1
|
Yang L, Guo CW, Luo QM, Guo ZF, Chen L, Ishihama Y, Li P, Yang H, Gao W. Thermostability-assisted limited proteolysis-coupled mass spectrometry for capturing drug target proteins and sites. Anal Chim Acta 2024; 1312:342755. [PMID: 38834267 DOI: 10.1016/j.aca.2024.342755] [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: 01/22/2024] [Revised: 04/28/2024] [Accepted: 05/20/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND Identifying drug-binding targets and their corresponding sites is crucial for drug discovery and mechanism studies. Limited proteolysis-coupled mass spectrometry (LiP-MS) is a sophisticated method used for the detection of compound and protein interactions. However, in some cases, LiP-MS cannot identify the target proteins due to the small structure changes or the lack of enrichment of low-abundant protein. To overcome this drawback, we developed a thermostability-assisted limited proteolysis-coupled mass spectrometry (TALiP-MS) approach for efficient drug target discovery. RESULTS We proved that the novel strategy, TALiP-MS, could efficiently identify target proteins of various ligands, including cyclosporin A (a calcineurin inhibitor), geldanamycin (an HSP90 inhibitor), and staurosporine (a kinase inhibitor), with accurately recognizing drug-binding domains. The TALiP protocol increased the number of target peptides detected in LiP-MS experiments by 2- to 8-fold. Meanwhile, the TALiP-MS approach can not only identify both ligand-binding stability and destabilization proteins but also shows high complementarity with the thermal proteome profiling (TPP) and machine learning-based limited proteolysis (LiP-Quant) methods. The developed TALiP-MS approach was applied to identify the target proteins of celastrol (CEL), a natural product known for its strong antioxidant and anti-cancer angiogenesis effect. Among them, four proteins, MTHFD1, UBA1, ACLY, and SND1 were further validated for their strong affinity to CEL by using cellular thermal shift assay. Additionally, the destabilized proteins induced by CEL such as TAGLN2 and CFL1 were also validated. SIGNIFICANCE Collectively, these findings underscore the efficacy of the TALiP-MS method for identifying drug targets, elucidating binding sites, and even detecting drug-induced conformational changes in target proteins in complex proteomes.
Collapse
Affiliation(s)
- Liu Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Chen-Wan Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Qi-Ming Luo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Zi-Fan Guo
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Ling Chen
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ping Li
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Hua Yang
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China.
| | - Wen Gao
- State Key Laboratory of Natural Medicines, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, PR China; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan.
| |
Collapse
|
2
|
Yin K, Wu R. Systematic Investigation of Dose-Dependent Protein Thermal Stability Changes to Uncover the Mechanisms of the Pleiotropic Effects of Metformin. ACS Pharmacol Transl Sci 2024; 7:467-477. [PMID: 38357277 PMCID: PMC10863438 DOI: 10.1021/acsptsci.3c00298] [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: 10/24/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024]
Abstract
Metformin is a widely used drug to treat type II diabetes. Beyond lowering blood sugar, it has been reported to have pleiotropic effects such as suppressing cancer growth and attenuating cell oxidative stress and inflammation. However, the underlying mechanisms of these effects remain to be explored. Here, we systematically study the thermal stability changes of proteins in liver cells (HepG2) induced by a wide dosage range of metformin by using the proteome integral solubility alteration (PISA) assay. The current results demonstrate that, besides the most accepted target of metformin (complex I), low concentrations of metformin (such as 0.2 μM) stabilize the complex IV subunits, suggesting its important role in the sugar-lowering effect. Low-dose metformin also results in stability alterations of ribosomal proteins, correlating with its inhibitive effect on cell proliferation. We further find that low-concentration metformin impacts mitochondrial cargo and vesicle transport, while high-concentration metformin affects cell redox responses and cell membrane protein sorting. This study provides mechanistic insights into the molecular mechanisms of lowering blood sugar and the pleiotropic effects of metformin.
Collapse
Affiliation(s)
- Kejun Yin
- School of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Ronghu Wu
- School of Chemistry and Biochemistry
and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
3
|
Li Y, Lyu J, Wang Y, Ye M, Wang H. Ligand Modification-Free Methods for the Profiling of Protein-Environmental Chemical Interactions. Chem Res Toxicol 2024; 37:1-15. [PMID: 38146056 DOI: 10.1021/acs.chemrestox.3c00282] [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: 12/27/2023]
Abstract
Adverse health outcomes caused by environmental chemicals are often initiated via their interactions with proteins. Essentially, one environmental chemical may interact with a number of proteins and/or a protein may interact with a multitude of environmental chemicals, forming an intricate interaction network. Omics-wide protein-environmental chemical interaction profiling (PECI) is of prominent importance for comprehensive understanding of these interaction networks, including the toxicity mechanisms of action (MoA), and for providing systematic chemical safety assessment. However, such information remains unknown for most environmental chemicals, partly due to their vast chemical diversity. In recent years, with the continuous efforts afforded, especially in mass spectrometry (MS) based omics technologies, several ligand modification-free methods have been developed, and new attention for systematic PECI profiling was gained. In this Review, we provide a comprehensive overview on these methodologies for the identification of ligand-protein interactions, including affinity interaction-based methods of affinity-driven purification, covalent modification profiling, and activity-based protein profiling (ABPP) in a competitive mode, physicochemical property changes assessment methods of ligand-directed nuclear magnetic resonance (ligand-directed NMR), MS integrated with equilibrium dialysis for the discovery of allostery systematically (MIDAS), thermal proteome profiling (TPP), limited proteolysis-coupled mass spectrometry (LiP-MS), stability of proteins from rates of oxidation (SPROX), and several intracellular downstream response characterization methods. We expect that the applications of these ligand modification-free technologies will drive a considerable increase in the number of PECI identified, facilitate unveiling the toxicological mechanisms, and ultimately contribute to systematic health risk assessment of environmental chemicals.
Collapse
Affiliation(s)
- Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
- State Key Laboratory of Medical Proteomics, Beijing, 102206, China
| | - Hailin Wang
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
- The State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Ye Y, Li K, Ma Y, Zhang X, Li Y, Yu T, Wang Y, Ye M. The Introduction of Detergents in Thermal Proteome Profiling Requires Lowering the Applied Temperatures for Efficient Target Protein Identification. Molecules 2023; 28:4859. [PMID: 37375414 DOI: 10.3390/molecules28124859] [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: 05/19/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
Although the use of detergents in thermal proteome profiling (TPP) has become a common practice to identify membrane protein targets in complex biological samples, surprisingly, there is no proteome-wide investigation into the impacts of detergent introduction on the target identification performance of TPP. In this study, we assessed the target identification performance of TPP in the presence of a commonly used non-ionic detergent or a zwitterionic detergent using a pan-kinase inhibitor staurosporine, our results showed that the addition of either of these detergents significantly impaired the identification performance of TPP at the optimal temperature for soluble target protein identification. Further investigation showed that detergents destabilized the proteome and increased protein precipitation. By lowering the applied temperature point, the target identification performance of TPP with detergents is significantly improved and is comparable to that in the absence of detergents. Our findings provide valuable insight into how to select the appropriate temperature range when detergents are used in TPP. In addition, our results also suggest that the combination of detergent and heat may serve as a novel precipitation-inducing force that can be applied for target protein identification.
Collapse
Affiliation(s)
- Yuying Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kejia Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanni Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanan Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Yu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Zhang X, Wang K, Wu S, Ruan C, Li K, Wang Y, Zhu H, Liu X, Liu Z, Li G, Hu L, Ye M. Highly effective identification of drug targets at the proteome level by pH-dependent protein precipitation. Chem Sci 2022; 13:12403-12418. [PMID: 36382280 PMCID: PMC9629037 DOI: 10.1039/d2sc03326g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 09/20/2022] [Indexed: 09/09/2023] Open
Abstract
Fully understanding the target spaces of drugs is essential for investigating the mechanism of drug action and side effects, as well as for drug discovery and repurposing. In this study, we present an energetics-based approach, termed pH-dependent protein precipitation (pHDPP), to probe the ligand-induced protein stability shift for proteome-wide drug target identification. We demonstrate that pHDPP works for a diverse array of ligands, including a folate derivative, an ATP analog, a CDK inhibitor and an immunosuppressant, enabling highly specific identification of target proteins from total cell lysates. This approach is compared to thermal and solvent-induced denaturation approaches with a pan-kinase inhibitor as the model drug, demonstrating its high sensitivity and high complementarity to other approaches. Dihydroartemisinin (DHA), a dominant derivative of artemisinin to treat malaria, is known to have an extraordinary effect on the treatment of various cancers. However, the anti-tumor mechanisms remain unknown. pHDPP was applied to reveal the target space of DHA and 45 potential target proteins were identified. Pathway analysis indicated that these target proteins were mainly involved in metabolism and apoptosis pathways. Two cancer-related target proteins, ALDH7A1 and HMGB1, were validated by structural simulation and AI-based target prediction methods. And they were further validated to have strong affinity to DHA by using cellular thermal shift assay (CETSA). In summary, pHDPP is a powerful tool to construct the target protein space to reveal the mechanism of drug action and would have broad application in drug discovery studies.
Collapse
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
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University Changchun 130012 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
| | - Sijin Wu
- 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
| | - Kejia Li
- 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
| | - 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
| | - He Zhu
- 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
| | - Zhen 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
| | - Guohui Li
- 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
| | - Lianghai Hu
- Center for Supramolecular Chemical Biology, State Key Laboratory of Supramolecular Structure and Materials, School of Life Sciences, Jilin University Changchun 130012 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
| |
Collapse
|
8
|
Ling S, Luo X, Lv B, Wang H, Xie M, Huang K, Sun J. Effect of miR-144-3p-Targeted Regulation of PTEN on Proliferation, Apoptosis, and Osteogenic Differentiation of Bone Marrow Mesenchymal Stem Cells under Stretch. Emerg Med Int 2022; 2022:5707504. [PMID: 35592654 PMCID: PMC9113913 DOI: 10.1155/2022/5707504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/15/2022] [Indexed: 12/04/2022] Open
Abstract
Objective To investigate the effects of miR-144-3p-targeted regulation of phosphatase and tensin homolog deleted on chromosome ten (PTEN) gene on proliferation, apoptosis, and osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) under retraction force. Methods The BMSCs of rats were randomly divided into the tension MSC group with detrusor stimulation and the MSC group without detrusor stimulation, after which osteogenic differentiation of BMSCs was induced in both groups. Alkaline phosphatase (ALP) staining and alizarin red staining were used to detect the osteogenic differentiation ability of the two groups of cells. Real-time quantitative reverse transcription PCR (qRT-PCR) was used to detect the expression of miR-144-3p and PTEN in the two groups of cells after osteogenic differentiation. Bioinformatics website and dual luciferase reporter were used to detect the relationship between miR-144-3p and PTEN. The tension MSC group was used as a control group, and miR-144-3p mimics (miR-144-3p mimic group), mimic controls (mimic-NC group), PTEN interferers (si-PTEN group), and interference controls (si-NC group) were transfected into BMSCs. The BMSCs were then continuously stimulated for 24 h using a Flexercell in vitro cellular mechanics loading device, applying a draft force at a frequency of 1 Hz and a deformation rate of 18%. The cell proliferation was detected by Cell Counting Kit-8 (CCK-8) colorimetric assay; the expression levels of cyclin, cyclin-dependent kinases (CDK), BCL2-associated X (BAX), B-cell lymphoma-2 (BCL-2), and other cell cycle and apoptosis related proteins were detected by western blot (WB); and the osteogenic differentiation ability of MSC cells was detected by ALP staining and alizarin red staining. Results Compared with the MSC group, the level of miR-144-3p was significantly lower and the level of PTEN was significantly higher in the tension MSC group. ALP staining showed normal activity in the MSC group and decreased ALP activity in the tension MSC group compared to the MSC group. Alizarin red staining in the MSC group showed scattered calcium nodule formation, and alizarin red staining showed red nodules with a more uniform color distribution. Compared to the MSC group, the tension MSC group showed fewer, smaller, and lighter staining mineralized nodules. Compared with the tension group and mimic-NC group (si-NC group), the proliferation rate of cells in the miR-144-3p mimic group (si-PTEN group) was significantly higher; the expression levels of PTEN and BAX were significantly lower; and the expression levels of cyclin, CDK, and BCL-2 protein were significantly higher. ALP staining results revealed that the miR-144-3p mimic group (si-PTEN group) showed significantly higher osteogenic differentiation ability and ALP activity of MSC than the tension group and mimic-NC group (si-NC group). Conclusion miR-144-3p may inhibit apoptosis and promote proliferation and osteogenic differentiation of BMSCs under tension by targeting and regulating PTEN.
Collapse
Affiliation(s)
- Shiyong Ling
- Department of Orthopedics, Zhabei Central Hospital, Jing'an District, Shanghai 200070, China
| | - Xi Luo
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Bo Lv
- Department of Orthopedics, Zhabei Central Hospital, Jing'an District, Shanghai 200070, China
| | - Hua Wang
- Department of Orthopedics, Zhabei Central Hospital, Jing'an District, Shanghai 200070, China
| | - Mengzhi Xie
- Department of Radiology, Zhabei Central Hospital, Jing'an District, Shanghai 200070, China
| | - Kai Huang
- Department of Orthopedics, Zhabei Central Hospital, Jing'an District, Shanghai 200070, China
| | - Jingchuan Sun
- Department of Orthopedic Surgery, Spine Center, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| |
Collapse
|
9
|
Beusch CM, Sabatier P, Zubarev RA. Ion-Based Proteome-Integrated Solubility Alteration Assays for Systemwide Profiling of Protein-Molecule Interactions. Anal Chem 2022; 94:7066-7074. [PMID: 35506705 PMCID: PMC9118197 DOI: 10.1021/acs.analchem.2c00391] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
![]()
Unbiased drug target
engagement deconvolution and mechanism of
action elucidation are major challenges in drug development. Modification-free
target engagement methods, such as thermal proteome profiling, have
gained increasing popularity in the last several years. However, these
methods have limitations, and, in any case, new orthogonal approaches
are needed. Here, we present a novel isothermal method for comprehensive
characterization of protein solubility alterations using the effect
on protein solubility of cations and anions in the Hofmeister series.
We combine the ion-based protein precipitation approach with Proteome-Integrated
Solubility Alteration (PISA) analysis and use this I-PISA assay to
delineate the targets of several anticancer drugs both in cell lysates
and intact cells. Finally, we demonstrate that I-PISA can detect solubility
changes in minute amounts of sample, opening chemical proteomics applications
to small and rare biological material.
Collapse
Affiliation(s)
- Christian M Beusch
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17177, Sweden
| | - Pierre Sabatier
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17177, Sweden
| | - Roman A Zubarev
- Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm 17177, Sweden.,Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow 119146, Russia.,The National Medical Research Centre for Endocrinology, Moscow 115478, Russia
| |
Collapse
|
10
|
Ruan C, Wang Y, Zhang X, Lyu J, Zhang N, Ma Y, Shi C, Qu G, Ye M. Matrix Thermal Shift Assay for Fast Construction of Multidimensional Ligand-Target Space. Anal Chem 2022; 94:6482-6490. [PMID: 35442643 DOI: 10.1021/acs.analchem.1c04627] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Existing thermal shift-based mass spectrometry approaches are able to identify target proteins without chemical modification of the ligand, but they are suffering from complicated workflows with limited throughput. Herein, we present a new thermal shift-based method, termed matrix thermal shift assay (mTSA), for fast deconvolution of ligand-binding targets and binding affinities at the proteome level. In mTSA, a sample matrix, treated horizontally with five different compound concentrations and vertically with five technical replicates of each condition, was denatured at a single temperature to induce protein precipitation, and then, data-independent acquisition was employed for quick protein quantification. Compared with previous thermal shift assays, the analysis throughput of mTSA was significantly improved, but the costs as well as efforts were reduced. More importantly, the matrix experiment design allowed simultaneous computation of the statistical significance and fitting of the dose-response profiles, which can be combined to enable a more accurate identification of target proteins, as well as reporting binding affinities between the ligand and individual targets. Using a pan-specific kinase inhibitor, staurosporine, we demonstrated a 36% improvement in screening sensitivity over the traditional thermal proteome profiling (TPP) and a comparable sensitivity with a latest two-dimensional TPP. Finally, mTSA was successfully applied to delineate the target landscape of perfluorooctanesulfonic acid (PFOS), a persistent organic pollutant that is hard to perform modification on, and revealed several potential targets that might account for the toxicities of PFOS.
Collapse
Affiliation(s)
- Chengfei Ruan
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Xiaolei Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| | - Jiawen Lyu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Na Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanni Ma
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunzhen Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian 116023, China
| |
Collapse
|
11
|
Odiwuor N, Xiong J, Ogolla F, Hong W, Li X, Khan FM, Wang N, Yu J, Wei H. A point-of-care SARS-CoV-2 test based on reverse transcription loop-mediated isothermal amplification without RNA extraction with diagnostic performance same as RT-PCR. Anal Chim Acta 2022; 1200:339590. [PMID: 35256137 PMCID: PMC8844505 DOI: 10.1016/j.aca.2022.339590] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 02/03/2022] [Accepted: 02/07/2022] [Indexed: 12/04/2022]
Abstract
The global public health crisis and economic losses resulting from the current novel coronavirus disease (COVID-19) pandemic have been dire. The most used real-time reverse transcription polymerase chain reaction (RT-PCR) method needs expensive equipment, technical expertise, and a long turnaround time. Therefore, there is a need for a rapid, accurate, and alternative technique of diagnosis that is deployable at resource-poor settings like point-of-care. This study combines heat deactivation and a novel mechanical lysis method by bead beating for quick and simple sample preparation. Then, using an optimized reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay to target genes encoding the open reading frame 8 (ORF8), spike and nucleocapsid proteins of the novel coronavirus, SARS-CoV-2. The test results can be read simultaneously in fluorometric and colorimetric readouts within 40 min from sample collection. We also calibrated a template transfer tool to simplify sample addition into LAMP reactions when pipetting skills are needed. Most importantly, validation of the direct RT-LAMP system based on multiplexing primers S1:ORF8 in a ratio (1:0.8) using 143 patients' nasopharyngeal swab samples showed a diagnostic performance of 99.30% accuracy, with 98.81% sensitivity and 100% selectivity, compared to commercial RT-PCR kits. Since our workflow does not rely on RNA extraction and purification, the time-to-result is two times faster than other workflows with FDA emergency use authorization. Considering all its strengths: speed, simplicity, accuracy and extraction-free, the system can be useful for optimal point-of-care testing of COVID-19.
Collapse
Affiliation(s)
- Nelson Odiwuor
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Jin Xiong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Faith Ogolla
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohong Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Fazal Mehmood Khan
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuo Wang
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Sino-Africa Joint Research Centre, Nairobi, 62000 - 00200, Kenya.
| |
Collapse
|
12
|
Unmodified methodologies in target discovery for small molecule drugs: A rising star. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2022.04.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|