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Breckels LM, Hutchings C, Ingole KD, Kim S, Lilley KS, Makwana MV, McCaskie KJA, Villanueva E. Advances in spatial proteomics: Mapping proteome architecture from protein complexes to subcellular localizations. Cell Chem Biol 2024; 31:1665-1687. [PMID: 39303701 DOI: 10.1016/j.chembiol.2024.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/12/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Proteins are responsible for most intracellular functions, which they perform as part of higher-order molecular complexes, located within defined subcellular niches. Localization is both dynamic and context specific and mislocalization underlies a multitude of diseases. It is thus vital to be able to measure the components of higher-order protein complexes and their subcellular location dynamically in order to fully understand cell biological processes. Here, we review the current range of highly complementary approaches that determine the subcellular organization of the proteome. We discuss the scale and resolution at which these approaches are best employed and the caveats that should be taken into consideration when applying them. We also look to the future and emerging technologies that are paving the way for a more comprehensive understanding of the functional roles of protein isoforms, which is essential for unraveling the complexities of cell biology and the development of disease treatments.
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Affiliation(s)
- Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Charlotte Hutchings
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kishor D Ingole
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Suyeon Kim
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Mehul V Makwana
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Kieran J A McCaskie
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
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2
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Wang T, Liang Y, Wang G, Ma S, Zhang L, Lu H, Zhang Y. Ultrafast and Chemoselective Biotinylation of Living Cell Surfaces for Time-Resolved Surfaceome Analysis. Anal Chem 2024; 96:14448-14455. [PMID: 39192718 DOI: 10.1021/acs.analchem.4c02271] [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: 08/29/2024]
Abstract
Cell surface proteins participate in many important biological processes, such as cell-to-cell interaction, signal transduction, cell adhesion, and protein transportation. In-depth study of the cell surface protein group is of great significance. Nevertheless, detection and analysis of the surfaceome remain a significant challenge due to their low abundance and hydrophobicity. Herein, we reported an ultrafast and chemoselective labeling method using our newly developed trifunctional probe, the OPA-S-S-alkyne, which labeled cell surface lysine residues, and then established a novel cell surfaceome profiling approach. According to our experimental results, the OPA-S-S-alkyne probe can react extremely fast with living cells, labeling cells in only 1 min, while traditional NHS (labeling cell surface lysine with N-hydroxysuccinimide ester probe) and CSC (labeling cell surface glycan with hydrazide biotin probe) methods normally take longer time of more than 30 min and 1 h, respectively. Taking advantage of this ultrafast property of the method, we highlight the utility of this method by exploring the temporal dynamic changes of surfaceome upon EGF stimulation in living Hela cells and reported "early" and "late" EGF-regulated cell surface proteins, which are difficult to be distinguished by the current cell surface profiling approaches.
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Affiliation(s)
- Ting Wang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yuying Liang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Guoli Wang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Shiyun Ma
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Haojie Lu
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
| | - Ying Zhang
- Department of Chemistry and Liver Cancer Institute of Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institutes of Biomedical Sciences and NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai 200032, China
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Liu X, Peng T, Xu M, Lin S, Hu B, Chu T, Liu B, Xu Y, Ding W, Li L, Cao C, Wu P. Spatial multi-omics: deciphering technological landscape of integration of multi-omics and its applications. J Hematol Oncol 2024; 17:72. [PMID: 39182134 PMCID: PMC11344930 DOI: 10.1186/s13045-024-01596-9] [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] [Received: 05/22/2024] [Accepted: 08/09/2024] [Indexed: 08/27/2024] Open
Abstract
The emergence of spatial multi-omics has helped address the limitations of single-cell sequencing, which often leads to the loss of spatial context among cell populations. Integrated analysis of the genome, transcriptome, proteome, metabolome, and epigenome has enhanced our understanding of cell biology and the molecular basis of human diseases. Moreover, this approach offers profound insights into the interactions between intracellular and intercellular molecular mechanisms involved in the development, physiology, and pathogenesis of human diseases. In this comprehensive review, we examine current advancements in multi-omics technologies, focusing on their evolution and refinement over the past decade, including improvements in throughput and resolution, modality integration, and accuracy. We also discuss the pivotal contributions of spatial multi-omics in revealing spatial heterogeneity, constructing detailed spatial atlases, deciphering spatial crosstalk in tumor immunology, and advancing translational research and cancer therapy through precise spatial mapping.
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Affiliation(s)
- Xiaojie Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ting Peng
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Miaochun Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Shitong Lin
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bai Hu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Tian Chu
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Binghan Liu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yashi Xu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wencheng Ding
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Li Li
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Canhui Cao
- Department of Gynecologic Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
| | - Peng Wu
- Department of Obstetrics and Gynecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- National Clinical Research Center for Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Martin RA, Viggars MR, Sanford JA, Taylor ZW, Hansen JR, Clair GC, Adkins JN, Douglas CM, Esser KA. Alterations of the skeletal muscle nuclear proteome after acute exercise reveals a post-transcriptional influence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607176. [PMID: 39149399 PMCID: PMC11326304 DOI: 10.1101/2024.08.08.607176] [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: 08/17/2024]
Abstract
Exercise is firmly established as a key contributor to overall well-being and is frequently employed as a therapeutic approach to mitigate various health conditions. One pivotal aspect of the impact of exercise lies in the systemic transcriptional response, which underpins its beneficial adaptations. While extensive research has been devoted to understanding the transcriptional response to exercise, our knowledge of the protein constituents of nuclear processes that accompany gene expression in skeletal muscle remains largely elusive. We hypothesize that alterations in the nuclear proteome following exercise hold vital clues for comprehending the transcriptional regulation and other related nuclear functions. We isolated skeletal muscle nuclei from C57BL/6 mice both sedentary control and one-hour post 30-minute treadmill running, to gain insights into the nuclear proteome after exercise. A substantial number of the 2,323 proteins identified, were related to nuclear functions. For instance, we found 59 proteins linked to nucleocytoplasmic transport were higher in sedentary mice compared to exercise, hinting at an exercise-induced modulation to nuclear trafficking. Furthermore, 135 proteins exhibited increased abundance after exercise (FDR < 0.1) while 89 proteins decreased, with the most prominent changes in proteins linked to mRNA processing and splicing. Super resolution microscopy further highlights potential localization change in mRNA processing proteins post-exercise, further suggesting changes in nuclear transport dynamics. Nonetheless, our data provide important considerations for the study of the nuclear proteome and supports a paradigm through which exercise downregulated mRNA processing and splicing, offering valuable insights into the broader landscape of the impact from acute exercise. New & Noteworthy Exercise plays a crucial role in promoting muscle health, but our understanding of nuclear proteins orchestrating exercise responses is limited. Isolation of skeletal muscle nuclei coupled with mass spectrometry enhanced the identification of nuclear proteins. This approach was used to investigate the effects of acute exercise, revealing changes in the muscle nuclear proteome 1-hour post-exercise, including proteins linked to post-transcriptional processing and splicing. Our findings offer insights into the exercise-induced changes within muscle nuclear proteins.
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Affiliation(s)
- Ryan A. Martin
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Mark R. Viggars
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | | | - Zane W. Taylor
- Pacific Northwest National Laboratory, Richland, WA, USA
| | | | | | - Joshua N. Adkins
- Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR, USA
| | - Collin M. Douglas
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
| | - Karyn A. Esser
- Department of Physiology and Aging, University of Florida, Gainesville, FL, USA
- Myology Institute, University of Florida, Gainesville, FL, USA
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5
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Ceasar SA, Prabhu S, Ebeed HT. Protein research in millets: current status and way forward. PLANTA 2024; 260:43. [PMID: 38958760 DOI: 10.1007/s00425-024-04478-z] [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: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
MAIN CONCLUSION Millets' protein studies are lagging behind those of major cereals. Current status and future insights into the investigation of millet proteins are discussed. Millets are important small-seeded cereals majorly grown and consumed by people in Asia and Africa and are considered crops of future food security. Although millets possess excellent climate resilience and nutrient supplementation properties, their research advancements have been lagging behind major cereals. Although considerable genomic resources have been developed in recent years, research on millet proteins and proteomes is currently limited, highlighting a need for further investigation in this area. This review provides the current status of protein research in millets and provides insights to understand protein responses for climate resilience and nutrient supplementation in millets. The reference proteome data is available for sorghum, foxtail millet, and proso millet to date; other millets, such as pearl millet, finger millet, barnyard millet, kodo millet, tef, and browntop millet, do not have any reference proteome data. Many studies were reported on stress-responsive protein identification in foxtail millet, with most studies on the identification of proteins under drought-stress conditions. Pearl millet has a few reports on protein identification under drought and saline stress. Finger millet is the only other millet to have a report on stress-responsive (drought) protein identification in the leaf. For protein localization studies, foxtail millet has a few reports. Sorghum has the highest number of 40 experimentally proven crystal structures, and other millets have fewer or no experimentally proven structures. Further proteomics studies will help dissect the specific proteins involved in climate resilience and nutrient supplementation and aid in breeding better crops to conserve food security.
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Affiliation(s)
- S Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India.
| | - Srinivasan Prabhu
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Cochin, Kerala, 683 104, India
| | - Heba T Ebeed
- Botany and Microbiology Department, Faculty of Science, Damietta University, Damietta, Egypt
- National Biotechnology Network of Expertise (NBNE), Academy of Scientific Research and Technology (ASRT), Cairo, Egypt
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6
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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 PMCID: PMC11381016 DOI: 10.1152/physrev.00026.2023] [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: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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Wang F, Ma L, Wang Q, Hammock BD, Xiao G, Liu R. Evaluation of the Immune Response of Patulin by Proteomics. BIOSENSORS 2024; 14:322. [PMID: 39056598 PMCID: PMC11274796 DOI: 10.3390/bios14070322] [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: 05/13/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/28/2024]
Abstract
Patulin, an emerging mycotoxin with high toxicity, poses great risks to public health. Considering the poor antibody production in patulin immunization, this study focuses on the four-dimensional data-independent acquisition (4D-DIA) quantitative proteomics to reveal the immune response of patulin in rabbits. The rabbit immunization was performed with the complete developed antigens of patulin, followed by the identification of the immune serum. A total of 554 differential proteins, including 292 up-regulated proteins and 262 down-regulated proteins, were screened; the differential proteins were annotated; and functional enrichment analysis was performed. The differential proteins were associated with the pathways of metabolism, gene information processing, environmental information processing, cellular processes, and organismal systems. The functional enrichment analysis indicated that the immunization procedures mostly resulted in the regulation of biochemical metabolic and signal transduction pathways, including the biosynthesis of amino acid (glycine, serine, and threonine), ascorbate, and aldarate metabolism; fatty acid degradation; and antigen processing and presentation. The 14 key proteins with high connectivity included G1U9T1, B6V9S9, G1SCN8, G1TMS5, G1U9U0, A0A0G2JH20, G1SR03, A0A5F9DAT4, G1SSA2, G1SZ14, G1T670, P30947, P29694, and A0A5F9C804, which were obtained by the analysis of protein-protein interaction networks. This study could provide potential directions for protein interaction and antibody production for food hazards in animal immunization.
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Affiliation(s)
- Feng Wang
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (L.M.); (Q.W.); (G.X.)
| | - Lukai Ma
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (L.M.); (Q.W.); (G.X.)
| | - Qin Wang
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (L.M.); (Q.W.); (G.X.)
| | - Bruce D. Hammock
- Department of Entomology and Nematology and UCD Comprehensive Cancer Center, University of California, Davis, CA 95616, USA;
| | - Gengsheng Xiao
- Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology, College of Light Industry and Food, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (L.M.); (Q.W.); (G.X.)
| | - Ruijing Liu
- Guangdong Engineering Technology Research Center for Pre-Cooked Food Processing and Quality Evaluation, Shunde Polytechnic, Foshan 528333, China
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8
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Reicher A, Reiniš J, Ciobanu M, Růžička P, Malik M, Siklos M, Kartysh V, Tomek T, Koren A, Rendeiro AF, Kubicek S. Pooled multicolour tagging for visualizing subcellular protein dynamics. Nat Cell Biol 2024; 26:745-756. [PMID: 38641660 PMCID: PMC11098740 DOI: 10.1038/s41556-024-01407-w] [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: 07/25/2023] [Accepted: 03/18/2024] [Indexed: 04/21/2024]
Abstract
Imaging-based methods are widely used for studying the subcellular localization of proteins in living cells. While routine for individual proteins, global monitoring of protein dynamics following perturbation typically relies on arrayed panels of fluorescently tagged cell lines, limiting throughput and scalability. Here, we describe a strategy that combines high-throughput microscopy, computer vision and machine learning to detect perturbation-induced changes in multicolour tagged visual proteomics cell (vpCell) pools. We use genome-wide and cancer-focused intron-targeting sgRNA libraries to generate vpCell pools and a large, arrayed collection of clones each expressing two different endogenously tagged fluorescent proteins. Individual clones can be identified in vpCell pools by image analysis using the localization patterns and expression level of the tagged proteins as visual barcodes, enabling simultaneous live-cell monitoring of large sets of proteins. To demonstrate broad applicability and scale, we test the effects of antiproliferative compounds on a pool with cancer-related proteins, on which we identify widespread protein localization changes and new inhibitors of the nuclear import/export machinery. The time-resolved characterization of changes in subcellular localization and abundance of proteins upon perturbation in a pooled format highlights the power of the vpCell approach for drug discovery and mechanism-of-action studies.
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Affiliation(s)
- Andreas Reicher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Jiří Reiniš
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Maria Ciobanu
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Pavel Růžička
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Monika Malik
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marton Siklos
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Victoria Kartysh
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Tatjana Tomek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Anna Koren
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - André F Rendeiro
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
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9
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Dowling P, Trollet C, Muraine L, Negroni E, Swandulla D, Ohlendieck K. The potential of proteomics for in-depth bioanalytical investigations of satellite cell function in applied myology. Expert Rev Proteomics 2024; 21:229-235. [PMID: 38753566 DOI: 10.1080/14789450.2024.2356578] [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: 02/19/2024] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
INTRODUCTION Regenerative myogenesis plays a crucial role in mature myofibers to counteract muscular injury or dysfunction due to neuromuscular disorders. The activation of specialized myogenic stem cells, called satellite cells, is intrinsically involved in proliferation and differentiation, followed by myoblast fusion and the formation of multinucleated myofibers. AREAS COVERED This report provides an overview of the role of satellite cells in the neuromuscular system and the potential future impact of proteomic analyses for biomarker discovery, as well as the identification of novel therapeutic targets in muscle disease. The article reviews the ways in which the systematic analysis of satellite cells, myoblasts, and myocytes by single-cell proteomics can help to better understand the process of myofiber regeneration. EXPERT OPINION In order to better comprehend satellite cell dysfunction in neuromuscular disorders, mass spectrometry-based proteomics is an excellent large-scale analytical tool for the systematic profiling of pathophysiological processes. The optimized isolation of muscle-derived cells can be routinely performed by mechanical/enzymatic dissociation protocols, followed by fluorescence-activated cell sorting in specialized flow cytometers. Ultrasensitive single-cell proteomics using label-free quantitation methods or approaches that utilize tandem mass tags are ideal bioanalytical approaches to study the pathophysiological role of stem cells in neuromuscular disease.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, KE, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, KE, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Laura Muraine
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, Paris, France
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, Bonn, Germany
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, Maynooth, KE, Ireland
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, KE, Ireland
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10
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Zhu Y, Akkaya KC, Ruta J, Yokoyama N, Wang C, Ruwolt M, Lima DB, Lehmann M, Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topologies. Nat Commun 2024; 15:3290. [PMID: 38632225 PMCID: PMC11024108 DOI: 10.1038/s41467-024-47569-x] [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: 03/04/2023] [Accepted: 04/05/2024] [Indexed: 04/19/2024] Open
Abstract
The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.
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Affiliation(s)
- Ying Zhu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Kerem Can Akkaya
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Julia Ruta
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Nanako Yokoyama
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Cong Wang
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Max Ruwolt
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Diogo Borges Lima
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Martin Lehmann
- Department of Molecular Physiology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany
| | - Fan Liu
- Department of Structural Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10 13125, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117, Berlin, Germany.
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11
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Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [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: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
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Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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12
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Currie J, Manda V, Robinson SK, Lai C, Agnihotri V, Hidalgo V, Ludwig RW, Zhang K, Pavelka J, Wang ZV, Rhee JW, Lam MPY, Lau E. Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions. Nat Commun 2024; 15:2207. [PMID: 38467653 PMCID: PMC10928085 DOI: 10.1038/s41467-024-46600-5] [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: 05/01/2023] [Accepted: 02/20/2024] [Indexed: 03/13/2024] Open
Abstract
The spatial and temporal distributions of proteins are critical to protein function, but cannot be directly assessed by measuring protein bundance. Here we describe a mass spectrometry-based proteomics strategy, Simultaneous Proteome Localization and Turnover (SPLAT), to measure concurrently protein turnover rates and subcellular localization in the same experiment. Applying the method, we find that unfolded protein response (UPR) has different effects on protein turnover dependent on their subcellular location in human AC16 cells, with proteome-wide slowdown but acceleration among stress response proteins in the ER and Golgi. In parallel, UPR triggers broad differential localization of proteins including RNA-binding proteins and amino acid transporters. Moreover, we observe newly synthesized proteins including EGFR that show a differential localization under stress than the existing protein pools, reminiscent of protein trafficking disruptions. We next applied SPLAT to an induced pluripotent stem cell derived cardiomyocyte (iPSC-CM) model of cancer drug cardiotoxicity upon treatment with the proteasome inhibitor carfilzomib. Paradoxically, carfilzomib has little effect on global average protein half-life, but may instead selectively disrupt sarcomere protein homeostasis. This study provides a view into the interactions of protein spatial and temporal dynamics and demonstrates a method to examine protein homeostasis regulations in stress and drug response.
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Affiliation(s)
- Jordan Currie
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Vyshnavi Manda
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Sean K Robinson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Celine Lai
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA, 94305, USA
| | - Vertica Agnihotri
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, CA, 91010, Duarte, USA
| | - Veronica Hidalgo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - R W Ludwig
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Kai Zhang
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - Jay Pavelka
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Zhao V Wang
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, 91010, USA
| | - June-Wha Rhee
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, CA, 91010, Duarte, USA
| | - Maggie P Y Lam
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Edward Lau
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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13
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Guo F, Qin S, Liu Z, Chen PR, Fan X. Decaging-to-labeling: Development and investigation of quinone methide warhead for protein labeling. Bioorg Chem 2024; 143:107088. [PMID: 38194902 DOI: 10.1016/j.bioorg.2023.107088] [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: 10/31/2023] [Revised: 12/28/2023] [Accepted: 12/30/2023] [Indexed: 01/11/2024]
Abstract
Biomolecule labeling in living systems is crucial for understanding biological processes and discovering therapeutic targets. A variety of labeling warheads have been developed for multiple biological applications, including proteomics, bioimaging, sequencing, and drug development. Quinone methides (QMs), a class of highly reactive Michael receptors, have recently emerged as prominent warheads for on-demand biomolecule labeling. Their highly flexible functionality and tunability allow for diverse biological applications, but remain poorly explored at present. In this regard, we designed, synthesized, and evaluated a series of new QM probes with a trifluoromethyl group at the benzyl position and substituents on the aromatic ring to manipulate their chemical properties for biomolecule labeling. The engineered QM warhead efficiently labeled proteins both in vitro and under living cell conditions, with significantly enhanced activity compared to previous QM warheads. We further analyzed the labeling efficacy with the assistance of density functional theory (DFT) calculations, which revealed that the QM generation process, rather than the reactivity of QM, contributes more predominantly to the labeling efficacy. Noteworthy, twelve nucleophilic residues on the BSA were labeled by the probe, including Cys, Asp, Glu, His, Lys, Asn, Gln, Arg, Ser, Thr, Trp and Tyr. Given their high efficiency and tunability, these new QM warheads may hold great promise for a broad range of applications, especially spatiotemporal proteomic profiling for in-depth biological studies.
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Affiliation(s)
- Fuhu Guo
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Shengnan Qin
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Ziqi Liu
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Peng R Chen
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Xinyuan Fan
- Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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14
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Currie J, Manda V, Robinson SK, Lai C, Agnihotri V, Hidalgo V, Ludwig RW, Zhang K, Pavelka J, Wang ZV, Rhee JW, Lam MPY, Lau E. Simultaneous proteome localization and turnover analysis reveals spatiotemporal features of protein homeostasis disruptions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.04.521821. [PMID: 36711879 PMCID: PMC9881985 DOI: 10.1101/2023.01.04.521821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The functions of proteins depend on their spatial and temporal distributions, which are not directly measured by static protein abundance. Under endoplasmic reticulum (ER) stress, the unfolded protein response (UPR) pathway remediates proteostasis in part by altering the turnover kinetics and spatial distribution of proteins. A global view of these spatiotemporal changes has yet to emerge and it is unknown how they affect different cellular compartments and pathways. Here we describe a mass spectrometry-based proteomics strategy and data analysis pipeline, termed Simultaneous Proteome Localization and Turnover (SPLAT), to measure concurrently the changes in protein turnover and subcellular distribution in the same experiment. Investigating two common UPR models of thapsigargin and tunicamycin challenge in human AC16 cells, we find that the changes in protein turnover kinetics during UPR varies across subcellular localizations, with overall slowdown but an acceleration in endoplasmic reticulum and Golgi proteins involved in stress response. In parallel, the spatial proteomics component of the experiment revealed an externalization of amino acid transporters and ion channels under UPR, as well as the migration of RNA-binding proteins toward an endosome co-sedimenting compartment. The SPLAT experimental design classifies heavy and light SILAC labeled proteins separately, allowing the observation of differential localization of new and old protein pools and capturing a partition of newly synthesized EGFR and ITGAV to the ER under stress that suggests protein trafficking disruptions. Finally, application of SPLAT toward human induced pluripotent stem cell derived cardiomyocytes (iPSC-CM) exposed to the cancer drug carfilzomib, identified a selective disruption of proteostasis in sarcomeric proteins as a potential mechanism of carfilzomib-mediated cardiotoxicity. Taken together, this study provides a global view into the spatiotemporal dynamics of human cardiac cells and demonstrates a method for inferring the coordinations between spatial and temporal proteome regulations in stress and drug response.
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Affiliation(s)
- Jordan Currie
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Vyshnavi Manda
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sean K. Robinson
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Celine Lai
- Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Vertica Agnihotri
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, Durante, CA 91010, USA
| | - Veronica Hidalgo
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - R. W. Ludwig
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Kai Zhang
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - Jay Pavelka
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Zhao V. Wang
- Department of Diabetes and Cancer Metabolism, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010, USA
| | - June-Wha Rhee
- Department of Medicine, Division of Cardiology, City of Hope Comprehensive Cancer Center, Durante, CA 91010, USA
| | - Maggie P. Y. Lam
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Edward Lau
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Consortium for Fibrosis Research and Translation, University of Colorado School of Medicine, Aurora, CO 80045, USA
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15
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Teraiya M, Krokhin O, Chen VC, Perreault H. Cytoplasmic Shotgun Proteomic Points to Key Proteins and Pathways in Temozolomide-Resistant Glioblastoma Multiforme. J Proteome Res 2024; 23:465-482. [PMID: 38147655 DOI: 10.1021/acs.jproteome.3c00669] [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: 12/28/2023]
Abstract
Temozolomide (TMZ) is the first line of chemotherapy to treat primary brain tumors of the type glioblastoma multiforme (GBM). TMZ resistance (TMZR) is one of the main barriers to successful treatment and is a principal factor in relapse, resulting in a poor median survival of 15 months. The present paper focuses on proteomic analyses of cytosolic fractions from TMZ-resistant (TMZR) LN-18 cells. The experimental workflow includes an easy, cost-effective, and reproducible method to isolate subcellular fraction of cytosolic (CYTO) proteins, mitochondria, and plasma membrane proteins for proteomic studies. For this study, enriched cytoplasmic fractions were analyzed in replicates by nanoflow liquid chromatography tandem high-resolution mass spectrometry (nLC-MS/MS), and proteins identified were quantified using a label-free approach (LFQ). Statistical analysis of control (CTRL) and temozolomide-resistant (TMZR) proteomes revealed proteins that appear to be differentially controlled in the cytoplasm. The functions of these proteins are discussed as well as their roles in other cancers and TMZ resistance in GBM. Key proteins are also described through biological processes related to gene ontology (GO), molecular functions, and cellular components. For protein-protein interactions (PPI), network and pathway involvement analyses have been performed, highlighting the roles of key proteins in the TMZ resistance phenotypes. This study provides a detailed insight into methods of subcellular fractionation for proteomic analysis of TMZ-resistant GBM cells and the potential to apply this approach to future large-scale studies. Several key proteins, protein-protein interactions (PPI), and pathways have been identified, underlying the TMZ resistance phenotype and highlighting the proteins' biological functions.
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Affiliation(s)
- Milan Teraiya
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
| | - Oleg Krokhin
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
- Manitoba Centre for Proteomics and Department of Internal Medicine, University of Manitoba, Winnipeg, Manitoba R3E3P4, Canada
| | - Vincent C Chen
- Chemistry Department, Brandon University, Brandon, Manitoba R7A 6A9, Canada
| | - Hélène Perreault
- Chemistry Department, University of Manitoba, Winnipeg, Manitoba R3T3C7, Canada
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16
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Mennillo E, Kim YJ, Lee G, Rusu I, Patel RK, Dorman LC, Flynn E, Li S, Bain JL, Andersen C, Rao A, Tamaki S, Tsui J, Shen A, Lotstein ML, Rahim M, Naser M, Bernard-Vazquez F, Eckalbar W, Cho SJ, Beck K, El-Nachef N, Lewin S, Selvig DR, Terdiman JP, Mahadevan U, Oh DY, Fragiadakis GK, Pisco A, Combes AJ, Kattah MG. Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.21.525036. [PMID: 36711576 PMCID: PMC9882264 DOI: 10.1101/2023.01.21.525036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.
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17
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Villanueva E, Smith T, Pizzinga M, Elzek M, Queiroz RML, Harvey RF, Breckels LM, Crook OM, Monti M, Dezi V, Willis AE, Lilley KS. System-wide analysis of RNA and protein subcellular localization dynamics. Nat Methods 2024; 21:60-71. [PMID: 38036857 PMCID: PMC10776395 DOI: 10.1038/s41592-023-02101-9] [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] [Received: 01/27/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023]
Abstract
Although the subcellular dynamics of RNA and proteins are key determinants of cell homeostasis, their characterization is still challenging. Here we present an integrative framework to simultaneously interrogate the dynamics of the transcriptome and proteome at subcellular resolution by combining two methods: localization of RNA (LoRNA) and a streamlined density-based localization of proteins by isotope tagging (dLOPIT) to map RNA and protein to organelles (nucleus, endoplasmic reticulum and mitochondria) and membraneless compartments (cytosol, nucleolus and cytosolic granules). Interrogating all RNA subcellular locations at once enables system-wide quantification of the proportional distribution of RNA. We obtain a cell-wide overview of localization dynamics for 31,839 transcripts and 5,314 proteins during the unfolded protein response, revealing that endoplasmic reticulum-localized transcripts are more efficiently recruited to cytosolic granules than cytosolic RNAs, and that the translation initiation factor eIF3d is key to sustaining cytoskeletal function. Overall, we provide the most comprehensive overview so far of RNA and protein subcellular localization dynamics.
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Affiliation(s)
- Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Tom Smith
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Mariavittoria Pizzinga
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
- Structural Biology Research Centre, Human Technopole, Milan, Italy
| | - Mohamed Elzek
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Rayner M L Queiroz
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Oliver M Crook
- Department of Statistics, University of Oxford, Oxford, UK
| | - Mie Monti
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Veronica Dezi
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Anne E Willis
- MRC Toxicology Unit, University of Cambridge, Cambridge, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, UK.
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18
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Li J, Wang X, Shi L, Liu B, Sheng Z, Chang S, Cai X, Shan G. A Mammalian Conserved Circular RNA CircLARP1B Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305902. [PMID: 37953462 PMCID: PMC10787103 DOI: 10.1002/advs.202305902] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Indexed: 11/14/2023]
Abstract
Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. In this study, a mammalian conserved circRNA circLARP1B is identified to play critical roles in hepatocellular carcinoma (HCC). Patients with high circLARP1B levels have advanced prognostic stage and poor overall survival. CircLARP1B facilitates cellular metastatic properties and lipid accumulation through promoting fatty acid synthesis in HCC. CircLARP1B deficient mice exhibit reduced metastasis and less lipid accumulation in an induced HCC model. Multiple lines of evidence demonstrate that circLARP1B binds to heterogeneous nuclear ribonucleoprotein D (HNRNPD) in the cytoplasm, and thus affects the binding of HNRNPD to sensitive transcripts including liver kinase B1 (LKB1) mRNA. This regulation causes decreased LKB1 mRNA stability and lower LKB1 protein levels. Antisense oligodeoxynucleotide complementary to theHNRNPD binding sites in circLARP1B increases the HNRNPD binding to LKB1 mRNA. Through the HNRNPD-LKB1-AMPK pathway, circLARP1B promotes HCC metastasis and lipid accumulation. Results from AAV8-mediated hepatocyte-directed knockdown of circLARP1B or Lkb1 in mouse models also demonstrate critical roles of hepatocytic circLARP1B regulatory pathway in HCC metastasis and lipid accumulation, and indicate that circLARP1B may be potential target of HCC treatment.
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Affiliation(s)
- Jingxin Li
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Xiaolin Wang
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Liang Shi
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Boqiang Liu
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Zhiyong Sheng
- School of Life ScienceBengbu Medical CollegeBengbu233030China
| | - Shuhui Chang
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Xiujun Cai
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Ge Shan
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
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19
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Deng B, Vanagas L, Alonso AM, Angel SO. Proteomics Applications in Toxoplasma gondii: Unveiling the Host-Parasite Interactions and Therapeutic Target Discovery. Pathogens 2023; 13:33. [PMID: 38251340 PMCID: PMC10821451 DOI: 10.3390/pathogens13010033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/23/2024] Open
Abstract
Toxoplasma gondii, a protozoan parasite with the ability to infect various warm-blooded vertebrates, including humans, is the causative agent of toxoplasmosis. This infection poses significant risks, leading to severe complications in immunocompromised individuals and potentially affecting the fetus through congenital transmission. A comprehensive understanding of the intricate molecular interactions between T. gondii and its host is pivotal for the development of effective therapeutic strategies. This review emphasizes the crucial role of proteomics in T. gondii research, with a specific focus on host-parasite interactions, post-translational modifications (PTMs), PTM crosstalk, and ongoing efforts in drug discovery. Additionally, we provide an overview of recent advancements in proteomics techniques, encompassing interactome sample preparation methods such as BioID (BirA*-mediated proximity-dependent biotin identification), APEX (ascorbate peroxidase-mediated proximity labeling), and Y2H (yeast two hybrid), as well as various proteomics approaches, including single-cell analysis, DIA (data-independent acquisition), targeted, top-down, and plasma proteomics. Furthermore, we discuss bioinformatics and the integration of proteomics with other omics technologies, highlighting its potential in unraveling the intricate mechanisms of T. gondii pathogenesis and identifying novel therapeutic targets.
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Affiliation(s)
- Bin Deng
- Department of Biology and VBRN Proteomics Facility, University of Vermont, Burlington, VT 05405, USA
| | - Laura Vanagas
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Andres M. Alonso
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
| | - Sergio O. Angel
- Laboratorio de Parasitología Molecular, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Chascomús 7130, Provincia de Buenos Aires, Argentina; (L.V.); (S.O.A.); (A.M.A.)
- Escuela de Bio y Nanotecnologías (UNSAM), 25 de Mayo y Francia. C.P., San Martín 1650, Provincia de Buenos Aires, Argentina
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20
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Xiang P, Liyu A, Kwon Y, Hu D, Williams SM, Veličković D, Markillie LM, Chrisler WB, Paša-Tolić L, Zhu Y. Spatial Proteomics toward Subcellular Resolution by Coupling Deep Ultraviolet Laser Ablation with Nanodroplet Sample Preparation. ACS MEASUREMENT SCIENCE AU 2023; 3:459-468. [PMID: 38145026 PMCID: PMC10740121 DOI: 10.1021/acsmeasuresciau.3c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 12/26/2023]
Abstract
Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling of laser microdissection with mass spectrometry-based proteomics has enabled deep and unbiased mapping of >1000 proteins. However, the throughput of laser microdissection is often limited due to tedious two-step procedures, sequential laser cutting, and sample collection. The two-step procedure also hinders the further improvement of spatial resolution to <10 μm as needed for subcellular proteomics. Herein, we developed a high-throughput and high-resolution spatial proteomics platform by seamlessly coupling deep ultraviolet (DUV) laser ablation (LA) with nanoPOTS (Nanodroplet Processing in One pot for Trace Samples)-based sample preparation. We demonstrated the DUV-LA system can quickly isolate and collect tissue samples at a throughput of ∼30 spots/min and a spatial resolution down to 2 μm from a 10 μm thick human pancreas tissue section. To improve sample recovery, we developed a proximity aerosol collection approach by placing DMSO droplets close to LA spots. We demonstrated the DUV-LA-nanoPOTS platform can detect an average of 1312, 1533, and 1966 proteins from ablation spots with diameters of 7, 13, and 19 μm, respectively. In a proof-of-concept study, we isolated and profiled two distinct subcellular regions of the pancreas tissue revealed by hematoxylin and eosin (H&E) staining. Quantitative proteomics revealed proteins specifically enriched to subcellular compartments.
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Affiliation(s)
- Piliang Xiang
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Andrey Liyu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Yumi Kwon
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- 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
| | - Lye Meng Markillie
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Department
of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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21
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Khwaja E, Song YS, Agarunov A, Huang B. CELL-E 2: Translating Proteins to Pictures and Back with a Bidirectional Text-to-Image Transformer. ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 2023; 36:4899-4914. [PMID: 39021511 PMCID: PMC11254339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We present CELL-E 2, a novel bidirectional transformer that can generate images depicting protein subcellular localization from the amino acid sequences (and vice versa). Protein localization is a challenging problem that requires integrating sequence and image information, which most existing methods ignore. CELL-E 2 extends the work of CELL-E, not only capturing the spatial complexity of protein localization and produce probability estimates of localization atop a nucleus image, but also being able to generate sequences from images, enabling de novo protein design. We train and finetune CELL-E 2 on two large-scale datasets of human proteins. We also demonstrate how to use CELL-E 2 to create hundreds of novel nuclear localization signals (NLS). Results and interactive demos are featured at https://bohuanglab.github.io/CELL-E_2/.
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Affiliation(s)
- Emaad Khwaja
- UC Berkeley - UCSF Joint Bioengineering Graduate Program
- Computer Science Division, UC Berkeley, CA 94720
| | - Yun S Song
- Department of Statistics, UC Berkeley, CA 94720
- Computer Science Division, UC Berkeley, CA 94720
| | - Aaron Agarunov
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 10065
| | - Bo Huang
- Department of Pharmaceutical Chemistry, UCSF, San Francisco, CA 94143
- Department of Biochemistry and Biophysics, UCSF, San Francisco, CA 94143
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA 94158
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22
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Abyadeh M, Alikhani M, Mirzaei M, Gupta V, Shekari F, Salekdeh GH. Proteomics provides insights into the theranostic potential of extracellular vesicles. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:101-133. [PMID: 38220422 DOI: 10.1016/bs.apcsb.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Extracellular vesicles (EVs) encompass a diverse range of membranous structures derived from cells, including exosomes and microvesicles. These vesicles are present in biological fluids and play vital roles in various physiological and pathological processes. They facilitate intercellular communication by enabling the exchange of proteins, lipids, and genetic material between cells. Understanding the cellular processes that govern EV biology is essential for unraveling their physiological and pathological functions and their potential clinical applications. Despite significant advancements in EV research in recent years, there is still much to learn about these vesicles. The advent of improved mass spectrometry (MS)-based techniques has allowed for a deeper characterization of EV protein composition, providing valuable insights into their roles in different physiological and pathological conditions. In this chapter, we provide an overview of proteomics studies conducted to identify the protein contents of EVs, which contribute to their therapeutic and pathological features. We also provided evidence on the potential of EV proteome contents as biomarkers for early disease diagnosis, progression, and treatment response, as well as factors that influence their composition. Additionally, we discuss the available databases containing information on EV proteome contents, and finally, we highlight the need for further research to pave the way toward their utilization in clinical settings.
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Affiliation(s)
- Morteza Abyadeh
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Alikhani
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Mehdi Mirzaei
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Vivek Gupta
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, North Ryde, Sydney, NSW, Australia
| | - Faezeh Shekari
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
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23
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Dai C, Guo X, Pan Z, Wan C, Yang D, Li Y, Lian C, An Y, Zhang T, Yang F, Zhu L, Yin F, Wang R, Li Z. Pyridinium-Based Strategy for a Bioorthogonal Conjugation-Assisted Purification Method for Profiling Cell Surface Proteome. Anal Chem 2023; 95:17125-17134. [PMID: 37934015 DOI: 10.1021/acs.analchem.3c04279] [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: 11/08/2023]
Abstract
Cell surface proteins (CSPs) are valuable targets for therapeutic agents, but achieving highly selective CSP enrichment in cellular physiology remains a technical challenge. To address this challenge, we propose a newly developed sulfo-pyridinium ester (SPE) cross-linking probe, followed by two-step imaging and enrichment. The SPE probe showed higher efficiency in labeling proteins than similar NHS esters at the level of cell lysates and demonstrated specificity for Lys in competitive experiments. More importantly, this probe could selectively label the cell membranes in cell imaging with only negligible labeling of the intracellular compartment. Moreover, we successfully performed this strategy on MCF-7 live cells to label 425 unique CSPs from 1162 labeled proteins. Finally, we employed our probe to label the CSPs of insulin-cultured MCF-7, revealing several cell surface targets of key functional biomarkers and insulin-associated pathogenesis. The above results demonstrate that the SPE method provides a promising tool for the selective labeling of cell surface proteins and monitoring transient cell surface events.
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Affiliation(s)
- Chuan Dai
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
- Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, P. R. China
| | - Xiaochun Guo
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Zhuoheng Pan
- School of Pharmacy, Macau University of Science and Technology, Taipa 999078, Macau, P. R. China
| | - Chuan Wan
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Dongyan Yang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Yongli Li
- China Medical System Holdings Limited, Shenzhen 518055, P. R. China
| | - Chenshan Lian
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Tuanjie Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Fadeng Yang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Lizhi Zhu
- Department of Pharmacy, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital (Shenzhen Institute of Translational Medicine), Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, National-Regional Key Technology Engineering Laboratory for Medical Ultrasound, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen 518060, P. R. China
| | - Feng Yin
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
| | - Zigang Li
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen 518118, P. R. China
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen 518055, P. R. China
- Frontiers Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, Sichuan, P. R. China
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24
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Lau CS, Dowle A, Thomas GH, Girr P, Mackinder LCM. A phase-separated CO2-fixing pyrenoid proteome determined by TurboID in Chlamydomonas reinhardtii. THE PLANT CELL 2023; 35:3260-3279. [PMID: 37195994 PMCID: PMC10473203 DOI: 10.1093/plcell/koad131] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/07/2023] [Indexed: 05/19/2023]
Abstract
Phase separation underpins many biologically important cellular events such as RNA metabolism, signaling, and CO2 fixation. However, determining the composition of a phase-separated organelle is often challenging due to its sensitivity to environmental conditions, which limits the application of traditional proteomic techniques like organellar purification or affinity purification mass spectrometry to understand their composition. In Chlamydomonas reinhardtii, Rubisco is condensed into a crucial phase-separated organelle called the pyrenoid that improves photosynthetic performance by supplying Rubisco with elevated concentrations of CO2. Here, we developed a TurboID-based proximity labeling technique in which proximal proteins in Chlamydomonas chloroplasts are labeled by biotin radicals generated from the TurboID-tagged protein. By fusing 2 core pyrenoid components with the TurboID tag, we generated a high-confidence pyrenoid proxiome that contains most known pyrenoid proteins, in addition to new pyrenoid candidates. Fluorescence protein tagging of 7 previously uncharacterized TurboID-identified proteins showed that 6 localized to a range of subpyrenoid regions. The resulting proxiome also suggests new secondary functions for the pyrenoid in RNA-associated processes and redox-sensitive iron-sulfur cluster metabolism. This developed pipeline can be used to investigate a broad range of biological processes in Chlamydomonas, especially at a temporally resolved suborganellar resolution.
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Affiliation(s)
- Chun Sing Lau
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Adam Dowle
- Department of Biology, University of York, York YO10 5DD, UK
| | - Gavin H Thomas
- Department of Biology, University of York, York YO10 5DD, UK
| | - Philipp Girr
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
| | - Luke C M Mackinder
- Centre for Novel Agricultural Products, Department of Biology, University of York, York YO10 5DD, UK
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25
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Schessner JP, Albrecht V, Davies AK, Sinitcyn P, Borner GHH. Deep and fast label-free Dynamic Organellar Mapping. Nat Commun 2023; 14:5252. [PMID: 37644046 PMCID: PMC10465578 DOI: 10.1038/s41467-023-41000-7] [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: 06/16/2022] [Accepted: 08/16/2023] [Indexed: 08/31/2023] Open
Abstract
The Dynamic Organellar Maps (DOMs) approach combines cell fractionation and shotgun-proteomics for global profiling analysis of protein subcellular localization. Here, we enhance the performance of DOMs through data-independent acquisition (DIA) mass spectrometry. DIA-DOMs achieve twice the depth of our previous workflow in the same mass spectrometry runtime, and substantially improve profiling precision and reproducibility. We leverage this gain to establish flexible map formats scaling from high-throughput analyses to extra-deep coverage. Furthermore, we introduce DOM-ABC, a powerful and user-friendly open-source software tool for analyzing profiling data. We apply DIA-DOMs to capture subcellular localization changes in response to starvation and disruption of lysosomal pH in HeLa cells, which identifies a subset of Golgi proteins that cycle through endosomes. An imaging time-course reveals different cycling patterns and confirms the quantitative predictive power of our translocation analysis. DIA-DOMs offer a superior workflow for label-free spatial proteomics as a systematic phenotype discovery tool.
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Affiliation(s)
- Julia P Schessner
- Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Vincent Albrecht
- Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Alexandra K Davies
- Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
- School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Pavel Sinitcyn
- Computational Systems Biochemistry Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg H H Borner
- Department of Proteomics and Signal Transduction, Systems Biology of Membrane Trafficking Research Group, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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26
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Wang X, Chen C, Yan J, Xu Y, Pan D, Wang L, Yang M. Druggability of Targets for Diagnostic Radiopharmaceuticals. ACS Pharmacol Transl Sci 2023; 6:1107-1119. [PMID: 37588760 PMCID: PMC10425999 DOI: 10.1021/acsptsci.3c00081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 08/18/2023]
Abstract
Targets play an indispensable and pivotal role in the development of radiopharmaceuticals. However, the initial stages of drug discovery projects are often plagued by frequent failures due to inadequate information on druggability and suboptimal target selection. In this context, we aim to present a comprehensive review of the factors that influence target druggability for diagnostic radiopharmaceuticals. Specifically, we explore the crucial determinants of target specificity, abundance, localization, and positivity rate and their respective implications. Through a detailed analysis of existing protein targets, we elucidate the significance of each factor. By carefully considering and balancing these factors during the selection of targets, more efficacious and targeted radiopharmaceuticals are expected to be designed for the diagnosis of a wide range of diseases in the future.
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Affiliation(s)
- Xinyu Wang
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Chongyang Chen
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
| | - Junjie Yan
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Yuping Xu
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
| | - Donghui Pan
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
| | - Lizhen Wang
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
| | - Min Yang
- NHC
Key Laboratory of Nuclear Medicine, Jiangsu Key Laboratory of Molecular
Nuclear Medicine, Jiangsu Institute of Nuclear
Medicine, Wuxi 214063, PR China
- School
of Pharmacy, Nanjing Medical University, Nanjing 211166, PR China
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27
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Husain SS, Ong EJ, Minskiy D, Bober-Irizar M, Irizar A, Bober M. Single-cell subcellular protein localisation using novel ensembles of diverse deep architectures. Commun Biol 2023; 6:489. [PMID: 37147530 PMCID: PMC10163260 DOI: 10.1038/s42003-023-04840-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 04/12/2023] [Indexed: 05/07/2023] Open
Abstract
Unravelling protein distributions within individual cells is vital to understanding their function and state and indispensable to developing new treatments. Here we present the Hybrid subCellular Protein Localiser (HCPL), which learns from weakly labelled data to robustly localise single-cell subcellular protein patterns. It comprises innovative DNN architectures exploiting wavelet filters and learnt parametric activations that successfully tackle drastic cell variability. HCPL features correlation-based ensembling of novel architectures that boosts performance and aids generalisation. Large-scale data annotation is made feasible by our AI-trains-AI approach, which determines the visual integrity of cells and emphasises reliable labels for efficient training. In the Human Protein Atlas context, we demonstrate that HCPL is best performing in the single-cell classification of protein localisation patterns. To better understand the inner workings of HCPL and assess its biological relevance, we analyse the contributions of each system component and dissect the emergent features from which the localisation predictions are derived.
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Affiliation(s)
| | - Eng-Jon Ong
- CVSSP, University of Surrey, Guildford, GU27XH, Surrey, UK
| | - Dmitry Minskiy
- CVSSP, University of Surrey, Guildford, GU27XH, Surrey, UK
| | - Mikel Bober-Irizar
- CVSSP, University of Surrey, Guildford, GU27XH, Surrey, UK
- ForecomAI, London, W1W 5PF, UK
| | | | - Miroslaw Bober
- CVSSP, University of Surrey, Guildford, GU27XH, Surrey, UK
- ForecomAI, London, W1W 5PF, UK
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28
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Sorour AA, Olama ZA, El-Naggar MY, Ali SM. Bioprocess development for extraction and purification of cellulases from Aspergillus niger 3ASZ using statistical experimental design techniques. Int J Biol Macromol 2023; 242:124759. [PMID: 37150365 DOI: 10.1016/j.ijbiomac.2023.124759] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 05/01/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
The amount of cellulosic materials is large and may lead to environmental pollution, so they can be converted into useful materials for use in food or energy. Statistical design (Plackett-Burman and Box-Behnken) was the main topic of this study and was used to optimize the effect of environmental factors on cellulase production by Aspergillus niger. Cellulase production using Plackett-Burman was 6.86-fold higher than the production of cellulase using the basal medium. B0X-Benken showed an increase in the cellulase production equal to 18 times compared to the basal medium, where the cellulase produced had an activity equal to 79.4 U/mL/min. Ammonium sulfate precipitation was applied to the crude enzyme, followed by sequential fractionation with an Amicon system. The Amicon was used to demonstrate the final volume, total enzyme activity, specific activity, purification fold, and yield of cellulase (partially purified enzyme). Numerous cellulolytic enzymes are abundant in Aspergillus species. All of the data showed that Aspergillus sp. might be a reliable source of industrially and economically useful cellulases. By statistically calculating the relevance of a large number of elements in one experiment using a multifactorial statistical design, time may be saved while still maintaining the validity of each component.
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Affiliation(s)
- Aman A Sorour
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Zakia A Olama
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Moustafa Y El-Naggar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Egypt
| | - Safaa M Ali
- Nucleic Acid Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, Alexandria, Egypt.
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29
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Rosenkranz AA, Slastnikova TA. Prospects of Using Protein Engineering for Selective Drug Delivery into a Specific Compartment of Target Cells. Pharmaceutics 2023; 15:pharmaceutics15030987. [PMID: 36986848 PMCID: PMC10055131 DOI: 10.3390/pharmaceutics15030987] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/13/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
A large number of proteins are successfully used to treat various diseases. These include natural polypeptide hormones, their synthetic analogues, antibodies, antibody mimetics, enzymes, and other drugs based on them. Many of them are demanded in clinical settings and commercially successful, mainly for cancer treatment. The targets for most of the aforementioned drugs are located at the cell surface. Meanwhile, the vast majority of therapeutic targets, which are usually regulatory macromolecules, are located inside the cell. Traditional low molecular weight drugs freely penetrate all cells, causing side effects in non-target cells. In addition, it is often difficult to elaborate a small molecule that can specifically affect protein interactions. Modern technologies make it possible to obtain proteins capable of interacting with almost any target. However, proteins, like other macromolecules, cannot, as a rule, freely penetrate into the desired cellular compartment. Recent studies allow us to design multifunctional proteins that solve these problems. This review considers the scope of application of such artificial constructs for the targeted delivery of both protein-based and traditional low molecular weight drugs, the obstacles met on the way of their transport to the specified intracellular compartment of the target cells after their systemic bloodstream administration, and the means to overcome those difficulties.
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Affiliation(s)
- Andrey A Rosenkranz
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
- Department of Biophysics, Faculty of Biology, Lomonosov Moscow State University, 1-12 Leninskie Gory St., 119234 Moscow, Russia
| | - Tatiana A Slastnikova
- Laboratory of Molecular Genetics of Intracellular Transport, Institute of Gene Biology of Russian Academy of Sciences, 34/5 Vavilov St., 119334 Moscow, Russia
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30
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Peng J, Chan C, Zhang S, Sklavounos AA, Olson ME, Scott EY, Hu Y, Rajesh V, Li BB, Chamberlain MD, Zhang S, Peng H, Wheeler AR. All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis. Chem Sci 2023; 14:2887-2900. [PMID: 36937585 PMCID: PMC10016607 DOI: 10.1039/d3sc00560g] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 02/24/2023] Open
Abstract
Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Calvin Chan
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Shuailong Zhang
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Mechatronical Engineering, Beijing Institute of Technology Beijing 100081 China
- Beijing Advanced Innovation Center for Intelligent Robots and Systems, Beijing Institute of Technology Beijing 100081 China
| | - Alexandros A Sklavounos
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
| | - Maxwell E Olson
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Erica Y Scott
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Yechen Hu
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - Vigneshwar Rajesh
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
| | - Bingyu B Li
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
| | - M Dean Chamberlain
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
- Saskatchewan Cancer Agency, University of Saskatchewan 107 Wiggins Road Saskatoon SK S7N 5E5 Canada
| | - Shen Zhang
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital 600 University Avenue Toronto ON M5G 1X5 Canada
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA Changsha Hunan 410000 China
| | - Hui Peng
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- School of Environment, University of Toronto 33 Willcocks Street Toronto ON M5S 3E8 Canada
| | - Aaron R Wheeler
- Department of Chemistry, University of Toronto 80 St. George Street Toronto ON M5S 3H6 Canada +1-416-946-3865 +1-416-946-3866
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto 160 College Street Toronto ON M5S 3E1 Canada
- Institute of Biomedical Engineering, University of Toronto 164 College Street Toronto ON M5S 3G9 Canada
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Wang RH, Luo T, Zhang HL, Du PF. PLA-GNN: Computational inference of protein subcellular location alterations under drug treatments with deep graph neural networks. Comput Biol Med 2023; 157:106775. [PMID: 36921458 DOI: 10.1016/j.compbiomed.2023.106775] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/21/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
The aberrant protein sorting has been observed in many conditions, including complex diseases, drug treatments, and environmental stresses. It is important to systematically identify protein mis-localization events in a given condition. Experimental methods for finding mis-localized proteins are always costly and time consuming. Predicting protein subcellular localizations has been studied for many years. However, only a handful of existing works considered protein subcellular location alterations. We proposed a computational method for identifying alterations of protein subcellular locations under drug treatments. We took three drugs, including TSA (trichostain A), bortezomib and tacrolimus, as instances for this study. By introducing dynamic protein-protein interaction networks, graph neural network algorithms were applied to aggregate topological information under different conditions. We systematically reported potential protein mis-localization events under drug treatments. As far as we know, this is the first attempt to find protein mis-localization events computationally in drug treatment conditions. Literatures validated that a number of proteins, which are highly related to pharmacological mechanisms of these drugs, may undergo protein localization alterations. We name our method as PLA-GNN (Protein Localization Alteration by Graph Neural Networks). It can be extended to other drugs and other conditions. All datasets and codes of this study has been deposited in a GitHub repository (https://github.com/quinlanW/PLA-GNN).
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Affiliation(s)
- Ren-Hua Wang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Tao Luo
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Han-Lin Zhang
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
| | - Pu-Feng Du
- College of Intelligence and Computing, Tianjin University, Tianjin, 300350, China.
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32
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Zhang L, Liang X, Takáč T, Komis G, Li X, Zhang Y, Ovečka M, Chen Y, Šamaj J. Spatial proteomics of vesicular trafficking: coupling mass spectrometry and imaging approaches in membrane biology. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:250-269. [PMID: 36204821 PMCID: PMC9884029 DOI: 10.1111/pbi.13929] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 06/16/2023]
Abstract
In plants, membrane compartmentalization requires vesicle trafficking for communication among distinct organelles. Membrane proteins involved in vesicle trafficking are highly dynamic and can respond rapidly to changes in the environment and to cellular signals. Capturing their localization and dynamics is thus essential for understanding the mechanisms underlying vesicular trafficking pathways. Quantitative mass spectrometry and imaging approaches allow a system-wide dissection of the vesicular proteome, the characterization of ligand-receptor pairs and the determination of secretory, endocytic, recycling and vacuolar trafficking pathways. In this review, we highlight major proteomics and imaging methods employed to determine the location, distribution and abundance of proteins within given trafficking routes. We focus in particular on methodologies for the elucidation of vesicle protein dynamics and interactions and their connections to downstream signalling outputs. Finally, we assess their biological applications in exploring different cellular and subcellular processes.
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Affiliation(s)
- Liang Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
- College of Life ScienceHenan Normal UniversityXinxiangChina
| | - Xinlin Liang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Tomáš Takáč
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - George Komis
- Department of Cell Biology, Centre of the Region Hana for Biotechnological and Agricultural Research, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Xiaojuan Li
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Yuan Zhang
- College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina
| | - Miroslav Ovečka
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
| | - Yanmei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Jozef Šamaj
- Department of Biotechnology, Faculty of SciencePalacky University OlomoucOlomoucCzech Republic
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33
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Albarnaz JD, Weekes MP. Proteomic analysis of antiviral innate immunity. Curr Opin Virol 2023; 58:101291. [PMID: 36529073 DOI: 10.1016/j.coviro.2022.101291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/03/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022]
Abstract
The capacity of host cells to detect and restrict an infecting virus rests on an array of cell-autonomous antiviral effectors and innate immune receptors that can trigger inflammatory processes at tissue and organismal levels. Dynamic changes in protein abundance, subcellular localisation, post-translational modifications and interactions with other biomolecules govern these processes. Proteomics is therefore an ideal experimental tool to discover novel mechanisms of host antiviral immunity. Additional information can be gleaned both about host and virus by systematic analysis of viral immune evasion strategies. In this review, we summarise recent advances in proteomic technologies and their application to antiviral innate immunity.
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Affiliation(s)
- Jonas D Albarnaz
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK
| | - Michael P Weekes
- Cambridge Institute for Medical Research, University of Cambridge, Hills Road, CB2 0XY Cambridge, UK.
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34
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Zhu XL, Bao LX, Xue MQ, Xu YY. Automatic recognition of protein subcellular location patterns in single cells from immunofluorescence images based on deep learning. Brief Bioinform 2023; 24:6964519. [PMID: 36577448 DOI: 10.1093/bib/bbac609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 11/16/2022] [Accepted: 12/11/2022] [Indexed: 12/30/2022] Open
Abstract
With the improvement of single-cell measurement techniques, there is a growing awareness that individual differences exist among cells, and protein expression distribution can vary across cells in the same tissue or cell line. Pinpointing the protein subcellular locations in single cells is crucial for mapping functional specificity of proteins and studying related diseases. Currently, research about single-cell protein location is still in its infancy, and most studies and databases do not annotate proteins at the cell level. For example, in the human protein atlas database, an immunofluorescence image stained for a particular protein shows multiple cells, but the subcellular location annotation is for the whole image, ignoring intercellular difference. In this study, we used large-scale immunofluorescence images and image-level subcellular locations to develop a deep-learning-based pipeline that could accurately recognize protein localizations in single cells. The pipeline consisted of two deep learning models, i.e. an image-based model and a cell-based model. The former used a multi-instance learning framework to comprehensively model protein distribution in multiple cells in each image, and could give both image-level and cell-level predictions. The latter firstly used clustering and heuristics algorithms to assign pseudo-labels of subcellular locations to the segmented cell images, and then used the pseudo-labels to train a classification model. Finally, the image-based model was fused with the cell-based model at the decision level to obtain the final ensemble model for single-cell prediction. Our experimental results showed that the ensemble model could achieve higher accuracy and robustness on independent test sets than state-of-the-art methods.
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Affiliation(s)
- Xi-Liang Zhu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China.,Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
| | - Lin-Xia Bao
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China.,Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
| | - Min-Qi Xue
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China.,Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
| | - Ying-Ying Xu
- School of Biomedical Engineering and Guangdong Provincial Key Laboratory of Medical Image Processing, Southern Medical University, Guangzhou 510515, China.,Guangdong Province Engineering Laboratory for Medical Imaging and Diagnostic Technology, Southern Medical University, Guangzhou 510515, China
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35
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Franciosa G, Kverneland AH, Jensen AWP, Donia M, Olsen JV. Proteomics to study cancer immunity and improve treatment. Semin Immunopathol 2023; 45:241-251. [PMID: 36598558 PMCID: PMC10121539 DOI: 10.1007/s00281-022-00980-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 12/12/2022] [Indexed: 01/05/2023]
Abstract
Cancer survival and progression depend on the ability of tumor cells to avoid immune recognition. Advances in the understanding of cancer immunity and tumor immune escape mechanisms enabled the development of immunotherapeutic approaches. In patients with otherwise incurable metastatic cancers, immunotherapy resulted in unprecedented response rates with the potential for durable complete responses. However, primary and acquired resistance mechanisms limit the efficacy of immunotherapy. Further therapeutic advances require a deeper understanding of the interplay between immune cells and tumors. Most high-throughput studies within the past decade focused on an omics characterization at DNA and RNA level. However, proteins are the molecular effectors of genomic information; therefore, the study of proteins provides deeper understanding of cellular functions. Recent advances in mass spectrometry (MS)-based proteomics at a system-wide scale may allow translational and clinical discoveries by enabling the analysis of understudied post-translational modifications, subcellular protein localization, cell signaling, and protein-protein interactions. In this review, we discuss the potential contribution of MS-based proteomics to preclinical and clinical research findings in the context of tumor immunity and cancer immunotherapies.
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Affiliation(s)
- Giulia Franciosa
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
| | - Anders H Kverneland
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.,National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Agnete W P Jensen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Marco Donia
- National Center of Cancer Immune Therapy, Department of Oncology, Copenhagen University Hospital - Herlev and Gentofte, Herlev, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark.
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36
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Samson R, Zangari F, Gingras AC. Studying Cellular Dynamics Using Proximity-Dependent Biotinylation: Somatic Cell Reprogramming. Methods Mol Biol 2023; 2718:23-52. [PMID: 37665453 DOI: 10.1007/978-1-0716-3457-8_3] [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: 09/05/2023]
Abstract
Assessing the reorganization of proteins and organelles following the induction of reprogramming and differentiation programs is crucial to understand the mechanistic underpinning of morphological and fate changes associated with these processes. The advent of proximity-dependent biotinylation (PDB) methods has overcome some of the limitations of biochemical purification methods, enabling proteomic characterization of most subcellular compartments. The first-generation PDB enzyme, the biotin ligase BirA* used in BioID, has now been used in multiple studies determining the cellular context in which proteins reside, typically under standard growth conditions and using long labeling (usually 8-24 h) times. Capitalizing on the generation of more active PDB enzymes such as miniTurbo that can generate strong biotinylation signals in minutes rather than hours, as well as the development of an inducible lentiviral toolkit for BioID, we define here protocols for time-resolved PDB in primary cells. Here, we report the optimization and application of lentivirally delivered miniTurbo constructs to a mouse fibroblast model of somatic cell reprogramming, allowing the study of this dynamic process. This detailed protocol also provides a baseline reference for researchers who wish to adapt these techniques to other dynamic cellular processes.
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Affiliation(s)
- Reuben Samson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Francesco Zangari
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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37
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Diamond A, Barnabé S, Desgagné‐Penix I. Is a spice missing from the recipe? The intra-cellular localization of vanillin biosynthesis needs further investigations. PLANT BIOLOGY (STUTTGART, GERMANY) 2023; 25:3-7. [PMID: 36066305 PMCID: PMC10087407 DOI: 10.1111/plb.13465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Vanillin is the most popular flavor compound in the world. Substantial effort were made in the last decades to completely elucidate the metabolic pathway that leads to vanillin in plants, with some controversy reported. In V. planifolia, vanillin biosynthesis occurs in plastids or in redifferentiated-plastids termed ''phenyloplasts''. More recently, it was shown that all enzymes required for the conversion of [14 C]-phenylalanine to [14 C]-vanillin-glucoside are confined within that organelle. However, knowing that some of these enzymes are cytosolic or ER-membrane bound in most plant species, it raises questions on the interpretation of data obtained from the technique used and on the true localization of the biosynthetic enzymes in V.planifolia. In addition, intense debate has emerged about the real participation of last enzyme of the pathway involving vanillin synthase (VpVAN) in the direct conversion of ferulic acid to vanillin. With the discovery of another enzyme capable of this conversion and the lack of activity of VpVAN in vitro, further disagreement emerged. One additional challenge to VpVAN being necessary and sufficient is that the transcript for this protein is abundant invarious non-vanillin-producing tissues of the vanilla plant. In this viewpoint, we discuss the findings surrounding the cellular-localization and activity of enzymes of vanillin biosynthesis. This will help to further understand the pathway and urge for additional research study to resolve the debate.
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Affiliation(s)
- A. Diamond
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQuébecCanada
| | - S. Barnabé
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQuébecCanada
| | - I. Desgagné‐Penix
- Department of Chemistry, Biochemistry and PhysicsUniversité du Québec à Trois‐RivièresTrois‐RivièresQuébecCanada
- Groupe de Recherche en Biologie Végétale (GRBV)Trois‐RivièresQuébecCanada
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38
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Das H, Zografakis A, Oeljeklaus S, Warscheid B. Analysis of Yeast Peroxisomes via Spatial Proteomics. Methods Mol Biol 2023; 2643:13-31. [PMID: 36952175 DOI: 10.1007/978-1-0716-3048-8_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Peroxisomes are ubiquitous organelles with essential functions in numerous cellular processes such as lipid metabolism, detoxification of reactive oxygen species, and signaling. Knowledge of the peroxisomal proteome including multi-localized proteins and, most importantly, changes of its composition induced by altering cellular conditions or impaired peroxisome biogenesis and function is of paramount importance for a holistic view on peroxisomes and their diverse functions in a cellular context. In this chapter, we provide a spatial proteomics protocol specifically tailored to the analysis of the peroxisomal proteome of baker's yeast that enables the definition of the peroxisomal proteome under distinct conditions and to monitor dynamic changes of the proteome including the relocation of individual proteins to a different cellular compartment. The protocol comprises subcellular fractionation by differential centrifugation followed by Nycodenz density gradient centrifugation of a crude peroxisomal fraction, quantitative mass spectrometric measurements of subcellular and density gradient fractions, and advanced computational data analysis, resulting in the establishment of organellar maps on a global scale.
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Affiliation(s)
- Hirak Das
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Alexandros Zografakis
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Silke Oeljeklaus
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
| | - Bettina Warscheid
- Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany.
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany.
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39
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Mou M, Pan Z, Lu M, Sun H, Wang Y, Luo Y, Zhu F. Application of Machine Learning in Spatial Proteomics. J Chem Inf Model 2022; 62:5875-5895. [PMID: 36378082 DOI: 10.1021/acs.jcim.2c01161] [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: 11/16/2022]
Abstract
Spatial proteomics is an interdisciplinary field that investigates the localization and dynamics of proteins, and it has gained extensive attention in recent years, especially the subcellular proteomics. Numerous evidence indicate that the subcellular localization of proteins is associated with various cellular processes and disease progression. Mass spectrometry (MS)-based and imaging-based experimental approaches have been developed to acquire large-scale spatial proteomic data. To allow the reliable analysis of increasingly complex spatial proteomics data, machine learning (ML) methods have been widely used in both MS-based and imaging-based spatial proteomic data analysis pipelines. Here, we comprehensively survey the applications of ML in spatial proteomics from following aspects: (1) data resources for spatial proteome are comprehensively introduced; (2) the roles of different ML algorithms in data analysis pipelines are elaborated; (3) successful applications of spatial proteomics and several analytical tools integrating ML methods are presented; (4) challenges existing in modern ML-based spatial proteomics studies are discussed. This review provides guidelines for researchers seeking to apply ML methods to analyze spatial proteomic data and can facilitate insightful understanding of cell biology as well as the future research in medical and drug discovery communities.
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Affiliation(s)
- Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziqi Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Mingkun Lu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yunxia Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yongchao Luo
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
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40
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Wang PS, Ma H, Yan S, Lu X, Tang H, Xi XH, Peng XH, Huang Y, Bao YF, Cao MF, Wang H, Huang J, Liu G, Wang X, Ren B. Correlation coefficient-directed label-free characterization of native proteins by surface-enhanced Raman spectroscopy. Chem Sci 2022; 13:13829-13835. [PMID: 36544733 PMCID: PMC9710310 DOI: 10.1039/d2sc04775f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/30/2022] [Indexed: 12/24/2022] Open
Abstract
Investigation of proteins in their native state is the core of proteomics towards better understanding of their structures and functions. Surface-enhanced Raman spectroscopy (SERS) has shown its unique advantages in protein characterization with fingerprint information and high sensitivity, which makes it a promising tool for proteomics. It is still challenging to obtain SERS spectra of proteins in the native state and evaluate the native degree. Here, we constructed 3D physiological hotspots for a label-free dynamic SERS characterization of a native protein with iodide-modified 140 nm Au nanoparticles. We further introduced the correlation coefficient to quantitatively evaluate the variation of the native degree, whose quantitative nature allows us to explicitly investigate the Hofmeister effect on the protein structure. We realized the classification of a protein of SARS-CoV-2 variants in 15 min, which has not been achieved before. This study offers an effective tool for tracking the dynamic structure of proteins and biomedical research.
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Affiliation(s)
- Ping-Shi Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Hao Ma
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Sen Yan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Xinyu Lu
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Hui Tang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Xiao-Han Xi
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Xiao-Hui Peng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Yajun Huang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Yi-Fan Bao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Mao-Feng Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Huimeng Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Jinglin Huang
- Laser Fusion Research Center, China Academy of Engineering Physics Mianyang 621900 China
| | - Guokun Liu
- State Key Laboratory of Marine Environmental Science, College of the Environment and Ecology, Xiamen University Xiamen 361005 China
| | - Xiang Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
| | - Bin Ren
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials (i-ChEM), Innovation Laboratory for Sciences and Technologies of Energy Materials of Fujian Province (IKKEM), Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University Xiamen 361005 China
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Watson J, Ferguson HR, Brady RM, Ferguson J, Fullwood P, Mo H, Bexley KH, Knight D, Howell G, Schwartz JM, Smith MP, Francavilla C. Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival. Nat Commun 2022; 13:6589. [PMID: 36329028 DOI: 10.1101/2021.01.17.427038] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/19/2022] [Indexed: 05/26/2023] Open
Abstract
Receptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we reveal FGFR signalling partners proximal to recycling endosomes by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphorylated peptides enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncover that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the recycling endosomes, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve cellular signalling.
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Affiliation(s)
- Joanne Watson
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Harriet R Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Rosie M Brady
- Division of Cancer Sciences, School of Medical Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester, M20 4GJ, UK
| | - Jennifer Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Paul Fullwood
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Hanyi Mo
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Katherine H Bexley
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - David Knight
- Bio-MS Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Gareth Howell
- Flow Cytometry Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Jean-Marc Schwartz
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Michael P Smith
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
- Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, M139PT, Manchester, UK.
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42
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Watson J, Ferguson HR, Brady RM, Ferguson J, Fullwood P, Mo H, Bexley KH, Knight D, Howell G, Schwartz JM, Smith MP, Francavilla C. Spatially resolved phosphoproteomics reveals fibroblast growth factor receptor recycling-driven regulation of autophagy and survival. Nat Commun 2022; 13:6589. [PMID: 36329028 PMCID: PMC9633600 DOI: 10.1038/s41467-022-34298-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Receptor Tyrosine Kinase (RTK) endocytosis-dependent signalling drives cell proliferation and motility during development and adult homeostasis, but is dysregulated in diseases, including cancer. The recruitment of RTK signalling partners during endocytosis, specifically during recycling to the plasma membrane, is still unknown. Focusing on Fibroblast Growth Factor Receptor 2b (FGFR2b) recycling, we reveal FGFR signalling partners proximal to recycling endosomes by developing a Spatially Resolved Phosphoproteomics (SRP) approach based on APEX2-driven biotinylation followed by phosphorylated peptides enrichment. Combining this with traditional phosphoproteomics, bioinformatics, and targeted assays, we uncover that FGFR2b stimulated by its recycling ligand FGF10 activates mTOR-dependent signalling and ULK1 at the recycling endosomes, leading to autophagy suppression and cell survival. This adds to the growing importance of RTK recycling in orchestrating cell fate and suggests a therapeutically targetable vulnerability in ligand-responsive cancer cells. Integrating SRP with other systems biology approaches provides a powerful tool to spatially resolve cellular signalling.
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Affiliation(s)
- Joanne Watson
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Harriet R Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Rosie M Brady
- Division of Cancer Sciences, School of Medical Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, Manchester, M20 4GJ, UK
| | - Jennifer Ferguson
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Paul Fullwood
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Hanyi Mo
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Katherine H Bexley
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - David Knight
- Bio-MS Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Gareth Howell
- Flow Cytometry Core Research Facility, FBMH, The University of Manchester, M139PT, Manchester, UK
| | - Jean-Marc Schwartz
- Division of Evolution, Infection and Genomics, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK
| | - Michael P Smith
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
| | - Chiara Francavilla
- Division of Molecular and Cellular Function, School of Biological Science, Faculty of Biology Medicine and Health (FBMH), The University of Manchester, M139PT, Manchester, UK.
- Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, M139PT, Manchester, UK.
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43
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Mitrea DM, Mittasch M, Gomes BF, Klein IA, Murcko MA. Modulating biomolecular condensates: a novel approach to drug discovery. Nat Rev Drug Discov 2022; 21:841-862. [PMID: 35974095 PMCID: PMC9380678 DOI: 10.1038/s41573-022-00505-4] [Citation(s) in RCA: 89] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2022] [Indexed: 12/12/2022]
Abstract
In the past decade, membraneless assemblies known as biomolecular condensates have been reported to play key roles in many cellular functions by compartmentalizing specific proteins and nucleic acids in subcellular environments with distinct properties. Furthermore, growing evidence supports the view that biomolecular condensates often form by phase separation, in which a single-phase system demixes into a two-phase system consisting of a condensed phase and a dilute phase of particular biomolecules. Emerging understanding of condensate function in normal and aberrant cellular states, and of the mechanisms of condensate formation, is providing new insights into human disease and revealing novel therapeutic opportunities. In this Perspective, we propose that such insights could enable a previously unexplored drug discovery approach based on identifying condensate-modifying therapeutics (c-mods), and we discuss the strategies, techniques and challenges involved.
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44
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Santos HJ, Nozaki T. The mitosome of the anaerobic parasitic protist Entamoeba histolytica: A peculiar and minimalist mitochondrion-related organelle. J Eukaryot Microbiol 2022; 69:e12923. [PMID: 35588086 PMCID: PMC9796589 DOI: 10.1111/jeu.12923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The simplest class of mitochondrion-related organelles (MROs) is the mitosome, an organelle present in a few anaerobic protozoan parasites such as Entamoeba histolytica, Giardia intestinalis, and Cryptosporidium parvum. E. histolytica causes amoebiasis in humans, deemed as one of the important, yet neglected tropical infections in the world. Much of the enigma of the E. histolytica mitosome circles around the obvious lack of a majority of known mitochondrial components and functions exhibited in other organisms. The identification of enzymes responsible for sulfate activation (AS, IPP, and APSK) and a number of lineage-specific proteins such as the outer membrane beta-barrel protein (MBOMP30), and transmembrane domain-containing proteins that bind to various organellar proteins (ETMP1, ETMP30, EHI_170120, and EHI_099350) showcased the remarkable divergence of this organelle compared to the other MROs of anaerobic protozoa. Here, we summarize the findings regarding the biology of the mitosomes in E. histolytica, from their discovery up to the present understanding of its roles and interactions. We also include current advances and future perspectives on the biology, biochemistry, and evolution of the mitosomes of E. histolytica.
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Affiliation(s)
- Herbert J. Santos
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
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Wang H, Wang Z, Gao H, Liu J, Qiao Z, Zhao B, Liang Z, Jiang B, Zhang L, Zhang Y. A photo-oxidation driven proximity labeling strategy enables profiling of mitochondrial proteome dynamics in living cells. Chem Sci 2022; 13:11943-11950. [PMID: 36320915 PMCID: PMC9580500 DOI: 10.1039/d2sc04087e] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/27/2022] [Indexed: 07/21/2023] Open
Abstract
Mapping the proteomic landscape of mitochondria with spatiotemporal precision plays a pivotal role in elucidating the delicate biological functions and complex relationship with other organelles in a variety of dynamic physiological processes which necessitates efficient and controllable chemical tools. We herein report a photo-oxidation driven proximity labeling strategy to profile the mitochondrial proteome by light dependence in living cells with high spatiotemporal resolution. Taking advantage of organelle-localizable organic photoactivated probes generating reactive species and nucleophilic substrates for proximal protein oxidation and trapping, mitochondrial proteins were selectively labeled by spatially limited reactions in their native environment. Integration of photo-oxidation driven proximity labeling and quantitative proteomics facilitated the plotting of the mitochondrial proteome in which up to 310 mitochondrial proteins were identified with a specificity of 64% in HeLa cells. Furthermore, mitochondrial proteome dynamics was deciphered in drug resistant Huh7 and LPS stimulated HMC3 cells which were hard-to-transfect. A number of differential proteins were quantified which were intimately linked to critical processes and provided insights into the related molecular mechanisms of drug resistance and neuroinflammation in the perspective of mitochondria. The photo-oxidation driven proximity labeling strategy offers solid technical support to a highly precise proteomic platform in time and finer space for more knowledge of subcellular biology.
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Affiliation(s)
- He Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhiting Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Hang Gao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Jianhui Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zichun Qiao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
- University of Chinese Academy of Sciences Beijing 100049 China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Bo Jiang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences Dalian 116023 China
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Dhakal S, Macreadie I. The Use of Yeast in Biosensing. Microorganisms 2022; 10:1772. [PMID: 36144374 PMCID: PMC9505958 DOI: 10.3390/microorganisms10091772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 11/18/2022] Open
Abstract
Yeast has been used as a model for several diseases as it is the simplest unicellular eukaryote, safe and easy to culture and harbors most of the fundamental processes that are present in almost all higher eukaryotes, including humans. From understanding the pathogenesis of disease to drug discovery studies, yeast has served as an important biosensor. It is not only due to the conservation of genetics, amenable modification of its genome and easily accessible analytical methods, but also some characteristic features such as its ability to survive with defective mitochondria, making it a highly flexible microbe for designing whole-cell biosensing systems. The aim of this review is to report on how yeasts have been utilized as biosensors, reporting on responses to various stimuli.
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Affiliation(s)
| | - Ian Macreadie
- School of Science, RMIT University, Bundoora, VIC 3083, Australia
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47
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Zhang S, Jiang H, Wu Q. Editorial: Exploring the subcellular proteome and its post-translational modifications. Front Mol Biosci 2022; 9:994961. [PMID: 36032683 PMCID: PMC9400011 DOI: 10.3389/fmolb.2022.994961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 07/19/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Shen Zhang
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-XIANGYA, Changsha, China
| | - Hao Jiang
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Qi Wu
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- *Correspondence: Qi Wu,
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48
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Spatial Proteomics Reveals Differences in the Cellular Architecture of Antibody-Producing CHO and Plasma Cell-Derived Cells. Mol Cell Proteomics 2022; 21:100278. [PMID: 35934186 PMCID: PMC9562429 DOI: 10.1016/j.mcpro.2022.100278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 07/28/2022] [Accepted: 07/30/2022] [Indexed: 01/18/2023] Open
Abstract
Most of the recombinant biotherapeutics employed today to combat severe illnesses, for example, various types of cancer or autoimmune diseases, are produced by Chinese hamster ovary (CHO) cells. To meet the growing demand of these pharmaceuticals, CHO cells are under constant development in order to enhance their stability and productivity. The last decades saw a shift from empirical cell line optimization toward rational cell engineering using a growing number of large omics datasets to alter cell physiology on various levels. Especially proteomics workflows reached new levels in proteome coverage and data quality because of advances in high-resolution mass spectrometry instrumentation. One type of workflow concentrates on spatial proteomics by usage of subcellular fractionation of organelles with subsequent shotgun mass spectrometry proteomics and machine learning algorithms to determine the subcellular localization of large portions of the cellular proteome at a certain time point. Here, we present the first subcellular spatial proteome of a CHO-K1 cell line producing high titers of recombinant antibody in comparison to the spatial proteome of an antibody-producing plasma cell-derived myeloma cell line. Both cell lines show colocalization of immunoglobulin G chains with chaperones and proteins associated in protein glycosylation within the endoplasmic reticulum compartment. However, we report differences in the localization of proteins associated to vesicle-mediated transport, transcription, and translation, which may affect antibody production in both cell lines. Furthermore, pairing subcellular localization data with protein expression data revealed elevated protein masses for organelles in the secretory pathway in plasma cell-derived MPC-11 (Merwin plasma cell tumor-11) cells. Our study highlights the potential of subcellular spatial proteomics combined with protein expression as potent workflow to identify characteristics of highly efficient recombinant protein-expressing cell lines. Data are available via ProteomeXchange with identifier PXD029115.
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49
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Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre LM, Lehtiö J. SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. Nat Protoc 2022; 17:1832-1867. [PMID: 35732783 DOI: 10.1038/s41596-022-00699-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/18/2022] [Indexed: 11/09/2022]
Abstract
The molecular functions of a protein are defined by its inherent properties in relation to its environment and interaction network. Within a cell, this environment and network are defined by the subcellular location of the protein. Consequently, it is crucial to know the localization of a protein to fully understand its functions. Recently, we have developed a mass spectrometry- (MS) and bioinformatics-based pipeline to generate a proteome-wide resource for protein subcellular localization across multiple human cancer cell lines ( www.subcellbarcode.org ). Here, we present a detailed wet-lab protocol spanning from subcellular fractionation to MS-sample preparation and analysis. A key feature of this protocol is that it includes all generated cell fractions without discarding any material during the fractionation process. We also describe the subsequent quantitative MS-data analysis, machine learning-based classification, differential localization analysis and visualization of the output. For broad applicability, we evaluated the pipeline by using MS data generated by two different peptide pre-fractionation approaches, namely high-resolution isoelectric focusing and high-pH reverse-phase fractionation, as well as direct analysis without pre-fractionation by using long-gradient liquid chromatography-MS. Moreover, an R package covering the dry-lab part of the method was developed and made available through Bioconductor. The method is straightforward and robust, and the entire protocol, from cell harvest to classification output, can be performed within 1-2 weeks. The protocol enables accurate classification of proteins to 15 compartments and 4 neighborhoods, visualization of the output data and differential localization analysis including treatment-induced protein relocalization, condition-dependent localization or cell type-specific localization. The SubCellBarCode package is freely available at https://bioconductor.org/packages/devel/bioc/html/SubCellBarCode.html .
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Affiliation(s)
- Taner Arslan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Yanbo Pan
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Georgios Mermelekas
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Mattias Vesterlund
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden
| | - Lukas M Orre
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden.
| | - Janne Lehtiö
- Department of Oncology and Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden.
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50
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Nakai K, Wei L. Recent Advances in the Prediction of Subcellular Localization of Proteins and Related Topics. FRONTIERS IN BIOINFORMATICS 2022; 2:910531. [PMID: 36304291 PMCID: PMC9580943 DOI: 10.3389/fbinf.2022.910531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Prediction of subcellular localization of proteins from their amino acid sequences has a long history in bioinformatics and is still actively developing, incorporating the latest advances in machine learning and proteomics. Notably, deep learning-based methods for natural language processing have made great contributions. Here, we review recent advances in the field as well as its related fields, such as subcellular proteomics and the prediction/recognition of subcellular localization from image data.
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Affiliation(s)
- Kenta Nakai
- Institute of Medical Science, The University of Tokyo, Minato-Ku, Japan
- *Correspondence: Kenta Nakai,
| | - Leyi Wei
- School of Software, Shandong University, Jinan, China
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