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Shoji H, Hirano H, Nojima Y, Gunji D, Shinkura A, Muraoka S, Abe Y, Narumi R, Nagao C, Aoki M, Obama K, Honda K, Mizuguchi K, Tomonaga T, Saito Y, Yoshikawa T, Kato K, Boku N, Adachi J. Phosphoproteomic subtyping of gastric cancer reveals dynamic transformation with chemotherapy and guides targeted cancer treatment. Cell Rep 2024:114774. [PMID: 39357518 DOI: 10.1016/j.celrep.2024.114774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 08/08/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024] Open
Abstract
There are only a few effective molecular targeted agents for advanced unresectable or recurrent advanced gastric cancer (AGC), which has a poor prognosis with a median survival time of less than 14 months. Focusing on phosphorylation signaling in cancer cells, we have been developing deep phosphoproteome analysis from minute endoscopic biopsy specimens frozen within 20 s of collection. Phosphoproteomic analysis of 127 fresh-frozen endoscopic biopsy samples from untreated patients with AGC revealed three subtypes reflecting different cellular signaling statuses. Subsequent serial biopsy analysis has revealed the dynamic mesenchymal transitions within cancer cells, along with the concomitant rewiring of the kinome network, ultimately resulting in the conversion to the epithelial-mesenchymal transition (EMT) subtype throughout treatment. We present our investigation of intracellular signaling related to the EMT in gastric cancer and propose therapeutic approaches targeting AXL. This study also provides a wealth of resources for the future development of treatments and biomarkers for AGC.
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Affiliation(s)
- Hirokazu Shoji
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan; Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo 104-0045, Japan.
| | - Hidekazu Hirano
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Yosui Nojima
- Center for Mathematical Modeling and Data Science, Osaka University, Osaka 560-8531, Japan; Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 566-0002, Japan
| | - Daigo Gunji
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Department of Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Akina Shinkura
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Department of Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Satoshi Muraoka
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan
| | - Yuichi Abe
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Immunoproteomics Laboratory, Institute for Glyco-core Research (iGCORE), Gifu University, Gifu 501-1112, Japan
| | - Ryohei Narumi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan
| | - Chioko Nagao
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 566-0002, Japan; Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Masahiko Aoki
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Kazutaka Obama
- Department of Gastrointestinal Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Kazufumi Honda
- Department of Bioregulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8602, Japan
| | - Kenji Mizuguchi
- Artificial Intelligence Center for Health and Biomedical Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 566-0002, Japan; Institute for Protein Research, Osaka University, Osaka 565-0871, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Proteobiologics Co., Ltd., Osaka 562-0011, Japan
| | - Yutaka Saito
- Endoscopy Division, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Takaki Yoshikawa
- Department of Gastric Surgery, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Ken Kato
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan; Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan
| | - Narikazu Boku
- Department of Gastrointestinal Medical Oncology, National Cancer Center Hospital, Tokyo 104-0045, Japan; Department of Medical Oncology and General Medicine, IMSUT Hospital, Institute of Medical Science, University of Tokyo, Tokyo 108-8639, Japan.
| | - Jun Adachi
- Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health, and Nutrition, Osaka 567-0085, Japan; Laboratory of Clinical and Analytical Chemistry, Center for Drug Design Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, Japan; Laboratory of Proteomics and Drug Discovery, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.
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Berryhill CA, Evans TN, Doud EH, Smith-Kinnaman WR, Hanquier JN, Mosley AL, Cornett EM. Quantitative analysis of non-histone lysine methylation sites and lysine demethylases in breast cancer cell lines. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.18.613658. [PMID: 39345446 PMCID: PMC11429713 DOI: 10.1101/2024.09.18.613658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Growing evidence shows that lysine methylation is a widespread protein post-translational modification that regulates protein function on histone and non-histone proteins. Numerous studies have demonstrated that dysregulation of lysine methylation mediators contributes to cancer growth and chemotherapeutic resistance. While changes in histone methylation are well documented with extensive analytical techniques available, there is a lack of high-throughput methods to reproducibly quantify changes in the abundances of the mediators of lysine methylation and non-histone lysine methylation (Kme) simultaneously across multiple samples. Recent studies by our group and others have demonstrated that antibody enrichment is not required to detect lysine methylation, prompting us to investigate the use of Tandem Mass Tag (TMT) labeling for global Kme quantification sans antibody enrichment in four different breast cancer cell lines (MCF-7, MDA-MB-231, HCC1806, and MCF10A). To improve the quantification of KDMs, we incorporated a lysine demethylase (KDM) isobaric trigger channel, which enabled 96% of all KDMs to be quantified while simultaneously quantifying 326 Kme sites. Overall, 142 differentially abundant Kme sites and eight differentially abundant KDMs were identified between the four cell lines, revealing cell line-specific patterning.
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Affiliation(s)
- Christine A Berryhill
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Taylor N Evans
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Emma H Doud
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Center for Proteome Analysis, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Whitney R Smith-Kinnaman
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Center for Proteome Analysis, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Jocelyne N Hanquier
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Amber L Mosley
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Center for Proteome Analysis, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
| | - Evan M Cornett
- Biochemistry and Molecular Biology, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
- Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indiana University School of Medicine (IUSM), 635 Barnhill Drive, Medical Science Building, Indianapolis, IN 46202-5122, U.S.A
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Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. Mol Cell Proteomics 2024:100841. [PMID: 39307423 DOI: 10.1016/j.mcpro.2024.100841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 08/19/2024] [Accepted: 08/23/2024] [Indexed: 09/25/2024] Open
Abstract
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ∼3500 proteins at a spatial resolution of 50 μm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Clayton E Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States.
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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4
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Sarkar S, Zheng X, Clair GC, Kwon YM, You Y, Swensen AC, Webb-Robertson BJM, Nakayasu ES, Qian WJ, Metz TO. Exploring new frontiers in type 1 diabetes through advanced mass-spectrometry-based molecular measurements. Trends Mol Med 2024:S1471-4914(24)00195-3. [PMID: 39152082 DOI: 10.1016/j.molmed.2024.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 07/17/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Type 1 diabetes (T1D) is a devastating autoimmune disease for which advanced mass spectrometry (MS) methods are increasingly used to identify new biomarkers and better understand underlying mechanisms. For example, integration of MS analysis and machine learning has identified multimolecular biomarker panels. In mechanistic studies, MS has contributed to the discovery of neoepitopes, and pathways involved in disease development and identifying therapeutic targets. However, challenges remain in understanding the role of tissue microenvironments, spatial heterogeneity, and environmental factors in disease pathogenesis. Recent advancements in MS, such as ultra-fast ion-mobility separations, and single-cell and spatial omics, can play a central role in addressing these challenges. Here, we review recent advancements in MS-based molecular measurements and their role in understanding T1D.
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Affiliation(s)
- Soumyadeep Sarkar
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Xueyun Zheng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Geremy C Clair
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yu Mi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Youngki You
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Adam C Swensen
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | | | - Ernesto S Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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5
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Veličković M, Fillmore TL, Attah IK, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD. Coupling Microdroplet-Based Sample Preparation, Multiplexed Isobaric Labeling, and Nanoflow Peptide Fractionation for Deep Proteome Profiling of the Tissue Microenvironment. Anal Chem 2024; 96:12973-12982. [PMID: 39089681 PMCID: PMC11325296 DOI: 10.1021/acs.analchem.4c00523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity in a cell-type-specific manner to better understand and predict the function of complex biological systems such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverage due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (microdroplet processing in one pot for trace samples), multiplexed isobaric labeling, and a nanoflow peptide fractionation approach. The integrated workflow allowed us to maximize proteome coverage of laser-isolated tissue samples containing nanogram levels of proteins. We demonstrated that the deep spatial proteomics platform can quantify more than 5000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 μm2) and differentiate unique protein abundance patterns in pancreas. Furthermore, the use of the microPOTS chip eliminated the requirement for advanced microfabrication capabilities and specialized nanoliter liquid handling equipment, making it more accessible to proteomic laboratories.
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Affiliation(s)
- Marija Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Isaac Kwame Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Camilo Posso
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - James C Pino
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Jon M Jacobs
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Kristin E Burnum-Johnson
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Paul D Piehowski
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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6
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Kwon Y, Woo J, Yu F, Williams SM, Markillie LM, Moore RJ, Nakayasu ES, Chen J, Campbell-Thompson M, Mathews CE, Nesvizhskii AI, Qian WJ, Zhu Y. Proteome-scale tissue mapping using mass spectrometry based on label-free and multiplexed workflows. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583367. [PMID: 38496682 PMCID: PMC10942300 DOI: 10.1101/2024.03.04.583367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Multiplexed bimolecular profiling of tissue microenvironment, or spatial omics, can provide deep insight into cellular compositions and interactions in healthy and diseased tissues. Proteome-scale tissue mapping, which aims to unbiasedly visualize all the proteins in a whole tissue section or region of interest, has attracted significant interest because it holds great potential to directly reveal diagnostic biomarkers and therapeutic targets. While many approaches are available, however, proteome mapping still exhibits significant technical challenges in both protein coverage and analytical throughput. Since many of these existing challenges are associated with mass spectrometry-based protein identification and quantification, we performed a detailed benchmarking study of three protein quantification methods for spatial proteome mapping, including label-free, TMT-MS2, and TMT-MS3. Our study indicates label-free method provided the deepest coverages of ~3500 proteins at a spatial resolution of 50 µm and the highest quantification dynamic range, while TMT-MS2 method holds great benefit in mapping throughput at >125 pixels per day. The evaluation also indicates both label-free and TMT-MS2 provide robust protein quantifications in identifying differentially abundant proteins and spatially co-variable clusters. In the study of pancreatic islet microenvironment, we demonstrated deep proteome mapping not only enables the identification of protein markers specific to different cell types, but more importantly, it also reveals unknown or hidden protein patterns by spatial co-expression analysis.
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Affiliation(s)
- Yumi Kwon
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jongmin Woo
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Fengchao Yu
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sarah M. Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lye Meng Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J. Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Martha Campbell-Thompson
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, United States
| | - Alexey I. Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Department of Proteomic and Genomic Technologies, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
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Pandey R, Roberts ML, Wang J, Pereckas M, Jensen D, Greene AS, Widlansky ME, Liang M. Proteomic Profiles of Human Arterioles Isolated From Fresh Adipose Tissue or Following Overnight Storage. J Transl Med 2024; 104:102036. [PMID: 38408704 PMCID: PMC11098693 DOI: 10.1016/j.labinv.2024.102036] [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: 08/25/2023] [Revised: 01/20/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024] Open
Abstract
Arterioles are key determinants of the total peripheral vascular resistance, which, in turn, is a key determinant of arterial blood pressure. However, the amount of protein available from one isolated human arteriole may be less than 5 μg, making proteomic analysis challenging. In addition, obtaining human arterioles requires manual dissection of unfrozen clinical specimens. This limits its feasibility, especially for powerful multicenter clinical studies in which clinical specimens need to be shipped overnight to a research laboratory for arteriole isolation. We performed a study to address low-input, test overnight tissue storage and develop a reference human arteriolar proteomic profile. In tandem mass tag proteomics, use of a booster channel consisting of human induced pluripotent stem cell-derived endothelial and vascular smooth muscle cells (1:5 ratio) increased the number of proteins detected in a human arteriole segment with a false discovery rate of <0.01 from 1051 to more than 3000. The correlation coefficient of proteomic profile was similar between replicate arterioles isolated freshly, following cold storage, or before and after the cold storage (1-way analysis of variance; P = .60). We built a human arteriolar proteomic profile consisting of 3832 proteins based on the analysis of 12 arteriole samples from 3 subjects. Of 1945 blood pressure-relevant proteins that we curated, 476 (12.5%) were detected in the arteriolar proteome, which was a significant overrepresentation (χ2 test; P < .05). These findings demonstrate that proteomic analysis is feasible with arterioles isolated from human adipose tissue following cold overnight storage and provide a reference human arteriolar proteome profile highly valuable for studies of arteriole-related traits.
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Affiliation(s)
- Rajan Pandey
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; Department of Physiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona
| | - Michelle L Roberts
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Jingli Wang
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Michaela Pereckas
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - David Jensen
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin
| | | | - Michael E Widlansky
- Division of Cardiovascular Medicine, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin.
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin; Department of Physiology, University of Arizona College of Medicine-Tucson, Tucson, Arizona.
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8
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Kim YK, Kim YR, Wells KL, Sarbaugh D, Guney M, Tsai CF, Zee T, Karsenty G, Nakayasu ES, Sussel L. PTPN2 Regulates Metabolic Flux to Affect β-Cell Susceptibility to Inflammatory Stress. Diabetes 2024; 73:434-447. [PMID: 38015772 PMCID: PMC10882156 DOI: 10.2337/db23-0355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
Protein tyrosine phosphatase N2 (PTPN2) is a type 1 diabetes (T1D) candidate gene identified from human genome-wide association studies. PTPN2 is highly expressed in human and murine islets and becomes elevated upon inflammation and models of T1D, suggesting that PTPN2 may be important for β-cell survival in the context of T1D. To test whether PTPN2 contributed to β-cell dysfunction in an inflammatory environment, we generated a β-cell-specific deletion of Ptpn2 in mice (PTPN2-β knockout [βKO]). Whereas unstressed animals exhibited normal metabolic profiles, low- and high-dose streptozotocin-treated PTPN2-βKO mice displayed hyperglycemia and accelerated death, respectively. Furthermore, cytokine-treated Ptpn2-KO islets resulted in impaired glucose-stimulated insulin secretion, mitochondrial defects, and reduced glucose-induced metabolic flux, suggesting β-cells lacking Ptpn2 are more susceptible to inflammatory stress associated with T1D due to maladaptive metabolic fitness. Consistent with the phenotype, proteomic analysis identified an important metabolic enzyme, ATP-citrate lyase, as a novel PTPN2 substrate. ARTICLE HIGHLIGHTS
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Affiliation(s)
- Yong Kyung Kim
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Youngjung Rachel Kim
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Kristen L. Wells
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Dylan Sarbaugh
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Michelle Guney
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Tiffany Zee
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Gerard Karsenty
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
| | - Ernesto S. Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA
| | - Lori Sussel
- Barbara Davis Center for Diabetes, University of Colorado Denver Anschutz Medical Campus, Aurora, CO
- Department of Genetics and Development, Columbia University Irving Medical Campus, New York, NY
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9
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Figueroa-Navedo AM, Ivanov AR. Experimental and data analysis advances in thermal proteome profiling. CELL REPORTS METHODS 2024; 4:100717. [PMID: 38412830 PMCID: PMC10921035 DOI: 10.1016/j.crmeth.2024.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.
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Affiliation(s)
- Amanda M Figueroa-Navedo
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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10
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [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] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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11
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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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12
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024; 2823:193-223. [PMID: 39052222 DOI: 10.1007/978-1-0716-3922-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).
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Affiliation(s)
| | | | | | - Bin Fang
- H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - John M Koomen
- H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Molecular Oncology/Pathology, Moffitt Cancer Center, Tampa, FL, USA.
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13
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Tsai CF, Hsu CC, Wang YT, Kim H, Liu T. A Tip-Based Workflow for Sensitive IMAC-Based Low Nanogram Level Phosphoproteomics. Methods Mol Biol 2024; 2823:129-140. [PMID: 39052218 DOI: 10.1007/978-1-0716-3922-1_9] [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] [Indexed: 07/27/2024]
Abstract
Analyzing the phosphoproteome at nanoscale poses a significant challenge, mainly due to the substantial sample loss from nonspecific surface adsorption during the enrichment of low stoichiometric phosphopeptides. Here, we describe a tandem tip-based phosphoproteomics sample preparation method capable of sequential sample cleanup and enrichment without the need for additional sample transfer, thereby minimizing sample loss. Integration of this method to our recently developed SOP (surfactant-assisted one-pot sample preparation) and iBASIL (improved boosting to amplify signal with isobaric labeling) approaches creates a streamlined workflow, enabling sensitive, high-throughput nanoscale phosphoproteomics measurements.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hyeyoon Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA.
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14
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Sarkar S, Syed F, Webb-Robertson BJ, Melchior JT, Chang G, Gritsenko M, Wang YT, Tsai CF, Liu J, Yi X, Cui Y, Eizirik DL, Metz TO, Rewers M, Evans-Molina C, Mirmira RG, Nakayasu ES. Protection of β cells against pro-inflammatory cytokine stress by the GDF15-ERBB2 signaling. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.27.23298904. [PMID: 38076918 PMCID: PMC10705646 DOI: 10.1101/2023.11.27.23298904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/13/2024]
Abstract
Aim/hypothesis Growth/differentiation factor 15 (GDF15) is a therapeutic target for a variety of metabolic diseases, including type 1 diabetes (T1D). However, the nausea caused by GDF15 is a challenging point for therapeutic development. In addition, it is unknown why the endogenous GDF15 fails to protect from T1D development. Here, we investigate the GDF15 signaling in pancreatic islets towards opening possibilities for therapeutic targeting in β cells and to understand why this protection fails to occur naturally. Methods GDF15 signaling in islets was determined by proximity-ligation assay, untargeted proteomics, pathway analysis, and treatment of cells with specific inhibitors. To determine if GDF15 levels would increase prior to disease onset, plasma levels of GDF15 were measured in a longitudinal prospective study of children during T1D development (n=132 cases vs. n=40 controls) and in children with islet autoimmunity but normoglycemia (n=47 cases vs. n=40 controls) using targeted mass spectrometry. We also investigated the regulation of GDF15 production in islets by fluorescence microscopy and western blot analysis. Results The proximity-ligation assay identified ERBB2 as the GDF15 receptor in islets, which was confirmed using its specific antagonist, tucatinib. The untargeted proteomics analysis and caspase assay showed that ERBB2 activation by GDF15 reduces β cell apoptosis by downregulating caspase 8. In plasma, GDF15 levels were higher (p=0.0024) during T1D development compared to controls, but not in islet autoimmunity with normoglycemia. However, in the pancreatic islets GDF15 was depleted via sequestration of its mRNA into stress granules, resulting in translation halting. Conclusions/interpretation GDF15 protects against T1D via ERBB2-mediated decrease of caspase 8 expression in pancreatic islets. Circulating levels of GDF15 increases pre-T1D onset, which is insufficient to promote protection due to its localized depletion in the islets. These findings open opportunities for targeting GDF15 downstream signaling for pancreatic β cell protection in T1D and help to explain the lack of natural protection by the endogenous protein.
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15
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Ahmad R, Budnik B. A review of the current state of single-cell proteomics and future perspective. Anal Bioanal Chem 2023; 415:6889-6899. [PMID: 37285026 PMCID: PMC10632274 DOI: 10.1007/s00216-023-04759-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 06/08/2023]
Abstract
Single-cell methodologies and technologies have started a revolution in biology which until recently has primarily been limited to deep sequencing and imaging modalities. With the advent and subsequent torrid development of single-cell proteomics over the last 5 years, despite the fact that proteins cannot be amplified like transcripts, it has now become abundantly clear that it is a worthy complement to single-cell transcriptomics. In this review, we engage in an assessment of the current state of the art of single-cell proteomics including workflow, sample preparation techniques, instrumentation, and biological applications. We investigate the challenges associated with working with very small sample volumes and the acute need for robust statistical methods for data interpretation. We delve into what we believe is a promising future for biological research at single-cell resolution and highlight some of the exciting discoveries that already have been made using single-cell proteomics, including the identification of rare cell types, characterization of cellular heterogeneity, and investigation of signaling pathways and disease mechanisms. Finally, we acknowledge that there are a number of outstanding and pressing problems that the scientific community vested in advancing this technology needs to resolve. Of prime importance is the need to set standards so that this technology becomes widely accessible allowing novel discoveries to be easily verifiable. We conclude with a plea to solve these problems rapidly so that single-cell proteomics can be part of a robust, high-throughput, and scalable single-cell multi-omics platform that can be ubiquitously applied to elucidating deep biological insights into the diagnosis and treatment of all diseases that afflict us.
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Affiliation(s)
- Rushdy Ahmad
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA
| | - Bogdan Budnik
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan Circle, Boston, MA, 02115, USA.
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16
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Bowser BL, Patterson KL, Robinson RA. Evaluating cPILOT Data toward Quality Control Implementation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2023; 34:1741-1752. [PMID: 37459602 DOI: 10.1021/jasms.3c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/03/2023]
Abstract
Multiplexing enables the monitoring of hundreds to thousands of proteins in quantitative proteomics analyses and increases sample throughput. In most mass-spectrometry-based proteomics workflows, multiplexing is achieved by labeling biological samples with heavy isotopes via precursor isotopic labeling or isobaric tagging. Enhanced multiplexing strategies, such as combined precursor isotopic labeling and isobaric tagging (cPILOT), combine multiple technologies to afford an even higher sample throughput. Critical to enhanced multiplexing analyses is ensuring that analytical performance is optimal and that missingness of sample channels is minimized. Automation of sample preparation steps and use of quality control (QC) metrics can be incorporated into multiplexing analyses and reduce the likelihood of missing information, thus maximizing the amount of usable quantitative data. Here, we implemented QC metrics previously developed in our laboratory to evaluate a 36-plex cPILOT experiment that encompassed 144 mouse samples of various tissue types, time points, genotypes, and biological replicates. The evaluation focuses on the use of a sample pool generated from all samples in the experiment to monitor the daily instrument performance and to provide a means for data normalization across sample batches. Our results show that tracking QC metrics enabled the quantification of ∼7000 proteins in each sample batch, of which ∼70% had minimal missing values across up to 36 sample channels. Implementation of QC metrics for future cPILOT studies as well as other enhanced multiplexing strategies will help yield high-quality data sets.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Khiry L Patterson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã As Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Memory & Alzheimer's Center, Nashville, Tennessee 37212, United States
- Vanderbilt Institute of Chemical Biology, Nashville, Tennessee 37232, United States
- Vanderbilt Brain Institute, Nashville, Tennessee 37232, United States
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17
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Kong L, Li F, Fang W, Du Z, Wang G, Zhang Y, Ge WP, Zhang W, Qin W. Sensitive N-Glycopeptide Profiling of Single and Rare Cells Using an Isobaric Labeling Strategy without Enrichment. Anal Chem 2023; 95:11326-11334. [PMID: 37409763 DOI: 10.1021/acs.analchem.3c01392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
Single-cell omics is critical in revealing population heterogeneity, discovering unique features of individual cells, and identifying minority subpopulations of interest. As one of the major post-translational modifications, protein N-glycosylation plays crucial roles in various important biological processes. Elucidation of the variation in N-glycosylation patterns at single-cell resolution may largely facilitate the understanding of their key roles in the tumor microenvironment and immune therapy. However, comprehensive N-glycoproteome profiling for single cells has not been achieved due to the extremely limited sample amount and incompatibility with the available enrichment strategies. Here, we have developed an isobaric labeling-based carrier strategy for highly sensitive intact N-glycopeptide profiling for single cells or a small number of rare cells without enrichment. Isobaric labeling has unique multiplexing properties, by which the "total" signal from all channels triggers MS/MS fragmentation for N-glycopeptide identification, while the reporter ions provide quantitative information. In our strategy, a carrier channel using N-glycopeptides obtained from bulk-cell samples significantly improved the "total" signal of N-glycopeptides and, therefore, promoted the first quantitative analysis of averagely 260 N-glycopeptides from single HeLa cells. We further applied this strategy to study the regional heterogeneity of N-glycosylation of microglia in mouse brain and discovered region-specific N-glycoproteome patterns and cell subtypes. In conclusion, the glycocarrier strategy provides an attractive solution for sensitive and quantitative N-glycopeptide profiling of single/rare cells that cannot be enriched by traditional workflows.
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Affiliation(s)
- Linlin Kong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Fengzhi Li
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Wei Fang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Zhuokun Du
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Guibin Wang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yangjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, Beijing 102206, China
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
- College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
- College of Chemistry and Materials Science, Hebei University, Baoding 071002, China
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18
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Mun DG, Bhat FA, Ding H, Madden BJ, Natesampillai S, Badley AD, Johnson KL, Kelly RT, Pandey A. Optimizing single cell proteomics using trapped ion mobility spectrometry for label-free experiments. Analyst 2023; 148:3466-3475. [PMID: 37395315 PMCID: PMC10370902 DOI: 10.1039/d3an00080j] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/10/2023] [Indexed: 07/04/2023]
Abstract
Although single cell RNA-seq has had a tremendous impact on biological research, a corresponding technology for unbiased mass spectrometric analysis of single cells has only recently become available. Significant technological breakthroughs including miniaturized sample handling have enabled proteome profiling of single cells. Furthermore, trapped ion mobility spectrometry (TIMS) in combination with parallel accumulation-serial fragmentation operated in data-dependent acquisition mode (DDA-PASEF) allowed improved proteome coverage from low-input samples. It has been demonstrated that modulating the ion flux in TIMS affects the overall performance of proteome profiling. However, the effect of TIMS settings on the analysis of low-input samples has been less investigated. Thus, we sought to optimize the conditions of TIMS with regard to ion accumulation/ramp times and ion mobility range for low-input samples. We observed that an ion accumulation time of 180 ms and monitoring a narrower ion mobility range from 0.7 to 1.3 V s cm-2 resulted in a substantial gain in the depth of proteome coverage and in detecting proteins with low abundance. We used these optimized conditions for proteome profiling of sorted human primary T cells, which yielded an average of 365, 804, 1116, and 1651 proteins from single, five, ten, and forty T cells, respectively. Notably, we demonstrated that the depth of proteome coverage from a low number of cells was sufficient to delineate several essential metabolic pathways and the T cell receptor signaling pathway. Finally, we showed the feasibility of detecting post-translational modifications including phosphorylation and acetylation from single cells. We believe that such an approach could be applied to label-free analysis of single cells obtained from clinically relevant samples.
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Affiliation(s)
- Dong-Gi Mun
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Firdous A Bhat
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | - Husheng Ding
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
| | | | | | - Andrew D Badley
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First ST SW, Rochester, MN 55905, USA.
- Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
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19
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Kim JH, Afridi R, Lee WH, Suk K. Analyzing the glial proteome in Alzheimer's disease. Expert Rev Proteomics 2023; 20:197-209. [PMID: 37724426 DOI: 10.1080/14789450.2023.2260955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/18/2023] [Indexed: 09/20/2023]
Abstract
INTRODUCTION Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive cognitive decline, memory loss, and changes in behavior. Accumulating evidence indicates that dysfunction of glial cells, including astrocytes, microglia, and oligodendrocytes, may contribute to the development and progression of AD. Large-scale analysis of glial proteins sheds light on their roles in cellular processes and diseases. In AD, glial proteomics has been utilized to understand glia-based pathophysiology and identify potential biomarkers and therapeutic targets. AREA COVERED In this review, we provide an updated overview of proteomic analysis of glia in the context of AD. Additionally, we discuss current challenges in the field, involving glial complexity and heterogeneity, and describe some cutting-edge proteomic technologies to address them. EXPERT OPINION Unbiased comprehensive analysis of glial proteomes aids our understanding of the molecular and cellular mechanisms of AD pathogenesis. These investigations highlight the crucial role of glial cells and provide novel insights into the mechanisms of AD pathology. A deeper understanding of the AD-related glial proteome could offer a repertoire of potential biomarkers and therapeutics. Further technical advancement of glial proteomics will enable us to identify proteins within individual cells and specific cell types, thus significantly enhancing our comprehension of AD pathogenesis.
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Affiliation(s)
- Jong-Heon Kim
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
| | - Ruqayya Afridi
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Won-Ha Lee
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, Republic of Korea
| | - Kyoungho Suk
- Brain Science & Engineering Institute, Kyungpook National University, Daegu, Republic of Korea
- Department of Pharmacology, BK21 Plus KNU Biomedical Convergence Program, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
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20
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Matzinger M, Mayer RL, Mechtler K. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing. Proteomics 2023; 23:e2200162. [PMID: 36806919 PMCID: PMC10909491 DOI: 10.1002/pmic.202200162] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/21/2023]
Abstract
The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field.
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Affiliation(s)
- Manuel Matzinger
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Rupert L. Mayer
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP)Vienna BioCenterViennaAustria
- Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
- Institute of Molecular Biotechnology (IMBA), Austrian Academy of SciencesVienna BioCenter (VBC)ViennaAustria
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21
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Bowser BL, Robinson RAS. Enhanced Multiplexing Technology for Proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:379-400. [PMID: 36854207 DOI: 10.1146/annurev-anchem-091622-092353] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The identification of thousands of proteins and their relative levels of expression has furthered understanding of biological processes and disease and stimulated new systems biology hypotheses. Quantitative proteomics workflows that rely on analytical assays such as mass spectrometry have facilitated high-throughput measurements of proteins partially due to multiplexing. Multiplexing allows proteome differences across multiple samples to be measured simultaneously, resulting in more accurate quantitation, increased statistical robustness, reduced analysis times, and lower experimental costs. The number of samples that can be multiplexed has evolved from as few as two to more than 50, with studies involving more than 10 samples being denoted as enhanced multiplexing or hyperplexing. In this review, we give an update on emerging multiplexing proteomics techniques and highlight advantages and limitations for enhanced multiplexing strategies.
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Affiliation(s)
- Bailey L Bowser
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
| | - Renã A S Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee, USA;
- Department of Neurology, Vanderbilt University Medical Center, Vanderbilt University, Nashville, Tennessee, USA
- Vanderbilt Memory and Alzheimer's Center, Nashville, Tennessee, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Brain Institute, Vanderbilt School of Medicine, Nashville, Tennessee, USA
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22
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Yin K, Tong M, Suttapitugsakul S, Xu S, Wu R. Global quantification of newly synthesized proteins reveals cell type- and inhibitor-specific effects on protein synthesis inhibition. PNAS NEXUS 2023; 2:pgad168. [PMID: 37275259 PMCID: PMC10235912 DOI: 10.1093/pnasnexus/pgad168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/15/2023] [Indexed: 06/07/2023]
Abstract
Manipulation of protein synthesis is commonly applied to uncover protein functions and cellular activities. Multiple inhibitors with distinct mechanisms have been widely investigated and employed in bio-related research, but it is extraordinarily challenging to measure and evaluate the synthesis inhibition efficiencies of individual proteins by different inhibitors at the proteome level. Newly synthesized proteins are the immediate and direct products of protein synthesis, and thus their comprehensive quantification provides a unique opportunity to study protein inhibition. Here, we systematically investigate protein inhibition and evaluate different popular inhibitors, i.e. cycloheximide, puromycin, and anisomycin, through global quantification of newly synthesized proteins in several types of human cells (A549, MCF-7, Jurkat, and THP-1 cells). The inhibition efficiencies of protein synthesis are comprehensively measured by integrating azidohomoalanine-based protein labeling, selective enrichment, a boosting approach, and multiplexed proteomics. The same inhibitor results in dramatic variation of the synthesis inhibition efficiencies for different proteins in the same cells, and each inhibitor exhibits unique preferences. Besides cell type- and inhibitor-specific effects, some universal rules are unraveled. For instance, nucleolar and ribosomal proteins have relatively higher inhibition efficiencies in every type of cells treated with each inhibitor. Moreover, proteins intrinsically resistant or sensitive to the inhibition are identified and found to have distinct functions. Systematic investigation of protein synthesis inhibition in several types of human cells by different inhibitors provides valuable information about the inhibition of protein synthesis, advancing our understanding of inhibiting protein synthesis.
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Affiliation(s)
| | | | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronghu Wu
- To whom correspondence should be addressed:
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23
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Phaneuf CG, Aizikov K, Grinfeld D, Kreutzmann A, Mourad D, Lange O, Dai D, Zhang B, Belenky A, Makarov AA, Ivanov AR. Experimental strategies to improve drug-target identification in mass spectrometry-based thermal stability assays. Commun Chem 2023; 6:64. [PMID: 37024568 PMCID: PMC10079678 DOI: 10.1038/s42004-023-00861-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Mass spectrometry (MS)-based thermal stability assays have recently emerged as one of the most promising solutions for the identification of protein-ligand interactions. Here, we have investigated eight combinations of several recently introduced MS-based advancements, including the Phase-Constrained Spectral Deconvolution Method, Field Asymmetric Ion Mobility Spectrometry, and the implementation of a carrier sample as improved MS-based acquisition approaches for thermal stability assays (iMAATSA). We used intact Jurkat cells treated with a commercially available MEK inhibitor, followed by heat treatment, to prepare a set of unfractionated isobarically-labeled proof-of-concept samples to compare the performance of eight different iMAATSAs. Finally, the best-performing iMAATSA was compared to a conventional approach and evaluated in a fractionation experiment. Improvements of up to 82% and 86% were demonstrated in protein identifications and high-quality melting curves, respectively, over the conventional approach in the proof-of-concept study, while an approximately 12% improvement in melting curve comparisons was achieved in the fractionation experiment.
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Affiliation(s)
- Clifford G Phaneuf
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | | | | | | | - Daniel Dai
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | - Bailin Zhang
- Sanofi, Disease Profiling and Functional Genomics, Cambridge, MA, USA
| | | | | | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.
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24
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Abelin JG, Bergstrom EJ, Rivera KD, Taylor HB, Klaeger S, Xu C, Verzani EK, Jackson White C, Woldemichael HB, Virshup M, Olive ME, Maynard M, Vartany SA, Allen JD, Phulphagar K, Harry Kane M, Rachimi S, Mani DR, Gillette MA, Satpathy S, Clauser KR, Udeshi ND, Carr SA. Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues. Nat Commun 2023; 14:1851. [PMID: 37012232 PMCID: PMC10070353 DOI: 10.1038/s41467-023-37547-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Serial multi-omic analysis of proteome, phosphoproteome, and acetylome provides insights into changes in protein expression, cell signaling, cross-talk and epigenetic pathways involved in disease pathology and treatment. However, ubiquitylome and HLA peptidome data collection used to understand protein degradation and antigen presentation have not together been serialized, and instead require separate samples for parallel processing using distinct protocols. Here we present MONTE, a highly sensitive multi-omic native tissue enrichment workflow, that enables serial, deep-scale analysis of HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome from the same tissue sample. We demonstrate that the depth of coverage and quantitative precision of each 'ome is not compromised by serialization, and the addition of HLA immunopeptidomics enables the identification of peptides derived from cancer/testis antigens and patient specific neoantigens. We evaluate the technical feasibility of the MONTE workflow using a small cohort of patient lung adenocarcinoma tumors.
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Affiliation(s)
- Jennifer G Abelin
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Erik J Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Keith D Rivera
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hannah B Taylor
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Susan Klaeger
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Charles Xu
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Eva K Verzani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - C Jackson White
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Hilina B Woldemichael
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Maya Virshup
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Meagan E Olive
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Myranda Maynard
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Stephanie A Vartany
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Joseph D Allen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Kshiti Phulphagar
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - M Harry Kane
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Suzanna Rachimi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
- Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Karl R Clauser
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA
| | - Namrata D Udeshi
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, 02142, USA.
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25
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Black HH, Hanson JL, Roberts JE, Leslie SN, Campodonico W, Ebmeier CC, Holling GA, Tay JW, Matthews AM, Ung E, Lau CI, Whiteley AM. UBQLN2 restrains the domesticated retrotransposon PEG10 to maintain neuronal health in ALS. eLife 2023; 12:e79452. [PMID: 36951542 PMCID: PMC10076021 DOI: 10.7554/elife.79452] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 03/15/2023] [Indexed: 03/24/2023] Open
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive motor neuron dysfunction and loss. A portion of ALS cases are caused by mutation of the proteasome shuttle factor Ubiquilin 2 (UBQLN2), but the molecular pathway leading from UBQLN2 dysfunction to disease remains unclear. Here, we demonstrate that UBQLN2 regulates the domesticated gag-pol retrotransposon 'paternally expressed gene 10 (PEG10)' in human cells and tissues. In cells, the PEG10 gag-pol protein cleaves itself in a mechanism reminiscent of retrotransposon self-processing to generate a liberated 'nucleocapsid' fragment, which uniquely localizes to the nucleus and changes the expression of genes involved in axon remodeling. In spinal cord tissue from ALS patients, PEG10 gag-pol is elevated compared to healthy controls. These findings implicate the retrotransposon-like activity of PEG10 as a contributing mechanism in ALS through the regulation of gene expression, and restraint of PEG10 as a primary function of UBQLN2.
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Affiliation(s)
- Holly H Black
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jessica L Hanson
- Institute for Behavioral Genetics, University of Colorado BoulderBoulderUnited States
| | - Julia E Roberts
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Shannon N Leslie
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Will Campodonico
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | | | - G Aaron Holling
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Jian Wei Tay
- Biofrontiers Institute, University of Colorado BoulderBoulderUnited States
| | - Autumn M Matthews
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Elizabeth Ung
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
| | - Cristina I Lau
- Department of Biochemistry, University of Colorado BoulderBoulderUnited States
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26
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Veličković M, Fillmore TL, Attah K, Posso C, Pino JC, Zhao R, Williams SM, Veličković D, Jacobs JM, Burnum-Johnson KE, Zhu Y, Piehowski PD. Coupling microdroplet-based sample preparation, multiplexed isobaric labeling, and nanoflow peptide fractionation for deep proteome profiling of tissue microenvironment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.13.531822. [PMID: 36993277 PMCID: PMC10055005 DOI: 10.1101/2023.03.13.531822] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
There is increasing interest in developing in-depth proteomic approaches for mapping tissue heterogeneity at a cell-type-specific level to better understand and predict the function of complex biological systems, such as human organs. Existing spatially resolved proteomics technologies cannot provide deep proteome coverages due to limited sensitivity and poor sample recovery. Herein, we seamlessly combined laser capture microdissection with a low-volume sample processing technology that includes a microfluidic device named microPOTS (Microdroplet Processing in One pot for Trace Samples), the multiplexed isobaric labelling, and a nanoflow peptide fractionation approach. The integrated workflow allowed to maximize proteome coverage of laser-isolated tissue samples containing nanogram proteins. We demonstrated the deep spatial proteomics can quantify more than 5,000 unique proteins from a small-sized human pancreatic tissue pixel (∼60,000 µm2) and reveal unique islet microenvironments.
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27
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Xu S, Yin K, Wu R. Combining Selective Enrichment and a Boosting Approach to Globally and Site-Specifically Characterize Protein Co-translational O-GlcNAcylation. Anal Chem 2023; 95:4371-4380. [PMID: 36802545 PMCID: PMC9996615 DOI: 10.1021/acs.analchem.2c04779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Protein O-GlcNAcylation plays extremely important roles in mammalian cells, regulating signal transduction and gene expression. This modification can happen during protein translation, and systematic and site-specific analysis of protein co-translational O-GlcNAcylation can advance our understanding of this important modification. However, it is extraordinarily challenging because normally O-GlcNAcylated proteins are very low abundant and the abundances of co-translational ones are even much lower. Here, we developed a method integrating selective enrichment, a boosting approach, and multiplexed proteomics to globally and site-specifically characterize protein co-translational O-GlcNAcylation. The boosting approach using the TMT labeling dramatically enhances the detection of co-translational glycopeptides with low abundance when enriched O-GlcNAcylated peptides from cells with a much longer labeling time was used as a boosting sample. More than 180 co-translational O-GlcNAcylated proteins were site-specifically identified. Further analyses revealed that among co-translational glycoproteins, those related to DNA binding and transcription are highly overrepresented using the total identified O-GlcNAcylated proteins in the same cells as the background. Compared with the glycosylation sites on all glycoproteins, co-translational sites have different local structures and adjacent amino acid residues. Overall, an integrative method was developed to identify protein co-translational O-GlcNAcylation, which is very useful to advance our understanding of this important modification.
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Affiliation(s)
- Senhan Xu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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28
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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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29
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Tsai CF, Wang YT, Hsu CC, Kitata RB, Chu RK, Velickovic M, Zhao R, Williams SM, Chrisler WB, Jorgensen ML, Moore RJ, Zhu Y, Rodland KD, Smith RD, Wasserfall CH, Shi T, Liu T. A streamlined tandem tip-based workflow for sensitive nanoscale phosphoproteomics. Commun Biol 2023; 6:70. [PMID: 36653408 PMCID: PMC9849344 DOI: 10.1038/s42003-022-04400-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 12/23/2022] [Indexed: 01/19/2023] Open
Abstract
Effective phosphoproteome of nanoscale sample analysis remains a daunting task, primarily due to significant sample loss associated with non-specific surface adsorption during enrichment of low stoichiometric phosphopeptide. We develop a tandem tip phosphoproteomics sample preparation method that is capable of sample cleanup and enrichment without additional sample transfer, and its integration with our recently developed SOP (Surfactant-assisted One-Pot sample preparation) and iBASIL (improved Boosting to Amplify Signal with Isobaric Labeling) approaches provides a streamlined workflow enabling sensitive, high-throughput nanoscale phosphoproteome measurements. This approach significantly reduces both sample loss and processing time, allowing the identification of >3000 (>9500) phosphopeptides from 1 (10) µg of cell lysate using the label-free method without a spectral library. It also enables precise quantification of ~600 phosphopeptides from 100 sorted cells (single-cell level input for the enriched phosphopeptides) and ~700 phosphopeptides from human spleen tissue voxels with a spatial resolution of 200 µm (equivalent to ~100 cells) in a high-throughput manner. The new workflow opens avenues for phosphoproteome profiling of mass-limited samples at the low nanogram level.
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Affiliation(s)
- Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Yi-Ting Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Chuan-Chih Hsu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Reta Birhanu Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rosalie K Chu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marija Velickovic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sarah M Williams
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Marda L Jorgensen
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Clive H Wasserfall
- Department of Pathology, Immunology, and Laboratory Medicine, Diabetes Institute, College of Medicine, University of Florida, Gainesville, FL, 32611, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
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30
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Ogata K, Takagi S, Sugiyama N, Ishihama Y. Motif-Targeting Phosphoproteome Analysis of Cancer Cells for Profiling Kinase Inhibitors. Cancers (Basel) 2022; 15:cancers15010078. [PMID: 36612075 PMCID: PMC9817674 DOI: 10.3390/cancers15010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
We present a motif-targeting phosphoproteome analysis workflow utilizing in vitro kinase reaction to enrich a subset of peptides with specific primary sequence motifs. Phosphopeptides are enriched and dephosphorylated with alkaline phosphatase, followed by in vitro kinase reaction to phosphorylate substrate peptides with specific primary-sequence motifs. These phosphopeptides are enriched again, TMT-labeled, dephosphorylated to enhance MS-detectability, and analyzed by LC/MS/MS. We applied this approach to inhibitor-treated cancer cells, and successfully profiled the inhibitory spectra of multiple kinase inhibitors. We anticipate this approach will be applicable to target specific subsets of the phosphoproteome using the wide variety of available recombinant protein kinases.
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31
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Le Sueur C, Hammarén HM, Sridharan S, Savitski MM. Thermal proteome profiling: Insights into protein modifications, associations, and functions. Curr Opin Chem Biol 2022; 71:102225. [PMID: 36368297 DOI: 10.1016/j.cbpa.2022.102225] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022]
Abstract
Tracking proteins' biophysical characteristics on a proteome-wide scale can provide valuable information on their functions and interactions. Thermal proteome profiling (TPP) is a multiplexed quantitative proteomics approach that measures changes in protein thermal stability-a key biophysical property-across different cellular states. Developed in 2014, as a target-deconvolution assay for drugs and other small molecules, TPP has since evolved to a system-level biochemical omics technique providing insights into context-dependent changes in protein states. In this review, we summarise key advances in the experimental and data analysis pipeline that have aided this transformation and discuss the recent developments and applications of TPP.
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Affiliation(s)
- Cecile Le Sueur
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Henrik M Hammarén
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Barts Brain Tumour Center, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
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32
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Day NJ, Zhang T, Gaffrey MJ, Zhao R, Fillmore TL, Moore RJ, Rodney GG, Qian WJ. A deep redox proteome profiling workflow and its application to skeletal muscle of a Duchenne Muscular Dystrophy model. Free Radic Biol Med 2022; 193:373-384. [PMID: 36306991 PMCID: PMC10072164 DOI: 10.1016/j.freeradbiomed.2022.10.300] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/06/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022]
Abstract
Perturbation to the redox state accompanies many diseases and its effects are viewed through oxidation of biomolecules, including proteins, lipids, and nucleic acids. The thiol groups of protein cysteine residues undergo an array of redox post-translational modifications (PTMs) that are important for regulation of protein and pathway function. To better understand what proteins are redox regulated following a perturbation, it is important to be able to comprehensively profile protein thiol oxidation at the proteome level. Herein, we report a deep redox proteome profiling workflow and demonstrate its application in measuring the changes in thiol oxidation along with global protein expression in skeletal muscle from mdx mice, a model of Duchenne Muscular Dystrophy (DMD). In-depth coverage of the thiol proteome was achieved with >18,000 Cys sites from 5,608 proteins in muscle being quantified. Compared to the control group, mdx mice exhibit markedly increased thiol oxidation, where a ∼2% shift in the median oxidation occupancy was observed. Pathway analysis for the redox data revealed that coagulation system and immune-related pathways were among the most susceptible to increased thiol oxidation in mdx mice, whereas protein abundance changes were more enriched in pathways associated with bioenergetics. This study illustrates the importance of deep redox profiling in gaining greater insight into oxidative stress regulation and pathways/processes that are perturbed in an oxidizing environment.
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Affiliation(s)
- Nicholas J Day
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Matthew J Gaffrey
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Rui Zhao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Thomas L Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - George G Rodney
- Department of Integrative Physiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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33
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Materials, workflows and applications of IMAC for phosphoproteome profiling in the recent decade: A review. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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34
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Cupp-Sutton KA, Fang M, Wu S. Separation methods in single-cell proteomics: RPLC or CE? INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2022; 481:116920. [PMID: 36211475 PMCID: PMC9542495 DOI: 10.1016/j.ijms.2022.116920] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Cellular heterogeneity is commonly investigated using single-cell genomics and transcriptomics to investigate biological questions such as disease mechanism, therapeutic screening, and genomic and transcriptomic diversity between cellular populations and subpopulations at the cellular level. Single-cell mass spectrometry (MS)-based proteomics enables the high-throughput examination of protein expression at the single-cell level with wide applicability, and with spatial and temporal resolution, applicable to the study of cellular development, disease, effect of treatment, etc. The study of single-cell proteomics has lagged behind genomics and transcriptomics largely because proteins from single-cell samples cannot be amplified as DNA and RNA can using well established techniques such as PCR. Therefore, analytical methods must be robust, reproducible, and sensitive enough to detect the very small amount of protein within a single cell. To this end, nearly every step of the proteomics process has been extensively altered and improved to facilitate the proteomics analysis of single cells including cell counting and sorting, lysis, protein digestion, sample cleanup, separation, MS data acquisition, and data analysis. Here, we have reviewed recent advances in single-cell protein separation using nano reversed phase liquid chromatography (nRPLC) and capillary electrophoresis (CE) to inform application driven selection of separation techniques in the laboratory setting.
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Affiliation(s)
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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35
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Sivanich MK, Gu T, Tabang DN, Li L. Recent advances in isobaric labeling and applications in quantitative proteomics. Proteomics 2022; 22:e2100256. [PMID: 35687565 PMCID: PMC9787039 DOI: 10.1002/pmic.202100256] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 05/21/2022] [Accepted: 06/07/2022] [Indexed: 12/30/2022]
Abstract
Mass spectrometry (MS) has emerged at the forefront of quantitative proteomic techniques. Liquid chromatography-mass spectrometry (LC-MS) can be used to determine abundances of proteins and peptides in complex biological samples. Several methods have been developed and adapted for accurate quantification based on chemical isotopic labeling. Among various chemical isotopic labeling techniques, isobaric tagging approaches rely on the analysis of peptides from MS2-based quantification rather than MS1-based quantification. In this review, we will provide an overview of several isobaric tags along with some recent developments including complementary ion tags, improvements in sensitive quantitation of analytes with lower abundance, strategies to increase multiplexing capabilities, and targeted analysis strategies. We will also discuss limitations of isobaric tags and approaches to alleviate these restrictions through bioinformatic tools and data acquisition methods. This review will highlight several applications of isobaric tags, including biomarker discovery and validation, thermal proteome profiling, cross-linking for structural investigations, single-cell analysis, top-down proteomics, along with applications to different molecules including neuropeptides, glycans, metabolites, and lipids, while providing considerations and evaluations to each application.
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Affiliation(s)
| | - Ting‐Jia Gu
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
| | | | - Lingjun Li
- Department of ChemistryUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
- School of PharmacyUniversity of Wisconsin‐MadisonMadisonWisconsinUSA
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36
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Yin K, Tong M, Sun F, Wu R. Quantitative Structural Proteomics Unveils the Conformational Changes of Proteins under the Endoplasmic Reticulum Stress. Anal Chem 2022; 94:13250-13260. [PMID: 36108266 PMCID: PMC9789690 DOI: 10.1021/acs.analchem.2c03076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Protein structures are decisive for their activities and interactions with other molecules. Global analysis of protein structures and conformational changes cannot be achieved by commonly used abundance-based proteomics. Here, we integrated cysteine covalent labeling, selective enrichment, and quantitative proteomics to study protein structures and structural changes on a large scale. This method was applied to globally investigate protein structures in HEK293T cells and protein structural changes in the cells with the tunicamycin (Tm)-induced endoplasmic reticulum (ER) stress. We quantified several thousand cysteine residues, which contain unprecedented and valuable information of protein structures. Combining this method with pulsed stable isotope labeling by amino acids in cell culture, we further analyzed the folding state differences between pre-existing and newly synthesized proteins in cells under the Tm treatment. Besides newly synthesized proteins, unexpectedly, many pre-existing proteins were found to become unfolded upon ER stress, especially those related to gene transcription and protein translation. Furthermore, the current results reveal that N-glycosylation plays a more important role in the folding process of the tertiary and quaternary structures than the secondary structures for newly synthesized proteins. Considering the importance of cysteine in protein structures, this method can be extensively applied in the biological and biomedical research fields.
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Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ming Tong
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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37
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Wang D, Ma M, Huang J, Gu TJ, Cui Y, Li M, Wang Z, Zetterberg H, Li L. Boost-DiLeu: Enhanced Isobaric N, N-Dimethyl Leucine Tagging Strategy for a Comprehensive Quantitative Glycoproteomic Analysis. Anal Chem 2022; 94:11773-11782. [PMID: 35960654 PMCID: PMC9966376 DOI: 10.1021/acs.analchem.2c01773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Intact glycopeptide analysis has been of great interest because it can elucidate glycosylation site information and glycan structural composition at the same time. However, mass spectrometry (MS)-based glycoproteomic analysis is hindered by the low abundance and poor ionization efficiency of glycopeptides. Relatively large amounts of starting materials are needed for the enrichment, which makes the identification and quantification of intact glycopeptides from samples with limited quantity more challenging. To overcome these limitations, we developed an improved isobaric labeling strategy with an additional boosting channel to enhance N,N-dimethyl leucine (DiLeu) tagging-based quantitative glycoproteomic analysis, termed as Boost-DiLeu. With the integration of a one-tube sample processing workflow and high-pH fractionation, 3514 quantifiable N-glycopeptides were identified from 30 μg HeLa cell tryptic digests with reliable quantification performance. Furthermore, this strategy was applied to human cerebrospinal fluid (CSF) samples to differentiate N-glycosylation profiles between Alzheimer's disease (AD) patients and non-AD donors. The results revealed processes and pathways affected by dysregulated N-glycosylation in AD, including platelet degranulation, cell adhesion, and extracellular matrix, which highlighted the involvement of N-glycosylation aberrations in AD pathogenesis. Moreover, weighted gene coexpression network analysis (WGCNA) showed nine modules of glycopeptides, two of which were associated with the AD phenotype. Our results demonstrated the feasibility of using this strategy for in-depth glycoproteomic analysis of size-limited clinical samples. Taken together, we developed and optimized a strategy for the enhanced comprehensive quantitative intact glycopeptide analysis with DiLeu labeling, showing significant promise for identifying novel therapeutic targets or biomarkers in biological systems with a limited sample quantity.
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Affiliation(s)
- Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Min Ma
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Junfeng Huang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ting-Jia Gu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Yusi Cui
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zicong Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, 43141, Sweden.,Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 43130, Sweden.,Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, U.K.,UK Dementia Research Institute at UCL, London, WC1N 3BG, U.K.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong, China
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.,School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA.,To whom correspondence should be addressed. . Phone: +1-(608)-265- 8491, Fax: +1-(608)-262-5345. Mailing Address: 5125 Rennebohm Hall, 777 Highland Avenue, Madison, WI 53705, USA
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38
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Beck L, Geiger T. MS-based technologies for untargeted single-cell proteomics. Curr Opin Biotechnol 2022; 76:102736. [DOI: 10.1016/j.copbio.2022.102736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/19/2022] [Accepted: 04/24/2022] [Indexed: 11/28/2022]
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39
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Steger M, Karayel Ö, Demichev V. Ubiquitinomics: history, methods and applications in basic research and drug discovery. Proteomics 2022; 22:e2200074. [PMID: 35353442 DOI: 10.1002/pmic.202200074] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/08/2022]
Abstract
The ubiquitin-proteasome system (UPS) was discovered about 40 years ago and is known to regulate a multitude of cellular processes including protein homeostasis. ubiquitylated proteins are recognized by downstream effectors, resulting in alterations of protein abundance, activity, or localization. Not surprisingly, the ubiquitylation machinery is dysregulated in numerous diseases, including cancers and neurodegeneration. Mass spectrometry (MS)-based proteomics has emerged as a transformative technology for characterizing protein ubiquitylation in an unbiased fashion. Here, we provide an overview of the different MS-based approaches for studying protein ubiquitylation. We review various methods for enriching and quantifying ubiquitin modifications at the peptide or protein level, outline MS acquisition and data processing approaches and discuss key challenges. Finally, we examine how MS-based ubiquitinomics can aid both basic biology and drug discovery research. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Martin Steger
- Evotec München GmbH, Martinsried, 82152, Germany.,Present address: Max Planck Institute of Biochemistry, Martinsried, 82152, Germany
| | - Özge Karayel
- Max Planck Institute of Biochemistry, Martinsried, 82152, Germany.,Current address: Department of Physiological Chemistry, Genentech, South San Francisco, CA, 94080, USA
| | - Vadim Demichev
- Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany
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40
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Kwon Y, Lee S, Park N, Ju S, Shin S, Yoo S, Lee H, Lee C. Phosphoproteome Profiling Using an Isobaric Carrier without the Need for Phosphoenrichment. Anal Chem 2022; 94:4192-4200. [PMID: 35239305 DOI: 10.1021/acs.analchem.1c04188] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Phosphorylation is a crucial component of cellular signaling cascades. It controls a variety of biological cellular functions, including cell growth and apoptosis. Owing to the low stoichiometry of phosphorylated proteins, the enrichment of phosphopeptides prior to LC-MS/MS is necessary for comprehensive phosphoproteome analysis, and quantitative phosphoproteomic workflows are typically limited by the amount of sample required. To address this issue, we developed an easy-to-establish, widely applicable, and reproducible strategy to increase phosphoproteomic signals from a small amount of sample without a phosphoenrichment step. By exploiting the multiplexing nature of isobaric labeling to generate a merged signal from multiple samples, and using a larger amount of enriched phosphopeptides as a carrier, we were able to increase trace amounts of phosphopeptides in the unpurified sample to an identifiable level and perform quantification using the reporter ion intensity of the isobaric tag. Our results showed that >1400 phosphopeptides were quantified from 250 ng of tryptic peptides prepared from cells. In a proof-of-concept of our strategy, we distinguished three types of lung cancer cell lines based on their quantitative phosphoproteomic data and identified changes in the phosphoproteome induced by drug treatment.
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Affiliation(s)
- Yumi Kwon
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Seonjeong Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
| | - Narae Park
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Shinyeong Ju
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea
| | - Sungho Shin
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Seongjin Yoo
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Hankyul Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,KHU-KIST Department of Converging Science and Technology, Kyung Hee University, Seoul 02447, Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul 02792, Korea.,Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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41
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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42
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Asleh K, Negri GL, Spencer Miko SE, Colborne S, Hughes CS, Wang XQ, Gao D, Gilks CB, Chia SKL, Nielsen TO, Morin GB. Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes. Nat Commun 2022; 13:896. [PMID: 35173148 PMCID: PMC8850446 DOI: 10.1038/s41467-022-28524-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 01/24/2022] [Indexed: 12/14/2022] Open
Abstract
Despite advances in genomic classification of breast cancer, current clinical tests and treatment decisions are commonly based on protein level information. Formalin-fixed paraffin-embedded (FFPE) tissue specimens with extended clinical outcomes are widely available. Here, we perform comprehensive proteomic profiling of 300 FFPE breast cancer surgical specimens, 75 of each PAM50 subtype, from patients diagnosed in 2008-2013 (n = 178) and 1986-1992 (n = 122) with linked clinical outcomes. These two cohorts are analyzed separately, and we quantify 4214 proteins across all 300 samples. Within the aggressive PAM50-classified basal-like cases, proteomic profiling reveals two groups with one having characteristic immune hot expression features and highly favorable survival. Her2-Enriched cases separate into heterogeneous groups differing by extracellular matrix, lipid metabolism, and immune-response features. Within 88 triple-negative breast cancers, four proteomic clusters display features of basal-immune hot, basal-immune cold, mesenchymal, and luminal with disparate survival outcomes. Our proteomic analysis characterizes the heterogeneity of breast cancer in a clinically-applicable manner, identifies potential biomarkers and therapeutic targets, and provides a resource for clinical breast cancer classification.
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Affiliation(s)
- Karama Asleh
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Interdisciplinary Oncology Program, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Sandra E Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Christopher S Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Xiu Q Wang
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Dongxia Gao
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Division of Anatomical Pathology, Vancouver General Hospital, University of British Columbia, Vancouver, Canada
- Canadian Immunohistochemistry Quality Control, University of British Columbia, Vancouver, BC, Canada
| | - Stephen K L Chia
- Division of Medical Oncology, British Columbia Cancer Centre, University of British Columbia, Vancouver, BC, Canada
| | - Torsten O Nielsen
- Genetic Pathology Evaluation Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
- Division of Anatomical Pathology, Vancouver General Hospital, University of British Columbia, Vancouver, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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43
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Dwivedi P, Rose CM. Understanding the effect of carrier proteomes in single cell proteomic studies - key lessons. Expert Rev Proteomics 2022; 19:5-15. [PMID: 35089822 DOI: 10.1080/14789450.2022.2036126] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Mass spectrometry based single cell proteomics (scMS) is experiencing rapid evolution due to the increased sensitivity of mass spectrometers as well as advances in multiplexing and sample preparation. To date, researchers have focused on two general approaches to scMS: label free and isobaric label based multiplexing. While label free analysis provides straightforward sample preparation and a clear path to automation, it currently lacks the throughput necessary to practically analyze thousands of single cells. Multiplexed analysis utilizing isobaric labels requires additional sample manipulation, but increases throughput such that analyzing thousands of cells is currently achievable. A key feature of multiplexed scMS experiments is a 'carrier proteome' - a sample added at 25x-500x the single cell samples that increases the number of proteins that can be identified in an MS analysis. AREAS COVERED Here, we review early examples of carrier proteomes in quantitative proteomics before summarizing advantages and challenges of using a carrier proteome in scMS experiments. EXPERT OPINION We conclude that the addition of carrier proteomes improves depth of identification for scMS, but high levels of carrier proteomes can have adverse effects on quantitative accuracy and precision.
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Affiliation(s)
- Pankaj Dwivedi
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
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44
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. CELL REPORTS METHODS 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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45
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Sanford J, Wang Y, Hansen JR, Gritsenko MA, Weitz KK, Sagendorf TJ, Tognon CE, Petyuk VA, Qian WJ, Liu T, Druker BJ, Rodland KD, Piehowski PD. Evaluation of Differential Peptide Loading on Tandem Mass Tag-Based Proteomic and Phosphoproteomic Data Quality. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:17-30. [PMID: 34813325 PMCID: PMC8739833 DOI: 10.1021/jasms.1c00169] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/27/2021] [Accepted: 11/04/2021] [Indexed: 06/13/2023]
Abstract
Global and phosphoproteome profiling has demonstrated great utility for the analysis of clinical specimens. One barrier to the broad clinical application of proteomic profiling is the large amount of biological material required, particularly for phosphoproteomics─currently on the order of 25 mg wet tissue weight. For hematopoietic cancers such as acute myeloid leukemia (AML), the sample requirement is ≥10 million peripheral blood mononuclear cells (PBMCs). Across large study cohorts, this requirement will exceed what is obtainable for many individual patients/time points. For this reason, we were interested in the impact of differential peptide loading across multiplex channels on proteomic data quality. To achieve this, we tested a range of channel loading amounts (approximately the material obtainable from 5E5, 1E6, 2.5E6, 5E6, and 1E7 AML patient cells) to assess proteome coverage, quantification precision, and peptide/phosphopeptide detection in experiments utilizing isobaric tandem mass tag (TMT) labeling. As expected, fewer missing values were observed in TMT channels with higher peptide loading amounts compared to lower loadings. Moreover, channels with a lower loading have greater quantitative variability than channels with higher loadings. A statistical analysis showed that decreased loading amounts result in an increase in the type I error rate. We then examined the impact of differential loading on the detection of known differences between distinct AML cell lines. Similar patterns of increased data missingness and higher quantitative variability were observed as loading was decreased resulting in fewer statistical differences; however, we found good agreement in features identified as differential, demonstrating the value of this approach.
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Affiliation(s)
- James
A. Sanford
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Yang Wang
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Joshua R. Hansen
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Marina A. Gritsenko
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Karl K. Weitz
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tyler J. Sagendorf
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Cristina E. Tognon
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Vladislav A. Petyuk
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Tao Liu
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Brian J. Druker
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
- Division
of Hematology and Medical Oncology, Oregon
Health & Science University, Portland, Oregon 97239, United States
| | - Karin D. Rodland
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
- Knight
Cancer Institute, Oregon Health & Science
University, Portland, Oregon 97239, United States
| | - Paul D. Piehowski
- Environmental
Molecular Sciences Division, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
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46
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Kwon YW, Jo HS, Bae S, Seo Y, Song P, Song M, Yoon JH. Application of Proteomics in Cancer: Recent Trends and Approaches for Biomarkers Discovery. Front Med (Lausanne) 2021; 8:747333. [PMID: 34631760 PMCID: PMC8492935 DOI: 10.3389/fmed.2021.747333] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 08/26/2021] [Indexed: 12/12/2022] Open
Abstract
Proteomics has become an important field in molecular sciences, as it provides valuable information on the identity, expression levels, and modification of proteins. For example, cancer proteomics unraveled key information in mechanistic studies on tumor growth and metastasis, which has contributed to the identification of clinically applicable biomarkers as well as therapeutic targets. Several cancer proteome databases have been established and are being shared worldwide. Importantly, the integration of proteomics studies with other omics is providing extensive data related to molecular mechanisms and target modulators. These data may be analyzed and processed through bioinformatic pipelines to obtain useful information. The purpose of this review is to provide an overview of cancer proteomics and recent advances in proteomic techniques. In particular, we aim to offer insights into current proteomics studies of brain cancer, in which proteomic applications are in a relatively early stage. This review covers applications of proteomics from the discovery of biomarkers to the characterization of molecular mechanisms through advances in technology. Moreover, it addresses global trends in proteomics approaches for translational research. As a core method in translational research, the continued development of this field is expected to provide valuable information at a scale beyond that previously seen.
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Affiliation(s)
- Yang Woo Kwon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Han-Seul Jo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Sungwon Bae
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Youngsuk Seo
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
| | - Parkyong Song
- Department of Convergence Medicine, Pusan National University School of Medicine, Yangsan, South Korea
| | - Minseok Song
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Jong Hyuk Yoon
- Neurodegenerative Diseases Research Group, Korea Brain Research Institute, Daegu, South Korea
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47
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Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND. Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment. Mol Cell Proteomics 2021; 20:100154. [PMID: 34592423 PMCID: PMC9357436 DOI: 10.1016/j.mcpro.2021.100154] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/23/2021] [Accepted: 09/22/2021] [Indexed: 01/11/2023] Open
Abstract
Robust methods for deep-scale enrichment and site-specific identification of ubiquitylation sites are necessary for characterizing the myriad roles of protein ubiquitylation. To this end we previously developed UbiFast, a sensitive method for highly multiplexed ubiquitylation profiling where K-ϵ-GG peptides are enriched with anti-K-ε-GG antibody and labeled on-antibody with isobaric labeling reagents for sample multiplexing. Here, we present robotic automation of the UbiFast method using a magnetic bead-conjugated K-ε-GG antibody (mK-ε-GG) and a magnetic particle processor. We report the identification of ∼20,000 ubiquitylation sites from a TMT10-plex with 500 μg input per sample processed in ∼2 h. Automation of the UbiFast method greatly increased the number of identified and quantified ubiquitylation sites, improved reproducibility, and significantly reduced processing time. The automated method also significantly reduced variability across process replicates compared with the manual method. The workflow enables processing of up to 96 samples in a single day making it suitable to study ubiquitylation in large sample sets. Here we demonstrate the applicability of the method to profile small amounts of tissue using breast cancer patient–derived xenograft (PDX) tissue samples. HS mag anti-K-ε-GG antibody increases sensitivity of ubiquitylation site detection. Automated UbiFast increases reproducibility and sample processing throughput. The automated UbiFast workflow enables processing of up to 96 samples in one day. UbiFast can be employed to profile ubiquitylomes from small amounts of tumor tissue.
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Affiliation(s)
- Keith D Rivera
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Meagan E Olive
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Erik J Bergstrom
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | | | - Shankha Satpathy
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - Namrata D Udeshi
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
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48
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Martin K, Zhang T, Lin TT, Habowski AN, Zhao R, Tsai CF, Chrisler WB, Sontag RL, Orton DJ, Lu YJ, Rodland KD, Yang B, Liu T, Smith RD, Qian WJ, Waterman ML, Wiley HS, Shi T. Facile One-Pot Nanoproteomics for Label-Free Proteome Profiling of 50-1000 Mammalian Cells. J Proteome Res 2021; 20:4452-4461. [PMID: 34351778 PMCID: PMC8945255 DOI: 10.1021/acs.jproteome.1c00403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recent advances in sample preparation enable label-free mass spectrometry (MS)-based proteome profiling of small numbers of mammalian cells. However, specific devices are often required to downscale sample processing volume from the standard 50-200 μL to sub-μL for effective nanoproteomics, which greatly impedes the implementation of current nanoproteomics methods by the proteomics research community. Herein, we report a facile one-pot nanoproteomics method termed SOPs-MS (surfactant-assisted one-pot sample processing at the standard volume coupled with MS) for convenient robust proteome profiling of 50-1000 mammalian cells. Building upon our recent development of SOPs-MS for label-free single-cell proteomics at a low μL volume, we have systematically evaluated its processing volume at 10-200 μL using 100 human cells. The processing volume of 50 μL that is in the range of volume for standard proteomics sample preparation has been selected for easy sample handling with a benchtop micropipette. SOPs-MS allows for reliable label-free quantification of ∼1200-2700 protein groups from 50 to 1000 MCF10A cells. When applied to small subpopulations of mouse colon crypt cells, SOPs-MS has revealed protein signatures between distinct subpopulation cells with identification of ∼1500-2500 protein groups for each subpopulation. SOPs-MS may pave the way for routine deep proteome profiling of small numbers of cells and low-input samples.
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Affiliation(s)
| | | | - Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amber N. Habowski
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - Rui Zhao
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Chia-Feng Tsai
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan L. Sontag
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Daniel J. Orton
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Yong-Jie Lu
- Centre for Cancer Biomarker and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, United Kingdom
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Bin Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Bioproducts, Sciences & Engineering Laboratory, Department of Biological Systems Engineering, Washington State University, Richland, Washington 99354, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Marian L. Waterman
- Department of Microbiology and Molecular Genetics, University of California Irvine, Irvine, California 92697, United States
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tujin Shi
- Corresponding Author Tujin Shi – Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States; Phone: (509) 371-6579;
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49
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Ogata K, Tsai CF, Ishihama Y. Nanoscale Solid-Phase Isobaric Labeling for Multiplexed Quantitative Phosphoproteomics. J Proteome Res 2021; 20:4193-4202. [PMID: 34292731 DOI: 10.1021/acs.jproteome.1c00444] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We established a workflow for highly sensitive multiplexed quantitative phosphoproteomics using a nanoscale solid-phase tandem mass tag (TMT) labeling reactor. Phosphopeptides were first enriched by titanium oxide chromatography and then labeled with isobaric TMT reagents in a StageTip packed with hydrophobic polymer-based sorbents. We found that TMT-labeled singly phosphorylated peptides tend to flow through the titanium oxide column. Therefore, TMT labeling should be performed after the enrichment step from tryptic peptides, resulting in the need for microscale reactions with small amounts of phosphopeptides. Using an optimized protocol for tens to hundreds of nanograms of phosphopeptides, we obtained a nearly 10-fold increase in sensitivity compared to the conventional solution-based TMT protocol. We demonstrate that this nanoscale phosphoproteomics protocol works for 50 μg of HeLa proteins treated with selumetinib, and we successfully quantified the selumetinib-regulated phosphorylated sites on a proteome scale. The MS raw data files have been deposited with the ProteomeXchange Consortium via the jPOST partner repository (https://jpostdb.org) with the data set identifier PXD025536.
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Affiliation(s)
- Kosuke Ogata
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Chia-Feng Tsai
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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50
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Friedrich C, Schallenberg S, Kirchner M, Ziehm M, Niquet S, Haji M, Beier C, Neudecker J, Klauschen F, Mertins P. Comprehensive micro-scaled proteome and phosphoproteome characterization of archived retrospective cancer repositories. Nat Commun 2021; 12:3576. [PMID: 34117251 PMCID: PMC8196151 DOI: 10.1038/s41467-021-23855-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 05/17/2021] [Indexed: 02/07/2023] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable resource for retrospective clinical studies. Here, we evaluate the feasibility of (phospho-)proteomics on FFPE lung tissue regarding protein extraction, quantification, pre-analytics, and sample size. After comparing protein extraction protocols, we use the best-performing protocol for the acquisition of deep (phospho-)proteomes from lung squamous cell and adenocarcinoma with >8,000 quantified proteins and >14,000 phosphosites with a tandem mass tag (TMT) approach. With a microscaled approach, we quantify 7,000 phosphosites, enabling the analysis of FFPE biopsies with limited tissue amounts. We also investigate the influence of pre-analytical variables including fixation time and heat-assisted de-crosslinking on protein extraction efficiency and proteome coverage. Our improved workflows provide quantitative information on protein abundance and phosphosite regulation for the most relevant oncogenes, tumor suppressors, and signaling pathways in lung cancer. Finally, we present general guidelines to which methods are best suited for different applications, highlighting TMT methods for comprehensive (phospho-)proteome profiling for focused clinical studies and label-free methods for large cohorts.
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Affiliation(s)
- Corinna Friedrich
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.419491.00000 0001 1014 0849Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), MDC graduate school, Berlin, Germany ,grid.7468.d0000 0001 2248 7639Humboldt Universität zu Berlin, Institute of Chemistry, Berlin, Germany
| | - Simon Schallenberg
- grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Marieluise Kirchner
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Ziehm
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Sylvia Niquet
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Christin Beier
- grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany
| | - Jens Neudecker
- grid.6363.00000 0001 2218 4662Department of Surgery - Campus Charité Mitte and Campus Virchow-Klinikum, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Frederick Klauschen
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.7468.d0000 0001 2248 7639Institute of Pathology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany ,grid.5252.00000 0004 1936 973XInstitute of Pathology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Philipp Mertins
- German Cancer Consortium (DKTK), partner site Berlin, Berlin, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.419491.00000 0001 1014 0849Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Proteomics Platform, Berlin, Germany ,grid.484013.aBerlin Institute of Health at Charité – Universitätsmedizin Berlin, Berlin, Germany
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