1
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Duez Q, van de Wiel J, van Sluijs B, Ghosh S, Baltussen MG, Derks MTGM, Roithová J, Huck WTS. Quantitative Online Monitoring of an Immobilized Enzymatic Network by Ion Mobility-Mass Spectrometry. J Am Chem Soc 2024; 146:20778-20787. [PMID: 39013149 PMCID: PMC11295183 DOI: 10.1021/jacs.4c04218] [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] [Received: 03/26/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024]
Abstract
The forward design of in vitro enzymatic reaction networks (ERNs) requires a detailed analysis of network kinetics and potentially hidden interactions between the substrates and enzymes. Although flow chemistry allows for a systematic exploration of how the networks adapt to continuously changing conditions, the analysis of the reaction products is often a bottleneck. Here, we report on the interface between a continuous stirred-tank reactor, in which an immobilized enzymatic network made of 12 enzymes is compartmentalized, and an ion mobility-mass spectrometer. Feeding uniformly 13C-labeled inputs to the enzymatic network generates all isotopically labeled reaction intermediates and products, which are individually detected by ion mobility-mass spectrometry (IMS-MS) based on their mass-to-charge ratios and inverse ion mobilities. The metabolic flux can be continuously and quantitatively monitored by diluting the ERN output with nonlabeled standards of known concentrations. The real-time quantitative data obtained by IMS-MS are then harnessed to train a model of network kinetics, which proves sufficiently predictive to control the ERN output after a single optimally designed experiment. The high resolution of the time-course data provided by this approach is an important stepping stone to design and control sizable and intricate ERNs.
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Affiliation(s)
| | | | - Bob van Sluijs
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Souvik Ghosh
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Mathieu G. Baltussen
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Max T. G. M. Derks
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Jana Roithová
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
| | - Wilhelm T. S. Huck
- Institute for Molecules and Materials, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, The Netherlands
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2
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Leal-Alves C, Deng Z, Kermeci N, Shih SCC. Integrating microfluidics and synthetic biology: advancements and diverse applications across organisms. LAB ON A CHIP 2024; 24:2834-2860. [PMID: 38712893 DOI: 10.1039/d3lc01090b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Synthetic biology is the design and modification of biological systems for specific functions, integrating several disciplines like engineering, genetics, and computer science. The field of synthetic biology is to understand biological processes within host organisms through the manipulation and regulation of their genetic pathways and the addition of biocontrol circuits to enhance their production capabilities. This pursuit serves to address global challenges spanning diverse domains that are difficult to tackle through conventional routes of production. Despite its impact, achieving precise, dynamic, and high-throughput manipulation of biological processes is still challenging. Microfluidics offers a solution to those challenges, enabling controlled fluid handling at the microscale, offering lower reagent consumption, faster analysis of biochemical reactions, automation, and high throughput screening. In this review, we diverge from conventional focus on automating the synthetic biology design-build-test-learn cycle, and instead, focus on microfluidic platforms and their role in advancing synthetic biology through its integration with host organisms - bacterial cells, yeast, fungi, animal cells - and cell-free systems. The review illustrates how microfluidic devices have been instrumental in understanding biological systems by showcasing microfluidics as an essential tool to create synthetic genetic circuits, pathways, and organisms within controlled environments. In conclusion, we show how microfluidics expedite synthetic biology applications across diverse domains including but not limited to personalized medicine, bioenergy, and agriculture.
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Affiliation(s)
- Chiara Leal-Alves
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Zhiyang Deng
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
| | - Natalia Kermeci
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
| | - Steve C C Shih
- Centre for Applied Synthetic Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada.
- Department of Electrical and Computer Engineering, Concordia University, 1515 Ste-Catherine St. W, Montréal, QC, H3G1M8 Canada
- Department of Biology, Concordia University, 7141 Sherbrooke St. W, Montréal, QC, H4B1R6 Canada
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3
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Guo Z, Zhao Y, Jin Z, Chang Y, Wang X, Guo G, Zhao Y. Monolithic 3D nanoelectrospray emitters based on a continuous fluid-assisted etching strategy for glass droplet microfluidic chip-mass spectrometry. Chem Sci 2024; 15:7781-7788. [PMID: 38784731 PMCID: PMC11110156 DOI: 10.1039/d4sc01700e] [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: 03/12/2024] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Glass microfluidic chips are suitable for coupling with mass spectrometry (MS) due to their flexible design, optical transparency and resistance to organic reagents. However, due to the high hardness and brittleness of glass, there is a lack of simple and feasible technology to manufacture a monolithic nanospray ionization (nESI) emitter on a glass microchip, which hinders its coupling with mass spectrometry. Here, a continuous fluid-assisted etching strategy is proposed to fabricate monolithic three-dimensional (3D) nESI emitters integrated into glass microchips. A continuous fluid of methanol is adopted to protect the inner wall of the channels and the bonding interface of the glass microfluidic chip from being wet-etched, forming sharp 3D nESI emitters. The fabricated 3D nESI emitter can form a stable electrospray plume, resulting in consistent nESI detection of acetylcholine with an RSD of 4.5% within 10 min. The fabricated 3D emitter is integrated on a glass microfluidic chip designed with a T-junction droplet generator, which can realize efficient analysis of acetylcholine in picoliter-volume droplets by nESI-MS. Stability testing of over 20 000 droplets detected by the established system resulted in an RSD of 9.1% over approximately 180 min. The detection of ten neurochemicals in rat cerebrospinal fluid droplets is achieved. The established glass droplet microfluidic chip-MS system exhibits potential for broad applications such as in vivo neurochemical monitoring and single-cell analysis in the future.
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Affiliation(s)
- Ziyang Guo
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Yingqi Zhao
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Zhao Jin
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Yaran Chang
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Xiayan Wang
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
| | - Guangsheng Guo
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
- Minzu University of China Beijing 100081 China
| | - Yaoyao Zhao
- Department of Chemistry, Beijing University of Technology Beijing 100124 China
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4
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Sun M, Zhang J, Xuanyuan T, Liu X, Liu W. Facile and Rapid Microcontact Printing of Additive-Free Polydimethylsiloxane for Biological Patterning Diversity. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 38597685 DOI: 10.1021/acsami.4c00460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The development and application of micropatterning technology play a promising role in the manipulation of biological substances and the exploration of life sciences at the microscale. However, the universally adaptable micropatterning method with user-friendly properties for acceptance in routine laboratories remains scarce. Herein, a green, facile, and rapid microcontact printing method is reported for upgrading popularization and diversification of biological patterning. The three-step printing can achieve high simplicity and fidelity of additive-free polydimethylsiloxane (PDMS) micropatterning and chip fabrication within 8 min as well as keep their high stability and diversity. A detailed experimental report is provided to support the advanced microcontact printing method. Furthermore, the applications of easy-to-operate PDMS-patterned chips are extensively validated to complete microdroplet array assembly with spatial control, cell pattern formation with high efficiency and geometry customization, and microtissue assembly and biomimetic tumor construction on a large scale. This straightforward method promotes diverse micropatternings with minimal time, effort, and expertise and maximal biocompatibility, which might broaden its applications in interdisciplinary scientific communities. This work also offers an insight into the establishment of popularized and market-oriented microtools for biomedical purposes such as biosensing, organs on a chip, cancer research, and bioscreening.
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Affiliation(s)
- Meilin Sun
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Jinwei Zhang
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Tingting Xuanyuan
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Xufang Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
| | - Wenming Liu
- Departments of Biomedical Engineering and Pathology, School of Basic Medical Science, Central South University, Changsha, Hunan 410013, China
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5
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Zohouri D, Lienard-Mayor T, Obeid S, Taverna M, Mai TD. A review on hyphenation of droplet microfluidics to separation techniques: From instrumental conception to analytical applications for limited sample volumes. Anal Chim Acta 2024; 1291:342090. [PMID: 38280779 DOI: 10.1016/j.aca.2023.342090] [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: 06/19/2023] [Revised: 11/17/2023] [Accepted: 11/28/2023] [Indexed: 01/29/2024]
Abstract
In this study, we review various strategies to couple sample processing in microfluidic droplets with different separation techniques, including liquid chromatography, mass spectrometry, and capillary electrophoresis. Separation techniques interfaced with droplet microfluidics represent an emerging trend in analytical chemistry, in which micro to femtoliter droplets serve as microreactors, a bridge between analytical modules, as well as carriers of target analytes between sample treatment and separation/detection steps. This allows to overcome the hurdles encountered in separation science, notably the low degree of module integration, working volume incompatibility, and cross contamination between different operational stages. For this droplet-separation interfacing purpose, this review covers different instrumental designs from all works on this topic up to May 2023, together with our viewpoints on respective advantages and considerations. Demonstration and performance of droplet-interfaced separation strategies for limited sample volumes are also discussed.
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Affiliation(s)
- Delaram Zohouri
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Théo Lienard-Mayor
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Sameh Obeid
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Myriam Taverna
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France
| | - Thanh Duc Mai
- Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 91400, Orsay, France.
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6
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Pourmasoumi F, Hengoju S, Beck K, Stephan P, Klopfleisch L, Hoernke M, Rosenbaum MA, Kries H. Analysing Megasynthetase Mutants at High Throughput Using Droplet Microfluidics. Chembiochem 2023; 24:e202300680. [PMID: 37804133 DOI: 10.1002/cbic.202300680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 10/05/2023] [Indexed: 10/08/2023]
Abstract
Nonribosomal peptide synthetases (NRPSs) are giant enzymatic assembly lines that deliver many pharmaceutically valuable natural products, including antibiotics. As the search for new antibiotics motivates attempts to redesign nonribosomal metabolic pathways, more robust and rapid sorting and screening platforms are needed. Here, we establish a microfluidic platform that reliably detects production of the model nonribosomal peptide gramicidin S. The detection is based on calcein-filled sensor liposomes yielding increased fluorescence upon permeabilization. From a library of NRPS mutants, the sorting platform enriches the gramicidin S producer 14.5-fold, decreases internal stop codons 250-fold, and generates enrichment factors correlating with enzyme activity. Screening for NRPS activity with a reliable non-binary sensor will enable more sophisticated structure-activity studies and new engineering applications in the future.
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Affiliation(s)
- Farzaneh Pourmasoumi
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Sundar Hengoju
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Katharina Beck
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Lukas Klopfleisch
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Hoernke
- Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität, Hermann-Herder-Str. 9, 79104, Freiburg i. Br., Germany
- Faculty of Chemistry, Martin-Luther-Universität, Von-Danckelmann-Platz 4, 06108, Halle (S.), Germany
| | - Miriam A Rosenbaum
- Bio Pilot Plant, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI), Beutenbergstr. 11a, 07745, Jena, Germany
- Department of Chemistry, University of Bayreuth, Universitätsstrasse 30, 95440, Bayreuth, Germany
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7
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Neuling NR, Allert RD, Bucher DB. Prospects of single-cell nuclear magnetic resonance spectroscopy with quantum sensors. Curr Opin Biotechnol 2023; 83:102975. [PMID: 37573624 DOI: 10.1016/j.copbio.2023.102975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 06/08/2023] [Accepted: 07/03/2023] [Indexed: 08/15/2023]
Abstract
Single-cell analysis can unravel functional heterogeneity within cell populations otherwise obscured by ensemble measurements. However, noninvasive techniques that probe chemical entities and their dynamics are still lacking. This challenge could be overcome by novel sensors based on nitrogen-vacancy (NV) centers in diamond, which enable nuclear magnetic resonance (NMR) spectroscopy on unprecedented sample volumes. In this perspective, we briefly introduce NV-based quantum sensing and review the progress made in microscale NV-NMR spectroscopy. Last, we discuss approaches to enhance the sensitivity of NV ensemble magnetometers to detect biologically relevant concentrations and provide a roadmap toward their application in single-cell analysis.
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Affiliation(s)
- Nick R Neuling
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85748 Garching b. München, Germany; Munich Center of Quantum Science and Technology (MCQST), Schellingstr. 4, 80779 München, Germany
| | - Robin D Allert
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85748 Garching b. München, Germany; Munich Center of Quantum Science and Technology (MCQST), Schellingstr. 4, 80779 München, Germany
| | - Dominik B Bucher
- Technical University of Munich, TUM School of Natural Sciences, Department of Chemistry, Lichtenbergstr. 4, 85748 Garching b. München, Germany; Munich Center of Quantum Science and Technology (MCQST), Schellingstr. 4, 80779 München, Germany.
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8
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Schirmer M, Dusny C. Microbial single-cell mass spectrometry: status, challenges, and prospects. Curr Opin Biotechnol 2023; 83:102977. [PMID: 37515936 DOI: 10.1016/j.copbio.2023.102977] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/31/2023]
Abstract
Single-cell analysis uncovers phenotypic differences between cells in a population and dissects their individual physiological states and differences on all omics levels from genome to phenome. Spectrometric observation allows label-free analysis of the metabolome and proteome of individual cells, but is still mainly limited to the analysis of mammalian single cells. Recent progress in mass spectrometry approaches now enables the analysis of microbial single cells - mainly by miniaturizing cell handling, incubation, and improving chip-coupling concepts for analyte ionization by interfacing microfluidic chips and mass spectrometers. This review aims at distilling the enabling principles behind microbial single-cell mass spectrometry and puts them into perspective for the future of the field.
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Affiliation(s)
- Martin Schirmer
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany
| | - Christian Dusny
- Department of Solar Materials - Microscale Analysis and Engineering, Helmholtz-Centre for Environmental Research - UFZ Leipzig, Leizpig, Germany.
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9
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Blöbaum L, Täuber S, Grünberger A. Protocol to perform dynamic microfluidic single-cell cultivation of C. glutamicum. STAR Protoc 2023; 4:102436. [PMID: 37543944 PMCID: PMC10425941 DOI: 10.1016/j.xpro.2023.102436] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/12/2023] [Accepted: 06/13/2023] [Indexed: 08/08/2023] Open
Abstract
Here, we present a protocol for the design, fabrication, and usage of a polydimethylsiloxane (PDMS)-based chip for dynamic microfluidic single-cell cultivation of Corynebacterium glutamicum. We describe steps for flow profile establishment and biological preparation. We then detail time-lapse imaging to observe reactions of C. glutamicum to repeated environmental changes in the range of seconds. This system can be adapted to other organisms with a cell wall and soluble non-gaseous environmental factors like nutrients. For complete details on the use and execution of this protocol, please refer to Täuber et al..1.
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Affiliation(s)
- Luisa Blöbaum
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, 33615 Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany.
| | - Sarah Täuber
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, 33615 Bielefeld, Germany; Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Alexander Grünberger
- Multiscale Bioengineering, Technical Faculty, Bielefeld University, 33615 Bielefeld, Germany; Microsystems in Bioprocess Engineering, Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany.
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10
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Murray BE, Penabad LI, Kennedy RT. Advances in coupling droplet microfluidics to mass spectrometry. Curr Opin Biotechnol 2023; 82:102962. [PMID: 37336080 DOI: 10.1016/j.copbio.2023.102962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 05/12/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023]
Abstract
Droplet microfluidics enables development of workflows with low sample consumption and high throughput. Fluorescence-based assays are most used with droplet microfluidics; however, the requirement of a fluorescent reporter restricts applicability of this approach. The coupling of droplets to mass spectrometry (MS) has enabled selective assays on complex mixtures to broaden the analyte scope. Droplet microfluidics has been interfaced to MS via electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI). The works reviewed herein outline the development of this nascent field as well as initial exploration of its application in biotechnology and bioanalysis, including synthetic biology, reaction development, and in vivo sensing.
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Affiliation(s)
- Bridget E Murray
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Laura I Penabad
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA
| | - Robert T Kennedy
- Department of Chemistry, University of Michigan, 930 N. University Ave, Ann Arbor, MI 48109-1055, USA.
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11
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Lee DK, Rubakhin SS, Sweedler JV. Chemical Decrosslinking-Based Peptide Characterization of Formaldehyde-Fixed Rat Pancreas Using Fluorescence-Guided Single-Cell Mass Spectrometry. Anal Chem 2023; 95:6732-6739. [PMID: 37040477 DOI: 10.1021/acs.analchem.3c00612] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Approaches for the characterization of proteins/peptides in single cells of formaldehyde-fixed (FF) tissues via mass spectrometry (MS) are still under development. The lack of a general method for selectively eliminating formaldehyde-induced crosslinking is a major challenge. A workflow is shown for the high-throughput peptide profiling of single cells isolated from FF tissues, here the rodent pancreas, which possesses multiple peptide hormones from the islets of Langerhans. The heat treatment is enhanced by a collagen-selective multistep thermal process assisting efficient isolation of islets from the FF pancreas and, subsequently, their dissociation into single islet cells. Hydroxylamine-based chemical decrosslinking helped restore intact peptide signals from individual isolated cells. Subsequently, an acetone/glycerol-assisted cell dispersion was optimized for spatially resolved cell deposition onto glass slides, while a glycerol solution maintained the hydrated state of the cells. This sample preparation procedure allowed peptide profiling in FF single cells by fluorescence-guided matrix-assisted laser desorption ionization MS. Here, 2594 single islet cells were analyzed and 28 peptides were detected, including insulin C-peptides and glucagon. T-distributed stochastic neighbor embedding (t-SNE) data visualization demonstrated that cells cluster based on cell-specific pancreatic peptide hormones. This workflow expands the sample availability for single-cell MS characterization to a wide range of formaldehyde-treated tissue specimens stored in biobanks.
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Affiliation(s)
- Dong-Kyu Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S Rubakhin
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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12
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Zhou S, Fatma Z, Xue P, Mishra S, Cao M, Zhao H, Sweedler JV. Mass Spectrometry-Based High-Throughput Quantification of Bioproducts in Liquid Culture. Anal Chem 2023; 95:4067-4076. [PMID: 36790390 DOI: 10.1021/acs.analchem.2c04845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
To meet the ever-increasing need for high-throughput screening in metabolic engineering, information-rich, fast screening methods are needed. Mass spectrometry (MS) provides an efficient and general approach for metabolite screening and offers the capability of characterizing a broad range of analytes in a label-free manner, but often requires a range of sample clean-up and extraction steps. Liquid extraction surface analysis (LESA) coupled MS is an image-guided MS surface analysis approach that directly samples and introduces metabolites from a surface to MS. Here, we combined the advantages of LESA-MS and an acoustic liquid handler with stable isotope-labeled internal standards. This approach provides absolute quantitation of target chemicals from liquid culture-dried droplets and enables high-throughput quantitative screening for microbial metabolites. In this study, LESA-MS was successfully applied to quantify several different metabolites (itaconic acid, triacetic acid lactone, and palmitic acid) from different yeast strains in different mediums, demonstrating its versatility, accuracy, and efficiency across a range of microbial engineering applications.
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Affiliation(s)
- Shuaizhen Zhou
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shekhar Mishra
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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Chantipmanee N, Xu Y. Toward nanofluidics‐based mass spectrometry for exploring the unknown complex and heterogenous subcellular worlds. VIEW 2022. [DOI: 10.1002/viw.20220036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nattapong Chantipmanee
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
| | - Yan Xu
- Department of Chemical Engineering Graduate School of Engineering Osaka Metropolitan University Sakai Japan
- Japan Science and Technology Agency (JST) PRESTO Kawaguchi Japan
- Japan Science and Technology Agency (JST) CREST Kawaguchi Japan
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Recent advances of integrated microfluidic systems for fungal and bacterial analysis. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Liu Y, Fan Z, Qiao L, Liu B. Advances in microfluidic strategies for single-cell research. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Heiligenthal L, van der Loh M, Polack M, Blaha ME, Moschütz S, Keim A, Sträter N, Belder D. Analysis of double-emulsion droplets with ESI mass spectrometry for monitoring lipase-catalyzed ester hydrolysis at nanoliter scale. Anal Bioanal Chem 2022; 414:6977-6987. [PMID: 35995875 PMCID: PMC9436884 DOI: 10.1007/s00216-022-04266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 11/11/2022]
Abstract
Microfluidic double-emulsion droplets allow the realization and study of biphasic chemical processes such as chemical reactions or extractions on the nanoliter scale. Double emulsions of the rare type (o1/w/o2) are used here to realize a lipase-catalyzed reaction in the non-polar phase. The surrounding aqueous phase induces the transfer of the hydrophilic product from the core oil phase, allowing on-the-fly MS analysis in single double droplets. A microfluidic two-step emulsification process is developed to generate the (o1/w/o2) double-emulsion droplets. In this first example of microfluidic double-emulsion MS coupling, we show in proof-of-concept experiments that the chemical composition of the water layer can be read online using ESI–MS. Double-emulsion droplets were further employed as two-phase micro-reactors for the hydrolysis of the lipophilic ester p-nitrophenyl palmitate catalyzed by the Candida antarctica lipase B (CalB). Finally, the formation of the hydrophilic reaction product p-nitrophenol within the double-emulsion droplet micro-reactors is verified by subjecting the double-emulsion droplets to online ESI–MS analysis.
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Affiliation(s)
- Laura Heiligenthal
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Marie van der Loh
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Matthias Polack
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Maximilian E Blaha
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany
| | - Susanne Moschütz
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Antje Keim
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Norbert Sträter
- Institute of Bioanalytical Chemistry, Leipzig University, Deutscher Platz 5, 04103, Leipzig, Germany
| | - Detlev Belder
- Institute of Analytical Chemistry, Leipzig University, Linnéstraße 3, 04103, Leipzig, Germany.
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