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Yang XY, Zheng XX, Zhai XJ, Tang T, Yu SC. Spindle apparatus coiled-coil protein 1 (SPDL1) serves as a novel prognostic biomarker in triple-negative breast cancer. Proteomics Clin Appl 2024; 18:e202300002. [PMID: 38316615 DOI: 10.1002/prca.202300002] [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: 01/04/2023] [Revised: 01/04/2024] [Accepted: 01/16/2024] [Indexed: 02/07/2024]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) has a poor prognosis, an ineffective diagnosis, and a high degree of aggressiveness. Therefore, novel therapeutic targets for TNBC urgently need to be identified. METHODS Through a series of bioinformatics analyses, including analysis of differential gene expression, protein-protein interaction (PPI) network, univariate cox regression, immune infiltration, pathway enrichment, etc, as well as auxiliary immunohistochemistry (IHC) and protein quantitativae analysis, to explore prognostic marker for TNBC. RESULTS In TNBC tissues, we found that SPDL1 (CCDC99) was considerably overexpressed at both the mRNA and protein levels compared to that in normal and non-TNBC tissues. Additionally, we found that SPDL1-high expression was strongly linked to poor prognosis in TNBC patients. Excessive SPDL1 expression was positively correlated with tumor growth and strongly linked to the cell cycle, DNA replication, and the p53 signaling pathway. In addition, CIBERSORT analysis revealed that SPDL1 can affect the tumor immune microenvironment (TME) in TNBC, encourage the development of TNBC and act as a potential prognostic biomarker for TNBC. Patients with SPDL1-high expression were more sensitive to AZD8055. Notably, we discovered that SPDL1 is highly expressed in the majority of malignancies and may have an impact on the pancancer prognosis. CONCLUSIONS SPDL1 can serve as a novel prognostic marker for TNBC and pancancer patients.
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Affiliation(s)
- Xian-Yan Yang
- Department of Stem Cell and Regenerative Medicine, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), ChongQing, China
- Key Laboratory of Cancer Immunopathology, Ministry of Education, ChongQing, China
- International Joint Research Center for Precision Biotherapy, Ministry of Science and Technology, ChongQing, China
| | - Xiao-Xia Zheng
- Department of Stem Cell and Regenerative Medicine, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), ChongQing, China
- Key Laboratory of Cancer Immunopathology, Ministry of Education, ChongQing, China
- International Joint Research Center for Precision Biotherapy, Ministry of Science and Technology, ChongQing, China
| | - Xue-Jia Zhai
- Department of Stem Cell and Regenerative Medicine, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), ChongQing, China
- Key Laboratory of Cancer Immunopathology, Ministry of Education, ChongQing, China
- International Joint Research Center for Precision Biotherapy, Ministry of Science and Technology, ChongQing, China
| | - Tao Tang
- Department of Stem Cell and Regenerative Medicine, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), ChongQing, China
- Key Laboratory of Cancer Immunopathology, Ministry of Education, ChongQing, China
- International Joint Research Center for Precision Biotherapy, Ministry of Science and Technology, ChongQing, China
| | - Shi-Cang Yu
- Department of Stem Cell and Regenerative Medicine, Institute of Pathology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), ChongQing, China
- Key Laboratory of Cancer Immunopathology, Ministry of Education, ChongQing, China
- International Joint Research Center for Precision Biotherapy, Ministry of Science and Technology, ChongQing, China
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2
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Neagu AN, Whitham D, Bruno P, Morrissiey H, Darie CA, Darie CC. Omics-Based Investigations of Breast Cancer. Molecules 2023; 28:4768. [PMID: 37375323 DOI: 10.3390/molecules28124768] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/08/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer (BC) is characterized by an extensive genotypic and phenotypic heterogeneity. In-depth investigations into the molecular bases of BC phenotypes, carcinogenesis, progression, and metastasis are necessary for accurate diagnoses, prognoses, and therapy assessments in predictive, precision, and personalized oncology. This review discusses both classic as well as several novel omics fields that are involved or should be used in modern BC investigations, which may be integrated as a holistic term, onco-breastomics. Rapid and recent advances in molecular profiling strategies and analytical techniques based on high-throughput sequencing and mass spectrometry (MS) development have generated large-scale multi-omics datasets, mainly emerging from the three "big omics", based on the central dogma of molecular biology: genomics, transcriptomics, and proteomics. Metabolomics-based approaches also reflect the dynamic response of BC cells to genetic modifications. Interactomics promotes a holistic view in BC research by constructing and characterizing protein-protein interaction (PPI) networks that provide a novel hypothesis for the pathophysiological processes involved in BC progression and subtyping. The emergence of new omics- and epiomics-based multidimensional approaches provide opportunities to gain insights into BC heterogeneity and its underlying mechanisms. The three main epiomics fields (epigenomics, epitranscriptomics, and epiproteomics) are focused on the epigenetic DNA changes, RNAs modifications, and posttranslational modifications (PTMs) affecting protein functions for an in-depth understanding of cancer cell proliferation, migration, and invasion. Novel omics fields, such as epichaperomics or epimetabolomics, could investigate the modifications in the interactome induced by stressors and provide PPI changes, as well as in metabolites, as drivers of BC-causing phenotypes. Over the last years, several proteomics-derived omics, such as matrisomics, exosomics, secretomics, kinomics, phosphoproteomics, or immunomics, provided valuable data for a deep understanding of dysregulated pathways in BC cells and their tumor microenvironment (TME) or tumor immune microenvironment (TIMW). Most of these omics datasets are still assessed individually using distinct approches and do not generate the desired and expected global-integrative knowledge with applications in clinical diagnostics. However, several hyphenated omics approaches, such as proteo-genomics, proteo-transcriptomics, and phosphoproteomics-exosomics are useful for the identification of putative BC biomarkers and therapeutic targets. To develop non-invasive diagnostic tests and to discover new biomarkers for BC, classic and novel omics-based strategies allow for significant advances in blood/plasma-based omics. Salivaomics, urinomics, and milkomics appear as integrative omics that may develop a high potential for early and non-invasive diagnoses in BC. Thus, the analysis of the tumor circulome is considered a novel frontier in liquid biopsy. Omics-based investigations have applications in BC modeling, as well as accurate BC classification and subtype characterization. The future in omics-based investigations of BC may be also focused on multi-omics single-cell analyses.
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Affiliation(s)
- Anca-Narcisa Neagu
- Laboratory of Animal Histology, Faculty of Biology, "Alexandru Ioan Cuza" University of Iasi, Carol I Bvd, No. 20A, 700505 Iasi, Romania
| | - Danielle Whitham
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Pathea Bruno
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Hailey Morrissiey
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Celeste A Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, USA
| | - Costel C Darie
- Biochemistry & Proteomics Laboratories, Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, NY 13699, 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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Kang S, Zhu X, Wu Q, Wang S, Crickmore N, Zhang Y, Guo Z. Critical Analysis of Multi-Omic Data from a Strain of Plutella xylostella Resistant to Bacillus thuringiensis Cry1Ac Toxin. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:11419-11428. [PMID: 36040024 DOI: 10.1021/acs.jafc.2c03618] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Rapid evolution of resistance in crop pests to Bacillus thuringiensis (Bt) products threatens their widespread use, especially as pests appear to develop resistance through a range of different physiological adaptations. With such a diverse range of mechanisms reported, researchers have resorted to multi-omic approaches to understand the molecular basis of resistance. Such approaches generate a lot of data making it difficult to establish where causal links between physiological changes and resistance exist. In this study, a combination of RNA-Seq and iTRAQ was used with a strain of diamondback moth, Plutella xylostella (L.), whose resistance mechanism is well understood. While some of the causal molecular changes in the resistant strain were detected, other previously verified changes were not detected. We suggest that while multi-omic studies have use in validating a proposed resistance mechanism, they are of limited value in identifying such a mechanism in the first place.
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Affiliation(s)
- Shi Kang
- School of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002, China
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Qingjun Wu
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shaoli Wang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Neil Crickmore
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, United Kingdom
| | - Youjun Zhang
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhaojiang Guo
- Department of Plant Protection, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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5
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Srinivasan A, Sing JC, Gingras AC, Röst HL. Improving Phosphoproteomics Profiling Using Data-Independent Mass Spectrometry. J Proteome Res 2022; 21:1789-1799. [PMID: 35877786 DOI: 10.1021/acs.jproteome.2c00172] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass spectrometry-based profiling of the phosphoproteome is a powerful method of identifying phosphorylation events at a systems level. Most phosphoproteomics studies have used data-dependent acquisition (DDA) mass spectrometry as their method of choice. In this Perspective, we review some recent studies benchmarking DDA and DIA methods for phosphoproteomics and discuss data analysis options for DIA phosphoproteomics. In order to evaluate the impact of data-dependent and data-independent acquisition (DIA) on identification and quantification, we analyze a previously published phosphopeptide-enriched data set consisting of 10 replicates acquired by DDA and DIA each. We find that though more unique identifications are made in DDA data, phosphopeptides are identified more consistently across replicates in DIA. We further discuss the challenges of identifying chromatographically coeluting phosphopeptide isomers and investigate the impact on reproducibility of identifying high-confidence site-localized phosphopeptides in replicates.
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Affiliation(s)
- Aparna Srinivasan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Justin C Sing
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Hannes L Röst
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
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6
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Futami Y, Takeda Y, Koba T, Narumi R, Nojima Y, Ito M, Nakayama M, Ishida M, Yoshimura H, Naito Y, Fukushima K, Takimoto T, Edahiro R, Matsuki T, Nojima S, Hirata H, Koyama S, Iwahori K, Nagatomo I, Shirai Y, Suga Y, Satoh S, Futami S, Miyake K, Shiroyama T, Inoue Y, Adachi J, Tomonaga T, Ueda K, Kumanogoh A. CD14 and lipopolysaccharide-binding protein as novel biomarkers for sarcoidosis by proteomics of serum extracellular vesicles. Int Immunol 2022; 34:327-340. [PMID: 35294531 PMCID: PMC9166566 DOI: 10.1093/intimm/dxac009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/15/2022] [Indexed: 11/14/2022] Open
Abstract
Sarcoidosis is a complex, polygenic, inflammatory granulomatous multi-organ disease of unknown cause. The granulomatous inflammation in sarcoidosis is driven by the interplay between T cells and macrophages. Extracellular vesicles (EVs) play important roles in intercellular communication. We subjected serum EVs, isolated by size exclusion chromatography, from seven patients with sarcoidosis and five control subjects to non-targeted proteomics analysis. Non-targeted, label-free proteomics analysis detected 2292 proteins in serum EVs; 42 proteins were up-regulated in patients with sarcoidosis relative to control subjects; and 324 proteins were down-regulated. The protein signature of EVs from patients with sarcoidosis reflected disease characteristics such as antigen presentation and immunological disease. Candidate biomarkers were further verified by targeted proteomics analysis (selected reaction monitoring) in 46 patients and 10 control subjects. Notably, CD14 and lipopolysaccharide-binding protein (LBP) were validated by targeted proteomics analysis. Up-regulation of these proteins was further confirmed by immunoblotting, and their expression was strongly increased in macrophages of lung granulomatous lesions. Consistent with these findings, CD14 levels were increased in lipopolysaccharide-stimulated macrophages during multinucleation, concomitant with increased levels of CD14 and LBP in EVs. The area under the curve values of CD14 and LBP were 0.81 and 0.84, respectively, and further increased to 0.98 in combination with angiotensin-converting enzyme and soluble interleukin-2 receptor. These findings suggest that CD14 and LBP in serum EVs, which are associated with granulomatous pathogenesis, can improve the diagnostic accuracy in patients with sarcoidosis.
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Affiliation(s)
- Yu Futami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoshito Takeda
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Taro Koba
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Yosui Nojima
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Mari Ito
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Mana Nakayama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Mimiko Ishida
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Hanako Yoshimura
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yujiro Naito
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Takayuki Takimoto
- Department of Respiratory Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Centre, Kita-Ku, Sakai, Osaka, Japan
| | - Ryuya Edahiro
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Tomonori Matsuki
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Satoshi Nojima
- Department of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Haruhiko Hirata
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Shohei Koyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Kota Iwahori
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Izumi Nagatomo
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuya Shirai
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yasuhiko Suga
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Shingo Satoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Shinji Futami
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Kotaro Miyake
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Takayuki Shiroyama
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoshikazu Inoue
- Clinical Research Centre, National Hospital Organization Kinki-Chuo Chest Medical Centre, Nagasone-Cho, Kita-Ku, Osaka, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Centre, Japanese Foundation for Cancer Research, Ariake, Koto, Tokyo, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Osaka University, Graduate School of Medicine, Suita, Osaka, Japan.,Laboratory of Immunopathology, World Premier International Immunology Frontier Research Centre, Osaka University, Suita, Osaka, Japan.,Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives (OTRI), Osaka University, Suita, Osaka, Japan
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7
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Cao A, Chen Y, Ni Z, Zhang C, Cao M, Cai L. Production mechanism of semicarbazide from protein in Chinese softshell turtles at different drying temperatures based on TMT-tagged quantitative proteomics. J Food Compost Anal 2021. [DOI: 10.1016/j.jfca.2021.103872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Reyes AJF, Kitata RB, Dela Rosa MAC, Wang YT, Lin PY, Yang PC, Friedler A, Yitzchaik S, Chen YJ. Integrating site-specific peptide reporters and targeted mass spectrometry enables rapid substrate-specific kinase assay at the nanogram cell level. Anal Chim Acta 2021; 1155:338341. [PMID: 33766317 DOI: 10.1016/j.aca.2021.338341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/04/2021] [Accepted: 02/16/2021] [Indexed: 11/25/2022]
Abstract
Dysregulation of phosphorylation-mediated signaling drives the initiation and progression of many diseases. A substrate-specific kinase assay capable of quantifying the altered site-specific phosphorylation of its phenotype-dependent substrates provides better specificity to monitor a disease state. We report a sensitive and rapid substrate-specific kinase assay by integrating site-specific peptide reporter and multiple reaction monitoring (MRM)-MS platform for relative and absolute quantification of substrate-specific kinase activity at the sensitivity of nanomolar kinase and nanogram cell lysate. Using non-small cell lung cancer as a proof-of-concept, three substrate peptides selected from constitutive phosphorylation in tumors (HDGF-S165, RALY-S135, and NRD1-S94) were designed to demonstrate the feasibility. The assay showed good accuracy (<15% nominal deviation) and reproducibility (<15% CV). In PC9 cells, the measured activity for HDGF-S165 was 3.2 ± 0.2 fmol μg-1 min-1, while RALY-S135 and NRD1-S94 showed 4- and 20-fold higher activity at the sensitivity of 25 ng and 5 ng lysate, respectively, suggesting different endogenous kinases for each substrate peptide. Without the conventional shotgun phosphoproteomics workflow, the overall pipeline from cell lysate to MS data acquisition only takes 3 h. The multiplexed analysis revealed differences in the phenotype-dependent substrate phosphorylation profiles across six NSCLC cell lines and suggested a potential association of HDGF-S165 and NRD1-S94 with TKI resistance. With the ease of design, sensitivity, accuracy, and reproducibility, this approach may offer rapid and sensitive assays for targeted quantification of the multiplexed substrate-specific kinase activity of small amounts of sample.
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Affiliation(s)
- Aaron James F Reyes
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Road, Hsinchu, 30013, Taiwan
| | - Reta Birhanu Kitata
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Mira Anne C Dela Rosa
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Yi-Ting Wang
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pei-Yi Lin
- Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Pan-Chyr Yang
- Department of Internal Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Assaf Friedler
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Shlomo Yitzchaik
- Institute of Chemistry and the Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem, 91904, Israel
| | - Yu-Ju Chen
- Molecular Science and Technology Program, Taiwan International Graduate Program, Academia Sinica and National Tsing Hua University, Taiwan; Institute of Chemistry, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan; Department of Chemistry, National Taiwan University, No. 1, Section 4, Roosevelt Road, Taipei, 10617, Taiwan.
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9
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Thomas S, Kumar R, Sharma K, Barpanda A, Sreelakshmi Y, Sharma R, Srivastava S. iTRAQ-based proteome profiling revealed the role of Phytochrome A in regulating primary metabolism in tomato seedling. Sci Rep 2021; 11:7540. [PMID: 33824368 PMCID: PMC8024257 DOI: 10.1038/s41598-021-87208-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 03/22/2021] [Indexed: 12/30/2022] Open
Abstract
In plants, during growth and development, photoreceptors monitor fluctuations in their environment and adjust their metabolism as a strategy of surveillance. Phytochromes (Phys) play an essential role in plant growth and development, from germination to fruit development. FR-light (FR) insensitive mutant (fri) carries a recessive mutation in Phytochrome A and is characterized by the failure to de-etiolate in continuous FR. Here we used iTRAQ-based quantitative proteomics along with metabolomics to unravel the role of Phytochrome A in regulating central metabolism in tomato seedlings grown under FR. Our results indicate that Phytochrome A has a predominant role in FR-mediated establishment of the mature seedling proteome. Further, we observed temporal regulation in the expression of several of the late response proteins associated with central metabolism. The proteomics investigations identified a decreased abundance of enzymes involved in photosynthesis and carbon fixation in the mutant. Profound accumulation of storage proteins in the mutant ascertained the possible conversion of sugars into storage material instead of being used or the retention of an earlier profile associated with the mature embryo. The enhanced accumulation of organic sugars in the seedlings indicates the absence of photomorphogenesis in the mutant.
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Affiliation(s)
- Sherinmol Thomas
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, 400076, India
| | - Rakesh Kumar
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
- Deptartment of Life Science, Central University of Karnataka, Kadaganchi, Kalaburagi, Karnataka, 585367, India
| | - Kapil Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Abhilash Barpanda
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, 400076, India
| | - Yellamaraju Sreelakshmi
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Rameshwar Sharma
- Repository of Tomato Genomics Resources, Department of Plant Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Sanjeeva Srivastava
- Proteomics Lab, Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, Maharashtra, 400076, India.
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10
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Koba T, Takeda Y, Narumi R, Shiromizu T, Nojima Y, Ito M, Kuroyama M, Futami Y, Takimoto T, Matsuki T, Edahiro R, Nojima S, Hayama Y, Fukushima K, Hirata H, Koyama S, Iwahori K, Nagatomo I, Suzuki M, Shirai Y, Murakami T, Nakanishi K, Nakatani T, Suga Y, Miyake K, Shiroyama T, Kida H, Sasaki T, Ueda K, Mizuguchi K, Adachi J, Tomonaga T, Kumanogoh A. Proteomics of serum extracellular vesicles identifies a novel COPD biomarker, fibulin-3 from elastic fibres. ERJ Open Res 2021; 7:00658-2020. [PMID: 33778046 PMCID: PMC7983195 DOI: 10.1183/23120541.00658-2020] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/18/2020] [Indexed: 12/28/2022] Open
Abstract
There is an unmet need for novel biomarkers in the diagnosis of multifactorial COPD. We applied next-generation proteomics to serum extracellular vesicles (EVs) to discover novel COPD biomarkers. EVs from 10 patients with COPD and six healthy controls were analysed by tandem mass tag-based non-targeted proteomics, and those from elastase-treated mouse models of emphysema were also analysed by non-targeted proteomics. For validation, EVs from 23 patients with COPD and 20 healthy controls were validated by targeted proteomics. Using non-targeted proteomics, we identified 406 proteins, 34 of which were significantly upregulated in patients with COPD. Of note, the EV protein signature from patients with COPD reflected inflammation and remodelling. We also identified 63 upregulated candidates from 1956 proteins by analysing EVs isolated from mouse models. Combining human and mouse biomarker candidates, we validated 45 proteins by targeted proteomics, selected reaction monitoring. Notably, levels of fibulin-3, tripeptidyl-peptidase 2, fibulin-1, and soluble scavenger receptor cysteine-rich domain-containing protein were significantly higher in patients with COPD. Moreover, six proteins; fibulin-3, tripeptidyl-peptidase 2, UTP-glucose-1-phosphate uridylyl transferase, CD81, CD177, and oncoprotein-induced transcript 3, were correlated with emphysema. Upregulation of fibulin-3 was confirmed by immunoblotting of EVs and immunohistochemistry in lungs. Strikingly, fibulin-3 knockout mice spontaneously developed emphysema with age, as evidenced by alveolar enlargement and elastin destruction. We discovered potential pathogenic biomarkers for COPD using next-generation proteomics of EVs. This is a novel strategy for biomarker discovery and precision medicine. This study identified novel biomarkers for COPD using next-generation proteomics of serum extracellular vesicles. Notably, the expression of fibulin-3 is correlated with lung function and emphysema. This could be useful for personalised medicine.https://bit.ly/2JfRCgk
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Affiliation(s)
- Taro Koba
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoshito Takeda
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryohei Narumi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Takashi Shiromizu
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Yosui Nojima
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Mari Ito
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Muneyoshi Kuroyama
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yu Futami
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takayuki Takimoto
- Dept of Respiratory Internal Medicine, National Hospital Organization Kinki-Chuo Chest Medical Center, Kita-Ku, Sakai, Osaka, Japan
| | - Takanori Matsuki
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Ryuya Edahiro
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Satoshi Nojima
- Dept of Pathology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yoshitomo Hayama
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kiyoharu Fukushima
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Haruhiko Hirata
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Shohei Koyama
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kota Iwahori
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Izumi Nagatomo
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Mayumi Suzuki
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yuya Shirai
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Teruaki Murakami
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kaori Nakanishi
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takeshi Nakatani
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yasuhiko Suga
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Kotaro Miyake
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takayuki Shiroyama
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Hiroshi Kida
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Takako Sasaki
- Dept of Biochemistry II, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | - Koji Ueda
- Cancer Proteomics Group, Cancer Precision Medicine Center, Japanese Foundation for Cancer Research, Koto, Tokyo, Japan
| | - Kenji Mizuguchi
- Laboratory of Bioinformatics, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
| | - Atsushi Kumanogoh
- Dept of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
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11
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Hara Y, Zhang B, Suzuki A, Yamaguchi S, Adachi J, Tomonaga T, Yasunaga S, Saku K, Aoyama T, Hirano KI. Effect of Tricaprin on Cardiac Proteome in a Mouse Model for Triglyceride Deposit Cardiomyovasculopathy. J Oleo Sci 2020; 69:1569-1577. [PMID: 33177279 DOI: 10.5650/jos.ess20185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Triglyceride deposit cardiomyovasculopathy (TGCV), a rare cardiovascular disorder caused by genetic or acquired dysfunction of adipose triglyceride lipase (ATGL), is marked by defective intracellular lipolysis that results in excessive accumulation of triglycerides (TGs) in the myocardium and coronary arteries, leading to intractable heart failure (HF). We have developed a specific treatment for TGCV using tricaprin, a medium chain TG, as part of a governmental rare disease project in Japan. We recently reported that tricaprin diet improved cardiac TG metabolism and left ventricular function in an ATGL-knockout (KO) mouse, a mouse model for TGCV. Here, we report the effect of tricaprin on the myocardial proteome of KO mice to elucidate the mechanisms of action of tricaprin at protein expression levels. We compared proteomic changes in the hearts of KO mice fed control or tricaprin diet. Tandem mass tag-based shotgun proteomics identified 1832 proteins common to all sample groups. Whole proteomic distribution in the heart was largely up-regulated in KO mice fed control diet. When using cut-off values (>1.5 or <0.67, FDR-adjusted p value<0.01), in fact, 65 proteins were up-regulated whereas only 2 proteins were down-regulated in the hearts of KO mice fed control diet. The former included proteins assigned to "Cardiac Arrhythmia", and "Cardiac Damage" reflecting HF by a toxicity function analysis. One of the latter was Ces1d, which is known to regulate intracellular TG metabolism. These proteomic changes observed in KO mice were dramatically rescued by the tricaprin diet. These results indicated that tricaprin diet ameliorated HF in a TGCV mouse model at protein expression levels and also provided important clues to understand mechanisms for the beneficial effect of tricaprin.
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Affiliation(s)
- Yasuhiro Hara
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Bo Zhang
- Department of Biochemistry, Fukuoka University Medical School
| | - Akira Suzuki
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Satoshi Yamaguchi
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition
| | | | - Keijiro Saku
- General Medical Research Center, Fukuoka University Medical School
| | - Toshiaki Aoyama
- Food Biotechnology Platform Promoting Project, New industry Creation Hatchery Center (NICHe) at Tohoku University
| | - Ken-Ichi Hirano
- Laboratory of Cardiovascular Disease, Novel, Non-Invasive, and Nutritional Therapeutics (CNT), Graduate School of Medicine, Osaka University
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12
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Abe Y, Hirano H, Shoji H, Tada A, Isoyama J, Kakudo A, Gunji D, Honda K, Boku N, Adachi J, Tomonaga T. Comprehensive characterization of the phosphoproteome of gastric cancer from endoscopic biopsy specimens. Theranostics 2020; 10:2115-2129. [PMID: 32089736 PMCID: PMC7019165 DOI: 10.7150/thno.37623] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 12/09/2019] [Indexed: 12/26/2022] Open
Abstract
Rationale: Cancer phosphoproteomics can provide insights regarding kinases that can be targeted for therapeutic applications. Monitoring the phosphoproteomics in cancer is expected to play a key role in optimizing treatments with kinase inhibitors. Clinical phosphoproteomics in surgical tissues and patient-derived models has been studied intensively. However, the reported data may not accurately reflect the phosphosignaling status in patients due to the effect of ischemia occurring during surgery or changes in the characteristics of cancer cells when establishing the models. In contrast, endoscopic biopsies have an advantage for clinical phosphoproteomics because they can be rapidly cryo-preserved. We aimed to develop a highly sensitive method for phosphoproteomics in endoscopic biopsies of gastric cancer. Methods: Three tumor biopsies and three normal gastric biopsies were obtained by endoscopy at one time, and subjected to our optimized phosphoproteomics. Phosphopeptides were enriched with an immobilized metal affinity chromatography, and labeled with Tandem Mass Tag reagent. Quantified phosphosites were compared between the pairs of tumor/normal biopsies within same patient. Cancer-specific activated pathways and kinases were identified by pathway enrichment analysis and kinase-substrate enrichment analysis. Results: Our protocol enabled the identification of more than 10,000 class 1 phosphosites from endoscopic biopsies. A comparison between samples from cancer tissue and normal mucosa demonstrated differences in the phosphosignaling, including biomarkers of response to DNA damage. Finally, cancer-specific activation of DNA damage response signaling was validated by additional phosphoproteomics of other patients and western blotting of gastric cancer/normal cells. Conclusion: In summary, our pioneering approach will facilitate more accurate clinical phosphoproteomics in endoscopic biopsies, which can be applied to monitor the activities of therapeutic kinases and, ultimately, can be a useful tool to precision medicine.
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13
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Affiliation(s)
- Yasushi ISHIHAMA
- Department of Molecular & Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University
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14
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Abstract
Castration-resistant prostate cancer (CRPC) remains incurable despite the approval of several new treatments. Identification of new biomarkers and therapeutic targets to enable personalization of CRPC therapy, with the aim of maximizing therapeutic responses and minimizing toxicity in patients, is urgently needed. Prostate cancer progression and therapeutic resistance are frequently driven by aberrantly activated kinase signalling pathways that are amenable to pharmacological inhibition. Personalized phosphoproteomics, which enables the analysis of signalling networks in individual tumours, is a promising approach to advance personalized therapy by discovering biomarkers of pathway activity and clinically actionable targets. Several technologies for global and targeted phosphoproteomic analysis exist, each with its own strengths and shortcomings. Global discovery phosphoproteomics is predominantly conducted using liquid chromatography-tandem mass spectrometry coupled with data-dependent or data-independent acquisition technologies. Multiplexed targeted phosphoproteomics can be divided into platforms based on mass spectrometry or antibodies, including selected or parallel reaction monitoring and triggered by offset, multiplexed, accurate mass, high-resolution, absolute quantification (known as TOMAHAQ) or forward-phase or reverse-phase protein arrays, respectively. Several obstacles still need to be overcome before the full potential of phosphoproteomics can be realized in routine clinical practice, but a future phosphoproteomics-centric trans-omic profiling approach should enable optimized personalized CRPC management through improved biomarkers and targeted treatments.
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15
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Haymond A, Davis JB, Espina V. Proteomics for cancer drug design. Expert Rev Proteomics 2019; 16:647-664. [PMID: 31353977 PMCID: PMC6736641 DOI: 10.1080/14789450.2019.1650025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 07/26/2019] [Indexed: 12/29/2022]
Abstract
Introduction: Signal transduction cascades drive cellular proliferation, apoptosis, immune, and survival pathways. Proteins have emerged as actionable drug targets because they are often dysregulated in cancer, due to underlying genetic mutations, or dysregulated signaling pathways. Cancer drug development relies on proteomic technologies to identify potential biomarkers, mechanisms-of-action, and to identify protein binding hot spots. Areas covered: Brief summaries of proteomic technologies for drug discovery include mass spectrometry, reverse phase protein arrays, chemoproteomics, and fragment based screening. Protein-protein interface mapping is presented as a promising method for peptide therapeutic development. The topic of biosimilar therapeutics is presented as an opportunity to apply proteomic technologies to this new class of cancer drug. Expert opinion: Proteomic technologies are indispensable for drug discovery. A suite of technologies including mass spectrometry, reverse phase protein arrays, and protein-protein interaction mapping provide complimentary information for drug development. These assays have matured into well controlled, robust technologies. Recent regulatory approval of biosimilar therapeutics provides another opportunity to decipher the molecular nuances of their unique mechanisms of action. The ability to identify previously hidden protein hot spots is expanding the gamut of potential drug targets. Proteomic profiling permits lead compound evaluation beyond the one drug, one target paradigm.
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Affiliation(s)
- Amanda Haymond
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Justin B Davis
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
| | - Virginia Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University , Manassas , VA , USA
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16
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Sum of peak intensities outperforms peak area integration in iTRAQ protein expression measurement by LC-MS/MS using a TripleTOF 5600+ platform. Biosci Rep 2019; 39:BSR20190904. [PMID: 31110078 PMCID: PMC6554230 DOI: 10.1042/bsr20190904] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/08/2019] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
In the field of quantitative proteomics, the Isobaric Tags for Relative and Absolute Quantitation (iTRAQ) technology has demonstrated efficacy for proteome monitoring despite its lack of a consensus for data handling. In the present study, after peptide and protein identification, we compared the widespread quantitation method based on the calculation of MS/MS reporter ion peaks areas ratios (ProteinPilot) to the alternative method based on the calculation of ratios of the sum of peak intensities (jTRAQx [Quant]) and we processed output data with the in-house Customizable iTRAQ Ratios Calculator (CiR-C) algorithm. Quantitation based on peak area ratios displayed no significant linear correlation with Western blot quantitation. In contrast, quantitation based on the sum of peak intensities displayed a significant linear association with Western blot quantitation (non-zero slope; Pearson correlation coefficient test, r = 0.296, P=0.010**) with an average bias of 0.087 ± 0.500 and 95% Limits of Agreement from −0.893 to 1.068. We proposed the Mascot-jTRAQx-CiR-C strategy as a simple yet powerful data processing adjunct to the iTRAQ technology.
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17
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Hama N, Nishimura K, Hasegawa A, Yuki A, Kume H, Adachi J, Kinoshita M, Ogawa Y, Nakajima S, Nomura T, Watanabe H, Mizukawa Y, Tomonaga T, Shimizu H, Abe R. Galectin-7 as a potential biomarker of Stevens-Johnson syndrome/toxic epidermal necrolysis: identification by targeted proteomics using causative drug-exposed peripheral blood cells. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2019; 7:2894-2897.e7. [PMID: 31100551 DOI: 10.1016/j.jaip.2019.05.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/22/2019] [Accepted: 05/03/2019] [Indexed: 12/20/2022]
Affiliation(s)
- Natsumi Hama
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Keiko Nishimura
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Akito Hasegawa
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akihiko Yuki
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideaki Kume
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Manao Kinoshita
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Youichi Ogawa
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Saeko Nakajima
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Nomura
- Department of Dermatology, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Hideaki Watanabe
- Department of Dermatology, Showa University School of Medicine, Tokyo, Japan
| | - Yoshiko Mizukawa
- Department of Dermatology, Kyorin University, School of Medicine, Tokyo, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan; Laboratory of Proteomics for Drug Discovery, Center for Drug Design Research, National Institute of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Dermatology, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Riichiro Abe
- Division of Dermatology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
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18
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Cui YH, Liu Q, Xu ZY, Li JH, Hu ZX, Li MJ, Zheng WL, Li ZJ, Pan HW. Quantitative proteomic analysis of human corneal epithelial cells infected with HSV-1. Exp Eye Res 2019; 185:107664. [PMID: 31085182 DOI: 10.1016/j.exer.2019.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/22/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023]
Abstract
HSV-1 infection in corneal epithelium initiates the process of herpes simplex keratitis. We investigated the dynamic change of the host proteins in corneal epithelial cells infected with HSV-1 to understand the virus-host interaction. iTRAQ coupled with LC-MS/MS was applied to quantitatively analyze the protein profiles in HSV-1 infected corneal epithelial cells at 6 and 24 h post-infection (hpi), and the results were validated by multiple reaction monitoring (MRM). We also performed bioinformatic analysis to investigate the potentially important signal pathways and protein interaction networks in the host response to HSV-1 infection. We identified 292 proteins were up-regulated and 168 proteins were down-regulated at 6 hpi, while 132 proteins were up-regulated and 89 proteins were down-regulated at 24 hpi, which were validated by MRM analysis. We found the most enriched GO terms were translational initiation, cytosol, poly(A) RNA binding, mRNA splicing via spliceosome and extracellular exosome for the dysregulated proteins. KEGG pathway analysis revealed significant changes in metabolism pathway characterized by decreased tricarboxylic acid cycle activity and increased glycolysis. Proteins interaction network analysis indicated several proteins including P4HB, ACLY, HSP90AA1 and EIF4A3, might be critical proteins in the host-virus response. Our study for the first time analyzed the protein profile of HSV-1 infected primary corneal epithelial cells by quantitative proteomics. These findings help to better understand the host-virus interaction and the pathogenesis of herpes simplex keratitis.
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Affiliation(s)
- Yu-Hong Cui
- Guangzhou Institute of Cardiovascular Disease, The Second Affiliated Hospital, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China; Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Qun Liu
- Department of Histology and Embryology, School of Basic Medical Sciences, Guangzhou Medical University, Guangzhou, China
| | - Zhi-Yi Xu
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Jia-Hui Li
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Zi-Xuan Hu
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Mei-Jun Li
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Wen-Lin Zheng
- Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China
| | - Zhi-Jie Li
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China
| | - Hong-Wei Pan
- Institute of Ophthalmology, School of Medicine, Jinan University, Guangzhou, China; Department of Ophthalmology, The First Affiliated Hospital, Jinan University, Guangzhou, China; Department of Public Health and Preventive Medicine, Jinan University, Guangzhou, China.
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19
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Mehta K, Jaiswal D, Nayak M, Prasannan CB, Wangikar PP, Srivastava S. Elevated carbon dioxide levels lead to proteome-wide alterations for optimal growth of a fast-growing cyanobacterium, Synechococcus elongatus PCC 11801. Sci Rep 2019; 9:6257. [PMID: 31000743 PMCID: PMC6472392 DOI: 10.1038/s41598-019-42576-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/29/2019] [Indexed: 12/21/2022] Open
Abstract
The environmental considerations attributing to the escalation of carbon dioxide emissions have raised alarmingly. Consequently, the concept of sequestration and biological conversion of CO2 by photosynthetic microorganisms is gaining enormous recognition. In this study, in an attempt to discern the synergistic CO2 tolerance mechanisms, metabolic responses to increasing CO2 concentrations were determined for Synechococcus elongatus PCC 11801, a fast-growing, novel freshwater strain, using quantitative proteomics. The protein expression data revealed that the organism responded to elevated CO2 by not only regulating the cellular transporters involved in carbon-nitrogen uptake and assimilation but also by inducing photosynthesis, carbon fixation and glycolysis. Several components of photosynthetic machinery like photosystem reaction centers, phycobilisomes, cytochromes, etc. showed a marked up-regulation with a concomitant downshift in proteins involved in photoprotection and redox maintenance. Additionally, enzymes belonging to the TCA cycle and oxidative pentose phosphate pathway exhibited a decline in their expression, further highlighting that the demand for reduced cofactors was fulfilled primarily through photosynthesis. The present study brings the first-ever comprehensive assessment of intricate molecular changes in this novel strain while shifting from carbon-limited to carbon-sufficient conditions and may pave the path for future host and pathway engineering for production of sustainable fuels through efficient CO2 capture.
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Affiliation(s)
- Kanika Mehta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Damini Jaiswal
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Monalisha Nayak
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Charulata B Prasannan
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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20
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Winter M, Mayer R, Warnken U, Debus J, Abdollahi A, Schnölzer M. Synthetic phosphopeptides: From spike-in standards to affinity tools for protein-protein interaction studies. Anal Biochem 2019; 568:73-77. [PMID: 30597127 DOI: 10.1016/j.ab.2018.12.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 12/04/2018] [Accepted: 12/21/2018] [Indexed: 11/27/2022]
Abstract
Synthetic isotope labeled phosphopeptides are valuable tools for the quantification and validation of phosphoproteome data. Here, we report that the same set of phosphopeptides, which are used as spike-in standards, can be successfully applied for identification of stimulus specific protein-protein interactions mediated by the respective phosphorylation sites. As a proof-of-concept, binding of two γH2AX (pS139) phosphosite specific interaction partners, MDC1 and 53BP1, was confirmed and elevated binding affinity was revealed in response to ionizing radiation. Our strategy is generally applicable and enables multiplexed validation and functional analysis of phosphorylation sites offering great potential for the follow-up of phosphoproteome studies.
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Affiliation(s)
- Martin Winter
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany; Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ramona Mayer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Uwe Warnken
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Jürgen Debus
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120, Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- Translational Radiation Oncology, National Center for Tumor Diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120, Heidelberg, Germany; German Cancer Consortium (DKTK), Heidelberg, Germany; Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120, Heidelberg, Germany; Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Martina Schnölzer
- Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
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21
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Pierobon M, Wulfkuhle J, Liotta LA, Petricoin Iii EF. Utilization of Proteomic Technologies for Precision Oncology Applications. Cancer Treat Res 2019; 178:171-187. [PMID: 31209845 DOI: 10.1007/978-3-030-16391-4_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Genomic analysis of tumor specimens has revealed that cancer is fundamentally a proteomic disease at the functional level: driven by genomically defined derangements, but selected for in the proteins that are encoded and the aberrant activation of signaling and biochemical networks. This activation is measured by posttranslational modifications such as phosphorylation and other modifications that modulate cellular signaling, and these events cannot be effectively measured by genomic analysis alone. Moreover, these signaling networks by and large represent the targets for many FDA-approved and experimental molecularly targeted therapeutics. Consequently, it is important that we consider new classification schemas for oncology based not on tumor site of origin or histology under the microscope but on the functional protein signaling architecture. There are numerous proteomic technologies that could be discussed from a purely technological standpoint, but this chapter will concentrate on an overview of the main proteomic technologies available for conducting protein pathway activation analysis of clinical specimens such as multiplex immunoassays, phospho-specific flow cytometry, reverse phase protein microarrays, quantitative immunohistochemistry, and mass spectrometry. This chapter will focus on the application of these technologies to cancer-based clinical studies evaluating prognostic/predictive markers or for stratifying patients to personalized treatments.
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Affiliation(s)
- Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Julie Wulfkuhle
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA
| | - Emanuel F Petricoin Iii
- Center for Applied Proteomics and Molecular Medicine, George Mason University, 20110, Manassas, VA, USA.
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22
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Horiuchi M, Kuga T, Saito Y, Nagano M, Adachi J, Tomonaga T, Yamaguchi N, Nakayama Y. The tyrosine kinase v-Src causes mitotic slippage by phosphorylating an inhibitory tyrosine residue of Cdk1. J Biol Chem 2018; 293:15524-15537. [PMID: 30135207 DOI: 10.1074/jbc.ra118.002784] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 08/17/2018] [Indexed: 11/06/2022] Open
Abstract
The nonreceptor tyrosine kinase v-Src is an oncogene first identified in Rous sarcoma virus. The oncogenic effects of v-Src have been intensively studied; however, its effects on chromosomal integrity are not fully understood. Here, using HeLa S3/v-Src cells having inducible v-Src expression, we found that v-Src causes mitotic slippage in addition to cytokinesis failure, even when the spindle assembly checkpoint is not satisfied because of the presence of microtubule-targeting agents. v-Src's effect on mitotic slippage was also observed in cells after a knockdown of C-terminal Src kinase (Csk), a protein-tyrosine kinase that inhibits Src-family kinases and was partially inhibited by PP2, an Src-family kinase inhibitor. Proteomic analysis and in vitro kinase assay revealed that v-Src phosphorylates cyclin-dependent kinase 1 (Cdk1) at Tyr-15. This phosphorylation attenuated Cdk1 kinase activity, resulting in a decrease in the phosphorylation of Cdk1 substrates. Furthermore, v-Src-induced mitotic slippage reduced the sensitivity of the cells to microtubule-targeting agents, and cells that survived the microtubule-targeting agents exhibited polyploidy. These results suggest that v-Src causes mitotic slippage by attenuating Cdk1 kinase activity via direct phosphorylation of Cdk1 at Tyr-15. On the basis of these findings, we propose a model for v-Src-induced oncogenesis, in which v-Src-promoted mitotic slippage due to Cdk1 phosphorylation generates genetic diversity via abnormal cell division of polyploid cells and also increases the tolerance of cancer cells to microtubule-targeting agents.
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Affiliation(s)
- Maria Horiuchi
- From the Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414
| | - Takahisa Kuga
- From the Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414
| | - Youhei Saito
- From the Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414
| | - Maiko Nagano
- the Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, and
| | - Jun Adachi
- the Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, and
| | - Takeshi Tomonaga
- the Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka 567-0085, and
| | - Naoto Yamaguchi
- the Laboratory of Molecular Cell Biology, Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 260-8675, Japan
| | - Yuji Nakayama
- From the Department of Biochemistry and Molecular Biology, Kyoto Pharmaceutical University, Kyoto 607-8414,
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23
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Gianazza E, Banfi C. Post-translational quantitation by SRM/MRM: applications in cardiology. Expert Rev Proteomics 2018; 15:477-502. [DOI: 10.1080/14789450.2018.1484283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Erica Gianazza
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
| | - Cristina Banfi
- Unit of Proteomics, Centro Cardiologico Monzino IRCCS, Milan, Italy
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24
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Selvan LDN, Danda R, Madugundu AK, Puttamallesh VN, Sathe GJ, Krishnan UM, Khetan V, Rishi P, Prasad TSK, Pandey A, Krishnakumar S, Gowda H, Elchuri SV. Phosphoproteomics of Retinoblastoma: A Pilot Study Identifies Aberrant Kinases. Molecules 2018; 23:molecules23061454. [PMID: 29914080 PMCID: PMC6100359 DOI: 10.3390/molecules23061454] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 05/31/2018] [Accepted: 06/07/2018] [Indexed: 01/09/2023] Open
Abstract
Retinoblastoma is a malignant tumour of the retina which most often occurs in children. Earlier studies on retinoblastoma have concentrated on the identification of key players in the disease and have not provided information on activated/inhibited signalling pathways. The dysregulation of protein phosphorylation in cancer provides clues about the affected signalling cascades in cancer. Phosphoproteomics is an ideal tool for the study of phosphorylation changes in proteins. Hence, global phosphoproteomics of retinoblastoma (RB) was carried out to identify signalling events associated with this cancer. Over 350 proteins showed differential phosphorylation in RB compared to control retina. Our study identified stress response proteins to be hyperphosphorylated in RB which included H2A histone family member X (H2AFX) and sirtuin 1. In particular, Ser140 of H2AFX also known as gamma-H2AX was found to be hyperphosphorylated in retinoblastoma, which indicated the activation of DNA damage response pathways. We also observed the activation of anti-apoptosis in retinoblastoma compared to control. These observations showed the activation of survival pathways in retinoblastoma. The identification of hyperphosphorylated protein kinases including Bromodomain containing 4 (BRD4), Lysine deficient protein kinase 1 (WNK1), and Cyclin-dependent kinase 1 (CDK1) in RB opens new avenues for the treatment of RB. These kinases can be considered as probable therapeutic targets for RB, as small-molecule inhibitors for some of these kinases are already in clinical trials for the treatment other cancers.
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Affiliation(s)
| | - Ravikanth Danda
- L&T Opthalmic Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
- Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamil Nadu 613 401, India.
| | - Anil K Madugundu
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Vinuth N Puttamallesh
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Gajanan J Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- Manipal Academy of Higher Education (MAHE), Manipal, Karnataka 576 104, India.
| | - Uma Maheswari Krishnan
- Centre for Nanotechnology and Advanced Biomaterials, Shanmugha Arts, Science, Technology and Research Academy University, Tanjore, Tamil Nadu 613 401, India.
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Pukhraj Rishi
- Shri Bhagwan Mahavir Vitreoretinal Services, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Thottethodi Subrahmanya Keshava Prasad
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, Karnataka 575 108, India.
| | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
- Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
| | - Subramanian Krishnakumar
- L&T Opthalmic Pathology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka 560 066, India.
| | - Sailaja V Elchuri
- Department of Nanotechnology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu 600 006, India.
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25
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Dekker LJM, Zeneyedpour L, Snoeijers S, Joore J, Leenstra S, Luider TM. Determination of Site-Specific Phosphorylation Ratios in Proteins with Targeted Mass Spectrometry. J Proteome Res 2018; 17:1654-1663. [PMID: 29457462 DOI: 10.1021/acs.jproteome.7b00911] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We show that parallel reaction monitoring (PRM) can be used for exact quantification of phosphorylation ratios of proteins using stable-isotope-labeled peptides. We have compared two different PRM approaches on a digest of a U87 cell culture, namely, direct-PRM (tryptic digest measured by PRM without any further sample preparation) and TiO2-PRM (tryptic digest enriched with TiO2 cartridges, followed by PRM measurement); these approaches are compared for the following phosphorylation sites: neuroblast differentiation-associated protein (AHNAK S5480-p), calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D T337-p), and epidermal growth factor receptor (EGFR S1166-p). A reproducible percentage of phosphorylation could be determined (CV 6-13%) using direct-PRM or TiO2-PRM. In addition, we tested the approaches in a cell culture experiment in which U87 cells were deprived of serum. As a "gold standard" we included immune precipitation of EGFR followed by PRM (IP-PRM). For EGFR (S1166) and AHNAK (S5480) a statistical significant change in the percentage of phosphorylation could be observed as a result of serum deprivation; for EGFR (S1166) this change was observed for both TiO2-PRM and IP-PRM. The presented approach has the potential to multiplex and to quantify the ratio of phosphorylation in a single analysis.
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Affiliation(s)
- Lennard J M Dekker
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | - Lona Zeneyedpour
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
| | | | - Jos Joore
- Pepscope , Dantelaan 83 , 3533 VB Utrecht , The Netherlands
| | - Sieger Leenstra
- Erasmus MC , Department of Neurosurgery , 3015 CN Rotterdam , The Netherlands
| | - Theo M Luider
- Erasmus MC , Department of Neurology , Wytemaweg 80 , 3015 CN Rotterdam , The Netherlands
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26
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Thygesen C, Boll I, Finsen B, Modzel M, Larsen MR. Characterizing disease-associated changes in post-translational modifications by mass spectrometry. Expert Rev Proteomics 2018; 15:245-258. [DOI: 10.1080/14789450.2018.1433036] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Camilla Thygesen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Inga Boll
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Bente Finsen
- Department of Neuroscience, University of Southern Denmark, Institute of Molecular Medicine, Denmark
| | - Maciej Modzel
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
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27
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Chen Y, Britton D, Wood ER, Brantley S, Magliocco A, Pike I, Koomen JM. Quantitative proteomics of breast tumors: Tissue quality assessment to clinical biomarkers. Proteomics 2017; 17. [PMID: 28127872 DOI: 10.1002/pmic.201600335] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Revised: 11/11/2016] [Accepted: 01/23/2017] [Indexed: 01/07/2023]
Abstract
Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM) is not only a proven tool for clinical chemistry, but also a versatile method to enhance the capability to quantify biomarkers for tumor biology research. As the treatment of cancer continues to evolve, the ability to assess multiple biomarkers to assign cancer phenotypes based on the genetic background and the signaling of the individual tumor becomes paramount to our ability to treat the patient. In breast cancer, the American Society of Clinical Oncology has defined biomarkers for patient assessment to guide selection of therapy: estrogen receptor, progesterone receptor, and the HER2/Neu receptor tyrosine kinase; therefore, these proteins were selected for LC-SRM assay development. Detailed molecular characterization of these proteins is necessary for patient treatment, so expression and phosphorylation assays have been developed and applied. In addition, other LC-SRM assays were developed to further evaluate tumor biology (e.g. Ki-67 for proliferation and vimentin for tumor aggressiveness related to the epithelial-to-mesenchymal transition). These measurements combined with biomarkers for tissue quality and histological content are implemented in a three-tier multiplexed assay platform, which is translated from cell line models into frozen tumor tissues banked from breast cancer patients.
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Affiliation(s)
- Yi Chen
- Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - Ian Pike
- Proteome Sciences plc., Cobham, UK
| | - John M Koomen
- Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA.,Chemical Biology and Molecular Medicine, Moffitt Cancer Center, Tampa, FL, USA
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28
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Quantitation of putative colorectal cancer biomarker candidates in serum extracellular vesicles by targeted proteomics. Sci Rep 2017; 7:12782. [PMID: 28986585 PMCID: PMC5630664 DOI: 10.1038/s41598-017-13092-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 09/19/2017] [Indexed: 02/07/2023] Open
Abstract
At the moment, there is no sensitive clinical test for detecting early-stage colorectal cancer (CRC). Target proteomics has enabled high-throughput verification of hundreds of biomarker candidate proteins. Using this technology, we verified 725 previously reported CRC biomarker candidate proteins that are functionally correlated with CRC in extracellular vesicles (EVs) from patients. Of these, 356 proteins were quantified, and 34 peptides (22 proteins) showed significant differences in the serum EVs between healthy controls and CRC patients of two independent cohorts (n = 77 and 84). These peptides were evaluated as single or multiple markers, and four single peptides in annexin family proteins and eight combinations of peptides showed area under the curve > 0.9 for discriminating between healthy controls and CRC patients. The sensitivities of annexins A3, A4, and A11 peptides for detecting early-stage CRC greatly exceed those of carcinoembryonic antigen. These peptides are promising biomarkers for early detection of CRC.
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29
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Zavialova MG, Zgoda VG, Nikolaev EN. [Analysis of contribution of protein phosphorylation in the development of the diseases]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2017; 63:101-114. [PMID: 28414281 DOI: 10.18097/pbmc20176302101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In recent decades, studies in the molecular origins of socially significant diseases have made a big step forward with the development and using of high-performance methods in genomics and proteomics. Numerous studies in the framework of the global program "Human Proteome" were aimed at the identification of all possible proteins in various cell cultures and tissues, including cancer. One of the objectives was to identify biomarkers - proteins with high specificity to certain pathologies. However, in many cases, it is shown that the development of the disease is not associated with the appearance of new proteins, but depends on the level of gene expression or forming of proteoforms - splice variants, single amino acid substitutions (SAP variants), and post-translational modifications (PTM) of proteins. PTM may play a key role in the development of pathology because they activate a variety of regulatory or structural proteins in the majority of cell physiological processes. Phosphorylation is among the most significant of these protein modifications.This review will describe methods for analysis of protein phosphorylation used in the studies of such diseases as cancer and neurodegenerative diseases, as well as examples of cases when the modified proteins are involved directly to their development, and screening such significant PTM is used for the diagnosis and choice of treatment.
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Affiliation(s)
| | - V G Zgoda
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E N Nikolaev
- Institute of Biomedical Chemistry, Moscow, Russia; Skolkovo Institute of Science and Technology (Skoltech), Moscow, Russia
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30
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Henry M, Power M, Kaushik P, Coleman O, Clynes M, Meleady P. Differential Phosphoproteomic Analysis of Recombinant Chinese Hamster Ovary Cells Following Temperature Shift. J Proteome Res 2017; 16:2339-2358. [DOI: 10.1021/acs.jproteome.6b00868] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Michael Henry
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Power
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Prashant Kaushik
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Orla Coleman
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Martin Clynes
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Paula Meleady
- National Institute for Cellular
Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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31
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Quan Q, Feng J, Lui LT, Shi T, Chu IK. Phosphoproteome of crab-eating macaque cerebral cortex characterized through multidimensional reversed-phase liquid chromatography/mass spectrometry with tandem anion/cation exchange columns. J Chromatogr A 2017; 1498:196-206. [DOI: 10.1016/j.chroma.2017.01.048] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 01/13/2017] [Accepted: 01/21/2017] [Indexed: 02/06/2023]
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32
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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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33
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Rai V, Muthuraj M, Gandhi MN, Das D, Srivastava S. Real-time iTRAQ-based proteome profiling revealed the central metabolism involved in nitrogen starvation induced lipid accumulation in microalgae. Sci Rep 2017; 7:45732. [PMID: 28378827 PMCID: PMC5381106 DOI: 10.1038/srep45732] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 03/06/2017] [Indexed: 02/06/2023] Open
Abstract
To understand the post-transcriptional molecular mechanisms attributing to oleaginousness in microalgae challenged with nitrogen starvation (N-starvation), the longitudinal proteome dynamics of Chlorella sp. FC2 IITG was investigated using multipronged quantitative proteomics and multiple reaction monitoring assays. Physiological data suggested a remarkably enhanced lipid accumulation with concomitant reduction in carbon flux towards carbohydrate, protein and chlorophyll biosynthesis. The proteomics-based investigations identified the down-regulation of enzymes involved in chlorophyll biosynthesis (porphobilinogen deaminase) and photosynthetic carbon fixation (sedoheptulose-1,7 bisphosphate and phosphoribulokinase). Profound up-regulation of hydroxyacyl-ACP dehydrogenase and enoyl-ACP reductase ascertained lipid accumulation. The carbon skeletons to be integrated into lipid precursors were regenerated by glycolysis, β-oxidation and TCA cycle. The enhanced expression of glycolysis and pentose phosphate pathway enzymes indicates heightened energy needs of FC2 cells for the sustenance of N-starvation. FC2 cells strategically reserved nitrogen by incorporating it into the TCA-cycle intermediates to form amino acids; particularly the enzymes involved in the biosynthesis of glutamate, aspartate and arginine were up-regulated. Regulation of arginine, superoxide dismutase, thioredoxin-peroxiredoxin, lipocalin, serine-hydroxymethyltransferase, cysteine synthase, and octanoyltransferase play a critical role in maintaining cellular homeostasis during N-starvation. These findings may provide a rationale for genetic engineering of microalgae, which may enable synchronized biomass and lipid synthesis.
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Affiliation(s)
- Vineeta Rai
- Department of Biosciences and Bioengineering, Wadhwani Research Center for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Muthusivaramapandian Muthuraj
- Department of Biosciences and Bioengineering, Centre for Energy, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Mayuri N. Gandhi
- Centre for Research in Nanotechnology & Science, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debasish Das
- Department of Biosciences and Bioengineering, Centre for Energy, Indian Institute of Technology Guwahati, Assam 781039, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, Powai - 400067, India
| | - Sanjeeva Srivastava
- Department of Biosciences and Bioengineering, Wadhwani Research Center for Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
- DBT PAN IIT Centre for Bioenergy, Indian Institute of Technology Bombay, Mumbai, Powai - 400067, India
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34
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Winter M, Dokic I, Schlegel J, Warnken U, Debus J, Abdollahi A, Schnölzer M. Deciphering the Acute Cellular Phosphoproteome Response to Irradiation with X-rays, Protons and Carbon Ions. Mol Cell Proteomics 2017; 16:855-872. [PMID: 28302921 DOI: 10.1074/mcp.m116.066597] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/15/2017] [Indexed: 12/15/2022] Open
Abstract
Radiotherapy is a cornerstone of cancer therapy. The recently established particle therapy with raster-scanning protons and carbon ions landmarks a new era in the field of high-precision cancer medicine. However, molecular mechanisms governing radiation induced intracellular signaling remain elusive. Here, we present the first comprehensive proteomic and phosphoproteomic study applying stable isotope labeling by amino acids in cell culture (SILAC) in combination with high-resolution mass spectrometry to decipher cellular response to irradiation with X-rays, protons and carbon ions. At protein expression level limited alterations were observed 2 h post irradiation of human lung adenocarcinoma cells. In contrast, 181 phosphorylation sites were found to be differentially regulated out of which 151 sites were not hitherto attributed to radiation response as revealed by crosscheck with the PhosphoSitePlus database.Radiation-induced phosphorylation of the p(S/T)Q motif was the prevailing regulation pattern affecting proteins involved in DNA damage response signaling. Because radiation doses were selected to produce same level of cell kill and DNA double-strand breakage for each radiation quality, DNA damage responsive phosphorylation sites were regulated to same extent. However, differential phosphorylation between radiation qualities was observed for 55 phosphorylation sites indicating the existence of distinct signaling circuitries induced by X-ray versus particle (proton/carbon) irradiation beyond the canonical DNA damage response. This unexpected finding was confirmed in targeted spike-in experiments using synthetic isotope labeled phosphopeptides. Herewith, we successfully validated uniform DNA damage response signaling coexisting with altered signaling involved in apoptosis and metabolic processes induced by X-ray and particle based treatments.In summary, the comprehensive insight into the radiation-induced phosphoproteome landscape is instructive for the design of functional studies aiming to decipher cellular signaling processes in response to radiotherapy, space radiation or ionizing radiation per se Further, our data will have a significant impact on the ongoing debate about patient treatment modalities.
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Affiliation(s)
- Martin Winter
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany.,§Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Ivana Dokic
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Julian Schlegel
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Uwe Warnken
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Jürgen Debus
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Amir Abdollahi
- §Translational Radiation Oncology, National Center for Tumor diseases (NCT), German Cancer Research Center (DKFZ), Im Neuenheimer Feld 460, D-69120 Heidelberg, Germany.,¶German Cancer Consortium (DKTK), Heidelberg, Germany.,‖Heidelberg Ion Beam Therapy Center (HIT), Department of Radiation Oncology, University of Heidelberg Medical School, Im Neuenheimer Feld 450, D-69120 Heidelberg, Germany.,**Heidelberg Institute of Radiation Oncology (HIRO), National Center for Radiation Research in Oncology (NCRO), Heidelberg, Germany
| | - Martina Schnölzer
- From the ‡Functional Proteome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany;
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35
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Lin YT, Chien KY, Wu CC, Chang WY, Chu LJ, Chen MC, Yeh CT, Yu JS. Super-SILAC mix coupled with SIM/AIMS assays for targeted verification of phosphopeptides discovered in a large-scale phosphoproteome analysis of hepatocellular carcinoma. J Proteomics 2017; 157:40-51. [DOI: 10.1016/j.jprot.2017.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/23/2017] [Accepted: 02/08/2017] [Indexed: 01/04/2023]
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Faria SS, Morris CFM, Silva AR, Fonseca MP, Forget P, Castro MS, Fontes W. A Timely Shift from Shotgun to Targeted Proteomics and How It Can Be Groundbreaking for Cancer Research. Front Oncol 2017; 7:13. [PMID: 28265552 PMCID: PMC5316539 DOI: 10.3389/fonc.2017.00013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 01/17/2017] [Indexed: 01/10/2023] Open
Abstract
The fact that cancer is a leading cause of death all around the world has naturally sparked major efforts in the pursuit of novel and more efficient biomarkers that could better serve as diagnostic tools, prognostic predictors, or therapeutical targets in the battle against this type of disease. Mass spectrometry-based proteomics has proven itself as a robust and logical alternative to the immuno-based methods that once dominated the field. Nevertheless, intrinsic limitations of classic proteomic approaches such as the natural gap between shotgun discovery-based methods and clinically applicable results have called for the implementation of more direct, hypothesis-based studies such as those made available through targeted approaches, that might be able to streamline biomarker discovery and validation as a means to increase survivability of affected patients. In fact, the paradigm shifting potential of modern targeted proteomics applied to cancer research can be demonstrated by the large number of advancements and increasing examples of new and more useful biomarkers found during the course of this review in different aspects of cancer research. Out of the many studies dedicated to cancer biomarker discovery, we were able to devise some clear trends, such as the fact that breast cancer is the most common type of tumor studied and that most of the research for any given type of cancer is focused on the discovery diagnostic biomarkers, with the exception of those that rely on samples other than plasma and serum, which are generally aimed toward prognostic markers. Interestingly, the most common type of targeted approach is based on stable isotope dilution-selected reaction monitoring protocols for quantification of the target molecules. Overall, this reinforces that notion that targeted proteomics has already started to fulfill its role as a groundbreaking strategy that may enable researchers to catapult the number of viable, effective, and validated biomarkers in cancer clinical practice.
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Affiliation(s)
- Sara S Faria
- Mastology Program, Federal University of Uberlandia (UFU) , Uberlandia , Brazil
| | - Carlos F M Morris
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Adriano R Silva
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Micaella P Fonseca
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasília, Brazil; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patrice Forget
- Department of Anesthesiology and Perioperative Medicine, Universitair Ziekenhuis Brussel, Vrije Universiteit of Brussel , Brussels , Belgium
| | - Mariana S Castro
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
| | - Wagner Fontes
- Laboratory of Biochemistry and Protein Chemistry, Department of Cell Biology, Institute of Biology, University of Brasilia , Brasília , Brazil
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von Stechow L, Olsen JV. Proteomics insights into DNA damage response and translating this knowledge to clinical strategies. Proteomics 2017; 17:1600018. [PMID: 27682984 PMCID: PMC5333460 DOI: 10.1002/pmic.201600018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 09/07/2016] [Accepted: 09/26/2016] [Indexed: 12/31/2022]
Abstract
Genomic instability is a critical driver in the process of cancer formation. At the same time, inducing DNA damage by irradiation or genotoxic compounds constitutes a key therapeutic strategy to kill fast-dividing cancer cells. Sensing of DNA lesions initiates a complex set of signalling pathways, collectively known as the DNA damage response (DDR). Deciphering DDR signalling pathways with high-throughput technologies could provide insights into oncogenic transformation, metastasis formation and therapy responses, and could build a basis for better therapeutic interventions in cancer treatment. Mass spectrometry (MS)-based proteomics emerged as a method of choice for global studies of proteins and their posttranslational modifications (PTMs). MS-based studies of the DDR have aided in delineating DNA damage-induced signalling responses. Those studies identified changes in abundance, interactions and modification of proteins in the context of genotoxic stress. Here we review ground-breaking MS-based proteomics studies, which analysed changes in protein abundance, protein-protein and protein-DNA interactions, phosphorylation, acetylation, ubiquitylation, SUMOylation and Poly(ADP-ribose)ylation (PARylation) in the DDR. Finally, we provide an outlook on how proteomics studies of the DDR could aid clinical developments on multiple levels.
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Affiliation(s)
- Louise von Stechow
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
| | - Jesper V. Olsen
- Proteomics ProgramNovo Nordisk Foundation Center for Protein ResearchFaculty of Health and Medical SciencesUniversity of CopenhagenCopenhagenDenmark
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38
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Adachi J, Narumi R, Tomonaga T. Targeted Phosphoproteome Analysis Using Selected/Multiple Reaction Monitoring (SRM/MRM). Methods Mol Biol 2016; 1394:87-100. [PMID: 26700043 DOI: 10.1007/978-1-4939-3341-9_7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Mass spectrometry-based phosphoproteomics has been rapidly spread based on the advancement of mass spectrometry and development of efficient enrichment techniques for phosphorylated proteins or peptides. Non-targeted approach has been employed in most of the studies for phosphoproteome analysis. However, targeted approach using selected/multiple reaction monitoring (SRM/MRM) is an indispensible technique used for the quantitation of known targets especially when we have many samples to quantitate phosphorylation events on proteins in biological or clinical samples. We herein describe the application of a large-scale phosphoproteome analysis and SRM-based quantitation for the systematic discovery and validation of biomarkers.
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Affiliation(s)
- Jun Adachi
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, 7-6-8 Saitoasagi Ibaraki-shi, Osaka, 567-0085, Japan
| | - Ryohei Narumi
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Kobe, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, 7-6-8 Saitoasagi Ibaraki-shi, Osaka, 567-0085, Japan.
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39
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Casein kinase 1 is recruited to nuclear speckles by FAM83H and SON. Sci Rep 2016; 6:34472. [PMID: 27681590 PMCID: PMC5041083 DOI: 10.1038/srep34472] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/14/2016] [Indexed: 11/29/2022] Open
Abstract
In some fibroblasts, casein kinase 1α (CK1α) is localized to nuclear speckles, which are sub-nuclear compartments supplying splicing factors, whereas it is recruited on keratin filaments in colorectal cancer cells such as DLD1 cells. In order to obtain a deeper understanding of why CK1α is localized to these different subcellular sites, we herein elucidated the mechanisms underlying its localization to nuclear speckles. CK1α and FAM83H were localized to nuclear speckles in RKO and WiDr colorectal cancer cells, which do not express simple epithelial keratins, and in DLD1 cells transfected with siRNAs for type I keratins. The localization of FAM83H to nuclear speckles was also detected in colorectal cancer cells with a poorly organized keratin cytoskeleton in colorectal cancer tissues. Using an interactome analysis of FAM83H, we identified SON, a protein present in nuclear speckles, as a scaffold protein to which FAM83H recruits CK1α. This result was supported by the knockdown of FAM83H or SON delocalizing CK1α from nuclear speckles. We also found that CK1δ and ε are localized to nuclear speckles in a FAM83H-dependent manner. These results suggest that CK1 is recruited to nuclear speckles by FAM83H and SON in the absence of an intact keratin cytoskeleton.
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40
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Adachi J, Hashiguchi K, Nagano M, Sato M, Sato A, Fukamizu K, Ishihama Y, Tomonaga T. Improved Proteome and Phosphoproteome Analysis on a Cation Exchanger by a Combined Acid and Salt Gradient. Anal Chem 2016; 88:7899-903. [DOI: 10.1021/acs.analchem.6b01232] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jun Adachi
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Kazunari Hashiguchi
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Maiko Nagano
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Misako Sato
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Ayako Sato
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Kazuna Fukamizu
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Yasushi Ishihama
- Graduate
School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Takeshi Tomonaga
- Laboratory
of Proteome Research, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
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41
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von Stechow L, Francavilla C, Olsen JV. Recent findings and technological advances in phosphoproteomics for cells and tissues. Expert Rev Proteomics 2016; 12:469-87. [PMID: 26400465 PMCID: PMC4819829 DOI: 10.1586/14789450.2015.1078730] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Site-specific phosphorylation is a fast and reversible covalent post-translational modification that is tightly regulated in cells. The cellular machinery of enzymes that write, erase and read these modifications (kinases, phosphatases and phospho-binding proteins) is frequently deregulated in different diseases, including cancer. Large-scale studies of phosphoproteins – termed phosphoproteomics – strongly rely on the use of high-performance mass spectrometric instrumentation. This powerful technology has been applied to study a great number of phosphorylation-based phenotypes. Nevertheless, many technical and biological challenges have to be overcome to identify biologically relevant phosphorylation sites in cells and tissues. This review describes different technological strategies to identify and quantify phosphorylation sites with high accuracy, without significant loss of analysis speed and reproducibility in tissues and cells. Moreover, computational tools for analysis, integration and biological interpretation of phosphorylation events are discussed.
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Affiliation(s)
- Louise von Stechow
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | - Chiara Francavilla
- a Proteomics Program, The Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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42
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FAM83H and casein kinase I regulate the organization of the keratin cytoskeleton and formation of desmosomes. Sci Rep 2016; 6:26557. [PMID: 27222304 PMCID: PMC4879633 DOI: 10.1038/srep26557] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 05/05/2016] [Indexed: 12/23/2022] Open
Abstract
FAM83H is essential for the formation of dental enamel because a mutation in the FAM83H gene causes amelogenesis imperfecta (AI). We previously reported that the overexpression of FAM83H often occurs and disorganizes the keratin cytoskeleton in colorectal cancer cells. We herein show that FAM83H regulates the organization of the keratin cytoskeleton and maintains the formation of desmosomes in ameloblastoma cells. FAM83H is expressed and localized on keratin filaments in human ameloblastoma cell lines and in mouse ameloblasts and epidermal germinative cells in vivo. FAM83H shows preferential localization to keratin filaments around the nucleus that often extend to cell-cell junctions. Alterations in the function of FAM83H by its overexpression, knockdown, or an AI-causing truncated mutant prevent the proper organization of the keratin cytoskeleton in ameloblastoma cells. Furthermore, the AI-causing mutant prevents desmosomal proteins from being localized to cell-cell junctions. The effects of the AI-causing mutant depend on its binding to and possible inhibition of casein kinase I (CK-1). The suppression of CK-1 by its inhibitor, D4476, disorganizes the keratin cytoskeleton. Our results suggest that AI caused by the FAM83H mutation is mediated by the disorganization of the keratin cytoskeleton and subsequent disruption of desmosomes in ameloblasts.
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43
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Mass Spectrometric-Based Selected Reaction Monitoring of Protein Phosphorylation during Symbiotic Signaling in the Model Legume, Medicago truncatula. PLoS One 2016; 11:e0155460. [PMID: 27203723 PMCID: PMC4874550 DOI: 10.1371/journal.pone.0155460] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Accepted: 04/29/2016] [Indexed: 11/19/2022] Open
Abstract
Unlike the major cereal crops corn, rice, and wheat, leguminous plants such as soybean and alfalfa can meet their nitrogen requirement via endosymbiotic associations with soil bacteria. The establishment of this symbiosis is a complex process playing out over several weeks and is facilitated by the exchange of chemical signals between these partners from different kingdoms. Several plant components that are involved in this signaling pathway have been identified, but there is still a great deal of uncertainty regarding the early events in symbiotic signaling, i.e., within the first minutes and hours after the rhizobial signals (Nod factors) are perceived at the plant plasma membrane. The presence of several protein kinases in this pathway suggests a mechanism of signal transduction via posttranslational modification of proteins in which phosphate is added to the hydroxyl groups of serine, threonine and tyrosine amino acid side chains. To monitor the phosphorylation dynamics and complement our previous untargeted 'discovery' approach, we report here the results of experiments using a targeted mass spectrometric technique, Selected Reaction Monitoring (SRM) that enables the quantification of phosphorylation targets with great sensitivity and precision. Using this approach, we confirm a rapid change in the level of phosphorylation in 4 phosphosites of at least 4 plant phosphoproteins that have not been previously characterized. This detailed analysis reveals aspects of the symbiotic signaling mechanism in legumes that, in the long term, will inform efforts to engineer this nitrogen-fixing symbiosis in important non-legume crops such as rice, wheat and corn.
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44
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Maes E, Tirez K, Baggerman G, Valkenborg D, Schoofs L, Encinar JR, Mertens I. The use of elemental mass spectrometry in phosphoproteomic applications. MASS SPECTROMETRY REVIEWS 2016; 35:350-360. [PMID: 25139451 DOI: 10.1002/mas.21440] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 05/14/2014] [Accepted: 05/14/2014] [Indexed: 06/03/2023]
Abstract
Reversible phosphorylation is one of the most important post-translational modifications in mammalian cells. Because this molecular switch is an important mechanism that diversifies and regulates proteins in cellular processes, knowledge about the extent and quantity of phosphorylation is very important to understand the complex cellular interplay. Although phosphoproteomics strategies are applied worldwide, they mainly include only molecular mass spectrometry (like MALDI or ESI)-based experiments. Although identification and relative quantification of phosphopeptides is straightforward with these techniques, absolute quantification is more complex and usually requires for specific isotopically phosphopeptide standards. However, the use of elemental mass spectrometry, and in particular inductively coupled plasma mass spectrometry (ICP-MS), in phosphoproteomics-based experiments, allow one to absolutely quantify phosphopeptides. Here, these phosphoproteomic applications with ICP-MS as elemental detector are reviewed. Pioneering work and recent developments in the field are both described. Additionally, the advantage of the parallel use of molecular and elemental mass spectrometry is stressed.
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Affiliation(s)
- Evelyne Maes
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Kristof Tirez
- Flemish Institute for Technological Research (VITO), Mol, Belgium
| | - Geert Baggerman
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
| | - Dirk Valkenborg
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
- Interuniversity Institute for Biostatistics and Statistical Bioinformatics, Hasselt University, Diepenbeek, Belgium
| | - Liliane Schoofs
- KU Leuven, Research Group of Functional Genomics and Proteomics, Leuven, Belgium
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Inge Mertens
- Flemish Institute for Technological Research (VITO), Mol, Belgium
- CFP-CeProMa, University of Antwerp, Antwerp, Belgium
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Quantitative proteomics and phosphoproteomics on serial tumor biopsies from a sorafenib-treated HCC patient. Proc Natl Acad Sci U S A 2016; 113:1381-6. [PMID: 26787912 DOI: 10.1073/pnas.1523434113] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Compensatory signaling pathways in tumors confer resistance to targeted therapy, but the pathways and their mechanisms of activation remain largely unknown. We describe a procedure for quantitative proteomics and phosphoproteomics on snap-frozen biopsies of hepatocellular carcinoma (HCC) and matched nontumor liver tissue. We applied this procedure to monitor signaling pathways in serial biopsies taken from an HCC patient before and during treatment with the multikinase inhibitor sorafenib. At diagnosis, the patient had an advanced HCC. At the time of the second biopsy, abdominal imaging revealed progressive disease despite sorafenib treatment. Sorafenib was confirmed to inhibit MAPK signaling in the tumor, as measured by reduced ribosomal protein S6 kinase phosphorylation. Hierarchical clustering and enrichment analysis revealed pathways broadly implicated in tumor progression and resistance, such as epithelial-to-mesenchymal transition and cell adhesion pathways. Thus, we describe a protocol for quantitative analysis of oncogenic pathways in HCC biopsies and obtained first insights into the effect of sorafenib in vivo. This protocol will allow elucidation of mechanisms of resistance and enable precision medicine.
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46
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Affiliation(s)
- Nicholas M. Riley
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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47
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Zhang H, Zhu NX, Huang K, Cai BZ, Zeng Y, Xu YM, Liu Y, Yuan YP, Lin CM. iTRAQ-Based Quantitative Proteomic Comparison of Early- and Late-Passage Human Dermal Papilla Cell Secretome in Relation to Inducing Hair Follicle Regeneration. PLoS One 2016; 11:e0167474. [PMID: 27907131 PMCID: PMC5132394 DOI: 10.1371/journal.pone.0167474] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 11/15/2016] [Indexed: 02/05/2023] Open
Abstract
Alopecia is an exceedingly prevalent problem that lacks effective therapy. Recently, research has focused on early-passage dermal papilla cells (DPCs), which have hair inducing activity both in vivo and in vitro. Our previous study indicated that factors secreted from early-passage DPCs contribute to hair follicle (HF) regeneration. To identify which factors are responsible for HF regeneration and why late-passage DPCs lose this potential, we collected 48-h-culture medium (CM) from both of passage 3 and 9 DPCs, and subcutaneously injected the DPC-CM into NU/NU mice. Passage 3 DPC-CM induced HF regeneration, based on the emergence of a white hair coat, but passage 9 DPC-CM did not. In order to identify the key factors responsible for hair induction, CM from passage 3 and 9 DPCs was analyzed by iTRAQ-based quantitative proteomic technology. We identified 1360 proteins, of which 213 proteins were differentially expressed between CM from early-passage vs. late-passage DPCs, including SDF1, MMP3, biglycan and LTBP1. Further analysis indicated that the differentially-expressed proteins regulated the Wnt, TGF-β and BMP signaling pathways, which directly and indirectly participate in HF morphogenesis and regeneration. Subsequently, we selected 19 proteins for further verification by multiple reaction monitoring (MRM) between the two types of CM. These results indicate DPC-secreted proteins play important roles in HF regeneration, with SDF1, MMP3, biglycan, and LTBP1 being potential key inductive factors secreted by dermal papilla cells in the regeneration of hair follicles.
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Affiliation(s)
- Huan Zhang
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong, China
| | - Ning-Xia Zhu
- Department of Cardiology, First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Keng Huang
- Emergency Department, Second Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Bo-Zhi Cai
- Tissue Engineering Laboratory, First Affiliated Hospital, Shantou University Medical College, Shantou, Guangdong, China
| | - Yang Zeng
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong, China
| | - Yan-Ming Xu
- Laboratory of Cancer Biology and Epigenetics, Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong, China
| | - Yang Liu
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong, China
| | - Yan-Ping Yuan
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong, China
| | - Chang-Min Lin
- Department of Histology and Embryology, Shantou University Medical College, Shantou, Guangdong, China
- * E-mail:
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48
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Narumi R, Tomonaga T. Quantitative Analysis of Tissue Samples by Combining iTRAQ Isobaric Labeling with Selected/Multiple Reaction Monitoring (SRM/MRM). Methods Mol Biol 2016; 1355:85-101. [PMID: 26584920 DOI: 10.1007/978-1-4939-3049-4_6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Mass spectrometry-based phosphoproteomics is an indispensible technique used in the discovery and quantification of phosphorylation events on proteins in biological samples. The application of this technique to tissue samples is especially useful for the discovery of biomarkers as well as biological studies. We herein describe the application of a large-scale phosphoproteome analysis and SRM/MRM-based quantitation to develop a strategy for the systematic discovery and validation of biomarkers using tissue samples.
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Affiliation(s)
- Ryohei Narumi
- Laboratory for Synthetic Biology, RIKEN Quantitative Biology Center, Osaka, Japan.,Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan
| | - Takeshi Tomonaga
- Laboratory of Proteome Research, National Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
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49
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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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Kennedy JJ, Yan P, Zhao L, Ivey RG, Voytovich UJ, Moore HD, Lin C, Pogosova-Agadjanyan EL, Stirewalt DL, Reding KW, Whiteaker JR, Paulovich AG. Immobilized Metal Affinity Chromatography Coupled to Multiple Reaction Monitoring Enables Reproducible Quantification of Phospho-signaling. Mol Cell Proteomics 2015; 15:726-39. [PMID: 26621847 DOI: 10.1074/mcp.o115.054940] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Indexed: 12/23/2022] Open
Abstract
A major goal in cell signaling research is the quantification of phosphorylation pharmacodynamics following perturbations. Traditional methods of studying cellular phospho-signaling measure one analyte at a time with poor standardization, rendering them inadequate for interrogating network biology and contributing to the irreproducibility of preclinical research. In this study, we test the feasibility of circumventing these issues by coupling immobilized metal affinity chromatography (IMAC)-based enrichment of phosphopeptides with targeted, multiple reaction monitoring (MRM) mass spectrometry to achieve precise, specific, standardized, multiplex quantification of phospho-signaling responses. A multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay targeting phospho-analytes responsive to DNA damage was configured, analytically characterized, and deployed to generate phospho-pharmacodynamic curves from primary and immortalized human cells experiencing genotoxic stress. The multiplexed assays demonstrated linear ranges of ≥3 orders of magnitude, median lower limit of quantification of 0.64 fmol on column, median intra-assay variability of 9.3%, median inter-assay variability of 12.7%, and median total CV of 16.0%. The multiplex immobilized metal affinity chromatography- multiple reaction monitoring assay enabled robust quantification of 107 DNA damage-responsive phosphosites from human cells following DNA damage. The assays have been made publicly available as a resource to the community. The approach is generally applicable, enabling wide interrogation of signaling networks.
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Affiliation(s)
- Jacob J Kennedy
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Ping Yan
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Lei Zhao
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Richard G Ivey
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Uliana J Voytovich
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Heather D Moore
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Chenwei Lin
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | | | - Derek L Stirewalt
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Kerryn W Reding
- §University of Washington, 1959 NE Pacific St., Seattle, Washington 98195
| | - Jeffrey R Whiteaker
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109
| | - Amanda G Paulovich
- From the ‡ Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, Washington 98109;
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