1
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Feng S, Sanford JA, Weber T, Hutchinson-Bunch CM, Dakup PP, Paurus VL, Attah K, Sauro HM, Qian WJ, Wiley HS. A Phosphoproteomics Data Resource for Systems-level Modeling of Kinase Signaling Networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551714. [PMID: 37577496 PMCID: PMC10418157 DOI: 10.1101/2023.08.03.551714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Building mechanistic models of kinase-driven signaling pathways requires quantitative measurements of protein phosphorylation across physiologically relevant conditions, but this is rarely done because of the insensitivity of traditional technologies. By using a multiplexed deep phosphoproteome profiling workflow, we were able to generate a deep phosphoproteomics dataset of the EGFR-MAPK pathway in non-transformed MCF10A cells across physiological ligand concentrations with a time resolution of <12 min and in the presence and absence of multiple kinase inhibitors. An improved phosphosite mapping technique allowed us to reliably identify >46,000 phosphorylation sites on >6600 proteins, of which >4500 sites from 2110 proteins displayed a >2-fold increase in phosphorylation in response to EGF. This data was then placed into a cellular context by linking it to 15 previously published protein databases. We found that our results were consistent with much, but not all previously reported data regarding the activation and negative feedback phosphorylation of core EGFR-ERK pathway proteins. We also found that EGFR signaling is biphasic with substrates downstream of RAS/MAPK activation showing a maximum response at <3ng/ml EGF while direct substrates, such as HGS and STAT5B, showing no saturation. We found that RAS activation is mediated by at least 3 parallel pathways, two of which depend on PTPN11. There appears to be an approximately 4-minute delay in pathway activation at the step between RAS and RAF, but subsequent pathway phosphorylation was extremely rapid. Approximately 80 proteins showed a >2-fold increase in phosphorylation across all experiments and these proteins had a significantly higher median number of phosphorylation sites (~18) relative to total cellular phosphoproteins (~4). Over 60% of EGF-stimulated phosphoproteins were downstream of MAPK and included mediators of cellular processes such as gene transcription, transport, signal transduction and cytoskeletal arrangement. Their phosphorylation was either linear with respect to MAPK activation or biphasic, corresponding to the biphasic signaling seen at the level of the EGFR. This deep, integrated phosphoproteomics data resource should be useful in building mechanistic models of EGFR and MAPK signaling and for understanding how downstream responses are regulated.
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Affiliation(s)
- Song Feng
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - James A. Sanford
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Thomas Weber
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | | | - Panshak P. Dakup
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Vanessa L. Paurus
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Kwame Attah
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Herbert M. Sauro
- Department of Bioengineering, University of Washington, Seattle, WA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - H. Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
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2
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. MASS SPECTROMETRY REVIEWS 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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3
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Targeted Quantification of Protein Phosphorylation and Its Contributions towards Mathematical Modeling of Signaling Pathways. Molecules 2023; 28:molecules28031143. [PMID: 36770810 PMCID: PMC9919559 DOI: 10.3390/molecules28031143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Post-translational modifications (PTMs) are key regulatory mechanisms that can control protein function. Of these, phosphorylation is the most common and widely studied. Because of its importance in regulating cell signaling, precise and accurate measurements of protein phosphorylation across wide dynamic ranges are crucial to understanding how signaling pathways function. Although immunological assays are commonly used to detect phosphoproteins, their lack of sensitivity, specificity, and selectivity often make them unreliable for quantitative measurements of complex biological samples. Recent advances in Mass Spectrometry (MS)-based targeted proteomics have made it a more useful approach than immunoassays for studying the dynamics of protein phosphorylation. Selected reaction monitoring (SRM)-also known as multiple reaction monitoring (MRM)-and parallel reaction monitoring (PRM) can quantify relative and absolute abundances of protein phosphorylation in multiplexed fashions targeting specific pathways. In addition, the refinement of these tools by enrichment and fractionation strategies has improved measurement of phosphorylation of low-abundance proteins. The quantitative data generated are particularly useful for building and parameterizing mathematical models of complex phospho-signaling pathways. Potentially, these models can provide a framework for linking analytical measurements of clinical samples to better diagnosis and treatment of disease.
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4
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Urban J. A review on recent trends in the phosphoproteomics workflow. From sample preparation to data analysis. Anal Chim Acta 2022; 1199:338857. [DOI: 10.1016/j.aca.2021.338857] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022]
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Targeted Quantification of Phosphorylation Sites Identifies STRIPAK-Dependent Phosphorylation of the Hippo Pathway-Related Kinase SmKIN3. mBio 2021; 12:mBio.00658-21. [PMID: 33947760 PMCID: PMC8262875 DOI: 10.1128/mbio.00658-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
We showed recently that the germinal center kinase III (GCKIII) SmKIN3 from the fungus Sordaria macrospora is involved in sexual development and hyphal septation. Our recent extensive global proteome and phosphoproteome analysis revealed that SmKIN3 is a target of the striatin-interacting phosphatase and kinase (STRIPAK) multisubunit complex. Here, using protein samples from the wild type and three STRIPAK mutants, we applied absolute quantification by parallel-reaction monitoring (PRM) to analyze phosphorylation site occupancy in SmKIN3 and other septation initiation network (SIN) components, such as CDC7 and DBF2, as well as BUD4, acting downstream of SIN. For SmKIN3, we show that phosphorylation of S668 and S686 is decreased in mutants lacking distinct subunits of STRIPAK, while a third phosphorylation site, S589, was not affected. We constructed SmKIN3 mutants carrying phospho-mimetic and phospho-deficient codons for phosphorylation sites S589, S668, and S686. Investigation of hyphae in a ΔSmkin3 strain complemented by the S668 and S686 mutants showed a hyper-septation phenotype, which was absent in the wild type, the ΔSmkin3 strain complemented with the wild-type gene, and the S589 mutant. Furthermore, localization studies with SmKIN3 phosphorylation variants and STRIPAK mutants showed that SmKIN3 preferentially localizes at the terminal septa, which is distinctly different from the localization of the wild-type strains. We conclude that STRIPAK-dependent phosphorylation of SmKIN3 has an impact on controlled septum formation and on the time-dependent localization of SmKIN3 on septa at the hyphal tip. Thus, STRIPAK seems to regulate SmKIN3, as well as DBF2 and BUD4 phosphorylation, affecting septum formation.
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Salazar-Cavazos E, Nitta CF, Mitra ED, Wilson BS, Lidke KA, Hlavacek WS, Lidke DS. Multisite EGFR phosphorylation is regulated by adaptor protein abundances and dimer lifetimes. Mol Biol Cell 2020; 31:695-708. [PMID: 31913761 PMCID: PMC7202077 DOI: 10.1091/mbc.e19-09-0548] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Differential epidermal growth factor receptor (EGFR) phosphorylation is thought to couple receptor activation to distinct signaling pathways. However, the molecular mechanisms responsible for biased signaling are unresolved due to a lack of insight into the phosphorylation patterns of full-length EGFR. We extended a single-molecule pull-down technique previously used to study protein-protein interactions to allow for robust measurement of receptor phosphorylation. We found that EGFR is predominantly phosphorylated at multiple sites, yet phosphorylation at specific tyrosines is variable and only a subset of receptors share phosphorylation at the same site, even with saturating ligand concentrations. We found distinct populations of receptors as soon as 1 min after ligand stimulation, indicating early diversification of function. To understand this heterogeneity, we developed a mathematical model. The model predicted that variations in phosphorylation are dependent on the abundances of signaling partners, while phosphorylation levels are dependent on dimer lifetimes. The predictions were confirmed in studies of cell lines with different expression levels of signaling partners, and in experiments comparing low- and high-affinity ligands and oncogenic EGFR mutants. These results reveal how ligand-regulated receptor dimerization dynamics and adaptor protein concentrations play critical roles in EGFR signaling.
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Affiliation(s)
| | | | - Eshan D Mitra
- Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | | | - Keith A Lidke
- Comprehensive Cancer Center, and.,Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131
| | - William S Hlavacek
- Comprehensive Cancer Center, and.,Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545
| | - Diane S Lidke
- Department of Pathology.,Comprehensive Cancer Center, and
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7
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Sun F, Suttapitugsakul S, Xiao H, Wu R. Comprehensive Analysis of Protein Glycation Reveals Its Potential Impacts on Protein Degradation and Gene Expression in Human Cells. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2480-2490. [PMID: 31073893 PMCID: PMC6842084 DOI: 10.1007/s13361-019-02197-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 03/11/2019] [Accepted: 03/12/2019] [Indexed: 05/02/2023]
Abstract
Glycation as a type of non-enzymatic protein modification is related to aging and chronic diseases, especially diabetes. Global analysis of protein glycation will aid in a better understanding of its formation mechanism and biological significance. In this work, we comprehensively investigated protein glycation in human cells (HEK293T, Jurkat, and MCF7 cells). The current results indicated that this non-enzymatic modification was not random, and protein at the extracellular regions and the nucleus were more frequently glycated. Systematic and site-specific analysis of glycated proteins allowed us to study the effect of the primary sequences and secondary structures of proteins on glycation. Furthermore, nearly every enzyme in the glycolytic pathway was found to be glycated and a possible mechanism was proposed. Many glycation sites were also previously reported as acetylation and ubiquitination sites, which strongly suggested that this non-enzymatic modification may disturb protein degradation and gene expression. The current results will facilitate further studies of protein glycation in biomedical and clinical research.
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Affiliation(s)
- Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA.
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8
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Nielson CM, Jacobs JM, Orwoll ES. Proteomic studies of bone and skeletal health outcomes. Bone 2019; 126:18-26. [PMID: 30954730 PMCID: PMC7302501 DOI: 10.1016/j.bone.2019.03.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/12/2022]
Abstract
Proteins are an essential part of essentially all biological processes, and there is enormous variation in protein forms and concentrations that is not reflected in DNA or RNA. Recently there have been rapid advances in the ability to measure protein sequence, modification and concentration, particularly with methods based in mass spectrometry. Global measures of proteins in tissues or in the circulation provide a broad assessment of the proteome that can be extremely useful for discovery, and targeted proteomic measures can yield specific and sensitive assessments of specific peptides and proteins. While most proteomic measures are directed at the detection of consensus peptide sequences, mass spectrometry based proteomic methods also allow a detailed examination of the peptide sequence differences that result from genetic variants and that may have important effects on protein function. In evaluating proteomic data, a number of analytical considerations are important, including an understanding of missing data, the challenge of multiple testing and replication, and the use of rapidly evolving methods in systems biology. While proteomics has not yet had a major impact in skeletal research, interesting recent research has used these approaches in the study of bone cell biology and the discovery of biomarkers of skeletal disorders. Proteomics can be expected to have an increasing influence in the study of bone biology and pathophysiology.
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Affiliation(s)
| | - Jon M Jacobs
- Pacific Northwest National Laboratory, Richland, WA, USA
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9
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TAKAHASHI C, YAZAKI T, SUGIYAMA N, ISHIHAMA Y. Selected Reaction Monitoring of Kinase Activity-Targeted Phosphopeptides. CHROMATOGRAPHY 2019. [DOI: 10.15583/jpchrom.2019.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | - Tatsuya YAZAKI
- Graduate School of Pharmaceutical Science, Kyoto University
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10
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Zhang B, Whiteaker JR, Hoofnagle AN, Baird GS, Rodland KD, Paulovich AG. Clinical potential of mass spectrometry-based proteogenomics. Nat Rev Clin Oncol 2019; 16:256-268. [PMID: 30487530 PMCID: PMC6448780 DOI: 10.1038/s41571-018-0135-7] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cancer genomics research aims to advance personalized oncology by finding and targeting specific genetic alterations associated with cancers. In genome-driven oncology, treatments are selected for individual patients on the basis of the findings of tumour genome sequencing. This personalized approach has prolonged the survival of subsets of patients with cancer. However, many patients do not respond to the predicted therapies based on the genomic profiles of their tumours. Furthermore, studies pairing genomic and proteomic analyses of samples from the same tumours have shown that the proteome contains novel information that cannot be discerned through genomic analysis alone. This observation has led to the concept of proteogenomics, in which both types of data are leveraged for a more complete view of tumour biology that might enable patients to be more successfully matched to effective treatments than they would using genomics alone. In this Perspective, we discuss the added value of proteogenomics over the current genome-driven approach to the clinical characterization of cancers and summarize current efforts to incorporate targeted proteomic measurements based on selected/multiple reaction monitoring (SRM/MRM) mass spectrometry into the clinical laboratory to facilitate clinical proteogenomics.
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Affiliation(s)
- Bing Zhang
- Department of Molecular and Human Genetics, Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX, USA
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Andrew N Hoofnagle
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Geoffrey S Baird
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
- Department of Cell, Development and Cancer Biology, Oregon Health & Sciences University, Portland, OR, USA
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
- Division of Medical Oncology, University of Washington School of Medicine, Seattle, WA, USA.
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11
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Chen YT, Tsai CH, Chen CL, Yu JS, Chang YH. Development of biomarkers of genitourinary cancer using mass spectrometry-based clinical proteomics. J Food Drug Anal 2019; 27:387-403. [PMID: 30987711 PMCID: PMC9296213 DOI: 10.1016/j.jfda.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 09/19/2018] [Accepted: 09/20/2018] [Indexed: 12/23/2022] Open
Abstract
Prostate, bladder and kidney cancer are the three most common types of genitourinary cancer in the world. Of these, prostate and bladder cancers are within the top 10 most common cancers in men. Notably, kidney cancer causes no obvious symptoms in the early stages. To satisfy clinical-management requirements, researchers have developed numerous biomarkers by applying proteomic approaches using clinical serum, urine and tissue specimens, as well as cell and animal models. Through application of biomarker pipeline protocols, including discovery, verification and validation phases, and mass-spectrometric based proteomic platforms coupled with multiplexed quantification assays, these studies have led to recent rapid progress in this area. With improvements in mass-spectrometric based proteomic techniques, numerous promising biomarker candidates and marker panels for various clinical purposes have been proposed. Verification of novel protein biomarker candidates is very resource demanding (e.g. on the clinical and laboratory sides). With the support of national consortia, it is now possible to investigate the future clinical use of such biomarker strategies and assess their cost-effectiveness in personalized medicine.
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Affiliation(s)
- Yi-Ting Chen
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taiwan University, Taoyuan,
Taiwan
- Corresponding author. Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Han Tsai
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Chien-Lun Chen
- Department of Urology, Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- College of Medicine, Chang Gung University, Taoyuan,
Taiwan
| | - Jau-Song Yu
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Molecular Medicine Research Center, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou,
Taiwan
| | - Ying-Hsu Chang
- Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan,
Taiwan
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan,
Taiwan
- Corresponding author. Division of Urology, Department of Surgery, LinKou Chang Gung Memorial Hospital, Taoyuan, Taiwan. E-mail addresses: (Y.-T. Chen), (Y.-H. Chang)
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12
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Viodé A, Epelbaum S, Benyounes I, Verny M, Dubois B, Junot C, Fenaille F, Lamari F, Becher F. Simultaneous quantification of tau and α-synuclein in cerebrospinal fluid by high-resolution mass spectrometry for differentiation of Lewy Body Dementia from Alzheimer's Disease and controls. Analyst 2019; 144:6342-6351. [DOI: 10.1039/c9an00751b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A novel mass spectrometry assay offers simultaneous quantification of CSF α-synuclein and tau and has potential diagnostic value.
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Affiliation(s)
- Arthur Viodé
- Service de Pharmacologie et d'Immunoanalyse (SPI)
- Laboratoire d'Etude du Métabolisme des Médicaments (LEMM)
- CEA
- INRA
- Université Paris Saclay
| | - Stéphane Epelbaum
- Institut de la Mémoire et de Maladie d'Alzheimer (IM2A)
- Département de Neurologie
- Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix
- Paris
- France
| | - Imen Benyounes
- Service de Biochimie Métabolique
- Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix
- Paris
- France
| | - Marc Verny
- Service de Gériatrie
- Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix
- Paris
- France
| | - Bruno Dubois
- Institut de la Mémoire et de Maladie d'Alzheimer (IM2A)
- Département de Neurologie
- Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix
- Paris
- France
| | - Christophe Junot
- Service de Pharmacologie et d'Immunoanalyse (SPI)
- Laboratoire d'Etude du Métabolisme des Médicaments (LEMM)
- CEA
- INRA
- Université Paris Saclay
| | - François Fenaille
- Service de Pharmacologie et d'Immunoanalyse (SPI)
- Laboratoire d'Etude du Métabolisme des Médicaments (LEMM)
- CEA
- INRA
- Université Paris Saclay
| | - Foudil Lamari
- Service de Biochimie Métabolique
- Hôpitaux Universitaires Pitié-Salpêtrière-Charles Foix
- Paris
- France
| | - François Becher
- Service de Pharmacologie et d'Immunoanalyse (SPI)
- Laboratoire d'Etude du Métabolisme des Médicaments (LEMM)
- CEA
- INRA
- Université Paris Saclay
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13
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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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14
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Facile carrier-assisted targeted mass spectrometric approach for proteomic analysis of low numbers of mammalian cells. Commun Biol 2018; 1:103. [PMID: 30271983 PMCID: PMC6123794 DOI: 10.1038/s42003-018-0107-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 07/10/2018] [Indexed: 01/04/2023] Open
Abstract
There is an unmet technical challenge for mass spectrometry (MS)-based proteomic analysis of single mammalian cells. Quantitative proteomic analysis of single cells has been previously achieved by antibody-based immunoassays but is limited by the availability of high-quality antibodies. Herein we report a facile targeted MS-based proteomics method, termed cPRISM-SRM (carrier-assisted high-pressure, high-resolution separations with intelligent selection and multiplexing coupled to selected reaction monitoring), for reliable analysis of low numbers of mammalian cells. The method capitalizes on using “carrier protein” to assist processing of low numbers of cells with minimal loss, high-resolution PRISM separation for target peptide enrichment, and sensitive SRM for protein quantification. We have demonstrated that cPRISM-SRM has sufficient sensitivity to quantify proteins expressed at ≥200,000 copies per cell at the single-cell level and ≥3000 copies per cell in 100 mammalian cells. We envision that with further improvement cPRISM-SRM has the potential to move toward targeted MS-based single-cell proteomics. Tujin Shi et al. report a mass spectrometry-based proteomics approach, cPRISM-SRM, that allows for accurate quantification of proteins in small numbers of mammalian cells through the use of a carrier protein to prevent sample loss. The sensitivity of cPRISM-SRM allows for measurement of the 2500 most abundant proteins in a human cell.
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15
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Yi L, Shi T, Gritsenko MA, X'avia Chan CY, Fillmore TL, Hess BM, Swensen AC, Liu T, Smith RD, Wiley HS, Qian WJ. Targeted Quantification of Phosphorylation Dynamics in the Context of EGFR-MAPK Pathway. Anal Chem 2018; 90:5256-5263. [PMID: 29584399 DOI: 10.1021/acs.analchem.8b00071] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Large-scale phosphoproteomics with coverage of over 10,000 sites of phosphorylation have now been routinely achieved with advanced mass spectrometry (MS)-based workflows. However, accurate targeted MS-based quantification of phosphorylation dynamics, an important direction for gaining quantitative understanding of signaling pathways or networks, has been much less investigated. Herein, we report an assessment of the targeted workflow in the context of signal transduction pathways, using the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway as our model. A total of 43 phosphopeptides from the EGFR-MAPK pathway were selected for the study. The recovery and sensitivity of two commonly used enrichment methods, immobilized metal affinity chromatography (IMAC) and titanium oxide (TiO2), combined with selected reaction monitoring (SRM)-MS were evaluated. The recovery of phosphopeptides by IMAC and TiO2 enrichment was quantified to be 38 ± 5% and 58 ± 20%, respectively, based on internal standards. Moreover, both enrichment methods provided comparable sensitivity from 1 to 100 μg starting peptides. Robust quantification was consistently achieved for most targeted phosphopeptides when starting with 25-100 μg peptides. However, the numbers of quantified targets significantly dropped when peptide samples were in the 1-25 μg range. Finally, IMAC-SRM was applied to quantify signaling dynamics of EGFR-MAPK pathway in Hs578T cells following 10 ng/mL EGF treatment. The kinetics of phosphorylation clearly revealed early and late phases of phosphorylation, even for very low abundance proteins. These results demonstrate the feasibility of robust targeted quantification of phosphorylation dynamics for specific pathways, even starting with relatively small amounts of protein.
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16
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Nakedi KC, Calder B, Banerjee M, Giddey A, Nel AJM, Garnett S, Blackburn JM, Soares NC. Identification of Novel Physiological Substrates of Mycobacterium bovis BCG Protein Kinase G (PknG) by Label-free Quantitative Phosphoproteomics. Mol Cell Proteomics 2018; 17:1365-1377. [PMID: 29549130 PMCID: PMC6030727 DOI: 10.1074/mcp.ra118.000705] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Indexed: 01/09/2023] Open
Abstract
Mycobacterial Ser/Thr kinases play a critical role in bacterial physiology and pathogenesis. Linking kinases to the substrates they phosphorylate in vivo, thereby elucidating their exact functions, is still a challenge. The aim of this work was to associate protein phosphorylation in mycobacteria with important subsequent macro cellular events by identifying the physiological substrates of PknG in Mycobacterium bovis BCG. The study compared the phosphoproteome dynamics during the batch growth of M. bovis BCG versus the respective PknG knock-out mutant (ΔPknG-BCG) strains. We employed TiO2 phosphopeptide enrichment techniques combined with label-free quantitative phosphoproteomics workflow on LC-MS/MS. The comprehensive analysis of label-free data identified 603 phosphopeptides on 307 phosphoproteins with high confidence. Fifty-five phosphopeptides were differentially phosphorylated, of these, 23 phosphopeptides were phosphorylated in M. bovis BCG wild-type only and not in the mutant. These were further validated through targeted mass spectrometry assays (PRMs). Kinase-peptide docking studies based on a published crystal structure of PknG in complex with GarA revealed that the majority of identified phosphosites presented docking scores close to that seen in previously described PknG substrates, GarA, and ribosomal protein L13. Six out of the 22 phosphoproteins had higher docking scores than GarA, consistent with the proteins identified here being true PknG substrates. Based on protein functional analysis of the PknG substrates identified, this study confirms that PknG plays an important regulatory role in mycobacterial metabolism, through phosphorylation of ATP binding proteins and enzymes in the TCA cycle. This work also reinforces PknG's regulation of protein translation and folding machinery.
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Affiliation(s)
- Kehilwe C Nakedi
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Bridget Calder
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Mousumi Banerjee
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Alexander Giddey
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Andrew J M Nel
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Shaun Garnett
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Jonathan M Blackburn
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa.,§Institute of Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, South Africa
| | - Nelson C Soares
- From the ‡Division of Chemical & Systems Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, South Africa;
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17
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Manes NP, Nita-Lazar A. Application of targeted mass spectrometry in bottom-up proteomics for systems biology research. J Proteomics 2018; 189:75-90. [PMID: 29452276 DOI: 10.1016/j.jprot.2018.02.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/25/2018] [Accepted: 02/07/2018] [Indexed: 02/08/2023]
Abstract
The enormous diversity of proteoforms produces tremendous complexity within cellular proteomes, facilitates intricate networks of molecular interactions, and constitutes a formidable analytical challenge for biomedical researchers. Currently, quantitative whole-proteome profiling often relies on non-targeted liquid chromatography-mass spectrometry (LC-MS), which samples proteoforms broadly, but can suffer from lower accuracy, sensitivity, and reproducibility compared with targeted LC-MS. Recent advances in bottom-up proteomics using targeted LC-MS have enabled previously unachievable identification and quantification of target proteins and posttranslational modifications within complex samples. Consequently, targeted LC-MS is rapidly advancing biomedical research, especially systems biology research in diverse areas that include proteogenomics, interactomics, kinomics, and biological pathway modeling. With the recent development of targeted LC-MS assays for nearly the entire human proteome, targeted LC-MS is positioned to enable quantitative proteomic profiling of unprecedented quality and accessibility to support fundamental and clinical research. Here we review recent applications of bottom-up proteomics using targeted LC-MS for systems biology research. SIGNIFICANCE: Advances in targeted proteomics are rapidly advancing systems biology research. Recent applications include systems-level investigations focused on posttranslational modifications (such as phosphoproteomics), protein conformation, protein-protein interaction, kinomics, proteogenomics, and metabolic and signaling pathways. Notably, absolute quantification of metabolic and signaling pathway proteins has enabled accurate pathway modeling and engineering. Integration of targeted proteomics with other technologies, such as RNA-seq, has facilitated diverse research such as the identification of hundreds of "missing" human proteins (genes and transcripts that appear to encode proteins but direct experimental evidence was lacking).
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Affiliation(s)
- Nathan P Manes
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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18
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Ferraiuolo RM, Tubman J, Sinha I, Hamm C, Porter LA. The cyclin-like protein, SPY1, regulates the ERα and ERK1/2 pathways promoting tamoxifen resistance. Oncotarget 2017; 8:23337-23352. [PMID: 28423577 PMCID: PMC5410308 DOI: 10.18632/oncotarget.15578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 02/12/2017] [Indexed: 12/20/2022] Open
Abstract
The Ras/Raf/MEK/ERK pathway conveys growth factor and mitogen signalling to control the phosphorylation of a plethora of substrates regulating proliferation, survival, and migration. The Ras signalling pathway is frequently associated with poor prognosis and drug resistance in various cancers including those of the blood, breast and prostate. Activation of the downstream effector ERK does not always occur via a linear cascade of events; complicating the targeting of this pathway therapeutically. This work describes a novel positive feedback loop where the cell cycle regulatory factor Spy1 (RINGO; gene SPDYA) activates ERK1/2 in a MEK-independent fashion. Spy1 was originally isolated for the ability to stimulate Xenopus oocyte maturation via a MAPK-signalling pathway and is known to override apoptosis triggered by the DNA damage response. We demonstrate that mammalian Spy1-mediated ERK activation increases ligand-independent phosphorylation and activation of estrogen receptor α, correlating with a decrease in tamoxifen sensitivity. This could define a novel druggable mechanism driving proliferation and resistance in select cancers.
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Affiliation(s)
- Rosa-Maria Ferraiuolo
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Janice Tubman
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada.,Acenzia Inc, Tecumseh, ON N9A 6J3, Canada
| | | | - Caroline Hamm
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada.,Windsor Regional Hospital, Windsor, ON N8W 1L9, Canada
| | - Lisa Ann Porter
- Department of Biological Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
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19
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Suttapitugsakul S, Xiao H, Smeekens J, Wu R. Evaluation and optimization of reduction and alkylation methods to maximize peptide identification with MS-based proteomics. MOLECULAR BIOSYSTEMS 2017; 13:2574-2582. [PMID: 29019370 PMCID: PMC5698164 DOI: 10.1039/c7mb00393e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mass spectrometry (MS) has become an increasingly important technique to analyze proteins. In popular bottom-up MS-based proteomics, reduction and alkylation are routine steps to facilitate peptide identification. However, incomplete reactions and side reactions may occur, which compromise the experimental results. In this work, we systematically evaluated the reduction step with commonly used reagents, i.e., dithiothreitol, 2-mercaptoethanol, tris(2-carboxyethyl)phosphine, or tris(3-hydroxypropyl)phosphine, and alkylation with iodoacetamide, acrylamide, N-ethylmaleimide, or 4-vinylpyridine. By using digested peptides from a yeast whole-cell lysate, the number of proteins and peptides identified were very similar using four different reducing reagents. The results from four alkylating reagents, however, were dramatically different with iodoacetamide giving the highest number of peptides with alkylated cysteine and the lowest number of peptides with incomplete cysteine alkylation and side reactions. Alkylation conditions with iodoacetamide were further optimized. To identify more peptides with cysteine, thiopropyl-sepharose 6B resins were used to enrich them, and the optimal conditions were employed for the reduction and alkylation. The enrichment resulted in over three times more cysteine-containing peptides than without enrichment. Systematic evaluation of the reduction and alkylation with different reagents can aid in a better design of bottom-up proteomic experiments.
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Affiliation(s)
- Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.
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20
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Wang H, Barbieri CE, He J, Gao Y, Shi T, Wu C, Schepmoes AA, Fillmore TL, Chae SS, Huang D, Mosquera JM, Qian WJ, Smith RD, Srivastava S, Kagan J, Camp DG, Rodland KD, Rubin MA, Liu T. Quantification of mutant SPOP proteins in prostate cancer using mass spectrometry-based targeted proteomics. J Transl Med 2017; 15:175. [PMID: 28810879 PMCID: PMC5557563 DOI: 10.1186/s12967-017-1276-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Speckle-type POZ protein (SPOP) is an E3 ubiquitin ligase adaptor protein that functions as a potential tumor suppressor, and SPOP mutations have been identified in ~10% of human prostate cancers. However, it remains unclear if mutant SPOP proteins can be utilized as biomarkers for early detection, diagnosis, prognosis or targeted therapy of prostate cancer. Moreover, the SPOP mutation sites are distributed in a relatively short region with multiple lysine residues, posing significant challenges for bottom-up proteomics analysis of the SPOP mutations. METHODS To address this issue, PRISM (high-pressure, high-resolution separations coupled with intelligent selection and multiplexing)-SRM (selected reaction monitoring) mass spectrometry assays have been developed for quantifying wild-type SPOP protein and 11 prostate cancer-derived SPOP mutations. RESULTS Despite inherent limitations due to amino acid sequence constraints, all the PRISM-SRM assays developed using Arg-C digestion showed a linear dynamic range of at least two orders of magnitude, with limits of quantification ranged from 0.1 to 1 fmol/μg of total protein in the cell lysate. Applying these SRM assays to analyze HEK293T cells with and without expression of the three most frequent SPOP mutations in prostate cancer (Y87N, F102C or F133V) led to confident detection of all three SPOP mutations in corresponding positive cell lines but not in the negative cell lines. Expression of the F133V mutation and wild-type SPOP was at much lower levels compared to that of F102C and Y87N mutations; however, at present, it is unknown if this also affects the biological activity of the SPOP protein. CONCLUSIONS In summary, PRISM-SRM enables multiplexed, isoform-specific detection of mutant SPOP proteins in cell lysates, providing significant potential in biomarker development for prostate cancer.
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Affiliation(s)
- Hui Wang
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Christopher E. Barbieri
- Institute of Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY USA
| | - Jintang He
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Athena A. Schepmoes
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Thomas L. Fillmore
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Sung-Suk Chae
- Institute of Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY USA
| | - Dennis Huang
- Institute of Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY USA
| | - Juan Miguel Mosquera
- Institute of Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Sudhir Srivastava
- Division of Cancer Prevention, Cancer Biomarkers Research Group, National Cancer Institute, Bethesda, MD USA
| | - Jacob Kagan
- Division of Cancer Prevention, Cancer Biomarkers Research Group, National Cancer Institute, Bethesda, MD USA
| | - David G. Camp
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Karin D. Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
| | - Mark A. Rubin
- Institute of Precision Medicine of Weill Cornell Medical College and New York Presbyterian Hospital, New York, NY USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, MSIN: K8-98, Richland, WA 99354 USA
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21
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Targeted mass spectrometry: An emerging powerful approach to unblock the bottleneck in phosphoproteomics. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1055-1056:29-38. [PMID: 28441545 DOI: 10.1016/j.jchromb.2017.04.026] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 02/23/2017] [Accepted: 04/14/2017] [Indexed: 01/21/2023]
Abstract
Following the rapid expansion of the proteomics field, the investigation of post translational modifications (PTM) has become extremely popular changing our perspective of how proteins constantly fine tune cellular functions. Reversible protein phosphorylation plays a pivotal role in virtually all biological processes in the cell and it is one the most characterized PTM up to date. During the last decade, the development of phosphoprotein/phosphopeptide enrichment strategies and mass spectrometry (MS) technology has revolutionized the field of phosphoproteomics discovering thousands of new site-specific phosphorylations and unveiling unprecedented evidence about their modulation under distinct cellular conditions. The field has expanded so rapidly that the use of traditional methods to validate and characterize the biological role of the phosphosites is not feasible any longer. Targeted MS holds great promise for becoming the method of choice to study with high precision and sensitivity already known site-specific phosphorylation events. This review summarizes the contribution of large-scale unbiased MS analyses and highlights the need of targeted MS-based approaches for follow-up investigation. Additionally, the article illustrates the biological relevance of protein phosphorylation by providing examples of disease-related phosphorylation events and emphasizes the benefits of applying targeted MS in clinics for disease diagnosis, prognosis and drug-response evaluation.
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22
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Bilan V, Selevsek N, Kistemaker HAV, Abplanalp J, Feurer R, Filippov DV, Hottiger MO. New Quantitative Mass Spectrometry Approaches Reveal Different ADP-ribosylation Phases Dependent On the Levels of Oxidative Stress. Mol Cell Proteomics 2017; 16:949-958. [PMID: 28325851 DOI: 10.1074/mcp.o116.065623] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/20/2017] [Indexed: 11/06/2022] Open
Abstract
Oxidative stress is a potent inducer of protein ADP-ribosylation. Although individual oxidative stress-induced ADP-ribosylated proteins have been identified, it is so far not clear to which extent different degrees of stress severity quantitatively and qualitatively alter ADP-ribosylation. Here, we investigated both quantitative and qualitative changes of the hydrogen peroxide (H2O2)-induced ADP-ribosylome using a label-free shotgun quantification and a parallel reaction monitoring (PRM) mass spectrometry approach for a selected number of identified ADP-ribosylated peptides. Although the major part of the basal HeLa ADP-ribosylome remained unchanged upon all tested H2O2 concentrations, some selected peptides change the extent of ADP-ribosylation depending on the degree of the applied oxidative stress. Low oxidative stress (i.e. 4 μm and 16 μm H2O2) caused a reduction in ADP-ribosylation of modified proteins detected under untreated conditions. In contrast, mid to strong oxidative stress (62 μm to 1 mm H2O2) induced a significant increase in ADP-ribosylation of oxidative stress-targeted proteins. The application of the PRM approach to SKOV3 and A2780, ovarian cancer cells displaying different sensitivities to PARP inhibitors, revealed that the basal and the H2O2-induced ADP-ribosylomes of SKOV3 and A2780 differed significantly and that the sensitivity to PARP inhibitors correlated with the level of ARTD1 expression in these cells. Overall, this new PRM-MS approach has proven to be sensitive in monitoring alterations of the ADP-ribosylome and has revealed unexpected alterations in proteins ADP-ribosylation depending on the degree of oxidative stress.
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Affiliation(s)
- Vera Bilan
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,§Molecular Life Science (MLS) program of the Life Science Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Nathalie Selevsek
- ¶Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Hans A V Kistemaker
- ‖Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Jeannette Abplanalp
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.,§Molecular Life Science (MLS) program of the Life Science Zurich Graduate School, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Roxane Feurer
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Dmitri V Filippov
- ‖Leiden Institute of Chemistry, Department of Bio-organic Synthesis, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Michael O Hottiger
- From the ‡Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland;
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23
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Cifani P, Shakiba M, Chhangawala S, Kentsis A. ProteoModlR for functional proteomic analysis. BMC Bioinformatics 2017; 18:153. [PMID: 28259147 PMCID: PMC5336658 DOI: 10.1186/s12859-017-1563-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 02/24/2017] [Indexed: 11/10/2022] Open
Abstract
Background High-accuracy mass spectrometry enables near comprehensive quantification of the components of the cellular proteomes, increasingly including their chemically modified variants. Likewise, large-scale libraries of quantified synthetic peptides are becoming available, enabling absolute quantification of chemically modified proteoforms, and therefore systems-level analyses of changes of their absolute abundance and stoichiometry. Existing computational methods provide advanced tools for mass spectral analysis and statistical inference, but lack integrated functions for quantitative analysis of post-translationally modified proteins and their modification stoichiometry. Results Here, we develop ProteoModlR, a program for quantitative analysis of abundance and stoichiometry of post-translational chemical modifications across temporal and steady-state biological states. While ProteoModlR is intended for the analysis of experiments using isotopically labeled reference peptides for absolute quantitation, it also supports the analysis of labeled and label-free data, acquired in both data-dependent and data-independent modes for relative quantitation. Moreover, ProteoModlR enables functional analysis of sparsely sampled quantitative mass spectrometry experiments by inferring the missing values from the available measurements, without imputation. The implemented architecture includes parsing and normalization functions to control for common sources of technical variation. Finally, ProteoModlR’s modular design and interchangeable format are optimally suited for integration with existing computational proteomics tools, thereby facilitating comprehensive quantitative analysis of cellular signaling. Conclusions ProteoModlR and its documentation are available for download at http://github.com/kentsisresearchgroup/ProteoModlR as a stand-alone R package. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1563-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Paolo Cifani
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mojdeh Shakiba
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Sagar Chhangawala
- Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Physiology, Biophysics and Systems Biology Program, Weill Cornell Graduate School of Medical Sciences, New York, NY, USA. .,Department of Pediatrics and Memorial Sloan Kettering Cancer Center, Weill Medical College of Cornell University, New York, NY, USA.
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24
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Chan CYX, Gritsenko MA, Smith RD, Qian WJ. The current state of the art of quantitative phosphoproteomics and its applications to diabetes research. Expert Rev Proteomics 2016; 13:421-33. [PMID: 26960075 DOI: 10.1586/14789450.2016.1164604] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Protein phosphorylation is a fundamental regulatory mechanism in many cellular processes and aberrant perturbation of phosphorylation has been implicated in various human diseases. Kinases and their cognate inhibitors have been considered as hotspots for drug development. Therefore, the emerging tools, which enable a system-wide quantitative profiling of phosphoproteome, would offer a powerful impetus in unveiling novel signaling pathways, drug targets and/or biomarkers for diseases of interest. This review highlights recent advances in phosphoproteomics, the current state of the art of the technologies and the challenges and future perspectives of this research area. Finally, some exemplary applications of phosphoproteomics in diabetes research are underscored.
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Affiliation(s)
- Chi Yuet X'avia Chan
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Marina A Gritsenko
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Richard D Smith
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA , USA
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25
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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26
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Shi T, Niepel M, McDermott JE, Gao Y, Nicora CD, Chrisler WB, Markillie LM, Petyuk VA, Smith RD, Rodland KD, Sorger PK, Qian WJ, Wiley HS. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway. Sci Signal 2016; 9:rs6. [PMID: 27405981 DOI: 10.1126/scisignal.aaf0891] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components-16 core proteins and 10 feedback regulators-of the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Mario Niepel
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Jason E McDermott
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Yuqian Gao
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Carrie D Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - William B Chrisler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Lye M Markillie
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Vladislav A Petyuk
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA
| | - Karin D Rodland
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Peter K Sorger
- HMS LINCS Center and Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - H Steven Wiley
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99352 USA.
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27
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Venegas LA, Pershad K, Bankole O, Shah N, Kay BK. A comparison of phosphospecific affinity reagents reveals the utility of recombinant Forkhead-associated domains in recognizing phosphothreonine-containing peptides. N Biotechnol 2016; 33:537-43. [PMID: 26772725 DOI: 10.1016/j.nbt.2015.12.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/21/2015] [Accepted: 12/29/2015] [Indexed: 12/14/2022]
Abstract
Phosphorylation is an important post-translational event that has a wide array of functional consequences. With advances in the ability of various technologies in revealing and mapping new phosphosites in proteins, it is equally important to develop affinity reagents that can monitor such post-translational modifications in eukaryotic cells. While monoclonal and polyclonal antibodies have been shown to be useful in assessing the phosphoproteome, we have expanded our efforts to exploit the Forkhead-associated 1 (FHA1) domain as scaffold for generating recombinant affinity reagents that recognize phosphothreonine-containing peptides. A phage display library of FHA1 variants was screened by affinity selection with 15 phosphothreonine-containing peptides corresponding to various human transcription factors and kinases, including human Myc, calmodulin-dependent protein kinase II (CaMKII), and extracellular-signal regulated kinases 1 and 2 (ERK1/2). The library yielded binding variants against 10 targets (66% success rate); success was largely determined by what residue occurred at the +3 position (C-terminal) to the pThr moiety (i.e., pT+3). The FHA domains binding Myc, CaMKII, and ERK1/2 were characterized and compared against commercially available antibodies. All FHA domains were shown to be phosphorylation-dependent and phosphothreonine-specific in their binding, unlike several commercial monoclonal and polyclonal antibodies. Both the pThr and the residue at the pT+3 position were major factors in defining the specificity of the FHA domains.
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Affiliation(s)
- Leon A Venegas
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Kritika Pershad
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Oluwadamilola Bankole
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Noman Shah
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Brian K Kay
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.
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28
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Wang H, Shi T, Qian WJ, Liu T, Kagan J, Srivastava S, Smith RD, Rodland KD, Camp DG. The clinical impact of recent advances in LC-MS for cancer biomarker discovery and verification. Expert Rev Proteomics 2015; 13:99-114. [PMID: 26581546 DOI: 10.1586/14789450.2016.1122529] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mass spectrometry (MS) -based proteomics has become an indispensable tool with broad applications in systems biology and biomedical research. With recent advances in liquid chromatography (LC) and MS instrumentation, LC-MS is making increasingly significant contributions to clinical applications, especially in the area of cancer biomarker discovery and verification. To overcome challenges associated with analyses of clinical samples (for example, a wide dynamic range of protein concentrations in bodily fluids and the need to perform high throughput and accurate quantification of candidate biomarker proteins), significant efforts have been devoted to improve the overall performance of LC-MS-based clinical proteomics platforms. Reviewed here are the recent advances in LC-MS and its applications in cancer biomarker discovery and quantification, along with the potentials, limitations and future perspectives.
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Affiliation(s)
- Hui Wang
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tujin Shi
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Wei-Jun Qian
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Tao Liu
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Jacob Kagan
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Sudhir Srivastava
- b Division of Cancer Prevention , National Cancer Institute (NCI) , Rockville , MD , USA
| | - Richard D Smith
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - Karin D Rodland
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
| | - David G Camp
- a Biological Sciences Division , Pacific Northwest National Laboratory , Richland , WA , USA
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