151
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Benchmarking mass spectrometry based proteomics algorithms using a simulated database. ACTA ACUST UNITED AC 2021; 10. [PMID: 34012763 DOI: 10.1007/s13721-021-00298-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Protein sequencing algorithms process data from a variety of instruments that has been generated under diverse experimental conditions. Currently there is no way to predict the accuracy of an algorithm for a given data set. Most of the published algorithms and associated software has been evaluated on limited number of experimental data sets. However, these performance evaluations do not cover the complete search space the algorithmand the software might encounter in real-world. To this end, we present a database of simulated spectra that can be used to benchmark any spectra to peptide search engine. We demonstrate the usability of this database by bench marking two popular peptide sequencing engines. We show wide variation in the accuracy of peptide deductions and a complete quality profile of a given algorithm can be useful for practitioners and algorithm developers. All benchmarking data is available at https://users.cs.fiu.edu/~fsaeed/Benchmark.html.
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152
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Pfleiderer MM, Galej WP. Structure of the catalytic core of the Integrator complex. Mol Cell 2021; 81:1246-1259.e8. [PMID: 33548203 PMCID: PMC7980224 DOI: 10.1016/j.molcel.2021.01.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/29/2020] [Accepted: 01/05/2021] [Indexed: 12/17/2022]
Abstract
The Integrator is a specialized 3' end-processing complex involved in cleavage and transcription termination of a subset of nascent RNA polymerase II transcripts, including small nuclear RNAs (snRNAs). We provide evidence of the modular nature of the Integrator complex by biochemically characterizing its two subcomplexes, INTS5/8 and INTS10/13/14. Using cryoelectron microscopy (cryo-EM), we determined a 3.5-Å-resolution structure of the INTS4/9/11 ternary complex, which constitutes Integrator's catalytic core. Our structure reveals the spatial organization of the catalytic nuclease INTS11, bound to its catalytically impaired homolog INTS9 via several interdependent interfaces. INTS4, a helical repeat protein, plays a key role in stabilizing nuclease domains and other components. In this assembly, all three proteins form a composite electropositive groove, suggesting a putative RNA binding path within the complex. Comparison with other 3' end-processing machineries points to distinct features and a unique architecture of the Integrator's catalytic module.
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Affiliation(s)
- Moritz M Pfleiderer
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France
| | - Wojciech P Galej
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, 38042 Grenoble, France.
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153
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Xiang Y, Sang Z, Bitton L, Xu J, Liu Y, Schneidman-Duhovny D, Shi Y. Integrative proteomics identifies thousands of distinct, multi-epitope, and high-affinity nanobodies. Cell Syst 2021; 12:220-234.e9. [PMID: 33592195 PMCID: PMC7979497 DOI: 10.1016/j.cels.2021.01.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 10/13/2020] [Accepted: 01/20/2021] [Indexed: 12/15/2022]
Abstract
The antibody immune response is essential for the survival of mammals. However, we still lack a systematic understanding of the antibody repertoire. Here, we developed a proteomic strategy to survey, at an unprecedented scale, the landscape of antigen-engaged, circulating camelid heavy-chain antibodies, whose minimal binding fragments are called VHH antibodies or nanobodies. The sensitivity and robustness of this approach were validated with three antigens spanning orders of magnitude in immune responses; thousands of distinct, high-affinity nanobody families were reliably identified and quantified. Using high-throughput structural modeling, cross-linking mass spectrometry, mutagenesis, and deep learning, we mapped and analyzed the epitopes of >100,000 antigen-nanobody complexes. Our results revealed a surprising diversity of ultrahigh-affinity camelid nanobodies for specific antigen binding on various dominant epitope clusters. Nanobodies utilize both shape and charge complementarity to enable highly selective antigen binding. Interestingly, we found that nanobody-antigen binding can mimic conserved intracellular protein-protein interactions. A record of this paper's Transparent Peer Review process is included in the Supplemental information.
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Affiliation(s)
- Yufei Xiang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhe Sang
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA
| | - Lirane Bitton
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel
| | - Jianquan Xu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dina Schneidman-Duhovny
- School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Israel.
| | - Yi Shi
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, USA; University of Pittsburgh, Carnegie Mellon University Program for Computational Biology, Pittsburgh, PA, USA.
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154
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Zequan X, Yonggang S, Guangjuan L, Shijun X, Li Z, Mingrui Z, Yanli X, Zirong W. Proteomics analysis as an approach to understand the formation of pale, soft, and exudative (PSE) pork. Meat Sci 2021; 177:108353. [PMID: 33721680 DOI: 10.1016/j.meatsci.2020.108353] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 09/12/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022]
Abstract
We investigated ten pale, soft, and exudative (PSE), and ten normal meat samples from pig carcasses. The meat quality at 0, 5, 12, and 24 h post-mortem and the key enzyme activities at 0 and 24 h post-mortem were determined. We selected three PSE and three normal samples for proteomics analysis at 0 h and 24 h post-mortem. No remarkable differences in pyruvate kinase (PK) and lactate dehydrogenase (LDH) activity were observed between samples at 0 h post-mortem; however, creatine kinase (CK) activity was significantly higher in PSE meat. Hexokinase (HK) activity in PSE samples was higher than that in normal samples at 24 h post-mortem. Bioinformatics analysis of the proteome showed that PSE was related to glycolysis, TCA cycle, oxidative phosphorylation, muscle tissue structure, signal transduction, and molecular chaperones. This research found that proteins such as troponin T slow skeletal muscle isoform X, GADPH, L-lactate dehydrogenase A chain, and gamma-enolase isoform X1 might be responsible for PSE.
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Affiliation(s)
- Xu Zequan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China; Tecon Biology Ltd, Xinjiang, China
| | - Shao Yonggang
- College of Animal Science, Xinjiang Agricultural University, Xinjiang, China
| | - Liu Guangjuan
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China
| | - Xing Shijun
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China
| | - Zhang Li
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China
| | - Zhu Mingrui
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China
| | - Xu Yanli
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China
| | - Wang Zirong
- College of Food Science and Pharmaceutics, Xinjiang Agricultural University, Xinjiang, China.
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155
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Ivanov MV, Bubis JA, Gorshkov V, Abdrakhimov DA, Kjeldsen F, Gorshkov MV. Boosting MS1-only Proteomics with Machine Learning Allows 2000 Protein Identifications in Single-Shot Human Proteome Analysis Using 5 min HPLC Gradient. J Proteome Res 2021; 20:1864-1873. [PMID: 33720732 DOI: 10.1021/acs.jproteome.0c00863] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proteome-wide analyses rely on tandem mass spectrometry and the extensive separation of proteolytic mixtures. This imposes considerable instrumental time consumption, which is one of the main obstacles in the broader acceptance of proteomics in biomedical and clinical research. Recently, we presented a fast proteomic method termed DirectMS1 based on ultrashort LC gradients as well as MS1-only mass spectra acquisition and data processing. The method allows significant reduction of the proteome-wide analysis time to a few minutes at the depth of quantitative proteome coverage of 1000 proteins at 1% false discovery rate (FDR). In this work, to further increase the capabilities of the DirectMS1 method, we explored the opportunities presented by the recent progress in the machine-learning area and applied the LightGBM decision tree boosting algorithm to the scoring of peptide feature matches when processing MS1 spectra. Furthermore, we integrated the peptide feature identification algorithm of DirectMS1 with the recently introduced peptide retention time prediction utility, DeepLC. Additional approaches to improve the performance of the DirectMS1 method are discussed and demonstrated, such as using FAIMS for gas-phase ion separation. As a result of all improvements to DirectMS1, we succeeded in identifying more than 2000 proteins at 1% FDR from the HeLa cell line in a 5 min gradient LC-FAIMS/MS1 analysis. The data sets generated and analyzed during the current study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD023977.
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Affiliation(s)
- Mark V Ivanov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Julia A Bubis
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
| | - Vladimir Gorshkov
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Daniil A Abdrakhimov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia.,Moscow Institute of Physics and Technology, Institutsky lane 9, Dolgoprudny, Moscow Region 141700, Russia
| | - Frank Kjeldsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Mikhail V Gorshkov
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, 38 Leninsky Pr., Bld. 2, Moscow 119334, Russia
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156
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Huang C, Chen L, Savage SR, Eguez RV, Dou Y, Li Y, da Veiga Leprevost F, Jaehnig EJ, Lei JT, Wen B, Schnaubelt M, Krug K, Song X, Cieślik M, Chang HY, Wyczalkowski MA, Li K, Colaprico A, Li QK, Clark DJ, Hu Y, Cao L, Pan J, Wang Y, Cho KC, Shi Z, Liao Y, Jiang W, Anurag M, Ji J, Yoo S, Zhou DC, Liang WW, Wendl M, Vats P, Carr SA, Mani DR, Zhang Z, Qian J, Chen XS, Pico AR, Wang P, Chinnaiyan AM, Ketchum KA, Kinsinger CR, Robles AI, An E, Hiltke T, Mesri M, Thiagarajan M, Weaver AM, Sikora AG, Lubiński J, Wierzbicka M, Wiznerowicz M, Satpathy S, Gillette MA, Miles G, Ellis MJ, Omenn GS, Rodriguez H, Boja ES, Dhanasekaran SM, Ding L, Nesvizhskii AI, El-Naggar AK, Chan DW, Zhang H, Zhang B. Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma. Cancer Cell 2021; 39:361-379.e16. [PMID: 33417831 PMCID: PMC7946781 DOI: 10.1016/j.ccell.2020.12.007] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 09/13/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023]
Abstract
We present a proteogenomic study of 108 human papilloma virus (HPV)-negative head and neck squamous cell carcinomas (HNSCCs). Proteomic analysis systematically catalogs HNSCC-associated proteins and phosphosites, prioritizes copy number drivers, and highlights an oncogenic role for RNA processing genes. Proteomic investigation of mutual exclusivity between FAT1 truncating mutations and 11q13.3 amplifications reveals dysregulated actin dynamics as a common functional consequence. Phosphoproteomics characterizes two modes of EGFR activation, suggesting a new strategy to stratify HNSCCs based on EGFR ligand abundance for effective treatment with inhibitory EGFR monoclonal antibodies. Widespread deletion of immune modulatory genes accounts for low immune infiltration in immune-cold tumors, whereas concordant upregulation of multiple immune checkpoint proteins may underlie resistance to anti-programmed cell death protein 1 monotherapy in immune-hot tumors. Multi-omic analysis identifies three molecular subtypes with high potential for treatment with CDK inhibitors, anti-EGFR antibody therapy, and immunotherapy, respectively. Altogether, proteogenomics provides a systematic framework to inform HNSCC biology and treatment.
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Affiliation(s)
- Chen Huang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lijun Chen
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Sara R Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rodrigo Vargas Eguez
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Yongchao Dou
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | | | - Eric J Jaehnig
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bo Wen
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael Schnaubelt
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Xiaoyu Song
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcin Cieślik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Hui-Yin Chang
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew A Wyczalkowski
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Kai Li
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Antonio Colaprico
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Qing Kay Li
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - David J Clark
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Yingwei Hu
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Liwei Cao
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jianbo Pan
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA; Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Yuefan Wang
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Kyung-Cho Cho
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Zhiao Shi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxing Liao
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wen Jiang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jiayi Ji
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel Cui Zhou
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Wen-Wei Liang
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Michael Wendl
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Steven A Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Zhen Zhang
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jiang Qian
- Department of Ophthalmology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Xi S Chen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Biostatistics, Department of Public Health Science, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences and Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Christopher R Kinsinger
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Eunkyung An
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Mathangi Thiagarajan
- Leidos Biomedical Research Inc., Frederick NaVonal Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Andrew G Sikora
- Department of Head and Neck Surgery, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, 71-252 Szczecin, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland
| | - Małgorzata Wierzbicka
- Poznań University of Medical Sciences, 61-701 Poznań, Poland; Institute of Human Genetics Polish Academy of Sciences, 60-479 Poznań, Poland
| | - Maciej Wiznerowicz
- International Institute for Molecular Oncology, 60-203 Poznań, Poland; Poznań University of Medical Sciences, 61-701 Poznań, Poland
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - George Miles
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gilbert S Omenn
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily S Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Saravana M Dhanasekaran
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Li Ding
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Alexey I Nesvizhskii
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adel K El-Naggar
- Department of Pathology, Division of Pathology and Laboratory Medicine, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Daniel W Chan
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
| | - Hui Zhang
- Department of Pathology and Oncology, Johns Hopkins University, Baltimore, MD 21231, USA.
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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157
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Zhang M, Zhen Y, Mi T, Lin S. Integrated RNA-seq and Proteomic Studies Reveal Resource Reallocation towards Energy Metabolism and Defense in Skeletonema marinoi in Response to CO 2 Increase. Appl Environ Microbiol 2021; 87:AEM.02614-20. [PMID: 33355106 PMCID: PMC8090871 DOI: 10.1128/aem.02614-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 12/05/2020] [Indexed: 11/20/2022] Open
Abstract
Rising atmospheric CO2 concentrations are causing ocean acidification (OA) with significant consequences for marine organisms. Because CO2 is essential for photosynthesis, the effect of elevated CO2 on phytoplankton is more complex and the mechanism is poorly understood. Here we applied RNA-seq and iTRAQ proteomics to investigate the impacts of CO2 increase (from ∼400 to 1000 ppm) on the temperate coastal marine diatom Skeletonema marinoi We identified 32,389 differentially expressed genes (DEGs) and 1,826 differentially expressed proteins (DEPs) from elevated CO2 conditions, accounting for 48.5% of total genes and 25.9% of total proteins we detected, respectively. Elevated pCO2 significantly inhibited the growth of S marinoi, and the 'omic' data suggested that this might be due to compromised photosynthesis in the chloroplast and raised mitochondrial energy metabolism. Furthermore, many genes/proteins associated with nitrogen metabolism, transcriptional regulation, and translational regulation were markedly up-regulated, suggesting enhanced protein synthesis. In addition, S marinoi exhibited higher capacity of ROS production and resistance to oxidative stress. Overall, elevated pCO2 seems to repress photosynthesis and growth of S marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.Importance Rising atmospheric CO2 concentrations are causing ocean acidification with significant consequences for marine organisms. Chain-forming centric diatoms of Skeletonema is one of the most successful groups of eukaryotic primary producers with widespread geographic distribution. Among the recognized 28 species, S. marinoi can be a useful model for investigating the ecological, genetic, physiological, and biochemical characteristics of diatoms in temperate coastal regions. In this study, we found that the elevated pCO2 seems to repress photosynthesis and growth of S. marinoi, and through massive gene expression reconfiguration induce cells to increase investment in protein synthesis, energy metabolism and antioxidative stress defense, likely to maintain pH homeostasis and population survival. This survival strategy may deprive this usually dominant diatom in temperate coastal waters of its competitive advantages in acidified environments.
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Affiliation(s)
- Mei Zhang
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
- Department of marine science, University of Connecticut, Groton, CT 06340, USA
| | - Yu Zhen
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Tiezhu Mi
- Key Laboratory of Marine Environment and Ecology, Ocean University of China, Ministry of Education, Qingdao 266100, China
- Laboratory for Marine Ecology and Environmental Science, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- College of Environmental Science and Engineering, Ocean University of China, Qingdao 266100, China
| | - Senjie Lin
- Department of marine science, University of Connecticut, Groton, CT 06340, USA
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158
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Omenn GS. Reflections on the HUPO Human Proteome Project, the Flagship Project of the Human Proteome Organization, at 10 Years. Mol Cell Proteomics 2021; 20:100062. [PMID: 33640492 PMCID: PMC8058560 DOI: 10.1016/j.mcpro.2021.100062] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 02/08/2023] Open
Abstract
We celebrate the 10th anniversary of the launch of the HUPO Human Proteome Project (HPP) and its major milestone of confident detection of at least one protein from each of 90% of the predicted protein-coding genes, based on the output of the entire proteomics community. The Human Genome Project reached a similar decadal milestone 20 years ago. The HPP has engaged proteomics teams around the world, strongly influenced data-sharing, enhanced quality assurance, and issued stringent guidelines for claims of detecting previously "missing proteins." This invited perspective complements papers on "A High-Stringency Blueprint of the Human Proteome" and "The Human Proteome Reaches a Major Milestone" in special issues of Nature Communications and Journal of Proteome Research, respectively, released in conjunction with the October 2020 virtual HUPO Congress and its celebration of the 10th anniversary of the HUPO HPP.
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Affiliation(s)
- Gilbert S Omenn
- University of Michigan Medical School, Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, and School of Public Health, Ann Arbor, Michigan, USA.
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159
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Mohammadi A, Tschanz A, Leitner A. Expanding the Cross-Link Coverage of a Carboxyl-Group Specific Chemical Cross-Linking Strategy for Structural Proteomics Applications. Anal Chem 2021; 93:1944-1950. [PMID: 33399445 DOI: 10.1021/acs.analchem.0c03926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carboxyl-group specific chemical cross-linking is gaining an increased interest as a structural mass spectrometry/structural proteomics technique that is complementary to the more commonly used amine-specific chemistry using succinimide esters. One of these protocols uses a combination of dihydrazide linkers and the coupling reagent DMTMM [4-(4,6-dimethoxy-1,3,5-triazin-2-yl)-4-methylmorpholinium] chloride, which allows performing the reaction at neutral pH. The reaction yields two types of products, carboxyl-carboxyl cross-links that incorporate the dihydrazide linker and zero-length carboxyl-amine cross-links induced by DMTMM alone. Until now, it has not been systematically investigated how the balance between the two products is affected by experimental conditions. Here, we studied the role of the ratios of the two reagents (using pimelic dihydrazide and DMTMM) and demonstrate that the concentration of the two reagents can be systematically adjusted to favor one reaction product over the other. Using a set of five model proteins, we observed that the number of identified cross-linked peptides could be more than doubled by a combination of three different reaction conditions. We also applied this strategy to the bovine 20S proteasome and the Escherichia coli 70S ribosome, again demonstrating complementarity and increased cross-link coverage.
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Affiliation(s)
- Azadeh Mohammadi
- Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, bd. du Triomphe, Access 2 - 1050 Brussels, Belgium.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Aline Tschanz
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
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160
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Wang SN, Yao ZW, Zhao CB, Ding YS, Bian LH, Li QY, Wang XM, Shi JL, Guo JY, Wang CG. Discovery and proteomics analysis of effective compounds in Valeriana jatamansi jones for the treatment of anxiety. JOURNAL OF ETHNOPHARMACOLOGY 2021; 265:113452. [PMID: 33069789 DOI: 10.1016/j.jep.2020.113452] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 09/18/2020] [Accepted: 10/02/2020] [Indexed: 06/11/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Zhizhu Xiang (ZZX for short) is the root and rhizome of Valeriana jatamansi Jones, which is a Traditional Chinese Medicine (TCM) used to treat various mood disorders for more than 2000 years, especially anxiety. However, there have been few investigations to clarify the compounds in ZZX for the treatment of anxiety. AIM OF THE STUDY Our previous study has identified five anti-anxiety components, including hesperidin, isochlorogenic acid A, isochlorogenic acid B and isochlorogenic acid C and chlorogenic acid, from extract of ZZX. In order to find the optimal combination and the underlying mechanism of these five components in the treatment of anxiety disorder, researches were designed based on uniform design method and proteomic technology. MATERIALS AND METHODS The samples with different proportion and content of the five active components were arranged by uniform design method. Then a mathematical model was formulated using partial least square method and stepwise regression analysis. Moreover, the empty bottle stress-induced anxiety rat model was established, and the anti-anxiety effect was recorded by the unconditioned reflex elevated maze test and the open field test. In addition, the isobaric tags for relative and absolute quantitation (iTRAQ) technique, along with the multidimensional liquid chromatography and high-resolution mass spectrometry were applied in proteomic study. At last, the result of proteomic analysis was further confirmed by Western blot. RESULTS The optimal combination of the components from the extract of ZZX was 1.153 mg/kg hesperidin, 2.197 mg/kg Isochlorogenic acid A, 0.699 mg/kg Isochlorogenic acid B and 1.249 mg/kg Chlorogenic acid. Total 6818 proteins were identified using proteomic analysis and 80 differentially expressed proteins were used for further bioinformatic analysis. These proteins were involved in the neuroactive ligand-receptor interaction, protein digestion and absorption, cholesterol metabolism, Chagas disease, and AGE/RAGE signaling pathway. CONCLUSIONS The composition and proportion of anti-anxiety components in extract of ZZX was disclosed, and there was an anti-anxiety effect for the combined components of flavonoids and phenolic acids. Through proteomic analysis and Western blot, it was found that the effective components of extract of ZZX can exert synergistic anti-anxiety effects via the regulation of multi-signaling pathways. These findings could provide a preliminary research basis for the development of new low-toxic, efficient, stable and controllable anti-anxiety drugs.
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Affiliation(s)
- Shao-Nan Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China; School of Pharmacy, Hebei University of Chinese Medicine, 3 Xingyuan Road, Luquan District, Shijiazhuang City, Hebei, 050200, China.
| | - Zi-Wei Yao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Cheng-Bowen Zhao
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Yong-Sheng Ding
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Li-Hua Bian
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Qiu-Yu Li
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Xiao-Mei Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Jin-Li Shi
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
| | - Jian-You Guo
- CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of Sciences, 4A DatunRoad, Chaoyang District, Beijing, 100101, China.
| | - Chun-Guo Wang
- School of Chinese Materia Medica, Beijing University of Chinese Medicine, 11A North Third Ring East Road, Chaoyang District, Beijing, 100029, China.
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161
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Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol 2021; 22:50. [PMID: 33504367 PMCID: PMC7839219 DOI: 10.1186/s13059-021-02267-5] [Citation(s) in RCA: 283] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/07/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative single-cell protein analysis. RESULTS To overcome this limitation, we develop SCoPE2, which substantially increases quantitative accuracy and throughput while lowering cost and hands-on time by introducing automated and miniaturized sample preparation. These advances enable us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiate into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantifies over 3042 proteins in 1490 single monocytes and macrophages in 10 days of instrument time, and the quantified proteins allow us to discern single cells by cell type. Furthermore, the data uncover a continuous gradient of proteome states for the macrophages, suggesting that macrophage heterogeneity may emerge in the absence of polarizing cytokines. Parallel measurements of transcripts by 10× Genomics suggest that our measurements sample 20-fold more protein copies than RNA copies per gene, and thus, SCoPE2 supports quantification with improved count statistics. This allowed exploring regulatory interactions, such as interactions between the tumor suppressor p53, its transcript, and the transcripts of genes regulated by p53. CONCLUSIONS Even in a homogeneous environment, macrophage proteomes are heterogeneous. This heterogeneity correlates to the inflammatory axis of classically and alternatively activated macrophages. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass spectrometry and demonstrates the potential for inferring transcriptional and post-transcriptional regulation from variability across single cells.
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Affiliation(s)
- Harrison Specht
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA.
| | - Edward Emmott
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Present Address: Department of Biochemistry, Centre for Proteome Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Aleksandra A Petelski
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - R Gray Huffman
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - David H Perlman
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Present Address: Merck Exploratory Sciences Center, Merck Sharp & Dohme Corp., 320 Bent St., Cambridge, MA, 02141, USA
| | - Marco Serra
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Antonius Koller
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA.
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162
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Specht H, Emmott E, Petelski AA, Huffman RG, Perlman DH, Serra M, Kharchenko P, Koller A, Slavov N. Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2. Genome Biol 2021; 22:50. [PMID: 33504367 DOI: 10.1101/665307] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 01/07/2021] [Indexed: 05/27/2023] Open
Abstract
BACKGROUND Macrophages are innate immune cells with diverse functional and molecular phenotypes. This diversity is largely unexplored at the level of single-cell proteomes because of the limitations of quantitative single-cell protein analysis. RESULTS To overcome this limitation, we develop SCoPE2, which substantially increases quantitative accuracy and throughput while lowering cost and hands-on time by introducing automated and miniaturized sample preparation. These advances enable us to analyze the emergence of cellular heterogeneity as homogeneous monocytes differentiate into macrophage-like cells in the absence of polarizing cytokines. SCoPE2 quantifies over 3042 proteins in 1490 single monocytes and macrophages in 10 days of instrument time, and the quantified proteins allow us to discern single cells by cell type. Furthermore, the data uncover a continuous gradient of proteome states for the macrophages, suggesting that macrophage heterogeneity may emerge in the absence of polarizing cytokines. Parallel measurements of transcripts by 10× Genomics suggest that our measurements sample 20-fold more protein copies than RNA copies per gene, and thus, SCoPE2 supports quantification with improved count statistics. This allowed exploring regulatory interactions, such as interactions between the tumor suppressor p53, its transcript, and the transcripts of genes regulated by p53. CONCLUSIONS Even in a homogeneous environment, macrophage proteomes are heterogeneous. This heterogeneity correlates to the inflammatory axis of classically and alternatively activated macrophages. Our methodology lays the foundation for automated and quantitative single-cell analysis of proteins by mass spectrometry and demonstrates the potential for inferring transcriptional and post-transcriptional regulation from variability across single cells.
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Affiliation(s)
- Harrison Specht
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA.
| | - Edward Emmott
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Present Address: Department of Biochemistry, Centre for Proteome Research, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Aleksandra A Petelski
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - R Gray Huffman
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - David H Perlman
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
- Present Address: Merck Exploratory Sciences Center, Merck Sharp & Dohme Corp., 320 Bent St., Cambridge, MA, 02141, USA
| | - Marco Serra
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Peter Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, 02115, USA
| | - Antonius Koller
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA
| | - Nikolai Slavov
- Department of Bioengineering and Barnett Institute, Northeastern University, Boston, MA, 02115, USA.
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163
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Karkampouna S, De Filippo MR, Ng CKY, Klima I, Zoni E, Spahn M, Stein F, Haberkant P, Thalmann GN, Kruithof-de Julio M. Stroma Transcriptomic and Proteomic Profile of Prostate Cancer Metastasis Xenograft Models Reveals Prognostic Value of Stroma Signatures. Cancers (Basel) 2020; 12:cancers12123786. [PMID: 33334054 PMCID: PMC7768471 DOI: 10.3390/cancers12123786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023] Open
Abstract
Resistance acquisition to androgen deprivation treatment and metastasis progression are a major clinical issue associated with prostate cancer (PCa). The role of stroma during disease progression is insufficiently defined. Using transcriptomic and proteomic analyses on differentially aggressive patient-derived xenografts (PDXs), we investigated whether PCa tumors predispose their microenvironment (stroma) to a metastatic gene expression pattern. RNA sequencing was performed on the PCa PDXs BM18 (castration-sensitive) and LAPC9 (castration-resistant), representing different disease stages. Using organism-specific reference databases, the human-specific transcriptome (tumor) was identified and separated from the mouse-specific transcriptome (stroma). To identify proteomic changes in the tumor (human) versus the stroma (mouse), we performed human/mouse cell separation and subjected protein lysates to quantitative Tandem Mass Tag labeling and mass spectrometry. Tenascin C (TNC) was among the most abundant stromal genes, modulated by androgen levels in vivo and highly expressed in castration-resistant LAPC9 PDX. The tissue microarray of primary PCa samples (n = 210) showed that TNC is a negative prognostic marker of the clinical progression to recurrence or metastasis. Stroma markers of osteoblastic PCa bone metastases seven-up signature were induced in the stroma by the host organism in metastatic xenografts, indicating conserved mechanisms of tumor cells to induce a stromal premetastatic signature. A 50-gene list stroma signature was identified based on androgen-dependent responses, which shows a linear association with the Gleason score, metastasis progression and progression-free survival. Our data show that metastatic PCa PDXs, which differ in androgen sensitivity, trigger differential stroma responses, which show the metastasis risk stratification and prognostic biomarker potential.
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Affiliation(s)
- Sofia Karkampouna
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Maria R. De Filippo
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Charlotte K. Y. Ng
- Oncogenomics Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 40, 3008 Bern, Switzerland;
| | - Irena Klima
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Eugenio Zoni
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
| | - Martin Spahn
- Lindenhofspital Bern, Prostate Center Bern, 3012 Bern, Switzerland;
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; (F.S.); (P.H.)
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; (F.S.); (P.H.)
| | - George N. Thalmann
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
- Department of Urology, Inselspital, Anna Seiler Haus, Bern University Hospital, 3010 Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Urology Research Laboratory, Department for BioMedical Research, University of Bern, Murtenstrasse 35, 3008 Bern, Switzerland; (S.K.); (M.R.D.F.); (I.K.); (E.Z.); (G.N.T.)
- Department of Urology, Inselspital, Anna Seiler Haus, Bern University Hospital, 3010 Bern, Switzerland
- Correspondence:
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164
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Smolikova G, Gorbach D, Lukasheva E, Mavropolo-Stolyarenko G, Bilova T, Soboleva A, Tsarev A, Romanovskaya E, Podolskaya E, Zhukov V, Tikhonovich I, Medvedev S, Hoehenwarter W, Frolov A. Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. Int J Mol Sci 2020; 21:E9162. [PMID: 33271881 PMCID: PMC7729594 DOI: 10.3390/ijms21239162] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
For centuries, crop plants have represented the basis of the daily human diet. Among them, cereals and legumes, accumulating oils, proteins, and carbohydrates in their seeds, distinctly dominate modern agriculture, thus play an essential role in food industry and fuel production. Therefore, seeds of crop plants are intensively studied by food chemists, biologists, biochemists, and nutritional physiologists. Accordingly, seed development and germination as well as age- and stress-related alterations in seed vigor, longevity, nutritional value, and safety can be addressed by a broad panel of analytical, biochemical, and physiological methods. Currently, functional genomics is one of the most powerful tools, giving direct access to characteristic metabolic changes accompanying plant development, senescence, and response to biotic or abiotic stress. Among individual post-genomic methodological platforms, proteomics represents one of the most effective ones, giving access to cellular metabolism at the level of proteins. During the recent decades, multiple methodological advances were introduced in different branches of life science, although only some of them were established in seed proteomics so far. Therefore, here we discuss main methodological approaches already employed in seed proteomics, as well as those still waiting for implementation in this field of plant research, with a special emphasis on sample preparation, data acquisition, processing, and post-processing. Thereby, the overall goal of this review is to bring new methodologies emerging in different areas of proteomics research (clinical, food, ecological, microbial, and plant proteomics) to the broad society of seed biologists.
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Affiliation(s)
- Galina Smolikova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Daria Gorbach
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Elena Lukasheva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Gregory Mavropolo-Stolyarenko
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Tatiana Bilova
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alena Soboleva
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Alexander Tsarev
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
| | - Ekaterina Romanovskaya
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
| | - Ekaterina Podolskaya
- Institute of Analytical Instrumentation, Russian Academy of Science; 190103 St. Petersburg, Russia;
- Institute of Toxicology, Russian Federal Medical Agency; 192019 St. Petersburg, Russia
| | - Vladimir Zhukov
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
| | - Igor Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology; 196608 St. Petersburg, Russia; (V.Z.); (I.T.)
- Department of Genetics and Biotechnology, St. Petersburg State University; 199034 St. Petersburg, Russia
| | - Sergei Medvedev
- Department of Plant Physiology and Biochemistry, St. Petersburg State University; 199034 St. Petersburg, Russia; (G.S.); (T.B.); (S.M.)
| | - Wolfgang Hoehenwarter
- Proteome Analytics Research Group, Leibniz Institute of Plant Biochemistry, 06120 Halle (Saale), Germany;
| | - Andrej Frolov
- Department of Biochemistry, St. Petersburg State University; 199178 St. Petersburg, Russia; (D.G.); (E.L.); (G.M.-S.); (A.S.); (A.T.); (E.R.)
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry; 06120 Halle (Saale), Germany
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165
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Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM. A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles. Nat Commun 2020; 11:5783. [PMID: 33188197 PMCID: PMC7666118 DOI: 10.1038/s41467-020-19529-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 10/14/2020] [Indexed: 02/06/2023] Open
Abstract
Detecting ligand-protein interactions in living cells is a fundamental challenge in molecular biology and drug research. Proteome-wide profiling of thermal stability as a function of ligand concentration promises to tackle this challenge. However, current data analysis strategies use preset thresholds that can lead to suboptimal sensitivity/specificity tradeoffs and limited comparability across datasets. Here, we present a method based on statistical hypothesis testing on curves, which provides control of the false discovery rate. We apply it to several datasets probing epigenetic drugs and a metabolite. This leads us to detect off-target drug engagement, including the finding that the HDAC8 inhibitor PCI-34051 and its analog BRD-3811 bind to and inhibit leucine aminopeptidase 3. An implementation is available as an R package from Bioconductor (https://bioconductor.org/packages/TPP2D). We hope that our method will facilitate prioritizing targets from thermal profiling experiments. 2D-thermal proteome profiling (2D-TPP) is a powerful assay for probing interactions of proteins with small molecules in their native context. Here the authors provide a statistical method for false discovery rate controlled analysis for 2D-TPP applications.
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Affiliation(s)
- Nils Kurzawa
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, 69120, Germany
| | - Isabelle Becher
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Sindhuja Sridharan
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.,Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Holger Franken
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - André Mateus
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany
| | - Simon Anders
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, Heidelberg, 69120, Germany
| | - Marcus Bantscheff
- Cellzome GmbH, GlaxoSmithKline, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Wolfgang Huber
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, Meyerhofstrasse 1, Heidelberg, 69117, Germany.
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166
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Zhao X, Li J, Zhu Q, Liang G, Xia W, He X, Zhu C, Qi H, Deng B, Chen X, Zhang J. HLA-A and HLA-DRB1 may play a unique role in ovarian teratoma-associated anti-N-methyl-D-aspartate receptor encephalitis. Reprod Biol Endocrinol 2020; 18:107. [PMID: 33160385 PMCID: PMC7648266 DOI: 10.1186/s12958-020-00661-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ovarian teratoma-associated anti-N-methyl-D-aspartate receptor encephalitis (NMDAR-E) is a severe autoimmune neurological disorder, and the influence of teratoma-induced autoantibodies on the pathogenesis remains unclear. METHODS Ovarian teratoma tissues were collected from teratoma patients with and without NMDAR-E. Proteins were extracted and then analyzed using iTRAQ-coupled LC-MS/MS, which was followed by bioinformatics analysis. Candidate proteins were verified by Western blotting and immunohistochemistry. RESULTS In total, 36 differentially expressed proteins (DEPs) were identified between the control group and NMDAR-E group, and the bioinformatics analysis revealed that the DEPs were mainly involved in immune-related pathways, especially HLA-A and HLA-DRB1. The western blotting results for HLA-A and HLA-DRB1 were consistent with the results of the iTRAQ analysis. Additionally, the immunohistochemical data revealed that the aggregation of HLA-A (+) and HLA-DRB1 (+) cells was more apparent in the teratoma tissues of NMDAR-E patients compared with that in the tissues of controls. CONCLUSION Our investigation indicated that HLA-A and HLA-DRB1 might be involved in mediating ovarian teratoma-associated NMDAR-E. These findings provide new insights into the pathophysiological mechanisms and provide information for the functional exploration of proteins in the future.
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Affiliation(s)
- Xiaoya Zhao
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Juan Li
- Department of Pathology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, 200030, China
| | - Qian Zhu
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Guiling Liang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Wei Xia
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Xiaoqing He
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Chenfeng Zhu
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Hang Qi
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China
| | - Bo Deng
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, No. 12 Wulumuqi Zhong Road, Shanghai, 200040, China
| | - Xiangjun Chen
- Department of Neurology, Huashan Hospital and Institute of Neurology, Fudan University, No. 12 Wulumuqi Zhong Road, Shanghai, 200040, China.
| | - Jian Zhang
- Department of Obstetrics and Gynecology, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiaotong University, No. 910, Hengshan Rd, Shanghai, 200030, China.
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167
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Couté Y, Bruley C, Burger T. Beyond Target-Decoy Competition: Stable Validation of Peptide and Protein Identifications in Mass Spectrometry-Based Discovery Proteomics. Anal Chem 2020; 92:14898-14906. [PMID: 32970414 DOI: 10.1021/acs.analchem.0c00328] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In bottom-up discovery proteomics, target-decoy competition (TDC) is the most popular method for false discovery rate (FDR) control. Despite unquestionable statistical foundations, this method has drawbacks, including its hitherto unknown intrinsic lack of stability vis-à-vis practical conditions of application. Although some consequences of this instability have already been empirically described, they may have been misinterpreted. This article provides evidence that TDC has become less reliable as the accuracy of modern mass spectrometers improved. We therefore propose to replace TDC by a totally different method to control the FDR at the spectrum, peptide, and protein levels, while benefiting from the theoretical guarantees of the Benjamini-Hochberg framework. As this method is simpler to use, faster to compute, and more stable than TDC, we argue that it is better adapted to the standardization and throughput constraints of current proteomic platforms.
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Affiliation(s)
- Yohann Couté
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Christophe Bruley
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
| | - Thomas Burger
- Université Grenoble Alpes, CNRS, CEA, INSERM, IRIG, BGE, F-38000 Grenoble, France
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168
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Abstract
Chinese black truffle (Tuber indicum) is rich in nutrition. However, commercial interests lead to the aroma components and nutrients of T. indicum being greatly affected by overexploitation without consideration of their maturity. This study investigated the proteomic and metabolomic profiles of truffle fruiting bodies at different maturities using a meta-proteomic approach. Among the 3007 identified proteins, the most up-expressed protein in the mature ascocarps was involved in the peptidyl-diphthamide biosynthetic process, while thiamine metabolism was the most differentially expressed pathway. Furthermore, a total of 54 metabolites identified upon LC-MS differed significantly, with 30 being up-expressed in the mature ascocarps, including organic acids, carnitine substances and polysaccharides. Additionally, the ash, protein, fat, crude fiber and total sugar contents were all higher in the mature ascocarps. Overall, our findings reveal that mature truffles have a higher nutritional value, providing a basis for further exploring protein functionality of T. indicum at different maturities.
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169
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Li J, Paulo JA, Nusinow DP, Huttlin EL, Gygi SP. Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. Cell Rep 2020; 29:2092-2104.e4. [PMID: 31722220 PMCID: PMC7382779 DOI: 10.1016/j.celrep.2019.10.034] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/30/2019] [Accepted: 10/09/2019] [Indexed: 12/25/2022] Open
Abstract
Governance of protein phosphorylation by kinases and phosphatases constitutes an essential regulatory network in eukaryotic cells. Network dysregulation leads to severe consequences and is often a key factor in disease pathogenesis. Previous studies revealed multiple roles for protein phosphorylation and pathway structures in cellular functions from different perspectives. We seek to understand the roles of kinases and phosphatases from a protein homeostasis point of view. Using a streamlined tandem mass tag (SL-TMT) strategy, we systematically measure proteomic and phosphoproteomic responses to perturbations of phosphorylation signaling networks in yeast deletion strains. Our results emphasize the requirement for protein normalization for more complete interpretation of phosphorylation data. Functional relationships between kinases and phosphatases were characterized at both proteome and phosphoproteome levels in three ways: (1) Gene Ontology enrichment analysis, (2) Δgene-Δgene correlation networks, and (3) molecule covariance networks. This resource illuminates kinase and phosphatase functions and pathway organizations.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David P Nusinow
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.
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170
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Zhang B, Zhang X, Yan L, Kang Z, Tan H, Jia D, Yang L, Ye L, Li X. WITHDRAWN: Different maturities drive proteomic and metabolomic changes in Chinese black truffle. Food Chem X 2020. [DOI: 10.1016/j.fochx.2020.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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171
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Cao X, Han Y, Gu M, Du H, Song M, Zhu X, Ma G, Pan C, Wang W, Zhao E, Goulette T, Yuan B, Zhang G, Xiao H. Foodborne Titanium Dioxide Nanoparticles Induce Stronger Adverse Effects in Obese Mice than Non-Obese Mice: Gut Microbiota Dysbiosis, Colonic Inflammation, and Proteome Alterations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2001858. [PMID: 32519440 DOI: 10.1002/smll.202001858] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 05/23/2023]
Abstract
The recent ban of titanium dioxide (TiO2 ) as a food additive (E171) in France intensified the controversy on safety of foodborne-TiO2 nanoparticles (NPs). This study determines the biological effects of TiO2 NPs and TiO2 (E171) in obese and non-obese mice. Oral consumption (0.1 wt% in diet for 8 weeks) of TiO2 (E171, 112 nm) and TiO2 NPs (33 nm) does not cause severe toxicity in mice, but significantly alters composition of gut microbiota, for example, increased abundance of Firmicutes phylum and decreased abundance of Bacteroidetes phylum and Bifidobacterium and Lactobacillus genera, which are accompanied by decreased cecal levels of short-chain fatty acids. Both TiO2 (E171) and TiO2 NPs increase abundance of pro-inflammatory immune cells and cytokines in the colonic mucosa, indicating an inflammatory state. Importantly, TiO2 NPs cause stronger colonic inflammation than TiO2 (E171), and obese mice are more susceptible to the effects. A microbiota transplant study demonstrates that altered fecal microbiota by TiO2 NPs directly mediate inflammatory responses in the mouse colon. Furthermore, proteomic analysis shows that TiO2 NPs cause more alterations in multiple pathways in the liver and colon of obese mice than non-obese mice. This study provides important information on the health effects of foodborne inorganic nanoparticles.
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Affiliation(s)
- Xiaoqiong Cao
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Yanhui Han
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Min Gu
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Hengjun Du
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Mingyue Song
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Xiaoai Zhu
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, Henan, 450001, P. R. China
| | - Gaoxing Ma
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
- College of Food Science and Engineering, Nanjing University of Finance and Economics, Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing, 210023, P. R. China
| | - Che Pan
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Weicang Wang
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Ermin Zhao
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Timothy Goulette
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Biao Yuan
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Food Quality and Safety/National R&D Center for Chinese Herbal Medicine Processing, College of Engineering, China Pharmaceutical University, Nanjing, Jiangsu, 211198, P. R. China
| | - Guodong Zhang
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
| | - Hang Xiao
- Department of Food Science, University of Massachusetts, Amherst, MA, 01003, USA
- Department of Microbiology, University of Massachusetts, Amherst, MA, 01003, USA
- Institute for Applied Life Sciences, University of Massachusetts, Amherst, MA, 01003, USA
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172
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Manohar S, Yu Q, Gygi SP, King RW. The Insulin Receptor Adaptor IRS2 is an APC/C Substrate That Promotes Cell Cycle Protein Expression and a Robust Spindle Assembly Checkpoint. Mol Cell Proteomics 2020; 19:1450-1467. [PMID: 32554797 PMCID: PMC8143631 DOI: 10.1074/mcp.ra120.002069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/01/2020] [Indexed: 01/21/2023] Open
Abstract
Insulin receptor substrate 2 (IRS2) is an essential adaptor that mediates signaling downstream of the insulin receptor and other receptor tyrosine kinases. Transduction through IRS2-dependent pathways is important for coordinating metabolic homeostasis, and dysregulation of IRS2 causes systemic insulin signaling defects. Despite the importance of maintaining proper IRS2 abundance, little is known about what factors mediate its protein stability. We conducted an unbiased proteomic screen to uncover novel substrates of the Anaphase Promoting Complex/Cyclosome (APC/C), a ubiquitin ligase that controls the abundance of key cell cycle regulators. We found that IRS2 levels are regulated by APC/C activity and that IRS2 is a direct APC/C target in G1 Consistent with the APC/C's role in degrading cell cycle regulators, quantitative proteomic analysis of IRS2-null cells revealed a deficiency in proteins involved in cell cycle progression. We further show that cells lacking IRS2 display a weakened spindle assembly checkpoint in cells treated with microtubule inhibitors. Together, these findings reveal a new pathway for IRS2 turnover and indicate that IRS2 is a component of the cell cycle control system in addition to acting as an essential metabolic regulator.
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Affiliation(s)
- Sandhya Manohar
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Randall W King
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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173
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Bartel J, Varadarajan AR, Sura T, Ahrens CH, Maaß S, Becher D. Optimized Proteomics Workflow for the Detection of Small Proteins. J Proteome Res 2020; 19:4004-4018. [DOI: 10.1021/acs.jproteome.0c00286] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Adithi R. Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Thomas Sura
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Christian H. Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, D-17489 Greifswald, Germany
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174
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Sinha NK, Ordureau A, Best K, Saba JA, Zinshteyn B, Sundaramoorthy E, Fulzele A, Garshott DM, Denk T, Thoms M, Paulo JA, Harper JW, Bennett EJ, Beckmann R, Green R. EDF1 coordinates cellular responses to ribosome collisions. eLife 2020; 9:e58828. [PMID: 32744497 PMCID: PMC7486125 DOI: 10.7554/elife.58828] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/02/2020] [Indexed: 12/11/2022] Open
Abstract
Translation of aberrant mRNAs induces ribosomal collisions, thereby triggering pathways for mRNA and nascent peptide degradation and ribosomal rescue. Here we use sucrose gradient fractionation combined with quantitative proteomics to systematically identify proteins associated with collided ribosomes. This approach identified Endothelial differentiation-related factor 1 (EDF1) as a novel protein recruited to collided ribosomes during translational distress. Cryo-electron microscopic analyses of EDF1 and its yeast homolog Mbf1 revealed a conserved 40S ribosomal subunit binding site at the mRNA entry channel near the collision interface. EDF1 recruits the translational repressors GIGYF2 and EIF4E2 to collided ribosomes to initiate a negative-feedback loop that prevents new ribosomes from translating defective mRNAs. Further, EDF1 regulates an immediate-early transcriptional response to ribosomal collisions. Our results uncover mechanisms through which EDF1 coordinates multiple responses of the ribosome-mediated quality control pathway and provide novel insights into the intersection of ribosome-mediated quality control with global transcriptional regulation.
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Affiliation(s)
- Niladri K Sinha
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Katharina Best
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - James A Saba
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Boris Zinshteyn
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Elayanambi Sundaramoorthy
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Amit Fulzele
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Danielle M Garshott
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Timo Denk
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Matthias Thoms
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute of Harvard Medical SchoolBostonUnited States
| | - Eric J Bennett
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San DiegoSan DiegoUnited States
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität MünchenMunichGermany
| | - Rachel Green
- Department of Molecular Biology and Genetics, Howard Hughes Medical Institute, Johns Hopkins University School of MedicineBaltimoreUnited States
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175
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Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Mooijman D, Benes V, Savitski MM, Gebauer F, Hennig J. Pseudo-RNA-Binding Domains Mediate RNA Structure Specificity in Upstream of N-Ras. Cell Rep 2020; 32:107930. [PMID: 32697992 PMCID: PMC7383231 DOI: 10.1016/j.celrep.2020.107930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
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Affiliation(s)
- Nele Merret Hollmann
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | | | - Pawel Masiewicz
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Tanit Guitart
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
| | - Bernd Simon
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jan Provaznik
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Lara Jayne Sweetapple
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Laura Villacorta
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Dylan Mooijman
- Developmental Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Mikhail M Savitski
- Proteomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Genome Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Fátima Gebauer
- Gene Regulation, Stem Cells and Cancer Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Janosch Hennig
- Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
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176
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The gain-of-function allele bamA E470K bypasses the essential requirement for BamD in β-barrel outer membrane protein assembly. Proc Natl Acad Sci U S A 2020; 117:18737-18743. [PMID: 32675245 DOI: 10.1073/pnas.2007696117] [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] [Indexed: 12/24/2022] Open
Abstract
The outer membrane (OM) of gram-negative bacteria confers innate resistance to toxins and antibiotics. Integral β-barrel outer membrane proteins (OMPs) function to establish and maintain the selective permeability of the OM. OMPs are assembled into the OM by the β-barrel assembly machine (BAM), which is composed of one OMP-BamA-and four lipoproteins-BamB, C, D, and E. BamB, C, and E can be removed individually with only minor effects on barrier function; however, depletion of either BamA or BamD causes a global defect in OMP assembly and results in cell death. We have identified a gain-of-function mutation, bamA E470K , that bypasses the requirement for BamD. Although bamD::kan bamA E470K cells exhibit growth and OM barrier defects, they assemble OMPs with surprising robustness. Our results demonstrate that BamD does not play a catalytic role in OMP assembly, but rather functions to regulate the activity of BamA.
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177
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Tian JJ, Zhang JM, Yu EM, Sun JH, Xia Y, Zhang K, Li ZF, Gong WB, Wang GJ, Xie J. Identification and analysis of lipid droplet-related proteome in the adipose tissue of grass carp (Ctenopharyngodon idella) under fed and starved conditions. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2020; 36:100710. [PMID: 32659607 DOI: 10.1016/j.cbd.2020.100710] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/02/2020] [Accepted: 07/04/2020] [Indexed: 11/29/2022]
Abstract
Fat accumulation in the mesenteric adipose tissue is a serious problem in grass carp (Ctenopharyngodon idella) culture. Lipid droplet-related proteins (LDRPs) are involved in the formation, degradation, and biological functions of lipid droplets. In this study, we aimed to provide reference proteomics data to study lipid droplet regulation in fish. We isolated LDRPs from the mesenteric adipose tissue of grass carp (1-year-old) after normal feeding and 7 days of starvation, and identified and analysed them using isobaric tags for relative and absolute quantitation (iTRAQ) technology. Short-term starvation had no significant effect on the body weight, condition factor, visceral index, hepatopancreas index, intraperitoneal fat index, adipose tissue triglyceride content, and adipocyte size of grass carp. Nine hundred and fifty proteins were identified and annotated using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases; they are involved in a variety of metabolic and signalling pathways, including amino acid, lipid, and carbohydrate metabolism, and the PI3K-Akt signalling pathway. There were 296 differentially expressed proteins (DEPs), with 143 up-regulated and 153 down-regulated proteins. Three proteins involved in triglyceride and fatty acid syntheses and two proteins involved in autophagy were up-regulated, and six proteins involved in lipid catabolism were down-regulated. These results indicate that under short-term starvation, lipid droplets in the adipose tissue of grass carp may maintain their shape by promoting fat production and inhibiting lipolysis, and autophagy may be one of the main strategies for coping with short-term energy deprivation.
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Affiliation(s)
- Jing-Jing Tian
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jun-Ming Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Tianjin Key Lab of Aqua-Ecology and Aquaculture, Tianjin Agricultural University, Tianjin 300384, China
| | - Er-Meng Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
| | - Jin-Hui Sun
- Tianjin Key Lab of Aqua-Ecology and Aquaculture, Tianjin Agricultural University, Tianjin 300384, China
| | - Yun Xia
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Kai Zhang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Zhi-Fei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wang-Bao Gong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Guang-Jun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Jun Xie
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
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178
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An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature 2020; 583:303-309. [PMID: 32612236 PMCID: PMC7351614 DOI: 10.1038/s41586-020-2446-y] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022]
Abstract
Mammalian cells reorganize their proteomes in response to nutrient stress through translational suppression and degradative mechanisms using the proteasome and autophagy systems1,2. Ribosomes are central targets of this response, as they are responsible for translation and subject to lysosomal turnover during nutrient stress3-5. The abundance of ribosomal (r)-proteins (around 6% of the proteome; 107 copies per cell)6,7 and their high arginine and lysine content has led to the hypothesis that they are selectively used as a source of basic amino acids during nutrient stress through autophagy4,7. However, the relative contributions of translational and degradative mechanisms to the control of r-protein abundance during acute stress responses is poorly understood, as is the extent to which r-proteins are used to generate amino acids when specific building blocks are limited7. Here, we integrate quantitative global translatome and degradome proteomics8 with genetically encoded Ribo-Keima5 and Ribo-Halo reporters to interrogate r-protein homeostasis with and without active autophagy. In conditions of acute nutrient stress, cells strongly suppress the translation of r-proteins, but, notably, r-protein degradation occurs largely through non-autophagic pathways. Simultaneously, the decrease in r-protein abundance is compensated for by a reduced dilution of pre-existing ribosomes and a reduction in cell volume, thereby maintaining the density of ribosomes within single cells. Withdrawal of basic or hydrophobic amino acids induces translational repression without differential induction of ribophagy, indicating that ribophagy is not used to selectively produce basic amino acids during acute nutrient stress. We present a quantitative framework that describes the contributions of biosynthetic and degradative mechanisms to r-protein abundance and proteome remodelling in conditions of nutrient stress.
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Affiliation(s)
- Heeseon An
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Alban Ordureau
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Maria Körner
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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179
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Quantitative Proteomics of the Cancer Cell Line Encyclopedia. Cell 2020; 180:387-402.e16. [PMID: 31978347 DOI: 10.1016/j.cell.2019.12.023] [Citation(s) in RCA: 499] [Impact Index Per Article: 124.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 10/14/2019] [Accepted: 12/13/2019] [Indexed: 01/22/2023]
Abstract
Proteins are essential agents of biological processes. To date, large-scale profiling of cell line collections including the Cancer Cell Line Encyclopedia (CCLE) has focused primarily on genetic information whereas deep interrogation of the proteome has remained out of reach. Here, we expand the CCLE through quantitative profiling of thousands of proteins by mass spectrometry across 375 cell lines from diverse lineages to reveal information undiscovered by DNA and RNA methods. We observe unexpected correlations within and between pathways that are largely absent from RNA. An analysis of microsatellite instable (MSI) cell lines reveals the dysregulation of specific protein complexes associated with surveillance of mutation and translation. These and other protein complexes were associated with sensitivity to knockdown of several different genes. These data in conjunction with the wider CCLE are a broad resource to explore cellular behavior and facilitate cancer research.
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180
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The Archaeal Proteome Project advances knowledge about archaeal cell biology through comprehensive proteomics. Nat Commun 2020; 11:3145. [PMID: 32561711 PMCID: PMC7305310 DOI: 10.1038/s41467-020-16784-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 11/08/2022] Open
Abstract
While many aspects of archaeal cell biology remain relatively unexplored, systems biology approaches like mass spectrometry (MS) based proteomics offer an opportunity for rapid advances. Unfortunately, the enormous amount of MS data generated often remains incompletely analyzed due to a lack of sophisticated bioinformatic tools and field-specific biological expertise for data interpretation. Here we present the initiation of the Archaeal Proteome Project (ArcPP), a community-based effort to comprehensively analyze archaeal proteomes. Starting with the model archaeon Haloferax volcanii, we reanalyze MS datasets from various strains and culture conditions. Optimized peptide spectrum matching, with strict control of false discovery rates, facilitates identifying > 72% of the reference proteome, with a median protein sequence coverage of 51%. These analyses, together with expert knowledge in diverse aspects of cell biology, provide meaningful insights into processes such as N-terminal protein maturation, N-glycosylation, and metabolism. Altogether, ArcPP serves as an invaluable blueprint for comprehensive prokaryotic proteomics.
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181
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Song W, Tang F, Cai W, Zhang Q, Zhou F, Ning M, Tian H, Shan C. iTRAQ-based quantitative proteomics analysis of cantaloupe (Cucumis melo var. saccharinus) after cold storage. BMC Genomics 2020; 21:390. [PMID: 32493266 PMCID: PMC7268308 DOI: 10.1186/s12864-020-06797-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/26/2020] [Indexed: 12/25/2022] Open
Abstract
Background Cantaloupe is susceptible to cold stress when it is stored at low temperatures, resulting in the loss of edible and commercial quality. To ascertain the molecular mechanisms of low temperatures resistance in cantaloupe, a cold-sensitive cultivar, Golden Empress-308 (GE) and a cold-tolerant cultivar, Jia Shi-310 (JS), were selected in parallel for iTRAQ quantitative proteomic analysis. Results The two kinds of commercial cultivars were exposed to a temperature of 0.5 °C for 0, 12 and 24 days. We found that the cold-sensitive cultivar (GE) suffered more severe damage as the length of the cold treatment increased. Proteomic analysis of both cultivars indicated that the number of differentially expressed proteins (DEPs) changed remarkably during the chilly treatment. JS expressed cold-responsive proteins more rapidly and mobilized more groups of proteins than GE. Furthermore, metabolic analysis revealed that more amino acids were up-regulated in JS during the early phases of low temperatures stress. The DEPs we found were mainly related to carbohydrate and energy metabolism, structural proteins, reactive oxygen species scavenging, amino acids metabolism and signal transduction. The consequences of phenotype assays, metabolic analysis and q-PCR validation confirm the findings of the iTRAQ analysis. Conclusion We found that the prompt response and mobilization of proteins in JS allowed it to maintain a higher level of cold tolerance than GE, and that the slower cold responses in GE may be a vital reason for the severe chilling injury commonly found in this cultivar. The candidate proteins we identified will form the basis of future studies and may improve our understanding of the mechanisms of cold tolerance in cantaloupe.
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Affiliation(s)
- Wen Song
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fengxian Tang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Wenchao Cai
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Qin Zhang
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Fake Zhou
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Ming Ning
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Huan Tian
- College of Food, Shihezi University, Xinjiang, 832000, China
| | - Chunhui Shan
- College of Food, Shihezi University, Xinjiang, 832000, China.
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182
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Zhou Tran Y, Minozada R, Cao X, Johansson HJ, Branca RM, Seashore-Ludlow B, Orre LM. Immediate Adaptation Analysis Implicates BCL6 as an EGFR-TKI Combination Therapy Target in NSCLC. Mol Cell Proteomics 2020; 19:928-943. [PMID: 32234966 PMCID: PMC7261823 DOI: 10.1074/mcp.ra120.002036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Indexed: 01/10/2023] Open
Abstract
Drug resistance is a major obstacle to curative cancer therapies, and increased understanding of the molecular events contributing to resistance would enable better prediction of therapy response, as well as contribute to new targets for combination therapy. Here we have analyzed the early molecular response to epidermal growth factor receptor (EGFR) inhibition using RNA sequencing data covering 13,486 genes and mass spectrometry data covering 10,138 proteins. This analysis revealed a massive response to EGFR inhibition already within the first 24 h, including significant regulation of hundreds of genes known to control downstream signaling, such as transcription factors, kinases, phosphatases and ubiquitin E3-ligases. Importantly, this response included upregulation of key genes in multiple oncogenic signaling pathways that promote proliferation and survival, such as ERBB3, FGFR2, JAK3, and BCL6, indicating an early adaptive response to EGFR inhibition. Using a library of more than 500 approved and experimental compounds in a combination therapy screen, we could show that several kinase inhibitors with targets including JAK3 and FGFR2 increased the response to EGFR inhibitors. Further, we investigated the functional impact of BCL6 upregulation in response to EGFR inhibition using siRNA-based silencing of BCL6. Proteomics profiling revealed that BCL6 inhibited transcription of multiple target genes including p53, resulting in reduced apoptosis which implicates BCL6 upregulation as a new EGFR inhibitor treatment escape mechanism. Finally, we demonstrate that combined treatment targeting both EGFR and BCL6 act synergistically in killing lung cancer cells. In conclusion, or data indicates that multiple different adaptive mechanisms may act in concert to blunt the cellular impact of EGFR inhibition, and we suggest BCL6 as a potential target for EGFR inhibitor-based combination therapy.
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Affiliation(s)
- Yan Zhou Tran
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rezan Minozada
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Xiaofang Cao
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Henrik J Johansson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Rui M Branca
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Brinton Seashore-Ludlow
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden.
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183
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Samaras P, Schmidt T, Frejno M, Gessulat S, Reinecke M, Jarzab A, Zecha J, Mergner J, Giansanti P, Ehrlich HC, Aiche S, Rank J, Kienegger H, Krcmar H, Kuster B, Wilhelm M. ProteomicsDB: a multi-omics and multi-organism resource for life science research. Nucleic Acids Res 2020; 48:D1153-D1163. [PMID: 31665479 PMCID: PMC7145565 DOI: 10.1093/nar/gkz974] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 11/22/2022] Open
Abstract
ProteomicsDB (https://www.ProteomicsDB.org) started as a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. The data types and contents grew over time to include RNA-Seq expression data, drug-target interactions and cell line viability data. In this manuscript, we summarize new developments since the previous update that was published in Nucleic Acids Research in 2017. Over the past two years, we have enriched the data content by additional datasets and extended the platform to support protein turnover data. Another important new addition is that ProteomicsDB now supports the storage and visualization of data collected from other organisms, exemplified by Arabidopsis thaliana. Due to the generic design of ProteomicsDB, all analytical features available for the original human resource seamlessly transfer to other organisms. Furthermore, we introduce a new service in ProteomicsDB which allows users to upload their own expression datasets and analyze them alongside with data stored in ProteomicsDB. Initially, users will be able to make use of this feature in the interactive heat map functionality as well as the drug sensitivity prediction, but ultimately will be able to use all analytical features of ProteomicsDB in this way.
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Affiliation(s)
- Patroklos Samaras
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Tobias Schmidt
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Martin Frejno
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Siegfried Gessulat
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,Innovation Center Network, SAP SE, Potsdam, Germany
| | - Maria Reinecke
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,German Cancer Consortium (DKTK), Partner Site Munich, Munich, Germany.,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Jarzab
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Jana Zecha
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Julia Mergner
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Piero Giansanti
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
| | | | | | - Johannes Rank
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Harald Kienegger
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Helmut Krcmar
- Chair for Information Systems, Technical University of Munich (TUM), Garching, Germany.,SAP University Competence Center, Technical University of Munich (TUM), Garching, Germany
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany.,Bavarian Biomolecular Mass Spectrometry Center (BayBioMS), Technical University of Munich (TUM), Freising, Bavaria, Germany
| | - Mathias Wilhelm
- Chair of Proteomics and Bioanalytics, Technical University of Munich (TUM), Freising, Bavaria, Germany
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184
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Li H, Zhou R, Xu S, Chen X, Hong Y, Lu Q, Liu H, Zhou B, Liang X. Improving Gene Annotation of the Peanut Genome by Integrated Proteogenomics Workflow. J Proteome Res 2020; 19:2226-2235. [DOI: 10.1021/acs.jproteome.9b00723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Haifen Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Ruo Zhou
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Shaohang Xu
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Yanbin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Qing Lu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Hao Liu
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
| | - Baojin Zhou
- Deepxomics Co., Ltd., Shenzhen 518000, China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Key Laboratory for Crops Genetic Improvement, South China Peanut Sub-Center of National Center of Oilseed Crops Improvement, Guangzhou 510640, China
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185
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Yu Q, Paulo JA, Naverrete-Perea J, McAlister GC, Canterbury JD, Bailey DJ, Robitaille AM, Huguet R, Zabrouskov V, Gygi SP, Schweppe DK. Benchmarking the Orbitrap Tribrid Eclipse for Next Generation Multiplexed Proteomics. Anal Chem 2020; 92:6478-6485. [PMID: 32250601 DOI: 10.1021/acs.analchem.9b05685] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The rise of sample multiplexing in quantitative proteomics for the dissection of complex phenotypic comparisons has been advanced by the development of ever more sensitive and robust instrumentation. Here, we evaluated the utility of the Orbitrap Eclipse Tribrid mass spectrometer (advanced quadrupole filter, optimized FTMS scan overhead) and new instrument control software features (Precursor Fit filtering, TurboTMT and Real-time Peptide Search filtering). Multidimensional comparisons of these novel features increased total peptide identifications by 20% for SPS-MS3 methods and 14% for HRMS2 methods. Importantly Real-time Peptide Search filtering enabled a ∼2× throughput improvement for quantification. Across the board, these sensitivity increases were attained without sacrificing quantitative accuracy. New hardware and software features enable more efficient characterization in pursuit of comparative whole proteome insights.
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Affiliation(s)
- Qing Yu
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | | | | | | | - Derek J Bailey
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | | | - Romain Huguet
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Vlad Zabrouskov
- Thermo Fisher Scientific, San Jose, California 95134, United States
| | - Steven P Gygi
- Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Devin K Schweppe
- Harvard Medical School, Boston, Massachusetts 02115, United States
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186
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Li J, Van Vranken JG, Paulo JA, Huttlin EL, Gygi SP. Selection of Heating Temperatures Improves the Sensitivity of the Proteome Integral Solubility Alteration Assay. J Proteome Res 2020; 19:2159-2166. [PMID: 32243163 DOI: 10.1021/acs.jproteome.0c00063] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The thermal shift assay is a robust method of discovering protein-ligand interactions by measuring the alterations in protein thermal stability under various conditions. Several thermal shift assays have been developed and their throughput has been advanced greatly by the rapid progress in tandem mass tag-based quantitative proteomics. A recent paper by Gaetani et al. ( J. Proteome Res. 2019, 18 (11), 4027-4037) introduced the proteome integral solubility alteration (PISA) assay, further increasing throughput and simplifying the data analysis. Both ΔSm (a proxy of the difference between areas under the melting curves) and fold changes (ratios between integral samples) are readouts of the PISA assay and positively related to ΔTm (shift in melting temperatures). Here, we show that the magnitudes of these readouts are inherently small in PISA assay, which is a challenge for quantitation. Both simulation and experimental results show that the selection of a subset of heating temperatures ameliorates the small difference problem and improves the sensitivity of the PISA assay.
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Affiliation(s)
- Jiaming Li
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jonathan G Van Vranken
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Edward L Huttlin
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
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187
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Quantitative proteomic landscape of metaplastic breast carcinoma pathological subtypes and their relationship to triple-negative tumors. Nat Commun 2020; 11:1723. [PMID: 32265444 PMCID: PMC7138853 DOI: 10.1038/s41467-020-15283-z] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
Metaplastic breast carcinoma (MBC) is a highly aggressive form of triple-negative cancer (TNBC), defined by the presence of metaplastic components of spindle, squamous, or sarcomatoid histology. The protein profiles underpinning the pathological subtypes and metastatic behavior of MBC are unknown. Using multiplex quantitative tandem mass tag-based proteomics we quantify 5798 proteins in MBC, TNBC, and normal breast from 27 patients. Comparing MBC and TNBC protein profiles we show MBC-specific increases related to epithelial-to-mesenchymal transition and extracellular matrix, and reduced metabolic pathways. MBC subtypes exhibit distinct upregulated profiles, including translation and ribosomal events in spindle, inflammation- and apical junction-related proteins in squamous, and extracellular matrix proteins in sarcomatoid subtypes. Comparison of the proteomes of human spindle MBC with mouse spindle (CCN6 knockout) MBC tumors reveals a shared spindle-specific signature of 17 upregulated proteins involved in translation and 19 downregulated proteins with roles in cell metabolism. These data identify potential subtype specific MBC biomarkers and therapeutic targets. Metaplastic breast carcinoma (MBC) is among the most aggressive subtypes of triple-negative breast cancer (TNBC) but the underlying proteome profiles are unknown. Here, the authors characterize the protein signatures of human MBC tissue samples and their relationship to TNBC and normal breast tissue.
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188
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Wu S, Guo Y, Adil MF, Sehar S, Cai B, Xiang Z, Tu Y, Zhao D, Shamsi IH. Comparative Proteomic Analysis by iTRAQ Reveals that Plastid Pigment Metabolism Contributes to Leaf Color Changes in Tobacco ( Nicotiana tabacum) during Curing. Int J Mol Sci 2020; 21:E2394. [PMID: 32244294 PMCID: PMC7178154 DOI: 10.3390/ijms21072394] [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: 02/17/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 01/21/2023] Open
Abstract
Tobacco (Nicotiana tabacum), is a world's major non-food agricultural crop widely cultivated for its economic value. Among several color change associated biological processes, plastid pigment metabolism is of trivial importance in postharvest plant organs during curing and storage. However, the molecular mechanisms involved in carotenoid and chlorophyll metabolism, as well as color change in tobacco leaves during curing, need further elaboration. Here, proteomic analysis at different curing stages (0 h, 48 h, 72 h) was performed in tobacco cv. Bi'na1 with an aim to investigate the molecular mechanisms of pigment metabolism in tobacco leaves as revealed by the iTRAQ proteomic approach. Our results displayed significant differences in leaf color parameters and ultrastructural fingerprints that indicate an acceleration of chloroplast disintegration and promotion of pigment degradation in tobacco leaves due to curing. In total, 5931 proteins were identified, of which 923 (450 up-regulated, 452 down-regulated, and 21 common) differentially expressed proteins (DEPs) were obtained from tobacco leaves. To elucidate the molecular mechanisms of pigment metabolism and color change, 19 DEPs involved in carotenoid metabolism and 12 DEPs related to chlorophyll metabolism were screened. The results exhibited the complex regulation of DEPs in carotenoid metabolism, a negative regulation in chlorophyll biosynthesis, and a positive regulation in chlorophyll breakdown, which delayed the degradation of xanthophylls and accelerated the breakdown of chlorophylls, promoting the formation of yellow color during curing. Particularly, the up-regulation of the chlorophyllase-1-like isoform X2 was the key protein regulatory mechanism responsible for chlorophyll metabolism and color change. The expression pattern of 8 genes was consistent with the iTRAQ data. These results not only provide new insights into pigment metabolism and color change underlying the postharvest physiological regulatory networks in plants, but also a broader perspective, which prompts us to pay attention to further screen key proteins in tobacco leaves during curing.
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Affiliation(s)
- Shengjiang Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China;
- Key Laboratory of Molecular Genetics/Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, CNTC, Guiyang 550081, China; (Y.G.); (B.C.); (Z.X.); (Y.T.)
| | - Yushuang Guo
- Key Laboratory of Molecular Genetics/Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, CNTC, Guiyang 550081, China; (Y.G.); (B.C.); (Z.X.); (Y.T.)
| | - Muhammad Faheem Adil
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.F.A.); (S.S.)
| | - Shafaque Sehar
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.F.A.); (S.S.)
| | - Bin Cai
- Key Laboratory of Molecular Genetics/Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, CNTC, Guiyang 550081, China; (Y.G.); (B.C.); (Z.X.); (Y.T.)
| | - Zhangmin Xiang
- Key Laboratory of Molecular Genetics/Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, CNTC, Guiyang 550081, China; (Y.G.); (B.C.); (Z.X.); (Y.T.)
| | - Yonggao Tu
- Key Laboratory of Molecular Genetics/Upland Flue-cured Tobacco Quality and Ecology Key Laboratory, Guizhou Academy of Tobacco Science, CNTC, Guiyang 550081, China; (Y.G.); (B.C.); (Z.X.); (Y.T.)
| | - Degang Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang 550025, China;
- Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
| | - Imran Haider Shamsi
- Department of Agronomy, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou 310058, China; (M.F.A.); (S.S.)
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189
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Gouveia L, Kraut S, Hadzic S, Vazquéz-Liébanas E, Kojonazarov B, Wu CY, Veith C, He L, Mermelekas G, Schermuly RT, Weissmann N, Betsholtz C, Andrae J. Lung developmental arrest caused by PDGF-A deletion: consequences for the adult mouse lung. Am J Physiol Lung Cell Mol Physiol 2020; 318:L831-L843. [PMID: 32186397 DOI: 10.1152/ajplung.00295.2019] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
PDGF-A is a key contributor to lung development in mice. Its expression is needed for secondary septation of the alveoli and deletion of the gene leads to abnormally enlarged alveolar air spaces in mice. In humans, the same phenotype is the hallmark of bronchopulmonary dysplasia (BPD), a disease that affects premature babies and may have long lasting consequences in adulthood. So far, the knowledge regarding adult effects of developmental arrest in the lung is limited. This is attributable to few follow-up studies of BPD survivors and lack of good experimental models that could help predict the outcomes of this early age disease for the adult individual. In this study, we used the constitutive lung-specific Pdgfa deletion mouse model to analyze the consequences of developmental lung defects in adult mice. We assessed lung morphology, physiology, cellular content, ECM composition and proteomics data in mature mice, that perinatally exhibited lungs with a BPD-like morphology. Histological and physiological analyses both revealed that enlarged alveolar air spaces remained until adulthood, resulting in higher lung compliance and higher respiratory volume in knockout mice. Still, no or only small differences were seen in cellular, ECM and protein content when comparing knockout and control mice. Taken together, our results indicate that Pdgfa deletion-induced lung developmental arrest has consequences for the adult lung at the morphological and functional level. In addition, these mice can reach adulthood with a BPD-like phenotype, which makes them a robust model to further investigate the pathophysiological progression of the disease and test putative regenerative therapies.
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Affiliation(s)
- Leonor Gouveia
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Simone Kraut
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Stefan Hadzic
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Elisa Vazquéz-Liébanas
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Baktybek Kojonazarov
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Cheng-Yu Wu
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Christine Veith
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Georgios Mermelekas
- Cancer Proteomics Mass Spectrometry, Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Ralph Theo Schermuly
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Norbert Weissmann
- Justus-Liebig University of Giessen (JLUG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Giessen, Germany
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Integrated Cardio Metabolic Centre, Karolinska Institutet, Huddinge, Sweden
| | - Johanna Andrae
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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190
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TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples. Nat Methods 2020; 17:399-404. [PMID: 32203386 DOI: 10.1038/s41592-020-0781-4] [Citation(s) in RCA: 256] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 02/12/2020] [Indexed: 02/07/2023]
Abstract
Isobaric labeling empowers proteome-wide expression measurements simultaneously across multiple samples. Here an expanded set of 16 isobaric reagents based on an isobutyl-proline immonium ion reporter structure (TMTpro) is presented. These reagents have similar characteristics to existing tandem mass tag reagents but with increased fragmentation efficiency and signal. In a proteome-scale example dataset, we compared eight common cell lines with and without Torin1 treatment with three replicates, quantifying more than 8,800 proteins (mean of 7.5 peptides per protein) per replicate with an analysis time of only 1.1 h per proteome. Finally, we modified the thermal stability assay to examine proteome-wide melting shifts after treatment with DMSO, 1 or 20 µM staurosporine with five replicates. This assay identified and dose-stratified staurosporine binding to 228 cellular kinases in just one, 18-h experiment. TMTpro reagents allow complex experimental designs-all with essentially no missing values across the 16 samples and no loss in quantitative integrity.
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191
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Yeung E, McFann S, Marsh L, Dufresne E, Filippi S, Harrington HA, Shvartsman SY, Wühr M. Inference of Multisite Phosphorylation Rate Constants and Their Modulation by Pathogenic Mutations. Curr Biol 2020; 30:877-882.e6. [PMID: 32059766 PMCID: PMC7085240 DOI: 10.1016/j.cub.2019.12.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/03/2019] [Accepted: 12/16/2019] [Indexed: 01/03/2023]
Abstract
Multisite protein phosphorylation plays a critical role in cell regulation [1-3]. It is widely appreciated that the functional capabilities of multisite phosphorylation depend on the order and kinetics of phosphorylation steps, but kinetic aspects of multisite phosphorylation remain poorly understood [4-6]. Here, we focus on what appears to be the simplest scenario, when a protein is phosphorylated on only two sites in a strict, well-defined order. This scenario describes the activation of ERK, a highly conserved cell-signaling enzyme. We use Bayesian parameter inference in a structurally identifiable kinetic model to dissect dual phosphorylation of ERK by MEK, a kinase that is mutated in a large number of human diseases [7-12]. Our results reveal how enzyme processivity and efficiencies of individual phosphorylation steps are altered by pathogenic mutations. The presented approach, which connects specific mutations to kinetic parameters of multisite phosphorylation mechanisms, provides a systematic framework for closing the gap between studies with purified enzymes and their effects in the living organism.
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Affiliation(s)
- Eyan Yeung
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Sarah McFann
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Chemical and Biological Engineering, Engineering Quad, Princeton University, Princeton, NJ 08544, USA
| | - Lewis Marsh
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Emilie Dufresne
- Department of Mathematics, James College, Campus West, University of York, York YO10 5DD, UK
| | - Sarah Filippi
- Department of Epidemiology and Biostatistics, Imperial College London, Medical School Building, St Mary's Campus, Norfolk Place, London W2 1PG, UK; Department of Mathematics, South Kensington Campus, Imperial College London, London SW7 2AZ, UK
| | - Heather A Harrington
- Mathematical Institute, University of Oxford, Andrew Wiles Building, Woodstock Road, Oxford OX2 6GG, UK
| | - Stanislav Y Shvartsman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA; Flatiron Institute, Simons Foundation, New York, NY 10010, USA.
| | - Martin Wühr
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Carl Icahn Laboratory, Washington Road, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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192
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Prieto G, Vázquez J. Protein Probability Model for High-Throughput Protein Identification by Mass Spectrometry-Based Proteomics. J Proteome Res 2020; 19:1285-1297. [PMID: 32037837 DOI: 10.1021/acs.jproteome.9b00819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Shotgun proteomics is the method of choice for high-throughput protein identification; however, robust statistical methods are essential to automatize this task while minimizing the number of false identifications. The standard method for estimating the false discovery rate (FDR) of individual identifications and keeping it below a threshold (typically 1%) is the target-decoy approach. However, numerous works have shown that FDR at the protein level may become much larger than FDR at the peptide level. The development of an appropriate scoring model to identify proteins from their peptides using high-throughput shotgun proteomics is highly needed. In this study, we present a novel protein-level scoring algorithm that uses the scores of the identified peptides and maintains all of the properties expected for a true protein probability. We also present a refinement of the picked method to calculate FDR at the protein level. These algorithms can be used together as a robust identification workflow suitable for large-scale proteomics, and we show that the identification performance of this workflow is superior to that of other widely used methods in several samples and using different search engines. Our protein probability model offers the scientific community an algorithm that is easy to integrate into protein identification workflows for the automated analysis of shotgun proteomics data.
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Affiliation(s)
- Gorka Prieto
- Department of Communications Engineering, University of the Basque Country (UPV/EHU), 48013 Bilbao, Spain
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28049 Madrid, Spain
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193
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Pfeuffer J, Sachsenberg T, Dijkstra TMH, Serang O, Reinert K, Kohlbacher O. EPIFANY: A Method for Efficient High-Confidence Protein Inference. J Proteome Res 2020; 19:1060-1072. [PMID: 31975601 DOI: 10.1021/acs.jproteome.9b00566] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate protein inference in the presence of shared peptides is still one of the key problems in bottom-up proteomics. Most protein inference tools employing simple heuristic inference strategies are efficient but exhibit reduced accuracy. More advanced probabilistic methods often exhibit better inference quality but tend to be too slow for large data sets. Here, we present a novel protein inference method, EPIFANY, combining a loopy belief propagation algorithm with convolution trees for efficient processing of Bayesian networks. We demonstrate that EPIFANY combines the reliable protein inference of Bayesian methods with significantly shorter runtimes. On the 2016 iPRG protein inference benchmark data, EPIFANY is the only tested method that finds all true-positive proteins at a 5% protein false discovery rate (FDR) without strict prefiltering on the peptide-spectrum match (PSM) level, yielding an increase in identification performance (+10% in the number of true positives and +14% in partial AUC) compared to previous approaches. Even very large data sets with hundreds of thousands of spectra (which are intractable with other Bayesian and some non-Bayesian tools) can be processed with EPIFANY within minutes. The increased inference quality including shared peptides results in better protein inference results and thus increased robustness of the biological hypotheses generated. EPIFANY is available as open-source software for all major platforms at https://OpenMS.de/epifany.
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Affiliation(s)
- Julianus Pfeuffer
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany.,Algorithmic Bioinformatics, Department of Bioinformatics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Timo Sachsenberg
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany
| | - Tjeerd M H Dijkstra
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Oliver Serang
- Department of Computer Science, University of Montana, Missoula, Montana 59812, United States
| | - Knut Reinert
- Algorithmic Bioinformatics, Department of Bioinformatics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, 72076 Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076 Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, 72076 Tübingen, Germany.,Quantitative Biology Center, University of Tübingen, 72076 Tübingen, Germany
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194
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Ye F, Wang Y, He Q, Cui C, Yu H, Lu Y, Zhu S, Xu H, Zhao X, Yin H, Li D, Li H, Zhu Q. Exosomes Transmit Viral Genetic Information and Immune Signals may cause Immunosuppression and Immune Tolerance in ALV-J Infected HD11 cells. Int J Biol Sci 2020; 16:904-920. [PMID: 32140061 PMCID: PMC7053331 DOI: 10.7150/ijbs.35839] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/06/2019] [Indexed: 01/13/2023] Open
Abstract
Avian leukosis virus (ALV) is oncogenic retrovirus that not only causes immunosuppression but also enhances the host's susceptibility to secondary infection. Exosomes play vital role in the signal transduction cascades that occur in response to viral infection. We want to explore the function of exosomes in the spread of ALV and the body's subsequent immunological response. RNA-sequencing and the isobaric tags for relative and absolute quantitation (iTRAQ) method were used to detect differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) in exosomes secreted by macrophage cells in response to injection with ALV subgroup J (ALV-J). RNA-sequencing identified 513 DEGs in infected cells, with specific differential regulation in mRNA involved in tight junction signaling, TNF signaling, salmonella infection response, and immune response, among other important cellular processes. Differential regulation was observed in 843 lncRNAs, with particular enrichment in those lncRNA targets involved in Rap1 signaling, HTLV-I infection, tight junction signaling, and other signaling pathways. A total of 50 DEPs were identified in the infected cells by iTRAQ. The proteins enriched are involved in immune response, antigen processing, the formation of both MHC protein and myosin complexes, and transport. Combined analysis of the transcriptome and proteome revealed that there were 337 correlations between RNA and protein enrichment, five of which were significant. Pathways that were enriched on both the RNA and protein levels were involved in pathways in cancer, PI3K-Akt signaling pathway, Endocytosis, Epstein-Barr virus infection. These data show that exosomes are transmitters of intercellular signaling in response to viral infection. Exosomes can carry both viral nucleic acids and proteins, making it possible for exosomes to be involved in the viral infection of other cells and the transmission of immune signals between cells. Our sequencing results confirme previous studies on exosomes and further find exosomes may cause immunosuppression and immune tolerance.
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Affiliation(s)
- Fei Ye
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan, 528231, Guangdong, China
| | - Yan Wang
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Qijian He
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Can Cui
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Heling Yu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Yuxiang Lu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Shiliang Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Hengyong Xu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Xiaoling Zhao
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Huadong Yin
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
| | - Hua Li
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, Foshan University, Foshan, 528231, Guangdong, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Sichuan, Chengdu, China
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195
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Chen J, Jiang TT, Yi WJ, Jiao JL, Liu CM, Tu HH, Hu YT, Shi LY, Huang H, Li ZB, Gan L, Li ZJ, Li JC. A group of serum proteins as potential diagnostic biomarkers for Yin-deficiency-heat syndrome. Anat Rec (Hoboken) 2020; 303:2086-2094. [PMID: 31922655 DOI: 10.1002/ar.24351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/10/2019] [Accepted: 12/10/2019] [Indexed: 12/15/2022]
Abstract
Yin-deficiency-heat (YDH) syndrome is a very common subhealth status in Traditional Chinese Medicine. However, currently, there is no unified standard for diagnosing YDH syndrome. We applied the iTRAQ-2D LC-MS/MS method to explore the potential of serum protein profiles as biomarker for YDH syndrome. A total of 120 differentially expressed proteins (79 downregulated and 41 upregulated) were identified by the proteomic profiling. The results of KEGG pathway analysis showed that the functions of the differentially expressed proteins were mainly involved in complement and coagulation cascades. The clinical data showed that YDH syndrome was closely related to inflammation and coagulation, compared with the healthy controls. The ELISA validation results indicated that the expression levels of ALB, CFI, and KLKB1 were downregulated in the YDH syndrome group (p < .05). Moreover, we established a decision tree model based on the combination of these three proteins and achieved a sensitivity of 87.5%, a specificity of 84.4%, and AUC of 0.891. The results indicated that the combination of ALB, CFI, and KLKB1 may serve as potential biomarkers for diagnosing YDH syndrome. Our study can provide a new method for YDH syndrome diagnosis, and may also provide an experimental basis to understand the molecular mechanism of YDH syndrome.
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Affiliation(s)
- Jing Chen
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ting-Ting Jiang
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Wen-Jing Yi
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Jin-Ling Jiao
- Xiaoshan Hospital of Traditional Chinese Medicine, Hangzhou, China
| | - Chang-Ming Liu
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Hui-Hui Tu
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yu-Ting Hu
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Li-Ying Shi
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, China
| | - Huai Huang
- Medical Research Center, Yuebei People's Hospital, Shaoguan, China
| | - Zhi-Bin Li
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Lin Gan
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Zhong-Jie Li
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Ji-Cheng Li
- Department of Anatomy and Embryology, School of Medicine, Zhejiang University, Hangzhou, China.,Medical Research Center, Yuebei People's Hospital, Shaoguan, China
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196
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Wang H, Yan W, Feng Z, Gao Y, Zhang L, Feng X, Tian D. Plasma proteomic analysis of autoimmune hepatitis in an improved AIH mouse model. J Transl Med 2020; 18:3. [PMID: 31906950 PMCID: PMC6943959 DOI: 10.1186/s12967-019-02180-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 12/13/2019] [Indexed: 12/28/2022] Open
Abstract
Background The prevalence of autoimmune hepatitis (AIH) is increasing, and its early clinical diagnosis is difficult. The pathogenesis of AIH remains unclear, and AIH-related studies are largely limited because of lack of suitable mouse models. Methods To obtain a good tool for research on AIH, we first established an improved immune-mediated mouse model that can mimic the pathological process of AIH as in the human body, through repeated injections of human cytochrome P450 2D6 (CYP2D6) plasmid. Next, a proteomic analysis based on isobaric tag (IBT) technology was performed to detect the differentially expressed proteins (DEPs), and related biological functions and pathways in the plasma of AIH and normal mice. Finally, we performed enzyme-linked immunosorbent assay (ELISA) to further confirm the most abundant DEP in the plasma of patients with AIH. Results Autoantibodies and the characteristic pathology of AIH were observed in our mouse model. Inflammatory infiltration also increased in the livers of AIH mice over time and plateaued by day 42 post the first injection. Chronic hepatitis was most severe on day 35 with the development of fibrosis as well, and the plasma of AIH mice were collected for proteomic analysis. A total of 176 DEPs were found in this experiment, of which 148 DEPs were up-regulated and 28 DEPs were down-regulated. Thirty significant Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways (P < 0.05) were detected. Arginine biosynthesis was found to be the most significant pathway involved in the AIH process. During the Gene Ontology (GO) analysis, most DEPs were found to be involved in the binding, cellular, and metabolic processes. Using ELISA, the most overexpressed DEP, serum amyloid A 1 (SAA1), was confirmed to be increased specifically in the plasma of patients with AIH compared to other chronic hepatitis. Different plasma levels of SAA1 were also found related to different grades of inflammation and stages of fibrosis in the liver of patients with AIH. Conclusions Our study is the first to describe the proteomics analysis of a true sense of AIH mouse model, which is beneficial for a better understanding of AIH pathogenesis and identifying potential biomarkers for its clinical diagnosis.
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Affiliation(s)
- Han Wang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, People's Republic of China
| | - Wei Yan
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, People's Republic of China
| | - Zuohua Feng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Yuan Gao
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
| | - Liu Zhang
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, People's Republic of China
| | - Xinxia Feng
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, People's Republic of China.
| | - Dean Tian
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1095, Wuhan, 430030, People's Republic of China.
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197
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Abstract
Shotgun proteomics is the method of choice for large-scale protein identification. However, the use of a robust statistical workflow to validate such identification is mandatory to minimize false matches, ambiguities, and amplification of error rates from spectra to proteins. In this chapter we emphasize the key concepts to take into account when processing the output of a search engine to obtain reliable peptide or protein identifications. We assume that the reader is already familiar with tandem mass spectrometry so we can focus on the use of statistical confidence methods. After introducing the key concepts we present different software tools and how to use them with an example dataset.
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Affiliation(s)
- Gorka Prieto
- Department of Communications Engineering, Faculty of Engineering of Bilbao, University of the Basque Country (UPV/EHU), Bilbao, Spain.
| | - Jesús Vázquez
- Laboratory of Cardiovascular Proteomics, Centro Nacional de Investigaciones Cardiovasculares (CNIC) and CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
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198
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Haytural H, Mermelekas G, Emre C, Nigam SM, Carroll SL, Winblad B, Bogdanovic N, Barthet G, Granholm AC, Orre LM, Tjernberg LO, Frykman S. The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease. Mol Cell Proteomics 2020; 19:128-141. [PMID: 31699905 PMCID: PMC6944231 DOI: 10.1074/mcp.ra119.001737] [Citation(s) in RCA: 18] [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] [Received: 08/29/2019] [Revised: 11/05/2019] [Indexed: 01/13/2023] Open
Abstract
Synaptic dysfunction is an early pathogenic event in Alzheimer disease (AD) that contributes to network disturbances and cognitive decline. Some synapses are more vulnerable than others, including the synapses of the perforant path, which provides the main excitatory input to the hippocampus. To elucidate the molecular mechanisms underlying the dysfunction of these synapses, we performed an explorative proteomic study of the dentate terminal zone of the perforant path. The outer two-thirds of the molecular layer of the dentate gyrus, where the perforant path synapses are located, was microdissected from five subjects with AD and five controls. The microdissected tissues were dissolved and digested by trypsin. Peptides from each sample were labeled with different isobaric tags, pooled together and pre-fractionated into 72 fractions by high-resolution isoelectric focusing. Each fraction was then analyzed by liquid chromatography-mass spectrometry. We quantified the relative expression levels of 7322 proteins, whereof 724 showed significantly altered levels in AD. Our comprehensive data analysis using enrichment and pathway analyses strongly indicated that presynaptic signaling, such as exocytosis and synaptic vesicle cycle processes, is severely disturbed in this area in AD, whereas postsynaptic proteins remained unchanged. Among the significantly altered proteins, we selected three of the most downregulated synaptic proteins; complexin-1, complexin-2 and synaptogyrin-1, for further validation, using a new cohort consisting of six AD and eight control cases. Semi-quantitative analysis of immunohistochemical staining confirmed decreased levels of complexin-1, complexin-2 and synaptogyrin-1 in the outer two-thirds of the molecular layer of the dentate gyrus in AD. Our in-depth proteomic analysis provides extensive knowledge on the potential molecular mechanism underlying synaptic dysfunction related to AD and supports that presynaptic alterations are more important than postsynaptic changes in early stages of the disease. The specific synaptic proteins identified could potentially be targeted to halt synaptic dysfunction in AD.
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Affiliation(s)
- Hazal Haytural
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden.
| | - Georgios Mermelekas
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Ceren Emre
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | | | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina
| | - Bengt Winblad
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Karolinska University Hospital, Theme Aging, Stockholm, Sweden
| | - Nenad Bogdanovic
- Karolinska University Hospital, Theme Aging, Stockholm, Sweden; Division of Clinical geriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Huddinge, Sweden
| | - Gaël Barthet
- Interdisciplinary Institute for Neuroscience, CNRS UMR, Bordeaux, France; University of Bordeaux, Bordeaux, France
| | - Ann-Charlotte Granholm
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden; Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado
| | - Lukas M Orre
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Lars O Tjernberg
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
| | - Susanne Frykman
- Division of Neurogeriatrics, Center for Alzheimer Research, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, Solna, Sweden
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Chen X, Yi Y, You X, Liu J, Shi Q. High-Throughput Identification of Putative Antimicrobial Peptides from Multi-Omics Data of the Lined Seahorse ( Hippocampus erectus). Mar Drugs 2019; 18:md18010030. [PMID: 31905755 PMCID: PMC7024384 DOI: 10.3390/md18010030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 12/22/2019] [Accepted: 12/25/2019] [Indexed: 02/06/2023] Open
Abstract
Lined seahorse (Hippocampus erectus), the most widely cultivated seahorse in China, has been in short supply because of its important medicinal value; meanwhile, unnatural deaths caused by various diseases (especially enteritis) have limited their practical large-scale aquaculture. Antimicrobial peptides (AMPs), as the best alternative to antibiotics, have been extensively applied in agricultural practices. In this study, we identified 290 putative AMP sequences from our previously published genome and transcriptome data of the lined seahorse. Among them, 267 are novel, and 118 were validated by our proteome data generated in the present study. It seems that there is a tissue preference in the distribution of AMP/AMP precursor transcripts, such as lectins in the male pouch. In addition, their transcription levels usually varied during development. Interestingly, the representative lectins kept extremely high levels at the pre-pregnancy stage while at relatively lower levels at other stages. Especially Lectin25, with the highest transcription levels and significant developmental changes, has been reported to be involved in seahorse and human pregnancy. The comparison of transcriptome data between one-day and three-month juveniles indicated that Hemoglobin2 (Hemo2) was significantly upregulated in the body, haslet, and brain. Our proteome data of female and male individuals revealed three putative AMP precursors with sexual specificity, including two male-biased cyclin-dependent kinases (CDK-like16 and CDK-like23) and one female-biased bovine pancreatic trypsin inhibitor 2 (BPTI2). In conclusion, our present high-throughput identification of putative AMP sequences from multi-omics (including genomics, transcriptomics, and proteomics) data provides an overview of AMPs in the popular lined seahorse, which lays a solid foundation for further development of AMP-based fish food additives and human drugs.
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Affiliation(s)
- Xiyang Chen
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; (X.C.); (Y.Y.); (X.Y.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Yunhai Yi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; (X.C.); (Y.Y.); (X.Y.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; (X.C.); (Y.Y.); (X.Y.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
| | - Jie Liu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China;
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China; (X.C.); (Y.Y.); (X.Y.)
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China
- Laboratory of Aquatic Genomics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518060, China
- Correspondence: ; Tel.: +86-185-6627-9826; Fax: +86-755-3630-7807
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200
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Ivanova A, Gill-Hille M, Huang S, Branca RM, Kmiec B, Teixeira PF, Lehtiö J, Whelan J, Murcha MW. A Mitochondrial LYR Protein Is Required for Complex I Assembly. PLANT PHYSIOLOGY 2019; 181:1632-1650. [PMID: 31601645 PMCID: PMC6878026 DOI: 10.1104/pp.19.00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/25/2019] [Indexed: 05/04/2023]
Abstract
Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.
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Affiliation(s)
- Aneta Ivanova
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Mabel Gill-Hille
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Shaobai Huang
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Rui M Branca
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - Beata Kmiec
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Pedro F Teixeira
- Department of Biochemistry and Biophysics, Stockholm University, Arrhenius Laboratories for Natural Sciences, Stockholm SE-106 91, Sweden
| | - Janne Lehtiö
- Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory and Karolinska Institutet, Stockholm 171 77, Sweden
| | - James Whelan
- Department of Animal, Plant and Soil Science, School of Life Science, The ARC Centre of Excellence in Plant Energy Biology, La Trobe University, Bundoora 3086, Australia
| | - Monika W Murcha
- School of Chemistry and Biochemistry, The University of Western Australia, Crawley, Perth 6009, Australia
- The Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Perth 6009, Australia
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