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Wang R, Ren C, Gao T, Li H, Bo X, Zhu D, Zhang D, Chen H, Zhang Y. SEPDB: a database of secreted proteins. Database (Oxford) 2024; 2024:baae007. [PMID: 38345567 PMCID: PMC10878045 DOI: 10.1093/database/baae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/14/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024]
Abstract
Detecting changes in the dynamics of secreted proteins in serum has been a challenge for proteomics. Enter secreted protein database (SEPDB), an integrated secretory proteomics database offering human, mouse and rat secretory proteomics datasets collected from serum, exosomes and cell culture media. SEPDB compiles secreted protein information from secreted protein database, UniProt and Human Protein Atlas databases to annotate secreted proteomics data based on protein subcellular localization and disease markers. SEPDB integrates the latest predictive modeling techniques to measure deviations in the distribution of signal peptide structures of secreted proteins, extends signal peptide sequence prediction by excluding transmembrane structural domain proteins and updates the validation analysis pipeline for secreted proteins. To establish tissue-specific profiles, we have also created secreted proteomics datasets associated with different human tissues. In addition, we provide information on heterogeneous receptor network organizational relationships, reflective of the complex functional information inherent in the molecular structures of secreted proteins that serve as ligands. Users can take advantage of the Refreshed Search, Analyze, Browse and Download functions of SEPDB, which is available online at https://sysomics.com/SEPDB/. Database URL: https://sysomics.com/SEPDB/.
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Affiliation(s)
- Ruiqing Wang
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Chao Ren
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Tian Gao
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Hao Li
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Xiaochen Bo
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Dahai Zhu
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #96 South Xingdao Ring Road, Haizhu District, Guangzhou 510005, China
| | - Dan Zhang
- Experimental Center, Shandong University of Traditional Chinese Medicine, Key Laboratory of Traditional Chinese Medicine Classical Theory, Ministry of Education, Shandong University of Traditional Chinese Medicine, #4655 Daxue Road, Changqing District, Jinan, Shandong Province 250355, China
| | - Hebing Chen
- Institute of Health Service and Transfusion Medicine, #27 Taiping Road, Haidian District, Beijing 100850, China
| | - Yong Zhang
- The State Key Laboratory of Complex, Severe, and Rare Diseases, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, #5 Dong Dan San Tiao, Beijing 100005, China
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), #96 South Xingdao Ring Road, Haizhu District, Guangzhou 510005, China
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2
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Michaud SA, Pětrošová H, Sinclair NJ, Kinnear AL, Jackson AM, McGuire JC, Hardie DB, Bhowmick P, Ganguly M, Flenniken AM, Nutter LMJ, McKerlie C, Smith D, Mohammed Y, Schibli D, Sickmann A, Borchers CH. Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues. Commun Biol 2024; 7:6. [PMID: 38168632 PMCID: PMC10762018 DOI: 10.1038/s42003-023-05687-0] [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: 09/16/2020] [Accepted: 12/07/2023] [Indexed: 01/05/2024] Open
Abstract
Mouse is the mammalian model of choice to study human health and disease due to its size, ease of breeding and the natural occurrence of conditions mimicking human pathology. Here we design and validate multiple reaction monitoring mass spectrometry (MRM-MS) assays for quantitation of 2118 unique proteins in 20 murine tissues and organs. We provide open access to technical aspects of these assays to enable their implementation in other laboratories, and demonstrate their suitability for proteomic profiling in mice by measuring normal protein abundances in tissues from three mouse strains: C57BL/6NCrl, NOD/SCID, and BALB/cAnNCrl. Sex- and strain-specific differences in protein abundances are identified and described, and the measured values are freely accessible via our MouseQuaPro database: http://mousequapro.proteincentre.com . Together, this large library of quantitative MRM-MS assays established in mice and the measured baseline protein abundances represent an important resource for research involving mouse models.
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Affiliation(s)
- Sarah A Michaud
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada.
| | - Helena Pětrošová
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Nicholas J Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Andrea L Kinnear
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Angela M Jackson
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Jamie C McGuire
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Pallab Bhowmick
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Milan Ganguly
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | - Ann M Flenniken
- The Center for Phenogenomics, Toronto, ON, Canada
- Sinai Health Lunenfeld-Tanenbaum Research Institute, Toronto, ON, Canada
| | - Lauryl M J Nutter
- The Center for Phenogenomics, Toronto, ON, Canada
- The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Derek Smith
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - David Schibli
- University of Victoria-Genome British Columbia Proteomics Centre, Victoria, BC, Canada
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V, Dortmund, 44139, Germany
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.
- Department of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pathology, McGill University, Montreal, QC, Canada.
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Zlatic SA, Werner E, Surapaneni V, Lee CE, Gokhale A, Singleton K, Duong D, Crocker A, Gentile K, Middleton F, Dalloul JM, Liu WLY, Patgiri A, Tarquinio D, Carpenter R, Faundez V. Systemic proteome phenotypes reveal defective metabolic flexibility in Mecp2 mutants. Hum Mol Genet 2023; 33:12-32. [PMID: 37712894 PMCID: PMC10729867 DOI: 10.1093/hmg/ddad154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 09/01/2023] [Accepted: 09/11/2023] [Indexed: 09/16/2023] Open
Abstract
Genes mutated in monogenic neurodevelopmental disorders are broadly expressed. This observation supports the concept that monogenic neurodevelopmental disorders are systemic diseases that profoundly impact neurodevelopment. We tested the systemic disease model focusing on Rett syndrome, which is caused by mutations in MECP2. Transcriptomes and proteomes of organs and brain regions from Mecp2-null mice as well as diverse MECP2-null male and female human cells were assessed. Widespread changes in the steady-state transcriptome and proteome were identified in brain regions and organs of presymptomatic Mecp2-null male mice as well as mutant human cell lines. The extent of these transcriptome and proteome modifications was similar in cortex, liver, kidney, and skeletal muscle and more pronounced than in the hippocampus and striatum. In particular, Mecp2- and MECP2-sensitive proteomes were enriched in synaptic and metabolic annotated gene products, the latter encompassing lipid metabolism and mitochondrial pathways. MECP2 mutations altered pyruvate-dependent mitochondrial respiration while maintaining the capacity to use glutamine as a mitochondrial carbon source. We conclude that mutations in Mecp2/MECP2 perturb lipid and mitochondrial metabolism systemically limiting cellular flexibility to utilize mitochondrial fuels.
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Affiliation(s)
- Stephanie A Zlatic
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Erica Werner
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Veda Surapaneni
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Chelsea E Lee
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Avanti Gokhale
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Kaela Singleton
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
| | - Duc Duong
- Department of Biochemistry, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, United States
| | - Amanda Crocker
- Program in Neuroscience, Middlebury College, Bicentennial Way, Middlebury, VT 05753, United States
| | - Karen Gentile
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, 505 Irving Avenue, Syracuse, NY 13210, United States
| | - Frank Middleton
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, 505 Irving Avenue, Syracuse, NY 13210, United States
| | - Joseph Martin Dalloul
- Pharmacology and Chemical Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, United States
| | - William Li-Yun Liu
- Pharmacology and Chemical Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, United States
| | - Anupam Patgiri
- Pharmacology and Chemical Biology, Emory University, 1510 Clifton Rd NE, Atlanta, GA 30322, United States
| | - Daniel Tarquinio
- Center for Rare Neurological Diseases, 5600 Oakbrook Pkwy, Norcross, GA 30093, United States
| | - Randall Carpenter
- Rett Syndrome Research Trust, 67 Under Cliff Rd, Trumbull, CT 06611, United States
| | - Victor Faundez
- Department of Cell Biology, Emory University, 615 Michael Steet, Atlanta, GA 30322, United States
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Zlatic SA, Werner E, Surapaneni V, Lee CE, Gokhale A, Singleton K, Duong D, Crocker A, Gentile K, Middleton F, Dalloul JM, Liu WLY, Patgiri A, Tarquinio D, Carpenter R, Faundez V. Systemic Proteome Phenotypes Reveal Defective Metabolic Flexibility in Mecp2 Mutants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535431. [PMID: 37066332 PMCID: PMC10103972 DOI: 10.1101/2023.04.03.535431] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/24/2023]
Abstract
Genes mutated in monogenic neurodevelopmental disorders are broadly expressed. This observation supports the concept that monogenic neurodevelopmental disorders are systemic diseases that profoundly impact neurodevelopment. We tested the systemic disease model focusing on Rett syndrome, which is caused by mutations in MECP2. Transcriptomes and proteomes of organs and brain regions from Mecp2-null mice as well as diverse MECP2-null male and female human cells were assessed. Widespread changes in the steady-state transcriptome and proteome were identified in brain regions and organs of presymptomatic Mecp2-null male mice as well as mutant human cell lines. The extent of these transcriptome and proteome modifications was similar in cortex, liver, kidney, and skeletal muscle and more pronounced than in the hippocampus and striatum. In particular, Mecp2- and MECP2-sensitive proteomes were enriched in synaptic and metabolic annotated gene products, the latter encompassing lipid metabolism and mitochondrial pathways. MECP2 mutations altered pyruvate-dependent mitochondrial respiration while maintaining the capacity to use glutamine as a mitochondrial carbon source. We conclude that mutations in Mecp2/MECP2 perturb lipid and mitochondrial metabolism systemically limiting cellular flexibility to utilize mitochondrial fuels.
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Affiliation(s)
| | - Erica Werner
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Veda Surapaneni
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Chelsea E. Lee
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Kaela Singleton
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
| | - Duc Duong
- Department of Biochemistry, Emory University, Atlanta, GA, USA, 30322
| | - Amanda Crocker
- Program in Neuroscience, Middlebury College, Middlebury, Vermont 05753
| | - Karen Gentile
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Frank Middleton
- Department of Neuroscience and Physiology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Joseph Martin Dalloul
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | - William Li-Yun Liu
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | - Anupam Patgiri
- Department of Pharmacology & Chemical Biology, Emory University, Atlanta, GA, USA, 30322
| | | | | | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA, USA, 30322
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Mohammed Y, Goodlett D, Borchers CH. Bioinformatics Tools and Knowledgebases to Assist Generating Targeted Assays for Plasma Proteomics. Methods Mol Biol 2023; 2628:557-577. [PMID: 36781806 DOI: 10.1007/978-1-0716-2978-9_32] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In targeted proteomics experiments, selecting the appropriate proteotypic peptides as surrogate for the target protein is a crucial pre-acquisition step. This step is largely a bioinformatics exercise that involves integrating information on the peptides and proteins and using various software tools and knowledgebases. We present here a few resources that automate and simplify the selection process to a great degree. These tools and knowledgebases were developed primarily to streamline targeted proteomics assay development and include PeptidePicker, PeptidePickerDB, MRMAssayDB, MouseQuaPro, and PeptideTracker. We have used these tools to develop and document thousands of targeted proteomics assays, many of them for plasma proteins with focus on human and mouse. An important aspect in all these resources is the integrative approach on which they are based. Using these tools in the first steps of designing a singleplexed or multiplexed targeted proteomic experiment can reduce the necessary experimental steps tremendously. All the tools and knowledgebases we describe here are Web-based and freely accessible so scientists can query the information conveniently from the browser. This chapter provides an overview of these software tools and knowledgebases, their content, and how to use them for targeted plasma proteomics. We further demonstrate how to use them with the results of the HUPO Human Plasma Proteome Project to produce a new database of 3.8 k targeted assays for known human plasma proteins. Upon experimental validation, these assays should help in the further quantitative characterizing of the plasma proteome.
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Affiliation(s)
- Yassene Mohammed
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, ZA, Netherlands. .,University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada. .,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| | - David Goodlett
- University of Victoria - Genome BC Proteomics Centre, Victoria, BC, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.,University of Gdansk, International Centre for Cancer Vaccine Science, Gdansk, Poland
| | - Christoph H Borchers
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, QC, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Department of Pathology, McGill University, Montreal, QC, Canada
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Mouse tissue glycome atlas 2022 highlights inter-organ variation in major N-glycan profiles. Sci Rep 2022; 12:17804. [PMID: 36280747 PMCID: PMC9592591 DOI: 10.1038/s41598-022-21758-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/30/2022] [Indexed: 01/19/2023] Open
Abstract
This study presents "mouse tissue glycome atlas" representing the profiles of major N-glycans of mouse glycoproteins that may define their essential functions in the surface glycocalyx of mouse organs/tissues and serum-derived extracellular vesicles (exosomes). Cell surface glycocalyx composed of a variety of N-glycans attached covalently to the membrane proteins, notably characteristic "N-glycosylation patterns" of the glycocalyx, plays a critical role for the regulation of cell differentiation, cell adhesion, homeostatic immune response, and biodistribution of secreted exosomes. Given that the integrity of cell surface glycocalyx correlates significantly with maintenance of the cellular morphology and homeostatic immune functions, dynamic alterations of N-glycosylation patterns in the normal glycocalyx caused by cellular abnormalities may serve as highly sensitive and promising biomarkers. Although it is believed that inter-organs variations in N-glycosylation patterns exist, information of the glycan diversity in mouse organs/tissues remains to be elusive. Here we communicate for the first-time N-glycosylation patterns of 16 mouse organs/tissues, serum, and serum-derived exosomes of Slc:ddY mice using an established solid-phase glycoblotting platform for the rapid, easy, and high throughput MALDI-TOFMS-based quantitative glycomics. The present results elicited occurrence of the organ/tissue-characteristic N-glycosylation patterns that can be discriminated to each other. Basic machine learning analysis using this N-glycome dataset enabled classification between 16 mouse organs/tissues with the highest F1 score (69.7-100%) when neural network algorithm was used. A preliminary examination demonstrated that machine learning analysis of mouse lung N-glycome dataset by random forest algorithm allows for the discrimination of lungs among the different mouse strains such as the outbred mouse Slc:ddY, inbred mouse DBA/2Crslc, and systemic lupus erythematosus model mouse MRL-lpr/lpr with the highest F1 score (74.5-83.8%). Our results strongly implicate importance of "human organ/tissue glycome atlas" for understanding the crucial and diversified roles of glycocalyx determined by the organ/tissue-characteristic N-glycosylation patterns and the discovery research for N-glycome-based disease-specific biomarkers and therapeutic targets.
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