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Oh Y, Kim K, Kim HJ, Hong SB, Lim CM, Koh Y, Ahn HS, Huh JW. Proteome signature for differential diagnosis of patients with bilateral lung infiltrates. ERJ Open Res 2025; 11:00762-2024. [PMID: 39963163 PMCID: PMC11831621 DOI: 10.1183/23120541.00762-2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Accepted: 08/05/2024] [Indexed: 02/20/2025] Open
Abstract
Background The differential diagnosis of bilateral lung infiltrates and prognosis prediction can be challenging for clinicians in the intensive care unit (ICU). We analysed the proteome from bronchoalveolar lavage fluid (BALF) and determined its usefulness for evaluating the infectious causes and mortality associated with bilateral lung infiltrates. Methods In the ICU cohort, 136 patients with bilateral infiltrate on chest radiographs were selected, and bronchoscopy with bronchoalveolar lavage (BAL) was performed. Proteomic profiling of the exosomes in the BALF (n=20) was conducted to identify candidate protein biomarkers potentially associated with infection or mortality. The BAL samples (n=116) were used to measure the candidate biomarker levels. Results The candidate biomarkers, CD20, CLIC4, SCFD1 and TAP1, were selected for the differential diagnosis of infection or mortality. The levels of CD20 were significantly elevated in patients with non-infectious causes, compared with those with infectious causes (248.6±154.5 versus 177.6±150.9 ng·mL-1, p=0.014). The levels of CLIC4, SCFD1 and TAP1 did not differ between the two groups. As per the receiver operating characteristic analysis, CD20 was a significant predictor of non-infectious causes (area under curve 0.668; 95% confidence interval 0.567-0.769; p=0.002; cut-off value 167.6 ng·mL-1; sensitivity 74.1%; specificity 63.2%). There were no significant differences in the concentrations of the biomarkers between survivors and non-survivors. Conclusions Our results suggest that CD20 levels in BALF might be a useful biomarker for differentiating non-infectious and infectious diseases in patients with bilateral lung infiltrates.
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Affiliation(s)
- Yumi Oh
- Department of Digital Medicine, BK21 project, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
- These authors contributed equally
| | - Kyunggon Kim
- Department of Digital Medicine, BK21 project, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Asan Institute for Life Sciences, Asan Medical Center, Seoul, Republic of Korea
- These authors contributed equally
| | - Ho Jeong Kim
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Sang-Bum Hong
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Chae-Man Lim
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Younsuck Koh
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Hee-Sung Ahn
- AMC science, Asan Medical Center, Seoul, Republic of Korea
| | - Jin Won Huh
- Department of Digital Medicine, BK21 project, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
- Department of Pulmonary and Critical Care Medicine, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
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2
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Han M, Niu H, Duan F, Wang Z, Zhang Z, Ren H. Research status and development trends of omics in neuroblastoma a bibliometric and visualization analysis. Front Oncol 2024; 14:1383805. [PMID: 39450262 PMCID: PMC11499224 DOI: 10.3389/fonc.2024.1383805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 09/16/2024] [Indexed: 10/26/2024] Open
Abstract
Background Neuroblastoma (NB), a prevalent extracranial solid tumor in children, stems from the neural crest. Omics technologies are extensively employed in NB, and We analyzed published articles on NB omics to understand the research trends and hot topics in NB omics. Method We collected all articles related to NB omics published from 2005 to 2023 from the Web of Science Core Collection database. Subsequently, we conducted analyses using VOSviewer, CiteSpace, Bibliometrix, and the Bibliometric online analysis platform (https://bibliometric.com/ ). Results We included a total of 514 articles in our analysis. The increasing number of publications in this field since 2020 indicates growing attention to NB omics, gradually entering a mature development stage. These articles span 50 countries and 1,000 institutions, involving 3,669 authors and 292 journals. The United States has the highest publication output and collaboration with other countries, with Germany being the most frequent collaborator. Capital Medical University and the German Cancer Research Center are the institutions with the highest publication count. The Journal of Proteome Research and the Journal of Biological Chemistry are the most prolific journal and most co-cited journal, respectively. Wang, W, and Maris, JM are the scholars with the highest publication count and co-citations in this field. "Neuroblastoma" and "Expression" are the most frequent keywords, while "classification," "Metabolism," "Cancer," and "Diagnosis" are recent key terms. The article titled "Neuroblastoma" by John M. Maris is the most cited reference in this analysis. Conclusion The continuous growth in NB omics research underscores its increasing significance in the scientific community. Omics technologies have facilitated the identification of potential biomarkers, advancements in personalized medicine, and the development of novel therapeutic strategies. Despite these advancements, the field faces significant challenges, including tumor heterogeneity, data standardization issues, and the translation of research findings into clinical practice.
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Affiliation(s)
| | - Huizhong Niu
- First Department of General Surgery, Hebei Children’s Hospital,
Shijiazhuang, Hebei, China
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3
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Porreca V, Barbagallo C, Corbella E, Peres M, Stella M, Mignogna G, Maras B, Ragusa M, Mancone C. Unveil Intrahepatic Cholangiocarcinoma Heterogeneity through the Lens of Omics and Multi-Omics Approaches. Cancers (Basel) 2024; 16:2889. [PMID: 39199659 PMCID: PMC11352949 DOI: 10.3390/cancers16162889] [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: 07/24/2024] [Revised: 08/12/2024] [Accepted: 08/16/2024] [Indexed: 09/01/2024] Open
Abstract
Intrahepatic cholangiocarcinoma (iCCA) is recognized worldwide as the second leading cause of morbidity and mortality among primary liver cancers, showing a continuously increasing incidence rate in recent years. iCCA aggressiveness is revealed through its rapid and silent intrahepatic expansion and spread through the lymphatic system leading to late diagnosis and poor prognoses. Multi-omics studies have aggregated information derived from single-omics data, providing a more comprehensive understanding of the phenomena being studied. These approaches are gradually becoming powerful tools for investigating the intricate pathobiology of iCCA, facilitating the correlation between molecular signature and phenotypic manifestation. Consequently, preliminary stratifications of iCCA patients have been proposed according to their "omics" features opening the possibility of identifying potential biomarkers for early diagnosis and developing new therapies based on personalized medicine (PM). The focus of this review is to provide new and advanced insight into the molecular pathobiology of the iCCA, starting from single- to the latest multi-omics approaches, paving the way for translating new basic research into therapeutic practices.
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Affiliation(s)
- Veronica Porreca
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (E.C.); (M.P.)
| | - Cristina Barbagallo
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.B.); (M.S.); (M.R.)
| | - Eleonora Corbella
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (E.C.); (M.P.)
| | - Marco Peres
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (E.C.); (M.P.)
| | - Michele Stella
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.B.); (M.S.); (M.R.)
| | - Giuseppina Mignogna
- Department of Biochemistry Science, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (B.M.)
| | - Bruno Maras
- Department of Biochemistry Science, Sapienza University of Rome, 00185 Rome, Italy; (G.M.); (B.M.)
| | - Marco Ragusa
- Section of Biology and Genetics, Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy; (C.B.); (M.S.); (M.R.)
| | - Carmine Mancone
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (E.C.); (M.P.)
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Peters-Clarke TM, Coon JJ, Riley NM. Instrumentation at the Leading Edge of Proteomics. Anal Chem 2024; 96:7976-8010. [PMID: 38738990 PMCID: PMC11996003 DOI: 10.1021/acs.analchem.3c04497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Affiliation(s)
- Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
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5
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Nagy C, Andrasi M, Szabo R, Gaspar A. CZE-MS peptide mapping: To desalt or not to desalt? Anal Chim Acta 2024; 1288:342162. [PMID: 38220294 DOI: 10.1016/j.aca.2023.342162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 12/10/2023] [Accepted: 12/16/2023] [Indexed: 01/16/2024]
Abstract
BACKGROUND In "shotgun" approaches involving high-performance liquid chromatography or capillary zone electrophoresis (CZE), matrix removal prior to sample analysis is considered as an indispensable tool. Despite the fact that CZE offers a high tolerance towards salts, most publications reported on the use of desalting. There seems to be no clear consensus on the utilization of desalting in the CZE-MS community, most probably due to the absence of works addressing the comparison of desalted and non-desalted digests. Our aim was to fill this research gap using protein samples of varying complexity in different sample matrices. RESULTS First, standard protein digests were analyzed to build the knowledge on the effect of sample clean-up by solid-phase extraction (SPE) pipette tips and the possible stacking phenomena induced by different sample matrices. Desalting led to a somewhat altered peptide profile, the procedure affected mostly the hydrophilic peptides (although not to a devastating extent). Nevertheless, desalting samples allowed remarkable stacking efficiency owing to their low-conductivity sample background, enabling a so-called field-amplified sample stacking phenomenon. Non-desalted samples also produced a stacking event, the mechanism of which is based on transient-isotachophoresis due to the presence of high-mobility ions in the digestion buffer itself. Adding either extra ammonium ions or acetonitrile into the non-desalted digests enhanced the stacking efficiency. A complex sample (yeast cell lysate) was also analyzed with the optimal conditions, which yielded similar tendencies. SIGNIFICANCE Based on these results, we propose that sample clean-up in the bottom-up sample preparation process prior to CZE-MS analysis can be omitted. The preclusion of desalting can even enhance detection sensitivity, separation efficiency or sequence coverage.
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Affiliation(s)
- Cynthia Nagy
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary
| | - Melinda Andrasi
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary
| | - Ruben Szabo
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary
| | - Attila Gaspar
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem ter 1, Debrecen, 4032, Hungary.
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6
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Kitata RB, Yang JC, Chen YJ. Advances in data-independent acquisition mass spectrometry towards comprehensive digital proteome landscape. MASS SPECTROMETRY REVIEWS 2023; 42:2324-2348. [PMID: 35645145 DOI: 10.1002/mas.21781] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 12/17/2021] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
The data-independent acquisition mass spectrometry (DIA-MS) has rapidly evolved as a powerful alternative for highly reproducible proteome profiling with a unique strength of generating permanent digital maps for retrospective analysis of biological systems. Recent advancements in data analysis software tools for the complex DIA-MS/MS spectra coupled to fast MS scanning speed and high mass accuracy have greatly expanded the sensitivity and coverage of DIA-based proteomics profiling. Here, we review the evolution of the DIA-MS techniques, from earlier proof-of-principle of parallel fragmentation of all-ions or ions in selected m/z range, the sequential window acquisition of all theoretical mass spectra (SWATH-MS) to latest innovations, recent development in computation algorithms for data informatics, and auxiliary tools and advanced instrumentation to enhance the performance of DIA-MS. We further summarize recent applications of DIA-MS and experimentally-derived as well as in silico spectra library resources for large-scale profiling to facilitate biomarker discovery and drug development in human diseases with emphasis on the proteomic profiling coverage. Toward next-generation DIA-MS for clinical proteomics, we outline the challenges in processing multi-dimensional DIA data set and large-scale clinical proteomics, and continuing need in higher profiling coverage and sensitivity.
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Affiliation(s)
| | - Jhih-Ci Yang
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Applied Chemistry, National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan
- Sustainable Chemical Science and Technology, Taiwan International Graduate Program, Academia Sinica and National Yang Ming Chiao Tung University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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7
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Wang C, Xu S, Sun D, Liu ZP. ActivePPI: quantifying protein-protein interaction network activity with Markov random fields. Bioinformatics 2023; 39:btad567. [PMID: 37698984 PMCID: PMC10516639 DOI: 10.1093/bioinformatics/btad567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/11/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023] Open
Abstract
MOTIVATION Protein-protein interactions (PPI) are crucial components of the biomolecular networks that enable cells to function. Biological experiments have identified a large number of PPI, and these interactions are stored in knowledge bases. However, these interactions are often restricted to specific cellular environments and conditions. Network activity can be characterized as the extent of agreement between a PPI network (PPIN) and a distinct cellular environment measured by protein mass spectrometry, and it can also be quantified as a statistical significance score. Without knowing the activity of these PPI in the cellular environments or specific phenotypes, it is impossible to reveal how these PPI perform and affect cellular functioning. RESULTS To calculate the activity of PPIN in different cellular conditions, we proposed a PPIN activity evaluation framework named ActivePPI to measure the consistency between network architecture and protein measurement data. ActivePPI estimates the probability density of protein mass spectrometry abundance and models PPIN using a Markov-random-field-based method. Furthermore, empirical P-value is derived based on a nonparametric permutation test to quantify the likelihood significance of the match between PPIN structure and protein abundance data. Extensive numerical experiments demonstrate the superior performance of ActivePPI and result in network activity evaluation, pathway activity assessment, and optimal network architecture tuning tasks. To summarize it succinctly, ActivePPI is a versatile tool for evaluating PPI network that can uncover the functional significance of protein interactions in crucial cellular biological processes and offer further insights into physiological phenomena. AVAILABILITY AND IMPLEMENTATION All source code and data are freely available at https://github.com/zpliulab/ActivePPI.
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Affiliation(s)
- Chuanyuan Wang
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Shiyu Xu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
| | - Duanchen Sun
- School of Mathematics, Shandong University, Jinan, Shandong 250100, China
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China
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8
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Xu Y, Cao Z, Chen T, Ren J. Trends in metabolic dysfunction in polycystic ovary syndrome: a bibliometric analysis. Front Endocrinol (Lausanne) 2023; 14:1245719. [PMID: 37701893 PMCID: PMC10494444 DOI: 10.3389/fendo.2023.1245719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023] Open
Abstract
Polycystic ovary syndrome (PCOS) is a very common chronic disease and causes reproductive disorders in women of childbearing age worldwide. The cause of metabolic dysfunction in PCOS is unknown, and there is a lack of systematic bibliometric analysis for this disease. This study included 3,972 articles on metabolic dysfunction in PCOS published from 2012 to 2021. We applied the VOSviewer and the CiteSpace scientometric analysis software to analyze the data regarding the publication of the articles, countries, authors, institutions, scientific categories, cited journals, and keywords. Through this analysis, we determined the research efforts and their developing trends and anticipated the progress in understanding PCOS-related metabolic dysfunction.
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Affiliation(s)
- Yan Xu
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zhiqun Cao
- The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ting Chen
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Jian Ren
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
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9
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Kohler D, Staniak M, Tsai TH, Huang T, Shulman N, Bernhardt OM, MacLean BX, Nesvizhskii AI, Reiter L, Sabido E, Choi M, Vitek O. MSstats Version 4.0: Statistical Analyses of Quantitative Mass Spectrometry-Based Proteomic Experiments with Chromatography-Based Quantification at Scale. J Proteome Res 2023; 22:1466-1482. [PMID: 37018319 PMCID: PMC10629259 DOI: 10.1021/acs.jproteome.2c00834] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Indexed: 04/06/2023]
Abstract
The MSstats R-Bioconductor family of packages is widely used for statistical analyses of quantitative bottom-up mass spectrometry-based proteomic experiments to detect differentially abundant proteins. It is applicable to a variety of experimental designs and data acquisition strategies and is compatible with many data processing tools used to identify and quantify spectral features. In the face of ever-increasing complexities of experiments and data processing strategies, the core package of the family, with the same name MSstats, has undergone a series of substantial updates. Its new version MSstats v4.0 improves the usability, versatility, and accuracy of statistical methodology, and the usage of computational resources. New converters integrate the output of upstream processing tools directly with MSstats, requiring less manual work by the user. The package's statistical models have been updated to a more robust workflow. Finally, MSstats' code has been substantially refactored to improve memory use and computation speed. Here we detail these updates, highlighting methodological differences between the new and old versions. An empirical comparison of MSstats v4.0 to its previous implementations, as well as to the packages MSqRob and DEqMS, on controlled mixtures and biological experiments demonstrated a stronger performance and better usability of MSstats v4.0 as compared to existing methods.
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Affiliation(s)
- Devon Kohler
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | | | - Tsung-Heng Tsai
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Ting Huang
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Nicholas Shulman
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | | | - Brendan X. MacLean
- Department
of Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Alexey I. Nesvizhskii
- Department
of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - Eduard Sabido
- Center for
Genomic Regulation, Barcelona Institute
of Science and Technology, Barcelona 08003, Spain
- Universitat
Pompeu Fabra, Barcelona 08002, Spain
| | - Meena Choi
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
| | - Olga Vitek
- Khoury College
of Computer Science, Northeastern University, Boston, Massachusetts 02115, United States
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10
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Zhang H, Ni Y, Ji H, Liu H, Liu S. Research trends of omics in ulcerative colitis: A bibliometric analysis. Front Med (Lausanne) 2023; 10:1115240. [PMID: 37051213 PMCID: PMC10083299 DOI: 10.3389/fmed.2023.1115240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 02/20/2023] [Indexed: 03/28/2023] Open
Abstract
BackgroundOmics has emerged as a promising biological science to shed light on the etiology, pathogenesis, and treatment of ulcerative colitis (UC). At present, although research on the omics of UC has drawn global attention, there is still a lack of bibliometric analysis in this field. This study aimed to access the trends and hotspots of omics in UC research.MethodPublications related to omics in UC from 1 January 2000 to 15 October 2022 were retrieved from the Web of Science Core Collection database. VOSviewer, CiteSpace, and the online bibliometric analysis platform “Bibliometrix” were adopted to extract and visualize information.ResultsA total of 385 publications were finally included and the annual number of publications fluctuated. The trend in publications increased rapidly after 2019. The United States showed its dominant position in several publications, total citations, and international collaborations. The top five research organizations for publications on the research of omics in UC were Harvard Medical School, the Icahn School of Medicine at Mount Sinai, Karolinska Institutet, the Brigham and Women's Hospital, and the Massachusetts General Hospital. Ashwin Ananthakrishnan from the Massachusetts General Hospital was the most productive author, and Séverine Vermeire from the Catholic University of Leuven was co-cited most often. Inflammatory bowel disease was the most popular and co-cited journal in this field. The reference with citation bursts and trend topics showed that “ulcerative colitis,” “inflammatory bowel disease,” “microbiome,” “transcriptomics,” “genomics,” “metabolomics,” “proteomics,” “dysbiosis,” “biomarkers,” “loci,” and “therapy” are currently research hotspots.ConclusionOur study presents several important insights into the research trends and developments in the field of omics in UC, which will provide key information for further research.
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Affiliation(s)
- He Zhang
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Yuanyuan Ni
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hangyu Ji
- Office of Good Clinical Practice, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Hongliang Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
| | - Shaoneng Liu
- Department of Gastroenterology, Guang' anmen Hospital, China Academy of Traditional Chinese Medical Sciences, Beijing, China
- *Correspondence: Shaoneng Liu
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11
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Xu L, Zhang XM, Wen YQ, Zhao JL, Xu TC, Yong L, Lin H, Zhang HW, Li ZX. Comparison of tropomyosin released peptide and epitope mapping after in vitro digestion from fish (Larimichthys crocea), shrimp (Litopenaeus vannamei) and clam (Ruditapes philippinarum) through SWATH-MS based proteomics. Food Chem 2023; 403:134314. [DOI: 10.1016/j.foodchem.2022.134314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022]
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Mehta D, Ahkami AH, Walley J, Xu SL, Uhrig RG. The incongruity of validating quantitative proteomics using western blots. NATURE PLANTS 2022; 8:1320-1321. [PMID: 36456804 DOI: 10.1038/s41477-022-01314-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Affiliation(s)
- Devang Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
- Department of Biosystems, KU Leuven, Leuven, Belgium.
- Plant Cell Atlas Proteomics Committee, Stanford, CA, USA.
| | - Amir H Ahkami
- Plant Cell Atlas Proteomics Committee, Stanford, CA, USA
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratories, Richland, WA, USA
- School of Biological Science (SBS), Washington State University (WSU), Pullman, WA, USA
| | - Justin Walley
- Plant Cell Atlas Proteomics Committee, Stanford, CA, USA
- Iowa State University, Ames, IA, USA
| | - Shou-Ling Xu
- Plant Cell Atlas Proteomics Committee, Stanford, CA, USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - R Glen Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
- Plant Cell Atlas Proteomics Committee, Stanford, CA, USA.
- Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada.
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Recent Advances in Proteomics-Based Approaches to Studying Age-Related Macular Degeneration: A Systematic Review. Int J Mol Sci 2022; 23:ijms232314759. [PMID: 36499086 PMCID: PMC9735888 DOI: 10.3390/ijms232314759] [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: 10/06/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
Age-related macular degeneration (AMD) is a common ocular disease characterized by degeneration of the central area of the retina in the elderly population. Progression and response to treatment are influenced by genetic and non-genetic factors. Proteomics is a powerful tool to study, at the molecular level, the mechanisms underlying the progression of the disease, to identify new therapeutic targets and to establish biomarkers to monitor progression and treatment effectiveness. In this work, we systematically review the use of proteomics-based approaches for the study of the molecular mechanisms underlying the development of AMD, as well as the progression of the disease and on-treatment patient monitoring. The Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) reporting guidelines were followed. Proteomic approaches have identified key players in the onset of the disease, such as complement components and proteins involved in lipid metabolism and oxidative stress, but also in the progression to advanced stages, including factors related to extracellular matrix integrity and angiogenesis. Although anti-vascular endothelial growth factor (anti-VEGF)-based therapy has been crucial in the treatment of neovascular AMD, it is necessary to deepen our understanding of the underlying disease mechanisms to move forward to next-generation therapies for later-stage forms of this multifactorial disease.
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14
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Hao Y, Lu L, Liu A, Lin X, Xiao L, Kong X, Li K, Liang F, Xiong J, Qu L, Li Y, Li J. Integrating bioinformatic strategies in spatial life science research. Brief Bioinform 2022; 23:bbac415. [PMID: 36198665 PMCID: PMC9677476 DOI: 10.1093/bib/bbac415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/15/2022] [Accepted: 08/27/2022] [Indexed: 12/14/2022] Open
Abstract
As space exploration programs progress, manned space missions will become more frequent and farther away from Earth, putting a greater emphasis on astronaut health. Through the collaborative efforts of researchers from various countries, the effect of the space environment factors on living systems is gradually being uncovered. Although a large number of interconnected research findings have been produced, their connection seems to be confused, and many unknown effects are left to be discovered. Simultaneously, several valuable data resources have emerged, accumulating data measuring biological effects in space that can be used to further investigate the unknown biological adaptations. In this review, the previous findings and their correlations are sorted out to facilitate the understanding of biological adaptations to space and the design of countermeasures. The biological effect measurement methods/data types are also organized to provide references for experimental design and data analysis. To aid deeper exploration of the data resources, we summarized common characteristics of the data generated from longitudinal experiments, outlined challenges or caveats in data analysis and provided corresponding solutions by recommending bioinformatics strategies and available models/tools.
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Affiliation(s)
- Yangyang Hao
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Liang Lu
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Anna Liu
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Xue Lin
- Department of Bioinformatics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Nanjing, China
| | - Li Xiao
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Xiaoyue Kong
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Kai Li
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Fengji Liang
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Jianghui Xiong
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Lina Qu
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Yinghui Li
- The State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, No. 26 Beiqing Road, Haidian District, Beijing, 100094, China
| | - Jian Li
- Key Laboratory of DGHD, MOE, School of Life Science and Technology, Southeast University, Nanjing, China
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15
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Kar FM, Vogel C, Hochwagen A. Meiotic DNA breaks activate a streamlined phospho-signaling response that largely avoids protein-level changes. Life Sci Alliance 2022; 5:e202201454. [PMID: 36271494 PMCID: PMC9438802 DOI: 10.26508/lsa.202201454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/24/2022] Open
Abstract
Meiotic cells introduce a numerous programmed DNA breaks into their genome to stimulate meiotic recombination and ensure controlled chromosome inheritance and fertility. A checkpoint network involving key kinases and phosphatases coordinates the repair of these DNA breaks, but the precise phosphorylation targets remain poorly understood. It is also unknown whether meiotic DNA breaks change gene expression akin to the canonical DNA-damage response. To address these questions, we analyzed the meiotic DNA break response in Saccharomyces cerevisiae using multiple systems-level approaches. We identified 332 DNA break-dependent phosphorylation sites, vastly expanding the number of known events during meiotic prophase. Less than half of these events occurred in recognition motifs for the known meiotic checkpoint kinases Mec1 (ATR), Tel1 (ATM), and Mek1 (CHK2), suggesting that additional kinases contribute to the meiotic DNA-break response. We detected a clear transcriptional program but detected only very few changes in protein levels. We attribute this dichotomy to a decrease in transcript levels after meiotic entry that dampens the effects of break-induced transcription sufficiently to cause only minimal changes in the meiotic proteome.
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Affiliation(s)
- Funda M Kar
- Department of Biology, New York University, New York City, NY, USA
| | - Christine Vogel
- Department of Biology, New York University, New York City, NY, USA
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16
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Wang Z, Sun Y, Bian L, Zhang Y, Zhang Y, Wang C, Tian J, Lu T. The crosstalk signals of Sodium Tanshinone ⅡA Sulfonate in rats with cerebral ischemic stroke: Insights from proteomics. Biomed Pharmacother 2022; 151:113059. [PMID: 35561426 DOI: 10.1016/j.biopha.2022.113059] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/06/2022] [Accepted: 04/26/2022] [Indexed: 11/02/2022] Open
Abstract
BACKGROUND Stroke could cause long-term disability, even mortality around the world. Recently, Sodium tanshinone IIA sulfonate (STS), identified from Salvia miltiorrhiza Bunge and was found to have unique efficiency in clinical practice as a potential therapeutic agent for ischemic cerebral infarction. However, systematic investigation about the biological mechanism is still lacking. Herein, we utilized high-throughput proteomics approach to identify the underlying targets for the treatment of STS in stroke. METHODS We investigated the effect of STS on stroke outcomes on rat model of the Middle Cerebral Artery Occlusion and Reperfusion (MCAO/R), assessing by Z-Longa score, infarct volume and HE staining. Pharmacoproteomic profiling of ischemic penumbra in cortical (IPC) was performed using DIA-based label-free liquid chromatography-tandem mass spectrometry (LC-MS/MS) technique. Bioinformatics analysis was processed for further investigation. The expression of core proteins was semi-quantified by DIA, and the major protein correlating with stroke was examined using parallel reaction monitoring (PRM). RESULTS Rats in the MCAO/R group showed neurological function deterioration, which was improved by STS. There were 423 differentially expressed proteins (DEPs) in IPC being detected and quantified in both the sham group and the MCAO/R group. Meanwhile, 285 proteins were significantly changed in the STS treated group, compared to the MCAO/R model. Protein-protein interaction (PPI) network, pathway and biological function enrichment were processed for the DEPs across each two groups, the results of which were integrated for analysis. Alb, mTOR, Dync1h1, Stxbp1, Cltc, and Sptan1 were contained as the core proteins. Altered molecules were discovered to be enriched in 18 signal pathways such as phosphatidylinositol signaling system, PI3K/AKT signal pathway and HIF-1 signal pathway. The results also showed the correlation with sleep disturbances and depression post-stroke. CONCLUSIONS We concluded that STS could prevent penumbra from progressively ongoing damage and improve neurological deficits in MCAO/R model rats. The intersected pathways and protein networks predicted by proteomics might provide much more detailed information for the therapeutic mechanisms of STS in the treatment of CIS.
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Affiliation(s)
- Zheyi Wang
- Qilu Hospital, Shandong University, Jinan, Shandong 250012, China; Beijing University of Chinese Medicine, Beijing 100029, China; School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China; Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China
| | - Yize Sun
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Lihua Bian
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejing 32500, China
| | - Yiling Zhang
- Xiamen Municipal Health Commission, Xiamen, Fujian 361000, China
| | - Yue Zhang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China
| | - Chunguo Wang
- Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jinzhou Tian
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100010, China
| | - Tao Lu
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100026, China.
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17
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Walzer M, García-Seisdedos D, Prakash A, Brack P, Crowther P, Graham RL, George N, Mohammed S, Moreno P, Papatheodorou I, Hubbard SJ, Vizcaíno JA. Implementing the reuse of public DIA proteomics datasets: from the PRIDE database to Expression Atlas. Sci Data 2022; 9:335. [PMID: 35701420 PMCID: PMC9197839 DOI: 10.1038/s41597-022-01380-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 05/12/2022] [Indexed: 11/14/2022] Open
Abstract
The number of mass spectrometry (MS)-based proteomics datasets in the public domain keeps increasing, particularly those generated by Data Independent Acquisition (DIA) approaches such as SWATH-MS. Unlike Data Dependent Acquisition datasets, the re-use of DIA datasets has been rather limited to date, despite its high potential, due to the technical challenges involved. We introduce a (re-)analysis pipeline for public SWATH-MS datasets which includes a combination of metadata annotation protocols, automated workflows for MS data analysis, statistical analysis, and the integration of the results into the Expression Atlas resource. Automation is orchestrated with Nextflow, using containerised open analysis software tools, rendering the pipeline readily available and reproducible. To demonstrate its utility, we reanalysed 10 public DIA datasets from the PRIDE database, comprising 1,278 SWATH-MS runs. The robustness of the analysis was evaluated, and the results compared to those obtained in the original publications. The final expression values were integrated into Expression Atlas, making SWATH-MS experiments more widely available and combining them with expression data originating from other proteomics and transcriptomics datasets.
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Affiliation(s)
- Mathias Walzer
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom.
| | - David García-Seisdedos
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Ananth Prakash
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Paul Brack
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Peter Crowther
- Melandra Limited, 16 Brook Road, Urmston, Manchester, M41 5RY, United Kingdom
| | - Robert L Graham
- School of Biological Sciences, Chlorine Gardens, Queen's University Belfast, Belfast, BT9 5DL, United Kingdom
| | - Nancy George
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Suhaib Mohammed
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Pablo Moreno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Irene Papatheodorou
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom
| | - Simon J Hubbard
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester, M13 9PT, United Kingdom
| | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, CB10 1SD, United Kingdom.
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18
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Grossbach J, Gillet L, Clément‐Ziza M, Schmalohr CL, Schubert OT, Schütter M, Mawer JSP, Barnes CA, Bludau I, Weith M, Tessarz P, Graef M, Aebersold R, Beyer A. The impact of genomic variation on protein phosphorylation states and regulatory networks. Mol Syst Biol 2022; 18:e10712. [PMID: 35574625 PMCID: PMC9109056 DOI: 10.15252/msb.202110712] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/11/2022] Open
Abstract
Genomic variation impacts on cellular networks by affecting the abundance (e.g., protein levels) and the functional states (e.g., protein phosphorylation) of their components. Previous work has focused on the former, while in this context, the functional states of proteins have largely remained neglected. Here, we generated high-quality transcriptome, proteome, and phosphoproteome data for a panel of 112 genomically well-defined yeast strains. Genetic effects on transcripts were generally transmitted to the protein layer, but specific gene groups, such as ribosomal proteins, showed diverging effects on protein levels compared with RNA levels. Phosphorylation states proved crucial to unravel genetic effects on signaling networks. Correspondingly, genetic variants that cause phosphorylation changes were mostly different from those causing abundance changes in the respective proteins. Underscoring their relevance for cell physiology, phosphorylation traits were more strongly correlated with cell physiological traits such as chemical compound resistance or cell morphology, compared with transcript or protein abundance. This study demonstrates how molecular networks mediate the effects of genomic variants to cellular traits and highlights the particular importance of protein phosphorylation.
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Affiliation(s)
- Jan Grossbach
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | - Ludovic Gillet
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
| | - Mathieu Clément‐Ziza
- Center for Molecular Medicine Cologne (CMMC)Medical Faculty, University of CologneCologneGermany
- Lesaffre InternationalMarcq‐en‐BarœulFrance
| | - Corinna L Schmalohr
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | - Olga T Schubert
- Department of Human GeneticsUniversity of California, Los AngelesLos AngelesCAUSA
| | | | | | | | - Isabell Bludau
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Department of Proteomics and Signal TransductionMax Planck Institute of BiochemistryMartinsriedGermany
| | - Matthias Weith
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
| | - Peter Tessarz
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Martin Graef
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
- Max Planck Institute for Biology of AgeingCologneGermany
| | - Ruedi Aebersold
- Department of BiologyInstitute of Molecular Systems BiologyETH ZurichZurichSwitzerland
- Faculty of ScienceUniversity of ZurichZurichSwitzerland
| | - Andreas Beyer
- Excellence Cluster on Cellular Stress Responses in Aging Associated DiseasesUniversity of CologneCologneGermany
- Center for Molecular Medicine Cologne (CMMC)Medical Faculty, University of CologneCologneGermany
- Institute for GeneticsFaculty of Mathematics and Natural SciencesUniversity of CologneCologneGermany
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19
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Li Y, Liu S, Shawky E, Tao M, Liu A, Sulaiman K, Tian J, Zhu W. SWATH-based quantitative proteomic analysis of Morus alba L. leaves after exposure to ultraviolet-B radiation and incubation in the dark. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2022; 230:112443. [PMID: 35429828 DOI: 10.1016/j.jphotobiol.2022.112443] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 02/23/2022] [Accepted: 04/05/2022] [Indexed: 12/11/2022]
Abstract
Morus alba is a woody shrub of the family Moraceae and used as traditional Chinese medicine for a long history. Ultraviolet-B (UV-B) radiation, as a kind of abiotic stress factor, affected the growth and secondary metabolism in M. alba. Previous studies indicated that the contents of several secondary metabolites such as moracin N, chalcomaricin were significantly increased under high level UV-B radiation and dark incubation in M. alba leaves. To reveal the response mechanism under UV-B radiation and dark incubation in M. alba leaves, SWATH-based quantitative proteomic analysis was performed. Totally, 716 proteins were identified and quantified in the control, UVB, and UVD groups. Among them, 123 proteins and 96 proteins were identified as differentially abundant proteins in UVB group and UVD groups, respectively. Proteins related to photosynthesis, amino acid biosynthesis, and tocopherol biosynthesis were significantly altered in UVB group, while proteins related to the biosynthesis of phenolic compounds were significantly altered in UVD group. In addition, the abundances of proteins involved in the ubiquitin-proteasome system (UPS) were significantly increased in both UVB and UVD groups, indicating that UPS combined with secondary mechanism participated in the resistance to UV-B radiation and dark incubation. The obtained results provide novel insight into the effects of high level UV-B radiation on M. alba leaves and on the strategies used for maximizing the chemical constituents and the medicinal value of the M. alba leaves.
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Affiliation(s)
- Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China; The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Eman Shawky
- Department of Pharmacognosy, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou 310027, China
| | - Kaisa Sulaiman
- The Xinjiang Uygur Autonomous Region National Institute of Traditional Chinese Medicine, Urumchi 830092, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310002, China.
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20
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Oliver SG. From Petri Plates to Petri Nets, a revolution in yeast biology. FEMS Yeast Res 2022; 22:foac008. [PMID: 35142857 PMCID: PMC8862034 DOI: 10.1093/femsyr/foac008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 01/26/2022] [Accepted: 02/07/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, United Kingdom
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21
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Zhu Y, Bian JF, Lu DQ, To CH, Lam CSY, Li KK, Yu FJ, Gong BT, Wang Q, Ji XW, Zhang HM, Nian H, Lam TC, Wei RH. Alteration of EIF2 Signaling, Glycolysis, and Dopamine Secretion in Form-Deprived Myopia in Response to 1% Atropine Treatment: Evidence From Interactive iTRAQ-MS and SWATH-MS Proteomics Using a Guinea Pig Model. Front Pharmacol 2022; 13:814814. [PMID: 35153787 PMCID: PMC8832150 DOI: 10.3389/fphar.2022.814814] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
Purpose: Atropine, a non-selective muscarinic antagonist, effectively slows down myopia progression in human adolescents and several animal models. However, the underlying molecular mechanism is unclear. The current study investigated retinal protein changes of form-deprived myopic (FDM) guinea pigs in response to topical administration of 1% atropine gel (10 g/L). Methods: At the first stage, the differentially expressed proteins were screened using fractionated isobaric tags for a relative and absolute quantification (iTRAQ) approach, coupled with nano-liquid chromatography-tandem mass spectrometry (nano-LC-MS/MS) (n = 24, 48 eyes) using a sample pooling technique. At the second stage, retinal tissues from another cohort with the same treatment (n = 12, 24 eyes) with significant ocular changes were subjected to label-free sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics for orthogonal protein target confirmation. The localization of Alpha-synuclein was verified using immunohistochemistry and confocal imaging. Results: A total of 1,695 proteins (8,875 peptides) were identified with 479 regulated proteins (FC ≥ 1.5 or ≤0.67) found from FDM eyes and atropine-treated eyes receiving 4-weeks drug treatment using iTRAQ-MS proteomics. Combining the iTRAQ-MS and SWATH-MS datasets, a total of 29 confident proteins at 1% FDR were consistently quantified and matched, comprising 12 up-regulated and 17 down-regulated proteins which differed between FDM eyes and atropine treated eyes (iTRAQ: FC ≥ 1.5 or ≤0.67, SWATH: FC ≥ 1.4 or ≤0.71, p-value of ≤0.05). Bioinformatics analysis using IPA and STRING databases of these commonly regulated proteins revealed the involvement of the three commonly significant pathways: EIF2 signaling; glycolysis; and dopamine secretion. Additionally, the most significantly regulated proteins were closely connected to Alpha-synuclein (SNCA). Using immunostaining (n = 3), SNCA was further confirmed in the inner margin of the inner nuclear layer (INL) and spread throughout the inner plexiform layer (IPL) of the retina of guinea pigs. Conclusion: The molecular evidence using next-generation proteomics (NGP) revealed that retinal EIF2 signaling, glycolysis, and dopamine secretion through SNCA are implicated in atropine treatment of myopia in the FDM-induced guinea pig model.
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Affiliation(s)
- Ying Zhu
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Jing Fang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Da Qian Lu
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Chi Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - King Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Feng Juan Yu
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
| | - Bo Teng Gong
- Department of Ophthalmology, Tianjin Medical University General Hospital, Tianjin, China
| | - Qiong Wang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Xiao Wen Ji
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Mei Zhang
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Hong Nian
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
- Centre for Eye and Vision Research (CEVR), Hong Kong SAR, China
- Research Centre for SHARP Vision (RCSV), The Hong Kong Polytechnic University, Hong Kong SAR, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen, China
- *Correspondence: Rui Hua Wei, ; Thomas Chuen Lam,
| | - Rui Hua Wei
- Tianjin Key Laboratory of Retinal Functions and Diseases, Tianjin Branch of National Clinical Research Center for Ocular Disease, Eye Institute and School of Optometry, Tianjin Medical University Eye Hospital, Tianjin, China
- *Correspondence: Rui Hua Wei, ; Thomas Chuen Lam,
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22
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Marsh AN, Sharma V, Mani SK, Vitek O, MacCoss MJ, MacLean BX. Skyline Batch: An Intuitive User Interface for Batch Processing with Skyline. J Proteome Res 2021; 21:289-294. [PMID: 34919405 PMCID: PMC8749956 DOI: 10.1021/acs.jproteome.1c00749] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Skyline Batch is
a newly developed Windows forms application that
enables the easy and consistent reprocessing of data with Skyline.
Skyline has made previous advances in this direction; however, none
enable seamless automated reprocessing of local and remote files.
Skyline keeps a log of all of the steps that were taken in the document;
however, reproducing these steps takes time and allows room for human
error. Skyline also has a command-line interface, enabling it to be
run from a batch script, but using the program in this way requires
expertise in editing these scripts. By formalizing the workflow of
a highly used set of batch scripts into an intuitive and powerful
user interface, Skyline Batch can reprocess data stored in remote
repositories just by opening and running a Skyline Batch configuration
file. When run, a Skyline Batch configuration downloads all necessary
remote files and then runs a four-step Skyline workflow. By condensing
the steps needed to reprocess the data into one file, Skyline Batch
gives researchers the opportunity to publish their processing along
with their data and other analysis files. These easily run configuration
files will greatly increase the transparency and reproducibility of
published work. Skyline Batch is freely available at https://skyline.ms/batch.url.
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Affiliation(s)
- Alexandra N Marsh
- Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Vagisha Sharma
- Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Surya K Mani
- Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts 02115, United States
| | - Michael J MacCoss
- Genome Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Brendan X MacLean
- Genome Sciences, University of Washington, Seattle, Washington 98195, United States
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23
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Che YQ, Zhang Y, Li HB, Shen D, Cui W. Serum KLKB1 as a Potential Prognostic Biomarker for Hepatocellular Carcinoma Based on Data-Independent Acquisition and Parallel Reaction Monitoring. J Hepatocell Carcinoma 2021; 8:1241-1252. [PMID: 34676182 PMCID: PMC8520450 DOI: 10.2147/jhc.s325629] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/08/2021] [Indexed: 12/12/2022] Open
Abstract
Purpose With the advancement of minimally invasive surgery and catheters for hepatocellular carcinoma (HCC), it is becoming more and more inconvenient to get tissues or the tissues gained are insufficient for testing. Screening of blood-derived markers is of great significance for prognosis assessment. Patients and Methods Data-independent acquisition (DIA) and parallel reaction monitoring (PRM) were implemented to identify valuable prognostic HCC biomarkers in 48 patients with different prognosis. The potential candidate biomarkers were examined in 205 HCC patients using enzyme-linked immunosorbent assay (ELISA) and then validated in The Cancer Genome Atlas (TCGA) HCC cohort. Results DIA screened 86 significantly differentially regulated proteins between patients with poor prognosis and those with good prognosis. Eight proteins from the DIA proteomic analyses were quantified by PRM, and six of them (KLKB1, IGFBP3, SHBG, SAA1, C7, and CD44) presented consistent expression trends between DIA and PRM. Then, the results of ELISA indicated that KLKB1 was abnormally expressed in HCC patients, and the serum level of KLKB1 also exhibited significant changes before and after treatment (P = 0.016). Patients with higher KLKB1 serum levels had significantly superior overall survival (P = 0.035) and progression-free survival (P = 0.027) than those with lower KLKB1 expression. In the TCGA-HCC cohort, Cox regression analysis suggested that KLKB1 was an independent prognostic factor for overall survival (P = 0.032) of HCC patients. Conclusion Aberrant expression of KLKB1 was strongly associated with the prognosis of HCC patients. KLKB1 may be used to evaluate the prognosis and guide the treatment for HCC.
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Affiliation(s)
- Yi-Qun Che
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China.,Center for Clinical Laboratory, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, People's Republic of China
| | - Yue Zhang
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Han-Bing Li
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Di Shen
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
| | - Wei Cui
- Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, People's Republic of China
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24
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Messner CB, Demichev V, Bloomfield N, Yu JSL, White M, Kreidl M, Egger AS, Freiwald A, Ivosev G, Wasim F, Zelezniak A, Jürgens L, Suttorp N, Sander LE, Kurth F, Lilley KS, Mülleder M, Tate S, Ralser M. Ultra-fast proteomics with Scanning SWATH. Nat Biotechnol 2021; 39:846-854. [PMID: 33767396 PMCID: PMC7611254 DOI: 10.1038/s41587-021-00860-4] [Citation(s) in RCA: 165] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 02/18/2021] [Indexed: 01/31/2023]
Abstract
Accurate quantification of the proteome remains challenging for large sample series and longitudinal experiments. We report a data-independent acquisition method, Scanning SWATH, that accelerates mass spectrometric (MS) duty cycles, yielding quantitative proteomes in combination with short gradients and high-flow (800 µl min-1) chromatography. Exploiting a continuous movement of the precursor isolation window to assign precursor masses to tandem mass spectrometry (MS/MS) fragment traces, Scanning SWATH increases precursor identifications by ~70% compared to conventional data-independent acquisition (DIA) methods on 0.5-5-min chromatographic gradients. We demonstrate the application of ultra-fast proteomics in drug mode-of-action screening and plasma proteomics. Scanning SWATH proteomes capture the mode of action of fungistatic azoles and statins. Moreover, we confirm 43 and identify 11 new plasma proteome biomarkers of COVID-19 severity, advancing patient classification and biomarker discovery. Thus, our results demonstrate a substantial acceleration and increased depth in fast proteomic experiments that facilitate proteomic drug screens and clinical studies.
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Affiliation(s)
- Christoph B Messner
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Vadim Demichev
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | | | - Jason S L Yu
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Matthew White
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Marco Kreidl
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anna-Sophia Egger
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
| | - Anja Freiwald
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Aleksej Zelezniak
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | - Linda Jürgens
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Leif Erik Sander
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Florian Kurth
- Department of Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Department of Tropical Medicine, Bernhard Nocht Institute for Tropical Medicine & I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kathryn S Lilley
- Department of Biochemistry, Cambridge Centre for Proteomics, University of Cambridge, Cambridge, UK
| | - Michael Mülleder
- Core Facility - High Throughput Mass Spectrometry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Markus Ralser
- Molecular Biology of Metabolism Laboratory, The Francis Crick Institute, London, UK.
- Department of Biochemistry, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
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25
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Uchida Y, Higuchi T, Shirota M, Kagami S, Saigusa D, Koshiba S, Yasuda J, Tamiya G, Kuriyama S, Kinoshita K, Yaegashi N, Yamamoto M, Terasaki T, Sugawara J. Identification and Validation of Combination Plasma Biomarker of Afamin, Fibronectin and Sex Hormone-Binding Globulin to Predict Pre-eclampsia. Biol Pharm Bull 2021; 44:804-815. [PMID: 34078812 DOI: 10.1248/bpb.b20-01043] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The purpose of the present study was to identify a plasma protein biomarker able to predict pre-eclampsia (PE). Comprehensive quantitative proteomics using mass spectrometry with sequential window acquisition of all theoretical fragment ion spectra (SWATH-MS) was applied to plasma samples of 7 PE and 14 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE), and 11 proteins were selected as candidates potentially able to differentiate the two groups. Plasmas collected at gestational weeks 14-24 from 36 PE and 120 healthy pregnant women (for PE subjects, plasma samples were taken before onset of PE) were used to conduct selected reaction monitoring quantification analysis, optimize protein combinations and conduct internal validation, which consisted of 30 iterations of 10-fold cross-validation using multivariate logistic regression and receiver operating characteristic (ROC) analysis. The combination of afamin, fibronectin, and sex-hormone-binding globulin was selected as the best candidate. The 3-protein combination predictive model (predictive equation and cut-off value) generated using the internal validation subjects was successfully validated in another group of validation subjects (36 PE and 54 healthy (for PE subjects, plasma samples were taken before onset of PE)) and showed good predictive performance, with the area under the curve (AUC) 0.835 and odds ratio 13.43. In conclusion, we newly identified a 3-protein combination biomarker and established a predictive equation and cut-off value that can predict the onset of PE based on analysis of plasma samples collected during gestational weeks 14-24.
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Affiliation(s)
- Yasuo Uchida
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | | | - Matsuyuki Shirota
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Satoshi Kagami
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Daisuke Saigusa
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Jun Yasuda
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute
| | - Gen Tamiya
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University.,Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project
| | - Shinichi Kuriyama
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Information Sciences, Tohoku University
| | - Nobuo Yaegashi
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
| | - Tetsuya Terasaki
- Faculty of Pharmaceutical Sciences, Tohoku University.,Graduate School of Pharmaceutical Sciences, Tohoku University.,Tohoku Medical Megabank Organization (ToMMo), Tohoku University
| | - Junichi Sugawara
- Tohoku Medical Megabank Organization (ToMMo), Tohoku University.,Graduate School of Medicine, Tohoku University
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26
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Bian J, Sze YH, Tse DYY, To CH, McFadden SA, Lam CSY, Li KK, Lam TC. SWATH Based Quantitative Proteomics Reveals Significant Lipid Metabolism in Early Myopic Guinea Pig Retina. Int J Mol Sci 2021; 22:4721. [PMID: 33946922 PMCID: PMC8124159 DOI: 10.3390/ijms22094721] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/25/2021] [Indexed: 12/14/2022] Open
Abstract
Most of the previous myopic animal studies employed a single-candidate approach and lower resolution proteomics approaches that were difficult to detect minor changes, and generated limited systems-wide biological information. Hence, a complete picture of molecular events in the retina involving myopic development is lacking. Here, to investigate comprehensive retinal protein alternations and underlying molecular events in the early myopic stage, we performed a data-independent Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH) based proteomic analysis coupled with different bioinformatics tools in pigmented guinea pigs after 4-day lens-induced myopia (LIM). Myopic eyes compared to untreated contralateral control eyes caused significant changes in refractive error and choroid thickness (p < 0.05, n = 5). Relative elongation of axial length and the vitreous chamber depth were also observed. Using pooled samples from all individuals (n = 10) to build a species-specific retinal ion library for SWATH analysis, 3202 non-redundant proteins (with 24,616 peptides) were identified at 1% global FDR. For quantitative analysis, the 10 individual retinal samples (5 pairs) were analyzed using a high resolution Triple-TOF 6600 mass spectrometry (MS) with technical replicates. In total, 37 up-regulated and 21 down-regulated proteins were found significantly changed after LIM treatment (log2 ratio (T/C) > 0.26 or < -0.26; p ≤ 0.05). Data are accepted via ProteomeXchange with identifier PXD025003. Through Ingenuity Pathways Analysis (IPA), "lipid metabolism" was found as the top function associated with the differentially expressed proteins. Based on the protein abundance and peptide sequences, expression patterns of two regulated proteins (SLC6A6 and PTGES2) identified in this pathway were further successfully validated with high confidence (p < 0.05) using a novel Multiple Reaction Monitoring (MRM) assay on a QTRAP 6500+ MS. In summary, through an integrated discovery and targeted proteomic approach, this study serves as the first report to detect and confirm novel retinal protein changes and significant biological functions in the early LIM mammalian guinea pigs. The study provides new workflow and insights for further research to myopia control.
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Affiliation(s)
- Jingfang Bian
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Ying-Hon Sze
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Dennis Yan-Yin Tse
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Chi-Ho To
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Sally A. McFadden
- School of Psychology, College of Engineering, Science and the Environment, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Carly Siu-Yin Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - King-Kit Li
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
| | - Thomas Chuen Lam
- Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Kowloon, Hong Kong, China; (J.B.); (Y.-H.S.); (D.Y.-Y.T.); (C.-H.T.); (C.S.-Y.L.); (K.-K.L.)
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
- Shenzhen Research Institute, The Hong Kong Polytechnic University, Shenzhen 518052, China
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27
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Turner N, Abeysinghe P, Sadowski P, Mitchell MD. Exosomal Cargo May Hold the Key to Improving Reproductive Outcomes in Dairy Cows. Int J Mol Sci 2021; 22:ijms22042024. [PMID: 33670752 PMCID: PMC7922264 DOI: 10.3390/ijms22042024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 02/15/2021] [Accepted: 02/15/2021] [Indexed: 12/25/2022] Open
Abstract
The reproductive status of dairy cows remains a challenge for dairy farmers worldwide, with impaired fertility linked to a significant reduction in herd profitability, due in part to impaired immunity, increased metabolic pressure, and longer postpartum anestrous interval (PPAI). Exosomes are nanovesicles released from a variety of cell types and end up in circulation, and carry proteins, bioactive peptides, lipids, and nucleic acids specific to the place of origin. As such, their role in health and disease has been investigated in humans and animals. This review discusses research into exosomes in the context of reproduction in dairy herds and introduces recent advances in mass-spectrometry (MS) based proteomics that have a potential to advance quantitative profiling of exosomal protein cargo in a search for early biomarkers of cattle fertility.
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Affiliation(s)
- Natalie Turner
- Institute of Health and Biomedical Innovation—Centre for Children’s Health Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4029, Australia; (N.T.); (P.A.)
| | - Pevindu Abeysinghe
- Institute of Health and Biomedical Innovation—Centre for Children’s Health Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4029, Australia; (N.T.); (P.A.)
| | - Pawel Sadowski
- Central Analytical Research Facility—Queensland University of Technology, Gardens Point, Brisbane, QLD 4000, Australia;
| | - Murray D. Mitchell
- Institute of Health and Biomedical Innovation—Centre for Children’s Health Research, School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4029, Australia; (N.T.); (P.A.)
- Correspondence: ; Tel.: +61-7-3069-7438
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28
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Dowell JA, Wright LJ, Armstrong EA, Denu JM. Benchmarking Quantitative Performance in Label-Free Proteomics. ACS OMEGA 2021; 6:2494-2504. [PMID: 33553868 PMCID: PMC7859943 DOI: 10.1021/acsomega.0c04030] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 01/11/2021] [Indexed: 05/07/2023]
Abstract
Previous benchmarking studies have demonstrated the importance of instrument acquisition methodology and statistical analysis on quantitative performance in label-free proteomics. However, the effects of these parameters in combination with replicate number and false discovery rate (FDR) corrections are not known. Using a benchmarking standard, we systematically evaluated the combined impact of acquisition methodology, replicate number, statistical approach, and FDR corrections. These analyses reveal a complex interaction between these parameters that greatly impacts the quantitative fidelity of protein- and peptide-level quantification. At a high replicate number (n = 8), both data-dependent acquisition (DDA) and data-independent acquisition (DIA) methodologies yield accurate protein quantification across statistical approaches. However, at a low replicate number (n = 4), only DIA in combination with linear models for microarrays (LIMMA) and reproducibility-optimized test statistic (ROTS) produced a high level of quantitative fidelity. Quantitative accuracy at low replicates is also greatly impacted by FDR corrections, with Benjamini-Hochberg and Storey corrections yielding variable true positive rates for DDA workflows. For peptide quantification, replicate number and acquisition methodology are even more critical. A higher number of replicates in combination with DIA and LIMMA produce high quantitative fidelity, while DDA performs poorly regardless of replicate number or statistical approach. These results underscore the importance of pairing instrument acquisition methodology with the appropriate replicate number and statistical approach for optimal quantification performance.
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Affiliation(s)
- James A. Dowell
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - Logan J. Wright
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - Eric A. Armstrong
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
| | - John M. Denu
- Wisconsin
Institute for Discovery, University of Wisconsin−Madison, 330 North Orchard Street, Madison, Wisconsin 53715, United States
- Department
of Biomolecular Chemistry, University of
Wisconsin−Madison, 420 Henry Mall Room 1135 Biochemistry Building, Madison, Wisconsin 53706, United States
- .
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29
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N α-terminal acetylation of proteins by NatA and NatB serves distinct physiological roles in Saccharomyces cerevisiae. Cell Rep 2021; 34:108711. [PMID: 33535049 DOI: 10.1016/j.celrep.2021.108711] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 10/10/2020] [Accepted: 01/09/2021] [Indexed: 11/22/2022] Open
Abstract
N-terminal (Nt) acetylation is a highly prevalent co-translational protein modification in eukaryotes, catalyzed by at least five Nt acetyltransferases (Nats) with differing specificities. Nt acetylation has been implicated in protein quality control, but its broad biological significance remains elusive. We investigate the roles of the two major Nats of S. cerevisiae, NatA and NatB, by performing transcriptome, translatome, and proteome profiling of natAΔ and natBΔ mutants. Our results reveal a range of NatA- and NatB-specific phenotypes. NatA is implicated in systemic adaptation control, because natAΔ mutants display altered expression of transposons, sub-telomeric genes, pheromone response genes, and nuclear genes encoding mitochondrial ribosomal proteins. NatB predominantly affects protein folding, because natBΔ mutants, to a greater extent than natA mutants, accumulate protein aggregates, induce stress responses, and display reduced fitness in the absence of the ribosome-associated chaperone Ssb. These phenotypic differences indicate that controlling Nat activities may serve to elicit distinct cellular responses.
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30
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Cao C, Ding B, Li Q, Kwok D, Wu J, Long Q. Power analysis of transcriptome-wide association study: Implications for practical protocol choice. PLoS Genet 2021; 17:e1009405. [PMID: 33635859 PMCID: PMC7946362 DOI: 10.1371/journal.pgen.1009405] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 03/10/2021] [Accepted: 02/06/2021] [Indexed: 12/12/2022] Open
Abstract
The transcriptome-wide association study (TWAS) has emerged as one of several promising techniques for integrating multi-scale 'omics' data into traditional genome-wide association studies (GWAS). Unlike GWAS, which associates phenotypic variance directly with genetic variants, TWAS uses a reference dataset to train a predictive model for gene expressions, which allows it to associate phenotype with variants through the mediating effect of expressions. Although effective, this core innovation of TWAS is poorly understood, since the predictive accuracy of the genotype-expression model is generally low and further bounded by expression heritability. This raises the question: to what degree does the accuracy of the expression model affect the power of TWAS? Furthermore, would replacing predictions with actual, experimentally determined expressions improve power? To answer these questions, we compared the power of GWAS, TWAS, and a hypothetical protocol utilizing real expression data. We derived non-centrality parameters (NCPs) for linear mixed models (LMMs) to enable closed-form calculations of statistical power that do not rely on specific protocol implementations. We examined two representative scenarios: causality (genotype contributes to phenotype through expression) and pleiotropy (genotype contributes directly to both phenotype and expression), and also tested the effects of various properties including expression heritability. Our analysis reveals two main outcomes: (1) Under pleiotropy, the use of predicted expressions in TWAS is superior to actual expressions. This explains why TWAS can function with weak expression models, and shows that TWAS remains relevant even when real expressions are available. (2) GWAS outperforms TWAS when expression heritability is below a threshold of 0.04 under causality, or 0.06 under pleiotropy. Analysis of existing publications suggests that TWAS has been misapplied in place of GWAS, in situations where expression heritability is low.
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Affiliation(s)
- Chen Cao
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Bowei Ding
- Department of Mathematics & Statistics, University of Calgary, Calgary, Canada
| | - Qing Li
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Devin Kwok
- Department of Mathematics & Statistics, University of Calgary, Calgary, Canada
| | - Jingjing Wu
- Department of Mathematics & Statistics, University of Calgary, Calgary, Canada
| | - Quan Long
- Department of Biochemistry & Molecular Biology, Alberta Children’s Hospital Research Institute, University of Calgary, Calgary, Canada
- Department of Mathematics & Statistics, University of Calgary, Calgary, Canada
- Department of Medical Genetics, University of Calgary, Calgary, Canada
- Hotchkiss Brain Institute, O’Brien Institute for Public Health, University of Calgary, Calgary, Canada
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31
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Jiang B, Hu L, Zhang X, Zhang H, Zhang F, Chen L, Li Z, Zhao X, Xue C, Jiang X. Uncovering proteome variations of differently heat-treated sea cucumber (Apostichopus japonicus) by label-free mass spectrometry. Food Chem 2020; 344:128575. [PMID: 33191009 DOI: 10.1016/j.foodchem.2020.128575] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 10/08/2020] [Accepted: 11/03/2020] [Indexed: 02/08/2023]
Abstract
The effects of heat treatment on the proteome of Apostichopus japonicus have been evaluated using label-free quantitative proteomics by ultrahigh performance liquid chromatography-quadrupole/time of flight (UHPLC-Q/TOF) mass spectrometry with sequential window acquisition of all the theoretical fragment ion (SWATH) acquisition mode. Chemometric tools are integrated to reveal proteomic changes by mining the protein quantitation data from fresh and differently heat-treated samples. SWATH allows the quantitation of 548 proteins, of which 24 proteins are significantly sensitive to heat treatment and 13 proteins vary significantly responding to different heat procedures (boiling, steaming, and microwave heating), and 5 of them are sharing proteins. Gene ontology (GO) annotation of the differentiating proteins highlights most of them are relevant to molecular functions. The results can be favorable to evaluate the effects of heat treatment on the nutrition and function of processed sea cucumbers and facilitate the selection of an optimal thermal treatment.
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Affiliation(s)
- Bingxue Jiang
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Lingping Hu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou 310058, PR China
| | - Xiaomei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China
| | - Hongwei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, PR China.
| | - Feng Zhang
- Chinese Academy of Inspection & Quarantine, Beijing 100176, PR China
| | - Lipin Chen
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Zhaojie Li
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Xue Zhao
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China
| | - Changhu Xue
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology, Qingdao, Shandong Province 266237, PR China
| | - Xiaoming Jiang
- College of Food Science and Technology, Ocean University of China, No. 5 Yu Shan Road, Qingdao, Shandong Province 266003, PR China.
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32
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Xu LL, Zhang HW, Zhang XM, Lin H, Guo YM, Yu C, Sun LR, Li ZX. Natural Shrimp ( Litopenaeus vannamei) Tropomyosin Shows Higher Allergic Properties than Recombinant Ones as Compared through SWATH-MS-Based Proteomics and Immunological Response. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11553-11567. [PMID: 32941022 DOI: 10.1021/acs.jafc.0c03840] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Tropomyosin (TM) is the major shrimp allergen that could trigger anaphylactic reactions. Recently, recombinant TM (rTM) has been accepted widely in the field of allergen-specific immunotherapy, but the allergenicity of rTM has not been compared with natural TM (nTM) based on an in vitro digestion profile. In this work, IgG-/IgE binding, allergen peptides, and degranulation ability of the digested samples in simulated gastric fluid/simulated intestinal fluid/gastrointestinal models from nTM and rTM were evaluated by immunoassays, proteomics, and basophil degranulation assay. Results showed that pepsin-digested and trypsin-digested samples of rTM exhibited lower IgG-/IgE binding and degranulation than those of nTM. More peptides of the digested samples from rTM (57.8%) matched shrimp allergic epitopes than those from nTM (33.3%). However, the peptide SITDELDQTF (269-278) appeared most frequently. These findings would supply foundation data for epitope-based immunotherapy to shrimp allergic individuals.
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Affiliation(s)
- Li Li Xu
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Hong Wei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, P. R. China
| | - Xiao Mei Zhang
- Technology Center of Qingdao Customs District, No.70 Qutangxia Road, Qingdao, Shandong Province 266002, P. R. China
| | - Hong Lin
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Yu Man Guo
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Chuang Yu
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Li Rui Sun
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
| | - Zhen Xing Li
- College of Food Science and Engineering, Ocean University of China, No.5, Yushan Road, Qingdao, Shandong Province 266003, P. R. China
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33
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Yan C, Guo H, Ding Q, Shao Y, Kang D, Yu T, Li C, Huang H, Du Y, Wang H, Hu K, Xie L, Wang G, Liang Y. Multiomics Profiling Reveals Protective Function of Schisandra Lignans against Acetaminophen-Induced Hepatotoxicity. Drug Metab Dispos 2020; 48:1092-1103. [PMID: 32719086 DOI: 10.1124/dmd.120.000083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
The action principles of traditional Chinese medicines (TCMs) feature multiactive components, multitarget sites, and weak combination with action targets. In the present study, we performed an integrated analysis of metabonomics, proteomics, and lipidomics to establish a scientific research system on the underlying mechanism of TCMs, and Schisandra lignan extract (SLE) was selected as a model TCM. In metabonomics, several metabolic pathways were found to mediate the liver injury induced by acetaminophen (APAP), and SLE could regulate the disorder of lipid metabolism. The proteomic study further proved that the hepatoprotective effect of SLE was closely related to the regulation of lipid metabolism. Indeed, the results of lipidomics demonstrated that SLE dosing has an obvious callback effect on APAP-induced lipidic profile shift. The contents of 25 diglycerides (DAGs) and 21 triglycerides (TAGs) were enhanced significantly by APAP-induced liver injury, which could further induce liver injury and inflammatory response by upregulating protein kinase C (PKCβ, PKCγ, PKCδ, and PKCθ). The upregulated lipids and PKCs could be reversed to the normal level by SLE dosing. More importantly, phosphatidic acid phosphatase, fatty acid transport protein 5, and diacylglycerol acyltransferase 2 were proved to be positively associated with the regulation of DAGs and TAGs. SIGNIFICANCE STATEMENT: Integrated multiomics was first used to reveal the mechanism of APAP-induced acute liver failure (ALF) and the hepatoprotective role of SLE. The results showed that the ALF caused by APAP was closely related to lipid regulation and that SLE dosing could exert a hepatoprotective role by reducing intrahepatic diglyceride and triglyceride levels. Our research can not only promote the application of multicomponent technology in the study of the mechanism of traditional Chinese medicines but also provide an effective approach for the prevention and treatment of ALF.
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Affiliation(s)
- Caixia Yan
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Huimin Guo
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Qingqing Ding
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Yuhao Shao
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Dian Kang
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Tengjie Yu
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Changjian Li
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Haoran Huang
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Yisha Du
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - He Wang
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Kangrui Hu
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Lin Xie
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Guangji Wang
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
| | - Yan Liang
- Key Laboratory of Drug Metabolism & Pharmacokinetics, State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, P.R. China (C.Y., H.G., Y.S., D.K., T.Y., C.L., H.H., Y.D., H.W., K.H., L.X., G.W., Y.L.) and Department of Geriatric Oncology, First Affiliated Hospital of Nanjing Medical University (Jiangsu People's Hospital), Nanjing, P.R. China (Q.D.)
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34
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Iacobucci I, Monaco V, Cozzolino F, Monti M. From classical to new generation approaches: An excursus of -omics methods for investigation of protein-protein interaction networks. J Proteomics 2020; 230:103990. [PMID: 32961344 DOI: 10.1016/j.jprot.2020.103990] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/11/2020] [Accepted: 08/31/2020] [Indexed: 01/24/2023]
Abstract
Functional Proteomics aims to the identification of in vivo protein-protein interaction (PPI) in order to piece together protein complexes, and therefore, cell pathways involved in biological processes of interest. Over the years, proteomic approaches used for protein-protein interaction investigation have relied on classical biochemical protocols adapted to a global overview of protein-protein interactions, within so-called "interactomics" investigation. In particular, their coupling with advanced mass spectrometry instruments and innovative analytical methods led to make great strides in the PPIs investigation in proteomics. In this review, an overview of protein complexes purification strategies, from affinity purification approaches, including proximity-dependent labeling techniques and cross-linking strategy for the identification of transient interactions, to Blue Native Gel Electrophoresis (BN-PAGE) and Size Exclusion Chromatography (SEC) employed in the "complexome profiling", has been reported, giving a look to their developments, strengths and weakness and providing to readers several recent applications of each strategy. Moreover, a section dedicated to bioinformatic databases and platforms employed for protein networks analyses was also included.
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Affiliation(s)
- Ilaria Iacobucci
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Vittoria Monaco
- CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy
| | - Flora Cozzolino
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
| | - Maria Monti
- Department of Chemical Sciences, University Federico II of Naples, Strada Comunale Cinthia, 26, 80126 Naples, Italy; CEINGE Advanced Biotechnologies, Via G. Salvatore 486, 80145 Naples, Italy.
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35
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Choi M, Carver J, Chiva C, Tzouros M, Huang T, Tsai TH, Pullman B, Bernhardt OM, Hüttenhain R, Teo GC, Perez-Riverol Y, Muntel J, Müller M, Goetze S, Pavlou M, Verschueren E, Wollscheid B, Nesvizhskii AI, Reiter L, Dunkley T, Sabidó E, Bandeira N, Vitek O. MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets. Nat Methods 2020; 17:981-984. [PMID: 32929271 PMCID: PMC7541731 DOI: 10.1038/s41592-020-0955-0] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/13/2020] [Indexed: 11/09/2022]
Abstract
MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational analysis tools. A branch structure enables MassIVE.quant to systematically store raw experimental data, metadata of the experimental design, scripts of the quantitative analysis workflow, intermediate input and output files, as well as alternative reanalyses of the same dataset.
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Affiliation(s)
- Meena Choi
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Jeremy Carver
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Cristina Chiva
- Proteomics Unit, Center for Genomics Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manuel Tzouros
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Ting Huang
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Tsung-Heng Tsai
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA
| | - Benjamin Pullman
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Ruth Hüttenhain
- Department of Molecular and Cellular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yasset Perez-Riverol
- Proteomics Services, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | | | - Maik Müller
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Maria Pavlou
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland
| | - Erik Verschueren
- Department of Molecular and Cellular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Translational Medicine, ETH, Zurich, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Tom Dunkley
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Eduard Sabidó
- Proteomics Unit, Center for Genomics Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Proteomics Unit, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuno Bandeira
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
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36
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Tsai TH, Choi M, Banfai B, Liu Y, MacLean BX, Dunkley T, Vitek O. Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments. Mol Cell Proteomics 2020; 19:944-959. [PMID: 32234965 PMCID: PMC7261813 DOI: 10.1074/mcp.ra119.001792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/27/2020] [Indexed: 12/11/2022] Open
Abstract
In bottom-up mass spectrometry-based proteomics, relative protein quantification is often achieved with data-dependent acquisition (DDA), data-independent acquisition (DIA), or selected reaction monitoring (SRM). These workflows quantify proteins by summarizing the abundances of all the spectral features of the protein (e.g. precursor ions, transitions or fragments) in a single value per protein per run. When abundances of some features are inconsistent with the overall protein profile (for technological reasons such as interferences, or for biological reasons such as post-translational modifications), the protein-level summaries and the downstream conclusions are undermined. We propose a statistical approach that automatically detects spectral features with such inconsistent patterns. The detected features can be separately investigated, and if necessary, removed from the data set. We evaluated the proposed approach on a series of benchmark-controlled mixtures and biological investigations with DDA, DIA and SRM data acquisitions. The results demonstrated that it could facilitate and complement manual curation of the data. Moreover, it can improve the estimation accuracy, sensitivity and specificity of detecting differentially abundant proteins, and reproducibility of conclusions across different data processing tools. The approach is implemented as an option in the open-source R-based software MSstats.
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Affiliation(s)
- Tsung-Heng Tsai
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts
| | - Meena Choi
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts
| | - Balazs Banfai
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Yansheng Liu
- Department of Pharmacology, Yale Cancer Biology Institute, Yale University School of Medicine, West Haven, Connecticut
| | - Brendan X MacLean
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Tom Dunkley
- Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
| | - Olga Vitek
- Khoury College of Computer Sciences, Northeastern University, Boston, Massachusetts.
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37
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Salivary proteome signatures in the early and middle stages of human pregnancy with term birth outcome. Sci Rep 2020; 10:8022. [PMID: 32415095 PMCID: PMC7229191 DOI: 10.1038/s41598-020-64483-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/11/2020] [Indexed: 02/07/2023] Open
Abstract
The establishment and maintenance of pregnancy in humans proceed through a continuous change of biochemical and biophysical processes. It requires a constant interaction between the fetus and the maternal system. The present prospective study aims to elucidate changes in salivary proteome from the early to middle stages of term pregnancy, and establishing an expressional trajectory for modulated proteins. To date, a comprehensive characterization of the longitudinal salivary proteome in pregnancy has not been performed and it is our immediate interest. In the discovery phase, maternal saliva (N = 20) at 6–13, 18–21, and 26–29 weeks of gestation was analyzed using level-free proteomics (SWATH-MS) approach. The expression levels of 65 proteins were found to change significantly with gestational age and distributed into two distinct clusters with a unique expression trajectory. The results revealed that altered proteins are involved in maternal immune modulation, metabolism, and host defense mechanism. Further, verification of 12 proteins was employed using targeted mass spectrometry (MRM-MS) in a separate subset of saliva (N = 14). The MRM results of 12 selected proteins confirmed a similar expression pattern as in SWATH-MS analysis. Overall, the results not only demonstrate the longitudinal maternal saliva proteome for the first time but also set the groundwork for comparative analysis between term birth and adverse pregnancy outcomes.
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38
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Baeza J, Lawton AJ, Fan J, Smallegan MJ, Lienert I, Gandhi T, Bernhardt OM, Reiter L, Denu JM. Revealing Dynamic Protein Acetylation across Subcellular Compartments. J Proteome Res 2020; 19:2404-2418. [PMID: 32290654 DOI: 10.1021/acs.jproteome.0c00088] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Protein acetylation is a widespread post-translational modification implicated in many cellular processes. Recent advances in mass spectrometry have enabled the cataloging of thousands of sites throughout the cell; however, identifying regulatory acetylation marks have proven to be a daunting task. Knowledge of the kinetics and stoichiometry of site-specific acetylation is an important factor to uncover function. Here, an improved method of quantifying acetylation stoichiometry was developed and validated, providing a detailed landscape of dynamic acetylation stoichiometry within cellular compartments. The dynamic nature of site-specific acetylation in response to serum stimulation was revealed. In two distinct human cell lines, growth factor stimulation led to site-specific, temporal acetylation changes, revealing diverse kinetic profiles that clustered into several groups. Overlap of dynamic acetylation sites among two different human cell lines suggested similar regulatory control points across major cellular pathways that include splicing, translation, and protein homeostasis. Rapid increases in acetylation on protein translational machinery suggest a positive regulatory role under progrowth conditions. Finally, higher median stoichiometry was observed in cellular compartments where active acetyltransferases are well described. Data sets can be accessed through ProteomExchange via the MassIVE repository (ProteomExchange: PXD014453; MassIVE: MSV000084029).
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Affiliation(s)
- Josue Baeza
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Alexis J Lawton
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Jing Fan
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States.,Morgridge Institute for Research, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Michael J Smallegan
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
| | - Ian Lienert
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | - Tejas Gandhi
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | | | - Lukas Reiter
- Biognosys AG, Wagistrasse 25, CH-8952 Schlieren, Switzerland
| | - John M Denu
- Biomolecular Chemistry Department, School of Medicine and Public Health, University of Wisconsin-Madison, 53706 Madison, Wisconsin, United States.,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 53715 Madison, Wisconsin, United States
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39
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Cho KC, Clark DJ, Schnaubelt M, Teo GC, Leprevost FDV, Bocik W, Boja ES, Hiltke T, Nesvizhskii AI, Zhang H. Deep Proteomics Using Two Dimensional Data Independent Acquisition Mass Spectrometry. Anal Chem 2020; 92:4217-4225. [PMID: 32058701 PMCID: PMC7255061 DOI: 10.1021/acs.analchem.9b04418] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Methodologies that facilitate high-throughput proteomic analysis are a key step toward moving proteome investigations into clinical translation. Data independent acquisition (DIA) has potential as a high-throughput analytical method due to the reduced time needed for sample analysis, as well as its highly quantitative accuracy. However, a limiting feature of DIA methods is the sensitivity of detection of low abundant proteins and depth of coverage, which other mass spectrometry approaches address by two-dimensional fractionation (2D) to reduce sample complexity during data acquisition. In this study, we developed a 2D-DIA method intended for rapid- and deeper-proteome analysis compared to conventional 1D-DIA analysis. First, we characterized 96 individual fractions obtained from the protein standard, NCI-7, using a data-dependent approach (DDA), identifying a total of 151,366 unique peptides from 11,273 protein groups. We observed that the majority of the proteins can be identified from just a few selected fractions. By performing an optimization analysis, we identified six fractions with high peptide number and uniqueness that can account for 80% of the proteins identified in the entire experiment. These selected fractions were combined into a single sample which was then subjected to DIA (referred to as 2D-DIA) quantitative analysis. Furthermore, improved DIA quantification was achieved using a hybrid spectral library, obtained by combining peptides identified from DDA data with peptides identified directly from the DIA runs with the help of DIA-Umpire. The optimized 2D-DIA method allowed for improved identification and quantification of low abundant proteins compared to conventional unfractionated DIA analysis (1D-DIA). We then applied the 2D-DIA method to profile the proteomes of two breast cancer patient-derived xenograft (PDX) models, quantifying 6,217 and 6,167 unique proteins in basal- and luminal- tumors, respectively. Overall, this study demonstrates the potential of high-throughput quantitative proteomics using a novel 2D-DIA method.
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Affiliation(s)
- Kyung-Cho Cho
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - David J Clark
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Michael Schnaubelt
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
| | - Guo Ci Teo
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | | | - William Bocik
- Antibody Characterization Laboratory, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland 20892, United States
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, United States
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40
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Tannous A, Boonen M, Zheng H, Zhao C, Germain CJ, Moore DF, Sleat DE, Jadot M, Lobel P. Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics. J Proteome Res 2020; 19:1718-1730. [PMID: 32134668 DOI: 10.1021/acs.jproteome.9b00862] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Knowledge of intracellular location can provide important insights into the function of proteins and their respective organelles, and there is interest in combining classical subcellular fractionation with quantitative mass spectrometry to create global cellular maps. To evaluate mass spectrometric approaches specifically for this application, we analyzed rat liver differential centrifugation and Nycodenz density gradient subcellular fractions by tandem mass tag (TMT) isobaric labeling with reporter ion measurement at the MS2 and MS3 level and with two different label-free peak integration approaches, MS1 and data independent acquisition (DIA). TMT-MS2 provided the greatest proteome coverage, but ratio compression from contaminating background ions resulted in a narrower accurate dynamic range compared to TMT-MS3, MS1, and DIA, which were similar. Using a protein clustering approach to evaluate data quality by assignment of reference proteins to their correct compartments, all methods performed well, with isobaric labeling approaches providing the highest quality localization. Finally, TMT-MS2 gave the lowest percentage of missing quantifiable data when analyzing orthogonal fractionation methods containing overlapping proteomes. In summary, despite inaccuracies resulting from ratio compression, data obtained by TMT-MS2 assigned protein localization as well as other methods but achieved the highest proteome coverage with the lowest proportion of missing values.
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Affiliation(s)
- Abla Tannous
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Marielle Boonen
- URPhyM-Intracellular Trafficking Biology, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Haiyan Zheng
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Caifeng Zhao
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Colin J Germain
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States
| | - Dirk F Moore
- Department of Biostatistics, School of Public Health, Rutgers - The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - David E Sleat
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
| | - Michel Jadot
- URPhyM-Physiological Chemistry, NARILIS, University of Namur, 61 rue de Bruxelles, Namur 5000, Belgium
| | - Peter Lobel
- Center for Advanced Biotechnology and Medicine, Piscataway, New Jersey 08854, United States.,Department of Biochemistry and Molecular Biology, Robert-Wood Johnson Medical School, Rutgers Biomedical Health Sciences, Piscataway, New Jersey 08854, United States
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41
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González-Fernández MJ, Fabrikov D, Ramos-Bueno RP, Guil-Guerrero JL, Ortea I. SWATH Differential Abundance Proteomics and Cellular Assays Show In Vitro Anticancer Activity of Arachidonic Acid- and Docosahexaenoic Acid-Based Monoacylglycerols in HT-29 Colorectal Cancer Cells. Nutrients 2019; 11:E2984. [PMID: 31817645 PMCID: PMC6950369 DOI: 10.3390/nu11122984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/02/2019] [Accepted: 12/04/2019] [Indexed: 12/20/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most common and mortal types of cancer. There is increasing evidence that some polyunsaturated fatty acids (PUFAs) exercise specific inhibitory actions on cancer cells through different mechanisms, as a previous study on CRC cells demonstrated for two very long-chain PUFA. These were docosahexaenoic acid (DHA, 22:6n3) and arachidonic acid (ARA, 20:4n6) in the free fatty acid (FFA) form. In this work, similar design and technology have been used to investigate the actions of both DHA and ARA as monoacylglycerol (MAG) molecules, and results have been compared with those obtained using the corresponding FFA. Cell assays revealed that ARA- and DHA-MAG exercised dose- and time-dependent antiproliferative actions, with DHA-MAG acting on cancer cells more efficiently than ARA-MAG. Sequential window acquisition of all theoretical mass spectra (SWATH) - mass spectrometry massive quantitative proteomics, validated by parallel reaction monitoring and followed by pathway analysis, revealed that DHA-MAG had a massive effect in the proteasome complex, while the ARA-MAG main effect was related to DNA replication. Prostaglandin synthesis also resulted as inhibited by DHA-MAG. Results clearly demonstrated the ability of both ARA- and DHA-MAG to induce cell death in colon cancer cells, which suggests a direct relationship between chemical structure and antitumoral actions.
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Affiliation(s)
- María José González-Fernández
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Dmitri Fabrikov
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Rebeca P. Ramos-Bueno
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - José Luis Guil-Guerrero
- Food Technology Division, Agrifood Campus of International Excellence, ceiA3, University of Almería, 40120 Almería, Spain; (M.J.G.-F.); (D.F.); (R.P.R.-B.); (J.L.G.-G.)
| | - Ignacio Ortea
- Proteomics Unit, IMIBIC, Reina Sofía University Hospital, University of Córdoba, 14004 Córdoba, Spain
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42
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43
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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44
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Bittremieux W, Laukens K, Noble WS. Extremely Fast and Accurate Open Modification Spectral Library Searching of High-Resolution Mass Spectra Using Feature Hashing and Graphics Processing Units. J Proteome Res 2019; 18:3792-3799. [PMID: 31448616 PMCID: PMC6886738 DOI: 10.1021/acs.jproteome.9b00291] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Open modification searching (OMS) is a powerful search strategy to identify peptides with any type of modification. OMS works by using a very wide precursor mass window to allow modified spectra to match against their unmodified variants, after which the modification types can be inferred from the corresponding precursor mass differences. A disadvantage of this strategy, however, is the large computational cost, because each query spectrum has to be compared against a multitude of candidate peptides. We have previously introduced the ANN-SoLo tool for fast and accurate open spectral library searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up OMS by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. Here we demonstrate how this candidate selection procedure can be further optimized using graphics processing units. Additionally, we introduce a feature hashing scheme to convert high-resolution spectra to low-dimensional vectors. On the basis of these algorithmic advances, along with low-level code optimizations, the new version of ANN-SoLo is up to an order of magnitude faster than its initial version. This makes it possible to efficiently perform open searches on a large scale to gain a deeper understanding about the protein modification landscape. We demonstrate the computational efficiency and identification performance of ANN-SoLo based on a large data set of the draft human proteome. ANN-SoLo is implemented in Python and C++. It is freely available under the Apache 2.0 license at https://github.com/bittremieux/ANN-SoLo .
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Affiliation(s)
- Wout Bittremieux
- Department of Mathematics and Computer Science , University of Antwerp , 2020 Antwerp , Belgium
- Biomedical Informatics Network Antwerpen (biomina) , 2020 Antwerp , Belgium
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
| | - Kris Laukens
- Department of Mathematics and Computer Science , University of Antwerp , 2020 Antwerp , Belgium
- Biomedical Informatics Network Antwerpen (biomina) , 2020 Antwerp , Belgium
| | - William Stafford Noble
- Department of Genome Sciences , University of Washington , Seattle , Washington 98195 , United States
- Department of Computer Science and Engineering , University of Washington , Seattle , Washington 98195 , United States
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45
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Wang K, Donnarumma F, Herke SW, Dong C, Herke PF, Murray KK. RNA sampling from tissue sections using infrared laser ablation. Anal Chim Acta 2019; 1063:91-98. [PMID: 30967191 DOI: 10.1016/j.aca.2019.02.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/17/2019] [Accepted: 02/24/2019] [Indexed: 10/27/2022]
Abstract
RNA was obtained from discrete locations of frozen rat brain tissue sections through infrared (IR) laser ablation using a 3-μm wavelength in transmission geometry. The ablated plume was captured in a microcentrifuge tube containing RNAse-free buffer and processed using a commercial RNA purification kit. RNA transfer efficiency and integrity were evaluated based on automated electrophoresis in microfluidic chips. Reproducible IR-laser ablation of intact RNA was demonstrated with purified RNA at laser fluences of 3-5 kJ/m2 (72 ± 12% transfer efficiency) and with tissue sections at a laser fluence of 13 kJ/m2 (79 ± 14% transfer efficiency); laser energies were attenuated ∼20% by the soda-lime glass slides used to support the samples. RNA integrity from tissue ablation was >90% of its original RIN value (∼7) and the purified RNA was sufficiently intact for conversion to cDNA and subsequent qPCR assay.
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Affiliation(s)
- Kelin Wang
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Scott W Herke
- Genomics Facility, College of Science, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Patrick F Herke
- Genomics Facility, College of Science, Louisiana State University, Baton Rouge, LA, 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, 70803, United States.
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46
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Lacerda MPF, Marcelino MY, Lourencetti NMS, Neto ÁB, Gattas EA, Mendes-Giannini MJS, Fusco-Almeida AM. Methodologies and Applications of Proteomics for Study of Yeast Strains: An Update. Curr Protein Pept Sci 2019; 20:893-906. [PMID: 31322071 DOI: 10.2174/1389203720666190715145131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 11/22/2022]
Abstract
Yeasts are one of the mostly used microorganisms as models in several studies. A wide range of applications in different processes can be attributed to their intrinsic characteristics. They are eukaryotes and therefore valuable expression hosts that require elaborate post-translational modifications. Their arsenal of proteins has become a valuable biochemical tool for the catalysis of several reactions of great value to the food (beverages), pharmaceutical and energy industries. Currently, the main challenge in systemic yeast biology is the understanding of the expression, function and regulation of the protein pool encoded by such microorganisms. In this review, we will provide an overview of the proteomic methodologies used in the analysis of yeasts. This research focuses on the advantages and improvements in their most recent applications with an understanding of the functionality of the proteins of these microorganisms, as well as an update of the advances of methodologies employed in mass spectrometry.
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Affiliation(s)
- Maria Priscila F Lacerda
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Mônica Yonashiro Marcelino
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Natália M S Lourencetti
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
| | - Álvaro Baptista Neto
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | - Edwil A Gattas
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Engineering of Bioprocesses and Biotechnology, Araraquara, Brazil
| | | | - Ana Marisa Fusco-Almeida
- Sao Paulo State University (UNESP), School of Pharmaceutical Sciences - Department of Clinical Analysis, Araraquara, Brazil
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47
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Kim KH, Kim JY, Yoo JS. Mass spectrometry analysis of glycoprotein biomarkers in human blood of hepatocellular carcinoma. Expert Rev Proteomics 2019; 16:553-568. [PMID: 31145639 DOI: 10.1080/14789450.2019.1626235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Kwang Hoe Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jin Young Kim
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - Jong Shin Yoo
- Biomedical Omics Group, Korea Basic Science Institute, Cheongju, Republic of Korea
- Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
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48
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Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS. Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules. J Proteome Res 2019; 18:2525-2534. [DOI: 10.1021/acs.jproteome.9b00076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Bertrand Fabre
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Dagmara Korona
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Jonathan G. Lees
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Ikrame Lazar
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Ido Livneh
- Technion Integrated Cancer Center (TICC), The Rappaport Faculty of Medicine and Research Institute, Haifa, Israel
| | - Manon Brunet
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Christine A. Orengo
- Institute of Structural and Molecular Biology, University College London, London WC1E 7HX, United Kingdom
| | - Steven Russell
- Department of Genetics, University of Cambridge, University of Cambridge, Cambridge CB2 3EH, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Kathryn S. Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge CB2 1QR, U.K
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge CB2 1GA, U.K
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, U.K
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Wilson RS, Rauniyar N, Sakaue F, Lam TT, Williams KR, Nairn AC. Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD). Proteomes 2019; 7:12. [PMID: 30986977 PMCID: PMC6630806 DOI: 10.3390/proteomes7020012] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 02/07/2023] Open
Abstract
The postsynaptic density (PSD) is a structural, electron-dense region of excitatory glutamatergic synapses, which is involved in a variety of cellular and signaling processes in neurons. The PSD is comprised of a large network of proteins, many of which have been implicated in a wide variety of neuropsychiatric disorders. Biochemical fractionation combined with mass spectrometry analyses have enabled an in-depth understanding of the protein composition of the PSD. However, the PSD composition may change rapidly in response to stimuli, and robust and reproducible methods to thoroughly quantify changes in protein abundance are warranted. Here, we report on the development of two types of targeted mass spectrometry-based assays for quantitation of PSD-enriched proteins. In total, we quantified 50 PSD proteins in a targeted, parallel reaction monitoring (PRM) assay using heavy-labeled, synthetic internal peptide standards and identified and quantified over 2100 proteins through a pre-determined spectral library using a data-independent acquisition (DIA) approach in PSD fractions isolated from mouse cortical brain tissue.
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Affiliation(s)
- Rashaun S Wilson
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | | | - Fumika Sakaue
- Department of Neurology and Neurological Science, Tokyo Medical and Dental University, Tokyo 113-8519, Japan.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
| | - TuKiet T Lam
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- W.M Keck Biotechnology Resource Laboratory, Yale University School of Medicine, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Kenneth R Williams
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06511, USA.
| | - Angus C Nairn
- Yale/NIDA Neuroproteomics Center, New Haven, CT 06511, USA.
- Department of Psychiatry, Yale School of Medicine, Connecticut Mental Health Center, New Haven, CT 06511, USA.
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50
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Comparative analysis of proteomic and metabolomic profiles of different species of Paris. J Proteomics 2019; 200:11-27. [PMID: 30890455 DOI: 10.1016/j.jprot.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/12/2019] [Accepted: 02/01/2019] [Indexed: 02/08/2023]
Abstract
An extract prepared from species of Paris is the most widely consumed herbal product in China. The genus Paris includes a variety of genotypes with different medicinal component contents but only two are defined as official sources. Closely related species have different medicinal properties because of differential expression of proteins and metabolites. To better understand the molecular basis of these differences, we examined proteomic and metabolomic changes in rhizomes of P. polyphylla var. chinensis, P. polyphylla var. yunnanensis, and P. fargesii var. fargesii using a technique known as sequential window acquisition of all theoretical mass spectra as well as gas chromatography-time-of-flight mass spectrometry. In total, 419 proteins showed significant abundance changes, and 33 metabolites could be used to discriminate Paris species. A complex analysis of proteomic and metabolomic data revealed a higher efficiency of sucrose utilization and an elevated protein abundance in the sugar metabolic pathway of P. polyphylla var. chinensis. The pyruvate content and efficiency of acetyl-CoA-utilization in saponin biosynthesis were also higher in P. polyphylla var. chinensis than in the other two species. The results expand our understanding of the proteome and metabolome of Paris and offer new insights into the species-specific traits of these herbaceous plants. SIGNIFICANCE: The traditional Chinese medicine Paris is the most widely consumed herbal product for the treatment of joint pain, rheumatoid arthritis and antineoplastic. All Paris species have roughly the same morphological characteristics; however, different members have different medicinal compound contents. Efficient exploitation of genetic diversity is a key factor in the development of rare medicinal plants with improved agronomic traits and malleability to challenging environmental conditions. Nevertheless, only a partial understanding of physiological and molecular mechanisms of different plants of Paris can be achieved without proteomics. To better understand the molecular basis of these differences and facilitate the use of other Paris species, we examine proteomic metabolomic changes in rhizomes of Paris using the technique known as SWATH-MS and GC/TOF-MS. Our research has provided information that can be used in other studies to compare metabolic traits in different Paris species. Our findings can also serve as a theoretical basis for the selection and cultivation of other Paris species with a higher medicinal value.
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