robust at quantifying poorly resolved protein bands (separation resolution, Rs < 0.6). With burgeoning needs for more single-cell protein analysis tools, we see microfluidic separations as benefitting substantially from segmentation-based analysis approaches.
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Affiliation(s)
- Anjali Gopal
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
| | - Amy E. Herr
- Department of Bioengineering, University of California, Berkeley, CA, USA
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, CA, USA
- Chan Zuckerberg BioHub, San Francisco, CA, USA
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6
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Moss AC, Herr AE. In-gel fluorescence detection by DNA polymerase elongation. APL Bioeng 2020; 4:046104. [PMID: 33263097 PMCID: PMC7680656 DOI: 10.1063/5.0021149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 10/07/2020] [Indexed: 11/14/2022] Open
Abstract
Fluorescence-based DNA readouts are increasingly important in biological research, owing to enhanced analytical sensitivity and multiplexing capability. In this study, we characterize an in-gel polymerase elongation process to understand the reaction kinetics and transport limitations, and we evaluate DNA sequence design to develop signal amplification strategies. Using fluorescently labeled nucleotides, we scrutinize polymerase elongation on single-stranded overhangs of DNA immobilized in polyacrylamide hydrogels. When polymerase elongation reactions were carried out with reactants diffused into the gels, we observed reaction completion after 2 h, indicating that the process was efficient but much slower than that predicted by models. Confocal microscopy revealed a nonuniform post-reaction fluorescence profile of the elongated DNA throughout the depth of the gel and that the time for complete fluorescence penetration was proportional to the immobilized DNA concentration. These observations suggest retarded diffusion of the polymerase, attributable to interactions between diffusing polymerase and immobilized DNA. This study will ultimately inform assay design by providing insight into the reaction completion time to ensure spatial uniformity of the fluorescence signal. In agreement with our hypothesis that incorporation of multiple labeled nucleotides per DNA strand results in an increased signal, incorporation of four labeled nucleotides resulted in a 2.3-fold increase in fluorescence intensity over one labeled nucleotide. Our results further suggest that the fluorescence signal increases with spacing between labeled nucleotides, validating the number of and spacing between labeled nucleotides as tunable parameters for signal amplification. In-gel polymerase-based fluorescence readout is promising for signal amplification when considering both transport limitations and DNA sequence design.
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Affiliation(s)
| | - Amy E. Herr
- Author to whom correspondence should be addressed:
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7
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Mourdoukoutas AP, Grist SM, Herr AE. Rapid electrotransfer probing for improved detection sensitivity in in-gel immunoassays. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4638-4648. [PMID: 33030469 PMCID: PMC7552878 DOI: 10.1039/d0ay01203c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Protein electrotransfer in conventional western blotting facilitates detection of size-separated proteins by diffusive immunoprobing, as analytes are transferred from a small-pore sizing gel to a blotting membrane for detection. This additional transfer step can, however, impair detection sensitivity through protein losses and confound protein localization. To overcome challenges associated with protein transfer, in-gel immunoassays immobilize target proteins to the hydrogel matrix for subsequent in-gel immunoprobing. Yet, detection sensitivity in diffusive immunoprobing of hydrogels is determined by the gel pore size relative to the probe size, and in-gel immunoprobing results in (i) reduced in-gel probe concentration compared to surrounding free-solution, and (ii) slow in-gel probe transfer compared to immunocomplex dissociation. Here, we demonstrate electrotransfer probing for effective and rapid immunoprobing of in-gel immunoassays. Critically, probe (rather than target protein) is electrotransferred from an inert, large-pore 'loading gel' to a small-pore protein sizing gel. Electric field is used as a tuneable parameter for electromigration velocity, providing electrotransfer probing with a fundamental advantage over diffusive probing. Using electrotransfer probing, we observe 6.5 ± 0.1× greater probe concentration loaded in-gel in ∼82× time reduction, and 2.7 ± 0.4× less probe concentration remaining in-gel after unloading in ∼180× time reduction (compared to diffusive probing). We then apply electrotransfer probing to detect OVA immobilized in-gel and achieve 4.1 ± 3.4× greater signal-to-noise ratio and 30× reduction in total immunoprobing duration compared to diffusive probing. We demonstrate electrotransfer probing as a substantially faster immunoprobing method for improved detection sensitivity of protein sizing in-gel immunoassays.
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Affiliation(s)
- Andoni P Mourdoukoutas
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California 94720, USA.
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8
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Jeeawoody S, Yamauchi KA, Su A, Herr AE. Laterally Aggregated Polyacrylamide Gels for Immunoprobed Isoelectric Focusing. Anal Chem 2020; 92:3180-3188. [PMID: 31985208 PMCID: PMC7861876 DOI: 10.1021/acs.analchem.9b04913] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Immunoprobed isoelectric focusing (IEF) resolves proteins based on differences in isoelectric point (pI) and then identifies protein targets through immunoprobing of IEF-separated proteins that have been immobilized onto a gel scaffold. During the IEF stage, the gel functions as an anti-convective medium and not as a molecular sieving matrix. During the immunoprobing stage, the gel acts as an immobilization scaffold for IEF-focused proteins via photoactive moieties. Here, we characterized the effect of gel pore size on IEF separation and in-gel immunoassay performance. We modulated polyacrylamide (PA) gel pore size via lateral chain aggregation initiated by PEG monomers. During IEF, the 2% PEG highly porous PA gel formulation offered higher resolution (minimum pI difference ∼0.07 ± 0.02) than unmodified 6%T, 3.3%C (benchmark) and 6%T, 8%C (negative control) PA gels. The highly porous gels supported a pH gradient with slope and linearity comparable to benchmark gels. The partition coefficient for antibodies into the highly porous gels (K = 0.35 ± 0.02) was greater than the benchmark (3×) and negative control (1.75×) gels. The highly porous gels also had lower immunoassay background signal than the benchmark (2×) and negative control (3×) gels. Taken together, lateral aggregation creates PA gels that are suitable for both IEF and subsequent in-gel immunoprobing by mitigating immunoprobe exclusion from the gels while facilitating removal of unbound immunoprobe.
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Affiliation(s)
- Shaheen Jeeawoody
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Kevin A Yamauchi
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Alison Su
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
| | - Amy E Herr
- Department of Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- The UC Berkeley/UCSF Graduate Program in Bioengineering , University of California Berkeley , Berkeley , California 94720 , United States
- Chan Zuckerberg Biohub , 499 Illinois Street , San Francisco , California 94158 , United States
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9
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Gumuscu B, Herr AE. Separation-encoded microparticles for single-cell western blotting. LAB ON A CHIP 2020; 20:64-73. [PMID: 31773114 PMCID: PMC7029799 DOI: 10.1039/c9lc00917e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Direct measurement of proteins from single cells has been realized at the microscale using microfluidic channels, capillaries, and semi-enclosed microwell arrays. Although powerful, these formats are constrained, with the enclosed geometries proving cumbersome for multistage assays, including electrophoresis followed by immunoprobing. We introduce a hybrid microfluidic format that toggles between a planar microwell array and a suspension of microparticles. The planar array is stippled in a thin sheet of polyacrylamide gel, for efficient single-cell isolation and protein electrophoresis of hundreds-to-thousands of cells. Upon mechanical release, array elements become a suspension of separation-encoded microparticles for more efficient immunoprobing due to enhanced mass transfer. Dehydrating microparticles offer improved analytical sensitivity owing to in-gel concentration of fluorescence signal for high-throughput single-cell targeted proteomics.
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Affiliation(s)
- Burcu Gumuscu
- Department of Bioengineering, University of California Berkeley, Berkeley, USA.
| | - Amy E Herr
- Department of Bioengineering, University of California Berkeley, Berkeley, USA.
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10
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Abstract
Thermodynamic partitioning dictates solute loading and release from a hydrogel. Design of drug delivery vehicles, cell and tissue matrices, and immunoassay scaffolds that utilize hydrogel materials is informed by an understanding of the thermodynamic partitioning properties of those hydrogels. We develop aberration-compensated laser scanning confocal microscopy (AC-LSCM), a technique that can be applied to all fluorescence microscopy-based equilibrium partition coefficient measurements where the fluorescence is uniformly distributed in the reference material (e.g., many solutes in thermodynamic equilibrium). In this paper, we use AC-LSCM to measure spatially resolved in situ equilibrium partition coefficients of various fluorescently labeled solutes in single-layer and multilayer open hydrogels. In considering a dynamic material, we scrutinize solute interactions with a UV photoactive polyacrylamide gel that incorporates a benzophenone methacrylamide backbone. We observed strong agreement with an adjusted version of Ogston's ideal size-exclusion model for spatially resolved in situ equilibrium partition coefficients across a wide range of polyacrylamide hydrogel densities (R2 = 0.98). Partition coefficients of solutes differing in hydrodynamic radius were consistent with size-based theory in the photoactive hydrogels, but exceed those in unmodified polyacrylamide gels. This observation suggests a deviation from the size-exclusion model and a shift in the thermodynamic equilibrium state of the solutes toward the gel phase. AC-LSCM also resolves differential partitioning behavior of the model solute in two-layer gels, providing insight into the transport phenomena governing the partitioning in multilaminate gel structures. Furthermore, AC-LSCM identifies and quantifies depth-dependent axial aberrations that could confound quantitation, highlighting the need for the "aberration compensated" aspect of AC-LSCM.
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Affiliation(s)
- Alison Su
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Benjamin E. Smith
- Department of Vision Sciences, University of California Berkeley, Berkeley, California 94720, United States
| | - Amy E. Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
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Gopal A, Herr AE. Multiplexed in-gel microfluidic immunoassays: characterizing protein target loss during reprobing of benzophenone-modified hydrogels. Sci Rep 2019; 9:15389. [PMID: 31659305 PMCID: PMC6817870 DOI: 10.1038/s41598-019-51849-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 09/27/2019] [Indexed: 12/28/2022] Open
Abstract
From whole tissues to single-cell lysate, heterogeneous immunoassays are widely utilized for analysis of protein targets in complex biospecimens. Recently, benzophenone-functionalized hydrogel scaffolds have been used to immobilize target protein for immunoassay detection with fluorescent antibody probes. In benzophenone-functionalized hydrogels, multiplex target detection occurs via serial rounds of chemical stripping (incubation with sodium-dodecyl-sulfate (SDS) and β-mercaptoethanol at 50-60 °C for ≥1 h), followed by reprobing (interrogation with additional antibody probes). Although benzophenone facilitates covalent immobilization of proteins to the hydrogel, we observe 50% immunoassay signal loss of immobilized protein targets during stripping rounds. Here, we identify and characterize signal loss mechanisms during stripping and reprobing. We posit that loss of immobilized target is responsible for ≥50% of immunoassay signal loss, and that target loss is attributable to disruption of protein immobilization by denaturing detergents (SDS) and incubation at elevated temperatures. Furthermore, our study suggests that protein losses under non-denaturing conditions are more sensitive to protein structure (i.e., hydrodynamic radius), than to molecular mass (size). We formulate design guidance for multiplexed in-gel immunoassays, including that low-abundance proteins be immunoprobed first, even when targets are covalently immobilized to the gel. We also recommend careful scrutiny of the order of proteins targets detected via multiple immunoprobing cycles, based on the protein immobilization buffer composition.
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Affiliation(s)
- Anjali Gopal
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94720, United States
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California, 94720, United States
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, Berkeley, California, 94720, United States.
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California, Berkeley, Berkeley, California, 94720, United States.
- Chan Zuckerberg BioHub, San Francisco, California, 94158, United States.
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12
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Murphy TW, Zhang Q, Naler LB, Ma S, Lu C. Recent advances in the use of microfluidic technologies for single cell analysis. Analyst 2017; 143:60-80. [PMID: 29170786 PMCID: PMC5839671 DOI: 10.1039/c7an01346a] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The inherent heterogeneity in cell populations has become of great interest and importance as analytical techniques have improved over the past decades. With the advent of personalized medicine, understanding the impact of this heterogeneity has become an important challenge for the research community. Many different microfluidic approaches with varying levels of throughput and resolution exist to study single cell activity. In this review, we take a broad view of the recent microfluidic developments in single cell analysis based on microwell, microchamber, and droplet platforms. We cover physical, chemical, and molecular biology approaches for cellular and molecular analysis including newly emerging genome-wide analysis.
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Affiliation(s)
- Travis W Murphy
- Department of Chemical Engineering, Virginia Tech, Blacksburg, VA 24061, USA.
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13
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Vlassakis J, Herr AE. Joule Heating-Induced Dispersion in Open Microfluidic Electrophoretic Cytometry. Anal Chem 2017; 89:12787-12796. [PMID: 29110464 DOI: 10.1021/acs.analchem.7b03096] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
While protein electrophoresis conducted in capillaries and microchannels offers high-resolution separations, such formats can be cumbersome to parallelize for single-cell analysis. One approach for realizing large numbers of concurrent separations is open microfluidics (i.e., no microchannels). In an open microfluidic device adapted for single-cell electrophoresis, we perform 100s to 1000s of simultaneous separations of endogenous proteins. The microscope slide-sized device contains cells isolated in microwells located in a ∼40 μm polyacrylamide gel. The gel supports protein electrophoresis after concurrent in situ chemical lysis of each isolated cell. During electrophoresis, Joule (or resistive) heating degrades separation performance. Joule heating effects are expected to be acute in open microfluidic devices, where a single, high-conductivity buffer expedites the transition from cell lysis to protein electrophoresis. Here, we test three key assertions. First, Joule heating substantially impacts analytical sensitivity due to diffusive losses of protein out of the open microfluidic electrophoretic (EP) cytometry device. Second, increased analyte diffusivity due to autothermal runaway Joule heating is a dominant mechanism that reduces separation resolution in EP cytometry. Finally, buffer exchange reduces diffusive losses and band broadening, even when handling single-cell lysate protein concentrations in an open device. We develop numerical simulations of Joule heating-enhanced diffusion during electrophoresis and observe ∼50% protein loss out of the gel, which is reduced using the buffer exchange. Informed by analytical model predictions of separation resolution (with Joule heating), we empirically demonstrate nearly fully resolved separations of proteins with molecular mass differences of just 4 kDa or 12% (GAPDH, 36 kDa; PS6, 32 kDa) in each of 129 single cells. The attained separation performance with buffer exchange is relevant to detection of currently unmeasurable protein isoforms responsible for cancer progression.
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Affiliation(s)
- Julea Vlassakis
- Department of Bioengineering and ‡The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley , Berkeley, California 94720, United States
| | - Amy E Herr
- Department of Bioengineering and ‡The UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley , Berkeley, California 94720, United States
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14
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Abstract
Measuring the catalytic activity of immobilized enzymes underpins development of biosensing, bioprocessing, and analytical chemistry tools. To expand the range of approaches available for measuring enzymatic activity, we report on a technique to probe activity of enzymes immobilized in porous materials in the absence of confounding mass transport artifacts. We measured reaction kinetics of calf intestinal alkaline phosphatase (CIAP) immobilized in benzophenone-modified polyacrylamide (BPMA-PAAm) gel films housed in an array of fluidically isolated chambers. To ensure kinetics measurements are not confounded by mass transport limitations, we employed Weisz's modulus (Φ), which compares observed enzyme-catalyzed reaction rates to characteristic substrate diffusion times. We characterized activity of CIAP immobilized in BPMA-PAAm gels in a reaction-limited regime (Φ ≪ 0.15 for all measurements), allowing us to isolate the effect of immobilization on enzymatic activity. Immobilization of CIAP in BPMA-PAAm gels produced a ∼2× loss in apparent enzyme-substrate affinity (Km) and ∼200× decrease in intrinsic catalytic activity (kcat) relative to in-solution measurements. As estimating Km and kcat requires multiple steps of data manipulation, we developed a computational approach (bootstrapping) to propagate uncertainty in calibration data through all data manipulation steps. Numerical simulation revealed that calibration error is only negligible when the normalized root-mean-squared error (NRMSE) in the calibration falls below 0.05%. Importantly, bootstrapping is independent of the mathematical model, and thus generalizable beyond enzyme kinetics studies. Furthermore, the measurement tool presented can be readily adapted to study other porous immobilization supports, facilitating rational design (immobilization method, geometry, enzyme loading) of immobilized-enzyme devices.
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Affiliation(s)
- Hector D. Neira
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
| | - Amy E. Herr
- UC Berkeley/UCSF Graduate Program in Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
- Department of Bioengineering, University of California Berkeley, Berkeley, California 94720, United States
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Kang CC, Yamauchi KA, Vlassakis J, Sinkala E, Duncombe TA, Herr AE. Single cell-resolution western blotting. Nat Protoc 2016; 11:1508-30. [PMID: 27466711 DOI: 10.1038/nprot.2016.089] [Citation(s) in RCA: 106] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
This protocol describes how to perform western blotting on individual cells to measure cell-to-cell variation in protein expression levels and protein state. Like conventional western blotting, single-cell western blotting (scWB) is particularly useful for protein targets that lack selective antibodies (e.g., isoforms) and in cases in which background signal from intact cells is confounding. scWB is performed on a microdevice that comprises an array of microwells molded in a thin layer of a polyacrylamide gel (PAG). The gel layer functions as both a molecular sieving matrix during PAGE and a blotting scaffold during immunoprobing. scWB involves five main stages: (i) gravity settling of cells into microwells; (ii) chemical lysis of cells in each microwell; (iii) PAGE of each single-cell lysate; (iv) exposure of the gel to UV light to blot (immobilize) proteins to the gel matrix; and (v) in-gel immunoprobing of immobilized proteins. Multiplexing can be achieved by probing with antibody cocktails and using antibody stripping/reprobing techniques, enabling detection of 10+ proteins in each cell. We also describe microdevice fabrication for both uniform and pore-gradient microgels. To extend in-gel immunoprobing to gels of small pore size, we describe an optional gel de-cross-linking protocol for more effective introduction of antibodies into the gel layer. Once the microdevice has been fabricated, the assay can be completed in 4-6 h by microfluidic novices and it generates high-selectivity, multiplexed data from single cells. The technique is relevant when direct measurement of proteins in single cells is needed, with applications spanning the fundamental biosciences to applied biomedicine.
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Affiliation(s)
- Chi-Chih Kang
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Kevin A Yamauchi
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Julea Vlassakis
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Elly Sinkala
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Todd A Duncombe
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Amy E Herr
- Department of Bioengineering, University of California, Berkeley, California, USA
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