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Petersen J, Englmaier L, Artemov AV, Poverennaya I, Mahmoud R, Bouderlique T, Tesarova M, Deviatiiarov R, Szilvásy-Szabó A, Akkuratov EE, Pajuelo Reguera D, Zeberg H, Kaucka M, Kastriti ME, Krivanek J, Radaszkiewicz T, Gömöryová K, Knauth S, Potesil D, Zdrahal Z, Ganji RS, Grabowski A, Buhl ME, Zikmund T, Kavkova M, Axelson H, Lindgren D, Kramann R, Kuppe C, Erdélyi F, Máté Z, Szabó G, Koehne T, Harkany T, Fried K, Kaiser J, Boor P, Fekete C, Rozman J, Kasparek P, Prochazka J, Sedlacek R, Bryja V, Gusev O, Adameyko I. A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology. Nat Commun 2023; 14:3092. [PMID: 37248239 DOI: 10.1038/s41467-023-38663-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/11/2023] [Indexed: 05/31/2023] Open
Abstract
In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.
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Affiliation(s)
- Julian Petersen
- Department of Orthodontics, University Leipzig Medical Center, Leipzig, Germany.
| | - Lukas Englmaier
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, 1090, Vienna, Austria
| | - Artem V Artemov
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Irina Poverennaya
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Ruba Mahmoud
- Department of Orthodontics, University Leipzig Medical Center, Leipzig, Germany
| | - Thibault Bouderlique
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Marketa Tesarova
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Ruslan Deviatiiarov
- Regulatory Genomics Research Center, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
- Endocrinology Research Center, Moscow, Russia
| | - Anett Szilvásy-Szabó
- Laboratory of Integrative Neuroendocrinology, Institute of Experimental Medicine, 1083, Budapest, Hungary
| | - Evgeny E Akkuratov
- Department of Applied Physics, Royal Institute of Technology, Science for Life Laboratory, 171 65, Stockholm, Sweden
- University of Oxford, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, Oxford, OX3 9DS, UK
| | - David Pajuelo Reguera
- Institute of Molecular Genetics of the Czech Academy of Science, Czech Centre for Phenogenomics, Vestec, Czech Republic
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Marketa Kaucka
- Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
| | - Maria Eleni Kastriti
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Krivanek
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomasz Radaszkiewicz
- Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristína Gömöryová
- Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Sarah Knauth
- Department of Orthodontics, University Leipzig Medical Center, Leipzig, Germany
| | - David Potesil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbynek Zdrahal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Ranjani Sri Ganji
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Anna Grabowski
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Miriam E Buhl
- Institute of Pathology & Electron Microscopy Facility, RWTH Aachen University Hospital, Aachen, Germany
| | - Tomas Zikmund
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Michaela Kavkova
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Håkan Axelson
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Scheelevägen 2, Lund, Sweden
| | - David Lindgren
- Translational Cancer Research, Department of Laboratory Medicine, Lund University, Medicon Village, Scheelevägen 2, Lund, Sweden
| | - Rafael Kramann
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Christoph Kuppe
- Institute of Experimental Medicine and Systems Biology, RWTH Aachen University, Aachen, Germany
| | - Ferenc Erdélyi
- Medical Gene Technology Unit, Institute of Experimental Medicine, Budapest, Hungary
| | - Zoltán Máté
- Medical Gene Technology Unit, Institute of Experimental Medicine, Budapest, Hungary
| | - Gábor Szabó
- Medical Gene Technology Unit, Institute of Experimental Medicine, Budapest, Hungary
| | - Till Koehne
- Department of Orthodontics, University Leipzig Medical Center, Leipzig, Germany
| | - Tibor Harkany
- Department of Molecular Neurosciences, Center for Brain Research, Medical University Vienna, Vienna, Austria
| | - Kaj Fried
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
| | - Jozef Kaiser
- Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Peter Boor
- Institute of Pathology & Electron Microscopy Facility, RWTH Aachen University Hospital, Aachen, Germany
| | - Csaba Fekete
- Laboratory of Integrative Neuroendocrinology, Institute of Experimental Medicine, 1083, Budapest, Hungary
| | - Jan Rozman
- Institute of Molecular Genetics of the Czech Academy of Science, Czech Centre for Phenogenomics, Vestec, Czech Republic
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, 6, avenue du Swing, 4367, Belvaux, Luxembourg
| | - Petr Kasparek
- Institute of Molecular Genetics of the Czech Academy of Science, Czech Centre for Phenogenomics, Vestec, Czech Republic
| | - Jan Prochazka
- Institute of Molecular Genetics of the Czech Academy of Science, Czech Centre for Phenogenomics, Vestec, Czech Republic
| | - Radislav Sedlacek
- Institute of Molecular Genetics of the Czech Academy of Science, Czech Centre for Phenogenomics, Vestec, Czech Republic
| | - Vitezslav Bryja
- Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Oleg Gusev
- Endocrinology Research Center, Moscow, Russia
- Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Center for Integrative Medical Sciences, RIKEN, Yokohama City, Kanagawa, Japan
| | - Igor Adameyko
- Department of Neuroimmunology, Center for Brain Research, Medical University Vienna, Vienna, Austria.
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden.
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2
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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3
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Roberts A, Gandhi S. A brief review on novel biomarkers identified and advanced biosensing technologies developed for rapid diagnosis of Japanese Encephalitis Virus. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [PMCID: PMC9483901 DOI: 10.1007/s43538-022-00113-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Advanced biosensor technology research is imperative for the management of infectious disease outbreaks such as Japanese Encephalitis (JE), a zoonotic disease caused by the flavivirus JE virus (JEV) which is transmitted to humans (dead-end hosts) from the amplification host, pigs, via mosquitoes. To avoid future pandemic scenarios, proactive research rather than responsive research in the field of diagnostics is a requirement for development of rapid, sensitive and specific screening detection methods. In this mini-review, we have critically compared and evaluated the different types of biomarkers (antigen, antibody, nucleic acid) identified for JEV diagnostics and their specific roles in the manifestation of the infection which may be potentially used for therapeutics and drug development as no treatment is available for JE. Furthermore, different biosensors developed for the detection of JEV biomarkers have been discussed in detail to give an overview of the working principles (electrochemical, optical, etc.), fabrication components (signal amplifier, bioreceptor, etc.), detection limits and response times. This review provides a compact compiled base on available JEV diagnostic research work being currently carried out along with their limitations, future prospective, and major challenges faced. This will enable future development of rapid point-of-care diagnostic screening methods for JEV infection management, which may help reduce number of fatalities.
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Affiliation(s)
- Akanksha Roberts
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana 500032 India
- DBT-Regional Centre for Biotechnology (RCB), Faridabad, Haryana 121001 India
| | - Sonu Gandhi
- DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, Telangana 500032 India
- DBT-Regional Centre for Biotechnology (RCB), Faridabad, Haryana 121001 India
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4
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Chen Q, Zhang Y, Zhang K, Liu J, Pan H, Wang X, Li S, Hu D, Lin Z, Zhao Y, Hou G, Guan F, Li H, Liu S, Ren Y. Profiling the Bisecting N-acetylglucosamine Modification in Amniotic Membrane via Mass Spectrometry. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:648-656. [PMID: 35123071 PMCID: PMC9880894 DOI: 10.1016/j.gpb.2021.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 01/31/2023]
Abstract
Bisecting N-acetylglucosamine (GlcNAc), a GlcNAc linked to the core β-mannose residue via a β1,4 linkage, is a special type of N-glycosylation that has been reported to be involved in various biological processes, such as cell adhesion and fetal development. This N-glycan structure is abundant in human trophoblasts, which is postulated to be resistant to natural killer cell-mediated cytotoxicity, enabling a mother to nourish a fetus without rejection. In this study, we hypothesized that the human amniotic membrane, which serves as the last barrier for the fetus, may also express bisected-type glycans. To test this hypothesis, glycomic analysis of the human amniotic membrane was performed, and bisected N-glycans were detected. Furthermore, our proteomic data, which have been previously employed to explore human missing proteins, were analyzed and the presence of bisecting GlcNAc-modified peptides was confirmed. A total of 41 glycoproteins with 43 glycopeptides were found to possess a bisecting GlcNAc, and 25 of these glycoproteins were reported to exhibit this type of modification for the first time. These results provide insights into the potential roles of bisecting GlcNAc modification in the human amniotic membrane, and can be beneficial to functional studies on glycoproteins with bisecting GlcNAc modifications and functional studies on immune suppression in human placenta.
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Affiliation(s)
| | | | | | - Jie Liu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | | | - Siqi Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Dandan Hu
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Yun Zhao
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - Feng Guan
- Joint International Research Laboratory of Glycobiology and Medical Chemistry, College of Life Sciences, Northwest University, Xi’an 710069, China
| | - Hong Li
- Shenzhen Seventh People's Hospital, Shenzhen 518081, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen 518083, China,Corresponding authors.
| | - Yan Ren
- BGI-Shenzhen, Shenzhen 518083, China,Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China,Corresponding authors.
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5
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Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova K, Koonin E, Shen Y, Söll D, Fu X. The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism. Nucleic Acids Res 2022; 50:4601-4615. [PMID: 35466371 PMCID: PMC9071458 DOI: 10.1093/nar/gkac271] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
Site-specific incorporation of distinct non-canonical amino acids into proteins via genetic code expansion requires mutually orthogonal aminoacyl-tRNA synthetase/tRNA pairs. Pyrrolysyl-tRNA synthetase (PylRS)/tRNAPyl pairs are ideal for genetic code expansion and have been extensively engineered for developing mutually orthogonal pairs. Here, we identify two novel wild-type PylRS/tRNAPyl pairs simultaneously present in the deep-rooted extremely halophilic euryarchaeal methanogen Candidatus Methanohalarchaeum thermophilum HMET1, and show that both pairs are functional in the model halophilic archaeon Haloferax volcanii. These pairs consist of two different PylRS enzymes and two distinct tRNAs with dissimilar discriminator bases. Surprisingly, these two PylRS/tRNAPyl pairs display mutual orthogonality enabled by two unique features, the A73 discriminator base of tRNAPyl2 and a shorter motif 2 loop in PylRS2. In vivo translation experiments show that tRNAPyl2 charging by PylRS2 is defined by the enzyme's shortened motif 2 loop. Finally, we demonstrate that the two HMET1 PylRS/tRNAPyl pairs can simultaneously decode UAG and UAA codons for incorporation of two distinct noncanonical amino acids into protein. This example of a single base change in a tRNA leading to additional coding capacity suggests that the growth of the genetic code is not yet limited by the number of identity elements fitting into the tRNA structure.
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Affiliation(s)
| | | | | | - Takahito Mukai
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Oscar Vargas-Rodriguez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Huiming Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuxing Zhang
- BGI-Shenzhen, Shenzhen, 518083, China,Sino-Danish College, University of the Chinese Academy of Sciences, Beijing, China
| | - Paul Wassel
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Kazuaki Amikura
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
| | - Julie Maupin-Furlow
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA,Genetics Institute, University of Florida, Gainesville, FL 32611, USA
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Yue Shen
- Correspondence may also be addressed to Yue Shen.
| | - Dieter Söll
- To whom correspondence should be addressed. Tel: +1 203 4326200;
| | - Xian Fu
- Correspondence may also be addressed to Xian Fu.
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6
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Bu F, Cheng Q, Zhang Y, Zhang X, Yan K, Liu F, Li Z, Lu X, Ren Y, Liu S. Discovery of Missing Proteins from an Aneuploidy Cell Line Using a Proteogenomic Approach. J Proteome Res 2021; 20:5329-5339. [PMID: 34748338 DOI: 10.1021/acs.jproteome.1c00772] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the steadfast development of proteomic technology, the number of missing proteins (MPs) has been continuously shrinking, with approximately 1470 MPs that have not been explored yet. Due to this phenomenon, the discovery of MPs has been increasingly more difficult and elusive. In order to face this challenge, we have hypothesized that a stable aneuploid cell line with increased chromosomes serves as a useful material for assisting MP exploration. Ker-CT cell line with trisomy at chromosome 5 and 20 was selected for this purpose. With a combination strategy of RNA-Seq and LC-MS/MS, a total of 22 178 transcripts and 8846 proteins were identified in Ker-CT. Although the transcripts corresponding to 15 and 15 MP genes located at chromosome 5 and 20 were detected, none of the MPs were found in Ker-CT. Surprisingly, 3 MPs containing at least two unique non-nest peptides of length ≥9 amino acids were identified in Ker-CT, whose genes are located on chromosome 3 and 10, respectively. Furthermore, the 3 MPs were verified using the method of parallel reaction monitoring (PRM). These results suggest that the abnormal status of chromosomes may not only impact the expression of the corresponding genes in trisomy chromosomes, but also influence that of other chromosomes, which benefits MP discovery. The data obtained in this study are available via ProteomeXchange (PXD028647) and PeptideAtlas (PASS01700), respectively.
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Affiliation(s)
- Fanyu Bu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Qingqiu Cheng
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yuxing Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Xia Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Keqiang Yan
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Frank Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Zelong Li
- Biological Resource Center of Plants, Animals and Microorganisms, China National Gene Bank, BGI-Shenzhen, Guangdong 518120, China
| | - Xiaomei Lu
- Clinical Laboratory Center of Dongguan Eighth People's Hospital, Dongguan 523325, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China.,Department of BGI Education, School of Life Sciences, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
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7
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Boschetti E, Zilberstein G, Righetti PG. Combinatorial peptides: A library that continuously probes low-abundance proteins. Electrophoresis 2021; 43:355-369. [PMID: 34498305 DOI: 10.1002/elps.202100131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/31/2021] [Accepted: 08/24/2021] [Indexed: 12/12/2022]
Abstract
After a decade of experimental applications, it is the objective of this review to make a point on combinatorial peptide ligand libraries dedicated to low-abundance proteins from animals to plants and to microorganism proteomics. It is, thus, at the light of the recent technical developments and applications that we will examine the state of the art, its usage within the scientific community, and its openness to unexplored fields. The improvements of the methodology and its implementation in connection with analytical determinations of combinatorial peptide ligand library (CPLL)-treated samples are extensively reviewed and commented upon. Relevant examples covering few critical aspects describe the performance of the technology. Finally, a reflection on the technological future is attempted in particular by involving new concepts adapted to the limited availability of certain biological samples.
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Affiliation(s)
| | | | - Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Milan, Italy
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8
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Mining the Royal Jelly Proteins: Combinatorial Hexapeptide Ligand Library Significantly Improves the MS-Based Proteomic Identification in Complex Biological Samples. MOLECULES (BASEL, SWITZERLAND) 2021; 26:molecules26092762. [PMID: 34067143 PMCID: PMC8125745 DOI: 10.3390/molecules26092762] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 12/18/2022]
Abstract
Royal jelly (RJ) is a complex, creamy secretion produced by the glands of worker bees. Due to its health-promoting properties, it is used by humans as a dietary supplement. However, RJ compounds are not fully characterized yet. Hence, in this research, we aimed to broaden the knowledge of the proteomic composition of fresh RJ. Water extracts of the samples were pre-treated using combinatorial hexapeptide ligand libraries (ProteoMinerTM kit), trypsin-digested, and analyzed by a nanoLC-MALDI-TOF/TOF MS system. To check the ProteoMinerTM performance in the MS-based protein identification, we also examined RJ extracts that were not prepared with the ProteoMinerTM kit. We identified a total of 86 proteins taxonomically classified to Apis spp. (bees). Among them, 74 proteins were detected in RJ extracts pre-treated with ProteoMinerTM kit, and only 50 proteins were found in extracts non-enriched with this technique. Ten of the identified features were hypothetical proteins whose existence has been predicted, but any experimental evidence proves their in vivo expression. Additionally, we detected four uncharacterized proteins of unknown functions. The results of this research indicate that the ProteoMinerTM strategy improves proteomic identification in complex biological samples. Broadening the knowledge of RJ composition may contribute to the development of standards and regulations, enhancing the quality of RJ, and consequently, the safety of its supplementation.
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9
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Omenn GS. Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Mol Cell Proteomics 2021; 20:100062. [PMID: 33640492 PMCID: PMC8058560 DOI: 10.1016/j.mcpro.2021.100062] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
We celebrate the 10th anniversary of the launch of the HUPO Human Proteome Project (HPP) and its major milestone of confident detection of at least one protein from each of 90% of the predicted protein-coding genes, based on the output of the entire proteomics community. The Human Genome Project reached a similar decadal milestone 20 years ago. The HPP has engaged proteomics teams around the world, strongly influenced data-sharing, enhanced quality assurance, and issued stringent guidelines for claims of detecting previously "missing proteins." This invited perspective complements papers on "A High-Stringency Blueprint of the Human Proteome" and "The Human Proteome Reaches a Major Milestone" in special issues of Nature Communications and Journal of Proteome Research, respectively, released in conjunction with the October 2020 virtual HUPO Congress and its celebration of the 10th anniversary of the HUPO HPP.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan Medical School, Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, Ann Arbor, Michigan, USA.
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10
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New Approaches to Identify Sepsis Biomarkers: The Importance of Model and Sample Source for Mass Spectrometry. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6681073. [PMID: 33425215 PMCID: PMC7775177 DOI: 10.1155/2020/6681073] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/17/2020] [Accepted: 11/27/2020] [Indexed: 02/06/2023]
Abstract
Septic shock is a systemic inflammatory response syndrome associated with circulatory failure leading to organ failure with a 40% mortality rate. Early diagnosis and prognosis of septic shock are necessary for specific and timely treatment. However, no predictive biomarker is available. In recent years, improvements in proteomics-based mass spectrometry have improved the detection of such biomarkers. This approach can be performed on different samples such as tissue or biological fluids. Working directly from human samples is complicated owing to interindividual variability. Indeed, patients are admitted at different stages of disease development and with signs of varying severity from one patient to another. All of these elements interfere with the identification of early, sensitive, and specific septic shock biomarkers. For these reasons, animal models of sepsis, although imperfect, are used to control the kinetics of the development of the pathology and to standardise experimentation, facilitating the identification of potential biomarkers. These elements underline the importance of the choice of animal model used and the sample to be studied during preclinical studies. The aim of this review is to discuss the relevance of different approaches to enable the identification of biomarkers that could indirectly be relevant to the clinical setting.
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11
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Zhang Y, Zhang K, Bu F, Hao P, Yang H, Liu S, Ren Y. D283 Med, a Cell Line Derived from Peritoneal Metastatic Medulloblastoma: A Good Choice for Missing Protein Discovery. J Proteome Res 2020; 19:4857-4866. [DOI: 10.1021/acs.jproteome.0c00743] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, Guangdong 518083, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th Building, Yantian District, Shenzhen, Guangdong 518083, China
- BGI-Genomics, BGI-Shenzhen, Shenzhen, Guangdong 518083, China
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12
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Chu W, Prodromou R, Day KN, Schneible JD, Bacon KB, Bowen JD, Kilgore RE, Catella CM, Moore BD, Mabe MD, Alashoor K, Xu Y, Xiao Y, Menegatti S. Peptides and pseudopeptide ligands: a powerful toolbox for the affinity purification of current and next-generation biotherapeutics. J Chromatogr A 2020; 1635:461632. [PMID: 33333349 DOI: 10.1016/j.chroma.2020.461632] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 02/08/2023]
Abstract
Following the consolidation of therapeutic proteins in the fight against cancer, autoimmune, and neurodegenerative diseases, recent advancements in biochemistry and biotechnology have introduced a host of next-generation biotherapeutics, such as CRISPR-Cas nucleases, stem and car-T cells, and viral vectors for gene therapy. With these drugs entering the clinical pipeline, a new challenge lies ahead: how to manufacture large quantities of high-purity biotherapeutics that meet the growing demand by clinics and biotech companies worldwide. The protein ligands employed by the industry are inadequate to confront this challenge: while featuring high binding affinity and selectivity, these ligands require laborious engineering and expensive manufacturing, are prone to biochemical degradation, and pose safety concerns related to their bacterial origin. Peptides and pseudopeptides make excellent candidates to form a new cohort of ligands for the purification of next-generation biotherapeutics. Peptide-based ligands feature excellent target biorecognition, low or no toxicity and immunogenicity, and can be manufactured affordably at large scale. This work presents a comprehensive and systematic review of the literature on peptide-based ligands and their use in the affinity purification of established and upcoming biological drugs. A comparative analysis is first presented on peptide engineering principles, the development of ligands targeting different biomolecular targets, and the promises and challenges connected to the industrial implementation of peptide ligands. The reviewed literature is organized in (i) conventional (α-)peptides targeting antibodies and other therapeutic proteins, gene therapy products, and therapeutic cells; (ii) cyclic peptides and pseudo-peptides for protein purification and capture of viral and bacterial pathogens; and (iii) the forefront of peptide mimetics, such as β-/γ-peptides, peptoids, foldamers, and stimuli-responsive peptides for advanced processing of biologics.
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Affiliation(s)
- Wenning Chu
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Raphael Prodromou
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kevin N Day
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Schneible
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kaitlyn B Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - John D Bowen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Ryan E Kilgore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Carly M Catella
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Brandyn D Moore
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Matthew D Mabe
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606
| | - Kawthar Alashoor
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, NY 14642
| | - Yiman Xu
- College of Material Science and Engineering, Donghua University, 201620 Shanghai, People's Republic of China
| | - Yuanxin Xiao
- College of Textile, Donghua University, Songjiang District, Shanghai, 201620, People's Republic of China
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, 911 Partners Way room 2-009, Raleigh, NC 27606.
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13
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Omenn GS, Lane L, Overall CM, Cristea IM, Corrales FJ, Lindskog C, Paik YK, Van Eyk JE, Liu S, Pennington SR, Snyder MP, Baker MS, Bandeira N, Aebersold R, Moritz RL, Deutsch EW. Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project. J Proteome Res 2020; 19:4735-4746. [PMID: 32931287 DOI: 10.1021/acs.jproteome.0c00485] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
According to the 2020 Metrics of the HUPO Human Proteome Project (HPP), expression has now been detected at the protein level for >90% of the 19 773 predicted proteins coded in the human genome. The HPP annually reports on progress made throughout the world toward credibly identifying and characterizing the complete human protein parts list and promoting proteomics as an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2020-01 classified 17 874 proteins as PE1, having strong protein-level evidence, up 180 from 17 694 one year earlier. These represent 90.4% of the 19 773 predicted coding genes (all PE1,2,3,4 proteins in neXtProt). Conversely, the number of neXtProt PE2,3,4 proteins, termed the "missing proteins" (MPs), was reduced by 230 from 2129 to 1899 since the neXtProt 2019-01 release. PeptideAtlas is the primary source of uniform reanalysis of raw mass spectrometry data for neXtProt, supplemented this year with extensive data from MassIVE. PeptideAtlas 2020-01 added 362 canonical proteins between 2019 and 2020 and MassIVE contributed 84 more, many of which converted PE1 entries based on non-MS evidence to the MS-based subgroup. The 19 Biology and Disease-driven B/D-HPP teams continue to pursue the identification of driver proteins that underlie disease states, the characterization of regulatory mechanisms controlling the functions of these proteins, their proteoforms, and their interactions, and the progression of transitions from correlation to coexpression to causal networks after system perturbations. And the Human Protein Atlas published Blood, Brain, and Metabolic Atlases.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan, Ann Arbor, Michigan 48109, United States.,Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | | | - Ileana M Cristea
- Princeton University, Princeton, New Jersey 08544, United States
| | | | | | | | | | - Siqi Liu
- BGI Group, Shenzhen 518083, China
| | | | | | - Mark S Baker
- Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Nuno Bandeira
- University of California, San Diego, La Jolla, California 92093, United States
| | - Ruedi Aebersold
- ETH-Zurich and University of Zurich, 8092 Zurich, Switzerland
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
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14
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Serum proteomics of active tuberculosis patients and contacts reveals unique processes activated during Mycobacterium tuberculosis infection. Sci Rep 2020; 10:3844. [PMID: 32123229 PMCID: PMC7052228 DOI: 10.1038/s41598-020-60753-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 02/17/2020] [Indexed: 01/24/2023] Open
Abstract
Tuberculosis (TB) is the most lethal infection among infectious diseases. The specific aim of this study was to establish panels of serum protein biomarkers representative of active TB patients and their household contacts who were either infected (LTBI) or uninfected (EMI-TB Discovery Cohort, Pontevedra Region, Spain). A TMT (Tamdem mass tags) 10plex-based quantitative proteomics study was performed in quintuplicate containing a total of 15 individual serum samples per group. Peptides were analyzed in an LC-Orbitrap Elite platform, and raw data were processed using Proteome Discoverer 2.1. A total of 418 proteins were quantified. The specific protein signature of active TB patients was characterized by an accumulation of proteins related to complement activation, inflammation and modulation of immune response and also by a decrease of a small subset of proteins, including apolipoprotein A and serotransferrin, indicating the importance of lipid transport and iron assimilation in the progression of the disease. This signature was verified by the targeted measurement of selected candidates in a second cohort (EMI-TB Verification Cohort, Maputo Region, Mozambique) by ELISA and nephelometry techniques. These findings will aid our understanding of the complex metabolic processes associated with TB progression from LTBI to active disease.
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15
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Zhang Y, Lin Z, Tan Y, Bu F, Hao P, Zhang K, Yang H, Liu S, Ren Y. Exploration of Missing Proteins by a Combination Approach to Enrich the Low-Abundance Hydrophobic Proteins from Four Cancer Cell Lines. J Proteome Res 2019; 19:401-408. [DOI: 10.1021/acs.jproteome.9b00590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yifan Tan
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Fanyu Bu
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone, 11th Building, Yantian District, Shenzhen 518083, Guangdong, China
- Clinical Laboratory of BGI Health, BGI-Shenzhen, Shenzhen 518083, China
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16
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Lin Z, Zhang Y, Pan H, Hao P, Li S, He Y, Yang H, Liu S, Ren Y. Alternative Strategy To Explore Missing Proteins with Low Molecular Weight. J Proteome Res 2019; 18:4180-4188. [PMID: 31592669 DOI: 10.1021/acs.jproteome.9b00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Identifying more missing proteins (MPs) is an important mission of C-HPP. With the number of identified MPs being attenuated year by year (2,949 to 2,129 MPs from 2016 to 2019), we have realized that the difficulty of exploring the remaining MPs is a challenge in technique. Herein, we propose a comprehensive strategy to effectively enrich, separate, and identify proteins with low molecular weights, aiming at the discovery of MPs. Basically, a protein extract from human placenta was passed through a C18 SPE column, and the bound proteins that were eluted were further separated with an SDS-PAGE gel or a 50 kDa cutoff filter. The separated proteins were subjected to trypsin digestion, and the MS/MS signals were searched against data sets with two different digestion modes (full-trypsin and semitrypsin). The strategy was adopted, resulting in the identification of 4 MPs with 8 unique peptides (≥2 non-nested unique peptides with ≥9 amino acids). Importantly, the identification of 6 out of 8 of the unique peptides derived from the MPs was further supported by parallel reaction monitoring, which confirmed the identification of 3 MPs from human placenta tissues (Q6NT89: TMF-regulated nuclear protein 1; A0A183: late cornified envelope protein 6A; and Q6UWQ7: insulin growth factor-like family member 2, mapped to chromosomes 1, 1, and 19, respectively). The three proteins ranged in length from 80 aa to 227 aa. The study not only establishes a feasible strategy for analyzing proteins with low molecular weights but also fills a small part of a large gap in the list of MPs. The data obtained in this study are available via ProteomeXchange (PXD014083) and PeptideAtlas (PASS01389).
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Affiliation(s)
- Zhilong Lin
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yuanliang Zhang
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Huozhen Pan
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Piliang Hao
- School of Life Science and Technology , ShanghaiTech University , 393 Middle Huaxia Road , Shanghai 201210 , China
| | - Siqi Li
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yanbin He
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Huanming Yang
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,James D. Watson Institute of Genome Sciences , Hangzhou 310058 , China
| | - Siqi Liu
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
| | - Yan Ren
- BGI-Shenzhen , Beishan Industrial Zone 11th building , Yantian District, Shenzhen , Guangdong 518083 , China.,Clinical laboratory of BGI Health , BGI-Shenzhen , Shenzhen 518083 , China
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17
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Zhou Y, Qin S, Sun M, Tang L, Yan X, Kim TK, Caballero J, Glusman G, Brunkow ME, Soloski MJ, Rebman AW, Scavarda C, Cooper D, Omenn GS, Moritz RL, Wormser GP, Price ND, Aucott JN, Hood L. Measurement of Organ-Specific and Acute-Phase Blood Protein Levels in Early Lyme Disease. J Proteome Res 2019; 19:346-359. [PMID: 31618575 DOI: 10.1021/acs.jproteome.9b00569] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Lyme disease results from infection of humans with the spirochete Borrelia burgdorferi. The first and most common clinical manifestation is the circular, inflamed skin lesion referred to as erythema migrans; later manifestations result from infections of other body sites. Laboratory diagnosis of Lyme disease can be challenging in patients with erythema migrans because of the time delay in the development of specific diagnostic antibodies against Borrelia. Reliable blood biomarkers for the early diagnosis of Lyme disease in patients with erythema migrans are needed. Here, we performed selected reaction monitoring, a targeted mass spectrometry-based approach, to measure selected proteins that (1) are known to be predominantly expressed in one organ (i.e., organ-specific blood proteins) and whose blood concentrations may change as a result of Lyme disease, or (2) are involved in acute immune responses. In a longitudinal cohort of 40 Lyme disease patients and 20 healthy controls, we identified 10 proteins with significantly altered serum levels in patients at the time of diagnosis, and we also developed a 10-protein panel identified through multivariate analysis. In an independent cohort of patients with erythema migrans, six of these proteins, APOA4, C9, CRP, CST6, PGLYRP2, and S100A9, were confirmed to show significantly altered serum levels in patients at time of presentation. Nine of the 10 proteins from the multivariate panel were also verified in the second cohort. These proteins, primarily innate immune response proteins or proteins specific to liver, skin, or white blood cells, may serve as candidate blood biomarkers requiring further validation to aid in the laboratory diagnosis of early Lyme disease.
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Affiliation(s)
- Yong Zhou
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Shizhen Qin
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Mingjuan Sun
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Second Military Medical University , Shanghai 200433 , China
| | - Li Tang
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Xiaowei Yan
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Taek-Kyun Kim
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Juan Caballero
- Molecular and Developmental Complexity Lab , Langebio-Cinvestav , Irapuato , Guanajuato 36821 , Mexico
| | - Gustavo Glusman
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Mary E Brunkow
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Mark J Soloski
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , Maryland 21093 , United States
| | - Alison W Rebman
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , Maryland 21093 , United States
| | - Carol Scavarda
- Division of Infectious Diseases, Department of Medicine , New York Medical College , Valhalla , New York 10595 , United States
| | - Denise Cooper
- Division of Infectious Diseases, Department of Medicine , New York Medical College , Valhalla , New York 10595 , United States
| | - Gilbert S Omenn
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Center for Computational Medicine & Bioinformatics , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Robert L Moritz
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - Gary P Wormser
- Division of Infectious Diseases, Department of Medicine , New York Medical College , Valhalla , New York 10595 , United States
| | - Nathan D Price
- Institute for Systems Biology , Seattle , Washington 98109 , United States
| | - John N Aucott
- Lyme Disease Research Center, Division of Rheumatology, Department of Medicine , Johns Hopkins University School of Medicine , Baltimore , Maryland 21093 , United States
| | - Leroy Hood
- Institute for Systems Biology , Seattle , Washington 98109 , United States.,Providence St. Joseph Health , Seattle , Washington 98109 , United States
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18
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Omenn GS, Lane L, Overall CM, Corrales FJ, Schwenk JM, Paik YK, Van Eyk JE, Liu S, Snyder M, Baker MS, Deutsch EW. Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project. J Proteome Res 2018; 17:4031-4041. [PMID: 30099871 PMCID: PMC6387656 DOI: 10.1021/acs.jproteome.8b00441] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The Human Proteome Project (HPP) annually reports on progress throughout the field in credibly identifying and characterizing the human protein parts list and making proteomics an integral part of multiomics studies in medicine and the life sciences. NeXtProt release 2018-01-17, the baseline for this sixth annual HPP special issue of the Journal of Proteome Research, contains 17 470 PE1 proteins, 89% of all neXtProt predicted PE1-4 proteins, up from 17 008 in release 2017-01-23 and 13 975 in release 2012-02-24. Conversely, the number of neXtProt PE2,3,4 missing proteins has been reduced from 2949 to 2579 to 2186 over the past two years. Of the PE1 proteins, 16 092 are based on mass spectrometry results, and 1378 on other kinds of protein studies, notably protein-protein interaction findings. PeptideAtlas has 15 798 canonical proteins, up 625 over the past year, including 269 from SUMOylation studies. The largest reason for missing proteins is low abundance. Meanwhile, the Human Protein Atlas has released its Cell Atlas, Pathology Atlas, and updated Tissue Atlas, and is applying recommendations from the International Working Group on Antibody Validation. Finally, there is progress using the quantitative multiplex organ-specific popular proteins targeted proteomics approach in various disease categories.
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Affiliation(s)
- Gilbert S. Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Avenue, Ann Arbor, Michigan 48109-2218, United States
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
| | - Lydie Lane
- CALIPHO Group, SIB Swiss Institute of Bioinformatics and Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Michel-Servet 1, 1211 Geneva 4, Switzerland
| | - Christopher M. Overall
- Life Sciences Institute, Faculty of Dentistry, University of British Columbia, 2350 Health Sciences Mall, Room 4.401, Vancouver, BC Canada V6T 1Z3
| | | | - Jochen M. Schwenk
- Science for Life Laboratory, KTH Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Young-Ki Paik
- Yonsei Proteome Research Center, Room 425, Building #114, Yonsei University,50 Yonsei-ro, Seodaemoon-ku, Seoul 120-749, Korea
| | - Jennifer E. Van Eyk
- Advanced Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Siqi Liu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, United States
| | - Michael Snyder
- Department of Genetics, Stanford University, Alway Building, 300 Pasteur Drive, 3165 Porter Drive, Palo Alto, 94304, United States
| | - Mark S. Baker
- Department of Biomedical Sciences, Macquarie University, NSW 2109, Australia
| | - Eric W. Deutsch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, Washington 98109-5263, United States
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19
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Zhang Y, Lin Z, Hao P, Hou K, Sui Y, Zhang K, He Y, Li H, Yang H, Liu S, Ren Y. Improvement of Peptide Separation for Exploring the Missing Proteins Localized on Membranes. J Proteome Res 2018; 17:4152-4159. [DOI: 10.1021/acs.jproteome.8b00409] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanliang Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Zhilong Lin
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Kexia Hou
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Yuanyuan Sui
- The Second Maternal and Child Health Care Center of Huangdao District, 236 Fuchunjiang Road, Qingdao 266555, Shandong, China
| | - Keren Zhang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yanbin He
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Hong Li
- Pulmonary Function Room, Shenzhen Seventh People’s Hospital, 2010 Wutong Road, Yantian District, Shenzhen, Guangdong 518081, China
| | - Huanming Yang
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Siqi Liu
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
| | - Yan Ren
- BGI-Shenzhen, Beishan Industrial Zone 11th building, Yantian District, Shenzhen, Guangdong 518083, China
- China National GeneBank, BGI-Shenzhen, Jinsha Road, Shenzhen 518120, China
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20
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Melaine N, Com E, Bellaud P, Guillot L, Lagarrigue M, Morrice NA, Guével B, Lavigne R, Velez de la Calle JF, Dojahn J, Pineau C. Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins. J Proteome Res 2018; 17:4197-4210. [DOI: 10.1021/acs.jproteome.8b00387] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathalie Melaine
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Pascale Bellaud
- H2P2 Core Facility, UMS BioSit, Univ Rennes, Rennes F-35040, France
| | - Laetitia Guillot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Mélanie Lagarrigue
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Nick A. Morrice
- Sciex, Phoenix House Lakeside Drive Centre Park, Warrington WA1 1RX, U.K
| | - Blandine Guével
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | - Régis Lavigne
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
| | | | - Jörg Dojahn
- Sciex, Landwehrstr. 54, 64293 Darmstadt, Germany
| | - Charles Pineau
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail)—UMR S 1085, F-35042 Rennes cedex, France
- Protim, Univ Rennes, F-35042 Rennes, France
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21
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Paik YK, Overall CM, Deutsch EW, Van Eyk JE, Omenn GS. Progress and Future Direction of Chromosome-Centric Human Proteome Project. J Proteome Res 2018; 16:4253-4258. [PMID: 29191025 DOI: 10.1021/acs.jproteome.7b00734] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This special issue of JPR celebrates the fifth anniversary of the Chromosome-Centric Human Proteome Project (C-HPP). We present 27 manuscripts in four categories: (i) Metrics of Progress and Resources, (ii) Missing Protein Detection and Validation, (iii) Analytical Methods and Quality Assessment, and (iv) Protein Functions and Disease. We briefly introduce key messages from each paper, mostly from C-HPP teams and some from the Biology and Disease-driven HPP. From the first few months of the C-HPP NeXt-MP50 Missing Proteins Challenge, authors report 73 missing protein detections that meet the HPP guidelines using several novel approaches. Finally, we discuss future directions.
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Affiliation(s)
- Young-Ki Paik
- Yonsei Proteome Research Center and Department of Biochemistry, Yonsei University
| | - Christopher M Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia
| | | | - Jennifer E Van Eyk
- Advanced Clinical BioSystems Research Institute , Department of Medicine, Cedars-Sinai Medical Centre
| | - Gilbert S Omenn
- Institute for Systems Biology.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan
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