201
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Jiang LG, Li B, Liu SX, Wang HW, Li CP, Song SH, Beatty M, Zastrow-Hayes G, Yang XH, Qin F, He Y. Characterization of Proteome Variation During Modern Maize Breeding. Mol Cell Proteomics 2019; 18:263-276. [PMID: 30409858 PMCID: PMC6356080 DOI: 10.1074/mcp.ra118.001021] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 11/06/2018] [Indexed: 12/21/2022] Open
Abstract
The success of modern maize breeding has been demonstrated by remarkable increases in productivity with tremendous modification of agricultural phenotypes over the last century. Although the underlying genetic changes of the maize adaptation from tropical to temperate regions have been extensively studied, our knowledge is limited regarding the accordance of protein and mRNA expression levels accompanying such adaptation. Here we conducted an integrative analysis of proteomic and transcriptomic changes in a maize association panel. The minimum extent of correlation between protein and RNA levels suggests that variation in mRNA expression is often not indicative of protein expression at a population scale. This is corroborated by the observation that mRNA- and protein-based coexpression networks are relatively independent of each other, and many pQTLs arise without the presence of corresponding eQTLs. Importantly, compared with transcriptome, the subtypes categorized by the proteome show a markedly high accuracy to resemble the genomic subpopulation. These findings suggest that proteome evolved under a greater evolutionary constraint than transcriptome during maize adaptation from tropical to temperate regions. Overall, the integrated multi-omics analysis provides a functional context to interpret gene expression variation during modern maize breeding.
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Affiliation(s)
- Lu-Guang Jiang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Bo Li
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Sheng-Xue Liu
- College of Biological Sciences, China Agricultural University, Beijing 100094, China
| | - Hong-Wei Wang
- Agricultural College, Hubei Collaborative Innovation Center for Grain Industry, Yangtze University, Hubei 434000, China
| | - Cui-Ping Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shu-Hui Song
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | - Xiao-Hong Yang
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Feng Qin
- College of Biological Sciences, China Agricultural University, Beijing 100094, China;.
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China;.
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202
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Tengstrand E, Zhang H, Liu N, Dunn K, Hsieh F. A multiplexed UPLC-MS/MS assay for the simultaneous measurement of urinary safety biomarkers of drug-induced kidney injury and phospholipidosis. Toxicol Appl Pharmacol 2019; 366:54-63. [PMID: 30653977 DOI: 10.1016/j.taap.2019.01.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/07/2018] [Accepted: 01/13/2019] [Indexed: 11/27/2022]
Abstract
Drug-induced kidney injury (DIKI) is a major concern in drug risk assessment given its clinical importance and the absence of a sensitive/specific method of diagnosis. Pharmaceutical regulatory agencies have qualified and issued letters of support for new biomarkers to better evaluate DIKI in nonclinical toxicity and clinical studies. Additional efforts have focused on drug-induced phospholipidosis (DIPL) and its potential link with collateral renal damage. The combined use of urinary biomarkers is an efficient way to evaluate renal safety in nonclinical and clinical studies. Eight FDA/EMA/PMDA qualified (or supported) urinary biomarkers, including kidney injury molecule-1 (KIM-1), β2-microglobulin (B2M), clusterin (CLU), cystatin C (CysC), trefoil factor 3 (TFF3), neutrophil gelatinase-associated lipocalin (NGAL), osteopontin (OPN), and alpha-glutathione S-transferase (α-GST), were quantified by multiplex UPLC-MS/MS in a repeat dose study of gentamicin in rats. Rats administered gentamicin at 100 mg/kg/day for 2 weeks developed renal lesions detected by histopathology. Biomarkers of tubular damage (CLU, KIM-1, OPN) increased 9.8, 34.7, and 35.6-fold (relative to concurrent controls), respectively, after 2 weeks of dosing. Biomarkers of glomerular damage and/or impairment of tubular reabsorption (CysC, B2M) increased 11.7 and 22.6-fold. NGAL and α-GST increased <3-fold after 2 weeks of dosing. TFF3 was comparable to concurrent controls. The elevated biomarker concentrations met PSTC threshold criteria and were consistent with mechanisms of gentamicin nephrotoxicity. Increased urinary di-22:6-BMP indicated concomitant DIPL as confirmed by TEM. This work provides evidence supporting the combined use of the DIKI biomarker panel and di-22:6-BMP as a biomarker of DIPL in drug risk assessment.
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Affiliation(s)
| | - Hannah Zhang
- Nextcea Inc., 500 West Cummings Park #4550, Woburn, MA 01801, USA
| | - Nanjun Liu
- Nextcea Inc., 500 West Cummings Park #4550, Woburn, MA 01801, USA
| | - Kelly Dunn
- Nextcea Inc., 500 West Cummings Park #4550, Woburn, MA 01801, USA
| | - Frank Hsieh
- Nextcea Inc., 500 West Cummings Park #4550, Woburn, MA 01801, USA.
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203
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Mariscal J, Fernandez-Puente P, Calamia V, Abalo A, Santacana M, Matias-Guiu X, Lopez-Lopez R, Gil-Moreno A, Alonso-Alconada L, Abal M. Proteomic Characterization of Epithelial-Like Extracellular Vesicles in Advanced Endometrial Cancer. J Proteome Res 2019; 18:1043-1053. [PMID: 30585730 DOI: 10.1021/acs.jproteome.8b00750] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Endometrial cancer (EC) is the most frequent gynecological cancer. Tumor dissemination affecting ∼20% of EC patients is characterized at the primary carcinoma by epithelial-to-mesenchymal transition (EMT) associated with myometrial infiltration. At distant sites, the interaction of circulating tumor cells (CTCs) with the microenvironment is crucial for metastatic colonization, with a participation of the extracellular vesicles (EVs). We comprehensively approached these primary and secondary sites to study the impact of tumor EVs on the metastatic efficiency of CTCs in EC. Tumor EVs in circulation reproduce the epithelial phenotype predominant in the primary carcinoma, whereas CTCs are characterized by an EMT phenotype. We modeled this EMT-related clinical scenario in the Hec1A endometrial cell line and characterized the epithelial-like EVs in circulation by SILAC proteome analysis. The identification of proteins involved in cell-cell and cell-matrix interaction and binding, together with in vitro evidence of an improved adhesion of CTC to a functionalized endothelium, suggests a contribution of the epithelial-like EVs in the homing of CTCs at metastatic sites. Accordingly, adhesion protein LGALS3BP was found to be significantly enriched in circulating EVs from a cohort of EC patients with a high risk of recurrence by targeted proteomics (multiple reaction monitoring), highlighting its potential in liquid biopsy in EC.
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Affiliation(s)
- Javier Mariscal
- Translational Medical Oncology, CIBERONC, Health Research Institute of Santiago (IDIS) , University Hospital of Santiago (SERGAS) , Santiago de Compostela 15706 , Spain
| | - Patricia Fernandez-Puente
- Proteomics Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC) , University Hospital A Coruña (SERGAS), Universidade da Coruña , A Coruña 15006 , Spain
| | - Valentina Calamia
- Proteomics Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC) , University Hospital A Coruña (SERGAS), Universidade da Coruña , A Coruña 15006 , Spain
| | - Alicia Abalo
- Translational Medical Oncology, CIBERONC, Health Research Institute of Santiago (IDIS) , University Hospital of Santiago (SERGAS) , Santiago de Compostela 15706 , Spain
| | - Maria Santacana
- Hospital Universitari Arnau de Vilanova , University of Lleida, IRBLLEIDA, CIBERONC , Lleida 08080 , Spain
| | - Xavier Matias-Guiu
- Hospital Universitari Arnau de Vilanova , University of Lleida, IRBLLEIDA, CIBERONC , Lleida 08080 , Spain
| | - Rafael Lopez-Lopez
- Translational Medical Oncology, CIBERONC, Health Research Institute of Santiago (IDIS) , University Hospital of Santiago (SERGAS) , Santiago de Compostela 15706 , Spain
| | - Antonio Gil-Moreno
- Biomedical Research Group in Gynecology, Vall Hebron Research Institute (VHIR) , Universitat Autonoma de Barcelona, CIBERONC , Barcelona 08035 , Spain
| | - Lorena Alonso-Alconada
- Translational Medical Oncology, CIBERONC, Health Research Institute of Santiago (IDIS) , University Hospital of Santiago (SERGAS) , Santiago de Compostela 15706 , Spain
| | - Miguel Abal
- Translational Medical Oncology, CIBERONC, Health Research Institute of Santiago (IDIS) , University Hospital of Santiago (SERGAS) , Santiago de Compostela 15706 , Spain
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204
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Steiner C, Lescuyer P, Tille JC, Cutler P, Ducret A. Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues. Methods Mol Biol 2019; 1959:185-203. [PMID: 30852824 DOI: 10.1007/978-1-4939-9164-8_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The search for novel and clinically relevant biomarkers still represents a major clinical challenge and mass-spectrometry-based technologies are essential tools to help in this process. In this application, we demonstrate how selected reaction monitoring (SRM) can be applied in a highly multiplexed way to analyze formalin-fixed paraffin-embedded (FFPE) tissues. Such an assay can be used to analyze numerous samples for narrowing down a list of potential biomarkers to the most relevant candidates. The use of FFPE tissues is of high relevance in this context as large sample collections linked with valuable clinical information are available in hospitals around the world. Here we describe in detail how we proceeded to develop such an assay for 200 proteins in breast tumor FFPE tissues. We cover the selection of suitable peptides, which are different in FFPE compared to fresh frozen tissues and show how we deliberately biased our assay toward proteins with a high probability of being measurable in human clinical samples.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland.
- Late Stage Analytical Development, Small Molecules Technical Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland.
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Paul Cutler
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
- Translational Biomarkers and Bioanalysis, Development Sciences, UCB Pharma, Slough, UK
| | - Axel Ducret
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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205
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Rinschen MM. Single glomerular proteomics: A novel tool for translational glomerular cell biology. Methods Cell Biol 2019; 154:1-14. [DOI: 10.1016/bs.mcb.2019.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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206
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Nguyen L, Brun V, Combes F, Loux V, Vandenbrouck Y. Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework. Methods Mol Biol 2019; 1959:275-289. [PMID: 30852829 DOI: 10.1007/978-1-4939-9164-8_18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Knowledge-based approaches using large-scale biological ("omics") data are a powerful way to identify mechanistic biomarkers, provided that scientists have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed a set of tools under the Galaxy framework to allow biologists to define their own strategy for reproducible biomarker selection. These tools rely on retrieving experimental data from public databases, and applying successive filters derived from information relating to disease pathophysiology. A step-by-step protocol linking these tools was implemented to select tissue-leakage biomarker candidates of myocardial infarction. A list of 24 candidates suitable for experimental assessment by MS-based proteomics is proposed. These tools have been made publicly available at http://www.proteore.org , allowing researchers to reuse them in their quest for biomarker discovery.
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Affiliation(s)
- Lien Nguyen
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
- INRA, MAIAGE Unit, University Paris-Saclay, Jouy-en-Josas, France
| | - Virginie Brun
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
| | - Florence Combes
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France
| | - Valentin Loux
- INRA, MAIAGE Unit, University Paris-Saclay, Jouy-en-Josas, France
| | - Yves Vandenbrouck
- Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France.
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207
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Jun J, Gim J, Kim Y, Kim H, Yu SJ, Yeo I, Park J, Yoo JJ, Cho YY, Lee DH, Cho EJ, Lee JH, Kim YJ, Lee S, Yoon JH, Kim Y, Park T. Analysis of significant protein abundance from multiple reaction-monitoring data. BMC SYSTEMS BIOLOGY 2018; 12:123. [PMID: 30598095 PMCID: PMC6311902 DOI: 10.1186/s12918-018-0656-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Background Discovering reliable protein biomarkers is one of the most important issues in biomedical research. The ELISA is a traditional technique for accurate quantitation of well-known proteins. Recently, the multiple reaction-monitoring (MRM) mass spectrometry has been proposed for quantifying newly discovered protein and has become a popular alternative to ELISA. For the MRM data analysis, linear mixed modeling (LMM) has been used to analyze MRM data. MSstats is one of the most widely used tools for MRM data analysis that is based on the LMMs. However, LMMs often provide various significance results, depending on model specification. Sometimes it would be difficult to specify a correct LMM method for the analysis of MRM data. Here, we propose a new logistic regression-based method for Significance Analysis of Multiple Reaction Monitoring (LR-SAM). Results Through simulation studies, we demonstrate that LMM methods may not preserve type I error, thus yielding high false- positive errors, depending on how random effects are specified. Our simulation study also shows that the LR-SAM approach performs similarly well as LMM approaches, in most cases. However, LR-SAM performs better than the LMMs, particularly when the effects sizes of peptides from the same protein are heterogeneous. Our proposed method was applied to MRM data for identification of proteins associated with clinical responses of treatment of 115 hepatocellular carcinoma (HCC) patients with the tyrosine kinase inhibitor sorafenib. Of 124 candidate proteins, LMM approaches provided 6 results varying in significance, while LR-SAM, by contrast, yielded 18 significant results that were quite reproducibly consistent. Conclusion As exemplified by an application to HCC data set, LR-SAM more effectively identified proteins associated with clinical responses of treatment than LMM did.
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Affiliation(s)
- Jongsu Jun
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Jungsoo Gim
- Graduate School of Public Health, Seoul National University, Seoul, South Korea
| | - Yongkang Kim
- Department of Statistics, Seoul National University, Seoul, South Korea
| | - Hyunsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Su Jong Yu
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Injun Yeo
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea
| | - Jiyoung Park
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea
| | - Jeong-Ju Yoo
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Young Youn Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Dong Hyeon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Eun Ju Cho
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Jeong-Hoon Lee
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Yoon Jun Kim
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Seungyeoun Lee
- Department of Mathematics and Statistics, Sejong University, Seoul, South Korea
| | - Jung-Hwan Yoon
- Department of Internal Medicine and Liver Research Institute, Seoul National University, Seoul, South Korea
| | - Youngsoo Kim
- Department of Biomedical Engineering, Seoul National University College of Medicine, Seoul, South Korea.,Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Taesung Park
- Department of Statistics, Seoul National University, Seoul, South Korea. .,Interdisciplinary program in Bioinformatics, Seoul National University, Seoul, South Korea.
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208
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Gibbons BC, Fillmore TL, Gao Y, Moore RJ, Liu T, Nakayasu ES, Metz TO, Payne SH. Rapidly Assessing the Quality of Targeted Proteomics Experiments through Monitoring Stable-Isotope Labeled Standards. J Proteome Res 2018; 18:694-699. [PMID: 30525668 DOI: 10.1021/acs.jproteome.8b00688] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Targeted proteomics experiments based on selected reaction monitoring (SRM) have gained wide adoption in the use of clinical biomarkers, cellular modeling, and numerous other biological experiments due to their highly accurate and reproducible quantification. The quantitative accuracy in targeted proteomics experiments is reliant on the stable-isotope, heavy-labeled peptide standards that are spiked into a sample and used as a reference when calculating the abundance of endogenous peptides. Therefore, the quality of measurement for these standards is a critical factor in determining whether data acquisition was successful. With improved mass spectrometry (MS) instrumentation that enables the monitoring of hundreds of peptides in hundreds to thousands of samples, quality assessment is increasingly important and cannot be performed manually. We present Q4SRM, a software tool that rapidly checks the signal from all heavy-labeled peptides and flags those that fail quality-control metrics. Using four metrics, the tool detects problems with both individual SRM transitions and the collective group of transitions that monitor a single peptide. The program's speed and simplicity enable its use at the point of data acquisition and can be ideally run immediately upon the completion of a liquid chromatography-SRM-MS analysis.
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Affiliation(s)
- Bryson C Gibbons
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas L Fillmore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Yuqian Gao
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ronald J Moore
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Tao Liu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Ernesto S Nakayasu
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Thomas O Metz
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
| | - Samuel H Payne
- Biological Sciences Division , Pacific Northwest National Laboratory , Richland Washington 99336 , United States
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209
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Rose CM, Erickson BK, Schweppe DK, Viner R, Choi J, Rogers J, Bomgarden R, Gygi SP, Kirkpatrick DS. TomahaqCompanion: A Tool for the Creation and Analysis of Isobaric Label Based Multiplexed Targeted Assays. J Proteome Res 2018; 18:594-605. [PMID: 30501201 DOI: 10.1021/acs.jproteome.8b00767] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Triggered by Offset, Multiplexed, Accurate mass, High resolution, and Absolute Quantitation (TOMAHAQ) is a recently introduced targeted proteomics method that combines peptide and sample multiplexing. TOMAHAQ assays enable sensitive and accurate multiplexed quantification by implementing an intricate data collection scheme that comprises multiple MSn scans, mass inclusion lists, and data-driven filters. Consequently, manual creation of TOMAHAQ methods can be time-consuming and error prone, while the resulting TOMAHAQ data may not be compatible with common mass spectrometry analysis pipelines. To address these concerns we introduce TomahaqCompanion, an open-source desktop application that enables rapid creation of TOMAHAQ methods and analysis of TOMAHAQ data. Starting from a list of peptide sequences, a user can perform each step of TOMAHAQ assay development including (1) generation of priming run target list, (2) analysis of priming run data, (3) generation of TOMAHAQ method file, and (4) analysis and export of quantitative TOMAHAQ data. We demonstrate the flexibility of TomahaqCompanion by creating a variety of methods testing TOMAHAQ parameters (e.g., number of SPS notches, run length, etc.). Lastly, we analyze an interference sample comprising heavy yeast peptides, a standard human peptide mixture, TMT11-plex, and super heavy TMT (shTMT) isobaric labels to demonstrate ∼10-200 attomol limit of quantification within a complex background using TOMAHAQ.
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Affiliation(s)
- Christopher M Rose
- Department of Microchemistry, Proteomics and Lipidomics , Genentech , South San Francisco , California 94080 , United States
| | - Brian K Erickson
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Devin K Schweppe
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Rosa Viner
- Thermo Fisher Scientific , San Jose , California 95134 , United States
| | - Jae Choi
- Thermo Fisher Scientific , Rockford , Illinois 61101 , United States
| | - John Rogers
- Thermo Fisher Scientific , Rockford , Illinois 61101 , United States
| | - Ryan Bomgarden
- Thermo Fisher Scientific , Rockford , Illinois 61101 , United States
| | - Steven P Gygi
- Department of Cell Biology , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Donald S Kirkpatrick
- Department of Microchemistry, Proteomics and Lipidomics , Genentech , South San Francisco , California 94080 , United States
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210
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Kiseleva OI, Ponomarenko EA, Romashova YA, Poverennaya EV, Lisitsa AV. Detectability of Plasma Proteins in SRM Measurements. CURR PROTEOMICS 2018. [DOI: 10.2174/1570164615666180718151135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Background: Liquid chromatography coupled with targeted mass spectrometry underwent
rapid technical evolution during last years and has become widely used technology in clinical laboratories.
It offers confident specificity and sensitivity superior to those of traditional immunoassays. However,
due to controversial reports on reproducibility of SRM measurements, the prospects of clinical appliance
of the method are worth discussing.
</P><P>
Objective: The study was aimed at assessment of capabilities of SRM to achieve a thorough assembly
of the human plasma proteome.
</P><P>
Method: We examined set of 19 human blood plasma samples to measure 100 proteins, including
FDA-approved biomarkers, via SRM-assay.
</P><P>
Results: Out of 100 target proteins 43 proteins were confidently detected in at least two blood plasma
sample runs, 36 and 21 proteins were either not detected in any run or inconsistently detected, respectively.
Empiric dependences on protein detectability were derived to predict the number of biological
samples required to detect with certainty a diagnostically relevant quantum of the human plasma proteome.
</P><P>
Conclusion: The number of samples exponentially increases with an increase in the number of protein
targets, while proportionally decreasing to the logarithm of the limit of detection. Analytical sensitivity
and enormous proteome heterogeneity are major bottlenecks of the human proteome exploration.
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Affiliation(s)
- Olga I. Kiseleva
- Department of Bioinformatics, Institute of Biomedical Chemistry, 10/8 Pogodinskaya Street, Moscow, 119121, Russian Federation
| | - Elena A. Ponomarenko
- Department of Bioinformatics, Institute of Biomedical Chemistry, 10/8 Pogodinskaya Street, Moscow, 119121, Russian Federation
| | - Yulia A. Romashova
- Department of Bioinformatics, Institute of Biomedical Chemistry, 10/8 Pogodinskaya Street, Moscow, 119121, Russian Federation
| | - Ekaterina V. Poverennaya
- Department of Bioinformatics, Institute of Biomedical Chemistry, 10/8 Pogodinskaya Street, Moscow, 119121, Russian Federation
| | - Andrey V. Lisitsa
- Department of Bioinformatics, Institute of Biomedical Chemistry, 10/8 Pogodinskaya Street, Moscow, 119121, Russian Federation
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211
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pRAD50: a novel and clinically applicable pharmacodynamic biomarker of both ATM and ATR inhibition identified using mass spectrometry and immunohistochemistry. Br J Cancer 2018; 119:1233-1243. [PMID: 30385821 PMCID: PMC6251026 DOI: 10.1038/s41416-018-0286-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 08/17/2018] [Accepted: 09/11/2018] [Indexed: 01/26/2023] Open
Abstract
Background AZD0156 and AZD6738 are potent and selective inhibitors of ataxia-telangiectasia-kinase (ATM) and ataxia-telangiectasia-mutated and Rad3-related (ATR), respectively, important sensors/signallers of DNA damage. Methods We used multiplexed targeted-mass-spectrometry to select pRAD50(Ser635) as a pharmacodynamic biomarker for AZD0156-mediated ATM inhibition from a panel of 45 peptides, then developed and tested a clinically applicable immunohistochemistry assay for pRAD50(Ser635) detection in FFPE tissue. Results We found moderate pRAD50 baseline levels across cancer indications. pRAD50 was detectable in 100% gastric cancers (n = 23), 99% colorectal cancers (n = 102), 95% triple-negative-breast cancers (TNBC) (n = 40) and 87.5% glioblastoma-multiformes (n = 16). We demonstrated AZD0156 target inhibition in TNBC patient-derived xenograft models; where AZD0156 monotherapy or post olaparib treatment, resulted in a 34–72% reduction in pRAD50. Similar inhibition of pRAD50 (68%) was observed following ATM inhibitor treatment post irinotecan in a colorectal cancer xenograft model. ATR inhibition, using AZD6738, increased pRAD50 in the ATM-proficient models whilst in ATM-deficient models the opposite was observed, suggesting pRAD50 pharmacodynamics post ATR inhibition may be ATM-dependent and could be useful to determine ATM functionality in patients treated with ATR inhibitors. Conclusion Together these data support clinical utilisation of pRAD50 as a biomarker of AZD0156 and AZD6738 pharmacology to elucidate clinical pharmacokinetic/pharmacodynamic relationships, thereby informing recommended Phase 2 dose/schedule.
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212
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Wiśniewski JR, Wegler C, Artursson P. Multiple-Enzyme-Digestion Strategy Improves Accuracy and Sensitivity of Label- and Standard-Free Absolute Quantification to a Level That Is Achievable by Analysis with Stable Isotope-Labeled Standard Spiking. J Proteome Res 2018; 18:217-224. [PMID: 30336047 DOI: 10.1021/acs.jproteome.8b00549] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Quantification of individual proteins is an essential task in understanding biological processes. For example, determination of concentrations of proteins transporting and metabolizing xenobiotics is a prerequisite for drug disposition predictions in humans based on in vitro data. So far, this task has frequently been accomplished by targeted proteomics. This type of analyses requires preparation of stable isotope labeled standards for each protein of interest. The selection of appropriate standard peptides is usually tedious and the number of proteins that can be studied in a single experiment by these approaches is limited. In addition, incomplete digestion of proteins often affects the accuracy of the quantification. To circumvent these constrains in proteomic protein quantification, label- and standard-free approaches, such as "total protein approach" (TPA) have been proposed. Here we directly compare an approach using stable isotope labeled (SIL) standards and TPA for quantification of transporters and enzymes in human liver samples within the same LC-MS/MS runs. We show that TPA is a convenient alternative to SIL-based methods. Optimization of the sample preparation beyond commonly used single tryptic digestion, by adding consecutive cleavage steps, improves accuracy and reproducibility of the TPA method to a level, which is achievable by analysis using stable isotope-labeled standard spiking.
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Affiliation(s)
- Jacek R Wiśniewski
- Biochemical Proteomics Group, Department of Proteomics and Signal Transduction , Max-Planck-Institute of Biochemistry , Am Klopferspitz 18 , D-82152 Martinsried , Germany
| | - Christine Wegler
- Department of Pharmacy , Uppsala University , S-751 23 Uppsala , Sweden.,Cardiovascular, Renal and Metabolism , Innovative Medicines and Early Development Biotech Unit , AstraZeneca , Gothenburg , Sweden
| | - Per Artursson
- Department of Pharmacy , Uppsala University , S-751 23 Uppsala , Sweden.,Science for Life Laboratory , Uppsala University , S-751 23 , Uppsala , Sweden
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213
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Vreeker GM, Nicolardi S, Bladergroen MR, van der Plas CJ, Mesker WE, Tollenaar RAEM, van der Burgt YEM, Wuhrer M. Automated Plasma Glycomics with Linkage-Specific Sialic Acid Esterification and Ultrahigh Resolution MS. Anal Chem 2018; 90:11955-11961. [PMID: 30230816 PMCID: PMC6209171 DOI: 10.1021/acs.analchem.8b02391] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/19/2018] [Indexed: 12/17/2022]
Abstract
High-throughput mass spectrometry (MS) glycomics is an emerging field driven by technological advancements including sample preparation and data processing. Previously, we reported an automated protocol for the analysis of N-glycans released from plasma proteins that included sialic acid derivatization with linkage-specificity, namely, ethylation of α2,6-linked sialic acid residues and lactone formation of α2,3-linked sialic acids. In the current study, each step in this protocol was further optimized. Method improvements included minimizing the extent of side-reaction during derivatization, an adjusted glycan purification strategy and mass analysis of the released N-glycans by ultrahigh resolution matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance MS. The latter resolved peak overlap and simplified spectral alignment due to high mass measurement precision. Moreover, this resulted in more confident glycan assignments and improved signal-to-noise for low-abundant species. The performance of the protocol renders high-throughput applications feasible in the exciting field of clinical glycomics.
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Affiliation(s)
- Gerda
C. M. Vreeker
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
- Department
of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Simone Nicolardi
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
- Department
of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Marco R. Bladergroen
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Corné J. van der Plas
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Wilma E. Mesker
- Department
of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Rob A. E. M. Tollenaar
- Department
of Surgery, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Center
for Proteomics and Metabolomics, Leiden
University Medical Center, 2300 RC Leiden, The Netherlands
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214
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Kuznetsova KG, Kliuchnikova AA, Ilina IU, Chernobrovkin AL, Novikova SE, Farafonova TE, Karpov DS, Ivanov MV, Goncharov AO, Ilgisonis EV, Voronko OE, Nasaev SS, Zgoda VG, Zubarev RA, Gorshkov MV, Moshkovskii SA. Proteogenomics of Adenosine-to-Inosine RNA Editing in the Fruit Fly. J Proteome Res 2018; 17:3889-3903. [DOI: 10.1021/acs.jproteome.8b00553] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Anna A. Kliuchnikova
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | | | | | | | - Dmitry S. Karpov
- Institute of Biomedical Chemistry, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mark V. Ivanov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Anton O. Goncharov
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | | | - Shamsudin S. Nasaev
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
| | | | - Roman A. Zubarev
- Karolinska Institutet, Stockholm, Sweden
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | - Mikhail V. Gorshkov
- Institute of Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, Russia
| | - Sergei A. Moshkovskii
- Institute of Biomedical Chemistry, Moscow, Russia
- Pirogov Russian National Research Medical University (RNRMU), Moscow, Russia
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215
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Verbeke F, Debunne N, Janssens Y, Tack L, Wynendaele E, Rigole P, Coenye T, De Spiegeleer B. Detection and quantification of Enterococcus faecalis RNPP-type quorum sensing peptides in bacterial culture media by UHPLC-MS. J Pharm Biomed Anal 2018; 160:55-63. [DOI: 10.1016/j.jpba.2018.07.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 07/08/2018] [Accepted: 07/14/2018] [Indexed: 11/29/2022]
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216
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Li D, Huang F, Zhao Y, Villata PW, Griffin TJ, Zhang L, Li L, Yu F. Plasma lipoproteome in Alzheimer's disease: a proof-of-concept study. Clin Proteomics 2018; 15:31. [PMID: 30250409 PMCID: PMC6147047 DOI: 10.1186/s12014-018-9207-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/15/2018] [Indexed: 12/11/2022] Open
Abstract
Background Although total plasma lipoproteome consists of proteins that have shown promises as biomarkers that can identify Alzheimer's disease (AD), effect sizes are modest. The objective of this study is to provide initial proof-of-concept that the plasma lipoproteome more likely differ between AD cases and controls when measured in individual plasma lipoprotein fractions than when measured as total in immunodepleted plasma. Methods We first developed a targeted proteomics method based on selected reaction monitoring (SRM) and liquid chromatography and tandem mass spectrometry for measurement of 120 tryptic peptides from 79 proteins that are commonly present in plasma lipoproteins. Then in a proof-of concept case-control study of 5 AD cases and 5 sex- and age-matched controls, we applied the targeted proteomic method and performed relatively quantification of 120 tryptic peptides in plasma lipoprotein fractions (fractionated by sequential gradient ultracentrifugation) and in immunodepleted plasma (of albumin and IgG). Unadjusted p values from two-sample t-tests and overall fold change was used to evaluate a peptide relative difference between AD cases and controls, with lower p values (< 0.05) or greater fold differences (> 1.05 or < 0.95) suggestive of greater peptide/protein differences. Results Within-day and between-days technical precisions (mean %CV [SD] of all SRM transitions) of the targeted proteomic method were 3.95% (2.65) and 9.31% (5.59), respectively. Between-days technical precisions (mean % CV [SD]) of the entire plasma lipoproteomic workflow including plasma lipoprotein fractionation was 27.90% (14.61). Ten tryptic peptides that belonged to 5 proteins in plasma lipoproteins had unadjusted p values < 0.05, compared to no peptides in immunodepleted plasma. Furthermore, 27, 32, 17, and 20 tryptic peptides in VLDL, IDL, LDL and HDL, demonstrated overall peptide fold differences > 1.05 or < 0.95, compared to only 6 tryptic peptides in immunodepleted plasma. The overall comparisons, therefore, suggested greater peptide/protein differences in plasma lipoproteome when measured in individual plasma lipoproteins than as total in immunodepleted plasma. Specifically, protein complement C3's peptide IHWESASLLR, had unadjusted p values of 0.00007, 0.00012, and 0.0006 and overall 1.25, 1.17, 1.14-fold changes in VLDL, IDL, and LDL, respectively. After positive False Discovery Rate (pFDR) adjustment, the complement C3 peptide IHWESASLLR in VLDL remained statistically different (adjusted p value < 0.05). Discussion The findings may warrant future studies to investigate plasma lipoproteome when measured in individual plasma lipoprotein fractions for AD diagnosis.
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Affiliation(s)
- Danni Li
- 1Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, MMC 609, Minneapolis, MN 55455 USA
| | - Fangying Huang
- 1Department of Laboratory Medicine and Pathology, University of Minnesota, 420 Delaware Street SE, MMC 609, Minneapolis, MN 55455 USA
| | - Yingchun Zhao
- 2Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Peter W Villata
- 2Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455 USA
| | - Timothy J Griffin
- 3Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Lin Zhang
- 4Department of Biostatistics, University of Minnesota, Minneapolis, MN 55455 USA
| | - Ling Li
- 5Department of Experimental and Clinical Pharmacology, University of Minnesota, Minneapolis, MN 55455 USA
| | - Fang Yu
- 6School of Nursing, University of Minnesota, Minneapolis, MN 55455 USA
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217
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Mato JM, Elortza F, Lu SC, Brun V, Paradela A, Corrales FJ. Liver cancer-associated changes to the proteome: what deserves clinical focus? Expert Rev Proteomics 2018; 15:749-756. [PMID: 30204005 DOI: 10.1080/14789450.2018.1521277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
INTRODUCTION Hepatocellular carcinoma (HCC) is recognized as the fifth most common neoplasm and currently represents the second leading form of cancer-related death worldwide. Despite great progress has been done in the understanding of its pathogenesis, HCC represents a heavy societal and economic burden as most patients are still diagnosed at advanced stages and the 5-year survival rate remain below 20%. Early detection and revolutionary therapies that rely on the discovery of new molecular biomarkers and therapeutic targets are therefore urgently needed to develop precision medicine strategies for a more efficient management of patients. Areas covered: This review intends to comprehensively analyse the proteomics-based research conducted in the last few years to address some of the principal still open riddles in HCC biology, based on the identification of molecular drivers of tumor progression and metastasis. Expert commentary: The technical advances in mass spectrometry experienced in the last decade have significantly improved the analytical capacity of proteome wide studies. Large-scale protein and protein variant (post-translational modifications) identification and quantification have allowed detailed dissections of molecular mechanisms underlying HCC progression and are already paving the way for the identification of clinically relevant proteins and the development of their use on patient care.
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Affiliation(s)
- José M Mato
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Félix Elortza
- a CIC bioGUNE, CIBERehd, ProteoRed-ISCIII, Bizkaia Science and Technology Park , Derio , Spain.,b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain
| | - Shelly C Lu
- c Division of Digestive and Liver Diseases , Cedars-Sinai Medical Center , LA , CA , USA
| | - Virginie Brun
- d Université Grenoble-Alpes, CEA, BIG, Biologie à Grande Echelle, Inserm , Grenoble , France
| | - Alberto Paradela
- e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
| | - Fernando J Corrales
- b National Institute for the Study of Liver and Gastrointestinal Diseases (CIBERehd), Carlos III National Institute of Health , Madrid , Spain.,e Functional Proteomics Laboratory , Centro Nacional de Biotecnología-CSIC, Proteored-ISCIII, CIBERehd , Madrid , Spain
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218
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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219
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Kopylov AT, Tikhonova OV, Farafonova TE, Novikova SE, Shushkova NA, Shevchenko VE, Liao PC, Archakov AI, Zgoda VG. [Quantitative targeted screening of proteins associated with lung adenocarcinoma cancer by the method of selected reaction monitoring]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2018; 64:368-375. [PMID: 30135285 DOI: 10.18097/pbmc20186404368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In the present study, we applied selected reaction monitoring (SRM) to a group of proteins that were previously reported to be associated with lung cancer (Novikova S.E. et al. (2017) Biomeditsinskaya khimiya, 63, 181-210. [1]). Measurements were performed on 59 plasma samples. These samples included: 23 samples of plasma of patients diagnosed with lung adenocarcinoma (LAC), 11 samples of plasma of patients diagnosed with squamous cell lung carcinoma (SqCC), 25 samples of donors with no previous history of oncological diseases, and one pooled sample from each of the above group. As a result of the SRM measurements 52 proteins were detected at least in one individual plasma sample. Statistical analysis showed that there were two groups confidently differentiated by the concentration value of 8 proteins wherein 5 proteins displayed increased level (P00738, P26639, P21926, P08603, P51149) in LAC group and 3 proteins (P51884, O15162, Q8N2K0) indicated diminishing the concentration level towards the control level. Data on protein concentrations obtained for LAC and SqCC did not distinguish the samples by statistical clustering analysis. These potential biomarkers can be used for further development of methods for early diagnostics of lung cancer.
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Affiliation(s)
- A T Kopylov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - S E Novikova
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | | | - Pao-Chi Liao
- National Cheng-Kung University, Tainan City, Taiwan
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
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220
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Ludwig C, Gillet L, Rosenberger G, Amon S, Collins BC, Aebersold R. Data-independent acquisition-based SWATH-MS for quantitative proteomics: a tutorial. Mol Syst Biol 2018; 14:e8126. [PMID: 30104418 PMCID: PMC6088389 DOI: 10.15252/msb.20178126] [Citation(s) in RCA: 622] [Impact Index Per Article: 103.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/11/2018] [Accepted: 05/15/2018] [Indexed: 01/16/2023] Open
Abstract
Many research questions in fields such as personalized medicine, drug screens or systems biology depend on obtaining consistent and quantitatively accurate proteomics data from many samples. SWATH-MS is a specific variant of data-independent acquisition (DIA) methods and is emerging as a technology that combines deep proteome coverage capabilities with quantitative consistency and accuracy. In a SWATH-MS measurement, all ionized peptides of a given sample that fall within a specified mass range are fragmented in a systematic and unbiased fashion using rather large precursor isolation windows. To analyse SWATH-MS data, a strategy based on peptide-centric scoring has been established, which typically requires prior knowledge about the chromatographic and mass spectrometric behaviour of peptides of interest in the form of spectral libraries and peptide query parameters. This tutorial provides guidelines on how to set up and plan a SWATH-MS experiment, how to perform the mass spectrometric measurement and how to analyse SWATH-MS data using peptide-centric scoring. Furthermore, concepts on how to improve SWATH-MS data acquisition, potential trade-offs of parameter settings and alternative data analysis strategies are discussed.
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Affiliation(s)
- Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich (TUM), Freising, Germany
| | - Ludovic Gillet
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - George Rosenberger
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Sabine Amon
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
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221
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Yin X, Baig F, Haudebourg E, Blankley RT, Gandhi T, Müller S, Reiter L, Hinterwirth H, Pechlaner R, Tsimikas S, Santer P, Willeit J, Kiechl S, Witztum JL, Sullivan A, Mayr M. Plasma Proteomics for Epidemiology: Increasing Throughput With Standard-Flow Rates. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001808. [PMID: 29237681 DOI: 10.1161/circgenetics.117.001808] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/03/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. METHODS AND RESULTS Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26-0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring-based measurements differed from antibody-based assays. CONCLUSIONS The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.
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Affiliation(s)
- Xiaoke Yin
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Ferheen Baig
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Eloi Haudebourg
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Richard T Blankley
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Tejas Gandhi
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Sebastian Müller
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Lukas Reiter
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Helmut Hinterwirth
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Raimund Pechlaner
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Sotirios Tsimikas
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Peter Santer
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Johann Willeit
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Stefan Kiechl
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Joseph L Witztum
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Anthony Sullivan
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Manuel Mayr
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.).
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222
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Proteoform Analysis to Fulfill Unmet Clinical Needs and Reach Global Standardization of Protein Measurands in Clinical Chemistry Proteomics. Clin Lab Med 2018; 38:487-497. [PMID: 30115393 DOI: 10.1016/j.cll.2018.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In clinical testing of protein markers, structure variants of the measurand are often not taken into account. This heterogeneous character of protein measurands in immunoassays often renders test standardization impossible. Consequently, test results from different methods can lead to underdiagnosis or overdiagnosis and, thus, undertreatment or overtreatment of patients. The systematic structural analysis of protein isoforms has been coined proteoform profiling and is performed through mass spectrometry-based proteomics strategies. Knowledge on proteoforms allows refining existing uni-marker tests and moreover has great potential to contribute to the urgent need for new tests to predict prognosis and severity of diseases.
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223
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Frantzi M, Latosinska A, Kontostathi G, Mischak H. Clinical Proteomics: Closing the Gap from Discovery to Implementation. Proteomics 2018; 18:e1700463. [PMID: 29785737 DOI: 10.1002/pmic.201700463] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/10/2018] [Indexed: 12/15/2022]
Abstract
Clinical proteomics, the application of proteome analysis to serve a clinical purpose, represents a major field in the area of proteome research. Over 1000 manuscripts on this topic are published each year, with numbers continuously increasing. However, the anticipated outcome, the transformation of the reported findings into improvements in patient management, is not immediately evident. In this article, the value and validity of selected clinical proteomics findings are investigated, and it is assessed how far implementation has progressed. A main conclusion from this assessment is that to achieve implementation, well-powered clinical studies are required in the appropriate population, addressing a specific clinical need and with a clear context-of-use. Efforts toward implementation, to be feasible, must be supported by the key players in science: publishers and funders. The authors propose a change on objectives, from additional discovery studies toward studies aiming at validation of the plethora of potential biomarkers that have been described, to demonstrate practical value of clinical proteomics. All elements required, potential biomarkers, technologies, and bio-banked samples are available (based on today's literature), hence a change in focus from discovery toward validation and application is not only urgently necessary, but also possible based on resources available today.
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Affiliation(s)
- Maria Frantzi
- Mosaiques Diagnostics GmbH, Hannover, 30659, Germany
| | | | - Georgia Kontostathi
- Department of Biotechnology, Biomedical Research Foundation Academy of Athens, Athens, 11527, Greece
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224
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Andjelković U, Josić D. Mass spectrometry based proteomics as foodomics tool in research and assurance of food quality and safety. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.04.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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225
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You J, Kao A, Dillon R, Croner LJ, Benz R, Blume JE, Wilcox B. A large-scale and robust dynamic MRM study of colorectal cancer biomarkers. J Proteomics 2018; 187:80-92. [PMID: 29953963 DOI: 10.1016/j.jprot.2018.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 05/10/2018] [Accepted: 06/20/2018] [Indexed: 12/13/2022]
Abstract
Over the past 20 years, mass spectrometry (MS) has emerged as a dynamic tool for proteomics biomarker discovery. However, published MS biomarker candidates often do not translate to the clinic, failing during attempts at independent replication. The cause can be shortcomings in study design, sample quality, assay quantitation, and/or quality/process control. To address these shortcomings, we developed an MS workflow in accordance with Tier 2 measurement requirements for targeted peptides, defined by the Clinical Proteomic Tumor Analysis Consortium (CPTAC) "fit-for-purpose" approach, using dynamic multiple reaction monitoring (dMRM), which measures specific peptide transitions during predefined retention time (RT) windows. We describe the development of a robust multipex dMRM assay measuring 641 proteotypic peptides from 392 colorectal cancer (CRC) related proteins, and the procedures to track and handle sample processing and instrument variation over a four-month study, during which the assay measured blood samples from 1045 patients with CRC symptoms. After data collection, transitions were filtered by signal quality metrics before entering receiver operating characteristic (ROC) analysis. The results demonstrated CRC signal carried by 127 proteins in the symptomatic population. The workflow might be further developed to build Tier 1 assays for clinical tests identifying symptomatic individuals at elevated risk of CRC. SIGNIFICANCE We developed a dMRM MS method with the rigor of a Tier 2 assay as defined by the CPTAC 'fit for purpose approach' [1]. Using quality and process control procedures, the assay was used to quantify 641 proteotypic peptides representing 392 CRC-related proteins in plasma from 1045 CRC-symptomatic patients. To our knowledge, this is the largest MRM method applied to the largest study to date. The results showed that 127 of the proteins carried univariate CRC signal in the symptomatic population. This large number of single biomarkers bodes well for future development of multivariate classifiers to distinguish CRC in the symptomatic population.
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Affiliation(s)
- Jia You
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - Athit Kao
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - Roslyn Dillon
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - Lisa J Croner
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - Ryan Benz
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - John E Blume
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA
| | - Bruce Wilcox
- Applied Proteomics, Inc., 3545 John Hopkins Court, San Diego, CA 92121, USA.
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226
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Ulke-Lemée A, Lau A, Nelson MC, James MT, Muruve DA, MacDonald JA. Quantification of Inflammasome Adaptor Protein ASC in Biological Samples by Multiple-Reaction Monitoring Mass Spectrometry. Inflammation 2018; 41:1396-1408. [DOI: 10.1007/s10753-018-0787-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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227
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Whiteaker JR, Zhao L, Saul R, Kaczmarczyk JA, Schoenherr RM, Moore HD, Jones-Weinert C, Ivey RG, Lin C, Hiltke T, Reding KW, Whiteley G, Wang P, Paulovich AG. A Multiplexed Mass Spectrometry-Based Assay for Robust Quantification of Phosphosignaling in Response to DNA Damage. Radiat Res 2018; 189:505-518. [PMID: 29474155 PMCID: PMC5939939 DOI: 10.1667/rr14963.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A lack of analytically robust and multiplexed assays has hampered studies of the large, branched phosphosignaling network responsive to DNA damage. To address this need, we developed and fully analytically characterized a 62-plex assay quantifying protein expression and post-translational modification (phosphorylation and ubiquitination) after induction of DNA damage. The linear range was over 3 orders of magnitude, the median inter-assay variability was 10% CV and the vast majority (∼85%) of assays were stable after extended storage. The multiplexed assay was applied in proof-of-principle studies to quantify signaling after exposure to genotoxic stress (ionizing radiation and 4-nitroquinoline 1-oxide) in immortalized cell lines and primary human cells. The effects of genomic variants and pharmacologic kinase inhibition (ATM/ATR) were profiled using the assay. This study demonstrates the utility of a quantitative multiplexed assay for studying cellular signaling dynamics, and the potential application to studies on inter-individual variation in the radiation response.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Rick Saul
- Antibody Characterization Laboratory, Leidos Biochemical Research, Inc., Frederick National Laboratory for Cancer Research ATRF, Frederick, Maryland
| | - Jan A. Kaczmarczyk
- Antibody Characterization Laboratory, Leidos Biochemical Research, Inc., Frederick National Laboratory for Cancer Research ATRF, Frederick, Maryland
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Heather D. Moore
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Corey Jones-Weinert
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, Maryland
| | - Kerryn W. Reding
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
- School of Public Health, University of Washington, Seattle, Washington
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research, Inc., Frederick National Laboratory for Cancer Research ATRF, Frederick, Maryland
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washingon
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228
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Manual method of visually identifying candidate signals for a targeted peptide. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1083:258-270. [PMID: 29554522 DOI: 10.1016/j.jchromb.2018.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 01/05/2018] [Accepted: 01/15/2018] [Indexed: 11/20/2022]
Abstract
The purpose of this study is to improve peptide signal identification in groups of extracted ion chromatograms (XICs) obtained with the liquid chromatography-selected reaction monitoring (LC-SRM) technique and a triple quadrupole mass spectrometer (QqQ) operating in one of the supported multiple reaction monitoring (MRM) modes. The imperfection of quadrupole mass analyzers causes ion interference, which impedes the identification of peptide signals as chromatographic peak groups in relevant retention time intervals. To investigate this problem in depth, the QqQ conversion of the eluate into XIC groups was considered as the consecutive transformations of the particles' abundances as the corresponding functions of retention time. In this study, the hypothesis that, during this conversion, the same chromatographic profile should be preserved as an implicit sign in each chromatographic peak of the signal was confirmed for peptides. To examine chromatographic profiles, continuous transformations of XIC groups were derived and implemented in srm2prot Express software (s2pe, http://msr.ibmc.msk.ru/s2pe). Because of ion interference, several peptide-like signals may appear in one XIC group. Therefore, these signals must be considered candidates for a targeted peptide's signal and should be resolved after identification. The theoretical investigation of intensity functions as XICs that are not distorted by noise produced three rules for Identifying Candidate Signals for a targeted Peptide (ICSP, http://msr.ibmc.msk.ru/ICSP) that constitute the proposed manual visual method. We theoretically and experimentally compared this method with the conventional semiempirical intuitive technique and found that the former significantly streamlines peptide signal identification and avoids typical errors.
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229
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Bostanci N, Selevsek N, Wolski W, Grossmann J, Bao K, Wahlander A, Trachsel C, Schlapbach R, Öztürk VÖ, Afacan B, Emingil G, Belibasakis GN. Targeted Proteomics Guided by Label-free Quantitative Proteome Analysis in Saliva Reveal Transition Signatures from Health to Periodontal Disease. Mol Cell Proteomics 2018; 17:1392-1409. [PMID: 29610270 DOI: 10.1074/mcp.ra118.000718] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 03/28/2018] [Indexed: 12/18/2022] Open
Abstract
Periodontal diseases are among the most prevalent worldwide, but largely silent, chronic diseases. They affect the tooth-supporting tissues with multiple ramifications on life quality. Their early diagnosis is still challenging, due to lack of appropriate molecular diagnostic methods. Saliva offers a non-invasively collectable reservoir of clinically relevant biomarkers, which, if utilized efficiently, could facilitate early diagnosis and monitoring of ongoing disease. Despite several novel protein markers being recently enlisted by discovery proteomics, their routine diagnostic application is hampered by the lack of validation platforms that allow for rapid, accurate and simultaneous quantification of multiple proteins in large cohorts. Here we carried out a pipeline of two proteomic platforms; firstly, we applied open ended label-free quantitative (LFQ) proteomics for discovery in saliva (n = 67, including individuals with health, gingivitis, and periodontitis), followed by selected-reaction monitoring (SRM)-targeted proteomics for validation in an independent cohort (n = 82). The LFQ platform led to the discovery of 119 proteins with at least 2-fold significant difference between health and disease. The 65 proteins chosen for the subsequent SRM platform included 50 functionally related proteins derived from the significantly enriched processes of the LFQ data, 11 from literature-mining, and four house-keeping ones. Among those, 60 were reproducibly quantifiable proteins (92% success rate), represented by a total of 143 peptides. Machine-learning modeling led to a narrowed-down panel of five proteins of high predictive value for periodontal diseases with maximum area under the receiver operating curve >0.97 (higher in disease: Matrix metalloproteinase-9, Ras-related protein-1, Actin-related protein 2/3 complex subunit 5; lower in disease: Clusterin, Deleted in Malignant Brain Tumors 1). This panel enriches the pool of credible clinical biomarker candidates for diagnostic assay development. Yet, the quantum leap brought into the field of periodontal diagnostics by this study is the application of the biomarker discovery-through-verification pipeline, which can be used for validation in further cohorts.
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Affiliation(s)
- Nagihan Bostanci
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden;
| | - Nathalie Selevsek
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Witold Wolski
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Kai Bao
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Asa Wahlander
- ¶AstraZeneca Translational Biomarkers and Bioanalysis, Drug Safety and Metabolism, Innovative Medicines, Mölndal, Sweden
| | - Christian Trachsel
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Ralph Schlapbach
- §Functional Genomics Center Zürich, University of Zürich/ETH Zürich, Zürich, Switzerland
| | - Veli Özgen Öztürk
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Beral Afacan
- ‖Department of Periodontology, School of Dentistry, Adnan Menderes University, Aydin, Turkey
| | - Gulnur Emingil
- **Department of Periodontology, School of Dentistry, Ege University, Izmir, Turkey
| | - Georgios N Belibasakis
- From the ‡Division of Oral Diseases, Department of Dental Medicine, Karolinska Institutet, Stockholm, Sweden
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230
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Achour B, Dantonio A, Niosi M, Novak JJ, Al-Majdoub ZM, Goosen TC, Rostami-Hodjegan A, Barber J. Data Generated by Quantitative Liquid Chromatography-Mass Spectrometry Proteomics Are Only the Start and Not the Endpoint: Optimization of Quantitative Concatemer-Based Measurement of Hepatic Uridine-5′-Diphosphate–Glucuronosyltransferase Enzymes with Reference to Catalytic Activity. Drug Metab Dispos 2018; 46:805-812. [DOI: 10.1124/dmd.117.079475] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 03/22/2018] [Indexed: 12/17/2022] Open
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231
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Whiteaker JR, Zhao L, Ivey RG, Sanchez-Bonilla M, Moore HD, Schoenherr RM, Yan P, Lin C, Shimamura A, Paulovich AG. Targeted mass spectrometry enables robust quantification of FANCD2 mono-ubiquitination in response to DNA damage. DNA Repair (Amst) 2018; 65:47-53. [PMID: 29605812 DOI: 10.1016/j.dnarep.2018.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/19/2018] [Accepted: 03/19/2018] [Indexed: 12/28/2022]
Abstract
The Fanconi anemia pathway is an important coordinator of DNA repair pathways and is particularly relevant to repair of DNA inter-strand crosslinks. Central to the pathway is monoubiquitination of FANCD2, requiring the function of multiple proteins in an upstream Fanconi core complex. We present development and analytical characterization of a novel assay for quantification of unmodified and monoubiquitinated FANCD2 proteoforms, based on peptide immunoaffinity enrichment and targeted multiple reaction monitoring mass spectrometry (immuno-MRM). The immuno-MRM assay is analytically characterized using fit-for-purpose method validation. The assay linear range is >3 orders of magnitude with total repeatability <16% CV. In proof-of-principle experiments, we demonstrate application of the multiplex assay by quantifying the FANCD2 proteoforms following mitomycin-c treatment in an isogenic pair of FancA-corrected and uncorrected cell lines, as well as primary peripheral blood mononuclear cells from Fanconi Anemia patients. Additionally, we demonstrate detection of endogenous FANCD2 monoubiquitination in human breast cancer tissue. The immuno-MRM assay provides a potential functional diagnostic for patients with Fanconi Anemia with defects in the upstream FA complex or FANCD2, and a potential test for predicting sensitivity to DNA cross-linking agents in human cancers.
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Affiliation(s)
- Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Richard G Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Marilyn Sanchez-Bonilla
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States; Seattle Children's Research Institute, Seattle, WA, United States
| | - Heather D Moore
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Regine M Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States
| | - Akiko Shimamura
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, United States
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, United States.
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232
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Top-down mass spectrometric immunoassay for human insulin and its therapeutic analogs. J Proteomics 2018; 175:27-33. [DOI: 10.1016/j.jprot.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/08/2023]
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233
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Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin Appl 2018; 12:1600180. [PMID: 28895300 PMCID: PMC6084352 DOI: 10.1002/prca.201600180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Indexed: 11/08/2022]
Abstract
PURPOSE Targeted proteomics using MRM with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept. Internal NAT-addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time. EXPERIMENTAL DESIGN To compare the following three methods, an MRM assay for 34 high-to-moderate abundance human plasma proteins is used: classical internal SIS-addition, internal NAT-addition, and external NAT-addition-generated in buffer using NAT and SIS peptides. Using endogenous-free chicken plasma, the accuracy is also evaluated. RESULTS The internal NAT-addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT-addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values. CONCLUSIONS AND CLINICAL RELEVANCE While the internal NAT-addition method may be "ideal", this new external NAT-addition can be used to determine the concentration of high-to-moderate abundance endogenous plasma proteins, providing a robust and cost-effective alternative for clinical analyses or other high-throughput applications.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenthe Netherlands
| | - Jingxi Pan
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Suping Zhang
- MRM Proteomics Inc.VictoriaBritish ColumbiaCanada
| | - Jun Han
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Christoph H. Borchers
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- University of VictoriaDepartment of Biochemistry and MicrobiologyVictoriaBCCanada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
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234
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Bateman NW, Conrads TP. Recent advances and opportunities in proteomic analyses of tumour heterogeneity. J Pathol 2018; 244:628-637. [PMID: 29344964 DOI: 10.1002/path.5036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/04/2018] [Accepted: 01/05/2018] [Indexed: 01/27/2023]
Abstract
Solid tumour malignancies comprise a highly variable admixture of tumour and non-tumour cellular populations, forming a complex cellular ecosystem and tumour microenvironment. This tumour heterogeneity is not incidental, and is known to correlate with poor patient prognosis for many cancer types. Indeed, non-malignant cell populations, such as vascular endothelial and immune cells, are known to play key roles supporting and, in some cases, driving aggressive tumour biology, and represent targets of emerging therapeutics, such as antiangiogenesis and immune checkpoint inhibitors. The biochemical interplay between these cellular populations and how they contribute to molecular tumour heterogeneity remains enigmatic, particularly from the perspective of the tumour proteome. This review focuses on recent advances in proteomic methods, namely imaging mass spectrometry, single-cell proteomic techniques, and preanalytical sample processing, that are uniquely positioned to enable detailed analysis of discrete cellular populations within tumours to improve our understanding of tumour proteomic heterogeneity. This review further emphasizes the opportunity afforded by the application of these techniques to the analysis of tumour heterogeneity in formalin-fixed paraffin-embedded archival tumour tissues, as these represent an invaluable resource for retrospective analyses that is now routinely accessible, owing to recent technological and methodological advances in tumour tissue proteomics. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Department of Obstetrics and Gynecology, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.,The John P. Murtha Cancer Center, Uniformed Services University of the Health Sciences and Walter Reed National Military Medical Center, Bethesda, MD, USA.,Inova Schar Cancer Institute, Inova Center for Personalized Health, Falls Church, VA, USA
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235
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Vildhede A, Nguyen C, Erickson BK, Kunz RC, Jones R, Kimoto E, Bourbonais F, Rodrigues AD, Varma MV. Comparison of Proteomic Quantification Approaches for Hepatic Drug Transporters: Multiplexed Global Quantitation Correlates with Targeted Proteomic Quantitation. Drug Metab Dispos 2018; 46:692-696. [DOI: 10.1124/dmd.117.079285] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 02/08/2018] [Indexed: 12/12/2022] Open
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236
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Perzanowska A, Fatalska A, Wojtas G, Lewandowicz A, Michalak A, Krasowski G, Borchers CH, Dadlez M, Domanski D. An MRM-Based Cytokeratin Marker Assay as a Tool for Cancer Studies: Application to Lung Cancer Pleural Effusions. Proteomics Clin Appl 2018; 12. [DOI: 10.1002/prca.201700084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 01/03/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Anna Perzanowska
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Agnieszka Fatalska
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Grzegorz Wojtas
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Andrzej Lewandowicz
- Department of Geriatrics; National Institute of Geriatrics, Rheumatology and Rehabilitation; Warsaw Poland
| | - Agata Michalak
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Grzegorz Krasowski
- Mazovian Center of Pulmonary Disease and Tuberculosis Treatment; Otwock Poland
| | - Christoph H. Borchers
- Proteomics Centre; Segal Cancer Centre; Lady Davis Institute; Jewish General Hospital; McGill University; Montreal Quebec Canada
- Gerald Bronfman Department of Oncology; Jewish General Hospital; McGill University; Montreal Quebec Canada
- Genome British Columbia Proteomics Centre; University of Victoria; Victoria British Columbia Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria British Columbia Canada
| | - Michal Dadlez
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
| | - Dominik Domanski
- Mass Spectrometry Laboratory; Institute of Biochemistry and Biophysics-Polish Academy of Sciences; Warsaw Poland
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237
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Mueller C, Haymond A, Davis JB, Williams A, Espina V. Protein biomarkers for subtyping breast cancer and implications for future research. Expert Rev Proteomics 2018; 15:131-152. [PMID: 29271260 PMCID: PMC6104835 DOI: 10.1080/14789450.2018.1421071] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
INTRODUCTION Breast cancer subtypes are currently defined by a combination of morphologic, genomic, and proteomic characteristics. These subtypes provide a molecular portrait of the tumor that aids diagnosis, prognosis, and treatment escalation/de-escalation options. Gene expression signatures describing intrinsic breast cancer subtypes for predicting risk of recurrence have been rapidly adopted in the clinic. Despite the use of subtype classifications, many patients develop drug resistance, breast cancer recurrence, or therapy failure. Areas covered: This review provides a summary of immunohistochemistry, reverse phase protein array, mass spectrometry, and integrative studies that are revealing differences in biological functions within and between breast cancer subtypes. We conclude with a discussion of rigor and reproducibility for proteomic-based biomarker discovery. Expert commentary: Innovations in proteomics, including implementation of assay guidelines and standards, are facilitating refinement of breast cancer subtypes. Proteomic and phosphoproteomic information distinguish biologically functional subtypes, are predictive of recurrence, and indicate likelihood of drug resistance. Actionable, activated signal transduction pathways can now be quantified and characterized. Proteomic biomarker validation in large, well-designed studies should become a public health priority to capitalize on the wealth of information gleaned from the proteome.
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Affiliation(s)
- Claudius Mueller
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Amanda Haymond
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Justin B Davis
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Alexa Williams
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Virginia Espina
- a Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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238
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Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer's Disease Brain. Methods Mol Biol 2018; 1523:161-177. [PMID: 27975250 DOI: 10.1007/978-1-4939-6598-4_10] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Recent advances in mass spectrometry (MS)-based proteomics have greatly facilitated the robust identification and quantification of posttranslational modifications (PTMs), including those that are present at substoichiometric site occupancies. The abnormal posttranslational modification and accumulation of the microtubule-associated protein tau has been implicated in the pathogenesis of Alzheimer's disease (AD), and it is thought that the primary mode of regulation of tau occurs through PTMs. Several studies have been published regarding tau phosphorylation; however, other tau PTMs such as ubiquitylation, acetylation, methylation, oxidation, sumoylation, nitration, and glycosylation have not been analyzed as extensively. The comprehensive detection and delineation of these PTMs is critical for drug target discovery and validation. Lysine-directed PTMs including ubiquitylation, acetylation, and methylation play key regulatory roles with respect to the rates of tau turnover and aggregation. MS-based analytical approaches have been used to gain insight into the tau lysine-directed PTM signature that is most closely associated with neurofibrillary lesion formation. This chapter provides details pertaining to the liquid chromatography tandem mass spectrometry (LC-MS/MS)-based analysis of the lysine-directed posttranslational modification of tau.
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239
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Aebersold R, Bensimon A, Collins BC, Ludwig C, Sabido E. Applications and Developments in Targeted Proteomics: From SRM to DIA/SWATH. Proteomics 2018; 16:2065-7. [PMID: 27542680 DOI: 10.1002/pmic.201600203] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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240
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Musunuru K, Ingelsson E, Fornage M, Liu P, Murphy AM, Newby LK, Newton-Cheh C, Perez MV, Voora D, Woo D. The Expressed Genome in Cardiovascular Diseases and Stroke: Refinement, Diagnosis, and Prediction: A Scientific Statement From the American Heart Association. ACTA ACUST UNITED AC 2018; 10:HCG.0000000000000037. [PMID: 28760750 DOI: 10.1161/hcg.0000000000000037] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There have been major advances in our knowledge of the contribution of DNA sequence variations to cardiovascular disease and stroke. However, the inner workings of the body reflect the complex interplay of factors beyond the DNA sequence, including epigenetic modifications, RNA transcripts, proteins, and metabolites, which together can be considered the "expressed genome." The emergence of high-throughput technologies, including epigenomics, transcriptomics, proteomics, and metabolomics, is now making it possible to address the contributions of the expressed genome to cardiovascular disorders. This statement describes how the expressed genome can currently and, in the future, potentially be used to diagnose diseases and to predict who will develop diseases such as coronary artery disease, stroke, heart failure, and arrhythmias.
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241
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242
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Miyamoto S, Stroble CD, Taylor S, Hong Q, Lebrilla CB, Leiserowitz GS, Kim K, Ruhaak LR. Multiple Reaction Monitoring for the Quantitation of Serum Protein Glycosylation Profiles: Application to Ovarian Cancer. J Proteome Res 2017; 17:222-233. [PMID: 29207246 DOI: 10.1021/acs.jproteome.7b00541] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein glycosylation fingerprints are widely recognized as potential markers for disease states, and indeed differential glycosylation has been identified in multiple types of autoimmune diseases and several types of cancer. However, releasing the glycans leave the glycoproteins unknown; therefore, there exists a need for high-throughput methods that allow quantification of site- and protein-specific glycosylation patterns from complex biological mixtures. In this study, a targeted multiple reaction monitoring (MRM)-based method for the protein- and site-specific quantitation involving serum proteins immunoglobulins A, G and M, alpha-1-antitrypsin, transferrin, alpha-2-macroglobulin, haptoglobin, alpha-1-acid glycoprotein and complement C3 was developed. The method is based on tryptic digestion of serum glycoproteins, followed by immediate reverse phase UPLC-QQQ-MS analysis of glycopeptides. To quantitate protein glycosylation independent of the protein serum concentration, a nonglycosylated peptide was also monitored. Using this strategy, 178 glycopeptides and 18 peptides from serum glycoproteins are analyzed with good repeatability (interday CVs of 3.65-21-92%) in a single 17 min run. To assess the potential of the method, protein glycosylation was analyzed in serum samples from ovarian cancer patients and controls. A training set consisting of 40 cases and 40 controls was analyzed, and differential analyses were performed to identify aberrant glycopeptide levels. All findings were validated in an independent test set (n = 44 cases and n = 44 controls). In addition to the differential glycosylation on the immunoglobulins, which was reported previously, aberrant glycosylation was also observed on each of the glycoproteins, which could be corroborated in the test set. This report shows the development of a method for targeted protein- and site-specific glycosylation analysis and the potential of such methods in biomarker development.
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Affiliation(s)
- Suzanne Miyamoto
- UC Davis Cancer Center , Sacramento, California 95817, United States
| | - Carol D Stroble
- UC Davis Cancer Center , Sacramento, California 95817, United States.,Department of Chemistry, University of California , Davis, California 95616, United States
| | - Sandra Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - Qiuting Hong
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Carlito B Lebrilla
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Gary S Leiserowitz
- Division of Gynecologic Oncology, UC Davis Medical Center , Sacramento, California 95817, United States
| | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California , Davis, California 95616, United States
| | - L Renee Ruhaak
- Department of Chemistry, University of California , Davis, California 95616, United States.,Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center , 2333 ZA Leiden, The Netherlands
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243
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Mercier C, Klich A, Truntzer C, Picaud V, Giovannelli JF, Ducoroy P, Grangeat P, Maucort-Boulch D, Roy P. Variance component analysis to assess protein quantification in biomarker discovery. Application to MALDI-TOF mass spectrometry. Biom J 2017; 60:262-274. [PMID: 29230881 DOI: 10.1002/bimj.201600198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 07/06/2017] [Accepted: 10/08/2017] [Indexed: 11/11/2022]
Abstract
Controlling the technological variability on an analytical chain is critical for biomarker discovery. The sources of technological variability should be modeled, which calls for specific experimental design, signal processing, and statistical analysis. Furthermore, with unbalanced data, the various components of variability cannot be estimated with the sequential or adjusted sums of squares of usual software programs. We propose a novel approach to variance component analysis with application to the matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) technology and use this approach for protein quantification by a classical signal processing algorithm and two more recent ones (BHI-PRO 1 and 2). Given the high technological variability, the quantification failed to restitute the known quantities of five out of nine proteins present in a controlled solution. There was a linear relationship between protein quantities and peak intensities for four out of nine peaks with all algorithms. The biological component of the variance was higher with BHI-PRO than with the classical algorithm (80-95% with BHI-PRO 1, 79-95% with BHI-PRO 2 vs. 56-90%); thus, BHI-PRO were more efficient in protein quantification. The technological component of the variance was higher with the classical algorithm than with BHI-PRO (6-25% vs. 2.5-9.6% with BHI-PRO 1 and 3.5-11.9% with BHI-PRO 2). The chemical component was also higher with the classical algorithm (3.6-18.7% vs. < 3.5%). Thus, BHI-PRO were better in removing noise from signal when the expected peaks are detected. Overall, either BHI-PRO algorithm may reduce the technological variance from 25 to 10% and thus improve protein quantification and biomarker validation.
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Affiliation(s)
- Catherine Mercier
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Département Biostatistiques et Modélisation pour la santé et l'environnement, Université Lyon 1, Villeurbanne, 69622, France.,Pôle Rhône-Alpes de Bioinformatique (PRABI), Villeurbanne, France.,CNRS UMR 5558, Laboratoire de Biométrie et Biologie Évolutive (LBBE), Équipe Biostatistique Santé, Villeurbanne, France
| | - Amna Klich
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Département Biostatistiques et Modélisation pour la santé et l'environnement, Université Lyon 1, Villeurbanne, 69622, France.,Pôle Rhône-Alpes de Bioinformatique (PRABI), Villeurbanne, France.,CNRS UMR 5558, Laboratoire de Biométrie et Biologie Évolutive (LBBE), Équipe Biostatistique Santé, Villeurbanne, France
| | - Caroline Truntzer
- Clinical and Innovation Proteomic Platform (CLIPP), Pôle de Recherche Université de Bourgogne, Dijon, France
| | - Vincent Picaud
- Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Gif-sur-Yvette, France.,Université Paris-Saclay, Saint-Aubin, France
| | - Jean-François Giovannelli
- CNRS UMR 5218, Laboratoire de l'Intégration du Matériau au Système (IMS), Talence, France.,Département micro Technologies pour la biologie et la santé, Université de Bordeaux, Talence, France.,Institut Polytechnique de Bordeaux (Bordeaux INP), Talence, France
| | - Patrick Ducoroy
- Clinical and Innovation Proteomic Platform (CLIPP), Pôle de Recherche Université de Bourgogne, Dijon, France
| | - Pierre Grangeat
- Innovation en micro et nanotechnologie, Université de Grenoble-Alpes, Grenoble, France.,Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Laboratoire d'Électronique et de Technologie de l'Information, MINATEC Campus, Grenoble, France
| | - Delphine Maucort-Boulch
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Département Biostatistiques et Modélisation pour la santé et l'environnement, Université Lyon 1, Villeurbanne, 69622, France.,Pôle Rhône-Alpes de Bioinformatique (PRABI), Villeurbanne, France.,CNRS UMR 5558, Laboratoire de Biométrie et Biologie Évolutive (LBBE), Équipe Biostatistique Santé, Villeurbanne, France
| | - Pascal Roy
- Service de Biostatistique-Bioinformatique, Hospices Civils de Lyon, Lyon, France.,Université de Lyon, Lyon, France.,Département Biostatistiques et Modélisation pour la santé et l'environnement, Université Lyon 1, Villeurbanne, 69622, France.,Pôle Rhône-Alpes de Bioinformatique (PRABI), Villeurbanne, France.,CNRS UMR 5558, Laboratoire de Biométrie et Biologie Évolutive (LBBE), Équipe Biostatistique Santé, Villeurbanne, France
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244
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Bowler RP, Wendt CH, Fessler MB, Foster MW, Kelly RS, Lasky-Su J, Rogers AJ, Stringer KA, Winston BW. New Strategies and Challenges in Lung Proteomics and Metabolomics. An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 2017; 14:1721-1743. [PMID: 29192815 PMCID: PMC5946579 DOI: 10.1513/annalsats.201710-770ws] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This document presents the proceedings from the workshop entitled, "New Strategies and Challenges in Lung Proteomics and Metabolomics" held February 4th-5th, 2016, in Denver, Colorado. It was sponsored by the National Heart Lung Blood Institute, the American Thoracic Society, the Colorado Biological Mass Spectrometry Society, and National Jewish Health. The goal of this workshop was to convene, for the first time, relevant experts in lung proteomics and metabolomics to discuss and overcome specific challenges in these fields that are unique to the lung. The main objectives of this workshop were to identify, review, and/or understand: (1) emerging technologies in metabolomics and proteomics as applied to the study of the lung; (2) the unique composition and challenges of lung-specific biological specimens for metabolomic and proteomic analysis; (3) the diverse informatics approaches and databases unique to metabolomics and proteomics, with special emphasis on the lung; (4) integrative platforms across genetic and genomic databases that can be applied to lung-related metabolomic and proteomic studies; and (5) the clinical applications of proteomics and metabolomics. The major findings and conclusions of this workshop are summarized at the end of the report, and outline the progress and challenges that face these rapidly advancing fields.
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245
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Cheow ESH, Cheng WC, Yap T, Dutta B, Lee CN, Kleijn DPVD, Sorokin V, Sze SK. Myocardial Injury Is Distinguished from Stable Angina by a Set of Candidate Plasma Biomarkers Identified Using iTRAQ/MRM-Based Approach. J Proteome Res 2017; 17:499-515. [DOI: 10.1021/acs.jproteome.7b00651] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Esther Sok Hwee Cheow
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Woo Chin Cheng
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
| | - Terence Yap
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Bamaprasad Dutta
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
| | - Chuen Neng Lee
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Cardiac, Thoracic & Vascular Surgery, National University Heart Centre, Singapore 119074, Singapore
- Department
of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore
| | - Dominique P. V. de Kleijn
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Vascular Surgery, University Medical Center Utrecht, The Netherlands & Interuniversity Cardiovascular Institute of The Netherlands, Utrecht 3508 GA, The Netherlands
| | - Vitaly Sorokin
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore & Cardiovascular Research Institute, Singapore 119228, Singapore
- Department of Cardiac, Thoracic & Vascular Surgery, National University Heart Centre, Singapore 119074, Singapore
| | - Siu Kwan Sze
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, Singapore 637551, Singapore
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246
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Kang T, Jensen P, Huang H, Lund Christensen G, Billestrup N, Larsen MR. Characterization of the Molecular Mechanisms Underlying Glucose Stimulated Insulin Secretion from Isolated Pancreatic β-cells Using Post-translational Modification Specific Proteomics (PTMomics). Mol Cell Proteomics 2017; 17:95-110. [PMID: 29113996 DOI: 10.1074/mcp.ra117.000217] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/20/2017] [Indexed: 01/01/2023] Open
Abstract
Normal pancreatic islet β-cells (PBCs) abundantly secrete insulin in response to elevated blood glucose levels, in order to maintain an adequate control of energy balance and glucose homeostasis. However, the molecular mechanisms underlying the insulin secretion are unclear. Improving our understanding of glucose-stimulated insulin secretion (GSIS) mechanisms under normal conditions is a prerequisite for developing better interventions against diabetes. Here, we aimed at identifying novel signaling pathways involved in the initial release of insulin from PBCs after glucose stimulation using quantitative strategies for the assessment of phosphorylated proteins and sialylated N-linked (SA) glycoproteins.Islets of Langerhans derived from newborn rats with a subsequent 9-10 days of maturation in vitro were stimulated with 20 mm glucose for 0 min (control), 5 min, 10 min, and 15 min. The isolated islets were subjected to time-resolved quantitative phosphoproteomics and sialiomics using iTRAQ-labeling combined with enrichment of phosphorylated peptides and formerly SA glycopeptides and high-accuracy LC-MS/MS. Using bioinformatics we analyzed the functional signaling pathways during GSIS, including well-known insulin secretion pathways. Furthermore, we identified six novel activated signaling pathways (e.g. agrin interactions and prolactin signaling) at 15 min GSIS, which may increase our understanding of the molecular mechanism underlying GSIS. Moreover, we validated some of the regulated phosphosites by parallel reaction monitoring, which resulted in the validation of eleven new phosphosites significantly regulated on GSIS. Besides protein phosphorylation, alteration in SA glycosylation was observed on several surface proteins on brief GSIS. Interestingly, proteins important for cell-cell interaction, cell movement, cell-ECM interaction and Focal Adhesion (e.g. integrins, semaphorins, and plexins) were found regulated at the level of sialylation, but not in protein expression. Collectively, we believe that this comprehensive Proteomics and PTMomics survey of signaling pathways taking place during brief GSIS of primary PBCs is contributing to understanding the complex signaling underlying GSIS.
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Affiliation(s)
- Taewook Kang
- From the ‡Department of Biochemistry and Molecular Biology, PR group, University of Southern Denmark, Odense, Denmark
| | - Pia Jensen
- From the ‡Department of Biochemistry and Molecular Biology, PR group, University of Southern Denmark, Odense, Denmark
| | - Honggang Huang
- From the ‡Department of Biochemistry and Molecular Biology, PR group, University of Southern Denmark, Odense, Denmark
| | - Gitte Lund Christensen
- §Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Nils Billestrup
- §Department of Biomedical Sciences, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin R Larsen
- From the ‡Department of Biochemistry and Molecular Biology, PR group, University of Southern Denmark, Odense, Denmark;
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247
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Kopylov AT, Ilgisonis EV, Tikhonova OV, Farafonova TE, Novikova SE, Zgoda VG, Ponomarenko EA, Lisitsa AV, Markin AA, Morukov BV, Grigoriev AI, Archakov AI. Quantitative target proteomics of chromosome 13 human blood plasma proteins. DOKL BIOCHEM BIOPHYS 2017; 476:326-328. [DOI: 10.1134/s160767291705009x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Indexed: 11/23/2022]
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248
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Poverennaya EV, Ilgisonis EV, Ponomarenko EA, Kopylov AT, Zgoda VG, Radko SP, Lisitsa AV, Archakov AI. Why Are the Correlations between mRNA and Protein Levels so Low among the 275 Predicted Protein-Coding Genes on Human Chromosome 18? J Proteome Res 2017; 16:4311-4318. [PMID: 28956606 DOI: 10.1021/acs.jproteome.7b00348] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work targeted (selected reaction monitoring, SRM, PASSEL: PASS00697) and panoramic (shotgun LC-MS/MS, PRIDE: PXD00244) mass-spectrometric methods as well as transcriptomic analysis of the same samples using RNA-Seq and PCR methods (SRA experiment IDs: SRX341198, SRX267708, SRX395473, SRX390071) were applied for quantification of chromosome 18 encoded transcripts and proteins in human liver and HepG2 cells. The obtained data was used for the estimation of quantitative mRNA-protein ratios for the 275 genes of the selected chromosome in the selected tissues. The impact of methodological limitations of existing analytical proteomic methods on gene-specific mRNA-protein ratios and possible ways of overcoming these limitations for detection of missing proteins are also discussed.
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Affiliation(s)
| | | | | | | | - Victor G Zgoda
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAS , 119121 Moscow, Russia
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249
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Adeola HA, Van Wyk JC, Arowolo A, Ngwanya RM, Mkentane K, Khumalo NP. Emerging Diagnostic and Therapeutic Potentials of Human Hair Proteomics. Proteomics Clin Appl 2017; 12. [PMID: 28960873 DOI: 10.1002/prca.201700048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Indexed: 01/22/2023]
Abstract
The use of noninvasive human substrates to interrogate pathophysiological conditions has become essential in the post- Human Genome Project era. Due to its high turnover rate, and its long term capability to incorporate exogenous and endogenous substances from the circulation, hair testing is emerging as a key player in monitoring long term drug compliance, chronic alcohol abuse, forensic toxicology, and biomarker discovery, among other things. Novel high-throughput 'omics based approaches like proteomics have been underutilized globally in comprehending human hair morphology and its evolving use as a diagnostic testing substrate in the era of precision medicine. There is paucity of scientific evidence that evaluates the difference in drug incorporation into hair based on lipid content, and very few studies have addressed hair growth rates, hair forms, and the biological consequences of hair grooming or bleaching. It is apparent that protein-based identification using the human hair proteome would play a major role in understanding these parameters akin to DNA single nucleotide polymorphism profiling, up to single amino acid polymorphism resolution. Hence, this work seeks to identify and discuss the progress made thus far in the field of molecular hair testing using proteomic approaches, and identify ways in which proteomics would improve the field of hair research, considering that the human hair is mostly composed of proteins. Gaps in hair proteomics research are identified and the potential of hair proteomics in establishing a historic medical repository of normal and disease-specific proteome is also discussed.
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Affiliation(s)
- Henry A Adeola
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Jennifer C Van Wyk
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Afolake Arowolo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Reginald M Ngwanya
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Khwezikazi Mkentane
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
| | - Nonhlanhla P Khumalo
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.,Hair and Skin Research Laboratory, Groote Schuur Hospital, Cape Town, South Africa
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Kilambi HV, Manda K, Rai A, Charakana C, Bagri J, Sharma R, Sreelakshmi Y. Green-fruited Solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4803-4819. [PMID: 29048567 PMCID: PMC5853803 DOI: 10.1093/jxb/erx288] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 07/21/2017] [Indexed: 05/22/2023]
Abstract
Members of the tomato clade exhibit a wide diversity in fruit color, but the mechanisms governing inter-species diversity of coloration are largely unknown. The carotenoid profiles, carotenogenic gene expression and proteome profiles of green-fruited Solanum habrochaites (SH), orange-fruited S. galapagense, and red-fruited S. pimpinellifolium were compared with cultivated tomato [S. lycopersicum cv. Ailsa Craig (SL)] to decipher the molecular basis of coloration diversity. Green-fruited SH, though it showed normal expression of chromoplast-specific phytoene synthase1 and lycopene β-cyclase genes akin to orange/red-fruited species, failed to accumulate lycopene and β-carotene. The SH phytoene synthase1 cDNA encoded an enzymatically active protein, whereas the lycopene β-cyclase cDNA was barely active. Consistent with its green-fruited nature, SH's fruits retained chloroplast structure and PSII activity, and had impaired chlorophyll degradation with high pheophorbide a levels. Comparison of the fruit proteomes with SL revealed retention of the proteome complement related to photosynthesis in SH. Targeted peptide monitoring revealed a low abundance of key carotenogenic and sequestration proteins in SH compared with tomato. The green-fruitedness of SH appears to stem from blocks at several critical steps regulating fruit-specific carotenogenesis namely the absence of chloroplast to chromoplast transformation, block in carotenoid biosynthesis, and a dearth of carotenoid sequestering proteins.
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Affiliation(s)
- Himabindu Vasuki Kilambi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Kalyani Manda
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Avanish Rai
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Chaitanya Charakana
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Jayram Bagri
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, India
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