1
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Cheng C, Katoch P, Zhong YP, Higgins CT, Moredock M, Chang MEK, Flory MR, Randell SH, Streeter PR. Identification of a Novel Subset of Human Airway Epithelial Basal Stem Cells. Int J Mol Sci 2024; 25:9863. [PMID: 39337350 PMCID: PMC11432080 DOI: 10.3390/ijms25189863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 09/06/2024] [Accepted: 09/06/2024] [Indexed: 09/30/2024] Open
Abstract
The basal cell maintains the airway's respiratory epithelium as the putative resident stem cell. Basal cells are known to self-renew and differentiate into airway ciliated and secretory cells. However, it is not clear if every basal cell functions as a stem cell. To address functional heterogeneity amongst the basal cell population, we developed a novel monoclonal antibody, HLO1-6H5, that identifies a subset of KRT5+ (cytokeratin 5) basal cells. We used HLO1-6H5 and other known basal cell-reactive reagents to isolate viable airway subsets from primary human airway epithelium by Fluorescence Activated Cell Sorting. Isolated primary cell subsets were assessed for the stem cell capabilities of self-renewal and differentiation in the bronchosphere assay, which revealed that bipotent stem cells were, at minimum 3-fold enriched in the HLO1-6H5+ cell subset. Crosslinking-mass spectrometry identified the HLO1-6H5 target as a glycosylated TFRC/CD71 (transferrin receptor) proteoform. The HLO1-6H5 antibody provides a valuable new tool for identifying and isolating a subset of primary human airway basal cells that are substantially enriched for bipotent stem/progenitor cells and reveals TFRC as a defining surface marker for this novel cell subset.
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Affiliation(s)
- Christopher Cheng
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Parul Katoch
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Yong-Ping Zhong
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Claire T. Higgins
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Maria Moredock
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Matthew E. K. Chang
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Mark R. Flory
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health and Science University, Portland, OR 97239-3098, USA
| | - Scott H. Randell
- Marsico Lung Institute/Cystic Fibrosis Research Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-7248, USA
| | - Philip R. Streeter
- Oregon Stem Cell Center, Papè Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239-3098, USA
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2
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Xu X, Yin K, Xu S, Wang Z, Wu R. Mass spectrometry-based methods for investigating the dynamics and organization of the surfaceome: exploring potential clinical implications. Expert Rev Proteomics 2024; 21:99-113. [PMID: 38300624 PMCID: PMC10928381 DOI: 10.1080/14789450.2024.2314148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 01/16/2024] [Indexed: 02/02/2024]
Abstract
INTRODUCTION Cell-surface proteins are extremely important for many cellular events, such as regulating cell-cell communication and cell-matrix interactions. Aberrant alterations in surface protein expression, modification (especially glycosylation), and interactions are directly related to human diseases. Systematic investigation of surface proteins advances our understanding of protein functions, cellular activities, and disease mechanisms, which will lead to identifying surface proteins as disease biomarkers and drug targets. AREAS COVERED In this review, we summarize mass spectrometry (MS)-based proteomics methods for global analysis of cell-surface proteins. Then, investigations of the dynamics of surface proteins are discussed. Furthermore, we summarize the studies for the surfaceome interaction networks. Additionally, biological applications of MS-based surfaceome analysis are included, particularly highlighting the significance in biomarker identification, drug development, and immunotherapies. EXPERT OPINION Modern MS-based proteomics provides an opportunity to systematically characterize proteins. However, due to the complexity of cell-surface proteins, the labor-intensive workflow, and the limit of clinical samples, comprehensive characterization of the surfaceome remains extraordinarily challenging, especially in clinical studies. Developing and optimizing surfaceome enrichment methods and utilizing automated sample preparation workflow can expand the applications of surfaceome analysis and deepen our understanding of the functions of cell-surface proteins.
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Affiliation(s)
- Xing Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Zeyu Wang
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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3
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Punzalan C, Wang L, Bajrami B, Yao X. Measurement and utilization of the proteomic reactivity by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024; 43:166-192. [PMID: 36924435 DOI: 10.1002/mas.21837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 02/17/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Chemical proteomics, which involves studying the covalent modifications of proteins by small molecules, has significantly contributed to our understanding of protein function and has become an essential tool in drug discovery. Mass spectrometry (MS) is the primary method for identifying and quantifying protein-small molecule adducts. In this review, we discuss various methods for measuring proteomic reactivity using MS and covalent proteomics probes that engage through reactivity-driven and proximity-driven mechanisms. We highlight the applications of these methods and probes in live-cell measurements, drug target identification and validation, and characterizing protein-small molecule interactions. We conclude the review with current developments and future opportunities in the field, providing our perspectives on analytical considerations for MS-based analysis of the proteomic reactivity landscape.
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Affiliation(s)
- Clodette Punzalan
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
| | - Lei Wang
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- AD Bio US, Takeda, Lexington, Massachusetts, 02421, USA
| | - Bekim Bajrami
- Chemical Biology & Proteomics, Biogen, Cambridge, Massachusetts, USA
| | - Xudong Yao
- Department of Chemistry, University of Connecticut, Storrs, Connecticut, USA
- Institute for Systems Biology, University of Connecticut, Storrs, Connecticut, USA
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4
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Zheng J, Zheng Z, Fu C, Weng Y, He A, Ye X, Gao W, Tian R. Deciphering intercellular signaling complexes by interaction-guided chemical proteomics. Nat Commun 2023; 14:4138. [PMID: 37438365 DOI: 10.1038/s41467-023-39881-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 07/14/2023] Open
Abstract
Indirect cell-cell interactions mediated by secreted proteins and their plasma membrane receptors play essential roles for regulating intercellular signaling. However, systematic profiling of the interactions between living cell surface receptors and secretome from neighboring cells remains challenging. Here we develop a chemical proteomics approach, termed interaction-guided crosslinking (IGC), to identify ligand-receptor interactions in situ. By introducing glycan-based ligation and click chemistry, the IGC approach via glycan-to-glycan crosslinking successfully captures receptors from as few as 0.1 million living cells using only 10 ng of secreted ligand. The unparalleled sensitivity and selectivity allow systematic crosslinking and identification of ligand-receptor complexes formed between cell secretome and surfaceome in an unbiased and all-to-all manner, leading to the discovery of a ligand-receptor interaction between pancreatic cancer cell-secreted urokinase (PLAU) and neuropilin 1 (NRP1) on pancreatic cancer-associated fibroblasts. This approach is thus useful for systematic exploring new ligand-receptor pairs and discovering critical intercellular signaling events.
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Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
| | - Zhendong Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Changying Fu
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yicheng Weng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - An He
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xueting Ye
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Weina Gao
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
- Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen, 518055, China.
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5
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Sun F, Suttapitugsakul S, Wu R. Systematic characterization of extracellular glycoproteins using mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:519-545. [PMID: 34047389 PMCID: PMC8627532 DOI: 10.1002/mas.21708] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 05/13/2023]
Abstract
Surface and secreted glycoproteins are essential to cells and regulate many extracellular events. Because of the diversity of glycans, the low abundance of many glycoproteins, and the complexity of biological samples, a system-wide investigation of extracellular glycoproteins is a daunting task. With the development of modern mass spectrometry (MS)-based proteomics, comprehensive analysis of different protein modifications including glycosylation has advanced dramatically. This review focuses on the investigation of extracellular glycoproteins using MS-based proteomics. We first discuss the methods for selectively enriching surface glycoproteins and investigating protein interactions on the cell surface, followed by the application of MS-based proteomics for surface glycoprotein dynamics analysis and biomarker discovery. We then summarize the methods to comprehensively study secreted glycoproteins by integrating various enrichment approaches with MS-based proteomics and their applications for global analysis of secreted glycoproteins in different biological samples. Collectively, MS significantly expands our knowledge of extracellular glycoproteins and enables us to identify extracellular glycoproteins as potential biomarkers for disease detection and drug targets for disease treatment.
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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6
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Discovery of antibodies and cognate surface targets for ovarian cancer by surface profiling. Proc Natl Acad Sci U S A 2023; 120:e2206751120. [PMID: 36574667 PMCID: PMC9910589 DOI: 10.1073/pnas.2206751120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Although antibodies targeting specific tumor-expressed antigens are the standard of care for some cancers, the identification of cancer-specific targets amenable to antibody binding has remained a bottleneck in development of new therapeutics. To overcome this challenge, we developed a high-throughput platform that allows for the unbiased, simultaneous discovery of antibodies and targets based on phenotypic binding profiles. Applying this platform to ovarian cancer, we identified a wide diversity of cancer targets including receptor tyrosine kinases, adhesion and migration proteins, proteases and proteins regulating angiogenesis in a single round of screening using genomics, flow cytometry, and mass spectrometry. In particular, we identified BCAM as a promising candidate for targeted therapy in high-grade serous ovarian cancers. More generally, this approach provides a rapid and flexible framework to identify cancer targets and antibodies.
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7
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Fostering "Education": Do Extracellular Vesicles Exploit Their Own Delivery Code? Cells 2021; 10:cells10071741. [PMID: 34359911 PMCID: PMC8305232 DOI: 10.3390/cells10071741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/06/2021] [Accepted: 07/08/2021] [Indexed: 12/15/2022] Open
Abstract
Extracellular vesicles (EVs), comprising large microvesicles (MVs) and exosomes (EXs), play a key role in intercellular communication, both in physiological and in a wide variety of pathological conditions. However, the education of EV target cells has so far mainly been investigated as a function of EX cargo, while few studies have focused on the characterization of EV surface membrane molecules and the mechanisms that mediate the addressability of specific EVs to different cell types and tissues. Identifying these mechanisms will help fulfill the diagnostic, prognostic, and therapeutic promises fueled by our growing knowledge of EVs. In this review, we first discuss published studies on the presumed EV “delivery code” and on the combinations of the hypothesized EV surface membrane “sender” and “recipient” molecules that may mediate EV targeting in intercellular communication. Then we briefly review the main experimental approaches and techniques, and the bioinformatic tools that can be used to identify and characterize the structure and functional role of EV surface membrane molecules. In the final part, we present innovative techniques and directions for future research that would improve and deepen our understandings of EV-cell targeting.
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8
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Abid MSR, Mousavi S, Checco JW. Identifying Receptors for Neuropeptides and Peptide Hormones: Challenges and Recent Progress. ACS Chem Biol 2021; 16:251-263. [PMID: 33539706 DOI: 10.1021/acschembio.0c00950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Intercellular signaling events mediated by neuropeptides and peptide hormones represent important targets for both basic science and drug discovery. For many bioactive peptides, the protein receptors that transmit information across the receiving cell membrane are not known, severely limiting these signaling pathways as potential therapeutic targets. Identifying the receptor(s) for a given peptide of interest is complicated by several factors. Most notably, cell-cell signaling peptides are generated through dynamic biosynthetic pathways, can act on many different families of receptor proteins, and can participate in complex ligand-receptor interactions that extend beyond a simple one-to-one archetype. Here, we discuss recent methodological advances to identify signaling partners for bioactive peptides. Recent efforts have centered on methods to identify candidate receptors via transcript expression, methods to match peptide-receptor pairs through high throughput screening, and methods to capture direct ligand-receptor interactions using chemical probes. Future applications of the receptor identification approaches discussed here, as well as technical advancements to address their limitations, promise to lead to a greater understanding of how cells communicate to deliver complex physiologies. Importantly, such advancements will likely provide novel targets for the treatment of human diseases within the central nervous and endocrine systems.
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Affiliation(s)
- Md Shadman Ridwan Abid
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Somayeh Mousavi
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - James W. Checco
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
- The Nebraska Center for Integrated Biomolecular Communication (NCIBC), University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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9
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 130] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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10
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Zheng J, Chen X, Yang Y, Tan CSH, Tian R. Mass Spectrometry-Based Protein Complex Profiling in Time and Space. Anal Chem 2020; 93:598-619. [DOI: 10.1021/acs.analchem.0c04332] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xiong Chen
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yun Yang
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology, Shenzhen 518055, China
- Guangdong Provincial Key Laboratory of Cell Microenvironment and Disease Research, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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11
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Tremblay TL, Hill JJ. Adding polyvinylpyrrolidone to low level protein samples significantly improves peptide recovery in FASP digests: An inexpensive and simple modification to the FASP protocol. J Proteomics 2020; 230:104000. [PMID: 33011348 DOI: 10.1016/j.jprot.2020.104000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/02/2020] [Accepted: 09/29/2020] [Indexed: 11/18/2022]
Abstract
Filter-aided sample preparation (FASP) remains a popular choice for proteomic sample preparation, particularly for its ability to produce a 'clean' peptide sample clear of large molecule contaminants. However, sample loss continues to be a problem particularly for sample inputs that contain less than ten micrograms of protein. Here, we describe that the simple addition of a polymer, polyvinylpyrrolidone-40 (PVP-40) to the protein sample prior to FASP digest significantly improves peptide recovery and identifications, especially with lower level sample inputs. PVP-FASP produces clean samples which required no additional sample clean-up prior to nanoLC-MS analysis. In addition, PVP-FASP is compatible with other FASP modifications, including the use of sodium deoxycholate (DOC) to improve trypsin digestion. SIGNIFICANCE: Simple modification to FASP procedure improves sample recovery during proteomic digests in SDS, improving peptide identifications and median peptide intensity.
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Affiliation(s)
- Tammy-Lynn Tremblay
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr., Ottawa, ON K1A 0R6, Canada
| | - Jennifer J Hill
- Human Health Therapeutics Research Centre, National Research Council Canada, 100 Sussex Dr., Ottawa, ON K1A 0R6, Canada.
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12
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Khan HS, Nair VR, Ruhl CR, Alvarez-Arguedas S, Galvan Rendiz JL, Franco LH, Huang L, Shaul PW, Kim J, Xie Y, Mitchell RB, Shiloh MU. Identification of scavenger receptor B1 as the airway microfold cell receptor for Mycobacterium tuberculosis. eLife 2020; 9:52551. [PMID: 32134383 PMCID: PMC7065847 DOI: 10.7554/elife.52551] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/04/2020] [Indexed: 12/19/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) can enter the body through multiple routes, including via specialized transcytotic cells called microfold cells (M cell). However, the mechanistic basis for M cell entry remains undefined. Here, we show that M cell transcytosis depends on the Mtb Type VII secretion machine and its major virulence factor EsxA. We identify scavenger receptor B1 (SR-B1) as an EsxA receptor on airway M cells. SR-B1 is required for Mtb binding to and translocation across M cells in mouse and human tissue. Together, our data demonstrate a previously undescribed role for Mtb EsxA in mucosal invasion and identify SR-B1 as the airway M cell receptor for Mtb.
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Affiliation(s)
- Haaris S Khan
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Vidhya R Nair
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Cody R Ruhl
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Samuel Alvarez-Arguedas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jorge L Galvan Rendiz
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Luis H Franco
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States
| | - Linzhang Huang
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, United States
| | - Yang Xie
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, United States.,Harold C Simmons Cancer Center, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, United States
| | - Ron B Mitchell
- Department of Otolaryngology, University of Texas Southwestern Medical Center, Dallas, United States
| | - Michael U Shiloh
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, United States.,Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
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13
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Barrass SV, Butcher SJ. Advances in high-throughput methods for the identification of virus receptors. Med Microbiol Immunol 2019; 209:309-323. [PMID: 31865406 PMCID: PMC7248041 DOI: 10.1007/s00430-019-00653-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 12/02/2019] [Indexed: 12/26/2022]
Abstract
Viruses have evolved many mechanisms to invade host cells and establish successful infections. The interaction between viral attachment proteins and host cell receptors is the first and decisive step in establishing such infections, initiating virus entry into the host cells. Therefore, the identification of host receptors is fundamental in understanding pathogenesis and tissue tropism. Furthermore, receptor identification can inform the development of antivirals, vaccines, and diagnostic technologies, which have a substantial impact on human health. Nevertheless, due to the complex nature of virus entry, the redundancy in receptor usage, and the limitations in current identification methods, many host receptors remain elusive. Recent advances in targeted gene perturbation, high-throughput screening, and mass spectrometry have facilitated the discovery of virus receptors in recent years. In this review, we compare the current methods used within the field to identify virus receptors, focussing on genomic- and interactome-based approaches.
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Affiliation(s)
- Sarah V Barrass
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
| | - Sarah J Butcher
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Bioscience Research Programme and Helsinki Institute of Life Sciences, Institute of Biotechnology, University of Helsinki, P.O. Box 56, 00014, Helsinki, Finland.
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14
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Li Y, Qin H, Ye M. An overview on enrichment methods for cell surface proteome profiling. J Sep Sci 2019; 43:292-312. [PMID: 31521063 DOI: 10.1002/jssc.201900700] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Accepted: 09/11/2019] [Indexed: 12/17/2022]
Abstract
Cell surface proteins are essential for many important biological processes, including cell-cell interactions, signal transduction, and molecular transportation. With the characteristics of low abundance, high hydrophobicity, and high heterogeneity, it is difficult to get a comprehensive view of cell surface proteome by direct analysis. Thus, it is important to selectively enrich the cell surface proteins before liquid chromatography with mass spectrometry analysis. In recent years, a variety of enrichment methods have been developed. Based on the separation mechanism, these methods could be mainly classified into three types. The first type is based on their difference in the physicochemical property, such as size, density, charge, and hydrophobicity. The second one is based on the bimolecular affinity interaction with lectin or antibody. And the third type is based on the chemical covalent coupling to free side groups of surface-exposed proteins or carbohydrate chains, such as primary amines, carboxyl groups, glycan side chains. In addition, metabolic labeling and enzymatic reaction-based methods have also been employed to selectively isolate cell surface proteins. In this review, we will provide a comprehensive overview of the enrichment methods for cell surface proteome profiling.
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Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, P. R. China
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15
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Antigen Identification for Cell-Binding Antibodies Using Ligand-Directed Crosslinking and Biotin Transfer. Methods Mol Biol 2019. [PMID: 31364049 DOI: 10.1007/978-1-4939-9597-4_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Panning approaches using antibody libraries often result in the isolation of antibodies that bind to cells through an unknown cellular receptor. Here, we describe a protocol that uses ligand-directed crosslinking with the aminooxy-sulfhydryl-biotin (ASB) trifunctional crosslinker followed by a proteomic analysis to identify the cellular receptors for orphan ligands. We describe the synthesis of the ASB crosslinker, labelling of the ligand with ASB, and cell binding of the labelled ligands. Next, biotin affinity purification and trypsin digestion of cell surface proteins that have been crosslinked by ASB are described. Lastly, several hints and tips to improve the proteomic analysis for these types of samples are provided.
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Wood L, Wright GJ. Approaches to identify extracellular receptor–ligand interactions. Curr Opin Struct Biol 2019; 56:28-36. [DOI: 10.1016/j.sbi.2018.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/25/2022]
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Müskens FM, Ward RJ, Herkt D, van de Langemheen H, Tobin AB, Liskamp RMJ, Milligan G. Design, Synthesis, and Evaluation of a Diazirine Photoaffinity Probe for Ligand-Based Receptor Capture Targeting G Protein-Coupled Receptors. Mol Pharmacol 2019; 95:196-209. [PMID: 30514721 PMCID: PMC6324650 DOI: 10.1124/mol.118.114249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Chemoproteomic approaches to identify ligand-receptor interactions have gained popularity. However, identifying transmembrane receptors remains challenging. A new trifunctional probe to aid the nonbiased identification of such receptors was developed and synthesized using a convenient seven-step synthesis. This probe contained three functional groups: 1) an N-hydroxysuccinimide ester for ligand-coupling through free amines, 2) a diazirine moiety to capture the receptor of interest upon irradiation with UV light, and 3) a biotin group which allowed affinity purification of the final adduct using streptavidin. The interaction between the G protein-coupled tachykinin neurokinin 1 (NK1) receptor, expressed in an inducible manner, and the peptidic ligand substance P was used as a test system. Liquid chromatography-mass spectrometry analysis confirmed successful coupling of the probe to substance P, while inositol monophosphate accumulation assays demonstrated that coupling of the probe did not interfere substantially with the substance P-NK1 receptor interaction. Confocal microscopy and western blotting provided evidence of the formation of a covalent bond between the probe and the NK1 receptor upon UV activation. As proof of concept, the probe was used in full ligand-based receptor-capture experiments to identify the substance P-binding receptor via liquid chromatography-tandem mass spectrometry, resulting in the successful identification of only the NK1 receptor. This provides proof of concept toward general utilization of this probe to define interactions between ligands and previously unidentified plasma-membrane receptors.
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Affiliation(s)
- Frederike M Müskens
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Richard J Ward
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Dominik Herkt
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Helmus van de Langemheen
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Andrew B Tobin
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Rob M J Liskamp
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
| | - Graeme Milligan
- School of Chemistry, College of Science and Engineering (F.M.M., D.H., H.L., R.M.J.L.) and Centre for Translational Pharmacology, Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences (F.M.M., R.J.W., A.B.T., G.M.), University of Glasgow, Glasgow, United Kingdom
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Lasswitz L, Chandra N, Arnberg N, Gerold G. Glycomics and Proteomics Approaches to Investigate Early Adenovirus-Host Cell Interactions. J Mol Biol 2018; 430:1863-1882. [PMID: 29746851 PMCID: PMC7094377 DOI: 10.1016/j.jmb.2018.04.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/24/2018] [Accepted: 04/30/2018] [Indexed: 12/14/2022]
Abstract
Adenoviruses as most viruses rely on glycan and protein interactions to attach to and enter susceptible host cells. The Adenoviridae family comprises more than 80 human types and they differ in their attachment factor and receptor usage, which likely contributes to the diverse tropism of the different types. In the past years, methods to systematically identify glycan and protein interactions have advanced. In particular sensitivity, speed and coverage of mass spectrometric analyses allow for high-throughput identification of glycans and peptides separated by liquid chromatography. Also, developments in glycan microarray technologies have led to targeted, high-throughput screening and identification of glycan-based receptors. The mapping of cell surface interactions of the diverse adenovirus types has implications for cell, tissue, and species tropism as well as drug development. Here we review known adenovirus interactions with glycan- and protein-based receptors, as well as glycomics and proteomics strategies to identify yet elusive virus receptors and attachment factors. We finally discuss challenges, bottlenecks, and future research directions in the field of non-enveloped virus entry into host cells.
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Affiliation(s)
- Lisa Lasswitz
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany
| | - Naresh Chandra
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden
| | - Niklas Arnberg
- Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90185 Umea, Sweden.
| | - Gisa Gerold
- Institute for Experimental Virology, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Medical School Hannover and the Helmholtz Centre for Infection Research, 30625 Hannover, Germany; Department of Clinical Microbiology, Virology, Umeå University, SE-90185 Umeå, Sweden; Wallenberg Centre for Molecular Medicine (WCMM), Umeå University, SE-90185 Umea, Sweden.
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Sobotzki N, Schafroth MA, Rudnicka A, Koetemann A, Marty F, Goetze S, Yamauchi Y, Carreira EM, Wollscheid B. HATRIC-based identification of receptors for orphan ligands. Nat Commun 2018; 9:1519. [PMID: 29666374 PMCID: PMC5904110 DOI: 10.1038/s41467-018-03936-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 03/22/2018] [Indexed: 12/14/2022] Open
Abstract
Cellular responses depend on the interactions of extracellular ligands, such as nutrients, growth factors, or drugs, with specific cell-surface receptors. The sensitivity of these interactions to non-physiological conditions, however, makes them challenging to study using in vitro assays. Here we present HATRIC-based ligand receptor capture (HATRIC-LRC), a chemoproteomic technology that successfully identifies target receptors for orphan ligands on living cells ranging from small molecules to intact viruses. HATRIC-LRC combines a click chemistry-based, protein-centric workflow with a water-soluble catalyst to capture ligand-receptor interactions at physiological pH from as few as 1 million cells. We show HATRIC-LRC utility for general antibody target validation within the native nanoscale organization of the surfaceome, as well as receptor identification for a small molecule ligand. HATRIC-LRC further enables the identification of complex extracellular interactomes, such as the host receptor panel for influenza A virus (IAV), the causative agent of the common flu. Technologies for identifying receptor-ligand pairs on living cells at physiological conditions remain scarce. Here, the authors develop a mass spectrometry-based ligand receptor capture technology that can identify receptors for a diverse range of ligands at physiological pH with as few as a million cells.
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Affiliation(s)
- Nadine Sobotzki
- Department of Health Sciences and Technology & Institute of Molecular Systems Biology & BioMedical Proteomics Platform (BMPP), ETH Zurich, Zurich, Switzerland.,Merck Ventures B. V., Gustav Mahlerplein 102, 1082MA, Amsterdam, The Netherlands
| | - Michael A Schafroth
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Alina Rudnicka
- University of Zurich, Institute of Molecular Life Sciences, Winterthurerstrasse 190, Zurich, CH-8057, Switzerland.,School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Anika Koetemann
- Department of Health Sciences and Technology & Institute of Molecular Systems Biology & BioMedical Proteomics Platform (BMPP), ETH Zurich, Zurich, Switzerland
| | - Florian Marty
- Dualsystems Biotech AG, Wagistrasse 12, Schlieren, 8952, Switzerland.,Biognosys AG, Wagistrasse 21, Schlieren, 8952, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology & Institute of Molecular Systems Biology & BioMedical Proteomics Platform (BMPP), ETH Zurich, Zurich, Switzerland
| | - Yohei Yamauchi
- School of Cellular and Molecular Medicine, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, BS8 1TD, UK
| | - Erick M Carreira
- Department of Chemistry and Applied Biosciences, Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, Zürich, 8093, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology & Institute of Molecular Systems Biology & BioMedical Proteomics Platform (BMPP), ETH Zurich, Zurich, Switzerland.
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