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Liao Y, Remsing Rix LL, Li X, Fang B, Izumi V, Welsh EA, Monastyrskyi A, Haura EB, Koomen JM, Doebele RC, Rix U. Differential network analysis of ROS1 inhibitors reveals lorlatinib polypharmacology through co-targeting PYK2. Cell Chem Biol 2024; 31:284-297.e10. [PMID: 37848034 PMCID: PMC10922442 DOI: 10.1016/j.chembiol.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 08/02/2023] [Accepted: 09/19/2023] [Indexed: 10/19/2023]
Abstract
Multiple tyrosine kinase inhibitors (TKIs) are often developed for the same indication. However, their relative overall efficacy is frequently incompletely understood and they may harbor unrecognized targets that cooperate with the intended target. We compared several ROS1 TKIs for inhibition of ROS1-fusion-positive lung cancer cell viability, ROS1 autophosphorylation and kinase activity, which indicated disproportionately higher cellular potency of one TKI, lorlatinib. Quantitative chemical and phosphoproteomics across four ROS1 TKIs and differential network analysis revealed that lorlatinib uniquely impacted focal adhesion signaling. Functional validation using pharmacological probes, RNA interference, and CRISPR-Cas9 knockout uncovered a polypharmacology mechanism of lorlatinib by dual targeting ROS1 and PYK2, which form a multiprotein complex with SRC. Rational multi-targeting of this complex by combining lorlatinib with SRC inhibitors exhibited pronounced synergy. Taken together, we show that systems pharmacology-based differential network analysis can dissect mixed canonical/non-canonical polypharmacology mechanisms across multiple TKIs enabling the design of rational drug combinations.
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Affiliation(s)
- Yi Liao
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Lily L Remsing Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Xueli Li
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Victoria Izumi
- Proteomics and Metabolomics Core, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric A Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Andrii Monastyrskyi
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - John M Koomen
- Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Robert C Doebele
- Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA; Department of Oncologic Sciences, University of South Florida, Tampa, FL 33620, USA.
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2
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Xu X, Bok I, Jasani N, Wang K, Chadourne M, Mecozzi N, Deng O, Welsh EA, Kinose F, Rix U, Karreth FA. PTEN Lipid Phosphatase Activity Suppresses Melanoma Formation by Opposing an AKT/mTOR/FRA1 Signaling Axis. Cancer Res 2024; 84:388-404. [PMID: 38193852 PMCID: PMC10842853 DOI: 10.1158/0008-5472.can-23-1730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/27/2023] [Accepted: 11/17/2023] [Indexed: 01/10/2024]
Abstract
Inactivating mutations in PTEN are prevalent in melanoma and are thought to support tumor development by hyperactivating the AKT/mTOR pathway. Conversely, activating mutations in AKT are relatively rare in melanoma, and therapies targeting AKT or mTOR have shown disappointing outcomes in preclinical models and clinical trials of melanoma. This has led to the speculation that PTEN suppresses melanoma by opposing AKT-independent pathways, potentially through noncanonical functions beyond its lipid phosphatase activity. In this study, we examined the mechanisms of PTEN-mediated suppression of melanoma formation through the restoration of various PTEN functions in PTEN-deficient cells or mouse models. PTEN lipid phosphatase activity predominantly inhibited melanoma cell proliferation, invasion, and tumor growth, with minimal contribution from its protein phosphatase and scaffold functions. A drug screen underscored the exquisite dependence of PTEN-deficient melanoma cells on the AKT/mTOR pathway. Furthermore, activation of AKT alone was sufficient to counteract several aspects of PTEN-mediated melanoma suppression, particularly invasion and the growth of allograft tumors. Phosphoproteomics analysis of the lipid phosphatase activity of PTEN validated its potent inhibition of AKT and many of its known targets, while also identifying the AP-1 transcription factor FRA1 as a downstream effector. The restoration of PTEN dampened FRA1 translation by inhibiting AKT/mTOR signaling, and FRA1 overexpression negated aspects of PTEN-mediated melanoma suppression akin to AKT. This study supports AKT as the key mediator of PTEN inactivation in melanoma and identifies an AKT/mTOR/FRA1 axis as a driver of melanomagenesis. SIGNIFICANCE PTEN suppresses melanoma predominantly through its lipid phosphatase function, which when lost, elevates FRA1 levels through AKT/mTOR signaling to promote several aspects of melanomagenesis.
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Affiliation(s)
- Xiaonan Xu
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Ilah Bok
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Neel Jasani
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Kaizhen Wang
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Manon Chadourne
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Nicol Mecozzi
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Cancer Biology PhD program, University of South Florida, Tampa, Florida
| | - Ou Deng
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Eric A. Welsh
- Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Fumi Kinose
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Uwe Rix
- Department of Drug Discovery, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida, Tampa, Florida
| | - Florian A. Karreth
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
- Department of Oncologic Sciences, University of South Florida, Tampa, Florida
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3
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Liu F, Wu T, Tian A, He C, Bi X, Lu Y, Yang K, Xia W, Ye J. Intracellular metabolic profiling of drug resistant cells by surface enhanced Raman scattering. Anal Chim Acta 2023; 1279:341809. [PMID: 37827617 DOI: 10.1016/j.aca.2023.341809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Intracellular metabolic profiling reveals real-time metabolic information useful for the study of underlying mechanisms of cells in particular conditions such as drug resistance. However, mass spectrometry (MS), one of the leading metabolomics technologies, usually requires a large number of cells and complex pretreatments. Surface enhanced Raman scattering (SERS) has an ultrahigh detection sensitivity and specificity, favorable for metabolomics analysis. However, some targeted SERS methods focus on very limited metabolite without global bioprofiling, and some label-free approaches try to fingerprint the metabolic response based on whole SERS spectral classification, but comprehensive interpretation of biological mechanisms was lacking. (95) RESULTS: We proposed a label-free SERS technique for intracellular metabolic profiling in complex cellular lysates within 3 min. We first compared three kinds of cellular lysis methods and sonication lysis shows the highest extraction efficiency of metabolites. To obtain comprehensive metabolic information, we collected a spectral set for each sample and further qualified them by the Pearson correlation coefficient (PCC) to calculate how many spectra should be acquired at least to gain the adequate information from a statistical and global view. In addition, according to our measurements with 10 pure metabolites, we can understand the spectra acquired from complex cellular lysates of different cell lines more precisely. Finally, we further disclosed the variations of 22 SERS bands in enzalutamide-resistant prostate cancer cells and some are associated with the androgen receptor signaling activity and the methionine salvage pathway in the drug resistance process, which shows the same metabolic trends as MS. (149) SIGNIFICANCE: Our technique has the capability to capture the intracellular metabolic fingerprinting with the optimized lysis approach and spectral set collection, showing high potential in rapid, sensitive and global metabolic profiling in complex biosamples and clinical liquid biopsy. This gives a new perspective to the study of SERS in insightful understanding of relevant biological mechanisms. (54).
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Affiliation(s)
- Fugang Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Tingyu Wu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Ao Tian
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Chang He
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Xinyuan Bi
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Yao Lu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Kai Yang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China
| | - Weiliang Xia
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, PR China.
| | - Jian Ye
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, PR China; State Key Laboratory of Systems Medicine for Cancer, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032, PR China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200240, PR China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, PR China.
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4
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Kong Q, Weng Y, Zheng Z, Chen W, Li P, Cai Z, Tian R. Integrated and High-Throughput Approach for Sensitive Analysis of Tyrosine Phosphoproteome. Anal Chem 2022; 94:13728-13736. [PMID: 36179360 DOI: 10.1021/acs.analchem.2c01807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosine phosphorylation (pTyr) regulates various signaling pathways under normal and cancerous states. Due to their low abundance and transient and dynamic natures, systematic profiling of pTyr sites is challenging. Antibody and engineered binding domain-based approaches have been well applied to pTyr peptide enrichment. However, traditional methods have the disadvantage of a long sample preparation process, which makes them unsuitable for processing limited amount of samples, especially in a high-throughput manner. In this study we developed a 96-well microplate-based approach to integrate all the sample preparation steps starting from cell culture to MS-compatible pTyr peptide enrichment in three consecutive 96-well microplates. By assembling an engineered SH2 domain onto a microplate, nonspecific adsorption of phosphopeptides is greatly reduced, which allows us to remove the Ti-IMAC purification and three C18 desalting steps (after digestion, pTyr enrichment, and Ti-IMAC purification) and, therefore, greatly simplifies the entire pTyr peptide enrichment workflow, especially when processing a large number of samples. Starting with 96-well microplate-cultured, pervanadate-stimulated cells, our approach could enrich 21% more pTyr sites than the traditional serial pTyr enrichment approach and showed good sensitivity and reproducibility in the range of 200 ng to 200 μg peptides. Importantly, we applied this approach to profile tyrosine kinase inhibitor-mediated EGFR signaling pathway and could well differentiate the distinct response of different pTyr sites. Collectively, the integrated 96-well microplate-based approach is valuable for profiling pTyr sites from limited biological samples and in a high-throughput manner.
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Affiliation(s)
- Qian Kong
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Yicheng Weng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zhendong Zheng
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Wendong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Pengfei Li
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR 999077, China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Research Center for Chemical Biology and Omics Analysis, College of Science, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China.,Shenzhen Grubbs Institute, Southern University of Science and Technology, 1088 Xueyuan Road, Shenzhen 518055, China
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5
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Webber KGI, Truong T, Johnston SM, Zapata SE, Liang Y, Davis JM, Buttars AD, Smith FB, Jones HE, Mahoney AC, Carson RH, Nwosu AJ, Heninger JL, Liyu AV, Nordin GP, Zhu Y, Kelly RT. Label-Free Profiling of up to 200 Single-Cell Proteomes per Day Using a Dual-Column Nanoflow Liquid Chromatography Platform. Anal Chem 2022; 94:6017-6025. [PMID: 35385261 PMCID: PMC9356711 DOI: 10.1021/acs.analchem.2c00646] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Single-cell proteomics (SCP) has great potential to advance biomedical research and personalized medicine. The sensitivity of such measurements increases with low-flow separations (<100 nL/min) due to improved ionization efficiency, but the time required for sample loading, column washing, and regeneration in these systems can lead to low measurement throughput and inefficient utilization of the mass spectrometer. Herein, we developed a two-column liquid chromatography (LC) system that dramatically increases the throughput of label-free SCP using two parallel subsystems to multiplex sample loading, online desalting, analysis, and column regeneration. The integration of MS1-based feature matching increased proteome coverage when short LC gradients were used. The high-throughput LC system was reproducible between the columns, with a 4% difference in median peptide abundance and a median CV of 18% across 100 replicate analyses of a single-cell-sized peptide standard. An average of 621, 774, 952, and 1622 protein groups were identified with total analysis times of 7, 10, 15, and 30 min, corresponding to a measurement throughput of 206, 144, 96, and 48 samples per day, respectively. When applied to single HeLa cells, we identified nearly 1000 protein groups per cell using 30 min cycles and 660 protein groups per cell for 15 min cycles. We explored the possibility of measuring cancer therapeutic targets with a pilot study comparing the K562 and Jurkat leukemia cell lines. This work demonstrates the feasibility of high-throughput label-free single-cell proteomics.
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Affiliation(s)
- Kei G I Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - S Madisyn Johnston
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Sebastian E Zapata
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jacob M Davis
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Alexander D Buttars
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Fletcher B Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Hailey E Jones
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Arianna C Mahoney
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Richard H Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Andikan J Nwosu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jacob L Heninger
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Andrey V Liyu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Gregory P Nordin
- Department of Electrical Engineering, Brigham Young University, Provo, Utah 84602, United States
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States.,Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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6
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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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Dwivedi P, Rose CM. Understanding the effect of carrier proteomes in single cell proteomic studies - key lessons. Expert Rev Proteomics 2022; 19:5-15. [PMID: 35089822 DOI: 10.1080/14789450.2022.2036126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Mass spectrometry based single cell proteomics (scMS) is experiencing rapid evolution due to the increased sensitivity of mass spectrometers as well as advances in multiplexing and sample preparation. To date, researchers have focused on two general approaches to scMS: label free and isobaric label based multiplexing. While label free analysis provides straightforward sample preparation and a clear path to automation, it currently lacks the throughput necessary to practically analyze thousands of single cells. Multiplexed analysis utilizing isobaric labels requires additional sample manipulation, but increases throughput such that analyzing thousands of cells is currently achievable. A key feature of multiplexed scMS experiments is a 'carrier proteome' - a sample added at 25x-500x the single cell samples that increases the number of proteins that can be identified in an MS analysis. AREAS COVERED Here, we review early examples of carrier proteomes in quantitative proteomics before summarizing advantages and challenges of using a carrier proteome in scMS experiments. EXPERT OPINION We conclude that the addition of carrier proteomes improves depth of identification for scMS, but high levels of carrier proteomes can have adverse effects on quantitative accuracy and precision.
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Affiliation(s)
- Pankaj Dwivedi
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
| | - Christopher M Rose
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc. 1 DNA Way, South San Francisco CA 94080
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8
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Tsai CF, Ogata K, Sugiyama N, Ishihama Y. Motif-centric phosphoproteomics to target kinase-mediated signaling pathways. CELL REPORTS METHODS 2022; 2:100138. [PMID: 35474870 PMCID: PMC9017188 DOI: 10.1016/j.crmeth.2021.100138] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/08/2021] [Accepted: 12/13/2021] [Indexed: 12/27/2022]
Abstract
Identifying cellular phosphorylation pathways based on kinase-substrate relationships is a critical step to understanding the regulation of physiological functions in cells. Mass spectrometry-based phosphoproteomics workflows have made it possible to comprehensively collect information on individual phosphorylation sites in a variety of samples. However, there is still no generic approach to uncover phosphorylation networks based on kinase-substrate relationships in rare cell populations. Here, we describe a motif-centric phosphoproteomics approach combined with multiplexed isobaric labeling, in which in vitro kinase reactions are used to generate targeted phosphopeptides, which are spiked into one of the isobaric channels to increase detectability. Proof-of-concept experiments demonstrate selective and comprehensive quantification of targeted phosphopeptides by using multiple kinases for motif-centric channels. More than 7,000 tyrosine phosphorylation sites were quantified from several tens of micrograms of starting materials. This approach enables the quantification of multiple phosphorylation pathways under physiological or pathological regulation in a motif-centric manner.
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Affiliation(s)
- Chia-Feng Tsai
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Kosuke Ogata
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Naoyuki Sugiyama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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9
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Ulhaq ZS, Tse WKF. A Brief Analysis of Proteomic Profile Changes during Zebrafish Regeneration. Biomolecules 2021; 12:biom12010035. [PMID: 35053182 PMCID: PMC8773715 DOI: 10.3390/biom12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 12/21/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike mammals, zebrafish are capable to regenerate many of their organs, however, the response of tissue damage varies across tissues. Understanding the molecular mechanism behind the robust regenerative capacity in a model organism may help to identify and develop novel treatment strategies for mammals (including humans). Hence, we systematically analyzed the current literature on the proteome profile collected from different regenerated zebrafish tissues. Our analyses underlining that several proteins and protein families responsible as a component of cytoskeleton and structure, protein synthesis and degradation, cell cycle control, and energy metabolism were frequently identified. Moreover, target proteins responsible for the initiation of the regeneration process, such as inflammation and immune response were less frequently detected. This highlights the limitation of previous proteomic analysis and suggested a more sensitive modern proteomics analysis is needed to unfold the mechanism. This brief report provides a list of target proteins with predicted functions that could be useful for further biological studies.
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Affiliation(s)
- Zulvikar Syambani Ulhaq
- Department of Biochemistry, Faculty of Medicine and Health Sciences, Maulana Malik Ibrahim State Islamic University of Malang, Batu 65144, Indonesia;
- National Research and Innovation Agency, Central Jakarta 10340, Indonesia
| | - William Ka Fai Tse
- Laboratory of Developmental Disorders and Toxicology, Center for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka 819-0395, Japan
- Correspondence:
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10
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Stopfer LE, Conage-Pough JE, White FM. Quantitative Consequences of Protein Carriers in Immunopeptidomics and Tyrosine Phosphorylation MS 2 Analyses. Mol Cell Proteomics 2021; 20:100104. [PMID: 34052394 PMCID: PMC8240026 DOI: 10.1016/j.mcpro.2021.100104] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/07/2023] Open
Abstract
Utilizing a protein carrier in combination with isobaric labeling to “boost” the signal of other low-level samples in multiplexed analyses has emerged as an attractive strategy to enhance data quantity while minimizing protein input in mass spectrometry analyses. Recent applications of this approach include pMHC profiling and tyrosine phosphoproteomics, two applications that are often limited by large sample requirements. While including a protein carrier has been shown to increase the number of identifiable peptides in both applications, the impact of a protein carrier on quantitative accuracy remains to be thoroughly explored, particularly in relevant biological contexts where samples exhibit dynamic changes in abundance across peptides. Here, we describe two sets of analyses comparing MS2-based quantitation using a 20× protein carrier in pMHC analyses and a high (~100×) and low (~9×) protein carrier in pTyr analyses, using CDK4/6 inhibitors and EGF stimulation to drive dynamic changes in the immunopeptidome and phosphoproteome, respectively. In both applications, inclusion of a protein carrier resulted in an increased number of MHC peptide or phosphopeptide identifications, as expected. At the same time, quantitative accuracy was adversely affected by the presence of the protein carrier, altering interpretation of the underlying biological response to perturbation. Moreover, for tyrosine phosphoproteomics, the presence of high levels of protein carrier led to a large number of missing values for endogenous phosphopeptides, leading to fewer quantifiable peptides relative to the “no-boost” condition. These data highlight the unique limitations and future experimental considerations for both analysis types and provide a framework for assessing quantitative accuracy in protein carrier experiments moving forward. A carrier proteome may enhance detection of low abundance pMHC and pTyr peptides. A carrier boosted IDs in pMHC analyses; quantitation suffered from ratio compression. A 9× carrier provided higher quantitative accuracy over a 100× carrier in pTyr analyses but offered minimal benefit in data quantity. Experimental design should be rigorously evaluated to ensure quantitative accuracy.
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Affiliation(s)
- Lauren E Stopfer
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jason E Conage-Pough
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Forest M White
- Department of Biological Engineering, Koch Institute for Integrative Cancer Research, Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.
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