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Wang Y, Wang Y, Lü J, Li X. Unraveling the Drug Response Heterogeneity with Single-Cell Vibrational Phenomics. Cell Biochem Biophys 2024:10.1007/s12013-024-01363-0. [PMID: 38914839 DOI: 10.1007/s12013-024-01363-0] [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] [Accepted: 06/12/2024] [Indexed: 06/26/2024]
Abstract
Drug responses heterogeneity is often highlighted to justify the need for precision medicine. However, due to the highly complex nature of cell phenotypes in many diseases, one of key challenges is how to obtain the high content features in a cellular population. Here we present a single-cell vibrational phenomics approach, integrating synchrotron infrared microspectroscopy and multivariate calculation, for quantitatively evaluating the cellular responses to drug perturbation with single cell resolution. In a human hepatocellular carcinoma HepG2 cell model, the phenotypic changes induced by two types of drugs, taxol (TAX) and protopanaxadiol (PPD), were analyzed and revealed the response heterogeneity in drug concentration and chemical components. These findings not only provide a label-free strategy for determining the drug response at the single cell level, but also demonstrate the great potential of vibrational phenomics as a drug discovery platform.
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Affiliation(s)
- Yue Wang
- Collage of Public Health, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yadi Wang
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China.
| | - Junhong Lü
- College of Pharmacy, Binzhou Medical University, Yantai, 264003, China.
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Xueling Li
- Collage of Public Health, Shanghai University of Medicine & Health Sciences, Shanghai, 201318, China.
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Wang Y, Wang Y, Li X, Lü J. Vibrational phenomics decoding of the stem cell stepwise aging process at single-cell resolution. Chem Commun (Camb) 2024; 60:3263-3266. [PMID: 38389443 DOI: 10.1039/d4cc00193a] [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: 02/24/2024]
Abstract
We introduce vibrational spectroscopy to quantitatively measure the phenotypic heterogeneity of senescent stem cells in the aging process at the single cell level. Using an aging model of serially passaged human mesenchymal stem cells (MSCs), we characterized the phenotypic changes of MSCs during different aged stages and discovered a stepwise aging process with several distinct subtypes.
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Affiliation(s)
- Yue Wang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yadi Wang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
| | - Xueling Li
- Shanghai University of Medicine & Health Sciences, Shanghai 201318, China
| | - Junhong Lü
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China.
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Wang Y, Gao Y, Li X, Tian G, Lü J. Single-cell infrared phenomics identifies cell heterogeneity of individual pancreatic islets in mouse model. Anal Chim Acta 2023; 1258:341185. [PMID: 37087295 DOI: 10.1016/j.aca.2023.341185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/27/2023] [Accepted: 04/05/2023] [Indexed: 04/08/2023]
Abstract
Identifying the islet heterogeneity (cell types and the proportion of each subpopulation) and their relevance to function and disease will lead to fundamental information for the prevention and therapies of diabetes. Here, we introduce a single-cell phenotypic essay on the heterogeneity within individual pancreatic islets by using the combination of synchrotron infrared microspectroscopy and quantitative calculation. In a mouse model, the cellular heterogeneities at both the whole pancreas and single intact islet level were identified. The variation of biochemical phenotypes successfully subdivided islet cells into five main groups and quantitatively determined their proportion. These findings not only demonstrate single-cell infrared phenomics as a value complementary technique and strategy for the description of cellular heterogeneity within the pancreatic islets but also provide a quick, label-free optical platform for investigating phenotypic heterogeneity at the small-organelle level with single cell resolution.
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Zhong J, Yu W, Tang Y, Zhou X. Synchrotron Radiation FTIR Microspectroscopy Study of Biomolecular Alterations in Vincristine-Treated WRL68 Cells at the Single-Cell Level. ACS OMEGA 2022; 7:47274-47284. [PMID: 36570260 PMCID: PMC9773350 DOI: 10.1021/acsomega.2c06622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
The toxic effect of vincristine on hepatocytes has rarely been studied. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) microspectroscopy is a novel technique for investigating drug-cell interaction systems. In this research, the biomolecular alterations in WRL68 cells induced by vincristine treatment were investigated by SR-FTIR microspectroscopy and were further analyzed by multivariate statistical analysis and semiquantitative methods, including principal component analysis (PCA), orthogonal partial least square-discriminant analysis (OPLS-DA), and the peak area ratios of several characteristic IR bands. In vincristine-treated WRL68 cells, alterations in lipid structures and the presence of more long-chain fatty acids were found. A decrease in protein α-helical content relative to β-sheet structures in vincristine-treated WRL68 cells was identified. The nucleic acid content was decreased relative to that of lipids and proteins in WRL68 cells treated with vincristine. These results provide important information about the toxic effect of vincristine on normal liver cells. This research also provides a new approach to reveal the biomolecular alterations in drug-treated hepatocytes by combining SR-FTIR with multivariate statistical analysis and semiquantitative methods.
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Zhou X, Zhong J, Yu W, Tang Y. Synchrotron radiation-based Fourier transform infrared microspectroscopy investigation of WRL68 cells treated with doxorubicin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121773. [PMID: 36007348 DOI: 10.1016/j.saa.2022.121773] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/22/2022] [Accepted: 08/15/2022] [Indexed: 06/15/2023]
Abstract
Doxorubicin is an effective chemotherapeutic agent applied in a wide variety of cancers. Despite its potent anticancer activity towards cancer cells, doxorubicin is also toxic to noncancerous cells. Therefore, doxorubicin can cause serious side effects in various organs, especially when dose escalation is required for patients with advanced disease. The liver is the major detoxification organ that metabolizes drugs, and hepatotoxicity is one of the most common adverse effects of doxorubicin administration. However, the exact mechanisms of doxorubicin-induced hepatotoxicity have not been clearly identified, and how doxorubicin treatment affects the biomolecular contents of normal human hepatocytes has rarely been studied. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) microspectroscopy is a state-of-the-art analytical technique for characterizing the biomolecules present in cells. In this research, the biomolecular alterations of doxorubicin-treated normal human hepatocytes compared to untreated control cells were investigated at the single-cell level by combining SR-FTIR microspectroscopy with the Cell Counting Kit-8 (CCK-8) assay and flow cytometry. WRL68 human normal embryonic liver cells, which have been shown to be very promising for assessing the cytotoxicity of toxic compounds and investigating hepato-toxicology, were used in this research. Principal component analysis (PCA) and orthogonal partial least squares-discriminant analysis (OPLS-DA) were used to further analyse the biomolecular contents of WRL68 cells. The order of lipid acyl chains and protein α-helix structures in doxorubicin-treated WRL68 cells was found to be distinctly changed, while the nucleic acids were altered relatively less. No alteration in the carbohydrate content was distinguishable after doxorubicin treatment. These results provide more comprehensive information about the biomolecular changes in hepatocytes induced by doxorubicin treatment and help to elucidate the mechanism of doxorubicin-induced hepatotoxicity. This research also proves that SR-FTIR microspectroscopy, combined with PCA and OPLS-DA, is a promising approach for investigating drug-cell interaction systems.
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Affiliation(s)
- Xiaojie Zhou
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99, Haike Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai 201210, PR China.
| | - Jiajia Zhong
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99, Haike Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai 201210, PR China
| | - Wenjie Yu
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99, Haike Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai 201210, PR China
| | - Yuzhao Tang
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 99, Haike Road, Zhangjiang Hi-Tech Park, Pudong, Shanghai 201210, PR China.
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Synchrotron Infrared Microspectroscopy for Stem Cell Research. Int J Mol Sci 2022; 23:ijms23179878. [PMID: 36077277 PMCID: PMC9456088 DOI: 10.3390/ijms23179878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/23/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022] Open
Abstract
Stem cells have shown great potential functions for tissue regeneration and repair because of their unlimited self-renewal and differentiation. Stem cells reside in their niches, making them a hotspot for the development and diagnosis of diseases. Complex interactions between niches and stem cells create the balance between differentiation, self-renewal, maturation, and proliferation. However, the multi-facet applications of stem cells have been challenged since the complicated responses of stem cells to biological processes were explored along with the limitations of current systems or methods. Emerging evidence highlights that synchrotron infrared microspectroscopy, known as synchrotron radiation-based Fourier transform infrared microspectroscopy, has been investigated as a potentially attractive technology with its non-invasive and non-biological probes in stem cell research. With their unique vibration bands, the quantitative mapping of the content and distribution of biomolecules can be detected and characterized in cells or tissues. In this review, we focus on the potential applications of synchrotron infrared microspectroscopy for investigating the differentiation and fate determination of stem cells.
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Yang S, Zhang Q, Yang H, Shi H, Dong A, Wang L, Yu S. Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure. Int J Biol Macromol 2022; 206:175-187. [PMID: 35217087 DOI: 10.1016/j.ijbiomac.2022.02.104] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022]
Abstract
Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H2O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H2O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.
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Affiliation(s)
- Shouning Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | | | - Huayan Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, USA.
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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Liao X, Xu Q, Tan Z, Liu Y, Wang C. Recent Advances in Plasmonic Nanostructures Applied for Label‐free Single‐cell Analysis. ELECTROANAL 2021. [DOI: 10.1002/elan.202100330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Xue‐Wei Liao
- Analytical & Testing Center Nanjing Normal University Nanjing 210023 China
| | - Qiu‐Yang Xu
- Department of Chemistry China Pharmaceutical University Nanjing 211198 China
| | - Zheng Tan
- Department of Chemistry China Pharmaceutical University Nanjing 211198 China
| | - Yang Liu
- School of Environment Nanjing Normal University Nanjing 210023 China
| | - Chen Wang
- School of Chemistry and Materials Science Nanjing Normal University Nanjing 210023 China
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Wang Y, Dai W, Liu Z, Liu J, Cheng J, Li Y, Li X, Hu J, Lü J. Single-Cell Infrared Microspectroscopy Quantifies Dynamic Heterogeneity of Mesenchymal Stem Cells during Adipogenic Differentiation. Anal Chem 2020; 93:671-676. [PMID: 33290049 DOI: 10.1021/acs.analchem.0c04110] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The central relevance of cellular heterogeneity to biological phenomena raises the rational needs for analytical techniques with single-cell resolution. Here, we developed a single-cell FTIR microspectroscopy-based method for the quantitative evaluation of cellular heterogeneity by calculating the cell-to-cell similarity distance of the infrared spectral data. Based on this method, we revealed the infrared phenotypes might reflect the dynamic heterogeneity changes in the cell population during the adipogenic differentiation of the human mesenchymal stem cells. These findings provide an alternative label-free optical approach for quantifying the cellular heterogeneity, and the combination with other single-cell analysis tools will be very helpful for understanding the genotype-to-phenotype relationship in cellular populations.
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Affiliation(s)
- Yadi Wang
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 2019 Jia Luo Road, Jiading District, Shanghai 201800, China.,University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Wentao Dai
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Huangpu District, Shanghai 200025, China.,Shanghai Center for Bioinformation Technology, No.1278 Ke Yuan Road, Pudong New District, Shanghai 201203, China
| | - Zhixiao Liu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 2019 Jia Luo Road, Jiading District, Shanghai 201800, China
| | - Jixiang Liu
- Shanghai Center for Bioinformation Technology, No.1278 Ke Yuan Road, Pudong New District, Shanghai 201203, China
| | - Jie Cheng
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 2019 Jia Luo Road, Jiading District, Shanghai 201800, China
| | - Yuanyuan Li
- Shanghai Key Laboratory of Gastric Neoplasms, Shanghai Institute of Digestive Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Huangpu District, Shanghai 200025, China.,Shanghai Center for Bioinformation Technology, No.1278 Ke Yuan Road, Pudong New District, Shanghai 201203, China
| | - Xueling Li
- Shanghai University of Medicine and Health Sciences, National Engineering Research Center for Nanotechnology, No. 28 Jiangchuan East Road, Minhang District, Shanghai 201318, China
| | - Jun Hu
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 2019 Jia Luo Road, Jiading District, Shanghai 201800, China
| | - Junhong Lü
- Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, No. 239 Zhangheng Road, Pudong New District, Shanghai 201203, China.,Shanghai Institute of Applied Physics, Chinese Academy of Sciences, No. 2019 Jia Luo Road, Jiading District, Shanghai 201800, China
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Wang Y, Wang Y, Qian J, Pan X, Li X, Chen F, Hu J, Lü J. Single-cell infrared phenomics: phenotypic screening with infrared microspectroscopy. Chem Commun (Camb) 2020; 56:13237-13240. [PMID: 33030170 DOI: 10.1039/d0cc05721e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
We conceptually demonstrate single-cell infrared phenomics as a novel strategy of phenotypic screening with infrared microspectroscopy. Based on this development, the cancer cell HepG2 glycocalyx was first identified as a potential target of protopanaxadiol, an herbal medicine. These findings provide a powerful tool to accurately evaluate the cell stress response and to largely expand the phenotypic screening toolkit for drug discovery.
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Affiliation(s)
- Yadi Wang
- College of Pharmacy, Binzhou Medical University, Yantai 264003, China
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