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Humphries EM, Loudon C, Craft GE, Hains PG, Robinson PJ. Quantitative Comparison of Deparaffinization, Rehydration, and Extraction Methods for FFPE Tissue Proteomics and Phosphoproteomics. Anal Chem 2024; 96:13358-13370. [PMID: 39102789 DOI: 10.1021/acs.analchem.3c04479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/07/2024]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are suitable for proteomic and phosphoproteomic biomarker studies by data-independent acquisition mass spectrometry. The choice of the sample preparation method influences the number, intensity, and reproducibility of identifications. By comparing four deparaffinization and rehydration methods, including heptane, histolene, SubX, and xylene, we found that heptane and methanol produced the lowest coefficients of variation (CVs). Using this, five extraction methods from the literature were modified and evaluated for their performance using kidney, leg muscle, lung, and testicular rat organs. All methods performed well, except for SP3 due to insufficient tissue lysis. Heat n' Beat was the fastest and most reproducible method with the highest digestion efficiency and lowest CVs. S-Trap produced the highest peptide yield, while TFE produced the best phosphopeptide enrichment efficiency. The quantitation of FFPE-derived peptides remains an ongoing challenge with bias in UV and fluorescence assays across methods, most notably in SPEED. Functional enrichment analysis demonstrated that each method favored extracting some gene ontology cellular components over others including chromosome, cytoplasmic, cytoskeleton, endoplasmic reticulum, membrane, mitochondrion, and nucleoplasm protein groups. The outcome is a set of recommendations for choosing the most appropriate method for different settings.
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Affiliation(s)
- Erin M Humphries
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Clare Loudon
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - George E Craft
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Peter G Hains
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
| | - Phillip J Robinson
- ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales 2145, Australia
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2
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Pandey D, Ghosh D. Proteomics-based host-specific biomarkers for tuberculosis: The future of TB diagnosis. J Proteomics 2024; 305:105245. [PMID: 38942234 DOI: 10.1016/j.jprot.2024.105245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/23/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Tuberculosis (TB) is an infectious disease that remains one of the major global public health concerns. Early detection of Active Pulmonary TB is therefore of utmost importance for controlling lethality and disease spreading. Currently available TB diagnostics can be broadly categorized into microscopy, culture-based, and molecular approaches, all of which come with compromised sensitivity, limited efficacy, and high expenses. Hence, rapid, sensitive, and affordable diagnostic methods for TB is the current prerequisite for disease management. This review summarizes the proteomics investigations for host-specific biomarkers from serum, sputum, saliva, and urine samples of TB patients, along with patients having comorbidity. Thorough data mining from available literature led us to conclude that the host-specific proteins involved in immunity and defense, metabolic regulation, cellular adhesion, and motility, inflammatory responses, and tissue remodelling have shown significant deregulation upon Mycobacterium tuberculosis (Mtb) infection. Notably, the immunoregulatory protein orosomucoid (ORM) was up-regulated in active TB compared to non-TB individuals, as observed in multiple studies from diverse sample types. Mannose receptor C type 2 (MRC2) was identified as an upregulated, treatment response biomarker in two independent serum proteomics investigations. Thorough mechanistic investigation on these candidate proteins would be fascinating to dig into potential drug targets and customized therapeutics for TB patients, along with their diagnostic potentials.
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Affiliation(s)
- Divya Pandey
- Department of Pharmaceutical Sciences, School of Health Sciences and Technology, UPES, Dehradun 248007, Uttarakhand, India
| | - Dipanjana Ghosh
- School of Biomolecular Engineering & Biotechnology, Rajiv Gandhi Technological University, Airport Bypass Road, Bhopal 462033, India.
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3
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Song C, Wang G, Liu M, Han S, Dong M, Peng M, Wang W, Wang Y, Xu Y, Liu L. Deciphering the SOX4/MAPK1 regulatory axis: a phosphoproteomic insight into IQGAP1 phosphorylation and pancreatic Cancer progression. J Transl Med 2024; 22:602. [PMID: 38943117 PMCID: PMC11212360 DOI: 10.1186/s12967-024-05377-3] [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: 01/14/2024] [Accepted: 06/06/2024] [Indexed: 07/01/2024] Open
Abstract
OBJECTIVE This study aims to elucidate the functional role of IQGAP1 phosphorylation modification mediated by the SOX4/MAPK1 regulatory axis in developing pancreatic cancer through phosphoproteomics analysis. METHODS Proteomics and phosphoproteomics data of pancreatic cancer were obtained from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) database. Differential analysis, kinase-substrate enrichment analysis (KSEA), and independent prognosis analysis were performed on these datasets. Subtype analysis of pancreatic cancer patients was conducted based on the expression of prognostic-related proteins, and the prognosis of different subtypes was evaluated through prognosis analysis. Differential analysis of proteins in different subtypes was performed to identify differential proteins in the high-risk subtype. Clinical correlation analysis was conducted based on the expression of prognostic-related proteins, pancreatic cancer typing results, and clinical characteristics in the pancreatic cancer proteomics dataset. Functional pathway enrichment analysis was performed using GSEA/GO/KEGG, and most module proteins correlated with pancreatic cancer were selected using WGCNA analysis. In cell experiments, pancreatic cancer cells were grouped, and the expression levels of SOX4, MAPK1, and the phosphorylation level of IQGAP1 were detected by RT-qPCR and Western blot experiments. The effect of SOX4 on MAPK1 promoter transcriptional activity was assessed using a dual-luciferase assay, and the enrichment of SOX4 on the MAPK1 promoter was examined using a ChIP assay. The proliferation, migration, and invasion functions of grouped pancreatic cancer cells were assessed using CCK-8, colony formation, and Transwell assays. In animal experiments, the impact of SOX4 on tumor growth and metastasis through the regulation of MAPK1-IQGAP1 phosphorylation modification was studied by constructing subcutaneous and orthotopic pancreatic cancer xenograft models, as well as a liver metastasis model in nude mice. RESULTS Phosphoproteomics and proteomics data analysis revealed that the kinase MAPK1 may play an important role in pancreatic cancer progression by promoting IQGAP1 phosphorylation modification. Proteomics analysis classified pancreatic cancer patients into two subtypes, C1 and C2, where the high-risk C2 subtype was associated with poor prognosis, malignant tumor typing, and enriched tumor-related pathways. SOX4 may promote the occurrence of the high-risk C2 subtype of pancreatic cancer by regulating MAPK1-IQGAP1 phosphorylation modification. In vitro cell experiments confirmed that SOX4 promoted IQGAP1 phosphorylation modification by activating MAPK1 transcription while silencing SOX4 inhibited the proliferation, migration, and invasion of pancreatic cancer cells by reducing the phosphorylation level of MAPK1-IQGAP1. In vivo, animal experiments further confirmed that silencing SOX4 suppressed the growth and metastasis of pancreatic cancer by reducing the phosphorylation level of MAPK1-IQGAP1. CONCLUSION The findings of this study suggest that SOX4 promotes the phosphorylation modification of IQGAP1 by activating MAPK1 transcription, thereby facilitating the growth and metastasis of pancreatic cancer.
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Affiliation(s)
- Chao Song
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China
- Department of General Surgery, Qingpu Branch, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, No. 1158 Park Road East, Qingpu District, Shanghai, PR China
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, PR China
| | - Ganggang Wang
- Department of Hepatobiliary Surgery, Pudong Hospital, Fudan University, Shanghai, China
| | - Mengmeng Liu
- Department of Gastroenterology, Qingpu Branch, Affiliated Zhongshan Hospital of Fudan University, Shanghai, PR China
| | - Siyang Han
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China
| | - Meiyuan Dong
- Department of Endocrinology, Shanghai Pudong Hospital, Fudan University, Shanghai, PR China
| | - Maozhen Peng
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China
| | - Wenquan Wang
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China
| | - Yicun Wang
- Department of General Surgery, Qingpu Branch, Affiliated Zhongshan Hospital of Fudan University, Qingpu Branch, No. 1158 Park Road East, Qingpu District, Shanghai, PR China.
| | - Yaolin Xu
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China.
| | - Liang Liu
- Department of Pancreatic Surgery, Affiliated Zhongshan Hospital, Fudan University, No.180 Fenglin Road, Xuhui District, Shanghai, PR China.
- Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, PR China.
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4
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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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5
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Yaron-Barir TM, Joughin BA, Huntsman EM, Kerelsky A, Cizin DM, Cohen BM, Regev A, Song J, Vasan N, Lin TY, Orozco JM, Schoenherr C, Sagum C, Bedford MT, Wynn RM, Tso SC, Chuang DT, Li L, Li SSC, Creixell P, Krismer K, Takegami M, Lee H, Zhang B, Lu J, Cossentino I, Landry SD, Uduman M, Blenis J, Elemento O, Frame MC, Hornbeck PV, Cantley LC, Turk BE, Yaffe MB, Johnson JL. The intrinsic substrate specificity of the human tyrosine kinome. Nature 2024; 629:1174-1181. [PMID: 38720073 PMCID: PMC11136658 DOI: 10.1038/s41586-024-07407-y] [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: 08/24/2023] [Accepted: 04/10/2024] [Indexed: 05/31/2024]
Abstract
Phosphorylation of proteins on tyrosine (Tyr) residues evolved in metazoan organisms as a mechanism of coordinating tissue growth1. Multicellular eukaryotes typically have more than 50 distinct protein Tyr kinases that catalyse the phosphorylation of thousands of Tyr residues throughout the proteome1-3. How a given Tyr kinase can phosphorylate a specific subset of proteins at unique Tyr sites is only partially understood4-7. Here we used combinatorial peptide arrays to profile the substrate sequence specificity of all human Tyr kinases. Globally, the Tyr kinases demonstrate considerable diversity in optimal patterns of residues surrounding the site of phosphorylation, revealing the functional organization of the human Tyr kinome by substrate motif preference. Using this information, Tyr kinases that are most compatible with phosphorylating any Tyr site can be identified. Analysis of mass spectrometry phosphoproteomic datasets using this compendium of kinase specificities accurately identifies specific Tyr kinases that are dysregulated in cells after stimulation with growth factors, treatment with anti-cancer drugs or expression of oncogenic variants. Furthermore, the topology of known Tyr signalling networks naturally emerged from a comparison of the sequence specificities of the Tyr kinases and the SH2 phosphotyrosine (pTyr)-binding domains. Finally we show that the intrinsic substrate specificity of Tyr kinases has remained fundamentally unchanged from worms to humans, suggesting that the fidelity between Tyr kinases and their protein substrate sequences has been maintained across hundreds of millions of years of evolution.
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Affiliation(s)
- Tomer M Yaron-Barir
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Brian A Joughin
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander Kerelsky
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Daniel M Cizin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Benjamin M Cohen
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Amit Regev
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Junho Song
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Neil Vasan
- Department of Medicine, Division of Hematology/Oncology, Columbia University Irving Medical Center, New York, NY, USA
| | - Ting-Yu Lin
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Discovery Technologies, Calico Life Sciences, South San Francisco, CA, USA
| | - Jose M Orozco
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Christina Schoenherr
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Cari Sagum
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - R Max Wynn
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Shih-Chia Tso
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David T Chuang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lei Li
- School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, China
| | - Shawn S-C Li
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Pau Creixell
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Cancer Research UK Cambridge Institute, University of Cambridge Li Ka Shing Centre, Cambridge, UK
| | - Konstantin Krismer
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Mina Takegami
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Harin Lee
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Bin Zhang
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Jingyi Lu
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Ian Cossentino
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Sean D Landry
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Mohamed Uduman
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - John Blenis
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
- Department of Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Margaret C Frame
- Cancer Research United Kingdom Scotland Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Peter V Hornbeck
- Department Of Bioinformatics, Cell Signaling Technology, Danvers, MA, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Michael B Yaffe
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Division of Acute Care Surgery, Trauma, and Surgical Critical Care, and Division of Surgical Oncology, Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA.
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
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6
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Tong M, Liu Z, Li J, Wei X, Shi W, Liang C, Yu C, Huang R, Lin Y, Wang X, Wang S, Wang Y, Huang J, Wang Y, Li T, Qin J, Zhan D, Ji ZL. PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics. Comput Biol Med 2024; 174:108391. [PMID: 38613887 DOI: 10.1016/j.compbiomed.2024.108391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Liquid chromatography-mass spectrometry (LC-MS)-based quantitative phosphoproteomics has been widely used to detect thousands of protein phosphorylation modifications simultaneously from the biological specimens. However, the complicated procedures for analyzing phosphoproteomics data has become a bottleneck to widening its application. METHODS Here, we develop PhosMap, a versatile and scalable tool to accomplish phosphoproteomics data analysis. A standardized phosphorylation data format was created for data analyses, from data preprocessing to downstream bioinformatic analyses such as dimension reduction, differential phosphorylation analysis, kinase activity, survival analysis, and so on. For better usability, we distribute PhosMap as a Docker image for easy local deployment upon any of Windows, Linux, and Mac system. RESULTS The source code is deposited at https://github.com/BADD-XMU/PhosMap. A free PhosMap webserver (https://huggingface.co/spaces/Bio-Add/PhosMap), with easy-to-follow fashion of dashboards, is curated for interactive data analysis. CONCLUSIONS PhosMap fills the technical gap of large-scale phosphorylation research by empowering researchers to process their own phosphoproteomics data expediently and efficiently, and facilitates better data interpretation.
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Affiliation(s)
- Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiaao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xin Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wenhao Shi
- Analysis Center, Chemistry Department, Tsinghua University, Beijing, 100084, China
| | - Chenyu Liang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chunyu Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Rongting Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xinkang Wang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shun Wang
- Departments of Pathology, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi Wang
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yini Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Jun Qin
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dongdong Zhan
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China.
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
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7
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Stewart R, Sharma S, Wu T, Okuda S, Xie G, Zhou XZ, Shilton B, Lu KP. The role of the master cancer regulator Pin1 in the development and treatment of cancer. Front Cell Dev Biol 2024; 12:1343938. [PMID: 38745861 PMCID: PMC11091292 DOI: 10.3389/fcell.2024.1343938] [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: 11/24/2023] [Accepted: 03/28/2024] [Indexed: 05/16/2024] Open
Abstract
This review examines the complex role of Pin1 in the development and treatment of cancer. Pin1 is the only peptidyl-prolyl isomerase (PPIase) that can recognize and isomerize phosphorylated Ser/Thr-Pro peptide bonds. Pin1 catalyzes a structural change in phosphorylated Ser/Thr-Pro motifs that can modulate protein function and thereby impact cell cycle regulation and tumorigenesis. The molecular mechanisms by which Pin1 contributes to oncogenesis are reviewed, including Pin1 overexpression and its correlation with poor cancer prognosis, and the contribution of Pin1 to aggressive tumor phenotypes involved in therapeutic resistance is discussed, with an emphasis on cancer stem cells, the epithelial-to-mesenchymal transition (EMT), and immunosuppression. The therapeutic potential of Pin1 inhibition in cancer is discussed, along with the promise and the difficulties in identifying potent, drug-like, small-molecule Pin1 inhibitors. The available evidence supports the efficacy of targeting Pin1 as a novel cancer therapeutic by analyzing the role of Pin1 in a complex network of cancer-driving pathways and illustrating the potential of synergistic drug combinations with Pin1 inhibitors for treating aggressive and drug-resistant tumors.
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Affiliation(s)
- Robert Stewart
- Department of Biochemistry, Western University, London, ON, Canada
| | - Shaunik Sharma
- Department of Biochemistry, Western University, London, ON, Canada
| | - Timothy Wu
- Department of Biochemistry, Western University, London, ON, Canada
| | - Sho Okuda
- Department of Biochemistry, Western University, London, ON, Canada
| | - George Xie
- Department of Biochemistry, Western University, London, ON, Canada
| | - Xiao Zhen Zhou
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
| | - Brian Shilton
- Department of Biochemistry, Western University, London, ON, Canada
| | - Kun Ping Lu
- Department of Biochemistry, Western University, London, ON, Canada
- Robarts Research Institute, Western University, London, ON, Canada
- Lawson Health Research Institute, Schulich School of Medicine and Dentistry, Western University, London, ON, Canada
- Department of Oncology, Western University, London, ON, Canada
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8
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Jiménez C, Garrote-de-Barros A, López-Portugués C, Hernández-Sánchez M, Díez P. Characterization of Human B Cell Hematological Malignancies Using Protein-Based Approaches. Int J Mol Sci 2024; 25:4644. [PMID: 38731863 PMCID: PMC11083628 DOI: 10.3390/ijms25094644] [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: 03/19/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
The maturation of B cells is a complex, multi-step process. During B cell differentiation, errors can occur, leading to the emergence of aberrant versions of B cells that, finally, constitute a malignant tumor. These B cell malignancies are classified into three main groups: leukemias, myelomas, and lymphomas, the latter being the most heterogeneous type. Since their discovery, multiple biological studies have been performed to characterize these diseases, aiming to define their specific features and determine potential biomarkers for diagnosis, stratification, and prognosis. The rise of advanced -omics approaches has significantly contributed to this end. Notably, proteomics strategies appear as promising tools to comprehensively profile the final molecular effector of these cells. In this narrative review, we first introduce the main B cell malignancies together with the most relevant proteomics approaches. Then, we describe the core studies conducted in the field and their main findings and, finally, we evaluate the advantages and drawbacks of flow cytometry, mass cytometry, and mass spectrometry for the profiling of human B cell disorders.
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Affiliation(s)
- Cristina Jiménez
- Hematology Department, University Hospital of Salamanca (HUS/IBSAL), CIBERONC and Cancer Research Institute of Salamanca-IBMCC (USAL-CSIC), 37007 Salamanca, Spain;
| | - Alba Garrote-de-Barros
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Carlos López-Portugués
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, 28040 Madrid, Spain; (A.G.-d.-B.); (M.H.-S.)
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, 28029 Madrid, Spain
| | - Paula Díez
- Department of Physical and Analytical Chemistry Chemistry, Faculty of Chemistry, University of Oviedo, 33006 Oviedo, Spain;
- Health Research Institute of the Principality of Asturias (ISPA), 33011 Oviedo, Spain
- Department of Functional Biology, Faculty of Medicine and Health Science, University of Oviedo, 33006 Oviedo, Spain
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9
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Jiang W, Jaehnig EJ, Liao Y, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B. Illuminating the Dark Cancer Phosphoproteome Through a Machine-Learned Co-Regulation Map of 26,280 Phosphosites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585786. [PMID: 38562798 PMCID: PMC10983930 DOI: 10.1101/2024.03.19.585786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, but limited knowledge about the regulation and function of most phosphosites restricts our ability to extract meaningful biological insights from phosphoproteomics data. To address this, we combine machine learning and phosphoproteomic data from 1,195 tumor specimens spanning 11 cancer types to construct CoPheeMap, a network mapping the co-regulation of 26,280 phosphosites. Integrating network features from CoPheeMap into a machine learning model, CoPheeKSA, we achieve superior performance in predicting kinase-substrate associations. CoPheeKSA reveals 24,015 associations between 9,399 phosphosites and 104 serine/threonine kinases, including many unannotated phosphosites and under-studied kinases. We validate the accuracy of these predictions using experimentally determined kinase-substrate specificities. By applying CoPheeMap and CoPheeKSA to phosphosites with high computationally predicted functional significance and cancer-associated phosphosites, we demonstrate the effectiveness of these tools in systematically illuminating phosphosites of interest, revealing dysregulated signaling processes in human cancer, and identifying under-studied kinases as putative therapeutic targets.
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10
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Rii J, Sakamoto S, Mizokami A, Xu M, Fujimoto A, Saito S, Koike H, Tamura T, Arai T, Yamada Y, Goto Y, Sazuka T, Imamura Y, Suzuki K, Kanai Y, Anzai N, Ichikawa T. L-type amino acid transporter 1 inhibitor JPH203 prevents the growth of cabazitaxel-resistant prostate cancer by inhibiting cyclin-dependent kinase activity. Cancer Sci 2024; 115:937-953. [PMID: 38186218 PMCID: PMC10920979 DOI: 10.1111/cas.16062] [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: 05/25/2023] [Revised: 11/29/2023] [Accepted: 12/13/2023] [Indexed: 01/09/2024] Open
Abstract
L-type amino acid transporter 1 (LAT1, SLC7A5) is an amino acid transporter expressed in various carcinomas, and it is postulated to play an important role in the proliferation of cancer cells through the uptake of essential amino acids. Cabazitaxel is a widely used anticancer drug for treating castration-resistant prostate cancer (CRPC); however, its effectiveness is lost when cancer cells acquire drug resistance. In this study, we investigated the expression of LAT1 and the effects of a LAT1-specific inhibitor, JPH203, in cabazitaxel-resistant prostate cancer cells. LAT1 was more highly expressed in the cabazitaxel-resistant strains than in the normal strains. Administration of JPH203 inhibited the growth, migration, and invasive ability of cabazitaxel-resistant strains in vitro. Phosphoproteomics using liquid chromatography-mass spectrometry to comprehensively investigate changes in phosphorylation due to JPH203 administration revealed that cell cycle-related pathways were affected by JPH203, and that JPH203 significantly reduced the kinase activity of cyclin-dependent kinases 1 and 2. Moreover, JPH203 inhibited the proliferation of cabazitaxel-resistant cells in vivo. Taken together, the present study results suggest that LAT1 might be a valuable therapeutic target in cabazitaxel-resistant prostate cancer.
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Grants
- #20K09555 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20H03813 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20K09572 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
- #20K18087 Grants-in-Aid for Scientific Research of the Ministry of Education, Culture, Sports, Science and Technology of Japan
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Affiliation(s)
- Junryo Rii
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Shinichi Sakamoto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Atsushi Mizokami
- Department of Integrative Cancer Therapy and Urology, Graduate School of Medical ScienceKanazawa UniversityKanazawaJapan
| | - Minhui Xu
- Bio‐System PharmacologyOsaka University Graduate School of MedicineOsakaJapan
| | - Ayumi Fujimoto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Shinpei Saito
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
- Department of PharmacologyChiba University Graduate School of MedicineChibaJapan
| | - Hidekazu Koike
- Department of UrologyGunma University Graduate School of MedicineMaebashiJapan
| | - Takaaki Tamura
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Takayuki Arai
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yasutaka Yamada
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yusuke Goto
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Tomokazu Sazuka
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Yusuke Imamura
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
| | - Kazuhiro Suzuki
- Department of UrologyGunma University Graduate School of MedicineMaebashiJapan
| | - Yoshikatsu Kanai
- Bio‐System PharmacologyOsaka University Graduate School of MedicineOsakaJapan
| | - Naohiko Anzai
- Department of PharmacologyChiba University Graduate School of MedicineChibaJapan
| | - Tomohiko Ichikawa
- Department of UrologyChiba University Graduate School of MedicineChibaJapan
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11
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Chen E, Ling AL, Reardon DA, Chiocca EA. Lessons learned from phase 3 trials of immunotherapy for glioblastoma: Time for longitudinal sampling? Neuro Oncol 2024; 26:211-225. [PMID: 37995317 PMCID: PMC10836778 DOI: 10.1093/neuonc/noad211] [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] [Indexed: 11/25/2023] Open
Abstract
Glioblastoma (GBM)'s median overall survival is almost 21 months. Six phase 3 immunotherapy clinical trials have recently been published, yet 5/6 did not meet approval by regulatory bodies. For the sixth, approval is uncertain. Trial failures result from multiple factors, ranging from intrinsic tumor biology to clinical trial design. Understanding the clinical and basic science of these 6 trials is compelled by other immunotherapies reaching the point of advanced phase 3 clinical trial testing. We need to understand more of the science in human GBMs in early trials: the "window of opportunity" design may not be best to understand complex changes brought about by immunotherapeutic perturbations of the GBM microenvironment. The convergence of increased safety of image-guided biopsies with "multi-omics" of small cell numbers now permits longitudinal sampling of tumor and biofluids to dissect the complex temporal changes in the GBM microenvironment as a function of the immunotherapy.
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Affiliation(s)
- Ethan Chen
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alexander L Ling
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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12
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Ivanisevic T, Sewduth RN. Multi-Omics Integration for the Design of Novel Therapies and the Identification of Novel Biomarkers. Proteomes 2023; 11:34. [PMID: 37873876 PMCID: PMC10594525 DOI: 10.3390/proteomes11040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023] Open
Abstract
Multi-omics is a cutting-edge approach that combines data from different biomolecular levels, such as DNA, RNA, proteins, metabolites, and epigenetic marks, to obtain a holistic view of how living systems work and interact. Multi-omics has been used for various purposes in biomedical research, such as identifying new diseases, discovering new drugs, personalizing treatments, and optimizing therapies. This review summarizes the latest progress and challenges of multi-omics for designing new treatments for human diseases, focusing on how to integrate and analyze multiple proteome data and examples of how to use multi-proteomics data to identify new drug targets. We also discussed the future directions and opportunities of multi-omics for developing innovative and effective therapies by deciphering proteome complexity.
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Affiliation(s)
| | - Raj N. Sewduth
- VIB-KU Leuven Center for Cancer Biology (VIB), 3000 Leuven, Belgium;
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13
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Ramalhete L, Vigia E, Araújo R, Marques HP. Proteomics-Driven Biomarkers in Pancreatic Cancer. Proteomes 2023; 11:24. [PMID: 37606420 PMCID: PMC10443269 DOI: 10.3390/proteomes11030024] [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: 06/30/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/23/2023] Open
Abstract
Pancreatic cancer is a devastating disease that has a grim prognosis, highlighting the need for improved screening, diagnosis, and treatment strategies. Currently, the sole biomarker for pancreatic ductal adenocarcinoma (PDAC) authorized by the U.S. Food and Drug Administration is CA 19-9, which proves to be the most beneficial in tracking treatment response rather than in early detection. In recent years, proteomics has emerged as a powerful tool for advancing our understanding of pancreatic cancer biology and identifying potential biomarkers and therapeutic targets. This review aims to offer a comprehensive survey of proteomics' current status in pancreatic cancer research, specifically accentuating its applications and its potential to drastically enhance screening, diagnosis, and treatment response. With respect to screening and diagnostic precision, proteomics carries the capacity to augment the sensitivity and specificity of extant screening and diagnostic methodologies. Nonetheless, more research is imperative for validating potential biomarkers and establishing standard procedures for sample preparation and data analysis. Furthermore, proteomics presents opportunities for unveiling new biomarkers and therapeutic targets, as well as fostering the development of personalized treatment strategies based on protein expression patterns associated with treatment response. In conclusion, proteomics holds great promise for advancing our understanding of pancreatic cancer biology and improving patient outcomes. It is essential to maintain momentum in investment and innovation in this arena to unearth more groundbreaking discoveries and transmute them into practical diagnostic and therapeutic strategies in the clinical context.
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Affiliation(s)
- Luís Ramalhete
- Blood and Transplantation Center of Lisbon—Instituto Português do Sangue e da Transplantação, Alameda das Linhas de Torres, n° 117, 1769-001 Lisbon, Portugal
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- iNOVA4Health—Advancing Precision Medicine, RG11: Reno-Vascular Diseases Group, NOVA Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
| | - Emanuel Vigia
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
| | - Rúben Araújo
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- CHRC—Comprehensive Health Research Centre, NOVA Medical School, 1150-199 Lisbon, Portugal
| | - Hugo Pinto Marques
- Nova Medical School, Faculdade de Ciências Médicas, Universidade NOVA de Lisboa, 1169-056 Lisbon, Portugal
- Centro Hospitalar de Lisboa Central, Department of Hepatobiliopancreatic and Transplantation, 1050-099 Lisbon, Portugal
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14
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Wang F, Veth T, Kuipers M, Altelaar M, Stecker KE. Optimized Suspension Trapping Method for Phosphoproteomics Sample Preparation. Anal Chem 2023; 95:9471-9479. [PMID: 37319171 PMCID: PMC10308333 DOI: 10.1021/acs.analchem.3c00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023]
Abstract
A successful mass spectrometry-based phosphoproteomics analysis relies on effective sample preparation strategies. Suspension trapping (S-Trap) is a novel, rapid, and universal method of sample preparation that is increasingly applied in bottom-up proteomics studies. However, the performance of the S-Trap protocol for phosphoproteomics studies is unclear. In the existing S-Trap protocol, the addition of phosphoric acid (PA) and methanol buffer creates a fine protein suspension to capture proteins on a filter and is a critical step for subsequent protein digestion. Herein, we demonstrate that this addition of PA is detrimental to downstream phosphopeptide enrichment, rendering the standard S-Trap protocol suboptimal for phosphoproteomics. In this study, the performance of the S-Trap digestion for proteomics and phosphoproteomics is systematically evaluated in large-scale and small-scale samples. The results of this comparative analysis show that an optimized S-Trap approach, where trifluoroacetic acid is substituted for PA, is a simple and effective method to prepare samples for phosphoproteomics. Our optimized S-Trap protocol is applied to extracellular vesicles to demonstrate superior sample preparation workflow for low-abundance, membrane-rich samples.
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Affiliation(s)
- Fujia Wang
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Tim Veth
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Marije Kuipers
- Department
of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584
CM Utrecht, the Netherlands
| | - Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Kelly E. Stecker
- Biomolecular
Mass Spectrometry and Proteomics, Center for Biomolecular Research
and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
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15
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Guo M, Zhang Y, Wu L, Sheng Y, Zhao J, Wang Z, Wang H, Zhang L, Xiao H. Dynamic Phosphoproteomics of BRS3 Activation Reveals the Hippo Signaling Pathway for Cell Migration. J Proteome Res 2023. [PMID: 37368948 DOI: 10.1021/acs.jproteome.3c00116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Bombesin receptor subtype-3 (BRS3) is an orphan G-protein coupled receptor (GPCR) that is involved in a variety of pathological and physiological processes, while its biological functions and underlying regulatory mechanisms remain largely unknown. In this study, a quantitative phosphoproteomics approach was employed to comprehensively decipher the signal transductions that occurred upon intracellular BRS3 activation. The lung cancer cell line H1299-BRS3 was treated with MK-5046, an agonist of BRS3, for different durations. Harvested cellular proteins were digested and phosphopeptides were enriched by immobilized titanium (IV) ion affinity chromatography (Ti4+-IMAC) for label-free quantification (LFQ) analysis. A total of 11,938 phosphopeptides were identified, corresponding to 3,430 phosphoproteins and 10,820 phosphosites. Data analysis revealed that 27 phosphopeptides corresponding to six proteins were involved in the Hippo signaling pathway, which was significantly regulated by BRS3 activation. Verification experiments demonstrated that downregulation of the Hippo signaling pathway caused by BRS3 activation could induce the dephosphorylation and nucleus localization of the Yes-associated protein (YAP), and its association with cell migration was further confirmed by kinase inhibition. Our data collectively demonstrate that BRS3 activation contributes to cell migration through downregulation of the Hippo signaling pathway.
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Affiliation(s)
- Miao Guo
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lehao Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ye Sheng
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiaqi Zhao
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zeyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Huiyu Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lu Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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16
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Chen X, Ma L, Zhao J, Pan X, Chen S. Association between cognitive impairment promoted by high-fat diet and increase in PTEN phosphorylation. Behav Brain Res 2023; 447:114421. [PMID: 37028516 DOI: 10.1016/j.bbr.2023.114421] [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: 01/30/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
The purpose of this study was to observe the changes in memory impairment and hippocampal phosphorylated protein levels in mice caused by obesity, and to explore the key phosphorylation modification proteins and pathways of memory impairment induced by high-fat diet. First, sixteen C57BL/6J mice were randomly divided into simple obese group (group H, n=8) and normal control group (group C, n=8). And at the end of the experiment, the cognitive function of the mice was assessed by Morris water maze and serological indexes were measured. Finally, phosphoproteomics was used to identify the differentially phosphorylted protein expression in the hippocampus of obese mice. Compared with group C, mice in group H had significantly decreased learning and memory abilities, and significantly increased body weight, blood glucose and lipid levels. The results of the phosphoproteomics analysis showed 442 up-regulated differentially phosphorylated proteins and 402 down-regulated differentially phosphorylated proteins. Further protein-protein interaction (PPI) analysis revealed pathway hub proteins, including β-actin (ACTB), Phosphatase and tensin homolog deleted on chromosome ten (PTEN), Phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), mammalian target of rapamycin (mTOR), ribosomal protein 6 (RPS6), etc. Notably, the hub proteins PTEN, PIK3R1, and mTOR were jointly involved in the mTOR signaling pathway. Our study shows for the first time that a high-fat diet increases the phosphorylation of PTEN proteins, which may affect cognitive function.
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Affiliation(s)
- Xiaoyi Chen
- Graduate School of Hebei North University, Zhangjiakou, China; Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Liang Ma
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China
| | - Jingyu Zhao
- Department of Neurology, Hebei General Hospital, Shijiazhuang, China; Graduate School of North China University of Science and Technology, Tangshan, China
| | - Xiaoyu Pan
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China
| | - Shuchun Chen
- Department of Endocrinology, Hebei General Hospital, Shijiazhuang, China.
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17
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Current Trends in Toxicity Assessment of Herbal Medicines: A Narrative Review. Processes (Basel) 2022. [DOI: 10.3390/pr11010083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Even in modern times, the popularity level of medicinal plants and herbal medicines in therapy is still high. The World Health Organization estimates that 80% of the population in developing countries uses these types of remedies. Even though herbal medicine products are usually perceived as low risk, their potential health risks should be carefully assessed. Several factors can cause the toxicity of herbal medicine products: plant components or metabolites with a toxic potential, adulteration, environmental pollutants (heavy metals, pesticides), or contamination of microorganisms (toxigenic fungi). Their correct evaluation is essential for the patient’s safety. The toxicity assessment of herbal medicine combines in vitro and in vivo methods, but in the past decades, several new techniques emerged besides conventional methods. The use of omics has become a valuable research tool for prediction and toxicity evaluation, while DNA sequencing can be used successfully to detect contaminants and adulteration. The use of invertebrate models (Danio renio or Galleria mellonella) became popular due to the ethical issues associated with vertebrate models. The aim of the present article is to provide an overview of the current trends and methods used to investigate the toxic potential of herbal medicinal products and the challenges in this research field.
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18
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Ciancone AM, Hosseinibarkooie S, Bai DL, Borne AL, Ferris HA, Hsu KL. Global profiling identifies a stress-responsive tyrosine site on EDC3 regulating biomolecular condensate formation. Cell Chem Biol 2022; 29:1709-1720.e7. [PMID: 36476517 PMCID: PMC9779741 DOI: 10.1016/j.chembiol.2022.11.008] [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: 05/26/2022] [Revised: 09/01/2022] [Accepted: 11/14/2022] [Indexed: 12/12/2022]
Abstract
RNA granules are cytoplasmic condensates that organize biochemical and signaling complexes in response to cellular stress. Functional proteomic investigations under RNA-granule-inducing conditions are needed to identify protein sites involved in coupling stress response with ribonucleoprotein regulation. Here, we apply chemical proteomics using sulfonyl-triazole (SuTEx) probes to capture cellular responses to oxidative and nutrient stress. The stress-responsive tyrosine and lysine sites detected mapped to known proteins involved in processing body (PB) and stress granule (SG) pathways, including LSM14A, FUS, and Enhancer of mRNA-decapping protein 3 (EDC3). Notably, disruption of EDC3 tyrosine 475 (Y475) resulted in hypo-phosphorylation at S161 and S131 and altered protein-protein interactions (PPIs) with decapping complex components (DDX6, DCP1A/B) and 14-3-3 proteins. This resulting mutant form of EDC3 was capable of rescuing the PB-deficient phenotype of EDC3 knockout cells. Taken together, our findings identify Y475 as an arsenic-responsive site that regulates RNA granule formation by coupling EDC3 post-translational modification and PPI states.
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Affiliation(s)
- Anthony M Ciancone
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | | | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
| | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Heather A Ferris
- Department of Neuroscience, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA; Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA; University of Virginia Cancer Center, University of Virginia, Charlottesville, VA 22903, USA.
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19
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Sun C, Zou H, Yang Z, Yang M, Chen X, Huang Y, Fan W, Yuan R. Proteomics and phosphoproteomics analysis of vitreous in idiopathic epiretinal membrane patients. Proteomics Clin Appl 2022; 16:e2100128. [PMID: 35510950 DOI: 10.1002/prca.202100128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 03/18/2022] [Accepted: 05/02/2022] [Indexed: 12/30/2022]
Abstract
PURPOSE The purpose of the present study was to characterize the idiopathic epiretinal membrane (iERM) through proteomics and phosphoproteomics analysis to facilitate the diagnosis and treatment of iERM. EXPERIMENTAL DESIGN The vitreous of 25 patients with an iERM and 15 patients with an idiopathic macular hole were analyzed by proteomic and phosphoproteomic analysis based on tandem mass tag. PRM was used to verify the differential proteins. RESULTS Proteomic analysis identified a total of 878 proteins, including 50 differential proteins. Tenascin-C, galectin-3-binding protein, glucose-6-phosphate isomerase, neuroserpin, collagen alpha-1(XI) chain, and collagen alpha-1(II) chain were verified to be upregulated in iERM by PRM. Phosphoproteomic analysis identified a total of 401 phosphorylation sites on 213 proteins, including 27 differential phosphorylation sites on 24 proteins. Mitogen-activated protein kinase-activated protein kinase (MAPKAPK)3 and MAPKAPK5 were predicted as the major kinases in the vitreous of iERM. Twenty-six of the differential proteins and phosphorylated proteins may be closely related to fibrosis in iERM. CONCLUSION AND CLINICAL RELEVANCE Our results indicated the potential biomarkers or therapeutic targets for iERM, provided key kinases that may be involved in iERM. Fibrosis plays an essential role in iERM, and further exploration of related differential proteins has important clinical significance.
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Affiliation(s)
- Chao Sun
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Huan Zou
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Zhouquan Yang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Mei Yang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Xiaofan Chen
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Yanming Huang
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Wei Fan
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
| | - Rongdi Yuan
- Department of Ophthalmology, the Second Affiliated Hospital of Army Medical University, Chongqing, PR China
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20
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Zhu G, Jin L, Sun W, Wang S, Liu N. Proteomics of post-translational modifications in colorectal cancer: Discovery of new biomarkers. Biochim Biophys Acta Rev Cancer 2022; 1877:188735. [PMID: 35577141 DOI: 10.1016/j.bbcan.2022.188735] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the costliest health problems and ranks second in cancer-related mortality in developed countries. With the aid of proteomics, many protein biomarkers for the diagnosis, prognosis, and precise management of CRC have been identified. Furthermore, some protein biomarkers exhibit structural diversity after modifications. Post-translational modifications (PTMs), most of which are catalyzed by a variety of enzymes, extensively increase protein diversity and are involved in many complex and dynamic cellular processes through the regulation of protein function. Accumulating evidence suggests that abnormal PTM events are associated with a variety of human diseases, such as CRC, thus highlighting the need for studying PTMs to discover both the molecular mechanisms and therapeutic targets of CRC. In this review, we begin with a brief overview of the importance of protein PTMs, discuss the general strategies for proteomic profiling of several key PTMs (including phosphorylation, acetylation, glycosylation, ubiquitination, methylation, and citrullination), shift the emphasis to describing the specific methods used for delineating the global landscapes of each of these PTMs, and summarize the recent applications of these methods to explore the potential roles of the PTMs in CRC. Finally, we discuss the current status of PTM research on CRC and provide future perspectives on how PTM regulation can play an essential role in translational medicine for early diagnosis, prognosis stratification, and therapeutic intervention in CRC.
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Affiliation(s)
- Gengjun Zhu
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Lifang Jin
- Department Oncology and Hematology, The Second Hospital of Jilin University, Changchun, China
| | - Wanchun Sun
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Shuang Wang
- Dermatological department, The Second Hospital of Jilin University, Changchun, China.
| | - Ning Liu
- Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China; Central Laboratory, The Second Hospital of Jilin University, Changchun, China.
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