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Wang J, Tan H, Fu Y, Mishra A, Sun H, Wang Z, Wu Z, Wang X, Serrano GE, Beach TG, Peng J, High AA. Evaluation of Protein Identification and Quantification by the diaPASEF Method on timsTOF SCP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1253-1260. [PMID: 38754071 DOI: 10.1021/jasms.4c00067] [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: 05/18/2024]
Abstract
Accurate and precise quantification is crucial in modern proteomics, particularly in the context of exploring low-amount samples. While the innovative 4D-data-independent acquisition (DIA) quantitative proteomics facilitated by timsTOF mass spectrometers gives enhanced sensitivity and selectivity for protein identification, the diaPASEF (parallel accumulation-serial fragmentation combined with data-independent acquisition) parameters have not been systematically optimized, and a comprehensive evaluation of the quantification is currently lacking. In this study, we conducted a thorough optimization of key parameters on a timsTOF SCP instrument, including sample loading amount (50 ng), ramp/accumulation time (140 ms), isolation window width (20 m/z), and gradient time (60 min). To further improve the identification of proteins in low-amount samples, we utilized different column settings and introduced 0.02% n-dodecyl-β-d-maltoside (DDM) in the sample reconstitution solution, resulting in a remarkable 19-fold increase in protein identification at the single-cell-equivalent level. Moreover, a comprehensive comparison of protein quantification using a tandem mass tag reporter (TMT-reporter), complement TMT ions (TMTc), and diaPASEF revealed a strong correlation between these methods. Both diaPASEF and TMTc have effectively addressed the issue of ratio compression, highlighting the diaPASEF method's effectiveness in achieving accurate quantification data compared to TMT reporter quantification. Additionally, an in-depth analysis of in-group variation positioned diaPASEF between the TMT-reporter and TMTc methods. Therefore, diaPASEF quantification on the timsTOF SCP instrument emerges as a precise and accurate methodology for quantitative proteomics, especially for samples with small amounts.
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Affiliation(s)
- Ju Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yingxue Fu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Huan Sun
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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Li Z, Wang S, Cui H, Liu X, Zhang Y. Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification. Brief Bioinform 2024; 25:bbae280. [PMID: 38856171 PMCID: PMC11163383 DOI: 10.1093/bib/bbae280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/05/2024] [Accepted: 05/24/2024] [Indexed: 06/11/2024] Open
Abstract
The identification of protein complexes from protein interaction networks is crucial in the understanding of protein function, cellular processes and disease mechanisms. Existing methods commonly rely on the assumption that protein interaction networks are highly reliable, yet in reality, there is considerable noise in the data. In addition, these methods fail to account for the regulatory roles of biomolecules during the formation of protein complexes, which is crucial for understanding the generation of protein interactions. To this end, we propose a SpatioTemporal constrained RNA-protein heterogeneous network for Protein Complex Identification (STRPCI). STRPCI first constructs a multiplex heterogeneous protein information network to capture deep semantic information by extracting spatiotemporal interaction patterns. Then, it utilizes a dual-view aggregator to aggregate heterogeneous neighbor information from different layers. Finally, through contrastive learning, STRPCI collaboratively optimizes the protein embedding representations under different spatiotemporal interaction patterns. Based on the protein embedding similarity, STRPCI reweights the protein interaction network and identifies protein complexes with core-attachment strategy. By considering the spatiotemporal constraints and biomolecular regulatory factors of protein interactions, STRPCI measures the tightness of interactions, thus mitigating the impact of noisy data on complex identification. Evaluation results on four real PPI networks demonstrate the effectiveness and strong biological significance of STRPCI. The source code implementation of STRPCI is available from https://github.com/LI-jasm/STRPCI.
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Affiliation(s)
- Zeqian Li
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Shilong Wang
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Hai Cui
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
| | - Xiaoxia Liu
- Department of Neurology and Neurological Sciences, Stanford University, CA 94305, USA
| | - Yijia Zhang
- School of Information Science and Technology, Dalian Maritime University, Dalian, 116026, China
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Wanapat M, Dagaew G, Sommai S, Matra M, Suriyapha C, Prachumchai R, Muslykhah U, Phupaboon S. The application of omics technologies for understanding tropical plants-based bioactive compounds in ruminants: a review. J Anim Sci Biotechnol 2024; 15:58. [PMID: 38689368 PMCID: PMC11062008 DOI: 10.1186/s40104-024-01017-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 02/29/2024] [Indexed: 05/02/2024] Open
Abstract
Finding out how diet impacts health and metabolism while concentrating on the functional qualities and bioactive components of food is the crucial scientific objective of nutritional research. The complex relationship between metabolism and nutrition could be investigated with cutting-edge "omics" and bioinformatics techniques. This review paper provides an overview of the use of omics technologies in nutritional research, with a particular emphasis on the new applications of transcriptomics, proteomics, metabolomics, and genomes in functional and biological activity research on ruminant livestock and products in the tropical regions. A wealth of knowledge has been uncovered regarding the regulation and use of numerous physiological and pathological processes by gene, mRNA, protein, and metabolite expressions under various physiological situations and guidelines. In particular, the components of meat and milk were assessed using omics research utilizing the various methods of transcriptomics, proteomics, metabolomics, and genomes. The goal of this review is to use omics technologies-which have been steadily gaining popularity as technological tools-to develop new nutritional, genetic, and leadership strategies to improve animal products and their quality control. We also present an overview of the new applications of omics technologies in cattle production and employ nutriomics and foodomics technologies to investigate the microbes in the rumen ecology. Thus, the application of state-of-the-art omics technology may aid in our understanding of how species and/or breeds adapt, and the sustainability of tropical animal production, in the long run, is becoming increasingly important as a means of mitigating the consequences of climate change.
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Affiliation(s)
- Metha Wanapat
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Gamonmas Dagaew
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Sukruthai Sommai
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Maharach Matra
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Chaichana Suriyapha
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Rittikeard Prachumchai
- Department of Animal Science, Faculty of Agricultural Technology, University of Technology Thanyaburi, Rajamangala Pathum Thani, 12130, Thailand
| | - Uswatun Muslykhah
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Srisan Phupaboon
- Tropical Feed Resources Research and Development Center (TROFREC), Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen, 40002, Thailand.
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Iadarola P, Viglio S. Mass Spectrometric Proteomics 2.0. Int J Mol Sci 2024; 25:2960. [PMID: 38474207 DOI: 10.3390/ijms25052960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
This Special Issue, "Mass Spectrometric Proteomics 2 [...].
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Affiliation(s)
- Paolo Iadarola
- Department of Biology and Biotechnologies "L.Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Simona Viglio
- Department of Molecular Medicine, Biochemistry Unit, University of Pavia, 27100 Pavia, Italy
- Lung Transplantation Unit, IRCCS Policlinico San Matteo Foundation, 27100 Pavia, Italy
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Feng Q, Lu Y, Zhang R, Li Y, Zhao Z, Zhou H. Identification of differentially expressed exosome proteins in serum as potential biomarkers for cognitive impairments in cerebral small vessel disease. Neurosci Lett 2024; 822:137631. [PMID: 38211879 DOI: 10.1016/j.neulet.2024.137631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/25/2023] [Accepted: 01/08/2024] [Indexed: 01/13/2024]
Abstract
BACKGROUND Cognitive impairment arising from cerebral small vessel disease (CSVD) represents a critical subtype of vascular cognitive impairments (VCI) and is the primary cause of vascular dementia. However, identifying reliable clinical and laboratory indicators for this disease remain elusive. We hypothesize that plasma exosome proteins hold the potential to serve as biomarkers for the onset of cognitive dysfunction associated with cerebrovascular diseases. METHODS We employed TMT-based proteomics to discern variations in serum exosome proteomes between individuals with cognitive impairments due to CSVD and healthy volunteers. RESULTS Each group comprised 18 subjects, and through differential expression analysis, we identified 22 down-regulated and 8 up-regulated proteins between the two groups. Our research revealed 30 differentially expressed plasma exosome proteins, including histone, proteasome, clusterin and coagulation factor XIII, in individuals with cognitive impairments caused by CSVD. CONCLUSION The 30 differentially expressed plasma exosome proteins identified in our study are promising as biomarkers for diagnosing cognitive impairments resulting from CSVD. These findings may help us better understand the underlying pathological mechanisms involved in the diseases.
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Affiliation(s)
- Qian Feng
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yanjing Lu
- Department of Neurology, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Ruyang Zhang
- Department of Neurology, Suzhou Wuzhong People's Hospital, Suzhou, China
| | - Yifan Li
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zhong Zhao
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
| | - Hua Zhou
- Department of Neurology, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China.
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Smiley KO, Munley KM, Aghi K, Lipshutz SE, Patton TM, Pradhan DS, Solomon-Lane TK, Sun SED. Sex diversity in the 21st century: Concepts, frameworks, and approaches for the future of neuroendocrinology. Horm Behav 2024; 157:105445. [PMID: 37979209 PMCID: PMC10842816 DOI: 10.1016/j.yhbeh.2023.105445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/20/2023]
Abstract
Sex is ubiquitous and variable throughout the animal kingdom. Historically, scientists have used reductionist methodologies that rely on a priori sex categorizations, in which two discrete sexes are inextricably linked with gamete type. However, this binarized operationalization does not adequately reflect the diversity of sex observed in nature. This is due, in part, to the fact that sex exists across many levels of biological analysis, including genetic, molecular, cellular, morphological, behavioral, and population levels. Furthermore, the biological mechanisms governing sex are embedded in complex networks that dynamically interact with other systems. To produce the most accurate and scientifically rigorous work examining sex in neuroendocrinology and to capture the full range of sex variability and diversity present in animal systems, we must critically assess the frameworks, experimental designs, and analytical methods used in our research. In this perspective piece, we first propose a new conceptual framework to guide the integrative study of sex. Then, we provide practical guidance on research approaches for studying sex-associated variables, including factors to consider in study design, selection of model organisms, experimental methodologies, and statistical analyses. We invite fellow scientists to conscientiously apply these modernized approaches to advance our biological understanding of sex and to encourage academically and socially responsible outcomes of our work. By expanding our conceptual frameworks and methodological approaches to the study of sex, we will gain insight into the unique ways that sex exists across levels of biological organization to produce the vast array of variability and diversity observed in nature.
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Affiliation(s)
- Kristina O Smiley
- Department of Psychological and Brain Sciences, University of Massachusetts Amherst, 639 North Pleasant Street, Morrill IVN Neuroscience, Amherst, MA 01003, USA.
| | - Kathleen M Munley
- Department of Psychology, University of Houston, 3695 Cullen Boulevard, Houston, TX 77204, USA.
| | - Krisha Aghi
- Department of Integrative Biology and Physiology, University of California Los Angeles, 405 Hilgard Ave, Los Angeles, CA 90095, USA.
| | - Sara E Lipshutz
- Department of Biology, Duke University, 130 Science Drive, Durham, NC 27708, USA.
| | - Tessa M Patton
- Bioinformatics Program, Loyola University Chicago, 1032 West Sheridan Road, LSB 317, Chicago, IL 60660, USA.
| | - Devaleena S Pradhan
- Department of Biological Sciences, Idaho State University, 921 South 8th Avenue, Mail Stop 8007, Pocatello, ID 83209, USA.
| | - Tessa K Solomon-Lane
- Scripps, Pitzer, Claremont McKenna Colleges, 925 North Mills Avenue, Claremont, CA 91711, USA.
| | - Simón E D Sun
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Wang Y, Sun Y, Wang Y, Jia S, Qiao Y, Zhou Z, Shao W, Zhang X, Guo J, Zhang B, Niu X, Wang Y, Peng D. Identification of novel diagnostic panel for mild cognitive impairment and Alzheimer's disease: findings based on urine proteomics and machine learning. Alzheimers Res Ther 2023; 15:191. [PMID: 37925455 PMCID: PMC10625308 DOI: 10.1186/s13195-023-01324-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 11/06/2023]
Abstract
BACKGROUND Alzheimer's disease is a prevalent disease with a heavy global burden. Proteomics is the systematic study of proteins and peptides to provide comprehensive descriptions. Aiming to obtain a more accurate and convenient clinical diagnosis, researchers are working for better biomarkers. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels. METHODS We firstly enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples, and conducted an LC-MS/MS analysis. In parallel, clinical data were collected, and clinical examinations were performed. After statistical and bioinformatics analyses, significant risk factors and differential urinary proteins were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM. RESULTS Fifty-seven AD patients, 43 MCI patients, and 62 CN subjects were enrolled. A total of 3366 proteins were identified, and 608 urine proteins were finally included in the analysis. There were 33 significantly differential proteins between the AD and CN groups and 15 significantly differential proteins between the MCI and CN groups. AD diagnostic panel included DDC, CTSC, EHD4, GSTA3, SLC44A4, GNS, GSTA1, ANXA4, PLD3, CTSH, HP, RPS3, CPVL, age, and APOE ε4 with an AUC of 0.9989 in the training test and 0.8824 in the test set while MCI diagnostic panel included TUBB, SUCLG2, PROCR, TCP1, ACE, FLOT2, EHD4, PROZ, C9, SERPINA3, age, and APOE ε4 with an AUC of 0.9985 in the training test and 0.8143 in the test set. Besides, diagnostic proteins were weakly correlated with cognitive functions. CONCLUSIONS In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN.
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Affiliation(s)
- Yuye Wang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Sun
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yu Wang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Shuhong Jia
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Yanan Qiao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Zhi Zhou
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Wen Shao
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiangfei Zhang
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Jing Guo
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Bin Zhang
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
| | - Xiaoqian Niu
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dantao Peng
- China-Japan Friendship Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China.
- Department of Neurology, China-Japan Friendship Hospital, Beijing, 100029, China.
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China.
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Perkons I, Varunjikar MS, Rasinger JD. Unveiling the potential of proteomics in addressing food and feed safety challenges. EFSA J 2023; 21:e211013. [PMID: 38047126 PMCID: PMC10687763 DOI: 10.2903/j.efsa.2023.e211013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023] Open
Abstract
The food and feed sector in Europe is rapidly evolving to address contemporary challenges, striving for fairer, safer, greener and more sustainable food systems. This includes the exploration of new protein sources for human consumption and animal feed such as protein derived from insects, algae or novel plant-derived proteins, and the re-evaluation of existing sources like processed animal protein (PAP). To generate reliable data on the diverse array of emerging protein sources for future food and feed safety assessments, a growing demand for the development and implementation of advanced analytical techniques exists. New approach methodologies (NAMs) including, mass spectrometry (MS)-based proteomics methods have been emerging as valuable techniques which potentially can be implemented in regulatory laboratory settings to complement conventional approaches in this realm. These MS-driven strategies have already proven their utility in diverse applications, including the detection of prohibited substances in feed, identification of allergens, differentiation of fish species in complex mixtures for fraud detection and the verification of novel foods and alternative protein sources. This EU-FORA programme was focused on three core objectives namely: (i) the training of the fellow in utilising MS-based proteomics for food and feed safety analyses, (ii) the involvement of the fellow in the development of standardised operating procedures (SOP) for targeted and non-targeted proteomic MS-based workflows for species and tissues specific PAP identification in a national reference laboratory (NRL) and (iii) the transfer and implementation of MS-based approaches and standardised protocols for PAP analysis at the fellow's home institution. Altogether, this programme facilitates the broadening and diversification of use of MS-based proteomic methodologies for reinforcing their significance within the domains of food and feed safety research and regulatory science applications.
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Affiliation(s)
- Ingus Perkons
- Institute of Food SafetyAnimal Health and Environment ‘BIOR’, RigaLatvia
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Houston S, Gomez A, Geppert A, Eshghi A, Smith DS, Waugh S, Hardie DB, Goodlett DR, Cameron CE. Deep proteome coverage advances knowledge of Treponema pallidum protein expression profiles during infection. Sci Rep 2023; 13:18259. [PMID: 37880309 PMCID: PMC10600179 DOI: 10.1038/s41598-023-45219-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023] Open
Abstract
Comprehensive proteome-wide analysis of the syphilis spirochete, Treponema pallidum ssp. pallidum, is technically challenging due to high sample complexity, difficulties with obtaining sufficient quantities of bacteria for analysis, and the inherent fragility of the T. pallidum cell envelope which further complicates proteomic identification of rare T. pallidum outer membrane proteins (OMPs). The main aim of the present study was to gain a deeper understanding of the T. pallidum global proteome expression profile under infection conditions. This will corroborate and extend genome annotations, identify protein modifications that are unable to be predicted at the genomic or transcriptomic levels, and provide a foundational knowledge of the T. pallidum protein expression repertoire. Here we describe the optimization of a T. pallidum-specific sample preparation workflow and mass spectrometry-based proteomics pipeline which allowed for the detection of 77% of the T. pallidum protein repertoire under infection conditions. When combined with prior studies, this brings the overall coverage of the T. pallidum proteome to almost 90%. These investigations identified 27 known/predicted OMPs, including potential vaccine candidates, and detected expression of 11 potential OMPs under infection conditions for the first time. The optimized pipeline provides a robust and reproducible workflow for investigating T. pallidum protein expression during infection. Importantly, the combined results provide the deepest coverage of the T. pallidum proteome to date.
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Affiliation(s)
- Simon Houston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Alloysius Gomez
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Andrew Geppert
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Azad Eshghi
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Derek S Smith
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Sean Waugh
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Darryl B Hardie
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - David R Goodlett
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- University of Victoria-Genome BC Proteomics Centre, University of Victoria, Victoria, BC, Canada
| | - Caroline E Cameron
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA, USA.
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Ju Y, Jin C, Chen S, Wang J, Li C, Wang X, Wang P, Yue L, Jiang X, Tuohetaerbaike B, Li Y, Sheng Y, Qimanguli W, Wang J, Chen F. Proteomic analyses of smear-positive/negative tuberculosis patients uncover differential antigen-presenting cell activation and lipid metabolism. Front Cell Infect Microbiol 2023; 13:1240516. [PMID: 37908762 PMCID: PMC10613889 DOI: 10.3389/fcimb.2023.1240516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023] Open
Abstract
Background Tuberculosis (TB) remains a major global health concern, ranking as the second most lethal infectious disease following COVID-19. Smear-Negative Pulmonary Tuberculosis (SNPT) and Smear-Positive Pulmonary Tuberculosis (SPPT) are two common types of pulmonary tuberculosis characterized by distinct bacterial loads. To date, the precise molecular mechanisms underlying the differences between SNPT and SPPT patients remain unclear. In this study, we aimed to utilize proteomics analysis for identifying specific protein signatures in the plasma of SPPT and SNPT patients and further elucidate the molecular mechanisms contributing to different disease pathogenesis. Methods Plasma samples from 27 SPPT, 37 SNPT patients and 36 controls were collected and subjected to TMT-labeled quantitative proteomic analyses and targeted GC-MS-based lipidomic analysis. Ingenuity Pathway Analysis (IPA) was then performed to uncover enriched pathways and functionals of differentially expressed proteins. Results Proteomic analysis uncovered differential protein expression profiles among the SPPT, SNPT, and Ctrl groups, demonstrating dysfunctional immune response and metabolism in both SPPT and SNPT patients. Both groups exhibited activated innate immune responses and inhibited fatty acid metabolism, but SPPT patients displayed stronger innate immune activation and lipid metabolic inhibition compared to SNPT patients. Notably, our analysis uncovered activated antigen-presenting cells (APCs) in SNPT patients but inhibited APCs in SPPT patients, suggesting their critical role in determining different bacterial loads/phenotypes in SNPT and SPPT. Furthermore, some specific proteins were detected to be involved in the APC activation/acquired immune response, providing some promising therapeutic targets for TB. Conclusion Our study provides valuable insights into the differential molecular mechanisms underlying SNPT and SPPT, reveals the critical role of antigen-presenting cell activation in SNPT for effectively clearing the majority of Mtb in bodies, and shows the possibility of APC activation as a novel TB treatment strategy.
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Affiliation(s)
- Yingjiao Ju
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chengji Jin
- Department of Respiratory Medicine, Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Shan Chen
- Department of Respiratory Medicine, Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Jie Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Xiaotong Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Peihan Wang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Liya Yue
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Xiaoyuan Jiang
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
| | - Bahetibieke Tuohetaerbaike
- Respiratory Department, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Ying Li
- Respiratory Department, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Wushou’er Qimanguli
- Department of Respiratory Medicine, Second Affiliated Hospital of Xinjiang Medical University, Urumqi, Xinjiang, China
| | - Jing Wang
- Department of Respiratory Medicine, Second Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
- Respiratory Department, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
| | - Fei Chen
- Chinese Academy of Sciences (CAS) Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Respiratory Department, First Affiliated Hospital of Xinjiang Medical University, State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Urumqi, Xinjiang, China
- Beijing Key Laboratory of Genome and Precision Medicine Technologies, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, China
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11
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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12
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Birhanu AG. Mass spectrometry-based proteomics as an emerging tool in clinical laboratories. Clin Proteomics 2023; 20:32. [PMID: 37633929 PMCID: PMC10464495 DOI: 10.1186/s12014-023-09424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/03/2023] [Indexed: 08/28/2023] Open
Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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13
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Chaousis S, Leusch FDL, Nouwens A, Melvin SD, van de Merwe JP. Influence of chemical dose and exposure duration on protein synthesis in green sea turtle primary cells. J Proteomics 2023; 285:104942. [PMID: 37285907 DOI: 10.1016/j.jprot.2023.104942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 05/14/2023] [Accepted: 05/24/2023] [Indexed: 06/09/2023]
Abstract
Understanding the impacts of chemical exposure in marine wildlife is challenging, due to practical and ethical constraints that preclude traditional toxicology research on these animals. This study addressed some of these limitations by presenting an ethical and high throughput cell-based approach to elucidate molecular-level effects of contaminants on sea turtles. The experimental design addressed basic questions of cell-based toxicology, including chemical dose and exposure time. Primary green turtle skin cells were exposed to polychlorinated biphenyl (PCB) 153 and perfluorononanoic acid (PFNA) for 24 and 48 h, at three sub-lethal, environmentally relevant concentrations (1, 10 and 100 μg/L). Sequential window acquisition of all theoretical mass spectra (SWATH-MS) identified over 1000 differentially abundant proteins within the 1% false discovery rate (FDR) threshold. The 24 h exposure resulted in a greater number of differentially abundant proteins, compared to 48 h exposure, for both contaminants. However, there were no statistically significant dose-response relationships for the number of differentially synthesised proteins, nor differences in the proportion of increased vs decreased proteins between or within exposure times. Known in vivo markers of contaminant exposure, superoxide dismutase and glutathione S-transferase, were differentially abundant following exposure to PCB153 and PFNA. SIGNIFICANCE: Cell-based (in vitro) proteomics provides an ethical and high throughput approach to understanding the impacts of chemical contamination on sea turtles. Through investigating effects of chemical dose and exposure duration on unique protein abundance in vitro, this study provides an optimised framework for conducting cell-based studies in wildlife proteomics, and highlights that proteins detected in vitro could act as biomarkers of chemical exposure and effect in vivo.
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Affiliation(s)
- Stephanie Chaousis
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Frederic D L Leusch
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Amanda Nouwens
- School of Chemistry and Molecular Biology, The University of Queensland, Building 76, QLD 4067, Australia
| | - Steven D Melvin
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia
| | - Jason P van de Merwe
- Griffith School of Science and Environment and the Australian Rivers Institute, Griffith Univeristy, Building 51, Gold Coast Campus, QLD 4222, Australia.
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14
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Zhao WS, Chen KF, Liu M, Jia XL, Huang YQ, Hao BB, Hu H, Shen XY, Yu Q, Tan MJ. Investigation of targets and anticancer mechanisms of covalently acting natural products by functional proteomics. Acta Pharmacol Sin 2023; 44:1701-1711. [PMID: 36932232 PMCID: PMC10374574 DOI: 10.1038/s41401-023-01072-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
Eriocalyxin B (EB), 17-hydroxy-jolkinolide B (HJB), parthenolide (PN), xanthatin (XT) and andrographolide (AG) are terpenoid natural products with a variety of promising antitumor activities, which commonly bear electrophilic groups (α,β-unsaturated carbonyl groups and/or epoxides) capable of covalently modifying protein cysteine residues. However, their direct targets and underlying molecular mechanisms are still largely unclear, which limits the development of these compounds. In this study, we integrated activity-based protein profiling (ABPP) and quantitative proteomics approach to systematically characterize the covalent targets of these natural products and their involved cellular pathways. We first demonstrated the anti-proliferation activities of these five compounds in triple-negative breast cancer cell MDA-MB-231. Tandem mass tag (TMT)-based quantitative proteomics showed all five compounds commonly affected the ubiquitin mediated proteolysis pathways. ABPP platform identified the preferentially modified targets of EB and PN, two natural products with high anti-proliferation activity. Biochemical experiments showed that PN inhibited the cell proliferation through targeting ubiquitin carboxyl-terminal hydrolase 10 (USP10). Together, this study uncovered the covalently modified targets of these natural products and potential molecular mechanisms of their antitumor activities.
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Affiliation(s)
- Wen-Si Zhao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Kai-Feng Chen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Man Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xing-Long Jia
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Yu-Qi Huang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Bing-Bing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Hao Hu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Xiao-Yan Shen
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai, 201203, China
| | - Qiang Yu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Min-Jia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 101408, China.
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China.
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, College of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, China.
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15
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Increasing the production of the bioactive compounds in medicinal mushrooms: an omics perspective. Microb Cell Fact 2023; 22:11. [PMID: 36647087 PMCID: PMC9841694 DOI: 10.1186/s12934-022-02013-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Macroscopic fungi, mainly higher basidiomycetes and some ascomycetes, are considered medicinal mushrooms and have long been used in different areas due to their pharmaceutically/nutritionally valuable bioactive compounds. However, the low production of these bioactive metabolites considerably limits the utilization of medicinal mushrooms both in commerce and clinical trials. As a result, many attempts, ranging from conventional methods to novel approaches, have been made to improve their production. The novel strategies include conducting omics investigations, constructing genome-scale metabolic models, and metabolic engineering. So far, genomics and the combined use of different omics studies are the most utilized omics analyses in medicinal mushroom research (both with 31% contribution), while metabolomics (with 4% contribution) is the least. This article is the first attempt for reviewing omics investigations in medicinal mushrooms with the ultimate aim of bioactive compound overproduction. In this regard, the role of these studies and systems biology in elucidating biosynthetic pathways of bioactive compounds and their contribution to metabolic engineering will be highlighted. Also, limitations of omics investigations and strategies for overcoming them will be provided in order to facilitate the overproduction of valuable bioactive metabolites in these valuable organisms.
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16
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Mosavi Z, Bashi Zadeh Fakhar H, Rezaei-Tavirani M, Akbari ME, Rostami F. Proteome profiling of ductal carcinoma in situ. Breast Dis 2023; 41:513-520. [PMID: 36641653 DOI: 10.3233/bd-220017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
BACKGROUND AND AIM DCIS is the most common type of non-invasive breast cancer, accounting for about 15 to 30%. Proteome profile is used to detect biomarkers in the tissues of breast cancer patients by mass spectrometry. This study aimed to obtain the expression profile of DCIS proteome, and the expression profile of invasive biomarkers, and finally to introduce a dedicated biomarker panel to facilitate the prognosis and early detection for in situ breast cancer patients. METHODS AND MATERIALS In this study, 10 patients with breast cancer (DCIS) were studied. Benign (marginal) and cancerous tissue samples were obtained from patients for proteomics experiments. Initially, all tissue proteins were extracted using standard methods, and the proteins were separated using two-dimensional electrophoresis. Then, the expression amount of the extracted proteins was determined by ITRAQ. The data were analysed by R software, and gene ontology was utilised for describing the protein in detail. RESULTS 30 spots on gel electrophoresis were found in the tumor tissue group (sample), and 15 spots in the margin group (control) with P < 0.05. Healthy and cancerous tissue gels showed that 5 spots had different expression. VWF, MMP9, ITGAM, MPO and PLG protein spots were identified using the site www.ebi.ac.uk/IPI. Finally, protein biomarkers for breast tumor tissue with margin were introduced with the names of P04406, P49915, P05323, P06733, and P02768. DISCUSSION There are 5 critical proteins in inducing cancer pathways especially complement and coagulation cascades. The hall markers of a healthy cell to be cancerous are proliferation, invasion, angiogenesis, and changes in the immune system. Hence, regulation of protein plays a key role in developing recurrence to breast cancer in margins.
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Affiliation(s)
- Zeinb Mosavi
- Department of Medical Science, Islamic Azad University, Chalus Branch, Chalous, Iran
| | - Haniyeh Bashi Zadeh Fakhar
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Department of Laboratory Science, Islamic Azad University, Chalous Branch, Chalous, Iran
| | | | - Mohamd Esmaeel Akbari
- Cancer Research Centre (CRC), Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Forouzan Rostami
- Department of Nursing, Faculty of Nursing and Midwifery, Islamic Azad University, Chalous, Iran
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17
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Nisar N, Mir SA, Kareem O, Pottoo FH. Proteomics approaches in the identification of cancer biomarkers and drug discovery. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00001-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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18
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Cancer proteomics: An overview. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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19
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Chen J, Xiang Y, Wang P, Liu J, Lai W, Xiao M, Pei H, Fan C, Li L. Ensemble Modified Aptamer Based Pattern Recognition for Adaptive Target Identification. NANO LETTERS 2022; 22:10057-10065. [PMID: 36524831 DOI: 10.1021/acs.nanolett.2c03808] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The difficulty of the molecular design and chemical synthesis of artificial sensing receptors restricts their diagnostic and proteomic applications. Herein, we report a concept of "ensemble modified aptamers" (EMAmers) that exploits the collective recognition abilities of a small set of protein-like side-chain-modified nucleic acid ligands for discriminative identification of molecular or cellular targets. Different types and numbers of hydrophobic functional groups were incorporated at designated positions on nucleic acid scaffolds to mimic amino acid side chains. We successfully assayed 18 EMAmer probes with differential binding affinities to seven proteins. We constructed an EMAmer-based chemical nose sensor and demonstrated its application in blinded unknown protein identification, giving a 92.9% accuracy. Additionally, the sensor is generalizable to the detection of blinded unknown bacterial and cellular samples, which enabled identification accuracies of 96.3% and 94.8%, respectively. This sensing platform offers a discriminative means for adaptive target identification and holds great potential for diverse applications.
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Affiliation(s)
- Jing Chen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Ying Xiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Peipei Wang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Jingjing Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 201240, People's Republic of China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, People's Republic of China
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20
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Spermatozoa and seminal plasma proteomics: too many molecules, too few markers. The case of bovine and porcine semen. Anim Reprod Sci 2022; 247:107075. [DOI: 10.1016/j.anireprosci.2022.107075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/06/2022] [Accepted: 09/20/2022] [Indexed: 11/22/2022]
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21
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Lu W, Hu C. Molecular biomarkers for gestational diabetes mellitus and postpartum diabetes. Chin Med J (Engl) 2022; 135:1940-1951. [PMID: 36148588 PMCID: PMC9746787 DOI: 10.1097/cm9.0000000000002160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Indexed: 11/25/2022] Open
Abstract
ABSTRACT Gestational diabetes mellitus (GDM) is a growing public health problem worldwide that threatens both maternal and fetal health. Identifying individuals at high risk for GDM and diabetes after GDM is particularly useful for early intervention and prevention of disease progression. In the last decades, a number of studies have used metabolomics, genomics, and proteomic approaches to investigate associations between biomolecules and GDM progression. These studies clearly demonstrate that various biomarkers reflect pathological changes in GDM. The established markers have potential use as screening and diagnostic tools in GDM and in postpartum diabetes research. In the present review, we summarize recent studies of metabolites, single-nucleotide polymorphisms, microRNAs, and proteins associated with GDM and its transition to postpartum diabetes, with a focus on their predictive value in screening and diagnosis.
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Affiliation(s)
- Wenqian Lu
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510630, China
- Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to the Southern Medical University, Shanghai 201400, China
| | - Cheng Hu
- Shanghai Diabetes Institute, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, China
- The Third School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong 510630, China
- Department of Endocrinology and Metabolism, Fengxian Central Hospital Affiliated to the Southern Medical University, Shanghai 201400, China
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22
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Guo J, Zhang X, Chen X, Cai Y. Proteomics in Biomarker Discovery for Tuberculosis: Current Status and Future Perspectives. Front Microbiol 2022; 13:845229. [PMID: 35558124 PMCID: PMC9087271 DOI: 10.3389/fmicb.2022.845229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) continues to threaten many peoples' health worldwide, regardless of their country of residence or age. The current diagnosis of TB still uses mainly traditional, time-consuming, and/or culture-based techniques. Efforts have focused on discovering new biomarkers with higher efficiency and accuracy for TB diagnosis. Proteomics-the systematic study of protein diversity-is being applied to the discovery of novel protein biomarkers for different types of diseases. Mass spectrometry (MS) technology plays a revolutionary role in proteomics, and its applicability benefits from the development of other technologies, such as matrix-based and immune-based methods. MS and derivative strategies continuously contribute to disease-related discoveries, and some promising proteomic biomarkers for efficient TB diagnosis have been identified, but challenges still exist. For example, there are discrepancies in the biomarkers identified among different reports and the diagnostic accuracy of clinically applied proteomic biomarkers. The present review summarizes the current status and future perspectives of proteomics in the field of TB biomarker discovery and aims to elicit more promising findings for rapid and accurate TB diagnosis.
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Affiliation(s)
- Jiubiao Guo
- College of Pharmacy, Shenzhen Technology University, Shenzhen, China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Ximeng Zhang
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Xinchun Chen
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Yi Cai
- Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, School of Medicine, Shenzhen University, Shenzhen, China
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23
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Barbé C, Salles J, Chambon C, Giraudet C, Sanchez P, Patrac V, Denis P, Boirie Y, Walrand S, Gueugneau M. Characterization of the Skeletal Muscle Proteome in Undernourished Old Rats. Int J Mol Sci 2022; 23:ijms23094762. [PMID: 35563153 PMCID: PMC9101871 DOI: 10.3390/ijms23094762] [Citation(s) in RCA: 4] [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: 03/16/2022] [Revised: 04/10/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
Aging is associated with a progressive loss of skeletal muscle mass and function termed sarcopenia. Various metabolic alterations that occur with aging also increase the risk of undernutrition, which can worsen age-related sarcopenia. However, the impact of undernutrition on aged skeletal muscle remains largely under-researched. To build a deeper understanding of the cellular and molecular mechanisms underlying age-related sarcopenia, we characterized the undernutrition-induced changes in the skeletal muscle proteome in old rats. For this study, 20-month-old male rats were fed 50% or 100% of their spontaneous intake for 12 weeks, and proteomic analysis was performed on both slow- and fast-twitch muscles. Proteomic profiling of undernourished aged skeletal muscle revealed that undernutrition has profound effects on muscle proteome independently of its effect on muscle mass. Undernutrition-induced changes in muscle proteome appear to be muscle-type-specific: slow-twitch muscle showed a broad pattern of differential expression in proteins important for energy metabolism, whereas fast-twitch muscle mainly showed changes in protein turnover between undernourished and control rats. This first proteomic analysis of undernourished aged skeletal muscle provides new molecular-level insight to explain phenotypic changes in undernourished aged muscle. We anticipate this work as a starting point to define new biomarkers associated with undernutrition-induced muscle loss in the elderly.
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Affiliation(s)
- Caroline Barbé
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Jérôme Salles
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Christophe Chambon
- Animal Products Quality Unit (QuaPA), INRAE, 63122 Clermont-Ferrand, France;
- Metabolomic and Proteomic Exploration Facility, Clermont Auvergne University, INRAE, 63122 Clermont-Ferrand, France
| | - Christophe Giraudet
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Phelipe Sanchez
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Véronique Patrac
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Philippe Denis
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
| | - Yves Boirie
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Department of Clinical Nutrition, Clermont-Ferrand University Hospital Center, 63000 Clermont-Ferrand, France
| | - Stéphane Walrand
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Department of Clinical Nutrition, Clermont-Ferrand University Hospital Center, 63000 Clermont-Ferrand, France
| | - Marine Gueugneau
- Human Nutrition Unit, INRAE, Auvergne Human Nutrition Research Center, Clermont Auvergne University, 63000 Clermont-Ferrand, France; (C.B.); (J.S.); (C.G.); (P.S.); (V.P.); (P.D.); (Y.B.); (S.W.)
- Correspondence: ; Tel.: +33-4-73-60-82-65
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25
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Sultonova M, Pinto DM, Murphy JP. Multiplexed Quantitative Proteomic Profiling of Cancer Cells and Tissues Using Isobaric Labeling-Based Tags. Methods Mol Biol 2022; 2508:211-223. [PMID: 35737243 DOI: 10.1007/978-1-0716-2376-3_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Comparing cancer proteomes across many samples offers a window into cancer cell biology and may reveal new treatment options for specific subsets of cancer. Here we describe a method using tandem mass tag (TMT) technology to multiplex up to 18 samples in a single analysis, paving the way for the analysis of large cohorts of tumors, cell lines, and perturbations thereof. The procedure we describe will result in samples ready for in-depth LC-MS/MS analysis in 3-4 days.
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Affiliation(s)
- Mukhayyo Sultonova
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | | | - J Patrick Murphy
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada.
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26
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Chan ACY, Wong HY, Chong YF, Lai PS, Teoh HL, Ng AYY, Hung JHM, Chan YC, Ng KWP, Vijayan J, Ong JJY, Chandra B, Tan CH, Rutt NH, Tan TM, Ismail NH, Wilder-Smith E, Schwarz H, Choi H, Sharma VK, Mak A. Novel Autoantibodies in Idiopathic Small Fiber Neuropathy. Ann Neurol 2021; 91:66-77. [PMID: 34761434 PMCID: PMC9300200 DOI: 10.1002/ana.26268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 01/04/2023]
Abstract
Objective Small fiber neuropathy (SFN) is clinically and etiologically heterogeneous. Although autoimmunity has been postulated to be pathophysiologically important in SFN, few autoantibodies have been described. We aimed to identify autoantibodies associated with idiopathic SFN (iSFN) by a novel high‐throughput protein microarray platform that captures autoantibodies expressed in the native conformational state. Methods Sera from 58 SFN patients and 20 age‐ and gender‐matched healthy controls (HCs) were screened against >1,600 immune‐related antigens. Fluorescent unit readout and postassay imaging were performed, followed by composite data normalization and protein fold change (pFC) analysis. Analysis of an independent validation cohort of 33 SFN patients against the same 20 HCs was conducted to identify reproducible proteins in both cohorts. Results Nine autoantibodies were screened with statistical significance and pFC criteria in both cohorts, with at least 50% change in serum levels. Three proteins showed consistently high fold changes in main and validation cohorts: MX1 (FC = 2.99 and 3.07, respectively, p = 0.003, q = 0.076), DBNL (FC = 2.11 and 2.16, respectively, p = 0.009, q < 0.003), and KRT8 (FC = 1.65 and 1.70, respectively, p = 0.043, q < 0.003). Further subgroup analysis into iSFN and SFN by secondary causes (secondary SFN) in the main cohort showed that MX1 is higher in iSFN compared to secondary SFN (FC = 1.61 vs 0.106, p = 0.009). Interpretation Novel autoantibodies MX1, DBNL, and KRT8 are found in iSFN. MX1 may allow diagnostic subtyping of iSFN patients. ANN NEUROL 2022;91:66–77
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Affiliation(s)
- Amanda C Y Chan
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hiu Yi Wong
- Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong.,Hong Kong Center for Neurodegenerative Diseases, Hong Kong Science Park, Pak Shek Kok, China
| | - Yao Feng Chong
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Poh San Lai
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hock Luen Teoh
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alison Y Y Ng
- Division of Neurology, Department of Medicine, National University Health System, Singapore
| | - Jennifer H M Hung
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yee Cheun Chan
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kay W P Ng
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Joy Vijayan
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Jonathan J Y Ong
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bharatendu Chandra
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Medical Genetics, University of Iowa, Iowa City, IA, USA
| | - Chi Hsien Tan
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | | | | | | | - Einar Wilder-Smith
- Department of Neurology, Inselspital Bern, University of Bern, Bern, Switzerland
| | - Herbert Schwarz
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hyungwon Choi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Vijay K Sharma
- Division of Neurology, Department of Medicine, National University Health System, Singapore.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Anselm Mak
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Division of Rheumatology, University Medicine Cluster, National University Health System, Singapore
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27
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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28
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Yang X, Neta P, Mirokhin YA, Tchekhovskoi DV, Remoroza CA, Burke MC, Liang Y, Markey SP, Stein SE. MS_Piano: A Software Tool for Annotating Peaks in CID Tandem Mass Spectra of Peptides and N-Glycopeptides. J Proteome Res 2021; 20:4603-4609. [PMID: 34264676 DOI: 10.1021/acs.jproteome.1c00324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Annotating product ion peaks in tandem mass spectra is essential for evaluating spectral quality and validating peptide identification. This task is more complex for glycopeptides and is crucial for the confident determination of glycosylation sites in glycoproteins. MS_Piano (Mass Spectrum Peptide Annotation) software was developed for reliable annotation of peaks in collision induced dissociation (CID) tandem mass spectra of peptides or N-glycopeptides for given peptide sequences, charge states, and optional modifications. The program annotates each peak in high or low resolution spectra with possible product ion(s) and the mass difference between the measured and theoretical m/z values. Spectral quality is measured by two major parameters: the ratio between the sum of unannotated vs all peak intensities in the top 20 peaks, and the intensity of the highest unannotated peak. The product ions of peptides, glycans, and glycopeptides in spectra are labeled in different class-type colors to facilitate interpretation. MS_Piano assists validating peptide and N-glycopeptide identification from database and library searches and provides quality control and optimizes search reliability in custom developed peptide mass spectral libraries. The software is freely available in .exe and .dll formats for the Windows operating system.
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Affiliation(s)
- Xiaoyu Yang
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Pedatsur Neta
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Yuri A Mirokhin
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Dmitrii V Tchekhovskoi
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Concepcion A Remoroza
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Meghan C Burke
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Yuxue Liang
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Sanford P Markey
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Stephen E Stein
- Mass Spectrometry Data Center, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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Chung YS, Ahmed PK, Othman I, Shaikh MF. Orthosiphon stamineus Proteins Alleviate Hydrogen Peroxide Stress in SH-SY5Y Cells. Life (Basel) 2021; 11:life11060585. [PMID: 34202937 PMCID: PMC8235403 DOI: 10.3390/life11060585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/16/2021] [Accepted: 06/17/2021] [Indexed: 12/12/2022] Open
Abstract
The neuroprotective potential of Orthosiphon stamineus leaf proteins (OSLPs) has never been evaluated in SH-SY5Y cells challenged by hydrogen peroxide (H2O2). This work thus aims to elucidate OSLP neuroprotective potential in alleviating H2O2 stress. OSLPs at varying concentrations were evaluated for cytotoxicity (24 and 48 h) and neuroprotective potential in H2O2-induced SH-SY5Y cells (24 h). The protective mechanism of H2O2-induced SH-SY5Y cells was also explored via mass-spectrometry-based label-free quantitative proteomics (LFQ) and bioinformatics. OSLPs (25, 50, 125, 250, 500, and 1000 µg/mL; 24 and 48 h) were found to be safe. Pre-treatments with OSLP doses (250, 500, and 1000 µg/mL, 24 h) significantly increased the survival of SH-SY5Y cells in a concentration-dependent manner and improved cell architecture—pyramidal-shaped cells, reduced clumping and shrinkage, with apparent neurite formations. OSLP pre-treatment (1000 µg/mL, 24 h) lowered the expressions of two major heat shock proteins, HSPA8 (heat shock protein family A (Hsp70) member 8) and HSP90AA1 (heat shock protein 90), which promote cellular stress signaling under stress conditions. OSLP is, therefore, suggested to be anti-inflammatory by modulating the “signaling of interleukin-4 and interleukin-13” pathway as the predominant mechanism in addition to regulating the “attenuation phase” and “HSP90 chaperone cycle for steroid hormone receptors” pathways to counteract heat shock protein (HSP)-induced damage under stress conditions.
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Affiliation(s)
- Yin-Sir Chung
- Neuropharmacology Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (Y.-S.C.); (I.O.)
| | - Pervaiz Khalid Ahmed
- School of Business, Monash University Malaysia, Bandar Sunway 47500, Malaysia;
- Global Asia in the 21st Century (GA21), Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Iekhsan Othman
- Neuropharmacology Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (Y.-S.C.); (I.O.)
- Liquid Chromatography-Mass Spectrometry (LCMS) Platform, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia
| | - Mohd. Farooq Shaikh
- Neuropharmacology Research Laboratory, Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Bandar Sunway 47500, Malaysia; (Y.-S.C.); (I.O.)
- Global Asia in the 21st Century (GA21), Monash University Malaysia, Bandar Sunway 47500, Malaysia
- Correspondence:
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30
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Wang Z, Pisano S, Ghini V, Kadeřávek P, Zachrdla M, Pelupessy P, Kazmierczak M, Marquardsen T, Tyburn JM, Bouvignies G, Parigi G, Luchinat C, Ferrage F. Detection of Metabolite-Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR. J Am Chem Soc 2021; 143:9393-9404. [PMID: 34133154 DOI: 10.1021/jacs.1c01388] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Metabolomics, the systematic investigation of metabolites in biological fluids, cells, or tissues, reveals essential information about metabolism and diseases. Metabolites have functional roles in a myriad of biological processes, as substrates and products of enzymatic reactions but also as cofactors and regulators of large numbers of biochemical mechanisms. These functions involve interactions of metabolites with macromolecules. Yet, methods to systematically investigate these interactions are still scarce to date. In particular, there is a need for techniques suited to identify and characterize weak metabolite-macromolecule interactions directly in complex media such as biological fluids. Here, we introduce a method to investigate weak interactions between metabolites and macromolecules in biological fluids. Our approach is based on high-resolution NMR relaxometry and does not require any invasive procedure or separation step. We show that we can detect interactions between small and large molecules in human blood serum and quantify the size of the complex. Our work opens the way for investigations of metabolite (or other small molecules)-protein interactions in biological fluids for interactomics or pharmaceutical applications.
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Affiliation(s)
- Ziqing Wang
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Simone Pisano
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Veronica Ghini
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
| | - Pavel Kadeřávek
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Milan Zachrdla
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Philippe Pelupessy
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Morgan Kazmierczak
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | | | - Jean-Max Tyburn
- Bruker BioSpin, 34 rue de l'Industrie BP 10002, 67166 Cedex Wissembourg, France
| | - Guillaume Bouvignies
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Giacomo Parigi
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Claudio Luchinat
- Consorzio Interuniversitario Risonanze Magnetiche Metallo Proteine (CIRMMP), via Sacconi 6, Sesto Fiorentino, 50019 Italy
- Magnetic Resonance Center (CERM), University of Florence, via Sacconi 6, Sesto Fiorentino 50019, Italy
- Department of Chemistry "Ugo Schiff", University of Florence, via della Lastruccia 3, Sesto Fiorentino 50019, Italy
| | - Fabien Ferrage
- Laboratoire des Biomolécules, LBM, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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Dai X, Xu F, Wang S, Mundra PA, Zheng J. PIKE-R2P: Protein-protein interaction network-based knowledge embedding with graph neural network for single-cell RNA to protein prediction. BMC Bioinformatics 2021; 22:139. [PMID: 34078261 PMCID: PMC8170782 DOI: 10.1186/s12859-021-04022-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/11/2021] [Indexed: 12/05/2022] Open
Abstract
Background Recent advances in simultaneous measurement of RNA and protein abundances at single-cell level provide a unique opportunity to predict protein abundance from scRNA-seq data using machine learning models. However, existing machine learning methods have not considered relationship among the proteins sufficiently. Results We formulate this task in a multi-label prediction framework where multiple proteins are linked to each other at the single-cell level. Then, we propose a novel method for single-cell RNA to protein prediction named PIKE-R2P, which incorporates protein–protein interactions (PPI) and prior knowledge embedding into a graph neural network. Compared with existing methods, PIKE-R2P could significantly improve prediction performance in terms of smaller errors and higher correlations with the gold standard measurements. Conclusion The superior performance of PIKE-R2P indicates that adding the prior knowledge of PPI to graph neural networks can be a powerful strategy for cross-modality prediction of protein abundances at the single-cell level.
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Affiliation(s)
- Xinnan Dai
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong District, Shanghai, 201210, China
| | - Fan Xu
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong District, Shanghai, 201210, China
| | - Shike Wang
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong District, Shanghai, 201210, China
| | - Piyushkumar A Mundra
- Molecular Oncology Group, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, Manchester, UK
| | - Jie Zheng
- School of Information Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Pudong District, Shanghai, 201210, China.
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Shannon AE, Boos CE, Hummon AB. Co-culturing multicellular tumor models: Modeling the tumor microenvironment and analysis techniques. Proteomics 2021; 21:e2000103. [PMID: 33569922 PMCID: PMC8262778 DOI: 10.1002/pmic.202000103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 12/19/2020] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Advances in two-dimensional (2D) and three-dimensional (3D) cell culture over the last 10 years have led to the development of a plethora of methods for cultivating tumor models. More recently, cellular co-cultures have become a suitable testbed. The first portion of this review focuses on co-culturing methods that have been developed in recent years utilizing the multicellular tumor spheroid model. The latter portion describes techniques that are used to analyze the proteomes of mono- or co-cultured tumor models, with a focus on mass spectrometry (MS)-based analyses. Protein profiles are important indicators of the tumor heterogeneity. Therefore, there is a specific focus within this review on analysis by MS and MS imaging methods evaluating the proteomic profiles of 2D and 3D co-cultures. While these models are incredibly important for biological research, so far, they have not been widely explored on the proteomic level. With this review, we aim to introduce these systems to an analytical audience, with the goal of highlighting MS as an underutilized tool for proteomic analysis of tumor models.
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Affiliation(s)
- Ariana E. Shannon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Claire E. Boos
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
| | - Amanda B. Hummon
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, USA
- The Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
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Tolani P, Gupta S, Yadav K, Aggarwal S, Yadav AK. Big data, integrative omics and network biology. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2021; 127:127-160. [PMID: 34340766 DOI: 10.1016/bs.apcsb.2021.03.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A cell integrates various signals through a network of biomolecules that crosstalk to synergistically regulate the replication, transcription, translation and other metabolic activities of a cell. These networks regulate signal perception and processing that drives biological functions. The biological complexity cannot be fully captured by a single -omics discipline. The holistic study of an organism-in health, perturbation, exposure to environment and disease, is studied under systems biology. The bottom-up molecular approaches (genes, mRNA, protein, metabolite, etc.) have laid the foundation of current biological knowledge covering the horizon from viruses, bacteria, fungi, plants and animals. Yet, these techniques provide a rather myopic view of biology at the molecular level. To understand how the interconnected molecular components are formed and rewired in disease or exposure to environmental stimuli is the holy grail of modern biology. The omics era was heralded by the genomics revolution but advanced sequencing techniques are now also ubiquitous in transcriptomics, proteomics, metabolomics and lipidomics. Multi-omics data analysis and integration techniques are driving the quest for deeper insights into how the different layers of biomolecules talk to each other in diverse contexts.
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Affiliation(s)
- Priya Tolani
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Srishti Gupta
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Kirti Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; Department of Pharmaceutical Biotechnology, Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Suruchi Aggarwal
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India; Department of Molecular Biology and Biotechnology, Cotton University, Guwahati, Assam, India
| | - Amit Kumar Yadav
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India.
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34
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Abidin SAZ, Othman I, Naidu R. Shotgun Proteomics and Mass Spectrometry as a Tool for Protein Identification and Profiling of Bio-Carrier-Based Therapeutics on Human Cancer Cells. Methods Mol Biol 2021; 2211:233-240. [PMID: 33336281 DOI: 10.1007/978-1-0716-0943-9_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Shotgun proteomics has been widely applied to study proteins in complex biological samples. Combination of high-performance liquid chromatography with mass spectrometry has allowed for comprehensive protein analysis with high resolution, sensitivity, and mass accuracy. Prior to mass spectrometry analysis, proteins are extracted from biological samples and subjected to in-solution trypsin digestion. The digested proteins are subjected for clean-up and injected into the liquid chromatography-mass spectrometry system for peptide mass identification. Protein identification is performed by analyzing the mass spectrometry data on a protein search engine software such as PEAKS studio loaded with protein database for the species of interest. Results such as protein score, protein coverage, number of peptides, and unique peptides identified will be obtained and can be used to determine proteins identified with high confidence. This method can be applied to understand the proteomic changes or profile brought by bio-carrier-based therapeutics in vitro. In this chapter, we describe methods in which proteins can be extracted for proteomic analysis using a shotgun approach. The chapter outlines important in vitro techniques and data analysis that can be applied to investigate the proteome dynamics.
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Affiliation(s)
- Syafiq Asnawi Zainal Abidin
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Iekhsan Othman
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia
| | - Rakesh Naidu
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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35
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Li H, Zhang Y, Zhang J, Zhao C, Zhu Y, Han M. A quantitative proteomics analysis for small molecule Stemazole's effect on human neural stem cells. Proteome Sci 2020; 18:12. [PMID: 33298084 PMCID: PMC7724819 DOI: 10.1186/s12953-020-00168-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/26/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Stemazole is a novel small molecule that has been suggested to have the ability to protect multiple stem cells. The proliferation-promoting activity and promising neuroprotective effects of stemazole make it a prospective drug for neurodegenerative disease treatment. METHODS Since previous studies have shown that it protective effect in extreme conditions, to understand more aspects of stemazole, in this study, a systematic tandem mass tags (TMT)-labelled proteomics approach was used to address the whole proteome expression profile with or without stemazole in normal conditions instead of extreme conditions. Bioinformatics analyses, including Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and protein-protein interaction (PPI) network analyses, were employed. RESULTS The effect of stemazole on the expression profiles of neural stem cells was obtained. A total of 408 proteins with changes at the abundance level of two groups were identified: 178 proteins increase in abundance and 240 proteins decrease in abundance, respectively. Low abundance of some mitochondrial respiratory chain enzyme, overproduction of reactive oxygen species (ROS) and reduction of mitochondrial membrane potential may indicate stemazole has cytotoxicity. CONCLUSIONS It is the first proteomics research about stemazole, and the possible cytotoxicity of stemazole has been reported for the first time. The information about proteins that were affected by stemazole and more characteristics of stemazole will help obtain a complete picture of this small molecule drug. These findings provide a scientific basis for further stemazole treatment research.
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Affiliation(s)
- Huajun Li
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yubo Zhang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Jing Zhang
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Chaoran Zhao
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Yizi Zhu
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China
| | - Mei Han
- Key Laboratory of Radiopharmaceuticals, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, China.
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Antibody Arrays: Barcode Technology. Methods Mol Biol 2020. [PMID: 33237411 DOI: 10.1007/978-1-0716-1064-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Antibody microarray is a fundamental, high-content technology for analyzing biomarkers with a multiplexity even at the proteomic level. Recent advancement in this field has driven the antibody array into a new territory related with single-cell analysis. Here we describe a flow pattern-based method for producing a high-density barcode antibody microarray for the detection of proteins in fluidic samples and in single cells. The antibody microarray is fabricated by a perpendicularly oriented flow patterning of single-stranded barcode DNAs, which are then converted into DNA-antibody conjugates. Compared to conventional microarrays, this barcode antibody microarray features a simple and high-throughput assay while achieving both high sensitivity and specificity. This barcode technology provides new clues for developing next-generation antibody microarrays and can be widely used in protein biomarker discovery, cell signaling network analysis, and disease diagnosis and prognosis.
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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38
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Pavelić SK, Markova-Car E, Klobučar M, Sappe L, Spaventi R. Technological Advances in Preclinical Drug Evaluation: The Role of -Omics Methods. Curr Med Chem 2020; 27:1337-1349. [PMID: 31296156 DOI: 10.2174/0929867326666190711122819] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
Preclinical drug development is an essential step in the drug development process where the evaluation of new chemical entities occurs. In particular, preclinical drug development phases include deep analysis of drug candidates' interactions with biomolecules/targets, their safety, toxicity, pharmacokinetics, metabolism by use of assays in vitro and in vivo animal assays. Legal aspects of the required procedures are well-established. Herein, we present a comprehensive summary of current state-of-the art approaches and techniques used in preclinical studies. In particular, we will review the potential of new, -omics methods and platforms for mechanistic evaluation of drug candidates and speed-up of the preclinical evaluation steps.
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Affiliation(s)
- Sandra Kraljević Pavelić
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Elitza Markova-Car
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Marko Klobučar
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia
| | - Lana Sappe
- Department of Biotechnology, Centre for High-Throughput Technologies, University of Rijeka, 51000 Rijeka, Croatia.,Novartis Oncology Region Europe Headquarter, Largo Umberto Boccioni 1, 21040 Origgio, Italia
| | - Radan Spaventi
- Triadelta Partners d.o.o., Međimurska 19/2, Zagreb, Croatia
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Li M, Meng X, Zheng R, Wu FX, Li Y, Pan Y, Wang J. Identification of Protein Complexes by Using a Spatial and Temporal Active Protein Interaction Network. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020; 17:817-827. [PMID: 28885159 DOI: 10.1109/tcbb.2017.2749571] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The rapid development of proteomics and high-throughput technologies has produced a large amount of Protein-Protein Interaction (PPI) data, which makes it possible for considering dynamic properties of protein interaction networks (PINs) instead of static properties. Identification of protein complexes from dynamic PINs becomes a vital scientific problem for understanding cellular life in the post genome era. Up to now, plenty of models or methods have been proposed for the construction of dynamic PINs to identify protein complexes. However, most of the constructed dynamic PINs just focus on the temporal dynamic information and thus overlook the spatial dynamic information of the complex biological systems. To address the limitation of the existing dynamic PIN analysis approaches, in this paper, we propose a new model-based scheme for the construction of the Spatial and Temporal Active Protein Interaction Network (ST-APIN) by integrating time-course gene expression data and subcellular location information. To evaluate the efficiency of ST-APIN, the commonly used classical clustering algorithm MCL is adopted to identify protein complexes from ST-APIN and the other three dynamic PINs, NF-APIN, DPIN, and TC-PIN. The experimental results show that, the performance of MCL on ST-APIN outperforms those on the other three dynamic PINs in terms of matching with known complexes, sensitivity, specificity, and f-measure. Furthermore, we evaluate the identified protein complexes by Gene Ontology (GO) function enrichment analysis. The validation shows that the identified protein complexes from ST-APIN are more biologically significant. This study provides a general paradigm for constructing the ST-APINs, which is essential for further understanding of molecular systems and the biomedical mechanism of complex diseases.
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Kim J. Systematic approach to characterize the dynamics of protein adsorption on the surface of biomaterials using proteomics. Colloids Surf B Biointerfaces 2020; 188:110756. [DOI: 10.1016/j.colsurfb.2019.110756] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/03/2019] [Accepted: 12/23/2019] [Indexed: 01/08/2023]
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41
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Sun Z, Li L, Qu J, Li H, Chen H. Proteomic analysis of therapeutic effects of Qingyi pellet on rodent severe acute pancreatitis-associated lung injury. Biomed Pharmacother 2019; 118:109300. [DOI: 10.1016/j.biopha.2019.109300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 07/25/2019] [Accepted: 07/31/2019] [Indexed: 12/13/2022] Open
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Lindoso RS, Kasai-Brunswick TH, Monnerat Cahli G, Collino F, Bastos Carvalho A, Campos de Carvalho AC, Vieyra A. Proteomics in the World of Induced Pluripotent Stem Cells. Cells 2019; 8:cells8070703. [PMID: 31336746 PMCID: PMC6678893 DOI: 10.3390/cells8070703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 02/05/2023] Open
Abstract
Omics approaches have significantly impacted knowledge about molecular signaling pathways driving cell function. Induced pluripotent stem cells (iPSC) have revolutionized the field of biological sciences and proteomics and, in particular, has been instrumental in identifying key elements operating during the maintenance of the pluripotent state and the differentiation process to the diverse cell types that form organisms. This review covers the evolution of conceptual and methodological strategies in proteomics; briefly describes the generation of iPSC from a historical perspective, the state-of-the-art of iPSC-based proteomics; and compares data on the proteome and transcriptome of iPSC to that of embryonic stem cells (ESC). Finally, proteomics of healthy and diseased cells and organoids differentiated from iPSC are analyzed.
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Affiliation(s)
- Rafael Soares Lindoso
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Tais H Kasai-Brunswick
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Gustavo Monnerat Cahli
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
- Laboratory of Proteomics, LADETEC, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro 21941-598, Brazil
| | - Federica Collino
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
- Department of Biomedical Sciences, University of Padova, 35131 Padua, Italy
| | - Adriana Bastos Carvalho
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil
| | - Antonio Carlos Campos de Carvalho
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil.
| | - Adalberto Vieyra
- Carlos Chagas Filho Institute of Biophysics and National Center for Structural Biology and Bioimaging/CENABIO, Federal University of Rio de Janeiro, Rio de Janeiro 21941-102, Brazil.
- Graduate Program in Translational Biomedicine, Grande Rio University, Duque de Caxias 25071-202, Brazil.
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Rinschen MM, Limbutara K, Knepper MA, Payne DM, Pisitkun T. From Molecules to Mechanisms: Functional Proteomics and Its Application to Renal Tubule Physiology. Physiol Rev 2019; 98:2571-2606. [PMID: 30182799 DOI: 10.1152/physrev.00057.2017] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Classical physiological studies using electrophysiological, biophysical, biochemical, and molecular techniques have created a detailed picture of molecular transport, bioenergetics, contractility and movement, and growth, as well as the regulation of these processes by external stimuli in cells and organisms. Newer systems biology approaches are beginning to provide deeper and broader understanding of these complex biological processes and their dynamic responses to a variety of environmental cues. In the past decade, advances in mass spectrometry-based proteomic technologies have provided invaluable tools to further elucidate these complex cellular processes, thereby confirming, complementing, and advancing common views of physiology. As one notable example, the application of proteomics to study the regulation of kidney function has yielded novel insights into the chemical and physical processes that tightly control body fluids, electrolytes, and metabolites to provide optimal microenvironments for various cellular and organ functions. Here, we systematically review, summarize, and discuss the most significant key findings from functional proteomic studies in renal epithelial physiology. We also identify further improvements in technological and bioinformatics methods that will be essential to advance precision medicine in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Kavee Limbutara
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Mark A Knepper
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - D Michael Payne
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
| | - Trairak Pisitkun
- Department II of Internal Medicine, University Hospital Cologne , Cologne , Germany ; Center for Molecular Medicine Cologne, University of Cologne , Cologne , Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases, University of Cologne , Cologne , Germany ; Division of Nephrology, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand ; Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland ; and Center of Excellence in Systems Biology, Research Affairs, Faculty of Medicine, Chulalongkorn University , Bangkok , Thailand
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Ma Q, Adua E, Boyce MC, Li X, Ji G, Wang W. IMass Time: The Future, in Future! ACTA ACUST UNITED AC 2018; 22:679-695. [DOI: 10.1089/omi.2018.0162] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Qingwei Ma
- Bioyong (Beijing) Technology Co., Ltd., Beijing, China
| | - Eric Adua
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Mary C. Boyce
- School of Science, Edith Cowan University, Joondalup, Australia
| | - Xingang Li
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Guang Ji
- China-Canada Centre of Research for Digestive Diseases, University of Ottawa, Ottawa, Canada
- Institute of Digestive Diseases, Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Wei Wang
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
- School of Public Health, Taishan Medical University, Taian, China
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45
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A gold nanocluster chemical tongue sensor array for Alzheimer's disease diagnosis. Colloids Surf B Biointerfaces 2018; 173:478-485. [PMID: 30326364 DOI: 10.1016/j.colsurfb.2018.10.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/05/2018] [Accepted: 10/09/2018] [Indexed: 01/10/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder in elderly people, and is associated with a heavy financial burden on our society. The use of serologic biomarkers is an attractive method to diagnose AD. Although the determination of blood-based biomarkers for AD has been explored in many studies, few practical diagnosis methods have been used in the clinic. In this work, we constructed a "chemical tongue" sensor array that is easy to use and based on four kinds of fluorescent gold nanoclusters (Au NCs) for discriminating between multiple proteins at nanomolar concentrations. The device utilizes a linear discrimination analysis based on fluorescence intensity response patterns. Using this chemical tongue sensor array, multiple proteins can be confidently identified even in complex biological systems, such as human urine. Most importantly, sera of AD patients could be effectively discriminated from those of osteoarthritis patients, or of healthy people. Also, the results obtained for the AD patients by the chemical tongue sensor array were validated by CSF determination. We conclude that the chemical tongue sensor array manufactured in this work paves the way for designing an auxiliary diagnosis method for AD that is less invasive and more convenient for the large-scale screening of patients.
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46
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Gel-based proteomics in disease research: Is it still valuable? BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:9-16. [PMID: 30392562 DOI: 10.1016/j.bbapap.2018.08.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 06/30/2018] [Accepted: 08/09/2018] [Indexed: 12/17/2022]
Abstract
Gel electrophoresis had been the primary method in proteomics. In the early era of proteomics, gel electrophoresis was a dominant technique of sample preparation for mass spectrometry analysis. Particularly, two-dimensional electrophoresis provided high-resolution proteome separation, and was regarded as the standard methodology for the separation of wide-range proteomes. However, gel electrophoresis turned downwards due to the progress of other separations including liquid chromatography and ionization techniques, resulting gel-free proteomics finally becoming dominant players at present. There are numerous advantages in gel-free approach in aspects of current trends of disease research. Interestingly, gel-free approaches are still advanced, it seems that gel electrophoresis will not be disappeared. The unique features of gel electrophoresis can be complementary for gel-free and it is suitable for the new wave of top-down functional proteomics.
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Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors. INTERNATIONAL JOURNAL OF MEDICINAL CHEMISTRY 2018; 2018:2906519. [PMID: 30112206 PMCID: PMC6077552 DOI: 10.1155/2018/2906519] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 06/25/2018] [Indexed: 12/12/2022]
Abstract
Carbonic anhydrases (CAs) are thought to be important for regulating pH in the tumor microenvironment. A few of the CA isoforms are upregulated in cancer cells, with only limited expression in normal cells. For these reasons, there is interest in developing inhibitors that target these tumor-associated CA isoforms, with increased efficacy but limited nonspecific cytotoxicity. Here we present some of the biophysical, biochemical, and cell based techniques and approaches that can be used to evaluate the potency of CA targeted inhibitors and decipher the role of CAs in tumorigenesis, cancer progression, and metastatic processes. These techniques include esterase activity assays, stop flow kinetics, and mass inlet mass spectroscopy (MIMS), all of which measure enzymatic activity of purified protein, in the presence or absence of inhibitors. Also discussed is the application of X-ray crystallography and Cryo-EM as well as other structure-based techniques and thermal shift assays to the studies of CA structure and function. Further, large-scale genomic and proteomic analytical methods, as well as cell based techniques like those that measure cell growth, apoptosis, clonogenicity, and cell migration and invasion, are discussed. We conclude by reviewing approaches that test the metastatic potential of CAs and how the aforementioned techniques have contributed to the field of CA cancer research.
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48
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Liu W, Ma L, Jeon B, Chen L, Chen B. A Network Hierarchy-Based method for functional module detection in protein-protein interaction networks. J Theor Biol 2018; 455:26-38. [PMID: 29981337 DOI: 10.1016/j.jtbi.2018.06.026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Revised: 06/27/2018] [Accepted: 06/29/2018] [Indexed: 02/02/2023]
Abstract
In the post-genomic era, one of the important tasks is to identify protein complexes and functional modules from high-throughput protein-protein interaction data, so that we can systematically analyze and understand the molecular functions and biological processes of cells. Although a lot of functional module detection studies have been proposed, how to design correctly and efficiently functional modules detection algorithms is still a challenging and important scientific problem in computational biology. In this paper, we present a novel Network Hierarchy-Based method to detect functional modules in PPI networks (named NHB-FMD). NHB-FMD first constructs the hierarchy tree corresponding to the PPI network and then encodes the tree such that genetic algorithm is employed to obtain the hierarchy tree with Maximum Likelihood. After that functional module partitioning is performed based on it and the best partitioning is selected as the result. Experimental results in the real PPI networks have shown that the proposed algorithm not only significantly outperforms the state-of-the-art methods but also can detect protein modules more effectively and accurately.
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Affiliation(s)
- Wei Liu
- College of Information Engineering of Yangzhou University, Yangzhou 225127, China; The Laboratory for Internfet of Things and Mobile Internet Technology of Jiangsu Province, Huaiyin Institute of Technology, Huaiyin 223002, China; School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, South Korea.
| | - Liangyu Ma
- College of Information Engineering of Yangzhou University, Yangzhou 225127, China
| | - Byeungwoo Jeon
- School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, South Korea
| | - Ling Chen
- College of Information Engineering of Yangzhou University, Yangzhou 225127, China
| | - Bolun Chen
- The Laboratory for Internfet of Things and Mobile Internet Technology of Jiangsu Province, Huaiyin Institute of Technology, Huaiyin 223002, China
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49
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Bashizadeh Fakhar H, Rezaie-Tavirani M, Zali H, Darkhaneh RF, Nejad EK, Aghazadeh MH. Proteomic Analysis of Low-Grade Serous Ovarian Cancer and Comparing It with Non-cancerous Ovarian. INDIAN JOURNAL OF GYNECOLOGIC ONCOLOGY 2018. [DOI: 10.1007/s40944-018-0187-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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50
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Target Identification Using Cell Permeable and Cleavable Chloroalkane Derivatized Small Molecules. Methods Mol Biol 2018; 1647:91-108. [PMID: 28808997 DOI: 10.1007/978-1-4939-7201-2_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
An important aspect for gaining functional insight into the activity of small molecules revealed through phenotypic screening is the identification of their interacting proteins. Yet, isolating and validating these interacting proteins remains difficult. Here, we present a new approach utilizing a chloroalkane (CA) moiety capture handle, which can be chemically attached to small molecules to isolate their respective protein targets. Derivatization of small molecules with the CA moiety has been shown to not significantly impact their cell permeability or potency, allowing for phenotypic validation of the derivatized small molecule prior to capture. The retention of cell permeability also allows for treatment of live cells with the derivatized small molecule and the CA moiety enables rapid covalent capture onto HaloTag coated magnetic beads. Additionally, several options are available for the elution of interacting proteins, including chemical cleavage of the CA moiety, competitive elution using excess unmodified small molecule, or sodium dodecyl sulfate (SDS) elution. These features taken together yield a highly robust and efficient process for target identification, including capture of weak or low abundance interactors.
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