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Liu X, Shi L, Zhao Z, Shu J, Min W. VIBRANT: spectral profiling for single-cell drug responses. Nat Methods 2024; 21:501-511. [PMID: 38374266 PMCID: PMC11214684 DOI: 10.1038/s41592-024-02185-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 01/16/2024] [Indexed: 02/21/2024]
Abstract
High-content cell profiling has proven invaluable for single-cell phenotyping in response to chemical perturbations. However, methods with improved throughput, information content and affordability are still needed. We present a new high-content spectral profiling method named vibrational painting (VIBRANT), integrating mid-infrared vibrational imaging, multiplexed vibrational probes and an optimized data analysis pipeline for measuring single-cell drug responses. Three infrared-active vibrational probes were designed to measure distinct essential metabolic activities in human cancer cells. More than 20,000 single-cell drug responses were collected, corresponding to 23 drug treatments. The resulting spectral profile is highly sensitive to phenotypic changes under drug perturbation. Using this property, we built a machine learning classifier to accurately predict drug mechanism of action at single-cell level with minimal batch effects. We further designed an algorithm to discover drug candidates with new mechanisms of action and evaluate drug combinations. Overall, VIBRANT has demonstrated great potential across multiple areas of phenotypic screening.
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Affiliation(s)
- Xinwen Liu
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Lixue Shi
- Department of Chemistry, Columbia University, New York, NY, USA
- Shanghai Xuhui Central Hospital, Zhongshan-Xuhui Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhilun Zhao
- Department of Chemistry, Columbia University, New York, NY, USA
| | - Jian Shu
- Cutaneous Biology Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Wei Min
- Department of Chemistry, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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2
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Jiang YX, Shi WJ, Hu LX, Ma DD, Zhang H, Ong CN, Ying GG. Dydrogesterone disrupts lipid metabolism in zebrafish brain: A study based on metabolomics and Fourier transform infrared spectroscopy. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 317:120811. [PMID: 36470458 DOI: 10.1016/j.envpol.2022.120811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/26/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Brain is a potential target for neuroprogestogens and/or peripheral progestogens. Previous studies reported that expression of genes about steroidogenesis, reproduction, cell cycle, and circadian rhythm in zebrafish brain could be affected by progestogens. However, there are limited information from metabolites or biomacromolecules aspects, leaving an enormous gap in understanding toxic effects of progestogens on fish brain. In this study, we exposed zebrafish embryos to 2.8, 27.6, and 289.8 ng/L dydrogesterone (DDG, a synthetic progestogen) until sexual maturity (140 days). LC-MS and GC-MS based untargeted metabolomics and Fourier-transform infrared (FTIR) spectroscopy were then performed to investigate the metabolic profiles and macromolecular changes of brain of these zebrafish. The results from multivariate statistical analysis of metabolite features showed a clear separation between different treatment groups of both female and male zebrafish brains. DDG exposure increased the levels of cholesterol, saturated fatty acids, and nucleoside monophosphates, but decreased the contents of polyunsaturated fatty acids (PUFAs), lysophosphatides, and nucleosides in dose-dependent manner. FTIR results indicated that DDG exposure led to accumulation of saturated lipids, reduction of nucleic acids and carbohydrates, and alteration of protein secondary structures. The findings from this study demonstrated that DDG could affect contents of metabolites and biomacromolecules of zebrafish brain, which may finally lead to brain dysfunctions.
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Affiliation(s)
- Yu-Xia Jiang
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China; South China Institute of Environmental Sciences, Ministry of Ecology and Environment, Guangzhou 510535, China; State Key Laboratory of Organic Geochemistry, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, Guangzhou 510640, China
| | - Wen-Jun Shi
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China.
| | - Li-Xin Hu
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Dong-Dong Ma
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
| | - Hui Zhang
- NUS Environmental Research Institute, National University of Singapore, Singapore, 117411
| | - Choon Nam Ong
- School of Public Health, National University of Singapore, Singapore, 117547
| | - Guang-Guo Ying
- SCNU Environmental Research Institute, Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety & MOE Key Laboratory of Theoretical Chemistry of Environment, South China Normal University, Guangzhou 510006, China
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Malik F, Iqbal A, Zia S, Ranjha MMAN, Khalid W, Nadeem M, Selim S, Hadidi M, Moreno A, Manzoor MF, Kowalczewski PŁ, Aadil RM. Role and mechanism of fruit waste polyphenols in diabetes management. OPEN CHEM 2023. [DOI: 10.1515/chem-2022-0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Abstract
Among various diseases in humans, diabetes is one of the most complicated disorders resulting either from the malfunctioning of β cells, causing a poor discharge of insulin from them, or poor functioning of the liberated insulin. A wide array of chemical compounds so-called secondary metabolites are present in plants. These phytochemicals are produced as by-products of metabolism and play a key role in plant protection. However, in humans, they offer several beneficial functions. Polyphenols are an important class of phytochemicals and apart from fruits, they are also found in their major wastes mainly including the peel, pomace, and seed. The current review is aimed to focus on the potential sources, distribution, and extraction/isolation of polyphenols from major fruit wastes along with highlighting their medicinal and therapeutic benefits, especially in the management of diabetes.
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Affiliation(s)
- Faiqa Malik
- Institute of Food Science and Nutrition, University of Sargodha , Sargodha , Pakistan
| | - Aqsa Iqbal
- Institute of Food Science and Nutrition, University of Sargodha , Sargodha , Pakistan
| | - Sabika Zia
- Institute of Food Science and Nutrition, University of Sargodha , Sargodha , Pakistan
| | | | - Waseem Khalid
- Department of Food Science, Government College University Faisalabad , Faisalabad , Pakistan
| | - Muhammad Nadeem
- Institute of Food Science and Nutrition, University of Sargodha , Sargodha , Pakistan
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University , Sakaka 72341 , Saudi Arabia
| | - Milad Hadidi
- Department of Organic Chemistry, Faculty of Chemical Sciences and Technologies, University of Castilla-La Mancha , 13071 , Ciudad Real , Spain
| | - Andres Moreno
- Department of Organic Chemistry, Faculty of Chemical Sciences and Technologies, University of Castilla-La Mancha , 13071 , Ciudad Real , Spain
| | - Muhammad Faisal Manzoor
- Guangdong Provincial Key Laboratory of Intelligent Food Manufacturing, Foshan University , Foshan , China
| | | | - Rana Muhammad Aadil
- National Institute of Food Science and Technology, University of Agriculture , Faisalabad , 38000 , Pakistan
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Mohamed HT, Untereiner V, Cinque G, Ibrahim SA, Götte M, Nguyen NQ, Rivet R, Sockalingum GD, Brézillon S. Infrared Microspectroscopy and Imaging Analysis of Inflammatory and Non-Inflammatory Breast Cancer Cells and Their GAG Secretome. Molecules 2020; 25:molecules25184300. [PMID: 32961706 PMCID: PMC7570935 DOI: 10.3390/molecules25184300] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 12/11/2022] Open
Abstract
Glycosaminoglycans (GAGs)/proteoglycans (PGs) play a pivotal role in the metastasis of inflammatory breast cancer (IBC). They represent biomarkers and targets in diagnosis and treatment of different cancers including breast cancer. Thus, GAGs/PGs could represent potential prognostic/diagnostic biomarkers for IBC. In the present study, non-IBC MDA-MB-231, MCF7, SKBR3 cells and IBC SUM149 cells, as well as their GAG secretome were analyzed. The latter was measured in toto as dried drops with high-throughput (HT) Fourier Transform InfraRed (FTIR) spectroscopy and imaging. FTIR imaging was also employed to investigate single whole breast cancer cells while synchrotron-FTIR microspectroscopy was used to specifically target their cytoplasms. Data were analyzed by hierarchical cluster analysis and principal components analysis. Results obtained from HT-FTIR analysis of GAG drops showed that the inter-group variability enabled us to delineate between cell types in the GAG absorption range 1350–800 cm−1. Similar results were obtained for FTIR imaging of GAG extracts and fixed single whole cells. Synchrotron-FTIR data from cytoplasms allowed discrimination between non-IBC and IBC. Thus, by using GAG specific region, not only different breast cancer cell lines could be differentiated, but also non-IBC from IBC cells. This could be a potential diagnostic spectral marker for IBC detection useful for patient management.
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Affiliation(s)
- Hossam Taha Mohamed
- Laboratoire de Biochimie Médicale et Biologie Moléculaire, Université de Reims Champagne-Ardenne, 51097 Reims, France; (H.T.M.); (R.R.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire—MEDyC, 51097 Reims, France
- Zoology Department, Faculty of Science, Cairo University, Giza 12613, Egypt;
- Faculty of Biotechnology, October University for Modern Sciences and Arts, Giza 12613, Egypt
| | | | - Gianfelice Cinque
- MIRIAM Beamline B22, Diamond Light Source, Harwell Campus, Chilton-Didcot OX11 0DE, UK; (G.C.); (N.Q.N.)
| | | | - Martin Götte
- Department of Gynecology and Obstetrics, Münster University Hospital, 48149 Münster, Germany;
| | - Nguyet Que Nguyen
- MIRIAM Beamline B22, Diamond Light Source, Harwell Campus, Chilton-Didcot OX11 0DE, UK; (G.C.); (N.Q.N.)
| | - Romain Rivet
- Laboratoire de Biochimie Médicale et Biologie Moléculaire, Université de Reims Champagne-Ardenne, 51097 Reims, France; (H.T.M.); (R.R.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire—MEDyC, 51097 Reims, France
| | | | - Stéphane Brézillon
- Laboratoire de Biochimie Médicale et Biologie Moléculaire, Université de Reims Champagne-Ardenne, 51097 Reims, France; (H.T.M.); (R.R.)
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire—MEDyC, 51097 Reims, France
- Correspondence: ; Tel.: +33-326913734
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Gieroba B, Arczewska M, Sławińska-Brych A, Rzeski W, Stepulak A, Gagoś M. Prostate and breast cancer cells death induced by xanthohumol investigated with Fourier transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:118112. [PMID: 32014658 DOI: 10.1016/j.saa.2020.118112] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Fourier Transform Infrared spectroscopy was applied to detect in vitro cell death induced in prostate (PC-3) and breast (T47D) cancer cell lines treated with xanthohumol (XN). After incubation of the cancer cells with XN, specific spectral shifts in the infrared spectra arising from selected cellular components were identified that reflected biochemical changes characteristic for apoptosis and necrosis. Detailed analysis of specific absorbance intensity ratios revealed the compositional changes in the secondary structure of proteins and membrane lipids. In this study, for the first time we examined the changes in these molecular components and linked them to deduce the involvement of molecular mechanisms in the XN-induced death of the selected cancer cells. We showed that XN concentration-dependent changes were attributed to phospholipid ester carbonyl groups, especially in the case of T47D cells, suggesting that XN acts as an inhibitor of cell proliferation. Additionally, we observed distinct changes in the region assigned to the absorption of DNA, which were correlated with a specific marker of cell death and dependent on the XN dose and the type of cancer cells. The microscopic observation and flow cytometry analysis revealed that the decrease in cancer cell viability was mainly related to the induction of necrotic cell death. Moreover, the T47D cells were slightly more sensitive to XN than the PC-3 cells. Considering the results obtained, it can be assumed that apoptosis and necrosis induced by XN may contribute to the anti-proliferative and cytotoxic properties of this flavonoid against cancer cell lines PC-3 and T47D.
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Affiliation(s)
- Barbara Gieroba
- Department of Cell Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; Department of Biopharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland.
| | - Marta Arczewska
- Department of Biophysics, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Adrianna Sławińska-Brych
- Department of Cell Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
| | - Wojciech Rzeski
- Department of Virology and Immunology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland; Department of Medical Biology, Institute of Rural Health in Lublin, Jaczewskiego 2, 20-090 Lublin, Poland
| | - Andrzej Stepulak
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland
| | - Mariusz Gagoś
- Department of Cell Biology, Maria Curie-Skłodowska University, Akademicka 19, 20-033 Lublin, Poland
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de Camargo AC, Schwember AR, Parada R, Garcia S, Maróstica MR, Franchin M, Regitano-d'Arce MAB, Shahidi F. Opinion on the Hurdles and Potential Health Benefits in Value-Added Use of Plant Food Processing By-Products as Sources of Phenolic Compounds. Int J Mol Sci 2018; 19:E3498. [PMID: 30404239 PMCID: PMC6275048 DOI: 10.3390/ijms19113498] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 12/23/2022] Open
Abstract
Plant foods, their products and processing by-products are well recognized as important sources of phenolic compounds. Recent studies in this field have demonstrated that food processing by-products are often richer sources of bioactive compounds as compared with their original feedstock. However, their final application as a source of nutraceuticals and bioactives requires addressing certain hurdles and challenges. This review discusses recent knowledge advances in the use of plant food processing by-products as sources of phenolic compounds with special attention to the role of genetics on the distribution and biosynthesis of plant phenolics, as well as their profiling and screening, potential health benefits, and safety issues. The potentialities in health improvement from food phenolics in animal models and in humans is well substantiated, however, considering the emerging market of plant food by-products as potential sources of phenolic bioactives, more research in humans is deemed necessary.
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Affiliation(s)
- Adriano Costa de Camargo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
- Department of Food Science and Technology, Londrina State University, Londrina 86051-990, Parana State, Brazil.
- Department of Agri-Food Industry, Food & Nutrition, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba 13418-900, São Paulo State, Brazil.
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Roberto Parada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Sandra Garcia
- Department of Food Science and Technology, Londrina State University, Londrina 86051-990, Parana State, Brazil.
| | - Mário Roberto Maróstica
- Department of Food and Nutrition, University of Campinas-UNICAMP, Campinas 13083-862, São Paulo State, Brazil.
| | - Marcelo Franchin
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba 13414-903, São Paulo State, Brazil.
| | - Marisa Aparecida Bismara Regitano-d'Arce
- Department of Agri-Food Industry, Food & Nutrition, "Luiz de Queiroz" College of Agriculture, University of São Paulo, Piracicaba 13418-900, São Paulo State, Brazil.
| | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
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Smolina M, Goormaghtigh E. Gene expression data and FTIR spectra provide a similar phenotypic description of breast cancer cell lines in 2D and 3D cultures. Analyst 2018; 143:2520-2530. [DOI: 10.1039/c8an00145f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Gene expression patterns and FTIR spectral data are strongly correlated. Both identified the genotypes and phenotypes of breast cancer cell lines.
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Affiliation(s)
- Margarita Smolina
- Laboratory for the Structure and Function of Biological Membranes
- Center for Structural Biology and Bioinformatics
- Université Libre de Bruxelles
- Brussels
- Belgium
| | - Erik Goormaghtigh
- Laboratory for the Structure and Function of Biological Membranes
- Center for Structural Biology and Bioinformatics
- Université Libre de Bruxelles
- Brussels
- Belgium
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Mohamed HT, Untereiner V, Proult I, Ibrahim SA, Götte M, El-Shinawi M, Mohamed MM, Sockalingum GD, Brézillon S. Characterization of inflammatory breast cancer: a vibrational microspectroscopy and imaging approach at the cellular and tissue level. Analyst 2018; 143:6103-6112. [DOI: 10.1039/c8an01292j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Inflammatory breast cancer (IBC) has a poor prognosis because of the lack of specific biomarkers and its late diagnosis.
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Affiliation(s)
- Hossam Taha Mohamed
- Université de Reims Champagne-Ardenne
- Laboratoire de Biochimie Médicale et de Biologie Moléculaire
- UFR de Médecine
- Reims
- France
| | - Valérie Untereiner
- Plateforme d'imagerie Cellulaire et Tissulaire (PICT)
- Université de Reims Champagne-Ardenne
- Reims
- France
| | - Isabelle Proult
- Université de Reims Champagne-Ardenne
- Laboratoire de Biochimie Médicale et de Biologie Moléculaire
- UFR de Médecine
- Reims
- France
| | | | - Martin Götte
- Department of Gynecology and Obstetrics
- Münster University Hospital
- Münster
- Germany
| | - Mohamed El-Shinawi
- Department of General Surgery
- Faculty of Medicine
- Ain Shams University
- Egypt
| | | | - Ganesh D. Sockalingum
- BioSpecT-BioSpectroscopieTranslationnelle
- EA7506
- Université de Reims Champagne-Ardenne
- UFR de Pharmacie
- Reims
| | - Stéphane Brézillon
- Université de Reims Champagne-Ardenne
- Laboratoire de Biochimie Médicale et de Biologie Moléculaire
- UFR de Médecine
- Reims
- France
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