1
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Uversky VN. Functional unfoldomics: Roles of intrinsic disorder in protein (multi)functionality. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:179-210. [PMID: 38220424 DOI: 10.1016/bs.apcsb.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Intrinsically disordered proteins (IDPs), which are functional proteins without stable tertiary structure, and hybrid proteins containing ordered domains and intrinsically disordered regions (IDRs) constitute prominent parts of all proteomes collectively known as unfoldomes. IDPs/IDRs exist as highly dynamic structural ensembles of rapidly interconverting conformations and are characterized by the exceptional structural heterogeneity, where their different parts are (dis)ordered to different degree, and their overall structure represents a complex mosaic of foldons, inducible foldons, inducible morphing foldons, non-foldons, semifoldons, and even unfoldons. Despite their lack of unique 3D structures, IDPs/IDRs play crucial roles in the control of various biological processes and the regulation of different cellular pathways and are commonly involved in recognition and signaling, indicating that the disorder-based functional repertoire is complementary to the functions of ordered proteins. Furthermore, IDPs/IDRs are frequently multifunctional, and this multifunctionality is defined by their structural flexibility and heterogeneity. Intrinsic disorder phenomenon is at the roots of the structure-function continuum model, where the structure continuum is defined by the presence of differently (dis)ordered regions, and the function continuum arises from the ability of all these differently (dis)ordered parts to have different functions. In their everyday life, IDPs/IDRs utilize a broad spectrum of interaction mechanisms thereby acting as interaction specialists. They are crucial for the biogenesis of numerous proteinaceous membrane-less organelles driven by the liquid-liquid phase separation. This review introduces functional unfoldomics by representing some aspects of the intrinsic disorder-based functionality.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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2
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Dorl S, Winkler S, Mechtler K, Dorfer V. MS Ana: Improving Sensitivity in Peptide Identification with Spectral Library Search. J Proteome Res 2023; 22:462-470. [PMID: 36688604 PMCID: PMC9903325 DOI: 10.1021/acs.jproteome.2c00658] [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] [Indexed: 01/24/2023]
Abstract
Spectral library search can enable more sensitive peptide identification in tandem mass spectrometry experiments. However, its drawbacks are the limited availability of high-quality libraries and the added difficulty of creating decoy spectra for result validation. We describe MS Ana, a new spectral library search engine that enables high sensitivity peptide identification using either curated or predicted spectral libraries as well as robust false discovery control through its own decoy library generation algorithm. MS Ana identifies on average 36% more spectrum matches and 4% more proteins than database search in a benchmark test on single-shot human cell-line data. Further, we demonstrate the quality of the result validation with tests on synthetic peptide pools and show the importance of library selection through a comparison of library search performance with different configurations of publicly available human spectral libraries.
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Affiliation(s)
- Sebastian Dorl
- University
of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232Hagenberg, Austria,Department
of Computer Science, Johannes Kepler University
Linz, Altenbergerstraße
69, 4040Linz, Austria,E-mail: . Phone: +43 (0) 50804
27145
| | - Stephan Winkler
- University
of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232Hagenberg, Austria,Department
of Computer Science, Johannes Kepler University
Linz, Altenbergerstraße
69, 4040Linz, Austria
| | - Karl Mechtler
- Research
Institute of Molecular Pathology (IMP), Protein Chemistry, Campus-Vienna-Biocenter 1, 1030Vienna, Austria,Institute
of Molecular Biotechnology (IMBA), Protein Chemistry, Vienna Biocenter
(VBC), Dr. Bohr-Gasse 3, 1030Vienna, Austria,Gregor
Mendel Institute of Molecular Plant Biology of the Austrian Academy
of Sciences (GMI), Dr.
Bohr Gasse 3, 1030Vienna, Austria
| | - Viktoria Dorfer
- University
of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232Hagenberg, Austria,E-mail: . Phone: +43 (0) 50804
22740
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3
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La Ferlita A, Alaimo S, Ferro A, Pulvirenti A. Pathway Analysis for Cancer Research and Precision Oncology Applications. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1361:143-161. [DOI: 10.1007/978-3-030-91836-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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4
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Xiao X, Sun H, Liu X, Guo Z, Zheng S, Xu J, Sun J, Lan Y, Shao C, Sun W. Qualitative and quantitative proteomic and metaproteomic analyses of healthy human urine sediment. Proteomics Clin Appl 2021; 16:e2100007. [PMID: 34687263 DOI: 10.1002/prca.202100007] [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: 01/30/2021] [Revised: 09/30/2021] [Accepted: 10/17/2021] [Indexed: 11/07/2022]
Abstract
PURPOSE The healthy human urine sediment proteome and metaproteome are investigated, to shed light on the variations of urine sediment proteins and metaproteins associated with sex and age. EXPERIMENTAL DESIGN Urine sediment samples are collected from 19 healthy subjects. Protein identification and quantification are performed by liquid chromatography coupled high-resolution mass spectrometry. RESULTS A total of 2736 human proteins were identified, which were primarily associated with inflammatory response and energy metabolism. For the metaproteome, 65 genera were identified that were primarily involved in translation and carbohydrate metabolic processes. The median biological coefficient variation of the proteome/metaproteome of human urine sediment was 0.5/0.72, similar to the proteome of human urine supernatant. In addition, sex and age were observed to affect the proteome and metaproteome of healthy human urine sediment. CONCLUSION AND CLINICAL RELEVANCE The healthy human urine sediment were characterized, indicating that urine sediment might represent an alternative resource for disease research in addition to urine supernatant, but the influence of sex and age must be considered in the study design process.
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Affiliation(s)
- XiaoLian Xiao
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Haidan Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyan Liu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Zhengguang Guo
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Shuxin Zheng
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiyu Xu
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiameng Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Ying Lan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Chen Shao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Wei Sun
- Core Facility of Instrument, School of Basic Medicine, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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5
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Deutsch EW, Omenn GS, Sun Z, Maes M, Pernemalm M, Palaniappan KK, Letunica N, Vandenbrouck Y, Brun V, Tao SC, Yu X, Geyer PE, Ignjatovic V, Moritz RL, Schwenk JM. Advances and Utility of the Human Plasma Proteome. J Proteome Res 2021; 20:5241-5263. [PMID: 34672606 PMCID: PMC9469506 DOI: 10.1021/acs.jproteome.1c00657] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The study of proteins circulating in blood offers tremendous opportunities to diagnose, stratify, or possibly prevent diseases. With recent technological advances and the urgent need to understand the effects of COVID-19, the proteomic analysis of blood-derived serum and plasma has become even more important for studying human biology and pathophysiology. Here we provide views and perspectives about technological developments and possible clinical applications that use mass-spectrometry(MS)- or affinity-based methods. We discuss examples where plasma proteomics contributed valuable insights into SARS-CoV-2 infections, aging, and hemostasis and the opportunities offered by combining proteomics with genetic data. As a contribution to the Human Proteome Organization (HUPO) Human Plasma Proteome Project (HPPP), we present the Human Plasma PeptideAtlas build 2021-07 that comprises 4395 canonical and 1482 additional nonredundant human proteins detected in 240 MS-based experiments. In addition, we report the new Human Extracellular Vesicle PeptideAtlas 2021-06, which comprises five studies and 2757 canonical proteins detected in extracellular vesicles circulating in blood, of which 74% (2047) are in common with the plasma PeptideAtlas. Our overview summarizes the recent advances, impactful applications, and ongoing challenges for translating plasma proteomics into utility for precision medicine.
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Affiliation(s)
- Eric W Deutsch
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Gilbert S Omenn
- Institute for Systems Biology, Seattle, Washington 98109, United States.,Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, Michigan 48109-2218, United States
| | - Zhi Sun
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Michal Maes
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Maria Pernemalm
- Department of Oncology and Pathology/Science for Life Laboratory, Karolinska Institutet, 171 65 Stockholm, Sweden
| | | | - Natasha Letunica
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm U1292, Grenoble 38000, France
| | - Sheng-Ce Tao
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, B207 SCSB Building, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiaobo Yu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences-Beijing (PHOENIX Center), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Philipp E Geyer
- OmicEra Diagnostics GmbH, Behringstr. 6, 82152 Planegg, Germany
| | - Vera Ignjatovic
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville 3052, Victoria, Australia.,Department of Paediatrics, The University of Melbourne, 50 Flemington Road, Parkville 3052, Victoria, Australia
| | - Robert L Moritz
- Institute for Systems Biology, Seattle, Washington 98109, United States
| | - Jochen M Schwenk
- Affinity Proteomics, Science for Life Laboratory, Department of Protein Science, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
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6
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Marzullo L, Turco MC, Uversky VN. What's in the BAGs? Intrinsic disorder angle of the multifunctionality of the members of a family of chaperone regulators. J Cell Biochem 2021; 123:22-42. [PMID: 34339540 DOI: 10.1002/jcb.30123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/28/2021] [Accepted: 07/22/2021] [Indexed: 01/22/2023]
Abstract
In humans, the family of Bcl-2 associated athanogene (BAG) proteins includes six members characterized by exceptional multifunctionality and engagement in the pathogenesis of various diseases. All of them are capable of interacting with a multitude of often unrelated binding partners. Such binding promiscuity and related functional and pathological multifacetedness cannot be explained or understood within the frames of the classical "one protein-one structure-one function" model, which also fails to explain the presence of multiple isoforms generated for BAG proteins by alternative splicing or alternative translation initiation and their extensive posttranslational modifications. However, all these mysteries can be solved by taking into account the intrinsic disorder phenomenon. In fact, high binding promiscuity and potential to participate in a broad spectrum of interactions with multiple binding partners, as well as a capability to be multifunctional and multipathogenic, are some of the characteristic features of intrinsically disordered proteins and intrinsically disordered protein regions. Such functional proteins or protein regions lacking unique tertiary structures constitute a cornerstone of the protein structure-function continuum concept. The aim of this paper is to provide an overview of the functional roles of human BAG proteins from the perspective of protein intrinsic disorder which will provide a means for understanding their binding promiscuity, multifunctionality, and relation to the pathogenesis of various diseases.
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Affiliation(s)
- Liberato Marzullo
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Maria C Turco
- Department of Medicine, Surgery and Dentistry Schola Medica Salernitana, University of Salerno, Baronissi, Italy.,Research and Development Division, BIOUNIVERSA s.r.l., Baronissi, Italy
| | - Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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7
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Swensen AC, He J, Fang AC, Ye Y, Nicora CD, Shi T, Liu AY, Sigdel TK, Sarwal MM, Qian WJ. A Comprehensive Urine Proteome Database Generated From Patients With Various Renal Conditions and Prostate Cancer. Front Med (Lausanne) 2021; 8:548212. [PMID: 33928097 PMCID: PMC8076675 DOI: 10.3389/fmed.2021.548212] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 03/18/2021] [Indexed: 01/10/2023] Open
Abstract
Urine proteins can serve as viable biomarkers for diagnosing and monitoring various diseases. A comprehensive urine proteome database, generated from a variety of urine samples with different disease conditions, can serve as a reference resource for facilitating discovery of potential urine protein biomarkers. Herein, we present a urine proteome database generated from multiple datasets using 2D LC-MS/MS proteome profiling of urine samples from healthy individuals (HI), renal transplant patients with acute rejection (AR) and stable graft (STA), patients with non-specific proteinuria (NS), and patients with prostate cancer (PC). A total of ~28,000 unique peptides spanning ~2,200 unique proteins were identified with a false discovery rate of <0.5% at the protein level. Over one third of the annotated proteins were plasma membrane proteins and another one third were extracellular proteins according to gene ontology analysis. Ingenuity Pathway Analysis of these proteins revealed 349 potential biomarkers in the literature-curated database. Forty-three percentage of all known cluster of differentiation (CD) proteins were identified in the various human urine samples. Interestingly, following comparisons with five recently published urine proteome profiling studies, which applied similar approaches, there are still ~400 proteins which are unique to this current study. These may represent potential disease-associated proteins. Among them, several proteins such as serpin B3, renin receptor, and periostin have been reported as pathological markers for renal failure and prostate cancer, respectively. Taken together, our data should provide valuable information for future discovery and validation studies of urine protein biomarkers for various diseases.
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Affiliation(s)
- Adam C Swensen
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Jingtang He
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Alexander C Fang
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Yinyin Ye
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Carrie D Nicora
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Tujin Shi
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
| | - Alvin Y Liu
- Department of Urology, University of Washington, Seattle, WA, United States
| | - Tara K Sigdel
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Minnie M Sarwal
- Department of Surgery, University of California, San Francisco, San Francisco, CA, United States
| | - Wei-Jun Qian
- Integrative Omics, Pacific Northwest National Laboratory, Biological Sciences Division, Richland, WA, United States
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8
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Uversky VN. Functions of short lifetime biological structures at large: the case of intrinsically disordered proteins. Brief Funct Genomics 2020; 19:60-68. [PMID: 29982297 DOI: 10.1093/bfgp/ely023] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although for more than a century a protein function was intimately associated with the presence of unique structure in a protein molecule, recent years witnessed a skyrocket rise of the appreciation of protein intrinsic disorder concept that emphasizes the importance of the biologically active proteins without ordered structures. In different proteins, the depth and breadth of disorder penetrance are different, generating an amusing spatiotemporal heterogeneity of intrinsically disordered proteins (IDPs) and intrinsically disordered protein region regions (IDPRs), which are typically described as highly dynamic ensembles of rapidly interconverting conformations (or a multitude of short lifetime structures). IDPs/IDPRs constitute a substantial part of protein kingdom and have unique functions complementary to functional repertoires of ordered proteins. They are recognized as interaction specialists and global controllers that play crucial roles in regulation of functions of their binding partners and in controlling large biological networks. IDPs/IDPRs are characterized by immense binding promiscuity and are able to use a broad spectrum of binding modes, often resulting in the formation of short lifetime complexes. In their turn, functions of IDPs and IDPRs are controlled by various means, such as numerous posttranslational modifications and alternative splicing. Some of the functions of IDPs/IDPRs are briefly considered in this review to shed some light on the biological roles of short-lived structures at large.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA and Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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9
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Weisz J, Uversky VN. Zooming into the Dark Side of Human Annexin-S100 Complexes: Dynamic Alliance of Flexible Partners. Int J Mol Sci 2020; 21:ijms21165879. [PMID: 32824294 PMCID: PMC7461550 DOI: 10.3390/ijms21165879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Annexins and S100 proteins form two large families of Ca2+-binding proteins. They are quite different both structurally and functionally, with S100 proteins being small (10–12 kDa) acidic regulatory proteins from the EF-hand superfamily of Ca2+-binding proteins, and with annexins being at least three-fold larger (329 ± 12 versus 98 ± 7 residues) and using non-EF-hand-based mechanism for calcium binding. Members of both families have multiple biological roles, being able to bind to a large cohort of partners and possessing a multitude of functions. Furthermore, annexins and S100 proteins can interact with each other in either a Ca2+-dependent or Ca2+-independent manner, forming functional annexin-S100 complexes. Such functional polymorphism and binding indiscrimination are rather unexpected, since structural information is available for many annexins and S100 proteins, which therefore are considered as ordered proteins that should follow the classical “one protein–one structure–one function” model. On the other hand, the ability to be engaged in a wide range of interactions with multiple, often unrelated, binding partners and possess multiple functions represent characteristic features of intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs); i.e., functional proteins or protein regions lacking unique tertiary structures. The aim of this paper is to provide an overview of the functional roles of human annexins and S100 proteins, and to use the protein intrinsic disorder perspective to explain their exceptional multifunctionality and binding promiscuity.
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Affiliation(s)
- Judith Weisz
- Departments of Gynecology and Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA;
| | - Vladimir N. Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Correspondence: ; Tel.: +1-813-974-5816 (ext. 123); Fax: +1-813-974-7357
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10
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Deng N, Chen Y, Liang Z, Bian Y, Wang B, Sui Z, Zhang X, Yang K, Zhang L, Zhang Y. Ampholine immobilized polymer microspheres for increasing coverage of human urinary proteome. Talanta 2020; 215:120931. [DOI: 10.1016/j.talanta.2020.120931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/06/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
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11
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Dayhoff GW, Regenmortel MHV, Uversky VN. Intrinsic disorder in protein sense‐antisense recognition. J Mol Recognit 2020; 33:e2868. [DOI: 10.1002/jmr.2868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 05/04/2020] [Accepted: 05/18/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Guy W. Dayhoff
- Department of Chemistry, College of Art and SciencesUniversity of South Florida Tampa Florida USA
| | | | - Vladimir N. Uversky
- Laboratory of New Methods in BiologyInstitute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences” Pushchino Russia
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research InstituteMorsani College of Medicine, University of South Florida Tampa Florida USA
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12
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Ambrosino L, Colantuono C, Diretto G, Fiore A, Chiusano ML. Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PLANTS 2020; 9:plants9050591. [PMID: 32384671 PMCID: PMC7285221 DOI: 10.3390/plants9050591] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022]
Abstract
Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority. The rise of -omics approaches provides key strategies to promote effective research in the field, facilitating the investigations from reference models to an increasing number of species, tolerant and sensitive genotypes. Integrated multilevel approaches, based on molecular investigations at genomics, transcriptomics, proteomics and metabolomics levels, are now feasible, expanding the opportunities to clarify key molecular aspects involved in responses to abiotic stresses. To this aim, bioinformatics has become fundamental for data production, mining and integration, and necessary for extracting valuable information and for comparative efforts, paving the way to the modeling of the involved processes. We provide here an overview of bioinformatics resources for research on plant abiotic stresses, describing collections from -omics efforts in the field, ranging from raw data to complete databases or platforms, highlighting opportunities and still open challenges in abiotic stress research based on -omics technologies.
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Affiliation(s)
- Luca Ambrosino
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Chiara Colantuono
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
| | - Gianfranco Diretto
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Alessia Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), 00123 Rome, Italy; (G.D.); (A.F.)
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, University of Naples Federico II, 80055 Portici (Na), Italy; (L.A.); (C.C.)
- Department of Research Infrastructures for Marine Biological Resources (RIMAR), 80121 Naples, Italy
- Correspondence: ; Tel.: +39-081-253-9492
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13
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de Oliveira TM, de Lacerda JTJG, Leite GGF, Dias M, Mendes MA, Kassab P, E Silva CGS, Juliano MA, Forones NM. Label-free peptide quantification coupled with in silico mapping of proteases for identification of potential serum biomarkers in gastric adenocarcinoma patients. Clin Biochem 2020; 79:61-69. [PMID: 32097616 DOI: 10.1016/j.clinbiochem.2020.02.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/31/2020] [Accepted: 02/18/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVES We aimed to identify serum level variations in protein-derived peptides between patients diagnosed with gastric adenocarcinoma (GAC) and non-cancer persons (control) to detect the activity changes of proteases and explore the auxiliary diagnostic value in the context of GAC physiopathology. METHODS The label-free quantitative peptidome approach was applied to identify variants in serum levels of peptides that can differentiate GAC patients from the control group. Peptide sequences were submitted against Proteasix tool predicting proteases potentially involved in their generation. The activity change of proteases was subsequently estimated based on the peptides with significantly altered relative abundance. In turn, activity change prediction of proteases was correlated with relevant protease expression data from the literature. RESULTS A total of 191 peptide sequences generated by the cleavage of 36 precursor proteins were identified. Using the label-free quantification approach, 33 peptides were differentially quantified (adjusted fold change ≥ 1.5 and p-value < 0.05) in which 19 were up-regulated and 14 were down-regulated in GAC samples. Of these peptides, fibrinopeptide A was significantly decreased and its phosphorylated form ADpSGEGDFLAEGGGVR was upregulated in GAC samples. Activity change prediction yielded 10 proteases including 6 Matrix Metalloproteinases (MMPs), Thrombin, Plasmin, and kallikreins 4 and 14. Among predicted proteases in our analysis, MMP-7 was presented as a more promising biomarker associated with useful assays of clinical practice for GAC diagnosis. CONCLUSION Our experimental results demonstrate that the serum levels of peptides were significantly differentiated in GAC physiopathology. The hypotheses built on protease regulation could be used for further investigations to measure proteases and their activity levels that have been poorly studied for GAC diagnosis.
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Affiliation(s)
- Talita Mendes de Oliveira
- Department of Medicine, Division of Gastroenterology, Oncology Group, Federal University of São Paulo, São Paulo, SP, Brazil.
| | | | | | - Meriellen Dias
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil
| | - Maria Anita Mendes
- Department of Chemical Engineering, University of São Paulo, São Paulo, SP, Brazil
| | - Paulo Kassab
- Digestive Surgical Oncology Division, Santa Casa of São Paulo Medical School, São Paulo, SP, Brazil
| | | | | | - Nora Manoukian Forones
- Department of Medicine, Division of Gastroenterology, Oncology Group, Federal University of São Paulo, São Paulo, SP, Brazil
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14
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Abstract
Functions of intrinsically disordered proteins do not require structure. Such structure-independent functionality has melted away the classic rigid "lock and key" representation of structure-function relationships in proteins, opening a new page in protein science, where molten keys operate on melted locks and where conformational flexibility and intrinsic disorder, structural plasticity and extreme malleability, multifunctionality and binding promiscuity represent a new-fangled reality. Analysis and understanding of this new reality require novel tools, and some of the techniques elaborated for the examination of intrinsically disordered protein functions are outlined in this review.
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Affiliation(s)
- Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33620, USA
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russian Federation
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15
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Yi S, Zhu L, Mabury SA. First Report on In Vivo Pharmacokinetics and Biotransformation of Chlorinated Polyfluoroalkyl Ether Sulfonates in Rainbow Trout. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:345-354. [PMID: 31774655 DOI: 10.1021/acs.est.9b05258] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
This study provides the first in vivo pharmacokinetic data for chlorinated perfluorooctanesulfonate (Cl-PFOS), 6:2 and 8:2 chlorinated polyfluoroalkyl ether sulfonates (Cl-PFESAs), upon a 30 day dietary exposure and 34 day depuration phase in rainbow trout (Oncorhynchus mykiss). Biological handling of these three novel molecules and legacy PFOS were investigated via cross-comparison. PFOS and Cl-PFOS displayed comparable bioaccumulative potencies and similar distribution tendencies in tissues (blood > liver > kidneys), despite the presence of a terminal chlorine atom in Cl-PFOS molecule. The Cl-PFESAs, especially 8:2 Cl-PFESA, were predominantly assimilated from the bloodstream by liver and kidneys and resisted elimination, leading to higher bioaccumulation factors in liver than in blood (0.576 and 0.254, respectively, for 8:2 Cl-PFESA) and longer half-lives in liver and kidneys than PFOS, suggesting these alternatives may pose greater risks in terms of the great accumulation potentials in fish tissues. The present study provides the first report of the in vivo transformation of 6:2 and 8:2 Cl-PFESAs and identifies 6:2 and 8:2 H-PFESAs as their respective sole metabolites. This provides the first line of evidence suggesting that the transformation susceptibility of Cl-PFESAs in organisms is distinct from their environmental persistence.
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Affiliation(s)
- Shujun Yi
- State Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
| | - Lingyan Zhu
- State Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai University, Tianjin 300350, P. R. China
| | - Scott A Mabury
- Department of Chemistry, University of Toronto, Toronto M5S 3H6, Canada
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16
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Zhang Y, Mao Y, Zhao W, Su T, Zhong Y, Fu L, Zhu J, Cheng J, Yang H. Glyco-CPLL: An Integrated Method for In-Depth and Comprehensive N-Glycoproteome Profiling of Human Plasma. J Proteome Res 2019; 19:655-666. [PMID: 31860302 DOI: 10.1021/acs.jproteome.9b00557] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Yong Zhang
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yonghong Mao
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
- Thoracic Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Wanjun Zhao
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Tao Su
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yi Zhong
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Linru Fu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jingqiang Zhu
- Department of Thyroid Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jingqiu Cheng
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Hao Yang
- Key Lab of Transplant Engineering and Immunology, MOH, West China-Washington Mitochondria and Metabolism Research Center, West China Hospital, Sichuan University, Chengdu 610041, China
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17
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Djulbegovic MB, Uversky VN. Expanding the understanding of the heterogeneous nature of melanoma with bioinformatics and disorder-based proteomics. Int J Biol Macromol 2019; 150:1281-1293. [PMID: 31743721 DOI: 10.1016/j.ijbiomac.2019.10.139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/19/2019] [Accepted: 10/15/2019] [Indexed: 01/07/2023]
Abstract
The past few decades show that incidences of melanoma are on the rise. The risk associated with this disease is an interplay between genetic and host factors and sun exposure. While scientific progress in the treatment of melanoma is remarkable, additional research is needed to improve patient outcomes and to better understand the heterogenous nature of this disease. Fortunately, as the clinical community enters the era of "big data" and personalized medicine, the rise of bioinformatics that stems from recent advances in high throughout profiling of biological information offers potential for innovative treatment options. This study aims to provide an example of the usefulness of bioinformatics and disorder-based proteomics to identify the molecular pathway in melanoma, garner information on selected proteins from this pathway and uncover their intrinsically disordered proteins regions (IDPRs) and investigate functionality implicated in these IDPRs. The present study provides a new look at the melanoma heterogeneity and suggests that, in addition to the well-established genetic heterogeneity of melanoma, there is another level of heterogeneity that lies within the conformational ensembles that stem from intrinsic disorder in melanoma-related proteins. The hope is that these insights will inspire future drug discovery campaigns.
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Affiliation(s)
- Mak B Djulbegovic
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia.
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18
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Fonin AV, Darling AL, Kuznetsova IM, Turoverov KK, Uversky VN. Multi-functionality of proteins involved in GPCR and G protein signaling: making sense of structure-function continuum with intrinsic disorder-based proteoforms. Cell Mol Life Sci 2019; 76:4461-4492. [PMID: 31428838 PMCID: PMC11105632 DOI: 10.1007/s00018-019-03276-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 08/05/2019] [Accepted: 08/12/2019] [Indexed: 12/21/2022]
Abstract
GPCR-G protein signaling system recognizes a multitude of extracellular ligands and triggers a variety of intracellular signaling cascades in response. In humans, this system includes more than 800 various GPCRs and a large set of heterotrimeric G proteins. Complexity of this system goes far beyond a multitude of pair-wise ligand-GPCR and GPCR-G protein interactions. In fact, one GPCR can recognize more than one extracellular signal and interact with more than one G protein. Furthermore, one ligand can activate more than one GPCR, and multiple GPCRs can couple to the same G protein. This defines an intricate multifunctionality of this important signaling system. Here, we show that the multifunctionality of GPCR-G protein system represents an illustrative example of the protein structure-function continuum, where structures of the involved proteins represent a complex mosaic of differently folded regions (foldons, non-foldons, unfoldons, semi-foldons, and inducible foldons). The functionality of resulting highly dynamic conformational ensembles is fine-tuned by various post-translational modifications and alternative splicing, and such ensembles can undergo dramatic changes at interaction with their specific partners. In other words, GPCRs and G proteins exist as sets of conformational/basic, inducible/modified, and functioning proteoforms characterized by a broad spectrum of structural features and possessing various functional potentials.
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Affiliation(s)
- Alexander V Fonin
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - April L Darling
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Irina M Kuznetsova
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
| | - Konstantin K Turoverov
- Laboratory of structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, St. Petersburg, 194064, Russian Federation
- Department of Biophysics, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya av. 29, St. Petersburg, 195251, Russian Federation
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Moscow, Russian Federation.
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19
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Elguoshy A, Hirao Y, Yamamoto K, Xu B, Kinoshita N, Mitsui T, Yamamoto T. Utilization of the Proteome Data Deposited in SRMAtlas for Validating the Existence of the Human Missing Proteins in GPM. J Proteome Res 2019; 18:4197-4205. [PMID: 31646870 DOI: 10.1021/acs.jproteome.9b00355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Human Proteome Project (HPP) has made great efforts to clarify the existing evidence of human proteins since 2012. However, according to the recent release of neXtProt (2019-1), approximately 10% of all human genes still have inadequate or no experimental evidence of their translation at the protein level. They were categorized as missing proteins (PE2-PE4). To further the goal of HPP, we developed a two-step bioinformatic strategy addressing the utilization of the SRMAtlas synthetic peptides corresponding to the missing proteins as an exclusive reference in order to explore their natural counterparts within GPM. In the first step, we searched the GPM for the non-nested SRMAtlas peptides corresponding to the missing proteins, taking under consideration only those detected via ≥2 non-nested unitypic/proteotypic peptides "Stranded peptides" with length ≥9 amino acids in the same proteomic study. As a result, 51 missing proteins were newly detected in 35 different proteomic studies. In the second step, we validated these newly detected missing proteins based on matching the spectra of their synthetic and natural peptides in SRMAtlas and GPM, respectively. The results showed that 23 of the missing proteins with ≥2 non-nested peptides were validated by careful spectral matching.
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Affiliation(s)
- Amr Elguoshy
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan.,Graduate School of Science and Technology , Niigata University , Niigata 950-2181 , Japan.,Biotechnology Department, Faculty of Agriculture , Al-Azhar University , Cairo 11651 , Egypt
| | - Yoshitoshi Hirao
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan
| | - Keiko Yamamoto
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan
| | - Bo Xu
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan
| | - Naohiko Kinoshita
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan.,Department of Health Informatics , Niigata University of Health and Welfare , Niigata 950-3102 , Japan
| | - Toshiaki Mitsui
- Graduate School of Science and Technology , Niigata University , Niigata 950-2181 , Japan
| | - Tadashi Yamamoto
- Biofluid and Biomarker Center, Graduate School of Medical and Dental Sciences , Niigata University , Niigata 950-2181 , Japan.,Department of Clinical Laboratory , Shinrakuen Hospital , Niigata 950-2087 , Japan
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20
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The Structural and Functional Diversity of Intrinsically Disordered Regions in Transmembrane Proteins. J Membr Biol 2019; 252:273-292. [DOI: 10.1007/s00232-019-00069-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 05/17/2019] [Indexed: 10/26/2022]
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21
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Presnell KV, Alper HS. Systems Metabolic Engineering Meets Machine Learning: A New Era for Data-Driven Metabolic Engineering. Biotechnol J 2019; 14:e1800416. [PMID: 30927499 DOI: 10.1002/biot.201800416] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/20/2019] [Indexed: 12/30/2022]
Abstract
The recent increase in high-throughput capacity of 'omics datasets combined with advances and interest in machine learning (ML) have created great opportunities for systems metabolic engineering. In this regard, data-driven modeling methods have become increasingly valuable to metabolic strain design. In this review, the nature of 'omics is discussed and a broad introduction to the ML algorithms combining these datasets into predictive models of metabolism and metabolic rewiring is provided. Next, this review highlights recent work in the literature that utilizes such data-driven methods to inform various metabolic engineering efforts for different classes of application including product maximization, understanding and profiling phenotypes, de novo metabolic pathway design, and creation of robust system-scale models for biotechnology. Overall, this review aims to highlight the potential and promise of using ML algorithms with metabolic engineering and systems biology related datasets.
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Affiliation(s)
- Kristin V Presnell
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX, 78712, USA.,Institute for Cellular and Molecular Biology, The University of Texas at Austin, 100 E 24 St., Austin, TX, 78712, USA
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22
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Uversky VN. Protein intrinsic disorder and structure-function continuum. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:1-17. [DOI: 10.1016/bs.pmbts.2019.05.003] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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23
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Kulkarni P, Uversky VN. Intrinsically Disordered Proteins: The Dark Horse of the Dark Proteome. Proteomics 2018; 18:e1800061. [DOI: 10.1002/pmic.201800061] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 09/07/2018] [Indexed: 12/27/2022]
Affiliation(s)
- Prakash Kulkarni
- Department of Medical Oncology and Therapeutics Research; City of Hope National Medical Center; Duarte CA 91010 USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine; Morsani College of Medicine; University of South Florida; Tampa FL 33612 USA
- Laboratory of New methods in Biology; Institute for Biological Instrumentation; Russian Academy of Sciences; Pushchino Moscow Region 142290 Russia
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24
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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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25
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Jedinak A, Loughlin KR, Moses MA. Approaches to the discovery of non-invasive urinary biomarkers of prostate cancer. Oncotarget 2018; 9:32534-32550. [PMID: 30197761 PMCID: PMC6126692 DOI: 10.18632/oncotarget.25946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/23/2018] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) continues to be one of the most common cancers in men worldwide. Prostate specific antigen (PSA) measured in blood has been used for decades as an aid for physicians to detect the presence of prostate cancer. However, the PSA test has limited sensitivity and specificity, leading to unnecessary biopsies, overdiagnosis and overtreatment of patients. For these reasons, there is an urgent need for more accurate PCa biomarkers that can detect PCa with high sensitivity and specificity. Urine is a unique source of potential protein biomarkers that can be measured in a non-invasive way. This review comprehensively summarizes state of the art approaches used in the discovery and validation of urinary biomarkers for PCa. Numerous strategies are currently being used in the discovery of urinary biomarkers for prostate cancer including gel-based separation techniques, mass spectrometry, activity-based proteomic assays and software approaches. Antibody-based approaches remain preferred method for validation of candidate biomarkers with rapidly advancing multiplex immunoassays and MS-based targeted approaches. In the last decade, there has been a dramatic acceleration in the development of new techniques and approaches in the discovery of protein biomarkers for prostate cancer including computational, statistical and data mining methods. Many urinary-based protein biomarkers have been identified and have shown significant promise in initial studies. Examples of these potential biomarkers and the methods utilized in their discovery are also discussed in this review.
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Affiliation(s)
- Andrej Jedinak
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Kevin R Loughlin
- Department of Surgery, Harvard Medical School, Boston, MA, USA.,Department of Urology, Brigham and Women's Hospital, Boston, MA, USA
| | - Marsha A Moses
- Vascular Biology Program and Department of Surgery, Boston Children's Hospital, Boston, MA, USA.,Department of Surgery, Harvard Medical School, Boston, MA, USA
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26
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Zhao X, Zhang W, Liu T, Dong H, Huang J, Sun C, Wang G, Qian X, Qin W. A fast sample processing strategy for large-scale profiling of human urine phosphoproteome by mass spectrometry. Talanta 2018; 185:166-173. [DOI: 10.1016/j.talanta.2018.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 03/02/2018] [Accepted: 03/14/2018] [Indexed: 12/23/2022]
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27
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Darling AL, Uversky VN. Intrinsic Disorder and Posttranslational Modifications: The Darker Side of the Biological Dark Matter. Front Genet 2018; 9:158. [PMID: 29780404 PMCID: PMC5945825 DOI: 10.3389/fgene.2018.00158] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 04/17/2018] [Indexed: 01/05/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are functional proteins and domains that devoid stable secondary and/or tertiary structure. IDPs/IDPRs are abundantly present in various proteomes, where they are involved in regulation, signaling, and control, thereby serving as crucial regulators of various cellular processes. Various mechanisms are utilized to tightly regulate and modulate biological functions, structural properties, cellular levels, and localization of these important controllers. Among these regulatory mechanisms are precisely controlled degradation and different posttranslational modifications (PTMs). Many normal cellular processes are associated with the presence of the right amounts of precisely activated IDPs at right places and in right time. However, wrecked regulation of IDPs/IDPRs might be associated with various human maladies, ranging from cancer and neurodegeneration to cardiovascular disease and diabetes. Pathogenic transformations of IDPs/IDPRs are often triggered by altered PTMs. This review considers some of the aspects of IDPs/IDPRs and their normal and aberrant regulation by PTMs.
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Affiliation(s)
- April L Darling
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
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28
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Magalhães P, Pontillo C, Pejchinovski M, Siwy J, Krochmal M, Makridakis M, Carrick E, Klein J, Mullen W, Jankowski J, Vlahou A, Mischak H, Schanstra JP, Zürbig P, Pape L. Comparison of Urine and Plasma Peptidome Indicates Selectivity in Renal Peptide Handling. Proteomics Clin Appl 2018; 12:e1700163. [DOI: 10.1002/prca.201700163] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 02/21/2018] [Indexed: 01/02/2023]
Affiliation(s)
- Pedro Magalhães
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
| | - Claudia Pontillo
- Department of Toxicology and Pharmacology; Hannover Medical School; 30625 Hannover Germany
| | | | - Justyna Siwy
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | | | - Manousos Makridakis
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Emma Carrick
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Julie Klein
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - William Mullen
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joachim Jankowski
- RWTH Aachen University Hospital; 52074 Aachen Germany
- Department of Pathology, Cardiovascular Research Institute Maastricht; University of Maastricht; 6211 Maastricht The Netherlands
| | - Antonia Vlahou
- Biotechnology Division, Biomedical Research Foundation; Academy of Athens; 11527 Athens Greece
| | - Harald Mischak
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
- Institute of Cardiovascular and Medical Sciences, University of Glasgow; G12 8QQ Glasgow UK
| | - Joost P. Schanstra
- Institute of Cardiovascular and Metabolic Disease; Institut National de la Santé et de la Recherche Médicale,; 31432 Toulouse France
- Université Toulouse III Paul-Sabatier; 31330 Toulouse France
| | - Petra Zürbig
- Mosaiques Diagnostics GmbH; 30659 Hannover Germany
| | - Lars Pape
- Department of Pediatric Nephrology; Hannover Medical School; 30625 Hannover Germany
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29
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Chinello C, Stella M, Piga I, Smith AJ, Bovo G, Varallo M, Ivanova M, Denti V, Grasso M, Grasso A, Del Puppo M, Zaravinos A, Magni F. Proteomics of liquid biopsies: Depicting RCC infiltration into the renal vein by MS analysis of urine and plasma. J Proteomics 2018; 191:29-37. [PMID: 29689304 DOI: 10.1016/j.jprot.2018.04.029] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 04/03/2018] [Accepted: 04/14/2018] [Indexed: 01/12/2023]
Abstract
Liquid biopsies, as blood and urine, could offer an invaluable, easily accessible source of biomarkers, and evidences for elucidating the pathological processes. Only few studies integrated the proteomes driven by more than one biofluid. Furthermore, it is not clear which biofluid better mirrors the alterations triggered by disease. Venous infiltrating RCC(Renal Cell Carcinoma) could represent an advantageous model for exploring this aspect. Herein, we investigate how blood and urine "proteomically" reflect the changes occurring during RCC infiltration into renal vein(RV) by label-free nLC-ESI-MS/MS. We found 574 and 58 differentially expressed proteins(DEPs) in response to vascular involvement. To the augment of vascular involvement, the abundance of only three proteins in urine(UROM,RALA,CNDP1) and two in plasma(APOA1,K2C1) diminished while increased for twenty-six urinary proteins. 80 proteins were found both in urine and plasma, among which twenty-eight were DEPs. A huge overlap between the two biofluids was highlighted, as expected, being urine the filtrate of blood. However, this consistency decreases when RV-occlusion occurs suggesting alternative protein releases, and a loss of kidney architecture. Moreover, several proteomic and functional signatures were biofluid-specific. In conclusion, the complementarity between the specimens allowed to achieve a deeper level of molecular complexity of the RCC venous infiltration. SIGNIFICANCE: Although plasma and urine are strongly interconnected, only few proteomic studies investigated the complementarity of these fluids as bio-sources of information. Moreover, none of them was focused to their analysis and comparison in the context of vascular infiltration of renal cancer. Herein, new insights were gained regarding the impact into urinary and plasma proteome of the changes triggered by the ccRCC invasion into vascular system and renal vein. Furthermore, the integration of the information driven by the two liquid biopsies permits to unravel biological processes otherwise lost.
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Affiliation(s)
- Clizia Chinello
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy.
| | - Martina Stella
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | - Isabella Piga
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | - Andrew James Smith
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | - Giorgio Bovo
- Pathology Unit, Vimercate Hospital, Vimercate, Italy
| | | | - Mariia Ivanova
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | - Vanna Denti
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | | | | | - Marina Del Puppo
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
| | - Apostolos Zaravinos
- Department of Life Sciences, School of Sciences, European University Cyprus, 1516 Nicosia, Cyprus
| | - Fulvio Magni
- Department of Medicine and Surgery, University of Milano-Bicocca, Clinical Proteomics and Metabolomics Unit, Vedano al Lambro, Italy
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Abstract
PURPOSE OF REVIEW Despite modern immunosuppression, renal allograft rejection remains a major contributor to graft loss. Novel biomarkers may help improve posttransplant outcomes through the early detection and treatment of rejection. Our objective is to provide an overview of proteomics, review recent discovery-based rejection studies, and explore innovative approaches in biomarker development. RECENT FINDINGS Urine MMP7 was identified as a biomarker of subclinical and clinical rejection using two-dimensional liquid chromatography tandem-mass spectrometry (LC-MS/MS) and improved the overall diagnostic discrimination of urine CXCL10 : Cr alone for renal allograft inflammation. A novel peptide signature to classify stable allografts from acute rejection, chronic allograft injury, and polyoma virus (BKV) nephropathy was identified using isobaric tag for relative and absolute quantitation (TRAQ) and label-free MS, with independent validation by selected reaction monitoring mass spectrometry (SRM-MS). Finally, an in-depth exploration of peripheral blood mononuclear cells identified differential proteoform expression in healthy transplants versus rejection. SUMMARY There is still much in the human proteome that remains to be explored, and further integration of renal, urinary, and exosomal data may offer deeper insight into the pathophysiology of rejection. Functional proteomics may be more biologically relevant than protein/peptide quantity alone, such as assessment of proteoforms or activity-based protein profiling. Discovery-based studies have identified potential biomarker candidates, but external validation studies are required.
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31
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Powell JE, Fung JN, Shakhbazov K, Sapkota Y, Cloonan N, Hemani G, Hillman KM, Kaufmann S, Luong HT, Bowdler L, Painter JN, Holdsworth-Carson SJ, Visscher PM, Dinger ME, Healey M, Nyholt DR, French JD, Edwards SL, Rogers PAW, Montgomery GW. Endometriosis risk alleles at 1p36.12 act through inverse regulation of CDC42 and LINC00339. Hum Mol Genet 2018; 25:5046-5058. [PMID: 28171565 DOI: 10.1093/hmg/ddw320] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 08/28/2016] [Accepted: 09/12/2016] [Indexed: 01/16/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified markers within the WNT4 region on chromosome 1p36.12 showing consistent and strong association with increasing endometriosis risk. Fine mapping using sequence and imputed genotype data has revealed strong candidates for the causal SNPs within these critical regions; however, the molecular pathogenesis of these SNPs is currently unknown. We used gene expression data collected from whole blood from 862 individuals and endometrial tissue from 136 individuals from independent populations of European descent to examine the mechanism underlying endometriosis susceptibility. Association mapping results from 7,090 individuals (2,594 cases and 4,496 controls) supported rs3820282 as the SNP with the strongest association for endometriosis risk (P = 1.84 × 10−5, OR = 1.244 (1.126-1.375)). SNP rs3820282 is a significant eQTL in whole blood decreasing expression of LINC00339 (also known as HSPC157) and increasing expression of CDC42 (P = 2.0 ×10−54 and 4.5x10−4 respectively). The largest effects were for two LINC00339 probes (P = 2.0 ×10−54; 1.0 × 10−34). The eQTL for LINC00339 was also observed in endometrial tissue (P = 2.4 ×10−8) with the same direction of effect for both whole blood and endometrial tissue. There was no evidence for eQTL effects for WNT4. Chromatin conformation capture provides evidence for risk SNPs interacting with the promoters of both LINC00339 and CDC4 and luciferase reporter assays suggest the risk SNP rs12038474 is located in a transcriptional silencer for CDC42 and the risk allele increases expression of CDC42. However, no effect of rs3820282 was observed in the LINC00339 expression in Ishikawa cells. Taken together, our results suggest that SNPs increasing endometriosis risk in this region act through CDC42, but further functional studies are required to rule out inverse regulation of both LINC00339 and CDC42.
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Affiliation(s)
- Joseph E Powell
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia.,The Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Jenny N Fung
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Konstantin Shakhbazov
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia
| | - Yadav Sapkota
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicole Cloonan
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Gibran Hemani
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia.,MRC Integrative Epidemiology Unit, University of Bristol, Oakfield House, Bristol, UK
| | - Kristine M Hillman
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Susanne Kaufmann
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Hien T Luong
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Lisa Bowdler
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jodie N Painter
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Sarah J Holdsworth-Carson
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Peter M Visscher
- Centre for Neurogenetics and Statistical Genomics, Queensland Brain Institute, University of Queensland, St Lucia, Brisbane, Australia
| | - Marcel E Dinger
- Garvan Medical Research Institute, Sydney, Australia,St Vincent’s Clinical School, University of New South Wales, Sydney, NSW 2052, Australia and
| | - Martin Healey
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Dale R Nyholt
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, Australia
| | - Juliet D French
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Stacey L Edwards
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Peter A W Rogers
- Gynaecology Research Centre, University of Melbourne, Department of Obstetrics and Gynaecology, Royal Women's Hospital, Parkville VIC, Australia
| | - Grant W Montgomery
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Australia
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Jayapalan JJ, Lee CS, Lee CC, Ng KL, Junit SM, Hashim OH. iTRAQ analysis of urinary proteins: Potential use of gelsolin and osteopontin to distinguish benign thyroid goiter from papillary thyroid carcinoma. Clin Biochem 2018; 53:127-131. [PMID: 29355489 DOI: 10.1016/j.clinbiochem.2018.01.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 01/12/2018] [Indexed: 01/09/2023]
Abstract
BACKGROUND Benign thyroid goiter (BTG) and papillary thyroid carcinoma (PTC) are often interchangeably misdiagnosed. METHODS Pooled urine samples of patients with BTG (n=10), patients with PTC (n=9) and healthy controls (n=10) were subjected to iTRAQ analysis and immunoblotting. RESULTS The ITRAQ analysis of the urine samples detected 646 proteins, 18 of which showed significant altered levels (p<0.01; fold-change>1.5) between patients and controls. Whilst four urinary proteins were commonly altered in both BTG and PTC patients, 14 were unique to either BTG or PTC. Amongst these, four proteins were further chosen for validation using immunoblotting, and the enhanced levels of osteopontin in BTG patients and increased levels of a truncated gelsolin fragment in PTC patients, relative to controls, appeared to corroborate the findings of the iTRAQ analysis. CONCLUSION The data of the present study is suggestive of the potential application of urinary osteopontin and gelsolin to discriminate patients with BTG from those with PTC non-invasively. However, this needs to be further validated in studies of individual urine samples.
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Affiliation(s)
- Jaime Jacqueline Jayapalan
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Cheng-Siang Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Ching Chin Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Khoon Leong Ng
- Department of Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Sarni Mat Junit
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Onn Haji Hashim
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia; Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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Christensson A, Ash JA, DeLisle RK, Gaspar FW, Ostroff R, Grubb A, Lindström V, Bruun L, Williams SA. The Impact of the Glomerular Filtration Rate on the Human Plasma Proteome. Proteomics Clin Appl 2018; 12:e1700067. [DOI: 10.1002/prca.201700067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 10/08/2017] [Indexed: 01/02/2023]
Affiliation(s)
| | | | | | | | | | - Anders Grubb
- Department of Clinical Chemistry; Skåne University Hospital; Lund Sweden
| | - Veronica Lindström
- Department of Clinical Chemistry; Skåne University Hospital; Lund Sweden
| | - Laila Bruun
- Department of Nephrology; Skåne University Hospital; Malmö Sweden
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34
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Uversky VN. The roles of intrinsic disorder-based liquid-liquid phase transitions in the "Dr. Jekyll-Mr. Hyde" behavior of proteins involved in amyotrophic lateral sclerosis and frontotemporal lobar degeneration. Autophagy 2017; 13:2115-2162. [PMID: 28980860 DOI: 10.1080/15548627.2017.1384889] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Pathological developments leading to amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are associated with misbehavior of several key proteins, such as SOD1 (superoxide dismutase 1), TARDBP/TDP-43, FUS, C9orf72, and dipeptide repeat proteins generated as a result of the translation of the intronic hexanucleotide expansions in the C9orf72 gene, PFN1 (profilin 1), GLE1 (GLE1, RNA export mediator), PURA (purine rich element binding protein A), FLCN (folliculin), RBM45 (RNA binding motif protein 45), SS18L1/CREST, HNRNPA1 (heterogeneous nuclear ribonucleoprotein A1), HNRNPA2B1 (heterogeneous nuclear ribonucleoprotein A2/B1), ATXN2 (ataxin 2), MAPT (microtubule associated protein tau), and TIA1 (TIA1 cytotoxic granule associated RNA binding protein). Although these proteins are structurally and functionally different and have rather different pathological functions, they all possess some levels of intrinsic disorder and are either directly engaged in or are at least related to the physiological liquid-liquid phase transitions (LLPTs) leading to the formation of various proteinaceous membrane-less organelles (PMLOs), both normal and pathological. This review describes the normal and pathological functions of these ALS- and FTLD-related proteins, describes their major structural properties, glances at their intrinsic disorder status, and analyzes the involvement of these proteins in the formation of normal and pathological PMLOs, with the ultimate goal of better understanding the roles of LLPTs and intrinsic disorder in the "Dr. Jekyll-Mr. Hyde" behavior of those proteins.
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Affiliation(s)
- Vladimir N Uversky
- a Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute , Morsani College of Medicine , University of South Florida , Tampa , FL , USA.,b Institute for Biological Instrumentation of the Russian Academy of Sciences , Pushchino, Moscow region , Russia
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35
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Ho ME, Quek SI, True LD, Seiler R, Fleischmann A, Bagryanova L, Kim SR, Chia D, Goodglick L, Shimizu Y, Rosser CJ, Gao Y, Liu AY. Bladder cancer cells secrete while normal bladder cells express but do not secrete AGR2. Oncotarget 2017; 7:15747-56. [PMID: 26894971 PMCID: PMC4941274 DOI: 10.18632/oncotarget.7400] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 02/05/2016] [Indexed: 11/30/2022] Open
Abstract
Anterior gradient 2 (AGR2) is a cancer-associated secreted protein found predominantly in adenocarcinomas. Given its ubiquity in solid tumors, cancer-secreted AGR2 could be a useful biomarker in urine or blood for early detection. However, normal organs express and might also secrete AGR2, which would impact its utility as a cancer biomarker. Uniform AGR2 expression is found in the normal bladder urothelium. Little AGR2 is secreted by the urothelial cells as no measurable amounts could be detected in urine. The urinary proteomes of healthy people contain no listing for AGR2. Likewise, the blood proteomes of healthy people also contain no significant peptide counts for AGR2 suggesting little urothelial secretion into capillaries of the lamina propria. Expression of AGR2 is lost in urothelial carcinoma, with only 25% of primary tumors observed to retain AGR2 expression in a cohort of lymph node-positive cases. AGR2 is secreted by the urothelial carcinoma cells as urinary AGR2 was measured in the voided urine of 25% of the cases analyzed in a cohort of cancer vs. non-cancer patients. The fraction of AGR2-positive urine samples was consistent with the fraction of urothelial carcinoma that stained positive for AGR2. Since cancer cells secrete AGR2 while normal cells do not, its measurement in body fluids could be used to indicate tumor presence. Furthermore, AGR2 has also been found on the cell surface of cancer cells. Taken together, secretion and cell surface localization of AGR2 are characteristic of cancer, while expression of AGR2 by itself is not.
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Affiliation(s)
- Melissa E Ho
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.,Present address: University of California San Francisco Medical Center, San Francisco, CA, USA
| | - Sue-Ing Quek
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.,Present address: Singapore Polytechnic, Center for Biomedical & Life Sciences, Singapore
| | - Lawrence D True
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Roland Seiler
- Department of Urology, University Hospital of Bern, Bern, Switzerland
| | - Achim Fleischmann
- Institute of Pathology, University Hospital of Bern, Bern, Switzerland
| | - Lora Bagryanova
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sara R Kim
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - David Chia
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lee Goodglick
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | | | | | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Alvin Y Liu
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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36
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Schwenk JM, Omenn GS, Sun Z, Campbell DS, Baker MS, Overall CM, Aebersold R, Moritz RL, Deutsch EW. The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays. J Proteome Res 2017; 16:4299-4310. [PMID: 28938075 PMCID: PMC5864247 DOI: 10.1021/acs.jproteome.7b00467] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human blood plasma provides a highly accessible window to the proteome of any individual in health and disease. Since its inception in 2002, the Human Proteome Organization's Human Plasma Proteome Project (HPPP) has been promoting advances in the study and understanding of the full protein complement of human plasma and on determining the abundance and modifications of its components. In 2017, we review the history of the HPPP and the advances of human plasma proteomics in general, including several recent achievements. We then present the latest 2017-04 build of Human Plasma PeptideAtlas, which yields ∼43 million peptide-spectrum matches and 122,730 distinct peptide sequences from 178 individual experiments at a 1% protein-level FDR globally across all experiments. Applying the latest Human Proteome Project Data Interpretation Guidelines, we catalog 3509 proteins that have at least two non-nested uniquely mapping peptides of nine amino acids or more and >1300 additional proteins with ambiguous evidence. We apply the same two-peptide guideline to historical PeptideAtlas builds going back to 2006 and examine the progress made in the past ten years in plasma proteome coverage. We also compare the distribution of proteins in historical PeptideAtlas builds in various RNA abundance and cellular localization categories. We then discuss advances in plasma proteomics based on targeted mass spectrometry as well as affinity assays, which during early 2017 target ∼2000 proteins. Finally, we describe considerations about sample handling and study design, concluding with an outlook for future advances in deciphering the human plasma proteome.
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Affiliation(s)
- Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH Royal Institute of Technology, Tomtebodavägen 23, SE-171 65 Solna, Sweden
| | - Gilbert S. Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, and Human Genetics and School of Public Health, University of Michigan, Ann Arbor, MI, 48109-2218, USA
- Institute for Systems Biology, Seattle, WA, USA
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Mark S. Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Science, Macquarie University, NSW, 2109. Australia
| | - Christopher M. Overall
- Centre for Blood Research, Departments of Oral Biological & Medical Sciences, and Biochemistry & Molecular Biology, Faculty of Dentistry, University of British Columbia, Vancouver, Canada
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
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37
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Shi T, Quek SI, Gao Y, Nicora CD, Nie S, Fillmore TL, Liu T, Rodland KD, Smith RD, Leach RJ, Thompson IM, Vitello EA, Ellis WJ, Liu AY, Qian WJ. Multiplexed targeted mass spectrometry assays for prostate cancer-associated urinary proteins. Oncotarget 2017; 8:101887-101898. [PMID: 29254211 PMCID: PMC5731921 DOI: 10.18632/oncotarget.21710] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/04/2017] [Indexed: 02/07/2023] Open
Abstract
Biomarkers for effective early diagnosis and prognosis of prostate cancer are still lacking. Multiplexed assays for cancer-associated proteins could be useful for identifying biomarkers for cancer detection and stratification. Herein, we report the development of sensitive targeted mass spectrometry assays for simultaneous quantification of 10 prostate cancer-associated proteins in urine. The diagnostic utility of these markers was evaluated with an initial cohort of 20 clinical urine samples. Individual marker concentration was normalized against the measured urinary prostate-specific antigen level as a reference of prostate-specific secretion. The areas under the receiver-operating characteristic curves for the 10 proteins ranged from 0.75 for CXL14 to 0.87 for CEAM5. Furthermore, MMP9 level was found to be significantly higher in patients with high Gleason scores, suggesting a potential of MMP9 as a marker for risk level assessment. Taken together, our work illustrated the feasibility of accurate multiplexed measurements of low-abundance cancer-associated proteins in urine and provided a viable path forward for preclinical verification of candidate biomarkers for prostate cancer.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sue-Ing Quek
- Department of Urology, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.,Present address: Singapore Polytechnic, Center for Biomedical and Life Sciences T11A-412 (level 4), Singapore
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Thomas L Fillmore
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Robin J Leach
- Department of Urology and the Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Ian M Thompson
- Department of Urology and the Cancer Therapy and Research Center, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Elizabeth A Vitello
- Department of Urology, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - William J Ellis
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Alvin Y Liu
- Department of Urology, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
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38
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Harpole M, Davis J, Espina V. Current state of the art for enhancing urine biomarker discovery. Expert Rev Proteomics 2017; 13:609-26. [PMID: 27232439 DOI: 10.1080/14789450.2016.1190651] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Urine is a highly desirable biospecimen for biomarker analysis because it can be collected recurrently by non-invasive techniques, in relatively large volumes. Urine contains cellular elements, biochemicals, and proteins derived from glomerular filtration of plasma, renal tubule excretion, and urogenital tract secretions that reflect, at a given time point, an individual's metabolic and pathophysiologic state. AREAS COVERED High-resolution mass spectrometry, coupled with state of the art fractionation systems are revealing the plethora of diagnostic/prognostic proteomic information existing within urinary exosomes, glycoproteins, and proteins. Affinity capture pre-processing techniques such as combinatorial peptide ligand libraries and biomarker harvesting hydrogel nanoparticles are enabling measurement/identification of previously undetectable urinary proteins. Expert commentary: Future challenges in the urinary proteomics field include a) defining either single or multiple, universally applicable data normalization methods for comparing results within and between individual patients/data sets, and b) defining expected urinary protein levels in healthy individuals.
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Affiliation(s)
- Michael Harpole
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin Davis
- b Department of Chemistry/Biochemistry , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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39
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Wang Y, Zheng C, Wang X, Zuo K, Liu Z. Proteomic profile-based screening of potential protein biomarkers in the urine of patients with nephrotic syndrome. Mol Med Rep 2017; 16:6276-6284. [DOI: 10.3892/mmr.2017.7329] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 05/23/2017] [Indexed: 11/06/2022] Open
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40
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Keshishian H, Burgess MW, Specht H, Wallace L, Clauser KR, Gillette MA, Carr SA. Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry. Nat Protoc 2017; 12:1683-1701. [PMID: 28749931 PMCID: PMC6057147 DOI: 10.1038/nprot.2017.054] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Proteomic characterization of blood plasma is of central importance to clinical proteomics and particularly to biomarker discovery studies. The vast dynamic range and high complexity of the plasma proteome have, however, proven to be serious challenges and have often led to unacceptable tradeoffs between depth of coverage and sample throughput. We present an optimized sample-processing pipeline for analysis of the human plasma proteome that provides greatly increased depth of detection, improved quantitative precision and much higher sample analysis throughput as compared with prior methods. The process includes abundant protein depletion, isobaric labeling at the peptide level for multiplexed relative quantification and ultra-high-performance liquid chromatography coupled to accurate-mass, high-resolution tandem mass spectrometry analysis of peptides fractionated off-line by basic pH reversed-phase (bRP) chromatography. The overall reproducibility of the process, including immunoaffinity depletion, is high, with a process replicate coefficient of variation (CV) of <12%. Using isobaric tags for relative and absolute quantitation (iTRAQ) 4-plex, >4,500 proteins are detected and quantified per patient sample on average, with two or more peptides per protein and starting from as little as 200 μl of plasma. The approach can be multiplexed up to 10-plex using tandem mass tags (TMT) reagents, further increasing throughput, albeit with some decrease in the number of proteins quantified. In addition, we provide a rapid protocol for analysis of nonfractionated depleted plasma samples analyzed in 10-plex. This provides ∼600 quantified proteins for each of the ten samples in ∼5 h of instrument time.
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Affiliation(s)
| | | | - Harrison Specht
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Luke Wallace
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Karl R Clauser
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael A Gillette
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Massachusetts General Hospital, Boston, USA
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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41
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Prince JT, Smith R. Probabilistic Generation of Mass Spectrometry Molecular Abundance Variance for Case and Control Replicates. J Proteome Res 2017; 16:2429-2434. [DOI: 10.1021/acs.jproteome.7b00037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Rob Smith
- Department
of Computer Science, University of Montana, Missoula, Montana 59812, United States
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42
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A comprehensive analysis and annotation of human normal urinary proteome. Sci Rep 2017; 7:3024. [PMID: 28596590 PMCID: PMC5465101 DOI: 10.1038/s41598-017-03226-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 04/25/2017] [Indexed: 12/14/2022] Open
Abstract
Biomarkers are measurable changes associated with the disease. Urine can reflect the changes of the body while blood is under control of the homeostatic mechanisms; thus, urine is considered an important source for early and sensitive disease biomarker discovery. A comprehensive profile of the urinary proteome will provide a basic understanding of urinary proteins. In this paper, we present an in-depth analysis of the urinary proteome based on different separation strategies, including direct one dimensional liquid chromatography–tandem mass spectrometry (LC/MS/MS), two dimensional LC/MS/MS, and gel-eluted liquid fraction entrapment electrophoresis/liquid-phase isoelectric focusing followed by two dimensional LC/MS/MS. A total of 6085 proteins were identified in healthy urine, of which 2001 were not reported in previous studies and the concentrations of 2571 proteins were estimated (spanning a magnitude of 106) with an intensity-based absolute quantification algorithm. The urinary proteins were annotated by their tissue distribution. Detailed information can be accessed at the “Human Urine Proteome Database” (www.urimarker.com/urine).
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Alikhani M, Mirzaei M, Sabbaghian M, Parsamatin P, Karamzadeh R, Adib S, Sodeifi N, Gilani MAS, Zabet-Moghaddam M, Parker L, Wu Y, Gupta V, Haynes PA, Gourabi H, Baharvand H, Salekdeh GH. Quantitative proteomic analysis of human testis reveals system-wide molecular and cellular pathways associated with non-obstructive azoospermia. J Proteomics 2017; 162:141-154. [DOI: 10.1016/j.jprot.2017.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Revised: 01/22/2017] [Accepted: 02/13/2017] [Indexed: 12/17/2022]
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Shen B, Zhang W, Shi Z, Tian F, Deng Y, Sun C, Wang G, Qin W, Qian X. A novel strategy for global mapping of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry identification. Talanta 2017; 169:195-202. [PMID: 28411811 DOI: 10.1016/j.talanta.2017.03.049] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 01/07/2023]
Abstract
O-GlcNAcylation is a kind of dynamic O-linked glycosylation of nucleocytoplasmic and mitochondrial proteins. It serves as a major nutrient sensor to regulate numerous biological processes including transcriptional regulation, cell metabolism, cellular signaling, and protein degradation. Dysregulation of cellular O-GlcNAcylated levels contributes to the etiologies of many diseases such as diabetes, neurodegenerative disease and cancer. However, deeper insight into the biological mechanism of O-GlcNAcylation is hampered by its extremely low stoichiometry and the lack of efficient enrichment approaches for large-scale identification by mass spectrometry. Herein, we developed a novel strategy for the global identification of O-GlcNAc proteins and peptides using selective enzymatic deglycosylation, HILIC enrichment and mass spectrometry analysis. Standard O-GlcNAc peptides can be efficiently enriched even in the presence of 500-fold more abundant non-O-GlcNAc peptides and identified by mass spectrometry with a low nanogram detection sensitivity. This strategy successfully achieved the first large-scale enrichment and characterization of O-GlcNAc proteins and peptides in human urine. A total of 474 O-GlcNAc peptides corresponding to 457 O-GlcNAc proteins were identified by mass spectrometry analysis, which is at least three times more than that obtained by commonly used enrichment methods. A large number of unreported O-GlcNAc proteins related to cell cycle, biological regulation, metabolic and developmental process were found in our data. The above results demonstrated that this novel strategy is highly efficient in the global enrichment and identification of O-GlcNAc peptides. These data provide new insights into the biological function of O-GlcNAcylation in human urine, which is correlated with the physiological states and pathological changes of human body and therefore indicate the potential of this strategy for biomarker discovery from human urine.
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Affiliation(s)
- Bingquan Shen
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China; National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China
| | - Zhaomei Shi
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China
| | - Fang Tian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China
| | - Yulin Deng
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China
| | | | | | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China.
| | - Xiaohong Qian
- School of Life Science, Beijing Institute of Technology, Beijing 100081, PR China; National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, BPRC-Tianjin Baodi Hospital Joint Center, Beijing 102206, PR China.
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45
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McCord J, Sun Z, Deutsch EW, Moritz RL, Muddiman DC. The PeptideAtlas of the Domestic Laying Hen. J Proteome Res 2017; 16:1352-1363. [PMID: 28166638 DOI: 10.1021/acs.jproteome.6b00952] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proteomics-based biological research is greatly expanded by high-quality mass spectrometry studies, which are themselves enabled by access to quality mass spectrometry resources, such as high-quality curated proteome data repositories. We present a PeptideAtlas for the domestic chicken, containing an extensive and robust collection of chicken tissue and plasma samples with substantial value for the chicken proteomics community for protein validation and design of downstream targeted proteome quantitation. The chicken PeptideAtlas contains 6646 canonical proteins at a protein FDR of 1.3%, derived from ∼100 000 peptides at a peptide level FDR of 0.1%. The rich collection of readily accessible data is easily mined for the purposes of data validation and experimental planning, particularly in the realm of developing proteome quantitation workflows. Herein we demonstrate the use of the atlas to mine information on common chicken acute-phase proteins and biomarkers for cancer detection research, as well as their localization and polymorphisms. This wealth of information will support future proteome-based research using this highly important agricultural organism in pursuit of both chicken and human health outcomes.
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Affiliation(s)
- James McCord
- W.M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
| | - Zhi Sun
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - Eric W Deutsch
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - Robert L Moritz
- Institute for Systems Biology , Seattle, Washington 98109, United States
| | - David C Muddiman
- W.M. Keck FTMS Laboratory for Human Health Research, Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695, United States
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Russo P, Hood BL, Bateman NW, Conrads TP. Quantitative Mass Spectrometry by Isotope Dilution and Multiple Reaction Monitoring (MRM). Methods Mol Biol 2017; 1606:313-332. [PMID: 28502009 DOI: 10.1007/978-1-4939-6990-6_20] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Selected reaction monitoring (SRM) is used in molecular profiling to detect and quantify specific known proteins in complex mixtures. Using isotope dilution (Barnidge et al., Anal Chem 75(3):445-451, 2003) methodologies, peptides can be quantified without the need for an antibody-based method. Selected reaction monitoring assays employ electrospray ionization mass spectrometry (ESI-MS) followed by two stages of mass selection: a first stage where the mass of the peptide ion is selected and, after fragmentation by collision-induced dissociation (CID), a second stage (tandem MS) where either a single (e.g., SRM) or multiple (multiple reaction monitoring, MRM) specific peptide fragment ions are transmitted for detection. The MRM experiment is accomplished by specifying the parent masses of the selected endogenous and isotope-labeled peptides for MS/MS fragmentation and then monitoring fragment ions of interest, using their intensities/abundances and relative ratios to quantify the parent protein of interest. In this example protocol, we will utilize isotope dilution MRM-MS to quantify in absolute terms the total levels of the protein of interest, ataxia telangiectasia mutated (ATM) serine/threonine protein kinase. Ataxia telangiectasia mutated (ATM) phosphorylates several key proteins that initiate activation of the DNA damage checkpoint leading to cell cycle arrest.
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Affiliation(s)
- Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 10920 George Mason Circle MS1A9, Manassas, VA, 20110, USA.
| | - Brian L Hood
- DOD Gynecologic Cancer Center of Excellence, Annandale, VA, 22003, USA
| | | | - Thomas P Conrads
- Inova Dwight and Martha Schar Cancer Institute, 3300 Gallows Road, Falls Church, VA, 22042, USA. .,Gynecologic Cancer Center of Excellence, Women's Health Integrated Research Center, 3289 Woodburn Rd, Suite 375, Annandale, VA, 22003, USA.
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47
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Salivary and pellicle proteome: A datamining analysis. Sci Rep 2016; 6:38882. [PMID: 27966577 PMCID: PMC5155218 DOI: 10.1038/srep38882] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 11/16/2016] [Indexed: 01/06/2023] Open
Abstract
We aimed to comprehensively compare two compartmented oral proteomes, the salivary and the dental pellicle proteome. Systematic review and datamining was used to obtain the physico-chemical, structural, functional and interactional properties of 1,515 salivary and 60 identified pellicle proteins. Salivary and pellicle proteins did not differ significantly in their aliphatic index, hydrophaty, instability index, or isoelectric point. Pellicle proteins were significantly more charged at low and high pH and were significantly smaller (10–20 kDa) than salivary proteins. Protein structure and solvent accessible molecular surface did not differ significantly. Proteins of the pellicle were more phosphorylated and glycosylated than salivary proteins. Ion binding and enzymatic activities also differed significantly. Protein-protein-ligand interaction networks relied on few key proteins. The identified differences between salivary and pellicle proteins could guide proteome compartmentalization and result in specialized functionality. Key proteins could be potential targets for diagnostic or therapeutic application.
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Gaudet P, Michel PA, Zahn-Zabal M, Britan A, Cusin I, Domagalski M, Duek PD, Gateau A, Gleizes A, Hinard V, Rech de Laval V, Lin J, Nikitin F, Schaeffer M, Teixeira D, Lane L, Bairoch A. The neXtProt knowledgebase on human proteins: 2017 update. Nucleic Acids Res 2016; 45:D177-D182. [PMID: 27899619 PMCID: PMC5210547 DOI: 10.1093/nar/gkw1062] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 10/19/2016] [Accepted: 10/24/2016] [Indexed: 01/14/2023] Open
Abstract
The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update. All of the neXtProt data are available via our user interface and FTP site. We also provide an API access and a SPARQL endpoint for more technical applications.
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Affiliation(s)
- Pascale Gaudet
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206 .,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
| | - Pierre-André Michel
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Monique Zahn-Zabal
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Aurore Britan
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Isabelle Cusin
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Marcin Domagalski
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
| | - Paula D Duek
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Alain Gateau
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Anne Gleizes
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Valérie Hinard
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Valentine Rech de Laval
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
| | - JinJin Lin
- Sun Yat-sen University, 135 Xingang W Rd, Haizhu, Guangzhou, Guangdong, China
| | - Frederic Nikitin
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Mathieu Schaeffer
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
| | - Daniel Teixeira
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206
| | - Lydie Lane
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
| | - Amos Bairoch
- CALIPHO group, SIB Swiss Institute of Bioinformatics, Geneva, Switzerland, 1206.,Department of Human Protein Sciences, Faculty of Medicine, University of Geneva, Geneva, Switzerland, 1206
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Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E. The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine. Proteomics 2016; 16:634-44. [PMID: 26699206 DOI: 10.1002/pmic.201500195] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Revised: 11/02/2015] [Accepted: 12/16/2015] [Indexed: 01/14/2023]
Abstract
Biological research of Sus scrofa, the domestic pig, is of immediate relevance for food production sciences, and for developing pig as a model organism for human biomedical research. Publicly available data repositories play a fundamental role for all biological sciences, and protein data repositories are in particular essential for the successful development of new proteomic methods. Cumulative proteome data repositories, including the PeptideAtlas, provide the means for targeted proteomics, system-wide observations, and cross-species observational studies, but pigs have so far been underrepresented in existing repositories. We here present a significantly improved build of the Pig PeptideAtlas, which includes pig proteome data from 25 tissues and three body fluid types mapped to 7139 canonical proteins. The content of the Pig PeptideAtlas reflects actively ongoing research within the veterinary proteomics domain, and this article demonstrates how the expression of isoform-unique peptides can be observed across distinct tissues and body fluids. The Pig PeptideAtlas is a unique resource for use in animal proteome research, particularly biomarker discovery and for preliminary design of SRM assays, which are equally important for progress in research that supports farm animal production and veterinary health, as for developing pig models with relevance to human health research.
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Affiliation(s)
| | - Marius C Codrea
- Quantitative Biology Center (QBiC), Eberhard Karls Universität, Tübingen, Germany
| | - Zhi Sun
- Institute for Systems Biology, Seattle, WA, USA
| | | | - Tue B Bennike
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Louise Bundgaard
- Department of Large Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Emøke Bendixen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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50
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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept. Int J Mol Sci 2016; 17:ijms17111874. [PMID: 27834926 PMCID: PMC5133874 DOI: 10.3390/ijms17111874] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/27/2016] [Accepted: 11/03/2016] [Indexed: 01/10/2023] Open
Abstract
Although it is one of the most studied proteins, p53 continues to be an enigma. This protein has numerous biological functions, possesses intrinsically disordered regions crucial for its functionality, can form both homo-tetramers and isoform-based hetero-tetramers, and is able to interact with many binding partners. It contains numerous posttranslational modifications, has several isoforms generated by alternative splicing, alternative promoter usage or alternative initiation of translation, and is commonly mutated in different cancers. Therefore, p53 serves as an important illustration of the protein structure–function continuum concept, where the generation of multiple proteoforms by various mechanisms defines the ability of this protein to have a multitude of structurally and functionally different states. Considering p53 in the light of a proteoform-based structure–function continuum represents a non-canonical and conceptually new contemplation of structure, regulation, and functionality of this important protein.
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