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Wang D, Wang G, Wang X, Ren Z, Jia C. Native Mass Spectrometry-Centric Approaches Revealed That Neuropeptides Frequently Interact with Amyloid-β. ACS Chem Neurosci 2024; 15:2719-2728. [PMID: 39066700 DOI: 10.1021/acschemneuro.4c00075] [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] [Indexed: 07/30/2024] Open
Abstract
Amyloid-β (Aβ) aggregates are recognized as initiators of Alzheimer's disease, and their interaction with the nervous system contributes to the progression of neurodegeneration. Herein, we investigated the frequency at which neuropeptides interact with Aβ and affect the aggregation kinetics and cytotoxicity of Aβ. To this end, we established a native mass spectrometry (MS)-centric workflow for screening Aβ-interacting neuropeptides, and six out of 12 neuropeptides formed noncovalent complexes with Aβ species in the MS gas phase. Thioflavin-T fluorescence assays and gel separation indicated that leptin and cerebellin decreased Aβ aggregation, whereas kisspeptin increased this process. In addition, leptin and cerebellin attenuated Aβ-induced cytotoxicity, which was independent of the influence of metal ions. Leptin can chelate copper from copper-bound Aβ species, reducing the cytotoxicity caused by the aggregation of Aβ and metal ion complexes. Overall, our study demonstrated that neuropeptides frequently interact with Aβ and revealed that leptin and cerebellin are potential inhibitors of Aβ aggregation, providing great insight into understanding the molecular mechanism of Aβ interacting with the nervous system and facilitating drug development.
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Affiliation(s)
- Danyang Wang
- Department of Anatomy, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
- Beijing Proteome Research Center, State Key Laboratory of Medical Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences-Beijing, Beijing 102206, China
| | - Guibin Wang
- Beijing Proteome Research Center, State Key Laboratory of Medical Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences-Beijing, Beijing 102206, China
| | - Xiankun Wang
- Beijing Proteome Research Center, State Key Laboratory of Medical Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences-Beijing, Beijing 102206, China
| | - Zhenhua Ren
- Department of Anatomy, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chenxi Jia
- Department of Anatomy, School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
- Beijing Proteome Research Center, State Key Laboratory of Medical Proteomics, Beijing Institute of Lifeomics, National Center for Protein Sciences-Beijing, Beijing 102206, China
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Xu M, Wang X, Zhang Y, Ji N, Wang Q, Zhao T, Zhou C, Jia C. Profiling of the Proteins Interacting with Amyloid Beta Peptides in Clinical Samples by PACTS-TPP. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:1310-1319. [PMID: 38780475 DOI: 10.1021/jasms.4c00083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The accumulation of amyloid beta (Aβ1-42) results in neurotoxicity and is strongly related to neurodegenerative disorders, especially Alzheimer's disease (AD), but the underlying molecular mechanism is still poorly understood. Therefore, there is an urgent need for researchers to discover the proteins that interact with Aβ1-42 to determine the molecular basis. Previously, we developed peptide-ligand-induced changes in the abundance of proTeinS (PACTS)-assisted thermal proteome profiling (TPP) to identify proteins that interact with peptide ligands. In the present study, we applied this technique to analyze clinical samples to identify Aβ1-42-interacting proteins. We detected 115 proteins that interact with Aβ1-42 in human frontal lobe tissue. Pathway enrichment analysis revealed that the differentially expressed proteins were involved mainly in neurodegenerative diseases. Further orthogonal validation revealed that Aβ1-42 interacted with the AD-associated protein mitogen-activated protein kinase 3 (MAPK3), and knockdown of the Aβ1-42 amyloid precursor protein (APP) inhibited the MAPK signaling pathway, suggesting potential functional roles for Aβ1-42 in interacting with MAPK3. Overall, this study demonstrated the application of the PACTS-TPP in clinical samples and provided a valuable data source for research on neurodegenerative diseases.
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Affiliation(s)
- Mengting Xu
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui 230032, China
| | - Xiankun Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Yang Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, 100070, China
| | - Qianqian Wang
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Ting Zhao
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Congli Zhou
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Chenxi Jia
- State Key Laboratory of Medical Proteomics, National Center for Protein Sciences-Beijing, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, 102206, China
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Zhang X, Ruan C, Wang Y, Wang K, Liu X, Lyu J, Ye M. Integrated Protein Solubility Shift Assays for Comprehensive Drug Target Identification on a Proteome-Wide Scale. Anal Chem 2023; 95:13779-13787. [PMID: 37676971 DOI: 10.1021/acs.analchem.3c00072] [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: 09/09/2023]
Abstract
Target proteins are often stabilized after binding with a ligand and thereby typically become more resistant to denaturation. Based on this phenomenon, several methods without the need to covalently modify the ligand have been developed to identify target proteins for a specific ligand. These methods usually employ complicated workflows with high cost and limited throughput. Here, we develop an iso-pH shift assay (ipHSA) method, a proteome-wide target identification method that detects ligand-induced protein solubility shifts by precipitating proteins with a single concentration of acidic agent followed by protein quantification via data-independent acquisition (DIA). Using a pan-kinase inhibitor, staurosporine, we demonstrated that ipHSA increased throughput compared to the previously developed pH-dependent protein precipitation (pHDPP) method. ipHSA was found to have high complementarity in staurosporine target identification compared with the improved isothermal shift assay (iTSA) and isosolvent shift assay (iSSA) using DIA instead of tandem mass tags (TMTs) for quantification. To further improve target identification sensitivity, we developed an integrated protein solubility shift assay (IPSSA) by pooling the supernatants yielded from ipHSA, iTSA, and iSSA methods. IPSSA exhibited increased sensitivity in screening staurosporine targets by 38, 29, and 38% compared to individual methods. Increasing the number of replicate experiments further enhanced the sensitivity of target identification. Meanwhile, IPSSA also improved the throughput and reduced the cost compared with previous methods. As a fast and efficient tool for drug target identification, IPSSA is expected to have broad applications in the study of the mechanism of action.
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Affiliation(s)
- Xiaolei Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chengfei Ruan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Keyun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xiaoyan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R & A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Kang J, Seshadri M, Cupp-Sutton KA, Wu S. Toward the analysis of functional proteoforms using mass spectrometry-based stability proteomics. FRONTIERS IN ANALYTICAL SCIENCE 2023; 3:1186623. [PMID: 39072225 PMCID: PMC11281393 DOI: 10.3389/frans.2023.1186623] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Functional proteomics aims to elucidate biological functions, mechanisms, and pathways of proteins and proteoforms at the molecular level to examine complex cellular systems and disease states. A series of stability proteomics methods have been developed to examine protein functionality by measuring the resistance of a protein to chemical or thermal denaturation or proteolysis. These methods can be applied to measure the thermal stability of thousands of proteins in complex biological samples such as cell lysate, intact cells, tissues, and other biological fluids to measure proteome stability. Stability proteomics methods have been popularly applied to observe stability shifts upon ligand binding for drug target identification. More recently, these methods have been applied to characterize the effect of structural changes in proteins such as those caused by post-translational modifications (PTMs) and mutations, which can affect protein structures or interactions and diversify protein functions. Here, we discussed the current application of a suite of stability proteomics methods, including thermal proteome profiling (TPP), stability of proteomics from rates of oxidation (SPROX), and limited proteolysis (LiP) methods, to observe PTM-induced structural changes on protein stability. We also discuss future perspectives highlighting the integration of top-down mass spectrometry and stability proteomics methods to characterize intact proteoform stability and understand the function of variable protein modifications.
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Affiliation(s)
- Ji Kang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Meena Seshadri
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Kellye A. Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, United States
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Le Sueur C, Hammarén HM, Sridharan S, Savitski MM. Thermal proteome profiling: Insights into protein modifications, associations, and functions. Curr Opin Chem Biol 2022; 71:102225. [PMID: 36368297 DOI: 10.1016/j.cbpa.2022.102225] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/05/2022] [Accepted: 10/09/2022] [Indexed: 11/10/2022]
Abstract
Tracking proteins' biophysical characteristics on a proteome-wide scale can provide valuable information on their functions and interactions. Thermal proteome profiling (TPP) is a multiplexed quantitative proteomics approach that measures changes in protein thermal stability-a key biophysical property-across different cellular states. Developed in 2014, as a target-deconvolution assay for drugs and other small molecules, TPP has since evolved to a system-level biochemical omics technique providing insights into context-dependent changes in protein states. In this review, we summarise key advances in the experimental and data analysis pipeline that have aided this transformation and discuss the recent developments and applications of TPP.
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Affiliation(s)
- Cecile Le Sueur
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany; Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Henrik M Hammarén
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
| | - Sindhuja Sridharan
- Barts Brain Tumour Center, Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Mikhail M Savitski
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany.
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