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Li L, Zou Y, Shen C, Chen N, Tong M, Liu R, Wang J, Ning G. Hepatic Dyrk1b impairs systemic glucose homeostasis by modulating Wbp2 expression in a kinase activity-dependent manner. Heliyon 2024; 10:e36726. [PMID: 39296215 PMCID: PMC11407929 DOI: 10.1016/j.heliyon.2024.e36726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/05/2024] [Accepted: 08/21/2024] [Indexed: 09/21/2024] Open
Abstract
Patients with gain-of-function mutations of Dyrk1b have higher fasting blood glucose (FBG) levels. However, the role of Dyrk1b in glucose metabolism is not fully elucidated. Herein, we found that hepatic Dyrk1b overexpression in mice impaired systemic glucose tolerance and hepatic insulin signaling. Dyrk1b overexpression in vitro attenuated insulin signaling in a kinase activity-dependent manner, and its kinase activity was required for its effect on systemic glucose homeostasis and hepatic insulin signaling in vivo. Dyrk1b ablation improved systemic glucose tolerance and hepatic insulin signaling in mice. Quantitative proteomic analyses showed that Dyrk1b downregulated WW domain-binding protein 2 (Wbp2) protein abundance. Mechanistically, Dyrk1b enhanced Wbp2 ubiquitylation and proteasomal degradation. Restoration of hepatic Wbp2 partially rescued the impaired glucose homeostasis in Dyrk1b overexpression mice. In addition, Dyrk1b inhibition with AZ191 moderately improved systemic glucose homeostasis. Our study uncovers that hepatic Dyrk1b impairs systemic glucose homeostasis via its modulation of Wbp2 expression in a kinase activity-dependent manner.
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Affiliation(s)
- Lianju Li
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Yaoyu Zou
- Shanghai Ji Ai Genetics & IVF Institute, Obstetrics & Gynecology Hospital, Fudan University, Shanghai, 200025, China
| | - Chongrong Shen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Na Chen
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Muye Tong
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Ruixin Liu
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Jiqiu Wang
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
| | - Guang Ning
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai National Center for Translational Medicine, Shanghai, 200025, China
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Welter AS, Gerwien M, Kerridge R, Alp KM, Mertins P, Selbach M. Combining Data Independent Acquisition with Spike-in SILAC (DIA-SiS) Improves Proteome Coverage and Quantification. Mol Cell Proteomics 2024:100839. [PMID: 39271013 DOI: 10.1016/j.mcpro.2024.100839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 08/22/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024] Open
Abstract
Data Independent Acquisition (DIA) is increasingly preferred over Data Dependent Acquisition (DDA) due to its higher throughput and fewer missing values. Whereas DDA often utilizes stable isotope labeling to improve quantification, DIA mostly relies on label-free approaches. Efforts to integrate DIA with isotope labeling include chemical methods like mTRAQ and dimethyl labeling, which, while effective, complicate sample preparation. Stable isotope labeling by amino acids in cell culture (SILAC) achieves high labeling efficiency through the metabolic incorporation of heavy labels into proteins in vivo. However, the need for metabolic incorporation limits the direct use in clinical scenarios and certain high-throughput experiments. Spike-in SILAC methods utilize an externally generated heavy sample as an internal reference, enabling SILAC-based quantification even for samples that cannot be directly labeled. Here, we combine DIA with spike-in SILAC (DIA-SiS), leveraging the robust quantification of SILAC without the complexities associated with chemical labeling. We developed DIA-SiS and rigorously assessed its performance with mixed-species benchmark samples on bulk and single cell-like amount level. We demonstrate that DIA-SiS substantially improves proteome coverage and quantification compared to label-free approaches and reduces incorrectly quantified proteins. Additionally, DIA-SiS proves effective in analyzing proteins in low-input formalin-fixed paraffin-embedded (FFPE) tissue sections. DIA-SiS combines the precision of stable isotope-based quantification with the simplicity of label-free sample preparation, facilitating simple, accurate and comprehensive proteome profiling.
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Affiliation(s)
- Anna Sophie Welter
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
| | - Maximilian Gerwien
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
| | - Robert Kerridge
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Faculty of Life Sciences, Humboldt-Universität zu Berlin, Unter den Linden 6, 10117 Berlin, Germany
| | - Keziban Merve Alp
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Berlin Institute of Health, Berlin, Germany
| | - Matthias Selbach
- Max Delbrück Center for Molecular Medicine, Robert-Rössle-Str. 10, 13092 Berlin, Germany; Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany.
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3
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Calvete JJ, Lomonte B, Saviola AJ, Calderón Celis F, Ruiz Encinar J. Quantification of snake venom proteomes by mass spectrometry-considerations and perspectives. MASS SPECTROMETRY REVIEWS 2024; 43:977-997. [PMID: 37155340 DOI: 10.1002/mas.21850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 11/24/2022] [Accepted: 03/30/2023] [Indexed: 05/10/2023]
Abstract
The advent of soft ionization mass spectrometry-based proteomics in the 1990s led to the development of a new dimension in biology that conceptually allows for the integral analysis of whole proteomes. This transition from a reductionist to a global-integrative approach is conditioned to the capability of proteomic platforms to generate and analyze complete qualitative and quantitative proteomics data. Paradoxically, the underlying analytical technique, molecular mass spectrometry, is inherently nonquantitative. The turn of the century witnessed the development of analytical strategies to endow proteomics with the ability to quantify proteomes of model organisms in the sense of "an organism for which comprehensive molecular (genomic and/or transcriptomic) resources are available." This essay presents an overview of the strategies and the lights and shadows of the most popular quantification methods highlighting the common misuse of label-free approaches developed for model species' when applied to quantify the individual components of proteomes of nonmodel species (In this essay we use the term "non-model" organisms for species lacking comprehensive molecular (genomic and/or transcriptomic) resources, a circumstance that, as we detail in this review-essay, conditions the quantification of their proteomes.). We also point out the opportunity of combining elemental and molecular mass spectrometry systems into a hybrid instrumental configuration for the parallel identification and absolute quantification of venom proteomes. The successful application of this novel mass spectrometry configuration in snake venomics represents a proof-of-concept for a broader and more routine application of hybrid elemental/molecular mass spectrometry setups in other areas of the proteomics field, such as phosphoproteomics, metallomics, and in general in any biological process where a heteroatom (i.e., any atom other than C, H, O, N) forms integral part of its mechanism.
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Affiliation(s)
- Juan J Calvete
- Evolutionary and Translational Venomics Laboratory, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Bruno Lomonte
- Unidad de Proteómica, Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Anthony J Saviola
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | | | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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Wang Z, Liu PK, Li L. A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics. ACS MEASUREMENT SCIENCE AU 2024; 4:315-337. [PMID: 39184361 PMCID: PMC11342459 DOI: 10.1021/acsmeasuresciau.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/01/2024] [Accepted: 04/03/2024] [Indexed: 08/27/2024]
Abstract
Recent advancements in mass spectrometry (MS) have revolutionized quantitative proteomics, with multiplex isotope labeling emerging as a key strategy for enhancing accuracy, precision, and throughput. This tutorial review offers a comprehensive overview of multiplex isotope labeling techniques, including precursor-based, mass defect-based, reporter ion-based, and hybrid labeling methods. It details their fundamental principles, advantages, and inherent limitations along with strategies to mitigate the limitation of ratio-distortion. This review will also cover the applications and latest progress in these labeling techniques across various domains, including cancer biomarker discovery, neuroproteomics, post-translational modification analysis, cross-linking MS, and single-cell proteomics. This Review aims to provide guidance for researchers on selecting appropriate methods for their specific goals while also highlighting the potential future directions in this rapidly evolving field.
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Affiliation(s)
- Zicong Wang
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Peng-Kai Liu
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
| | - Lingjun Li
- School
of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Biophysics
Graduate program, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Department
of Chemistry, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
- Lachman
Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
- Wisconsin
Center for NanoBioSystems, School of Pharmacy, University of Wisconsin—Madison, Madison, Wisconsin 53705, United States
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Ergin EK, Myung JJ, Lange PF. Statistical Testing for Protein Equivalence Identifies Core Functional Modules Conserved across 360 Cancer Cell Lines and Presents a General Approach to Investigating Biological Systems. J Proteome Res 2024; 23:2169-2185. [PMID: 38804581 PMCID: PMC11166143 DOI: 10.1021/acs.jproteome.4c00131] [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: 02/23/2024] [Revised: 05/04/2024] [Accepted: 05/17/2024] [Indexed: 05/29/2024]
Abstract
Quantitative proteomics has enhanced our capability to study protein dynamics and their involvement in disease using various techniques, including statistical testing, to discern the significant differences between conditions. While most focus is on what is different between conditions, exploring similarities can provide valuable insights. However, exploring similarities directly from the analyte level, such as proteins, genes, or metabolites, is not a standard practice and is not widely adopted. In this study, we propose a statistical framework called QuEStVar (Quantitative Exploration of Stability and Variability through statistical hypothesis testing), enabling the exploration of quantitative stability and variability of features with a combined statistical framework. QuEStVar utilizes differential and equivalence testing to expand statistical classifications of analytes when comparing conditions. We applied our method to an extensive data set of cancer cell lines and revealed a quantitatively stable core proteome across diverse tissues and cancer subtypes. The functional analysis of this set of proteins highlighted the molecular mechanism of cancer cells to maintain constant conditions of the tumorigenic environment via biological processes, including transcription, translation, and nucleocytoplasmic transport.
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Affiliation(s)
- Enes K. Ergin
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
| | - Junia J.K. Myung
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
| | - Philipp F. Lange
- Department
of Pathology, University of British Columbia, Vancouver, British Columbia V6T 1Z7, Canada
- Michael
Cuccione Childhood Cancer Research Program, BC Children’s Hospital Research Institute, Vancouver, British Columbia V5Z 2H4, Canada
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [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: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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7
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Jurkovic CM, Boisvert FM. Evolution of techniques and tools for replication fork proteome and protein interaction studies. Biochem Cell Biol 2024; 102:135-144. [PMID: 38113480 DOI: 10.1139/bcb-2023-0215] [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: 12/21/2023] Open
Abstract
Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.
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Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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Lu T, Zhou L, Chu Z, Song Y, Wang Q, Zhao M, Dai C, Chen L, Cheng G, Wang J, Guo Q. Cordyceps sinensis relieves non-small cell lung cancer by inhibiting the MAPK pathway. Chin Med 2024; 19:54. [PMID: 38528546 DOI: 10.1186/s13020-024-00895-0] [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: 08/15/2023] [Accepted: 01/23/2024] [Indexed: 03/27/2024] Open
Abstract
OBJECTIVE To determine the pharmacodynamic mechanism underlying Cordyceps sinensis relief in a murine model of non-small cell lung cancer (NSCLC). METHODS We created a murine model of NSCLC and studied the potential molecular mechanism by which C. sinensis relieved NSCLC using a combination of transcriptomics, proteomics, and experimental validation. RESULTS C. sinensis markedly suppressed the fluorescence values in mice with NSCLC, improved the pathologic morphology of lung tissue, ameliorated inflammatory cytokines (tumor necrosis factor-alpha, interleukin-6, interleukin-10, and the oxidative stress indicators superoxide dismutase, malondialdehyde, and glutathione peroxidase). Transcriptomics results showed that the therapeutic effect of C. sinensis was primarily involved in the differentiation and activation of T cells. Based on the proteomic results, C. sinensis likely exerted a protective effect by recruiting immune cells and suppressing tumor cell proliferation via the MAPK pathway. Finally, the experimental validation results indicated that C. sinensis significantly decreased the VEGF and Ki67 expression, downregulated RhoA, Raf-1, and c-fos expression, which are related to cell migration and invasion, increased the serum concentration of hematopoietic factors (EPO and GM-CSF), and improved the percentage of immune cells (natural killer cells, dendritic cells, and CD4+ and CD8+ lymphocytes), which enhanced immune function. CONCLUSIONS Based on our preclinical study, C. sinensis was shown to exert a protective effect on NSCLC, primarily by inhibiting the MAPK pathway.
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Affiliation(s)
- Tianming Lu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Lirun Zhou
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zheng Chu
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yang Song
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Qixin Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Minghong Zhao
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Chuanhao Dai
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Lin Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Guangqing Cheng
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jigang Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
- Department of Oncology, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Qiuyan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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Muneer A, Xie L, Xie X, Zhang F, Wrobel JA, Xiong Y, Yu X, Wang C, Gheorghe C, Wu P, Song J, Ming GL, Jin J, Song H, Shi PY, Chen X. Targeting G9a translational mechanism of SARS-CoV-2 pathogenesis for multifaceted therapeutics of COVID-19 and its sequalae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.04.583415. [PMID: 38496599 PMCID: PMC10942352 DOI: 10.1101/2024.03.04.583415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
By largely unknown mechanism(s), SARS-CoV-2 hijacks the host translation apparatus to promote COVID-19 pathogenesis. We report that the histone methyltransferase G9a noncanonically regulates viral hijacking of the translation machinery to bring about COVID-19 symptoms of hyperinflammation, lymphopenia, and blood coagulation. Chemoproteomic analysis of COVID-19 patient peripheral mononuclear blood cells (PBMC) identified enhanced interactions between SARS-CoV-2-upregulated G9a and distinct translation regulators, particularly the N 6 -methyladenosine (m 6 A) RNA methylase METTL3. These interactions with translation regulators implicated G9a in translational regulation of COVID-19. Inhibition of G9a activity suppressed SARS-CoV-2 replication in human alveolar epithelial cells. Accordingly, multi-omics analysis of the same alveolar cells identified SARS-CoV-2-induced changes at the transcriptional, m 6 A-epitranscriptional, translational, and post-translational (phosphorylation or secretion) levels that were reversed by inhibitor treatment. As suggested by the aforesaid chemoproteomic analysis, these multi-omics-correlated changes revealed a G9a-regulated translational mechanism of COVID-19 pathogenesis in which G9a directs translation of viral and host proteins associated with SARS-CoV-2 replication and with dysregulation of host response. Comparison of proteomic analyses of G9a inhibitor-treated, SARS-CoV-2 infected cells, or ex vivo culture of patient PBMCs, with COVID-19 patient data revealed that G9a inhibition reversed the patient proteomic landscape that correlated with COVID-19 pathology/symptoms. These data also indicated that the G9a-regulated, inhibitor-reversed, translational mechanism outperformed G9a-transcriptional suppression to ultimately determine COVID-19 pathogenesis and to define the inhibitor action, from which biomarkers of serve symptom vulnerability were mechanistically derived. This cell line-to-patient conservation of G9a-translated, COVID-19 proteome suggests that G9a inhibitors can be used to treat patients with COVID-19, particularly patients with long-lasting COVID-19 sequelae.
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10
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Cardoso JMS, Manadas B, Abrantes I, Robertson L, Arcos SC, Troya MT, Navas A, Fonseca L. Pine wilt disease: what do we know from proteomics? BMC PLANT BIOLOGY 2024; 24:98. [PMID: 38331735 PMCID: PMC10854151 DOI: 10.1186/s12870-024-04771-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024]
Abstract
Pine wilt disease (PWD) is a devastating forest disease caused by the pinewood nematode (PWN), Bursaphelenchus xylophilus, a migratory endoparasite that infects several coniferous species. During the last 20 years, advances have been made for understanding the molecular bases of PWN-host trees interactions. Major advances emerged from transcriptomic and genomic studies, which revealed some unique features related to PWN pathogenicity and constituted fundamental data that allowed the development of postgenomic studies. Here we review the proteomic approaches that were applied to study PWD and integrated the current knowledge on the molecular basis of the PWN pathogenicity. Proteomics has been useful for understanding cellular activities and protein functions involved in PWN-host trees interactions, shedding light into the mechanisms associated with PWN pathogenicity and being promising tools to better clarify host trees PWN resistance/susceptibility.
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Affiliation(s)
- Joana M S Cardoso
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martins de Freitas, Coimbra, 3000-456, Portugal.
| | - Bruno Manadas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Rua Larga, Polo I, Coimbra, 3004-504, Portugal
- CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Rua Larga - Faculdade de Medicina, 1ºandar - POLO I, Coimbra, 3004-504, Portugal
| | - Isabel Abrantes
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martins de Freitas, Coimbra, 3000-456, Portugal
| | - Lee Robertson
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC. Instituto de Ciencias Forestales (ICIFOR), Ctra. de La Coruña Km 7.5, Madrid, 28040, Spain
| | - Susana C Arcos
- Museo Nacional de Ciencias Naturales, CSIC. Dpto Biodiversidad y Biología Evolutiva, C/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Maria Teresa Troya
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, CSIC. Instituto de Ciencias Forestales (ICIFOR), Ctra. de La Coruña Km 7.5, Madrid, 28040, Spain
| | - Alfonso Navas
- Museo Nacional de Ciencias Naturales, CSIC. Dpto Biodiversidad y Biología Evolutiva, C/ José Gutiérrez Abascal 2, Madrid, 28006, Spain
| | - Luís Fonseca
- Centre for Functional Ecology, Associate Laboratory TERRA, Department of Life Sciences, University of Coimbra, Calçada Martins de Freitas, Coimbra, 3000-456, Portugal
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11
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Henrion A, Arsene CG, Liebl M, O'Connor G. Label-free quantification of host cell protein impurity in recombinant hemoglobin materials. Anal Bioanal Chem 2024; 416:387-396. [PMID: 38008782 PMCID: PMC10761545 DOI: 10.1007/s00216-023-05024-8] [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: 07/17/2023] [Revised: 10/09/2023] [Accepted: 10/27/2023] [Indexed: 11/28/2023]
Abstract
Quantitative analysis relies on pure-substance primary calibrators with known mass fractions of impurity. Here, label-free quantification (LFQ) is being evaluated as a readily available, reliable method for determining the mass fraction of host cell proteins (HCPs) in bioengineered proteins which are intended for use as protein calibration standards. In this study a purified hemoglobin-A2 (HbA2) protein, obtained through its overexpression in E. coli, was used. Two different materials were produced: natural and U15N-labeled HbA2. For the quantification of impurities, precursor ion (MS1-) intensities were integrated over all E. coli proteins identified and divided by the intensities obtained for HbA2. This ratio was calibrated against the corresponding results for an E. coli cell lysate, which had been spiked at known mass ratios to pure HbA2. To demonstrate the universal applicability of LFQ, further proteomes (yeast and human K562) were then alternatively used for calibration and found to produce comparable results. Valid results were also obtained when the complexity of the calibrator was reduced to a mix of just nine proteins, and a minimum of five proteins was estimated to be sufficient to keep the sampling error below 15%. For the studied materials, HbA2 mass fractions (or purities) of 923 and 928 mg(HbA2)/g(total protein) were found with expanded uncertainties (U) of 2.8 and 1.3%, resp. Value assignment by LFQ thus contributes up to about 3% of the overall uncertainty of HbA2 quantification when these materials are used as calibrators. Further purification of the natural HbA2 yielded a mass fraction of 999.1 mg/g, with a negligible uncertainty (U = 0.02%), though at a significant loss of material. If an overall uncertainty of 5% is acceptable for protein quantification, working with the original materials would therefore definitely be viable, circumventing the need of further purification.
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Affiliation(s)
- André Henrion
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116, Braunschweig, Germany
| | | | - Maik Liebl
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116, Braunschweig, Germany
| | - Gavin O'Connor
- Physikalisch-Technische Bundesanstalt (PTB), Bundesallee 100, 38116, Braunschweig, Germany.
- Department of Biochemistry and Bioinformatics, Technische Universität Braunschweig, 38106, Braunschweig, Germany.
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12
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Degliesposti G. Probing Protein Complexes Composition, Stoichiometry, and Interactions by Peptide-Based Mass Spectrometry. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:41-57. [PMID: 38507199 DOI: 10.1007/978-3-031-52193-5_4] [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: 03/22/2024]
Abstract
The characterization of a protein complex by mass spectrometry can be conducted at different levels. Initial steps regard the qualitative composition of the complex and subunit identification. After that, quantitative information such as stoichiometric ratios and copy numbers for each subunit in a complex or super-complex is acquired. Peptide-based LC-MS/MS offers a wide number of methods and protocols for the characterization of protein complexes. This chapter concentrates on the applications of peptide-based LC-MS/MS for the qualitative, quantitative, and structural characterization of protein complexes focusing on subunit identification, determination of stoichiometric ratio and number of subunits per complex as well as on cross-linking mass spectrometry and hydrogen/deuterium exchange as methods for the structural investigation of the biological assemblies.
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13
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Chatterjee M, Roschitzki B, Grossmann J, Rathinam M, Kunz L, Wolski W, Panse C, Yadav J, Schlapbach R, Rao U, Sreevathsa R. Developmental stage-specific proteome analysis of the legume pod borer Maruca vitrata provides insights on relevant proteins. Int J Biol Macromol 2024; 254:127666. [PMID: 37890743 DOI: 10.1016/j.ijbiomac.2023.127666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/31/2023] [Accepted: 10/23/2023] [Indexed: 10/29/2023]
Abstract
The spotted pod borer, Maruca vitrata (Lepidoptera: Crambidae) is a destructive insect pest that inflicts significant productivity losses on important leguminous crops. Unravelling insect proteomes is vital to comprehend their fundamental molecular mechanisms. This research delved into the proteome profiles of four distinct stages -three larval and pupa of M. vitrata, utilizing LC-MS/MS label-free quantification-based methods. Employing comprehensive proteome analysis with fractionated datasets, we mapped 75 % of 3459 Drosophila protein orthologues out of which 2695 were identified across all developmental stages while, 137 and 94 were exclusive to larval and pupal stages respectively. Cluster analysis of 2248 protein orthologues derived from MaxQuant quantitative dataset depicted six clusters based on expression pattern similarity across stages. Consequently, gene ontology and protein-protein interaction network analyses using STRING database identified cluster 1 (58 proteins) and cluster 6 (25 proteins) associated with insect immune system and lipid metabolism. Furthermore, qRT-PCR-based expression analyses of ten selected proteins-coding genes authenticated the proteome data. Subsequently, functional validation of these chosen genes through gene silencing reduced their transcript abundance accompanied by a marked increase in mortality among dsRNA-injected larvae. Overall, this is a pioneering study to effectively develop a proteome atlas of M. vitrata as a potential resource for crop protection programs.
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Affiliation(s)
- Madhurima Chatterjee
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Bernd Roschitzki
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Maniraj Rathinam
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Laura Kunz
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Witold Wolski
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Christian Panse
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland; Swiss Institute of Bioinformatics, Quartier Sorge, Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Jyoti Yadav
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Ralph Schlapbach
- Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Uma Rao
- Division of Nematology, ICAR-Indian Agricultural Research Institute, New Delhi, India; Engrave Bio Labs Pvt.Ltd., Shanthipuram, Kukatpally, Hyderabad, India.
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14
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Zhao G, Dong H, Dai L, Xie H, Sun H, Zhang J, Wang Q, Xu C, Yin K. Proteomics analysis of Toxoplasma gondii merozoites reveals regulatory proteins involved in sexual reproduction. Microb Pathog 2024; 186:106484. [PMID: 38052278 DOI: 10.1016/j.micpath.2023.106484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 10/18/2023] [Accepted: 11/29/2023] [Indexed: 12/07/2023]
Abstract
Sexual reproduction plays a crucial role in the transmission and life cycle of toxoplasmosis. The merozoites are the only developmental stage capable of differentiation into male and female gametes, thereby initiating sexual reproduction to form oocysts that are excreted into the environment. Hence, our study aimed to perform proteomic analyses of T. gondii Pru strain merozoites, a pre-sexual developmental stage in cat IECs, and tachyzoites, an asexual developmental stage, using the tandem mass tag (TMT) method in order to identify the differentially expressed proteins (DEPs) of merozoites. Proteins functions were subjected to cluster analysis, and DEPs were validated through the qPCR method. The results showed that a total of 106 proteins were identified, out of which 85 proteins had quantitative data. Among these, 15 proteins were differentially expressed within merozoites, with four exhibiting up-regulation and being closely associated with the material and energy metabolism as well as the cell division of T. gondii. Two novel DEPs, namely S8GHL5 and A0A125YP41, were identified, and their homologous family members have been demonstrated to play regulatory roles in oocyte maturation and spermatogenesis in other species. Therefore, they may potentially exhibit regulatory functions during the differentiation of micro- and macro-gametophytes at the initiation stage of sexual reproduction in T. gondii. In conclusion, our results showed that the metabolic and divisional activities in the merozoites surpass those in the tachyzoites, thereby providing structural, material, and energetic support for gametophytes development. The discovery of two novel DEPs associated with sexual reproduction represents a significant advancement in understanding Toxoplasma sexual reproduction initiation and oocyst formation.
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Affiliation(s)
- Guihua Zhao
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Hongjie Dong
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Lisha Dai
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Huanhuan Xie
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Hang Sun
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Junmei Zhang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Qi Wang
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Chao Xu
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
| | - Kun Yin
- Shandong Institute of Parasitic Diseases, Shandong First Medical University & Shandong Academy of Medical Sciences, 11 Taibai Middle Road, Jining City, Shandong Province, 272033, China.
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15
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Muneer A, Wang L, Xie L, Zhang F, Wu B, Mei L, Lenarcic EM, Feng EH, Song J, Xiong Y, Yu X, Wang C, Jain K, Strahl BD, Cook JG, Wan YY, Moorman NJ, Song H, Jin J, Chen X. Non-canonical function of histone methyltransferase G9a in the translational regulation of chronic inflammation. Cell Chem Biol 2023; 30:1525-1541.e7. [PMID: 37858336 PMCID: PMC11095832 DOI: 10.1016/j.chembiol.2023.09.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 06/21/2023] [Accepted: 09/20/2023] [Indexed: 10/21/2023]
Abstract
We report a novel translation-regulatory function of G9a, a histone methyltransferase and well-understood transcriptional repressor, in promoting hyperinflammation and lymphopenia; two hallmarks of endotoxin tolerance (ET)-associated chronic inflammatory complications. Using multiple approaches, we demonstrate that G9a interacts with multiple translation regulators during ET, particularly the N6-methyladenosine (m6A) RNA methyltransferase METTL3, to co-upregulate expression of certain m6A-modified mRNAs that encode immune-checkpoint and anti-inflammatory proteins. Mechanistically, G9a promotes m6A methyltransferase activity of METTL3 at translational/post-translational level by regulating its expression, its methylation, and its cytosolic localization during ET. Additionally, from a broader view extended from the G9a-METTL3-m6A translation regulatory axis, our translatome proteomics approach identified numerous "G9a-translated" proteins that unite the networks associated with inflammation dysregulation, T cell dysfunction, and systemic cytokine response. In sum, we identified a previously unrecognized function of G9a in protein-specific translation that can be leveraged to treat ET-related chronic inflammatory diseases.
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Affiliation(s)
- Adil Muneer
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Li Wang
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ling Xie
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Feng Zhang
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bing Wu
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Liu Mei
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erik M Lenarcic
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Emerald Hillary Feng
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juan Song
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yan Xiong
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Charles Wang
- Center for Genomics, Division of Microbiology & Molecular Genetics, Department of Basic Sciences, Loma Linda University, Loma Linda, CA 92350, USA
| | - Kanishk Jain
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jeanette Gowen Cook
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yisong Y Wan
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nathaniel John Moorman
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Hongjun Song
- Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xian Chen
- Department of Biochemistry & Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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16
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Chen X, Xie L, Sheehy R, Xiong Y, Muneer A, Wrobel J, Park KS, Liu J, Velez J, Luo Y, Li YD, Quintanilla L, Li Y, Xu C, Wen Z, Song J, Jin J, Deshmukh M. Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer's disease proteopathology for precision medication. RESEARCH SQUARE 2023:rs.3.rs-2743792. [PMID: 38045363 PMCID: PMC10690335 DOI: 10.21203/rs.3.rs-2743792/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Current amyloid beta-targeting approaches for Alzheimer's disease (AD) therapeutics only slow cognitive decline for small numbers of patients. This limited efficacy exists because AD is a multifactorial disease whose pathological mechanism(s) and diagnostic biomarkers are largely unknown. Here we report a new mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of a hippocampal proteome that defines the proteopathic nature of AD. Accordingly, we developed a novel brain-penetrant inhibitor of G9a, MS1262, across the blood-brain barrier to block this G9a-regulated, proteopathologic mechanism. Intermittent MS1262 treatment of multiple AD mouse models consistently restored both cognitive and noncognitive functions to healthy levels. Comparison of proteomic/phosphoproteomic analyses of MS1262-treated AD mice with human AD patient data identified multiple pathological brain pathways that elaborate amyloid beta and neurofibrillary tangles as well as blood coagulation, from which biomarkers of early stage of AD including SMOC1 were found to be affected by MS1262 treatment. Notably, these results indicated that MS1262 treatment may reduce or avoid the risk of blood clot burst for brain bleeding or a stroke. This mouse-to-human conservation of G9a-translated AD proteopathology suggests that the global, multifaceted effects of MS1262 in mice could extend to relieve all symptoms of AD patients with minimum side effect. In addition, our mechanistically derived biomarkers can be used for stage-specific AD diagnosis and companion diagnosis of individualized drug effects.
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17
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Delafield DG, Miles HN, Ricke WA, Li L. Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation. J Proteome Res 2023; 22:3508-3518. [PMID: 37815119 PMCID: PMC10732698 DOI: 10.1021/acs.jproteome.3c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.
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Affiliation(s)
- Daniel G. Delafield
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Hannah N. Miles
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
| | - William A. Ricke
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- George M. O’Brien Urology Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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18
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Xie L, Sheehy RN, Xiong Y, Muneer A, Wrobel JA, Park KS, Velez J, Liu J, Luo YJ, Li YD, Quintanilla L, Li Y, Xu C, Deshmukh M, Wen Z, Jin J, Song J, Chen X. Novel brain-penetrant inhibitor of G9a methylase blocks Alzheimer's disease proteopathology for precision medication. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.25.23297491. [PMID: 37961307 PMCID: PMC10635198 DOI: 10.1101/2023.10.25.23297491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Current amyloid beta-targeting approaches for Alzheimer's disease (AD) therapeutics only slow cognitive decline for small numbers of patients. This limited efficacy exists because AD is a multifactorial disease whose pathological mechanism(s) and diagnostic biomarkers are largely unknown. Here we report a new mechanism of AD pathogenesis in which the histone methyltransferase G9a noncanonically regulates translation of a hippocampal proteome that defines the proteopathic nature of AD. Accordingly, we developed a novel brain-penetrant inhibitor of G9a, MS1262, across the blood-brain barrier to block this G9a-regulated, proteopathologic mechanism. Intermittent MS1262 treatment of multiple AD mouse models consistently restored both cognitive and noncognitive functions to healthy levels. Comparison of proteomic/phosphoproteomic analyses of MS1262-treated AD mice with human AD patient data identified multiple pathological brain pathways that elaborate amyloid beta and neurofibrillary tangles as well as blood coagulation, from which biomarkers of early stage of AD including SMOC1 were found to be affected by MS1262 treatment. Notably, these results indicated that MS1262 treatment may reduce or avoid the risk of blood clot burst for brain bleeding or a stroke. This mouse-to-human conservation of G9a-translated AD proteopathology suggests that the global, multifaceted effects of MS1262 in mice could extend to relieve all symptoms of AD patients with minimum side effect. In addition, our mechanistically derived biomarkers can be used for stage-specific AD diagnosis and companion diagnosis of individualized drug effects. One-Sentence Summary A brain-penetrant inhibitor of G9a methylase blocks G9a translational mechanism to reverse Alzheimer's disease related proteome for effective therapy.
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19
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KIM S, KAMARULZAMAN L, TANIGUCHI Y. Recent methodological advances towards single-cell proteomics. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2023; 99:306-327. [PMID: 37673661 PMCID: PMC10749393 DOI: 10.2183/pjab.99.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/20/2023] [Indexed: 09/08/2023]
Abstract
Studying the central dogma at the single-cell level has gained increasing attention to reveal hidden cell lineages and functions that cannot be studied using traditional bulk analyses. Nonetheless, most single-cell studies exploiting genomic and transcriptomic levels fail to address information on proteins that are central to many important biological processes. Single-cell proteomics enables understanding of the functional status of individual cells and is particularly crucial when the specimen is composed of heterogeneous entities of cells. With the growing importance of this field, significant methodological advancements have emerged recently. These include miniaturized and automated sample preparation, multi-omics analyses, and combined analyses of multiple techniques such as mass spectrometry and microscopy. Moreover, artificial intelligence and single-molecule detection technologies have advanced throughput and improved sensitivity limitations, respectively, over conventional methods. In this review, we summarize cutting-edge methodologies for single-cell proteomics and relevant emerging technologies that have been reported in the last 5 years, and provide an outlook on this research field.
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Affiliation(s)
- Sooyeon KIM
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
| | - Latiefa KAMARULZAMAN
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Yuichi TANIGUCHI
- Laboratory for Cell Systems Control, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Sakyo-ku, Kyoto, Japan
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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20
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Wang J, Yu W, D'Anna R, Przybyla A, Wilson M, Sung M, Bullen J, Hurt E, D'Angelo G, Sidders B, Lai Z, Zhong W. Pan-Cancer Proteomics Analysis to Identify Tumor-Enriched and Highly Expressed Cell Surface Antigens as Potential Targets for Cancer Therapeutics. Mol Cell Proteomics 2023; 22:100626. [PMID: 37517589 PMCID: PMC10494184 DOI: 10.1016/j.mcpro.2023.100626] [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: 01/23/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/01/2023] Open
Abstract
The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) provides unique opportunities for cancer target discovery using protein expression. Proteomics data from CPTAC tumor types have been primarily generated using a multiplex tandem mass tag (TMT) approach, which is designed to provide protein quantification relative to reference samples. However, relative protein expression data are suboptimal for prioritization of targets within a tissue type, which requires additional reprocessing of the original proteomics data to derive absolute quantitation estimation. We evaluated the feasibility of using differential protein analysis coupled with intensity-based absolute quantification (iBAQ) to identify tumor-enriched and highly expressed cell surface antigens, employing tandem mass tag (TMT) proteomics data from CPTAC. Absolute quantification derived from TMT proteomics data was highly correlated with that of label-free proteomics data from the CPTAC colon adenocarcinoma cohort, which contains proteomics data measured by both approaches. We validated the TMT-iBAQ approach by comparing the iBAQ value to the receptor density value of HER2 and TROP2 measured by flow cytometry in about 30 selected breast and lung cancer cell lines from the Cancer Cell Line Encyclopedia. Collections of these tumor-enriched and highly expressed cell surface antigens could serve as a valuable resource for the development of cancer therapeutics, including antibody-drug conjugates and immunotherapeutic agents.
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Affiliation(s)
- Jixin Wang
- Oncology Data Science, AstraZeneca, Gaithersburg, Maryland, USA
| | - Wen Yu
- Data Science and AI, BioPharmaceuticals R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Rachel D'Anna
- Oncology Data Science, AstraZeneca, Gaithersburg, Maryland, USA
| | | | - Matt Wilson
- Early TDE Discovery, AstraZeneca, Cambridge, UK
| | | | - John Bullen
- Early TTD Discovery, AstraZeneca, Cambridge, UK
| | - Elaine Hurt
- Early TTD Discovery, AstraZeneca, Cambridge, UK
| | - Gina D'Angelo
- Late Oncology Statistics, Oncology R&D, AstraZeneca, Gaithersburg, Maryland, USA
| | - Ben Sidders
- Oncology Data Science, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Zhongwu Lai
- Oncology Data Science, Oncology R&D, AstraZeneca, Waltham, Massachusetts, USA
| | - Wenyan Zhong
- Oncology Data Science, Oncology R&D, AstraZeneca, New York, New York, USA.
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21
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Filandrova R, Douglas P, Zhan X, Verhey TB, Morrissy S, Turner RW, Schriemer DC. Mouse Model of Fragile X Syndrome Analyzed by Quantitative Proteomics: A Comparison of Methods. J Proteome Res 2023; 22:3054-3067. [PMID: 37595185 DOI: 10.1021/acs.jproteome.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2023]
Abstract
Multiple methods for quantitative proteomics are available for proteome profiling. It is unclear which methods are most useful in situations involving deep proteome profiling and the detection of subtle distortions in the proteome. Here, we compared the performance of seven different strategies in the analysis of a mouse model of Fragile X Syndrome, involving the knockout of the fmr1 gene that is the leading cause of autism spectrum disorder. Focusing on the cerebellum, we show that data-independent acquisition (DIA) and the tandem mass tag (TMT)-based real-time search method (RTS) generated the most informative profiles, generating 334 and 329 significantly altered proteins, respectively, although the latter still suffered from ratio compression. Label-free methods such as BoxCar and a conventional data-dependent acquisition were too noisy to generate a reliable profile, while TMT methods that do not invoke RTS showed a suppressed dynamic range. The TMT method using the TMTpro reagents together with complementary ion quantification (ProC) overcomes ratio compression, but current limitations in ion detection reduce sensitivity. Overall, both DIA and RTS uncovered known regulators of the syndrome and detected alterations in calcium signaling pathways that are consistent with calcium deregulation recently observed in imaging studies. Data are available via ProteomeXchange with the identifier PXD039885.
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Affiliation(s)
- Ruzena Filandrova
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Pauline Douglas
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Xiaoqin Zhan
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Theodore B Verhey
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Sorana Morrissy
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Raymond W Turner
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - David C Schriemer
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Department of Chemistry, University of Calgary, Calgary, Alberta T2N 4N1, Canada
- Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
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22
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Moing A, Berton T, Roch L, Diarrassouba S, Bernillon S, Arrivault S, Deborde C, Maucourt M, Cabasson C, Bénard C, Prigent S, Jacob D, Gibon Y, Lemaire-Chamley M. Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites. BMC PLANT BIOLOGY 2023; 23:365. [PMID: 37479985 PMCID: PMC10362748 DOI: 10.1186/s12870-023-04370-0] [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: 04/18/2023] [Accepted: 07/11/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied. RESULTS We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways. CONCLUSIONS The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.
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Affiliation(s)
- Annick Moing
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Thierry Berton
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Léa Roch
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Salimata Diarrassouba
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Present Address: Laboratoire de Recherche en Sciences Végétales, UMR 5546 UPS/CNRS, Auzeville- Tolosane, F-31320 France
| | - Stéphane Bernillon
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Present Address: INRAE, Mycologie et Sécurité des Aliments, UR 1264, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Stéphanie Arrivault
- Max Planck Institute of Molecular Plant Physiology, am Muehlenberg 14476, Potsdam-Golm, Germany
| | - Catherine Deborde
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Present Address: INRAE, UR1268 BIA, Centre INRAE Pays de Loire – Nantes, Nantes, F-44000 France
- Present address: INRAE, BIBS Facility, Centre INRAE Pays de Loire – Nantes, Nantes, F-44000 France
| | - Mickaël Maucourt
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Cécile Cabasson
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Camille Bénard
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Sylvain Prigent
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Daniel Jacob
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Yves Gibon
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
| | - Martine Lemaire-Chamley
- INRAE, Univ. Bordeaux, Biologie du Fruit et Pathologie, UMR 1332, Centre INRAE de Nouvelle Aquitaine Bordeaux, Villenave d’Ornon, F-33140 France
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23
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Lu H, Wang B, Liu Y, Wang D, Fields L, Zhang H, Li M, Shi X, Zetterberg H, Li L. DiLeu Isobaric Labeling Coupled with Limited Proteolysis Mass Spectrometry for High-Throughput Profiling of Protein Structural Changes in Alzheimer's Disease. Anal Chem 2023; 95:9746-9753. [PMID: 37307028 PMCID: PMC10330787 DOI: 10.1021/acs.analchem.2c05731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
High-throughput quantitative analysis of protein conformational changes has a profound impact on our understanding of the pathological mechanisms of Alzheimer's disease (AD). To establish an effective workflow enabling quantitative analysis of changes in protein conformation within multiple samples simultaneously, here we report the combination of N,N-dimethyl leucine (DiLeu) isobaric tag labeling with limited proteolysis mass spectrometry (DiLeu-LiP-MS) for high-throughput structural protein quantitation in serum samples collected from AD patients and control donors. Twenty-three proteins were discovered to undergo structural changes, mapping to 35 unique conformotypic peptides with significant changes between the AD group and the control group. Seven out of 23 proteins, including CO3, CO9, C4BPA, APOA1, APOA4, C1R, and APOA, exhibited a potential correlation with AD. Moreover, we found that complement proteins (e.g., CO3, CO9, and C4BPA) related to AD exhibited elevated levels in the AD group compared to those in the control group. These results provide evidence that the established DiLeu-LiP-MS method can be used for high-throughput structural protein quantitation, which also showed great potential in achieving large-scale and in-depth quantitative analysis of protein conformational changes in other biological systems.
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Affiliation(s)
- Haiyan Lu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Bin Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuan Liu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Danqing Wang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Lauren Fields
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Hua Zhang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xudong Shi
- Division of Otolaryngology, Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53792, USA
| | - Henrik Zetterberg
- Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, 43141, Gothenburg, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, 43130, Sweden
- Department of Molecular Neuroscience, UCL Institute of Neurology, London, WC1N 3BG, UK
- UK Dementia Research Institute at UCL, London, WC1N 3BG, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, 999077, China
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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24
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Fu X, Hong J, Zhai Y, Liu K, Xu W. Deep Bottom-up Proteomics Enabled by the Integration of Liquid-Phase Ion Trap. Anal Chem 2023. [PMID: 37367992 DOI: 10.1021/acs.analchem.3c00532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
In bottom-up proteomics, the complexity of the proteome requires advanced peptide separation and/or fractionation methods to acquire an in-depth understanding of protein profiles. Proposed earlier as a solution-phase ion manipulation device, liquid phase ion traps (LPITs) were used in front of mass spectrometers to accumulate target ions for improved detection sensitivity. In this work, an LPIT-reversed phase liquid chromatography-tandem mass spectrometry (LPIT-RPLC-MS/MS) platform was established for deep bottom-up proteomics. LPIT was used here as a robust and effective method for peptide fractionation, which also shows good reproducibility and sensitivity on both qualitative and quantitative levels. LPIT separates peptides based on their effective charges and hydrodynamic radii, which is orthogonal to that of RPLC. With excellent orthogonality, the integration of LPIT with RPLC-MS/MS could effectively increase the number of peptides and proteins being detected. When HeLa cells were analyzed, peptide and protein coverages were increased by ∼89.2% and 50.3%, respectively. With high efficiency and low cost, this LPIT-based peptide fraction method could potentially be used in routine deep bottom-up proteomics.
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Affiliation(s)
- Xinyan Fu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Yanbing Zhai
- School of Medical Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Kefu Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China
| | - Wei Xu
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China
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25
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Bai M, Deng J, Dai C, Pfeuffer J, Sachsenberg T, Perez-Riverol Y. LFQ-Based Peptide and Protein Intensity Differential Expression Analysis. J Proteome Res 2023. [PMID: 37220883 DOI: 10.1021/acs.jproteome.2c00812] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Testing for significant differences in quantities at the protein level is a common goal of many LFQ-based mass spectrometry proteomics experiments. Starting from a table of protein and/or peptide quantities from a given proteomics quantification software, many tools and R packages exist to perform the final tasks of imputation, summarization, normalization, and statistical testing. To evaluate the effects of packages and settings in their substeps on the final list of significant proteins, we studied several packages on three public data sets with known expected protein fold changes. We found that the results between packages and even across different parameters of the same package can vary significantly. In addition to usability aspects and feature/compatibility lists of different packages, this paper highlights sensitivity and specificity trade-offs that come with specific packages and settings.
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Affiliation(s)
- Mingze Bai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Jingwen Deng
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Chengxin Dai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing 102206, China
| | - Julianus Pfeuffer
- Algorithmic Bioinformatics, Freie Universität Berlin, Berlin 14195, Germany
- Visualization and Data Analysis, Zuse Institute Berlin, Berlin 14195, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen 72076, Germany
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hixton, Cambridge CB10 1SD, United Kingdom
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26
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Escudero-Cernuda S, García de Pablos C, Celis FC, Fernández-Sánchez ML, Encinar JR. Certification of protein biomarker standards using element MS and generic standards: Application to human cytokines. Anal Chim Acta 2023; 1251:341002. [PMID: 36925291 DOI: 10.1016/j.aca.2023.341002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/11/2023] [Accepted: 02/21/2023] [Indexed: 02/27/2023]
Abstract
The availability of protein standards and methods for their characterization, quantification, and purity assessment are currently a bottleneck in absolute quantitative proteomics. In this work, we introduce an absolute quantitative analytical strategy based on ICP-MS sulfur detection that uses sulfate as generic standard to quantify and certify the mass purity of protein standards. The methodology combines capillary chromatographic separation with parallel detection with ICP-MS and ESI-MS to determine proteoforms concentration and identity, respectively. The workability of the methodology was demonstrated using recombinant human cytokine standards IP-10 and Flt3L (2 batches), which are relevant biomarkers for carcinoma or inflammatory diseases. Every key factor (transport efficiency, column recovery, signal stability and internal standard suitability) was taken into account and certified BSA standard was used as quality control for validation purposes. Protein quantification values and resulting mass purity certification of IP-10 and one batch of Flt3L were very high (100 and 86%, respectively). Lower mass purity obtained for another batch of Flt3L (<70%) concurred with the finding of significant proteoforms resulted from oxidation processes as observed by parallel ESI-MS.
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Affiliation(s)
- Sara Escudero-Cernuda
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
| | - Carlos García de Pablos
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
| | - Francisco Calderón Celis
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain.
| | - M Luisa Fernández-Sánchez
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain.
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Avda. Julián Clavería 8, Oviedo, 33006, Spain
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27
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Li YD, Luo YJ, Xie L, Tart DS, Sheehy RN, Zhang L, Coleman LG, Chen X, Song J. Activation of hypothalamic-enhanced adult-born neurons restores cognitive and affective function in Alzheimer's disease. Cell Stem Cell 2023; 30:415-432.e6. [PMID: 37028406 PMCID: PMC10150940 DOI: 10.1016/j.stem.2023.02.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 12/29/2022] [Accepted: 02/14/2023] [Indexed: 04/09/2023]
Abstract
Patients with Alzheimer's disease (AD) exhibit progressive memory loss, depression, and anxiety, accompanied by impaired adult hippocampal neurogenesis (AHN). Whether AHN can be enhanced in impaired AD brain to restore cognitive and affective function remains elusive. Here, we report that patterned optogenetic stimulation of the hypothalamic supramammillary nucleus (SuM) enhances AHN in two distinct AD mouse models, 5×FAD and 3×Tg-AD. Strikingly, the chemogenetic activation of SuM-enhanced adult-born neurons (ABNs) rescues memory and emotion deficits in these AD mice. By contrast, SuM stimulation alone or activation of ABNs without SuM modification fails to restore behavioral deficits. Furthermore, quantitative phosphoproteomics analyses reveal activation of the canonical pathways related to synaptic plasticity and microglia phagocytosis of plaques following acute chemogenetic activation of SuM-enhanced (vs. control) ABNs. Our study establishes the activity-dependent contribution of SuM-enhanced ABNs in modulating AD-related deficits and informs signaling mechanisms mediated by the activation of SuM-enhanced ABNs.
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Affiliation(s)
- Ya-Dong Li
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yan-Jia Luo
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Dalton S Tart
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ryan N Sheehy
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Pharmacology Curriculum, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Libo Zhang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Leon G Coleman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Bowles Center for Alcohol Studies, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Juan Song
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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28
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Bai JPF, Yu LR. Modeling Clinical Phenotype Variability: Consideration of Genomic Variations, Computational Methods, and Quantitative Proteomics. J Pharm Sci 2023; 112:904-908. [PMID: 36279954 DOI: 10.1016/j.xphs.2022.10.016] [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: 09/07/2022] [Revised: 10/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022]
Abstract
Advances in biomedical and computer technologies have presented the modeling community the opportunity for mechanistically modeling and simulating the variability in a disease phenotype or in a drug response. The capability to quantify response variability can inform a drug development program. Quantitative systems pharmacology scientists have published various computational approaches for creating virtual patient populations (VPops) to model and simulate drug response variability. Genomic variations can impact disease characteristics and drug exposure and response. Quantitative proteomics technologies are increasingly used to facilitate drug discovery and development and inform patient care. Incorporating variations in genomics and quantitative proteomics may potentially inform creation of VPops to model and simulate virtual patient trials, and may help account for, in a predictive manner, phenotypic variations observed clinically.
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Affiliation(s)
- Jane P F Bai
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20903, USA.
| | - Li-Rong Yu
- Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA
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29
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Bridel C, van Gils JHM, Miedema SSM, Hoozemans JJM, Pijnenburg YAL, Smit AB, Rozemuller AJM, Abeln S, Teunissen CE. Clusters of co-abundant proteins in the brain cortex associated with fronto-temporal lobar degeneration. Alzheimers Res Ther 2023; 15:59. [PMID: 36949537 PMCID: PMC10035199 DOI: 10.1186/s13195-023-01200-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/28/2023] [Indexed: 03/24/2023]
Abstract
BACKGROUND Frontotemporal lobar degeneration (FTLD) is characterized pathologically by neuronal and glial inclusions of hyperphosphorylated tau or by neuronal cytoplasmic inclusions of TDP43. This study aimed at deciphering the molecular mechanisms leading to these distinct pathological subtypes. METHODS To this end, we performed an unbiased mass spectrometry-based proteomic and systems-level analysis of the middle frontal gyrus cortices of FTLD-tau (n = 6), FTLD-TDP (n = 15), and control patients (n = 5). We validated these results in an independent patient cohort (total n = 24). RESULTS The middle frontal gyrus cortex proteome was most significantly altered in FTLD-tau compared to controls (294 differentially expressed proteins at FDR = 0.05). The proteomic modifications in FTLD-TDP were more heterogeneous (49 differentially expressed proteins at FDR = 0.1). Weighted co-expression network analysis revealed 17 modules of co-regulated proteins, 13 of which were dysregulated in FTLD-tau. These modules included proteins associated with oxidative phosphorylation, scavenger mechanisms, chromatin regulation, and clathrin-mediated transport in both the frontal and temporal cortex of FTLD-tau. The most strongly dysregulated subnetworks identified cyclin-dependent kinase 5 (CDK5) and polypyrimidine tract-binding protein 1 (PTBP1) as key players in the disease process. Dysregulation of 9 of these modules was confirmed in independent validation data sets of FLTD-tau and control temporal and frontal cortex (total n = 24). Dysregulated modules were primarily associated with changes in astrocyte and endothelial cell protein abundance levels, indicating pathological changes in FTD are not limited to neurons. CONCLUSIONS Using this innovative workflow and zooming in on the most strongly dysregulated proteins of the identified modules, we were able to identify disease-associated mechanisms in FTLD-tau with high potential as biomarkers and/or therapeutic targets.
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Affiliation(s)
- Claire Bridel
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Neurodegeneration, Amsterdam UMC, Amsterdam, The Netherlands
- Department of Clinical Neurosciences, Division of Neurology, Geneva University Hospital, Geneva, Switzerland
| | - Juami H. M. van Gils
- Department of Computer Science, Bioinformatics group, VU University, Amsterdam, The Netherlands
| | - Suzanne S. M. Miedema
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Jeroen J. M. Hoozemans
- Department of Pathology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
| | - Yolande A. L. Pijnenburg
- Alzheimer Center, Department of Neurology, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | | | - Sanne Abeln
- Department of Computer Science, Bioinformatics group, VU University, Amsterdam, The Netherlands
| | - Charlotte E. Teunissen
- Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Neurodegeneration, Amsterdam UMC, Amsterdam, The Netherlands
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30
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Chen H, Lai X, Zhu Y, Huang H, Zeng L, Zhang L. Quantitative proteomics identified circulating biomarkers in lung adenocarcinoma diagnosis. Clin Proteomics 2022; 19:44. [PMID: 36404333 PMCID: PMC9677906 DOI: 10.1186/s12014-022-09381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 11/06/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Lung cancer (LC) is a common malignant tumor with a high incidence and poor prognosis. Early LC could be cured, but the 5-year-survival rate for patients advanced is extremely low. Early screening of tumor biomarkers through plasma could allow more LC to be detected at an early stage, leading to a earlier treatment and a better prognosis. METHODS This study was based on total proteomic analysis and parallel reaction monitoring validation of peripheral blood from 20 lung adenocarcinoma patients and 20 healthy individuals. Furthermore, differentially expressed proteins closely related to prognosis were analysed using Kaplan-Meier Plotter and receiver operating characteristic curve (ROC) curve analysis. RESULTS The candidate proteins GAPDH and RAC1 showed the highest connectivity with other differentially expressed proteins between the lung adenocarcinoma group and the healthy group using STRING. Kaplan-Meier Plotter analysis showed that lung adenocarcinoma patients with positive ATCR2, FHL1, RAB27B, and RAP1B expression had observably longer overall survival than patients with negative expression (P < 0.05). The high expression of ARPC2, PFKP, PNP, RAC1 was observably negatively correlated with prognosis (P < 0.05). 17 out of 27 proteins showed a high area under the curve (> 0.80) between the lung adenocarcinoma and healthy plasma groups. Among those proteins, UQCRC1 had an area under the curve of 0.960, and 5 proteins had an area under the curve from 0.90 to 0.95, suggesting that these hub proteins might have discriminatory potential in lung adenocarcinoma, P < 0.05. CONCLUSIONS These findings provide UQCRC1, GAPDH, RAC1, PFKP have potential as novel biomarkers for the early screening of lung adenocarcinoma.
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Affiliation(s)
- Hongyu Chen
- grid.13291.380000 0001 0807 1581Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Xiaoqin Lai
- grid.412901.f0000 0004 1770 1022Day Surgery Center, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Yihan Zhu
- grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Hong Huang
- grid.412901.f0000 0004 1770 1022Laboratory of Pathology, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Lingyan Zeng
- grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
| | - Li Zhang
- grid.13291.380000 0001 0807 1581Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Institute of Respiratory Health, West China Hospital, Sichuan University, Chengdu, Sichuan China ,grid.412901.f0000 0004 1770 1022Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan China
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Chong L, Hsu CC, Zhu Y. Advances in mass spectrometry-based phosphoproteomics for elucidating abscisic acid signaling and plant responses to abiotic stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6547-6557. [PMID: 35959917 DOI: 10.1093/jxb/erac324] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses have significant impacts on crop yield and quality. Even though significant efforts during the past decade have been devoted to uncovering the core signaling pathways associated with the phytohormone abscisic acid (ABA) and abiotic stress in plants, abiotic stress signaling mechanisms in most crops remain largely unclear. The core components of the ABA signaling pathway, including early events in the osmotic stress-induced phosphorylation network, have recently been elucidated in Arabidopsis with the aid of phosphoproteomics technologies. We now know that SNF1-related kinases 2 (SnRK2s) are not only inhibited by the clade A type 2C protein phosphatases (PP2Cs) through dephosphorylation, but also phosphorylated and activated by upstream mitogen-activated protein kinase kinase kinases (MAP3Ks). Through describing the course of studies to elucidate abiotic stress and ABA signaling, we will discuss how we can take advantage of the latest innovations in mass-spectrometry-based phosphoproteomics and structural proteomics to boost our investigation of plant regulation and responses to ABA and abiotic stress.
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Affiliation(s)
- Leelyn Chong
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Chuan-Chih Hsu
- Department of Biochemistry, Purdue University, West Lafayette, IN, USA
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, Hainan, China
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Proteomics analysis of the phytopathogenic fungus Sclerotinia sclerotiorum: a narrative review. JOURNAL OF BIO-X RESEARCH 2022. [DOI: 10.1097/jbr.0000000000000130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Ai Y, Gunawardena HP, Li X, Kim YI, Dewald HD, Chen H. Standard-Free Absolute Quantitation of Antibody Deamidation Degradation and Host Cell Proteins by Coulometric Mass Spectrometry. Anal Chem 2022; 94:12490-12499. [PMID: 36018377 PMCID: PMC10492508 DOI: 10.1021/acs.analchem.2c02709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomic absolute quantitation strategies mainly rely on the use of synthetic stable isotope-labeled peptides or proteins as internal standards, which are highly costly and time-consuming to synthesize. To circumvent this limitation, we recently developed a coulometric mass spectrometry (CMS) approach for absolute quantitation of proteins without the use of standards, based on the electrochemical oxidation of oxidizable surrogate peptides, followed by mass spectrometry measurement of the peptide oxidation yield. Previously, CMS was only applied for single-protein quantitation. In this study, first, we demonstrated absolute quantitation of multiple proteins in a mixture (e.g., β-lactoglobulin B, α-lactalbumin, and carbonic anhydrase) by CMS in one run, without using any standards. The CMS quantitation result was validated with a traditional isotope dilution method. Second, CMS can be used for absolute quantitation of a low-level target protein in a mixture; for instance, 500 ppm of PLBL2, a problematic host cell protein (HCP), in the presence of a highly abundant monoclonal antibody (mAb) was successfully quantified by CMS with no use of standards. Third, taking one step further, this study demonstrated the unprecedented quantitative analysis of deamidated peptide products arising from the mAb heavy chain deamidation reaction. In particular, absolute quantitation of the deamidation succinimide intermediate which had not been performed before due to the lack of standard was conducted by CMS, for the first time. Overall, our data suggest that CMS has potential utilities for quantitative proteomics and biotherapeutic drug discovery.
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Affiliation(s)
- Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Harsha P Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, United States
| | - Xuanwen Li
- Analytical Research & Development, Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yong-Ick Kim
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Howard D Dewald
- Department of Chemistry and Biochemistry, Ohio University, Chemistry Building, 133 University Terrace, Athens, Ohio 45701, United States
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
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Surrogate peptide selection and internal standardization for accurate quantification of endogenous proteins. Bioanalysis 2022; 14:949-961. [PMID: 36017716 DOI: 10.4155/bio-2022-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Relative quantification techniques have dominated the field of proteomics. However, biomarker discovery, mathematical model development and studies on transporter-mediated drug disposition still need absolute quantification of proteins. The quality of data of trace-level protein quantification is solely dependent on the specific selection of surrogate peptides. Selection of surrogate peptides has a major impact on the accuracy of the method. In this article, the advanced approaches for selection of surrogate peptides, which can provide absolute quantification of the proteins are discussed. In addition, internal standardization, which accounts for variations in the quantitation process to achieve absolute protein quantification is discussed.
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Cao Z, Li G. MStoCIRC: A powerful tool for downstream analysis of MS/MS data to predict translatable circRNAs. Front Mol Biosci 2022; 9:791797. [PMID: 36072432 PMCID: PMC9441560 DOI: 10.3389/fmolb.2022.791797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
CircRNAs are formed by a non-canonical splicing method and appear circular in nature. CircRNAs are widely distributed in organisms and have the features of time- and tissue-specific expressions. CircRNAs have attracted increasing interest from scientists because of their non-negligible effects on the growth and development of organisms. The translation capability of circRNAs is a novel and valuable direction in the functional research of circRNAs. To explore the translation potential of circRNAs, some progress has been made in both experimental identification and computational prediction. For computational prediction, both CircCode and CircPro are ribosome profiling-based software applications for predicting translatable circRNAs, and the online databases riboCIRC and TransCirc analyze as many pieces of evidence as possible and list the predicted translatable circRNAs of high confidence. Simultaneously, mass spectrometry in proteomics is often recognized as an efficient method to support the identification of protein and peptide sequences from diverse complex templates. However, few applications fully utilize mass spectrometry to predict translatable circRNAs. Therefore, this research aims to build up a scientific analysis pipeline with two salient features: 1) it starts with the data analysis of raw tandem mass spectrometry data; and 2) it also incorporates other translation evidence such as IRES. The pipeline has been packaged into an analysis tool called mass spectrometry to translatable circRNAs (MStoCIRC). MStoCIRC is mainly implemented by Python3 language programming and could be downloaded from GitHub (https://github.com/QUMU00/mstocirc-master). The tool contains a main program and several small, independent function modules, making it more multifunctional. MStoCIRC can process data efficiently and has obtained hundreds of translatable circRNAs in humans and Arabidopsis thaliana.
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Schneider TD, Roschitzki B, Grossmann J, Kraemer T, Steuer AE. Determination of the Time since Deposition of Blood Traces Utilizing a Liquid Chromatography-Mass Spectrometry-Based Proteomics Approach. Anal Chem 2022; 94:10695-10704. [PMID: 35856936 DOI: 10.1021/acs.analchem.2c01009] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Knowledge about when a bloodstain was deposited at a crime scene can be of critical value in forensic investigation. A donor of a genetically identified bloodstain could be linked to a suspected time frame and the crime scene itself. Determination of the time since deposition (TsD) has been extensively studied before but has yet to reach maturity. We therefore conducted a proof-of-principle study to study time- and storage-dependent changes of the proteomes of dried blood stains. A bottom-up proteomics approach was employed, and high-resolution liquid-chromatography-mass-spectrometry (HR-LC-MS) and data-independent acquisition (DIA) were used to analyze samples aged over a 2 month period and two different storage conditions. In multivariate analysis, samples showed distinct clustering according to their TsD in both principal component analysis (PCA) and in partial least square discriminant analysis (PLS DA). The storage condition alters sample aging and yields different separation-driving peptides in hierarchical clustering and in TsD marker peptide selection. Certain peptides and amino acid modifications were identified and further assessed for their applicability in assessing passed TsD. A prediction model based on data resampling (Jackknife) was applied, and prediction values for selected peptide ratios were created. Depending on storage conditions and actual sample age, mean prediction performances ranges in between 70 and 130% for the majority of peptides and time points. This places this study as a first in investigating LC-MS based bottom-up proteomics approaches for TsD determination.
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Affiliation(s)
- Tom D Schneider
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland
| | - Bernd Roschitzki
- Functional Genomics Centre Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland
| | - Jonas Grossmann
- Functional Genomics Centre Zurich, ETH Zurich/University of Zurich, 8057 Zurich, Switzerland.,SIB Swiss Institute of Bioinformatics, 1015 792 Lausanne, Switzerland
| | - Thomas Kraemer
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland
| | - Andrea E Steuer
- Department of Forensic Pharmacology and Toxicology, Zurich Institute of Forensic Medicine, University of Zurich, 8057 Zurich, Switzerland
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Brandi J, Noberini R, Bonaldi T, Cecconi D. Advances in enrichment methods for mass spectrometry-based proteomics analysis of post-translational modifications. J Chromatogr A 2022; 1678:463352. [PMID: 35896048 DOI: 10.1016/j.chroma.2022.463352] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/08/2022] [Accepted: 07/17/2022] [Indexed: 10/17/2022]
Abstract
Post-translational modifications (PTMs) occur during or after protein biosynthesis and increase the functional diversity of proteome. They comprise phosphorylation, acetylation, methylation, glycosylation, ubiquitination, sumoylation (among many other modifications), and influence all aspects of cell biology. Mass-spectrometry (MS)-based proteomics is the most powerful approach for PTM analysis. Despite this, it is challenging due to low abundance and labile nature of many PTMs. Hence, enrichment of modified peptides is required for MS analysis. This review provides an overview of most common PTMs and a discussion of current enrichment methods for MS-based proteomics analysis. The traditional affinity strategies, including immunoenrichment, chromatography and protein pull-down, are outlined together with their strengths and shortcomings. Moreover, a special attention is paid to chemical enrichment strategies, such as capture by chemoselective probes, metabolic and chemoenzymatic labelling, which are discussed with an emphasis on their recent progress. Finally, the challenges and future trends in the field are discussed.
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Affiliation(s)
- Jessica Brandi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
| | - Roberta Noberini
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy.
| | - Tiziana Bonaldi
- Department of Experimental Oncology, European Institute of Oncology (IEO) IRCCS, Via Adamello 16, 20139 Milano, Italy; Department of Oncology and Haemato-Oncology, University of Milan, Via Festa del Perdono 7, 20122 Milano, Italy.
| | - Daniela Cecconi
- Department of Biotechnology, University of Verona, Strada le Grazie 15, 37134 Verona, Italy.
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Feng C, Wu Y, Chen Y, Xiong X, Li P, Peng X, Li C, Weng W, Zhu Y, Zhou D, Li Y. Arsenic trioxide increases apoptosis of SK-N-BE (2) cells partially by inducing GPX4-mediated ferroptosis. Mol Biol Rep 2022; 49:6573-6580. [PMID: 35598199 DOI: 10.1007/s11033-022-07497-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/21/2022] [Indexed: 01/18/2023]
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial tumor in central nervous system threatening children's health with limited therapeutic options. Arsenic trioxide (ATO) has been identified the cytotoxicity in NB cells but the potential mechanism remains unclear. In this study, we attempted to obtain some insight into the mechanisms of cell death induced by ATO in NB cells. METHODS AND RESULTS Proteomic analyses found that ATO can affect the signaling pathway associated with ferroptosis, including the upregulation of iron absorption (FTL, FTH1, HO-1), ferritinophagy (LC3, P62, ATG7, NCOA4) and modifier of glutathione synthesis (GCLM); downregulation of glutamine synthetase (GS) and GPX4, which was the critical inhibitor of ferroptosis. Western blot analysis revealing GPX4 expression in SK-N-BE (2) cells decreased after treatment with ATO (7.3 µM), resulting in a loss of GPX4 activity. Furthermore, Ferroptosis inhibitor ferrostatin-1 partially blocked ATO-induced cell death. CONCLUSIONS Our study revealed that ATO may induce ferroptosis in neuroblastoma cell SK-N-BE (2) by facilitating the downregulation of GPX4, ultimately resulting in iron-dependent oxidative death.
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Affiliation(s)
- Chuchu Feng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yu Wu
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yantao Chen
- Department of Orthopaedics, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Xilin Xiong
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Peng Li
- Key Laboratory of Regenerative Biology, South China Institute for Stem Cell Biology and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Kaiyuan Avenue, No. 190, Guangzhou, 510530, China
| | - Xiaomin Peng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Chunmou Li
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Wenjun Weng
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Yafeng Zhu
- Medical Researcher Center, Sun Yat-Sen University Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China
| | - Dunhua Zhou
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China.
| | - Yang Li
- Department of Pediatric Hematology/Oncology, Sun Yet-Sen Memorial Hospital, Sun Yet-Sen University, Yan Jiang Xi Road, No. 107, Guangzhou, 510120, China.
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De La Toba EA, Bell SE, Romanova EV, Sweedler JV. Mass Spectrometry Measurements of Neuropeptides: From Identification to Quantitation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2022; 15:83-106. [PMID: 35324254 DOI: 10.1146/annurev-anchem-061020-022048] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Neuropeptides (NPs), a unique class of neuronal signaling molecules, participate in a variety of physiological processes and diseases. Quantitative measurements of NPs provide valuable information regarding how these molecules are differentially regulated in a multitude of neurological, metabolic, and mental disorders. Mass spectrometry (MS) has evolved to become a powerful technique for measuring trace levels of NPs in complex biological tissues and individual cells using both targeted and exploratory approaches. There are inherent challenges to measuring NPs, including their wide endogenous concentration range, transport and postmortem degradation, complex sample matrices, and statistical processing of MS data required for accurate NP quantitation. This review highlights techniques developed to address these challenges and presents an overview of quantitative MS-based measurement approaches for NPs, including the incorporation of separation methods for high-throughput analysis, MS imaging for spatial measurements, and methods for NP quantitation in single neurons.
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Affiliation(s)
- Eduardo A De La Toba
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Sara E Bell
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Elena V Romanova
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
| | - Jonathan V Sweedler
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois, USA;
- Beckman Institute for Advanced Science and Technology, University of Illinois Urbana-Champaign, Urbana, Illinois, USA
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40
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Geddes-McAlister J, Prudhomme N, Gutierrez Gongora D, Cossar D, McLean MD. The emerging role of mass spectrometry-based proteomics in molecular pharming practices. Curr Opin Chem Biol 2022; 68:102133. [DOI: 10.1016/j.cbpa.2022.102133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/02/2022] [Accepted: 02/23/2022] [Indexed: 12/11/2022]
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41
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Liu J, Zhou Y, Hou X, Liu C, Zhao B, Shan Y, Sui Z, Liang Z, Zhang L, Zhang Y. A1 Ions: Peptide-Specific and Intensity-Enhanced Fragment Ions for Accurate and Multiplexed Proteome Quantitation. Anal Chem 2022; 94:7637-7646. [PMID: 35590477 DOI: 10.1021/acs.analchem.2c00876] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Accurate proteome quantitation is of great significance to deeply understand various cellular and physiological processes. Since a1 ions, generated from dimethyl-labeled peptides, exhibited high formation efficiency (up to 99%) and enhanced intensities (2.34-fold by average) in tandem mass spectra, herein, we proposed an a1 ion-based proteome quantitation (APQ) method, which showed high quantitation accuracy (relative errors < 7%) and precision (median coefficients of variation ≤ 11%) even in a 20-fold dynamic range. Notably, due to the mass differences of a1 ions from peptides with different N-terminal amino acids, APQ demonstrated interference-free capacity by distinguishing target peptides from the coisolated ones. By designing an isobaric dimethyl labeling strategy, we achieved simultaneous proteome-wide measurements across up to eight samples. Using APQ to quantify the time-resolved proteomic profiles during a TGF-β-induced epithelial-mesenchymal transition, we found many differentially expressed proteins associated with fatty acid degradation, indicating that fatty acid metabolism reprogramming occurred during the process. The APQ method combines high quantitation accuracy with multiplexing capacity, which is suitable for deep mining and understanding of dynamic biological processes.
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Affiliation(s)
- Jianhui Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yuan Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,School of Medical Technology, Xuzhou Medical University, Xuzhou 221004, China
| | - Xinhang Hou
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chao Liu
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, School of Engineering Medicine, School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Baofeng Zhao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yichu Shan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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42
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Zhang H, Situ C, Guo X. Recent progress of proteomic analysis on spermatogenesis. Biol Reprod 2022; 107:109-117. [DOI: 10.1093/biolre/ioac065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
Testis, the only organ responsible for generating sperm, is by far the organ with the largest variety of proteins and tissue-specific proteins in humans. In testis, spermatogenesis is a multi-step complex process well-accepted that protein and mRNA are decoupled in certain stages of spermatogenesis. With the fast development of mass spectrometry-based proteomics, it is possible to systemically study protein abundances and modifications in testis and sperm to help us understand the molecular mechanisms of spermatogenesis. This review provides an overview of the recent progress of proteomics analysis on spermatogenesis, including protein expression and multiple PTMs, such as phosphorylation, glycosylation, ubiquitylation, and acetylation.
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Affiliation(s)
- Haotian Zhang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Chenghao Situ
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, Nanjing Medical University, Nanjing 211166, China
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Cai K, Wang F, Lu JQ, Shen AN, Zhao SM, Zang WD, Gui YH, Zhao JY. Nicotinamide Mononucleotide Alleviates Cardiomyopathy Phenotypes Caused by Short-Chain Enoyl-Coa Hydratase 1 Deficiency. JACC Basic Transl Sci 2022; 7:348-362. [PMID: 35540099 PMCID: PMC9079797 DOI: 10.1016/j.jacbts.2021.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 02/08/2023]
Abstract
ECHS1 hydrates medium- and short-chain enoyl CoAs and catalyzes the oxidation of fatty acids and branched-chain amino acids. The mechanism driving ECHS1 deficiency–associated cardiomyopathy was investigated using conventional biochemistry and molecular biology methods, including immunoprecipitation and polymerase chain reaction. Echs1 heterogeneous knockout mice displayed cardiac dysfunction as evaluated by echocardiography. ECHS1 deficiency causes cardiomyopathy by enhancing p300-mediated H3K9ac. ECHS1 deficiency–induced cardiomyopathy can be prevented using an intervention approach targeting H3K9ac.
Short-chain enoyl-CoA hydratase 1 (ECHS1) deficiency plays a role in cardiomyopathy. Whether ECHS1 deficiency causes or is only associated with cardiomyopathy remains unclear. By using Echs1 heterogeneous knockout (Echs1+/-) mice, we found that ECHS1 deficiency caused cardiac dysfunction, as evidenced by diffuse myocardial fibrosis and upregulated fibrosis-related genes. Mechanistically, ECHS1 interacts with the p300 nuclear localization sequence, preventing its nuclear translocation in fibroblasts. ECHS1 deficiency promotes p300 nuclear translocation, leading to increased H3K9 acetylation, a known risk factor for cardiomyopathy. Nicotinamide mononucleotide–mediated acetylation targeting suppressed ECHS1 deficiency–induced cardiomyopathy phenotypes in Echs1+/- mice. Thus, enhancing p300-mediated H3K9ac is a potential interventional approach for preventing ECHS1 deficiency–induced cardiomyopathy.
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Key Words
- ANP, atrial natriuretic peptide
- BCAA, branched-chain amino acid
- BNP, brain natriuretic peptide
- DCM, dilated cardiomyopathy
- ECHS1, short-chain enoyl-CoA hydratase 1
- FA, fatty acid
- HCM, hypertrophic cardiomyopathy
- HFF, human foreskin fibroblast
- IVSd, interventricular septum in end-diastole
- IVSs, interventricular septum in end-systole
- LVEF, left ventricular ejection fraction
- LVFS, left ventricular fractional shortening
- LVIDd, left ventricular internal dimension in end-diastole
- LVIDs, left ventricular internal dimension in end-systole
- LVPWd, left ventricular posterior wall in end-diastole
- LVPWs, left ventricular posterior wall in end-systole
- NMN, nicotinamide mononucleotide
- acetylation of H3K9
- cardiomyopathy
- enoyl-CoA hydratase 1
- nicotinamide mononucleotide
- p300
- α-SMA, smooth muscle actin-α
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Affiliation(s)
- Ke Cai
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China
| | - Feng Wang
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China
| | - Jia-Quan Lu
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China
| | - An-Na Shen
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China
| | - Shi-Min Zhao
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Fudan University, Shanghai, China
| | - Wei-Dong Zang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yong-Hao Gui
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China
| | - Jian-Yuan Zhao
- NHC Key Laboratory of Neonatal Diseases, Cardiovascular Center, Children's Hospital of Fudan University, State Key Laboratory of Genetic Engineering, and School of Life Sciences, Fudan University, Shanghai, China.,School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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Identifying Potential Mitochondrial Proteome Signatures Associated with the Pathogenesis of Pulmonary Arterial Hypertension in the Rat Model. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:8401924. [PMID: 35237384 PMCID: PMC8885180 DOI: 10.1155/2022/8401924] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/12/2022] [Accepted: 02/05/2022] [Indexed: 01/09/2023]
Abstract
Pulmonary arterial hypertension (PAH) is a severe and progressive disease that affects the heart and lungs and a global health concern that impacts individuals and society. Studies have reported that some proteins related to mitochondrial metabolic functions could play an essential role in the pathogenesis of PAH, and their specific expression and biological function are still unclear. We successfully constructed a monocrotaline- (MCT-) induced PAH rat model in the present research. Then, the label-free quantification proteomic technique was used to determine mitochondrial proteins between the PAH group (n = 6) and the normal group (n = 6). Besides, we identified 1346 mitochondrial differentially expressed proteins (DEPs) between these two groups. Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) were used to analyze the mainly mitochondrial DEPs' biological functions and the signal pathways. Based on the protein-protein interaction (PPI) network construction and functional enrichment, we screened 19 upregulated mitochondrial genes (Psmd1, Psmc4, Psmd13, Psmc2, etc.) and 123 downregulated mitochondrial genes (Uqcrfs1, Uqcrc1, Atp5c1, Atp5a1, Uqcrc2, etc.) in rats with PAH. Furthermore, in an independent cohort dataset and experiments with rat lung tissue using qPCR, validation results consistently showed that 6 upregulated mitochondrial genes (Psmd2, Psmc4, Psmc3, Psmc5, Psmd13, and Psmc2) and 3 downregulated mitochondrial genes (Lipe, Cat, and Prkce) were significantly differentially expressed in the lung tissue of PAH rats. Using the RNAInter database, we predict potential miRNA target hub mitochondrial genes at the transcriptome level. We also identified bortezomib and carfilzomib as the potential drugs for treatment in PAH. Finally, this study provides us with a new perspective on critical biomarkers and treatment strategies in PAH.
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Liu B, Stevens-Green R, Johal D, Buchanan R, Geddes-McAlister J. Fungal pathogens of cereal crops: Proteomic insights into fungal pathogenesis, host defense, and resistance. JOURNAL OF PLANT PHYSIOLOGY 2022; 269:153593. [PMID: 34915227 DOI: 10.1016/j.jplph.2021.153593] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/28/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
Fungal infections of cereal crops pose a significant risk to global food security through reduced grain production and quality, as well as contamination of animal feed and human products for consumption. To combat fungal disease, we need to understand how the pathogen adapts and survives within the hostile environment of the host and how the host's defense response can be modulated for protection from disease. Such investigations offer insight into fungal pathogenesis, host immunity, the development of resistance, and mechanisms of action for currently-used control strategies. Mass spectrometry-based proteomics provides a technologically-advanced platform to define differences among fungal pathogens and their hosts at the protein level, supporting the discovery of proteins critical for disease, and uncovering novel host responses driving susceptibly or resistance of the host. In this Review, we explore the role of mass spectrometry-based proteomics in defining the intricate relationship between a pathogen and host during fungal disease of cereal crops with a focus on recent discoveries derived from the globally-devastating diseases of Fusarium head blight, Rice blast, and Powdery mildew. We highlight advances made for each of these diseases and discuss opportunities to extrapolate findings to further our fight against fungal pathogens on a global scale.
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Affiliation(s)
- B Liu
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Stevens-Green
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - D Johal
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - R Buchanan
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - J Geddes-McAlister
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Canadian Proteomics and Artificial Intelligence Research and Training Consortium, Canada.
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Synthesis of a metal oxide affinity chromatography magnetic mesoporous nanomaterial and development of a one-step selective phosphopeptide enrichment strategy for analysis of phosphorylated proteins. Anal Chim Acta 2022; 1195:339430. [DOI: 10.1016/j.aca.2022.339430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/05/2021] [Accepted: 01/01/2022] [Indexed: 11/23/2022]
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Comparison of Different Label-Free Techniques for the Semi-Absolute Quantification of Protein Abundance. Proteomes 2022; 10:proteomes10010002. [PMID: 35076627 PMCID: PMC8788469 DOI: 10.3390/proteomes10010002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
In proteomics, it is essential to quantify proteins in absolute terms if we wish to compare results among studies and integrate high-throughput biological data into genome-scale metabolic models. While labeling target peptides with stable isotopes allow protein abundance to be accurately quantified, the utility of this technique is constrained by the low number of quantifiable proteins that it yields. Recently, label-free shotgun proteomics has become the “gold standard” for carrying out global assessments of biological samples containing thousands of proteins. However, this tool must be further improved if we wish to accurately quantify absolute levels of proteins. Here, we used different label-free quantification techniques to estimate absolute protein abundance in the model yeast Saccharomyces cerevisiae. More specifically, we evaluated the performance of seven different quantification methods, based either on spectral counting (SC) or extracted-ion chromatogram (XIC), which were applied to samples from five different proteome backgrounds. We also compared the accuracy and reproducibility of two strategies for transforming relative abundance into absolute abundance: a UPS2-based strategy and the total protein approach (TPA). This study mentions technical challenges related to UPS2 use and proposes ways of addressing them, including utilizing a smaller, more highly optimized amount of UPS2. Overall, three SC-based methods (PAI, SAF, and NSAF) yielded the best results because they struck a good balance between experimental performance and protein quantification.
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48
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Deng D, Zi Z. Absolute Quantification of TGF-β Signaling Proteins Using Quantitative Western Blot. Methods Mol Biol 2022; 2488:1-12. [PMID: 35347678 DOI: 10.1007/978-1-0716-2277-3_1] [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: 06/14/2023]
Abstract
Cell signaling governs the basic functions of cells by molecular interactions that involve of many proteins. The abundance of signaling proteins can directly influence cellular responses to external signal, contributing to cellular heterogeneity. Absolute quantification of proteins is important for modeling and understanding the complex signaling network. Here, we introduce how to measure the amount of TGF-β signaling proteins using quantitative immunoblotting. In addition, we discuss how to convert the measurements of protein abundance to the quantities of absolute molecules per cell. This method is generally applicable to the absolute quantification of other proteins.
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Affiliation(s)
- Difan Deng
- Max Planck Institute for Molecular Genetics, Otto Warburg Laboratory, Berlin, Germany
| | - Zhike Zi
- Department of Experimental Toxicology and ZEBET, German Federal Institute for Risk Assessment, Berlin, Germany.
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Pu Y, Brandizzi F. Protein Preparation for Proteomic Analysis of the Unfolded Protein Response in Arabidopsis thaliana. Methods Mol Biol 2022; 2378:279-289. [PMID: 34985707 PMCID: PMC8935445 DOI: 10.1007/978-1-0716-1732-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Excessive accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) leads to a potentially cytotoxic condition known as the ER stress. Upon ER stress, cells initiate a homeostatic response called unfolded protein response (UPR) to assist proper folding the unfolded or misfolded proteins. Proteomics have been broadly used in plants with Liquid Chromatography coupled to tandem MS (LC-MS/MS) technologies. LC-MS/MS techniques have also been a great tool for studies of posttranslational modifications (PTMs). Here we describe our protocol of a fast method for large amount of seedling treatment and collection for UPR study in Arabidopsis thaliana and the preparation of total proteins for proteomic analysis.
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Affiliation(s)
- Yunting Pu
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI, USA.
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50
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Lan Y, Zeng X, Xiao J, Hu L, Tan L, Liang M, Wang X, Lu S, Long F, Peng T. New advances in quantitative proteomics research and current applications in asthma. Expert Rev Proteomics 2021; 18:1045-1057. [PMID: 34890515 DOI: 10.1080/14789450.2021.2017777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Asthma is the most common chronic respiratory disease and has been declared a global public health problem by the World Health Organization. Due to the high heterogeneity and complexity, asthma can be classified into different 'phenotypes' and it is still difficult to assess the phenotypes and stages of asthma by traditional methods. In recent years, mass spectrometry-based proteomics studies have made significant progress in sensitivity and accuracy of protein identification and quantitation, and are able to obtain differences in protein expression across samples, which provides new insights into the mechanisms and classification of asthma. AREAS COVERED In this article, we summarize research strategies in quantitative proteomics, including labeled, label-free and targeted quantification, and highlight the advantages and disadvantages of each. In addition, new applications of quantitative proteomics and the current status of research in asthma have also been discussed. In this study, online resources such as PubMed and Google Scholar were used for literature retrieval. EXPERT OPINION The application of quantitative proteomics in asthma has an important role in identifying asthma subphenotypes, revealing potential pathogenesis and therapeutic targets. But the proteomic studies on asthma are not sufficient, as most of them are in the phase of biomarker discovery.
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Affiliation(s)
- Yanting Lan
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyin Zeng
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Jing Xiao
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Longbo Hu
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Long Tan
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Mengdi Liang
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Xufei Wang
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Shaohua Lu
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Fei Long
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute of Immunology, State Key Laboratory of Respiratory Disease, School of Basic Medical Sciences, College of Basic-Medical Science, Guangzhou Medical University, Guangzhou, China.,Guangdong South China Vaccine Co. Ltd, Guangzhou, China
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