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Huang KY, Upadhyay G, Ahn Y, Sakakura M, Pagan-Diaz GJ, Cho Y, Weiss AC, Huang C, Mitchell JW, Li J, Tan Y, Deng YH, Ellis-Mohr A, Dou Z, Zhang X, Kang S, Chen Q, Sweedler JV, Im SG, Bashir R, Chung HJ, Popescu G, Gillette MU, Gazzola M, Kong H. Neuronal innervation regulates the secretion of neurotrophic myokines and exosomes from skeletal muscle. Proc Natl Acad Sci U S A 2024; 121:e2313590121. [PMID: 38683978 PMCID: PMC11087749 DOI: 10.1073/pnas.2313590121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 03/06/2024] [Indexed: 05/02/2024] Open
Abstract
Myokines and exosomes, originating from skeletal muscle, are shown to play a significant role in maintaining brain homeostasis. While exercise has been reported to promote muscle secretion, little is known about the effects of neuronal innervation and activity on the yield and molecular composition of biologically active molecules from muscle. As neuromuscular diseases and disabilities associated with denervation impact muscle metabolism, we hypothesize that neuronal innervation and firing may play a pivotal role in regulating secretion activities of skeletal muscles. We examined this hypothesis using an engineered neuromuscular tissue model consisting of skeletal muscles innervated by motor neurons. The innervated muscles displayed elevated expression of mRNAs encoding neurotrophic myokines, such as interleukin-6, brain-derived neurotrophic factor, and FDNC5, as well as the mRNA of peroxisome-proliferator-activated receptor γ coactivator 1α, a key regulator of muscle metabolism. Upon glutamate stimulation, the innervated muscles secreted higher levels of irisin and exosomes containing more diverse neurotrophic microRNAs than neuron-free muscles. Consequently, biological factors secreted by innervated muscles enhanced branching, axonal transport, and, ultimately, spontaneous network activities of primary hippocampal neurons in vitro. Overall, these results reveal the importance of neuronal innervation in modulating muscle-derived factors that promote neuronal function and suggest that the engineered neuromuscular tissue model holds significant promise as a platform for producing neurotrophic molecules.
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Affiliation(s)
- Kai-Yu Huang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gaurav Upadhyay
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yujin Ahn
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
| | - Masayoshoi Sakakura
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gelson J. Pagan-Diaz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Younghak Cho
- Department of Chemical and Biomolecular Engineering and KI for the Nano Century, Korea Advanced Institute of Science and Technology, Daejeon305-701, Republic of Korea
| | - Amanda C. Weiss
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Chen Huang
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jennifer W. Mitchell
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jiahui Li
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yanqi Tan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Yu-Heng Deng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Austin Ellis-Mohr
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Zhi Dou
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Xiaotain Zhang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Sehong Kang
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jonathan V. Sweedler
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Sung Gap Im
- Department of Chemical and Biomolecular Engineering and KI for the Nano Century, Korea Advanced Institute of Science and Technology, Daejeon305-701, Republic of Korea
| | - Rashid Bashir
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Gabriel Popescu
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Martha U. Gillette
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Mattia Gazzola
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Hyunjoon Kong
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Chan Zuckerberg Biohub Chicago, Chicago, IL60642
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Korea University-Korea Institute of Science and Technology Graduate School of Converging Science and Technology, Korea University, Seoul02841, Republic of Korea
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2
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Parmar D, Rosado-Rosa JM, Shrout JD, Sweedler JV. Metabolic insights from mass spectrometry imaging of biofilms: A perspective from model microorganisms. Methods 2024; 224:21-34. [PMID: 38295894 DOI: 10.1016/j.ymeth.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/17/2023] [Accepted: 01/16/2024] [Indexed: 02/05/2024] Open
Abstract
Biofilms are dense aggregates of bacterial colonies embedded inside a self-produced polymeric matrix. Biofilms have received increasing attention in medical, industrial, and environmental settings due to their enhanced survival. Their characterization using microscopy techniques has revealed the presence of structural and cellular heterogeneity in many bacterial systems. However, these techniques provide limited chemical detail and lack information about the molecules important for bacterial communication and virulence. Mass spectrometry imaging (MSI) bridges the gap by generating spatial chemical information with unmatched chemical detail, making it an irreplaceable analytical platform in the multi-modal imaging of biofilms. In the last two decades, over 30 species of biofilm-forming bacteria have been studied using MSI in different environments. The literature conveys both analytical advancements and an improved understanding of the effects of environmental variables such as host surface characteristics, antibiotics, and other species of microorganisms on biofilms. This review summarizes the insights from frequently studied model microorganisms. We share a detailed list of organism-wide metabolites, commonly observed mass spectral adducts, culture conditions, strains of bacteria, substrate, broad problem definition, and details of the MS instrumentation, such as ionization sources and matrix, to facilitate future studies. We also compared the spatial characteristics of the secretome under different study designs to highlight changes because of various environmental influences. In addition, we highlight the current limitations of MSI in relation to biofilm characterization to enable cross-comparison between experiments. Overall, MSI has emerged to become an important approach for the spatial/chemical characterization of bacterial biofilms and its use will continue to grow as MSI becomes more accessible.
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Affiliation(s)
- Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joenisse M Rosado-Rosa
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, IN 46556, United States; Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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3
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Su P, Hollas MAR, Butun FA, Kanchustambham VL, Rubakhin S, Ramani N, Greer JB, Early BP, Fellers RT, Caldwell MA, Sweedler JV, Kafader JO, Kelleher NL. Single Cell Analysis of Proteoforms. J Proteome Res 2024. [PMID: 38497708 DOI: 10.1021/acs.jproteome.4c00075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
We introduce single cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.
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Affiliation(s)
- Pei Su
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A R Hollas
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatma Ayaloglu Butun
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Vijaya Lakshmi Kanchustambham
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Stanislav Rubakhin
- Beckman Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Namrata Ramani
- Department of Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Joseph B Greer
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P Early
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael A Caldwell
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Jonathan V Sweedler
- Beckman Institute and Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Jared O Kafader
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- Departments of Molecular Biosciences, Chemistry, Chemical and Biological Engineering, and Feinberg School of Medicine, Northwestern University, Evanston, Illinois 60208, United States
- Proteomics Center of Excellence, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
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4
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Zhou Y, Zhou S, Lyons S, Sun H, Sweedler JV, Lu Y. Enhancing 2-Pyrone Synthase Efficiency by High-Throughput Mass-Spectrometric Quantification and In Vitro/In Vivo Catalytic Performance Correlation. Chembiochem 2024; 25:e202300849. [PMID: 38116888 DOI: 10.1002/cbic.202300849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/19/2023] [Indexed: 12/21/2023]
Abstract
Engineering efficient biocatalysts is essential for metabolic engineering to produce valuable bioproducts from renewable resources. However, due to the complexity of cellular metabolic networks, it is challenging to translate success in vitro into high performance in cells. To meet such a challenge, an accurate and efficient quantification method is necessary to screen a large set of mutants from complex cell culture and a careful correlation between the catalysis parameters in vitro and performance in cells is required. In this study, we employed a mass-spectrometry based high-throughput quantitative method to screen new mutants of 2-pyrone synthase (2PS) for triacetic acid lactone (TAL) biosynthesis through directed evolution in E. coli. From the process, we discovered two mutants with the highest improvement (46 fold) in titer and the fastest kcat (44 fold) over the wild type 2PS, respectively, among those reported in the literature. A careful examination of the correlation between intracellular substrate concentration, Michaelis-Menten parameters and TAL titer for these two mutants reveals that a fast reaction rate under limiting intracellular substrate concentrations is important for in-cell biocatalysis. Such properties can be tuned by protein engineering and synthetic biology to adopt these engineered proteins for the maximum activities in different intracellular environments.
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Affiliation(s)
- Yu Zhou
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX 78712, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
| | - Shuaizhen Zhou
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
| | - Scott Lyons
- Department of Molecular Bioscience, The University of Texas at Austin, 100 E 24th St, Austin, TX 78712, USA
| | - Haoran Sun
- Department of Molecular Bioscience, The University of Texas at Austin, 100 E 24th St, Austin, TX 78712, USA
| | - Jonathan V Sweedler
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 S Mathews Avenue, Urbana, IL, 61801, USA
| | - Yi Lu
- Department of Chemistry, The University of Texas at Austin, 105 E 24th St, Austin, TX 78712, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W Gregory Dr, Urbana, IL, 61801, USA
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5
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Multiscale biochemical mapping of the brain through deep-learning-enhanced high-throughput mass spectrometry. Nat Methods 2024; 21:521-530. [PMID: 38366241 PMCID: PMC10927565 DOI: 10.1038/s41592-024-02171-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
Spatial omics technologies can reveal the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive biochemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping using MEISTER, an integrative experimental and computational mass spectrometry (MS) framework. Our framework integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating three-dimensional (3D) molecular distributions and a data integration method fitting cell-specific mass spectra to 3D datasets. We imaged detailed lipid profiles in tissues with millions of pixels and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future development of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Daniel C Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Stanislav S Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Timothy J Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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Croslow SW, Trinklein TJ, Sweedler JV. Advances in multimodal mass spectrometry for single-cell analysis and imaging enhancement. FEBS Lett 2024; 598:591-601. [PMID: 38243373 PMCID: PMC10963143 DOI: 10.1002/1873-3468.14798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/11/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]
Abstract
Multimodal mass spectrometry (MMS) incorporates an imaging modality with probe-based mass spectrometry (MS) to enable precise, targeted data acquisition and provide additional biological and chemical data not available by MS alone. Two categories of MMS are covered; in the first, an imaging modality guides the MS probe to target individual cells and to reduce acquisition time by automatically defining regions of interest. In the second category, imaging and MS data are coupled in the data analysis pipeline to increase the effective spatial resolution using a higher resolution imaging method, correct for tissue deformation, and incorporate fine morphological features in an MS imaging dataset. Recent methodological and computational developments are covered along with their application to single-cell and imaging analyses.
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Affiliation(s)
- Seth W. Croslow
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Timothy J. Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V. Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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7
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Tan Y, De La Toba E, Rubakhin SS, Labriola LT, Canfield C, Pan D, Sweedler JV. NanoLC-timsTOF-Assisted Analysis of Glycated Albumin in Diabetes-Affected Plasma and Tears. J Am Soc Mass Spectrom 2024; 35:106-113. [PMID: 38016044 PMCID: PMC10843563 DOI: 10.1021/jasms.3c00331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Glycation is a spontaneous and nonenzymatic glycosylation. Glycated albumin (GA), which serves as an important biomarker in plasma in the diagnosis and characterization of diabetes, can be passively filtered from the plasma to tears. Tears are important targets for research in clinical diagnostics due to the ability to collect this biofluid noninvasively and repeatably. Therefore, the analysis of GA in tear film provides information for monitoring diabetes progression independent of blood pathologies. Due to the limited volume (1-5 μL) of natural tear film, we developed a small volume assay using a nano liquid chromatography-trapped ion mobility spectrometry-time-of-flight MS (nanoLC-timsTOF) platform for the analysis of glycated albumin in human plasma and tear films affected by diabetes. The peptides containing lysine 525, which is the main glycation site in GA, were relatively quantified and represented as the GA level. The results of the measurements showed that GA levels were significantly higher in diabetes-affected plasma and tears compared to controls with a p-value < 0.01. A strong correlation of glycated albumin levels was observed for the plasma and tear film in diabetes samples (Pearson coefficient 0.92 with a p-value 0.0012). Moreover, the number of GA glycation sites was significantly higher in diabetes-affected plasma and tear comparatively to controls. Among all the glycation sites in plasma albumin, the GA level quantified by lysine 136/137 had a strong correlation with more commonly used lysine 525, suggesting that lysine 136 /137 is an alternative diabetes biomarker in plasma. Overall, our findings demonstrate GA in tears as a biomarker for monitoring diabetes progression, highlighting new possibilities for quick and noninvasive diabetes detection and monitoring.
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Affiliation(s)
- Yanqi Tan
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Eduardo De La Toba
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S Rubakhin
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | | | | | - Dipanjan Pan
- Department of Nuclear Engineering and Materials Science and Engineering, Pennsylvania State University, State College, Pennsylvania 16802, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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8
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Southey BR, Romanova EV, Rodriguez-Zas SL, Sweedler JV. Bioinformatics for Prohormone and Neuropeptide Discovery. Methods Mol Biol 2024; 2758:151-178. [PMID: 38549013 PMCID: PMC11045269 DOI: 10.1007/978-1-0716-3646-6_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Neuropeptides and peptide hormones are signaling molecules produced via complex posttranslational modifications of precursor proteins known as prohormones. Neuropeptides activate specific receptors and are associated with the regulation of physiological systems and behaviors. The identification of prohormones-and the neuropeptides created by these prohormones-from genomic assemblies has become essential to support the annotation and use of the rapidly growing number of sequenced genomes. Here we describe a well-validated methodology for identifying the prohormone complement from genomic assemblies that employs widely available public toolsets and databases. The uncovered prohormone sequences can then be screened for putative neuropeptides to enable accurate proteomic discovery and validation.
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Affiliation(s)
- Bruce R Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Sandra L Rodriguez-Zas
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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9
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Okyem S, Romanova EV, Tai HC, Checco JW, Sweedler JV. Nontargeted Identification of D-Amino Acid-Containing Peptides Through Enzymatic Screening, Chiral Amino Acid Analysis, and LC-MS. Methods Mol Biol 2024; 2758:227-240. [PMID: 38549017 PMCID: PMC11034756 DOI: 10.1007/978-1-0716-3646-6_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
D-amino acid-containing peptides (DAACPs) in animals are a class of bioactive molecules formed via the posttranslational modification of peptides consisting of all-L-amino acid residues. Amino acid residue isomerization greatly impacts the function of the resulting DAACP. However, because isomerization does not change the peptide's mass, this modification is difficult to detect by most mass spectrometry-based peptidomic approaches. Here we describe a method for the identification of DAACPs that can be used to systematically survey peptides extracted from a tissue sample in a nontargeted manner.
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Affiliation(s)
- Samuel Okyem
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Hua-Chia Tai
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - James W Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE, USA
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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10
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Lee C, Lee DK, Wei IA, Qiu TA, Rubakhin SS, Roper MG, Sweedler JV. Relations between Glucose and d-Amino Acids in the Modulation of Biochemical and Functional Properties of Rodent Islets of Langerhans. ACS Omega 2023; 8:47723-47734. [PMID: 38144114 PMCID: PMC10733910 DOI: 10.1021/acsomega.3c05983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/26/2023]
Abstract
The cell-to-cell signaling role of d-amino acids (d-AAs) in the mammalian endocrine system, particularly in the islets of Langerhans, has drawn growing interest for their potential involvement in modulating glucose metabolism. Previous studies found colocalization of serine racemase [produces d-serine (d-Ser)] and d-alanine (d-Ala) within insulin-secreting beta cells and d-aspartate (d-Asp) within glucagon-secreting alpha cells. Expressed in the islets, functional N-methyl-d-aspartate receptors are involved in the modulation of glucose-stimulated insulin secretion and have binding sites for several d-AAs. However, knowledge of the regulation of d-AA levels in the islets during glucose stimulation as well as the response of islets to different levels of extracellular d-AAs is limited. In this study, we determined the intracellular and extracellular levels of d-Ser, d-Ala, and d-Asp in cultures of isolated rodent islets exposed to different levels of extracellular glucose. We found that the intracellular levels of the enantiomers demonstrated large variability and, in general, were not affected by extracellular glucose levels. However, significantly lower levels of extracellular d-Ser and d-Ala were observed in the islet media supplemented with 20 mM concentration of glucose compared to the control condition utilizing 3 mM glucose. Glucose-induced oscillations of intracellular free calcium concentration ([Ca2+]i), a proxy for insulin secretion, were modulated by the exogenous application of d-Ser and d-Ala but not by their l-stereoisomers. Our results provide new insights into the roles of d-AAs in the biochemistry and function of pancreatic islets.
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Affiliation(s)
- Cindy
J. Lee
- Department
of Chemistry and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Dong-Kyu Lee
- Department
of Chemistry and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - I-An Wei
- Department
of Chemistry and Biochemistry, Florida State
University, Tallahassee, Florida 32306, United States
| | - Tian A. Qiu
- Department
of Chemistry and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stanislav S. Rubakhin
- Department
of Chemistry and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Michael G. Roper
- Department
of Chemistry and Biochemistry, Florida State
University, Tallahassee, Florida 32306, United States
| | - Jonathan V. Sweedler
- Department
of Chemistry and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Sweedler JV. The Analytical Chemistry Virtual Issue Featuring our Advisory Boards. Anal Chem 2023; 95:17425. [PMID: 38050675 DOI: 10.1021/acs.analchem.3c05146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
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12
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Weaver AA, Parmar D, Junker EA, Sweedler JV, Shrout JD. Differential Spreading of Rhamnolipid Congeners from Pseudomonas aeruginosa. ACS Appl Bio Mater 2023; 6:4914-4921. [PMID: 37878954 DOI: 10.1021/acsabm.3c00641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2023]
Abstract
Rhamnolipids are surfactants produced by many Pseudomonad bacteria, including the species Pseudomonas aeruginosa. These rhamnolipids are known to aid and enable numerous phenotypic traits that improve the survival of the bacteria that make them. These surfactants are also important for industrial products ranging from pharmaceuticals to cleaning supplies to cosmetics, to name a few. Rhamnolipids have structural diversity that leads to an array of congeners; however, little is known about the localization and distribution of these congeners in two-dimensional space. Differential distribution of congeners can reduce the uniformity of applications in industrial settings and create heterogeneity within biological communities. We examined the distribution patterns of combinations of rhamnolipids in commercially available mixtures, cell-free spent media, and colony biofilms using mass spectrometry. We found that even in the absence of cells, congeners exhibit different distribution patterns, leading to different rhamnolipid congener distributions on a surface. Congeners with shorter fatty acid chains were more centrally located, while longer chains were more heterogeneous and distally located. We found that congeners with similar structures can distribute differently. Within developing colony biofilms, we found rhamnolipid distribution patterns differed from cell-free environments, lacking simple trends noted in cell-free environments. Most strikingly, we found the distribution patterns of individual congeners in the colony biofilms to be diverse. We note that the congener distribution is far from homogeneous but composed of numerous local microenvironments of varied rhamnolipid congener composition.
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Affiliation(s)
- Abigail A Weaver
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Dharmeshkumar Parmar
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ella A Junker
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
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13
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Xie YR, Castro DC, Rubakhin SS, Trinklein TJ, Sweedler JV, Lam F. Integrative Multiscale Biochemical Mapping of the Brain via Deep-Learning-Enhanced High-Throughput Mass Spectrometry. bioRxiv 2023:2023.05.31.543144. [PMID: 37398021 PMCID: PMC10312594 DOI: 10.1101/2023.05.31.543144] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Elucidating the spatial-biochemical organization of the brain across different scales produces invaluable insight into the molecular intricacy of the brain. While mass spectrometry imaging (MSI) provides spatial localization of compounds, comprehensive chemical profiling at a brain-wide scale in three dimensions by MSI with single-cell resolution has not been achieved. We demonstrate complementary brain-wide and single-cell biochemical mapping via MEISTER, an integrative experimental and computational mass spectrometry framework. MEISTER integrates a deep-learning-based reconstruction that accelerates high-mass-resolving MS by 15-fold, multimodal registration creating 3D molecular distributions, and a data integration method fitting cell-specific mass spectra to 3D data sets. We imaged detailed lipid profiles in tissues with data sets containing millions of pixels, and in large single-cell populations acquired from the rat brain. We identified region-specific lipid contents, and cell-specific localizations of lipids depending on both cell subpopulations and anatomical origins of the cells. Our workflow establishes a blueprint for future developments of multiscale technologies for biochemical characterization of the brain.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Daniel C. Castro
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Stanislav S. Rubakhin
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Timothy J. Trinklein
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Jonathan V. Sweedler
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carl R. Woese Institute for Genomic Biology. University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Fan Lam
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Department of Electrical and Computer Engineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carle-Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carl R. Woese Institute for Genomic Biology. University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
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14
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Choe K, Sweedler JV. Workflow for High-throughput Screening of Enzyme Mutant Libraries Using Matrix-assisted Laser Desorption/Ionization Mass Spectrometry Analysis of Escherichia coli Colonies. Bio Protoc 2023; 13:e4862. [PMID: 37969752 PMCID: PMC10632168 DOI: 10.21769/bioprotoc.4862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 11/17/2023] Open
Abstract
High-throughput molecular screening of microbial colonies and DNA libraries are critical procedures that enable applications such as directed evolution, functional genomics, microbial identification, and creation of engineered microbial strains to produce high-value molecules. A promising chemical screening approach is the measurement of products directly from microbial colonies via optically guided matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Measuring the compounds from microbial colonies bypasses liquid culture with a screen that takes approximately 5 s per sample. We describe a protocol combining a dedicated informatics pipeline and sample preparation method that can prepare up to 3,000 colonies in under 3 h. The screening protocol starts from colonies grown on Petri dishes and then transferred onto MALDI plates via imprinting. The target plate with the colonies is imaged by a flatbed scanner and the colonies are located via custom software. The target plate is coated with MALDI matrix, MALDI-MS analyzes the colony locations, and data analysis enables the determination of colonies with the desired biochemical properties. This workflow screens thousands of colonies per day without requiring additional automation. The wide chemical coverage and the high sensitivity of MALDI-MS enable diverse screening projects such as modifying enzymes and functional genomics surveys of gene activation/inhibition libraries. Key features • Mass spectrometry analyzes a range of compounds from E. coli colonies as a proxy for liquid culture testing enzyme mutant libraries. • Colonies are transferred to a MALDI target plate by a simple imprinting method. • The screen compares the ratio among several products or searches for the qualitative presence of specific compounds. • The protocol requires a MALDI mass spectrometer.
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Affiliation(s)
- Kisurb Choe
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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15
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Wu YF, De La Toba EA, Dvoretskiy S, Jung R, Kim N, Daniels L, Romanova EV, Drnevich J, Sweedler JV, Boppart MD. Development of a cell-free strategy to recover aged skeletal muscle after disuse. J Physiol 2023; 601:5011-5031. [PMID: 35318675 PMCID: PMC9492804 DOI: 10.1113/jp282867] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 03/14/2022] [Indexed: 12/25/2022] Open
Abstract
Extended periods of bed rest and limb immobilization are required for healing post-injury or disease, yet disuse can result in significant muscle atrophy and decreased quality of life in older adults. Physical rehabilitation is commonly prescribed to recover these deficits, yet accumulation of reactive oxygen species and sustained rates of protein degradation persist during the rehabilitation period that can significantly delay or prevent recovery. Pericytes, considered the primary mesenchymal and vascular stromal cell in skeletal muscle, secrete beneficial factors that maintain baseline muscle mass, yet minimal information exists regarding the pericyte response to disuse and recovery. In the current study, single-cell RNA sequencing and functional assays were performed to demonstrate that pericytes in mouse skeletal muscle lose the capacity to synthesize antioxidants during disuse and recovery. This information was used to guide the design of a strategy in which healthy donor pericytes were stimulated with hydrogen peroxide (H2 O2 ) to produce small extracellular vesicles (sEVs) that effectively restored myofibre size in adult and aged muscle after disuse. Proteomic assessment detected 11 differentially regulated proteins in primed sEVs that may account for recovery of muscle, including proteins associated with extracellular matrix composition and anti-inflammatory and antioxidant processes. This study demonstrates that healthy H2 O2 -primed pericyte-derived sEVs effectively improve skeletal muscle recovery after immobilization, presenting a novel acellular approach to rebuild muscle mass in older adults after a period of disuse. KEY POINTS: Previous studies suggest that prolonged oxidative stress is a barrier to skeletal muscle recovery after a period of immobilization. In this study we demonstrate that muscle-resident perivascular stromal cells (pericytes) become dysfunctional and lack the capacity to mount an antioxidant defence after disuse in mice. Hydrogen peroxide treatment of healthy pericytes in vitro simulates the release of small extracellular vesicles (sEVs) that effectively recover skeletal muscle fibre size and extracellular matrix remodelling in young adult and aged mice after disuse. Pericyte-derived sEVs present a novel acellular strategy to recover skeletal muscle after disuse.
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Affiliation(s)
- Yu-Fu Wu
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Eduardo A. De La Toba
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Svyatoslav Dvoretskiy
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Rebecca Jung
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Noah Kim
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Laureen Daniels
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Elena V. Romanova
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Jenny Drnevich
- Roy J. Carver Biotechnology Center, High Performance Biological Computing, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Jonathan V. Sweedler
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Marni D. Boppart
- Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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16
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De La Toba EA, Anapindi KDB, Sweedler JV. Assessment and Comparison of Database Search Engines for Peptidomic Applications. J Proteome Res 2023; 22:3123-3134. [PMID: 36809008 PMCID: PMC10440370 DOI: 10.1021/acs.jproteome.2c00307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Protein database search engines are an integral component of mass spectrometry-based peptidomic analyses. Given the unique computational challenges of peptidomics, many factors must be taken into consideration when optimizing search engine selection, as each platform has different algorithms by which tandem mass spectra are scored for subsequent peptide identifications. In this study, four different database search engines, PEAKS, MS-GF+, OMSSA, and X! Tandem, were compared with Aplysia californica and Rattus norvegicus peptidomics data sets, and various metrics were assessed such as the number of unique peptide and neuropeptide identifications, and peptide length distributions. Given the tested conditions, PEAKS was found to have the highest number of peptide and neuropeptide identifications out of the four search engines in both data sets. Furthermore, principal component analysis and multivariate logistic regression were employed to determine whether specific spectral features contribute to false C-terminal amidation assignments by each search engine. From this analysis, it was found that the primary features influencing incorrect peptide assignments were the precursor and fragment ion m/z errors. Finally, an assessment employing a mixed species protein database was performed to evaluate search engine precision and sensitivity when searched against an enlarged search space containing human proteins.
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Affiliation(s)
- Eduardo A. De La Toba
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801
| | - Krishna D. B. Anapindi
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801
| | - Jonathan V. Sweedler
- Beckman Institute of Advanced Science and Technology, University of Illinois at Urbana-Champaign, 61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, 61801
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17
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Long CC, Antevska A, Mast DH, Okyem S, Sweedler JV, Do TD. Nonenzymatic Posttranslational Modifications and Peptide Cleavages Observed in Peptide Epimers. J Am Soc Mass Spectrom 2023; 34:1898-1907. [PMID: 37102735 PMCID: PMC10524105 DOI: 10.1021/jasms.3c00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Posttranslational modifications (PTMs) play vital roles in cellular homeostasis and are implicated in various pathological conditions. This work uses two ion mobility spectrometry-mass spectrometry (IMS-MS) modalities, drift-tube IMS (DT-IMS) and trapped IMS (TIMS), to characterize three important nonenzymatic PTMs that induce no mass loss: l/d isomerization, aspartate/isoaspartate isomerization, and cis/trans proline isomerization. These PTMs are assessed in a single peptide system, the recently discovered pleurin peptides, Plrn2, from Aplysia californica. We determine that the DT-IMS-MS/MS can capture and locate asparagine deamidation into aspartate and its subsequent isomerization to isoaspartate, a key biomarker for age-related diseases. Additionally, nonenzymatic peptide cleavage via in-source fragmentation is evaluated for differences in the intensities and patterns of fragment peaks between these PTMs. Peptide fragments resulting from in-source fragmentation, preceded by peptide denaturation by liquid chromatography (LC) mobile phase, exhibited cis/trans proline isomerization. Finally, the effects of differing the fragmentation voltage at the source and solution-based denaturation conditions on in-source fragmentation profiles are evaluated, confirming that LC denaturation and in-source fragmentation profoundly impact N-terminal peptide bond cleavages of Plrn2 and the structures of their fragment ions. With that, LC-IMS-MS/MS coupled with in-source fragmentation could be a robust method to identify three important posttranslational modifications: l/d isomerization, Asn-deamidation leading to Asp/IsoAsp isomerization, and cis/trans proline isomerization.
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Affiliation(s)
- Connor C. Long
- Department of Biochemistry, Cellular, and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | | | - David H. Mast
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Samuel Okyem
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, 61801
| | - Thanh D. Do
- Department of Chemistry, University of Tennessee, Knoxville, TN 37996, USA
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18
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Qiu TA, Lee CJ, Huang C, Lee DK, Rubakhin SS, Romanova EV, Sweedler JV. Biodistribution and racemization of gut-absorbed L/D-alanine in germ-free mice. Commun Biol 2023; 6:851. [PMID: 37587187 PMCID: PMC10432453 DOI: 10.1038/s42003-023-05209-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 08/03/2023] [Indexed: 08/18/2023] Open
Abstract
Microbiome-derived metabolites are important for the microbiome-gut-brain axis and the discovery of new disease treatments. D-Alanine (D-Ala) is found in many animals as a potential co-agonist of the N-methyl-D-aspartate receptors (NMDAR), receptors widely used in the nervous and endocrine systems. The gut microbiome, diet and putative endogenous synthesis are the potential sources of D-Ala in animals, although there is no direct evidence to show the distribution and racemization of gut-absorbed L-/D-Ala with regards to host-microbe interactions in mammals. In this work, we utilized germ-free mice to control the interference from microbiota and isotopically labeled L-/D-Ala to track their biodistribution and racemization in vivo. Results showed time-dependent biodistribution of gut-absorbed D-Ala, particularly accumulation of gut-absorbed D-Ala in pancreatic tissues, brain, and pituitary. No endogenous synthesis of D-Ala via racemization was observed in germ-free mice. The sources of D-Ala in mice were revealed as microbiota and diet, but not endogenous racemization. This work indicates the importance of further investigating the in vivo biological functions of gut-microbiome derived D-Ala, particularly on NMDAR-related activities, for D-Ala as a potential signaling molecules in the microbiome-gut-brain axis.
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Affiliation(s)
- Tian Autumn Qiu
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Department of Chemistry, Michigan State University, East Lansing, MI, USA
| | - Cindy J Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Chen Huang
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Dong-Kyu Lee
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- College of Pharmacy, Chung-Ang University, Seoul, Republic of Korea
| | - Stanislav S Rubakhin
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL, USA.
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, USA.
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19
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Li G, Jeon CK, Ma M, Jia Y, Zheng Z, Delafield DG, Lu G, Romanova EV, Sweedler JV, Ruotolo BT, Li L. Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42. Chem Sci 2023; 14:5936-5944. [PMID: 37293657 PMCID: PMC10246695 DOI: 10.1039/d3sc00678f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/06/2023] [Indexed: 06/10/2023] Open
Abstract
Growing evidence supports the confident association between distinct amyloid beta (Aβ) isoforms and Alzheimer's Disease (AD) pathogenesis. As such, critical investigations seeking to uncover the translational factors contributing to Aβ toxicity represent a venture of significant value. Herein, we comprehensively assess full-length Aβ42 stereochemistry, with a specific focus on models that consider naturally-occurring isomerization of Asp and Ser residues. We customize various forms of d-isomerized Aβ as natural mimics, ranging from fragments containing a single d residue to full length Aβ42 that includes multiple isomerized residues, systematically evaluating their cytotoxicity against a neuronal cell line. Combining multidimensional ion mobility-mass spectrometry experimental data with replica exchange molecular dynamics simulations, we confirm that co-d-epimerization at Asp and Ser residues within Aβ42 in both N-terminal and core regions effectively reduces its cytotoxicity. We provide evidence that this rescuing effect is associated with the differential and domain-specific compaction and remodeling of Aβ42 secondary structure.
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Affiliation(s)
- Gongyu Li
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
- Haihe Laboratory of Sustainable Chemical Transformations Tianjin 300192 China
| | - Chae Kyung Jeon
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Min Ma
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Yifei Jia
- State Key Laboratory of Pharmaceutical Chemical Biology, Research Center for Analytical Science and Tianjin Key Laboratory of Biosensing and Molecular Recognition, Frontiers Science Center for New Organic Matter, College of Chemistry, Nankai University Tianjin 300071 China
| | - Zhen Zheng
- School of Pharmacy, Tianjin Medical University Tianjin 300070 China
| | - Daniel G Delafield
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Gaoyuan Lu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
| | - Elena V Romanova
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Jonathan V Sweedler
- Department of Chemistry and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign Urbana Illinois 61801 USA
| | - Brandon T Ruotolo
- Department of Chemistry, University of Michigan Ann Arbor MI 48109 USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison 777 Highland Ave. Madison WI 53705 USA
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20
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Choe K, Jindra MA, Hubbard SC, Pfleger BF, Sweedler JV. MALDI-MS screening of microbial colonies with isomer resolution to select fatty acid desaturase variants. Anal Biochem 2023; 672:115169. [PMID: 37146955 DOI: 10.1016/j.ab.2023.115169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/18/2023] [Accepted: 04/19/2023] [Indexed: 05/07/2023]
Abstract
Creating controlled lipid unsaturation locations in oleochemicals can be a key to many bioengineered products. However, evaluating the effects of modifications to the acyl-ACP desaturase on lipid unsaturation is not currently amenable to high-throughput assays, limiting the scale of redesign efforts to <200 variants. Here, we report a rapid MS assay for profiling the positions of double bonds on membrane lipids produced by Escherichia coli colonies after treatment with ozone gas. By MS measurement of the ozonolysis products of Δ6 and Δ8 isomers of membrane lipids from colonies expressing recombinant Thunbergia alata desaturase, we screened a randomly mutagenized library of the desaturase gene at 5 s per sample. Two variants with altered regiospecificity were isolated, indicated by an increase in 16:1 Δ8 proportion. We also demonstrated the ability of these desaturase variants to influence the membrane composition and fatty acid distribution of E. coli strains deficient in the native acyl-ACP desaturase gene, fabA. Finally, we used the fabA deficient chassis to concomitantly express a non-native acyl-ACP desaturase and a medium-chain thioesterase from Umbellularia californica, demonstrating production of only saturated free fatty acids.
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Affiliation(s)
- Kisurb Choe
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Michael A Jindra
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Susan C Hubbard
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Brian F Pfleger
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Jonathan V Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States; Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States.
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21
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Castro DC, Smith KW, Norsworthy MD, Rubakhin SS, Weisbrod CR, Hendrickson CL, Sweedler JV. Single-Cell and Subcellular Analysis Using Ultrahigh Resolution 21 T MALDI FTICR Mass Spectrometry. Anal Chem 2023; 95:6980-6988. [PMID: 37070980 PMCID: PMC10190686 DOI: 10.1021/acs.analchem.3c00393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The mammalian brain contains ∼20,000 distinct lipid species that contribute to its structural organization and function. The lipid profiles of cells change in response to a variety of cellular signals and environmental conditions that result in modulation of cell function through alteration of phenotype. The limited sample material combined with the vast chemical diversity of lipids makes comprehensive lipid profiling of individual cells challenging. Here, we leverage the resolving power of a 21 T Fourier-transform ion cyclotron resonance (FTICR) mass spectrometer for chemical characterization of individual hippocampal cells at ultrahigh mass resolution. The accuracy of the acquired data allowed differentiation of freshly isolated and cultured hippocampal cell populations, as well as finding differences in lipids between the soma and neuronal processes of the same cell. Differences in lipids include TG 42:2 observed solely in the cell bodies and SM 34:1;O2 found only in the cellular processes. The work represents the first mammalian single cells analyzed at ultrahigh resolution and is an advance in the performance of mass spectrometry (MS) for single-cell research.
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Affiliation(s)
- Daniel C. Castro
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
| | - Karl W. Smith
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Miles D. Norsworthy
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801 United States
| | - Stanislav S. Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana IL 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
| | - Chad R. Weisbrod
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Christopher L. Hendrickson
- National High Magnetic Field Laboratory, Florida State University, 1801 East Paul Dirac Drive, Tallahassee, FL 32310, United States
| | - Jonathan V. Sweedler
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 505 South Goodwin Avenue, Urbana, IL 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, 505 South Mathews Avenue, Urbana IL 61801, United States
- Neuroscience Program, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, 405 North Mathews Avenue, Urbana, IL 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, 1406 West Green Street, Urbana, IL 61801, United States
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22
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Osorio N, Martineau M, Fortea M, Rouget C, Penalba V, Lee CJ, Boesmans W, Rolli-Derkinderen M, Patel AV, Mondielli G, Conrod S, Labat-Gest V, Papin A, Sasabe J, Sweedler JV, Vanden Berghe P, Delmas P, Mothet JP. d-Serine agonism of GluN1-GluN3 NMDA receptors regulates the activity of enteric neurons and coordinates gut motility. bioRxiv 2023:2023.04.19.537136. [PMID: 37131687 PMCID: PMC10153202 DOI: 10.1101/2023.04.19.537136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The enteric nervous system (ENS) is a complex network of diverse molecularly defined classes of neurons embedded in the gastrointestinal wall and responsible for controlling the major functions of the gut. As in the central nervous system, the vast array of ENS neurons is interconnected by chemical synapses. Despite several studies reporting the expression of ionotropic glutamate receptors in the ENS, their roles in the gut remain elusive. Here, by using an array of immunohistochemistry, molecular profiling and functional assays, we uncover a new role for d-serine (d-Ser) and non-conventional GluN1-GluN3 N-methyl d-aspartate receptors (NMDARs) in regulating ENS functions. We demonstrate that d-Ser is produced by serine racemase (SR) expressed in enteric neurons. By using both in situ patch clamp recording and calcium imaging, we show that d-Ser alone acts as an excitatory neurotransmitter in the ENS independently of the conventional GluN1-GluN2 NMDARs. Instead, d-Ser directly gates the non-conventional GluN1-GluN3 NMDARs in enteric neurons from both mouse and guinea-pig. Pharmacological inhibition or potentiation of GluN1-GluN3 NMDARs had opposite effects on mouse colonic motor activities, while genetically driven loss of SR impairs gut transit and fluid content of pellet output. Our results demonstrate the existence of native GluN1-GluN3 NMDARs in enteric neurons and open new perspectives on the exploration of excitatory d-Ser receptors in gut function and diseases.
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Affiliation(s)
- Nancy Osorio
- Laboratoire de Neurosciences Cognitives (LNC), Aix-Marseille-Université, CNRS, UMR 7291, Marseille, France
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
| | | | - Marina Fortea
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
| | | | - Virginie Penalba
- Laboratoire de Neurosciences Cognitives (LNC), Aix-Marseille-Université, CNRS, UMR 7291, Marseille, France
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
| | - Cindy J. Lee
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Werend Boesmans
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
| | | | - Amit V. Patel
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Grégoire Mondielli
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
| | - Sandrine Conrod
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
| | | | - Amandine Papin
- Laboratoire de Neurosciences Cognitives (LNC), Aix-Marseille-Université, CNRS, UMR 7291, Marseille, France
| | - Jumpei Sasabe
- Department of Pharmacology, Keio University School of Medicine, Tokyo, Japan
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Pieter Vanden Berghe
- Laboratory for Enteric NeuroScience (LENS), Translational Research Center for Gastrointestinal Disorders (TARGID), University of Leuven, Leuven, Belgium
| | - Patrick Delmas
- Laboratoire de Neurosciences Cognitives (LNC), Aix-Marseille-Université, CNRS, UMR 7291, Marseille, France
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
| | - Jean-Pierre Mothet
- Neurocentre Magendie, INSERM UMR U862, Bordeaux, France
- Centre de Recherche en Neurophysiologie et Neuroscience de Marseille, UMR 7286, CNRS, Université Aix-Marseille, Marseille, France
- Université Paris-Saclay, École Normale Supérieure Paris-Saclay, Centre National de la Recherche Scientifique, CentraleSupélec, LuMIn UMR9024, Gif-sur-Yvette 91190, France
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23
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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24
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Castro DC, Chan-Andersen P, Romanova EV, Sweedler JV. Probe-based mass spectrometry approaches for single-cell and single-organelle measurements. Mass Spectrom Rev 2023:10.1002/mas.21841. [PMID: 37010120 PMCID: PMC10545815 DOI: 10.1002/mas.21841] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/09/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Exploring the chemical content of individual cells not only reveals underlying cell-to-cell chemical heterogeneity but is also a key component in understanding how cells combine to form emergent properties of cellular networks and tissues. Recent technological advances in many analytical techniques including mass spectrometry (MS) have improved instrumental limits of detection and laser/ion probe dimensions, allowing the analysis of micron and submicron sized areas. In the case of MS, these improvements combined with MS's broad analyte detection capabilities have enabled the rise of single-cell and single-organelle chemical characterization. As the chemical coverage and throughput of single-cell measurements increase, more advanced statistical and data analysis methods have aided in data visualization and interpretation. This review focuses on secondary ion MS and matrix-assisted laser desorption/ionization MS approaches for single-cell and single-organelle characterization, which is followed by advances in mass spectral data visualization and analysis.
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Affiliation(s)
- Daniel C. Castro
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Peter Chan-Andersen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Elena V. Romanova
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA
| | - Jonathan V. Sweedler
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL USA
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25
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Hellinger R, Sigurdsson A, Wu W, Romanova EV, Li L, Sweedler JV, Süssmuth RD, Gruber CW. Peptidomics. Nat Rev Methods Primers 2023; 3:25. [PMID: 37250919 PMCID: PMC7614574 DOI: 10.1038/s43586-023-00205-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/09/2023] [Indexed: 05/31/2023]
Abstract
Peptides are biopolymers, typically consisting of 2-50 amino acids. They are biologically produced by the cellular ribosomal machinery or by non-ribosomal enzymes and, sometimes, other dedicated ligases. Peptides are arranged as linear chains or cycles, and include post-translational modifications, unusual amino acids and stabilizing motifs. Their structure and molecular size render them a unique chemical space, between small molecules and larger proteins. Peptides have important physiological functions as intrinsic signalling molecules, such as neuropeptides and peptide hormones, for cellular or interspecies communication, as toxins to catch prey or as defence molecules to fend off enemies and microorganisms. Clinically, they are gaining popularity as biomarkers or innovative therapeutics; to date there are more than 60 peptide drugs approved and more than 150 in clinical development. The emerging field of peptidomics comprises the comprehensive qualitative and quantitative analysis of the suite of peptides in a biological sample (endogenously produced, or exogenously administered as drugs). Peptidomics employs techniques of genomics, modern proteomics, state-of-the-art analytical chemistry and innovative computational biology, with a specialized set of tools. The complex biological matrices and often low abundance of analytes typically examined in peptidomics experiments require optimized sample preparation and isolation, including in silico analysis. This Primer covers the combination of techniques and workflows needed for peptide discovery and characterization and provides an overview of various biological and clinical applications of peptidomics.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Arnar Sigurdsson
- Institut für Chemie, Technische Universität Berlin, Berlin, Germany
| | - Wenxin Wu
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois, Urbana, IL, USA
| | - Lingjun Li
- School of Pharmacy and Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
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26
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Eberwine J, Kim J, Anafi RC, Brem S, Bucan M, Fisher SA, Grady MS, Herr AE, Issadore D, Jeong H, Kim H, Lee D, Rubakhin S, Sul JY, Sweedler JV, Wolf JA, Zaret KS, Zou J. Subcellular omics: a new frontier pushing the limits of resolution, complexity and throughput. Nat Methods 2023; 20:331-335. [PMID: 36899160 PMCID: PMC10049458 DOI: 10.1038/s41592-023-01788-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
We argue that the study of single-cell subcellular organelle omics is needed to understand and regulate cell function. This requires and is being enabled by new technology development.
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Affiliation(s)
- James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
| | - Ron C Anafi
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Maja Bucan
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Amy E Herr
- Department of Bioengineering, University of California at Berkeley, Berkeley, CA, USA
| | - David Issadore
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Hyejoong Jeong
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemical and Biomolecular Engineering, , University of Pennsylvania, Philadelphia, PA, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daeyeon Lee
- Department of Chemical and Biomolecular Engineering, , University of Pennsylvania, Philadelphia, PA, USA
| | - Stanislav Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jai-Yoon Sul
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kenneth S Zaret
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - James Zou
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Xie YR, Chari VK, Castro DC, Grant R, Rubakhin SS, Sweedler JV. Data-Driven and Machine Learning-Based Framework for Image-Guided Single-Cell Mass Spectrometry. J Proteome Res 2023; 22:491-500. [PMID: 36695570 PMCID: PMC9901547 DOI: 10.1021/acs.jproteome.2c00714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Improved throughput of analysis and lowered limits of detection have allowed single-cell chemical analysis to go beyond the detection of a few molecules in such volume-limited samples, enabling researchers to characterize different functional states of individual cells. Image-guided single-cell mass spectrometry leverages optical and fluorescence microscopy in the high-throughput analysis of cellular and subcellular targets. In this work, we propose DATSIGMA (DAta-driven Tools for Single-cell analysis using Image-Guided MAss spectrometry), a workflow based on data-driven and machine learning approaches for feature extraction and enhanced interpretability of complex single-cell mass spectrometry data. Here, we implemented our toolset with user-friendly programs and tested it on multiple experimental data sets that cover a wide range of biological applications, including classifying various brain cell types. Because it is open-source, it offers a high level of customization and can be easily adapted to other types of single-cell mass spectrometry data.
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Affiliation(s)
- Yuxuan Richard Xie
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Varsha K. Chari
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Daniel C. Castro
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Romans Grant
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Stanislav S. Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Jonathan V. Sweedler
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States,Mailing Address: Department of Chemistry, University of Illinois, 71 RAL, Box 63-5, 600 South Mathews Avenue, Urbana, Illinois 61801, United States; Phone: (217) 244-7359;
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29
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Jia J, Parmar D, Ellis JF, Cao T, Cutri AR, Shrout JD, Sweedler JV, Bohn PW. Effect of Micro-Patterned Mucin on Quinolone and Rhamnolipid Profiles of Mucoid Pseudomonas aeruginosa under Antibiotic Stress. ACS Infect Dis 2023; 9:150-161. [PMID: 36538577 PMCID: PMC10116410 DOI: 10.1021/acsinfecdis.2c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is commonly implicated in hospital-acquired infections where its capacity to form biofilms on a variety of surfaces and the resulting enhanced antibiotic resistance seriously limit treatment choices. Because surface attachment sensitizes P. aeruginosa to quorum sensing (QS) and induces virulence through both chemical and mechanical cues, we investigate the effect of surface properties through spatially patterned mucin, combined with sub-inhibitory concentrations of tobramycin on QS and virulence factors in both mucoid and non-mucoid P. aeruginosa strains using multi-modal chemical imaging combining confocal Raman microscopy and matrix-assisted laser desorption/ionization-mass spectrometry. Samples comprise surface-adherent static biofilms at a solid-water interface, supernatant liquid, and pellicle biofilms at an air-water interface at various time points. Although the presence of a sub-inhibitory concentration of tobramycin in the supernatant retards growth and development of static biofilms independent of strain and surface mucin patterning, we observe clear differences in the behavior of mucoid and non-mucoid strains. Quinolone signals in a non-mucoid strain are induced earlier and are influenced by mucin surface patterning to a degree not exhibited in the mucoid strain. Additionally, phenazine virulence factors, such as pyocyanin, are observed in the pellicle biofilms of both mucoid and non-mucoid strains but are not detected in the static biofilms from either strain, highlighting the differences in stress response between pellicle and static biofilms. Differences between mucoid and non-mucoid strains are consistent with their strain-specific phenology, in which the mucoid strain develops highly protected biofilms.
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Affiliation(s)
- Jin Jia
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Dharmeshkumar Parmar
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Joanna F Ellis
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianyuan Cao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Allison R Cutri
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Joshua D Shrout
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Jonathan V Sweedler
- Department of Chemistry and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Paul W Bohn
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States.,Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, United States
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30
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Sweedler JV. Remembering Former Editor Royce Murray: January 9, 1937 - July 6, 2022. Anal Chem 2022. [PMID: 36214466 DOI: 10.1021/acs.analchem.2c04184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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31
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Ali A, Davidson S, Fraenkel E, Gilmore I, Hankemeier T, Kirwan JA, Lane AN, Lanekoff I, Larion M, McCall LI, Murphy M, Sweedler JV, Zhu C. Single cell metabolism: current and future trends. Metabolomics 2022; 18:77. [PMID: 36181583 PMCID: PMC10063251 DOI: 10.1007/s11306-022-01934-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022]
Abstract
Single cell metabolomics is an emerging and rapidly developing field that complements developments in single cell analysis by genomics and proteomics. Major goals include mapping and quantifying the metabolome in sufficient detail to provide useful information about cellular function in highly heterogeneous systems such as tissue, ultimately with spatial resolution at the individual cell level. The chemical diversity and dynamic range of metabolites poses particular challenges for detection, identification and quantification. In this review we discuss both significant technical issues of measurement and interpretation, and progress toward addressing them, with recent examples from diverse biological systems. We provide a framework for further directions aimed at improving workflow and robustness so that such analyses may become commonly applied, especially in combination with metabolic imaging and single cell transcriptomics and proteomics.
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Affiliation(s)
- Ahmed Ali
- Leiden Academic Centre for Drug Research, University of Leiden, Gorlaeus Building Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Shawn Davidson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Ernest Fraenkel
- Department of Biological Engineering and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ian Gilmore
- National Physical Laboratory, Teddington, TW11 0LW, Middlesex, UK
| | - Thomas Hankemeier
- Leiden Academic Centre for Drug Research, University of Leiden, Room number GW4.07, Gorlaeus Building, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jennifer A Kirwan
- Berlin Institute of Health, Metabolomics Platform, Translational Research Unit of the Charite-Universitätsmedizin Berlin, Anna-Louisa-Karsch-Str 2, 10178, Berlin, Germany
| | - Andrew N Lane
- Department of Toxicology and Cancer Biology, and Center for Environmental and Systems Biochemistry, University of Kentucky, 789 S. Limestone St, Lexington, KY, 40536, USA.
| | - Ingela Lanekoff
- Department of Chemistry-BMC, Uppsala University, Husargatan 3 (576), 751 23, Uppsala, Sweden
| | - Mioara Larion
- Center for Cancer Research, National Cancer Institute, Building 37, Room 1136A, Bethesda, MD, 20892, USA
| | - Laura-Isobel McCall
- Department of Chemistry & Biochemistry, Department of Microbiology and Plant Biology, Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, 101 Stephenson Parkway, room 3750, Norman, OK, 73019-5251, USA
| | - Michael Murphy
- Departments of Biological Engineering, Department of Electrical Engineering, and Computer Science and the Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, USA
| | - Jonathan V Sweedler
- Department of Chemistry, and the Beckman Institute, University of Illinois Urbana-Champaign, 505 South Mathews Avenue, Urbana, IL, 61801, USA
| | - Caigang Zhu
- Department of Biomedical Engineering, University of Kentucky, Lexington, KY, 40536, USA
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32
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Zhang Y, Li K, Zhao Y, Shi W, Iyer H, Kim S, Brenden C, Sweedler JV, Vlasov Y. Attomole-Level Multiplexed Detection of Neurochemicals in Picoliter Droplets by On-Chip Nanoelectrospray Ionization Coupled to Mass Spectrometry. Anal Chem 2022; 94:13804-13809. [PMID: 36166829 PMCID: PMC9558086 DOI: 10.1021/acs.analchem.2c02323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
While droplet microfluidics is becoming an effective
tool for biomedical research,
sensitive detection of droplet content is still challenging, especially
for multiplexed analytes compartmentalized within ultrasmall droplets
down to picoliter volumes. To enable such measurements, we demonstrate
a silicon-based integrated microfluidic platform for multiplexed analysis
of neurochemicals in picoliter droplets via nanoelectrospray ionization
(nESI)-mass spectrometry (MS). An integrated silicon microfluidic
chip comprising downscaled 7 μm-radius channels, a compact T-junction
for droplet generation, and an integrated nESI emitter tip is used
for segmentation of analytes into picoliter compartments and their
efficient delivery for subsequent MS detection. The developed system
demonstrates effective detection of multiple neurochemicals encapsulated
within oil-isolated plugs down to low picoliter volumes. Quantitative
measurements for each neurochemical demonstrate limits of detection
at the attomole level. Such results are promising for applications
involving label-free and small-volume detection for monitoring a range
of brain chemicals.
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Affiliation(s)
- Yan Zhang
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Keyin Li
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Yaoyao Zhao
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Weihua Shi
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Hrishikesh Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Sungho Kim
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Christopher Brenden
- Department of Bioengineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
| | - Yurii Vlasov
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States.,Department of Bioengineering, University of Illinois Urbana Champaign, Urbana, Illinois 61801, United States
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33
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Lee CJ, Schnieders JH, Rubakhin SS, Patel AV, Liu C, Naji A, Sweedler JV. d-Amino Acids and Classical Neurotransmitters in Healthy and Type 2 Diabetes-Affected Human Pancreatic Islets of Langerhans. Metabolites 2022; 12:metabo12090799. [PMID: 36144204 PMCID: PMC9501506 DOI: 10.3390/metabo12090799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/20/2022] [Accepted: 08/25/2022] [Indexed: 11/16/2022] Open
Abstract
The pancreatic islets of Langerhans are clusters of cells that function as endocrine units synthesizing and releasing insulin and a range of additional peptide hormones. The structural and chemical characteristics of islets change during type 2 diabetes development. Although a range of metabolites including neurotransmitters has been reported in rodent islets, the involvement of these cell-to-cell signaling molecules within human pancreatic islets in the pathophysiology of type 2 diabetes is not well known, despite studies suggesting that these molecules impact intra- and inter-islet signaling pathways. We characterize the enigmatic cell-to-cell signaling molecules, d-serine (d-Ser) and d-aspartate (d-Asp), along with multiple classical neurotransmitters and related molecules, in healthy versus type 2 diabetes-affected human islets using capillary electrophoresis separations. Significantly reduced d-Ser percentage and gamma-aminobutyric acid (GABA) levels were found in type 2 diabetes-affected islets compared to healthy islets. In addition, the negative correlations of many of the signaling molecules, such as d-Ser percentage (r = −0.35), d-Asp (r = −0.32), serotonin (r = −0.42), and GABA (r = −0.39) levels, with hemoglobin A1c (HbA1c) levels and thus with the progression of type 2 diabetes further demonstrate the disruption in intra- or inter-islet signaling pathways and suggest that these cell-to-cell signaling molecules may be potential therapeutic targets.
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Affiliation(s)
- Cindy J. Lee
- Department of Chemistry, The Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Jack H. Schnieders
- Department of Chemistry, The Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Stanislav S. Rubakhin
- Department of Chemistry, The Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Amit V. Patel
- Department of Chemistry, The Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Chengyang Liu
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ali Naji
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jonathan V. Sweedler
- Department of Chemistry, The Beckman Institute, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
- Correspondence:
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34
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Lee CJ, Qiu TA, Hong Z, Zhang Z, Min Y, Zhang L, Dai L, Zhao H, Si T, Sweedler JV. Profiling of d-alanine production by the microbial isolates of rat gut microbiota. FASEB J 2022; 36:e22446. [PMID: 35816159 DOI: 10.1096/fj.202101595r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 06/07/2022] [Accepted: 06/27/2022] [Indexed: 11/11/2022]
Abstract
d-alanine (d-Ala) and several other d-amino acids (d-AAs) act as hormones and neuromodulators in nervous and endocrine systems. Unlike the endogenously synthesized d-serine in animals, d-Ala may be from exogenous sources, e.g., diet and intestinal microorganisms. However, it is unclear if the capability to produce d-Ala and other d-AAs varies among different microbial strains in the gut. We isolated individual microorganisms of rat gut microbiota and profiled their d-AA production in vitro, focusing on d-Ala. Serial dilutions of intestinal contents from adult male rats were plated on agar to obtain clonal cultures. Using MALDI-TOF MS for rapid strain typing, we identified 38 unique isolates, grouped into 11 species based on 16S rRNA gene sequences. We then used two-tier screening to profile bacterial d-AA production, combining a d-amino acid oxidase-based enzymatic assay for rapid assessment of non-acidic d-AA amount and chiral LC-MS/MS to quantify individual d-AAs, revealing 19 out of the 38 isolated strains as d-AA producers. LC-MS/MS analysis of the eight top d-AA producers showed high levels of d-Ala in all strains tested, with substantial inter- and intra-species variations. Though results from the enzymatic assay and LC-MS/MS analysis aligned well, LC-MS/MS further revealed the existence of d-glutamate and d-aspartate, which are poor substrates for this enzymatic assay. We observed large inter- and intra-species variation of d-AA production profiles from rat gut microbiome species, demonstrating the importance of chemical profiling of gut microbiota in addition to sequencing, furthering the idea that microbial metabolites modulate host physiology.
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Affiliation(s)
- Cindy J Lee
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tian A Qiu
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Zhilai Hong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Zhenkun Zhang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yuhao Min
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Linzixuan Zhang
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Huimin Zhao
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Tong Si
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jonathan V Sweedler
- Department of Chemistry, Carl R. Woese Institute for Genomic Biology, and the Beckman Institute, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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35
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Anapindi KDB, Romanova EV, Checco JW, Sweedler JV. Mass Spectrometry Approaches Empowering Neuropeptide Discovery and Therapeutics. Pharmacol Rev 2022; 74:662-679. [PMID: 35710134 DOI: 10.1124/pharmrev.121.000423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The discovery of insulin in the early 1900s ushered in the era of research related to peptides acting as hormones and neuromodulators, among other regulatory roles. These essential gene products are found in all organisms, from the most primitive to the most evolved, and carry important biologic information that coordinates complex physiology and behavior; their misregulation has been implicated in a variety of diseases. The evolutionary origins of at least 30 neuropeptide signaling systems have been traced to the common ancestor of protostomes and deuterostomes. With the use of relevant animal models and modern technologies, we can gain mechanistic insight into orthologous and paralogous endogenous peptides and translate that knowledge into medically relevant insights and new treatments. Groundbreaking advances in medicine and basic science influence how signaling peptides are defined today. The precise mechanistic pathways for over 100 endogenous peptides in mammals are now known and have laid the foundation for multiple drug development pipelines. Peptide biologics have become valuable drugs due to their unique specificity and biologic activity, lack of toxic metabolites, and minimal undesirable interactions. This review outlines modern technologies that enable neuropeptide discovery and characterization, and highlights lessons from nature made possible by neuropeptide research in relevant animal models that is being adopted by the pharmaceutical industry. We conclude with a brief overview of approaches/strategies for effective development of peptides as drugs. SIGNIFICANCE STATEMENT: Neuropeptides, an important class of cell-cell signaling molecules, are involved in maintaining a range of physiological functions. Since the discovery of insulin's activity, over 100 bioactive peptides and peptide analogs have been used as therapeutics. Because these are complex molecules not easily predicted from a genome and their activity can change with subtle chemical modifications, mass spectrometry (MS) has significantly empowered peptide discovery and characterization. This review highlights contributions of MS-based research towards the development of therapeutic peptides.
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Affiliation(s)
- Krishna D B Anapindi
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Elena V Romanova
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - James W Checco
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois (K.D.B.A., E.V.R., J.V.S.) and Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska (J.W.C.)
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36
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Abstract
Metabolomics, the study of metabolites present in biological samples, can provide a global view of sample state as well as insights into biological changes caused by disease or environmental interactions. Mass spectrometry (MS) is commonly used for metabolomics analysis given its high-throughput capabilities, high sensitivity, and capacity to identify multiple compounds in complex samples simultaneously. MS can be coupled to separation methods that can handle small volumes, making it well suited for analyzing the metabolome of organoids, miniaturized three-dimensional aggregates of stem cells that model in vivo organs. Organoids are being used in research efforts to study human disease and development, and in the design of personalized drug treatments. For organoid models to be useful, they need to recapitulate morphological and chemical aspects, such as the metabolome, of the parent tissue. This review highlights the separation- and imaging-based MS-based metabolomics methods that have been used to analyze the chemical contents of organoids. Future perspectives on how MS techniques can be optimized to determine the accuracy of organoid models and expand the field of organoid research are also discussed.
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Affiliation(s)
- Shannon E Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois, 61801, USA.
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37
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. Annu Rev Anal Chem (Palo Alto Calif) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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38
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Clark KD, Rubakhin SS, Sweedler JV. Characterizing RNA Modifications in Single Neurons using Mass Spectrometry. J Vis Exp 2022. [DOI: 10.3791/63940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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39
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Xie YR, Castro DC, Rubakhin SS, Sweedler JV, Lam F. Enhancing the Throughput of FT Mass Spectrometry Imaging Using Joint Compressed Sensing and Subspace Modeling. Anal Chem 2022; 94:5335-5343. [PMID: 35324161 DOI: 10.1021/acs.analchem.1c05279] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry imaging (MSI) allows for untargeted mapping of the chemical composition of tissues with attomole detection limits. MSI using Fourier transform (FT)-based mass spectrometers, such as FT-ion cyclotron resonance (FT-ICR), grants the ability to examine the chemical space with unmatched mass resolution and mass accuracy. However, direct imaging of large tissue samples using FT-ICR is slow. In this work, we present an approach that combines the subspace modeling of ICR temporal signals with compressed sensing to accelerate high-resolution FT-ICR MSI. A joint subspace and spatial sparsity constrained model computationally reconstructs high-resolution MSI data from the sparsely sampled transients with reduced duration, allowing a significant reduction in imaging time. Simulation studies and experimental implementation of the proposed method in investigation of brain tissues demonstrate a 10-fold enhancement in throughput of FT-ICR MSI, without the need for instrumental or hardware modifications.
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40
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Lee CA, Romanova EV, Southey BR, Gillette R, Sweedler JV. Comparative Analysis of Neuropeptides in Homologous Interneurons and Prohormone Annotation in Nudipleuran Sea Slugs. Front Physiol 2022; 12:809529. [PMID: 35002782 PMCID: PMC8735849 DOI: 10.3389/fphys.2021.809529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/02/2021] [Indexed: 02/06/2023] Open
Abstract
Despite substantial research on neuronal circuits in nudipleuran gastropods, few peptides have been implicated in nudipleuran behavior. In this study, we expanded the understanding of peptides in this clade, using three species with well-studied nervous systems, Hermissenda crassicornis, Melibe leonina, and Pleurobranchaea californica. For each species, we performed sequence homology analysis of de novo transcriptome predictions to identify homologs to 34 of 36 prohormones previously characterized in the gastropods Aplysia californica and Lymnaea stagnalis. We then used single-cell mass spectrometry to characterize peptide profiles in homologous feeding interneurons: the multifunctional ventral white cell (VWC) in P. californica and the small cardioactive peptide B large buccal (SLB) cells in H. crassicornis and M. leonina. The neurons produced overlapping, but not identical, peptide profiles. The H. crassicornis SLB cells expressed peptides from homologs to the FMRFamide (FMRFa), small cardioactive peptide (SCP), LFRFamide (LFRFa), and feeding circuit activating peptides prohormones. The M. leonina SLB cells expressed peptides from homologs to the FMRFa, SCP, LFRFa, and MIP-related peptides prohormones. The VWC, previously shown to express peptides from the FMRFa and QNFLa (a homolog of A. californica pedal peptide 4) prohormones, was shown to also contain SCP peptides. Thus, each neuron expressed peptides from the FMRFa and SCP families, the H. crassicornis and M. leonina SLB cells expressed peptides from the LFRFa family, and each neuron contained peptides from a prohormone not found in the others. These data suggest each neuron performs complex co-transmission, which potentially facilitates a multifunctional role in feeding. Additionally, the unique feeding characteristics of each species may relate, in part, to differences in the peptide profiles of these neurons. These data add chemical insight to enhance our understanding of the neuronal basis of behavior in nudipleurans and other gastropods.
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Affiliation(s)
- Colin A Lee
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Elena V Romanova
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Bruce R Southey
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Rhanor Gillette
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Molecular and Integrative Physiology, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Jonathan V Sweedler
- Neuroscience Program, University of Illinois Urbana-Champaign, Urbana, IL, United States.,Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, IL, United States
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41
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Wang J, Serratrice N, Lee CJ, François F, Sweedler JV, Puel JL, Mothet JP, Ruel J. Physiopathological Relevance of D-Serine in the Mammalian Cochlea. Front Cell Neurosci 2022; 15:733004. [PMID: 34975405 PMCID: PMC8718999 DOI: 10.3389/fncel.2021.733004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 11/29/2021] [Indexed: 12/02/2022] Open
Abstract
NMDA receptors (NMDARs) populate the complex between inner hair cell (IHC) and spiral ganglion neurons (SGNs) in the developing and mature cochlea. However, in the mature cochlea, activation of NMDARs is thought to mainly occur under pathological conditions such as excitotoxicity. Ototoxic drugs such as aspirin enable cochlear arachidonic-acid-sensitive NMDAR responses, and induced chronic tinnitus was blocked by local application of NMDAR antagonists into the cochlear fluids. We largely ignore if other modulators are also engaged. In the brain, D-serine is the primary physiological co-agonist of synaptic NMDARs. Whether D-serine plays a role in the cochlea had remained unexplored. We now reveal the presence of D-serine and its metabolic enzymes prior to, and at hearing onset, in the sensory and non-neuronal cells of the cochlea of several vertebrate species. In vivo intracochlear perfusion of D-serine in guinea pigs reduces sound-evoked activity of auditory nerve fibers without affecting the receptor potentials, suggesting that D-serine acts specifically on the postsynaptic auditory neurons without altering the functional state of IHC or of the stria vascularis. Indeed, we demonstrate in vitro that agonist-induced activation of NMDARs produces robust calcium responses in rat SGN somata only in the presence of D-serine, but not of glycine. Surprisingly, genetic deletion in mice of serine racemase (SR), the enzyme that catalyzes D-serine, does not affect hearing function, but offers protection against noise-induced permanent hearing loss as measured 3 months after exposure. However, the mechanisms of activation of NMDA receptors in newborn rats may be different from those in adult guinea pigs. Taken together, these results demonstrate for the first time that the neuro-messenger D-serine has a pivotal role in the cochlea by promoting the activation of silent cochlear NMDAR in pathological situations. Thus, D-serine and its signaling pathway may represent a new druggable target for treating sensorineural hearing disorders (i.e., hearing loss, tinnitus).
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Affiliation(s)
- Jing Wang
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,ENT Department, Hospital and University of Montpellier, Montpellier, France
| | - Nicolas Serratrice
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France
| | - Cindy J Lee
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Florence François
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France
| | - Jonathan V Sweedler
- Department of Chemistry, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jean-Luc Puel
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France
| | - Jean-Pierre Mothet
- Laboratoire LuMin, Biophotonics and Synapse Physiopathology Team, Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS), ENS Paris Saclay, Centrale Supélec, Gif-sur-Yvette, France
| | - Jérôme Ruel
- Institute for Neurosciences of Montpellier (INM), University Montpellier, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier, France.,Aix-Marseille Université, Centre National de la Recherche Scientifique (CNRS), Laboratoire de Neurosciences Cognitives, Marseille, France
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42
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Bhaduri A, Neumann EK, Kriegstein AR, Sweedler JV. Identification of Lipid Heterogeneity and Diversity in the Developing Human Brain. JACS Au 2021; 1:2261-2270. [PMID: 34977897 PMCID: PMC8717369 DOI: 10.1021/jacsau.1c00393] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Indexed: 06/11/2023]
Abstract
The lipidome is currently understudied but fundamental to life. Within the brain, little is known about cell-type lipid heterogeneity, and even less is known about cell-to-cell lipid diversity because it is difficult to study the lipids within individual cells. Here, we used single-cell mass spectrometry-based protocols to profile the lipidomes of 154 910 single cells across ten individuals consisting of five developmental ages and five brain regions, resulting in a unique lipid atlas available via a web browser of the developing human brain. From these data, we identify differentially expressed lipids across brain structures, cortical areas, and developmental ages. We inferred lipid profiles of several major cell types from this data set and additionally detected putative cell-type specific lipids. This data set will enable further interrogation of the developing human brain lipidome.
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Affiliation(s)
- Aparna Bhaduri
- Department
of Neurology, University of California,
San Francisco, San Francisco, California 94143, United States
- The
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell
Research, University of California, San
Francisco, San Francisco, California 94143, United States
- Department
of Biological Chemistry, University of California,
Los Angeles, Los Angeles, California 90095, United States
| | - Elizabeth K. Neumann
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Arnold R. Kriegstein
- Department
of Neurology, University of California,
San Francisco, San Francisco, California 94143, United States
- The
Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell
Research, University of California, San
Francisco, San Francisco, California 94143, United States
| | - Jonathan V. Sweedler
- Department
of Chemistry, University of Illinois at
Urbana−Champaign, Urbana, Illinois 61801, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
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43
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Zhang Y, Kim S, Shi W, Zhao Y, Park I, Brenden C, Iyer H, Jha P, Bashir R, Sweedler JV, Vlasov Y. Droplet-assisted electrospray phase separation using an integrated silicon microfluidic platform. Lab Chip 2021; 22:40-46. [PMID: 34897344 PMCID: PMC8691365 DOI: 10.1039/d1lc00758k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/01/2021] [Indexed: 06/14/2023]
Abstract
We report a silicon microfluidic platform that enables monolithic integration of transparent micron-scale microfluidic channels, an on-chip segmentation of analyte flows into picoliter-volume droplets, and a nano-electrospray ionization emitter that enables spatial and temporal separation of oil and aqueous phases during electro-spray for subsequent mass spectrometry analysis.
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Affiliation(s)
- Yan Zhang
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Sungho Kim
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Weihua Shi
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Yaoyao Zhao
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, IL 61801, USA
| | - Insu Park
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
| | - Christopher Brenden
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
| | - Hrishikesh Iyer
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Prasoon Jha
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
| | - Jonathan V Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois Urbana Champaign, IL 61801, USA
| | - Yurii Vlasov
- Department of Electrical and Computer Engineering, University of Illinois Urbana Champaign, IL 61801, USA.
- Department of Bioengineering, University of Illinois Urbana Champaign, IL 61801, USA
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44
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Bell SE, Park I, Rubakhin SS, Bashir R, Vlasov Y, Sweedler JV. Droplet Microfluidics with MALDI-MS Detection: The Effects of Oil Phases in GABA Analysis. ACS Meas Sci Au 2021; 1:147-156. [PMID: 34939077 PMCID: PMC8679089 DOI: 10.1021/acsmeasuresciau.1c00017] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Indexed: 06/01/2023]
Abstract
Microfluidic and mass spectrometry (MS) methods are widely used to sample and probe the chemical composition of biological systems to elucidate chemical correlates of their healthy and disease states. Though matrix-assisted laser desorption/ionization-mass spectrometry (MALDI)-MS has been hyphenated to droplet microfluidics for offline analyses, the effects of parameters related to droplet generation, such as the type of oil phase used, have been understudied. To characterize these effects, five different oil phases were tested in droplet microfluidics for producing samples for MALDI-MS analysis. Picoliter to nanoliter aqueous droplets containing 0.1 to 100 mM γ-aminobutyric acid (GABA) and inorganic salts were generated inside a polydimethylsiloxane microfluidic chip and deposited onto a conductive glass slide. Optical microscopy, Raman spectroscopy, and MALDI-mass spectrometry imaging (MSI) of the droplet samples and surrounding areas revealed patterns of solvent and oil evaporation and analyte deposition. Optical microscopy detected the presence of salt crystals in 50-100 μm diameter dried droplets, and Raman and MSI were used to correlate GABA signals to the visible droplet footprints. MALDI-MS analyses revealed that droplets prepared in the presence of octanol oil led to the poorest detectability of GABA, whereas the oil phases containing FC-40 provided the best detectability; GABA signal was localized to the footprint of 65 pL droplets with a limit of detection of 23 amol. The effect of the surfactant perfluorooctanol on analyte detection was also investigated.
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Affiliation(s)
- Sara E. Bell
- 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
| | - Insu Park
- Holonyak
Micro & Nanotechnology Laboratory, 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
| | - Rashid Bashir
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak
Micro & Nanotechnology Laboratory, University
of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yurii Vlasov
- Beckman
Institute for Advanced Science and Technology, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Holonyak
Micro & Nanotechnology Laboratory, University
of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Electrical and Computer Engineering, University of Illinois Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Bioengineering, University of Illinois
at 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
- Department
of Bioengineering, University of Illinois
at Urbana−Champaign, Urbana, Illinois 61801, United States
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45
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Clark KD, Rubakhin SS, Sweedler JV. Single-Neuron RNA Modification Analysis by Mass Spectrometry: Characterizing RNA Modification Patterns and Dynamics with Single-Cell Resolution. Anal Chem 2021; 93:14537-14544. [PMID: 34672536 PMCID: PMC8608286 DOI: 10.1021/acs.analchem.1c03507] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The entire collection of post-transcriptional modifications to RNA, known as the epitranscriptome, has been increasingly recognized as a critical regulatory layer in the cellular translation machinery. However, contemporary methods for the analysis of RNA modifications are limited to the detection of highly abundant modifications in bulk tissue samples, potentially obscuring unique epitranscriptomes of individual cells with population averages. We developed an approach, single-neuron RNA modification analysis by mass spectrometry (SNRMA-MS), that enables the detection and quantification of numerous post-transcriptionally modified nucleosides in single cells. When compared to a conventional RNA extraction approach that does not allow detection of RNA modifications in single cells, SNRMA-MS leverages an optimized sample preparation approach to detect up to 16 RNA modifications in individual neurons from the central nervous system of Aplysia californica. SNRMA-MS revealed that the RNA modification profiles of identified A. californica neurons with different physiological functions were mostly cell specific. However, functionally homologous neurons tended to demonstrate similar modification patterns. Stable isotope labeling with CD3-Met showed significant differences in RNA methylation rates that were dependent on the identity of the modification and the cell, with metacerebral cells (MCCs) displaying the fastest incorporation of CD3 groups into endogenous RNAs. Quantitative SNRMA-MS showed higher intracellular concentrations for 2'-O-methyladenosine and 2'-O-methylcytidine in homologous R2/LPl1 cell pairs than in MCCs. Overall, SNRMA-MS is the first analytical approach capable of simultaneously quantifying numerous RNA modifications in single neurons and revealing cell-specific modification profiles.
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Affiliation(s)
- Kevin D. Clark
- Beckman Institute for Advanced Science and Technology, 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
| | - Stanislav S. Rubakhin
- Beckman Institute for Advanced Science and Technology, 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
- Beckman Institute for Advanced Science and Technology, 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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46
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Zhang P, Perez OC, Southey BR, Sweedler JV, Pradhan AA, Rodriguez-Zas SL. Alternative Splicing Mechanisms Underlying Opioid-Induced Hyperalgesia. Genes (Basel) 2021; 12:1570. [PMID: 34680965 PMCID: PMC8535871 DOI: 10.3390/genes12101570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/19/2021] [Accepted: 09/30/2021] [Indexed: 12/13/2022] Open
Abstract
Prolonged use of opioids can cause opioid-induced hyperalgesia (OIH). The impact of alternative splicing on OIH remains partially characterized. A study of the absolute and relative modes of action of alternative splicing further the understanding of the molecular mechanisms underlying OIH. Differential absolute and relative isoform profiles were detected in the trigeminal ganglia and nucleus accumbens of mice presenting OIH behaviors elicited by chronic morphine administration relative to control mice. Genes that participate in glutamatergic synapse (e.g., Grip1, Grin1, Wnk3), myelin protein processes (e.g., Mbp, Mpz), and axon guidance presented absolute and relative splicing associated with OIH. Splicing of genes in the gonadotropin-releasing hormone receptor pathway was detected in the nucleus accumbens while splicing in the vascular endothelial growth factor, endogenous cannabinoid signaling, circadian clock system, and metabotropic glutamate receptor pathways was detected in the trigeminal ganglia. A notable finding was the prevalence of alternatively spliced transcription factors and regulators (e.g., Ciart, Ablim2, Pbx1, Arntl2) in the trigeminal ganglia. Insights into the nociceptive and antinociceptive modulatory action of Hnrnpk were gained. The results from our study highlight the impact of alternative splicing and transcriptional regulators on OIH and expose the need for isoform-level research to advance the understanding of morphine-associated hyperalgesia.
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Affiliation(s)
- Pan Zhang
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Olivia C. Perez
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (O.C.P.); (B.R.S.)
| | - Bruce R. Southey
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (O.C.P.); (B.R.S.)
| | - Jonathan V. Sweedler
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
| | - Amynah A. Pradhan
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - Sandra L. Rodriguez-Zas
- Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA;
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; (O.C.P.); (B.R.S.)
- Department of Statistics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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47
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Jeon S, Li Q, Ranard KM, Rubakhin SS, Sweedler JV, Kuchan MJ, Erdman JW. Spatiotemporal biodistribution of α-tocopherol is impacted by the source of 13C-labeled α-tocopherol in mice following a single oral dose. Nutr Res 2021; 93:79-86. [PMID: 34428718 DOI: 10.1016/j.nutres.2021.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 10/20/2022]
Abstract
Natural (RRR-) α-tocopherol (αT) is more bioactive than synthetic (all racemic, all rac-) αT, but not enough is known about the tissue kinetics of the 2 αT sources. We examined the time-course bioaccumulation of natural versus synthetic αT in tissues of young, marginally vitamin E-deficient mice using 13C-RRR-αT or 13C-all rac-αT tracers. In experiment 1, 3-week old male wild-type mice were fed a vitamin E-deficient diet for 0, 1, 2, or 3 weeks (n = 5/time point). Tissue αT levels were analyzed by HPLC-PDA. Feeding a vitamin E-deficient diet for up to 3 weeks decreased total αT concentrations in all analyzed tissues except the brain, which maintained its αT level. In experiment 2, a 2-week αT-depletion period was followed by administration of a single oral dose of 0.5 mg of 13C-RRR-αT or 13C-all rac-αT. At 12 hr, 1, 2, and 4 days post-dose, serum and multiple tissues were collected (n = 3/time point). αT was quantified by HPLC-PDA, and 13C-αT enrichment was determined by LC-MS. Both sources of 13C-αT reached maximum serum levels at 12 hr post-dose. 13C-RRR-αT levels were significantly higher than 13C-all rac-αT in serum at 1 d post-dose, and in heart, lungs, and kidney at 2d post-dose. In brain, 13C-RRR-αT concentrations were significantly higher than 13C-all rac-αT at 2 and 4 d post-dose. At 4 d post-dose, 13C-αT levels were similar between the 2 sources in examined tissues except for brain and adipose tissue where 13C-RRR-αT was higher. In conclusion, αT bioaccumulation over time varied substantially depending on αT source and tissue type.
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Affiliation(s)
- Sookyoung Jeon
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Illinois
| | - Qiyao Li
- Department of Chemistry, University of Illinois at Urbana-Champaign, Illinois; The Beckman Institute, University of Illinois at Urbana-Champaign, Illinois
| | - Katherine M Ranard
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Illinois
| | - Stanislav S Rubakhin
- Department of Chemistry, University of Illinois at Urbana-Champaign, Illinois; The Beckman Institute, University of Illinois at Urbana-Champaign, Illinois
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois at Urbana-Champaign, Illinois; The Beckman Institute, University of Illinois at Urbana-Champaign, Illinois
| | | | - John W Erdman
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Illinois; The Beckman Institute, University of Illinois at Urbana-Champaign, Illinois; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Illinois.
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48
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Clark K, Lee C, Gillette R, Sweedler JV. Characterization of Neuronal RNA Modifications during Non-associative Learning in Aplysia Reveals Key Roles for tRNAs in Behavioral Sensitization. ACS Cent Sci 2021; 7:1183-1190. [PMID: 34345669 PMCID: PMC8323240 DOI: 10.1021/acscentsci.1c00351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Indexed: 05/12/2023]
Abstract
Subtle changes in the landscape of post-transcriptional modifications have emerged as putative regulators of central nervous system plasticity and activity-induced protein synthesis. However, simultaneous characterization of multiple RNA modifications and their covariation during learning and memory paradigms has been impeded by the complexity of animal models and lack of untargeted approaches for identifying pathway-relevant RNA modifications in small-volume samples. Here, we used mass spectrometry to profile spatiotemporal changes in dozens of neuronal RNA modifications in Aplysia californica during behavioral sensitization of a simple defensive reflex. Unique RNA modification patterns were observed in the major ganglia of trained and naı̇ve animals, with two tRNA modifications, namely, 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U) and 1-methyladenosine (m1A), at significantly higher levels in trained subjects. We report that tRNAs, and their modifications, correlate with increased polyglutamine synthesis and excitability in neurons, characterizing the first link between noncoding RNA modifications and non-associative learning.
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Affiliation(s)
- Kevin
D. Clark
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Colin Lee
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Rhanor Gillette
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Jonathan V. Sweedler
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Neuroscience
Program, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Department
of Molecular and Integrative Physiology, 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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Sweedler JV. The Inaugural Measurement Science Symposium: Do Not Miss It! Anal Chem 2021; 93:7151. [PMID: 33961392 DOI: 10.1021/acs.analchem.1c01894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Choe K, Xue P, Zhao H, Sweedler JV. macroMS: Image-Guided Analysis of Random Objects by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry. J Am Soc Mass Spectrom 2021; 32:1180-1188. [PMID: 33822609 PMCID: PMC8102432 DOI: 10.1021/jasms.1c00013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Mass spectrometry imaging is well-suited to characterizing sample surfaces for their chemical content in a spatially resolved manner. However, when the surface contains small objects with significant empty spaces between them, more efficient approaches to sample acquisition are possible. Image-guided mass spectrometry (MS) enables high-throughput analysis of a diverse range of sample types, such as microbial colonies, liquid microdroplets, and others, by recognizing and analyzing selected location targets in an image. Here, we describe an imaging protocol and macroMS, an online software suite that can be used to enhance MS measurements of macroscopic samples that are imaged by a camera or a flatbed scanner. The web-based tool enables users to find and filter targets from the optical images, correct optical distortion issues for improved spatial location of selected targets, input the custom geometry files into an MS device to acquire spectra at the selected locations, and finally, perform limited data analysis and use visualization tools to aid locating samples containing compounds of interest. Using the macroMS suite, an enzyme mutant library of Saccharomyces cerevisiae and nL droplet arrays of Escherichia coli and Pseudomonas fluorescens have been assayed at a rate of ∼2 s/sample.
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Affiliation(s)
- Kisurb Choe
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
| | - Pu Xue
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Huimin Zhao
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Jonathan V. Sweedler
- Department of Energy Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
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