1
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Sandt C. Identification and classification of proteins by FTIR microspectroscopy. A proof of concept. Biochim Biophys Acta Gen Subj 2024; 1868:130688. [PMID: 39117047 DOI: 10.1016/j.bbagen.2024.130688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 07/23/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
FTIR spectroscopy is well known for its molecule fingerprinting capability but is also able to differentiate classes in complex biological systems. This includes strain typing and species level identification of bacterial, yeast or fungal cells, as well as distinguishing between cell layers in eukaryotic tissues. However, its use for the identification of macromolecules such as proteins remains underexplored and rarely used in practice. Here we demonstrate the efficacy of FTIR microspectroscopy coupled with machine learning methods for rapid and accurate identification of proteins in their dry state within minutes, from very small quantities of material, if they are obtained in a pure aqueous solution. FTIR microspectroscopy can provide additional information beside identification: it can detect small differences among different purification batches potentially originating from post-translational modifications or distinct folding states. Moreover, it distinguishes glycoproteins and evaluate glycosylation while detecting contaminants. This methodology presents itself as a valuable quality control tool in protein purification processes or any process requiring the utilization of precisely identified, pure proteins.
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Affiliation(s)
- Christophe Sandt
- SMIS beamline, Synchrotron SOLEIL, RD128, 91190 Saint Aubin, France.
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2
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Dučić T, Sanchez-Mata A, Castillo-Sanchez J, Algarra M, Gonzalez-Munoz E. Monitoring oocyte-based human pluripotency acquisition using synchrotron-based FTIR microspectroscopy reveals specific biomolecular trajectories. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 297:122713. [PMID: 37084681 DOI: 10.1016/j.saa.2023.122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/09/2023] [Accepted: 04/03/2023] [Indexed: 05/03/2023]
Abstract
The reprogramming of human somatic cells to induced pluripotent cells (iPSCs) has become a milestone and a paradigm shift in the field of regenerative medicine and human disease modeling including drug testing and genome editing. However, the molecular processes occurring during reprogramming and affecting the pluripotent state acquired remain largely unknown. Of interest, different pluripotent states have been described depending on the reprogramming factors used and the oocyte has emerged as a valuable source of information for candidate factors. The present study investigates the molecular changes occurring in somatic cells during reprogramming with either canonical (OSK) or oocyte-based (AOX15) combinations using synchrotron-radiation Fourier transform infrared (SR FTIR) spectroscopy. The data acquired by SR FTIR indicates different representation and conformation of biological relevant macromolecules (lipids, nucleic acids, carbohydrates and proteins) depending on the reprogramming combination used and at different stages during the reprogramming process. Association analysis based on cells spectra suggest that pluripotency acquisition trajectories converge at late intermediate stages while they diverge at early stages. Our results suggest that OSK and AOX15 reprogramming operates through differential mechanisms affecting nucleic acids reorganization and day 10 comes out as a candidate hinge point to further study the molecular pathways involved in the reprogramming process. This study indicates that SR FTIR approach contribute unpaired information to distinguish pluripotent states and to decipher pluripotency acquisition roadmaps and landmarks that will enable advanced biomedical applications of iPSCs.
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Affiliation(s)
- Tanja Dučić
- ALBA Synchrotron Light Source, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Barcelona, Spain.
| | - Alicia Sanchez-Mata
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Jesus Castillo-Sanchez
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain
| | - Manuel Algarra
- INAMAT(2) Institute for Advanced Materials and Mathematics, Department of Sciences, Public University of Navarre, Campus de Arrosadia, 31006 Pamplona, Spain
| | - Elena Gonzalez-Munoz
- Biomedical Research Institute and Nanomedicine Platform (IBIMA-BIONAND), C/ Severo Ochoa, 35, Malaga, Spain; Department of Cell Biology, Genetics and Physiology, University of Málaga, 29071 Málaga, Spain.
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3
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Discrimination and Prediction of Lonicerae japonicae Flos and Lonicerae Flos and Their Related Prescriptions by Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy Combined with Multivariate Statistical Analysis. Molecules 2022; 27:molecules27144640. [PMID: 35889512 PMCID: PMC9322902 DOI: 10.3390/molecules27144640] [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: 06/15/2022] [Revised: 07/10/2022] [Accepted: 07/14/2022] [Indexed: 12/03/2022] Open
Abstract
LJF and LF are commonly used in Chinese patent drugs. In the Chinese Pharmacopoeia, LJF and LF once belonged to the same source. However, since 2005, the two species have been listed separately. Therefore, they are often misused, and medicinal materials are indiscriminately put in their related prescriptions in China. In this work, firstly, we established a model for discriminating LJF and LF using ATR-FTIR combined with multivariate statistical analysis. The spectra data were further preprocessed and combined with spectral filter transformations and normalization methods. These pretreated data were used to establish pattern recognition models with PLS-DA, RF, and SVM. Results demonstrated that the RF model was the optimal model, and the overall classification accuracy for LJF and LF samples reached 98.86%. Then, the established model was applied in the discrimination of their related prescriptions. Interestingly, the results show good accuracy and applicability. The RF model for discriminating the related prescriptions containing LJF or LF had an accuracy of 100%. Our results suggest that this method is a rapid and effective tool for the successful discrimination of LJF and LF and their related prescriptions.
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4
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Sandt C, Feraud O, Bonnet ML, Desterke C, Khedhir R, Flamant S, Bailey CG, Rasko JEJ, Dumas P, Bennaceur-Griscelli A, Turhan AG. Direct and rapid identification of T315I-Mutated BCR-ABL expressing leukemic cells using infrared microspectroscopy. Biochem Biophys Res Commun 2018; 503:1861-1867. [PMID: 30057314 DOI: 10.1016/j.bbrc.2018.07.127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 01/07/2023]
Abstract
Despite the major success obtained by the use of tyrosine kinase inhibitors (TKI) in chronic myeloid leukemia (CML), resistances to therapies occur due to mutations in the ABL-kinase domain of the BCR-ABL oncogene. Amongst these mutations, the "gatekeeper" T315I is a major concern as it renders leukemic cells resistant to all licenced TKI except Ponatinib. We report here that Fourier transform infrared (FTIR) microspectroscopy is a powerful methodology allowing rapid and direct identification of a spectral signature in single cells expressing T315I-mutated BCR-ABL. The specificity of this spectral signature is confirmed using a Dox-inducible T315I-mutated BCR-ABL-expressing human UT-7 cells as well as in murine embryonic stem cells. Transcriptome analysis of UT-7 cells expressing BCR-ABL as compared to BCR-ABL T315I clearly identified a molecular signature which could be at the origin of the generation of metabolic changes giving rise to the spectral signature. Thus, these results suggest that this new methodology can be applied to the identification of leukemic cells harbouring the T315I mutation at the single cell level and could represent a novel early detection tool of mutant clones. It could also be applied to drug screening strategies to target T315I-mutated leukemic cells.
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MESH Headings
- Animals
- Cell Line
- Fusion Proteins, bcr-abl/genetics
- Fusion Proteins, bcr-abl/metabolism
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/metabolism
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Mice
- Mutation
- Spectroscopy, Fourier Transform Infrared
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Affiliation(s)
| | | | | | | | | | | | - Charles G Bailey
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Locked Bag No 6, Newtown, NSW, 2042, Australia; Sydney Medical School, University of Sydney, 2006, NSW, Australia
| | - John E J Rasko
- Gene and Stem Cell Therapy Program, Centenary Institute, University of Sydney, Locked Bag No 6, Newtown, NSW, 2042, Australia; Sydney Medical School, University of Sydney, 2006, NSW, Australia; Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2052, NSW, Australia
| | - Paul Dumas
- SOLEIL Synchrotron, Saint Aubin, 91192, Gif sur Yvette, France
| | - Annelise Bennaceur-Griscelli
- INSERM UMR_S_935, Campus CNRS, Villejuif, France; Department of Hematology, Paris Sud Hematology Institute, AP-HP Hôpital Paul Brousse, Villejuif, France; INGESTEM National Pluripotent Stem Cell Infrastructure, University Paris Sud 11, Villejuif, France
| | - Ali G Turhan
- INSERM UMR_S_935, Campus CNRS, Villejuif, France; Department of Hematology, Paris Sud Hematology Institute, AP-HP Hôpital Paul Brousse, Villejuif, France; INGESTEM National Pluripotent Stem Cell Infrastructure, University Paris Sud 11, Villejuif, France.
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5
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Verdonck M, Denayer A, Delvaux B, Garaud S, De Wind R, Desmedt C, Sotiriou C, Willard-Gallo K, Goormaghtigh E. Characterization of human breast cancer tissues by infrared imaging. Analyst 2017; 141:606-19. [PMID: 26535413 DOI: 10.1039/c5an01512j] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fourier Transform InfraRed (FTIR) spectroscopy coupled to microscopy (IR imaging) has shown unique advantages in detecting morphological and molecular pathologic alterations in biological tissues. The aim of this study was to evaluate the potential of IR imaging as a diagnostic tool to identify characteristics of breast epithelial cells and the stroma. In this study a total of 19 breast tissue samples were obtained from 13 patients. For 6 of the patients, we also obtained Non-Adjacent Non-Tumor tissue samples. Infrared images were recorded on the main cell/tissue types identified in all breast tissue samples. Unsupervised Principal Component Analyses and supervised Partial Least Square Discriminant Analyses (PLS-DA) were used to discriminate spectra. Leave-one-out cross-validation was used to evaluate the performance of PLS-DA models. Our results show that IR imaging coupled with PLS-DA can efficiently identify the main cell types present in FFPE breast tissue sections, i.e. epithelial cells, lymphocytes, connective tissue, vascular tissue and erythrocytes. A second PLS-DA model could distinguish normal and tumor breast epithelial cells in the breast tissue sections. A patient-specific model reached particularly high sensitivity, specificity and MCC rates. Finally, we showed that the stroma located close or at distance from the tumor exhibits distinct spectral characteristics. In conclusion FTIR imaging combined with computational algorithms could be an accurate, rapid and objective tool to identify/quantify breast epithelial cells and differentiate tumor from normal breast tissue as well as normal from tumor-associated stroma, paving the way to the establishment of a potential complementary tool to ensure safe tumor margins.
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Affiliation(s)
- M Verdonck
- Laboratory of Structure and Function of Biological Membranes, Center of Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
| | - A Denayer
- Laboratory of Structure and Function of Biological Membranes, Center of Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
| | - B Delvaux
- Laboratory of Structure and Function of Biological Membranes, Center of Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
| | - S Garaud
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - R De Wind
- Pathological Anatomy Department, Institut Jules Bordet, Brussels, Belgium
| | - C Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - C Sotiriou
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Brussels, Belgium
| | - K Willard-Gallo
- Molecular Immunology Unit, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - E Goormaghtigh
- Laboratory of Structure and Function of Biological Membranes, Center of Structural Biology and Bioinformatics, Université Libre de Bruxelles, Brussels, Belgium.
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6
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Sandt C, Nadaradjane C, Richards R, Dumas P, Sée V. Use of infrared microspectroscopy to elucidate a specific chemical signature associated with hypoxia levels found in glioblastoma. Analyst 2016; 141:870-83. [DOI: 10.1039/c5an02112j] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Detection of the chemical signature associated with hypoxia in single glioblastoma cells by synchrotron infrared microspectroscopy.
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Affiliation(s)
- Christophe Sandt
- Synchrotron SOLEIL
- L'Orme des Merisiers
- 91192 Gif sur Yvette
- France
| | - Céline Nadaradjane
- Synchrotron SOLEIL
- L'Orme des Merisiers
- 91192 Gif sur Yvette
- France
- Department of Biochemistry
| | - Rosalie Richards
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool
- UK
| | - Paul Dumas
- Synchrotron SOLEIL
- L'Orme des Merisiers
- 91192 Gif sur Yvette
- France
| | - Violaine Sée
- Department of Biochemistry
- Institute of Integrative Biology
- University of Liverpool
- Liverpool
- UK
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7
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Kenig S, Bedolla DE, Birarda G, Faoro V, Mitri E, Vindigni A, Storici P, Vaccari L. Fourier transform infrared microspectroscopy reveals biochemical changes associated with glioma stem cell differentiation. Biophys Chem 2015; 207:90-6. [DOI: 10.1016/j.bpc.2015.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/22/2015] [Accepted: 09/22/2015] [Indexed: 02/08/2023]
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8
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Courtot AM, Magniez A, Oudrhiri N, Féraud O, Bacci J, Gobbo E, Proust S, Turhan AG, Bennaceur-Griscelli A. Morphological analysis of human induced pluripotent stem cells during induced differentiation and reverse programming. Biores Open Access 2014; 3:206-16. [PMID: 25371857 PMCID: PMC4215385 DOI: 10.1089/biores.2014.0028] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The fine analysis of cell components during the generation of pluripotent cells and their comparison to bone fide human embryonic stem cells (hESCs) are valuable tools to understand their biological behavior. In this report, human mesenchymal cells (hMSCs) generated from the human ES cell line H9, were reprogrammed back to induced pluripotent state using Oct-4, Sox2, Nanog, and Lin28 transgenes. Human induced pluripotent stem cells (hIPSCs) were analyzed using electron microscopy and compared with regard to the original hESCs and the hMSCs from which they were derived. This analysis shows that hIPSCs and the original hESCs are morphologically undistinguishable but differ from the hMSCs with respect to the presence of several morphological features of undifferentiated cells at both the cytoplasmic (ribosomes, lipid droplets, glycogen, scarce reticulum) and nuclear levels (features of nuclear plasticity, presence of euchromatin, reticulated nucleoli). We show that hIPSC colonies generated this way presented epithelial aspects with specialized junctions highlighting morphological criteria of the mesenchymal–epithelial transition in cells engaged in a successful reprogramming process. Electron microscopic analysis revealed also specific morphological aspects of partially reprogrammed cells. These results highlight the valuable use of electron microscopy for a better knowledge of the morphological aspects of IPSC and cellular reprogramming.
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Affiliation(s)
- Anne-Marie Courtot
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France . ; Université Paris Sud , Faculté de Médecine, Le Kremlin Bicêtre, France
| | - Aurélie Magniez
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France
| | - Noufissa Oudrhiri
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France . ; Service d'Hématologie Biologique APHP, Hôpital Paul Brousse , GHU Paris Sud Villejuif, France
| | - Olivier Féraud
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France
| | - Josette Bacci
- Service de Neurologie, Hôpital Bicêtre APHP , Le Kremlin Bicêtre, France
| | - Emilie Gobbo
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France
| | - Stéphanie Proust
- Service de Virologie, Hôpital Bicêtre APHP , Le Kremlin Bicêtre, France
| | - Ali G Turhan
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France . ; Université Paris Sud , Faculté de Médecine, Le Kremlin Bicêtre, France . ; Service d'Hématologie Biologique APHP, Hôpital Bicêtre , GHU Paris Sud, Le Kremlin Bicêtre, France
| | - Annelise Bennaceur-Griscelli
- Inserm U935, ES-TEAM Paris Sud, Ingestem , Villejuif, France . ; Université Paris Sud , Faculté de Médecine, Le Kremlin Bicêtre, France . ; Service d'Hématologie Biologique APHP, Hôpital Paul Brousse , GHU Paris Sud Villejuif, France
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9
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Cao J, Ng ES, McNaughton D, Stanley EG, Elefanty AG, Tobin MJ, Heraud P. Fourier transform infrared microspectroscopy reveals unique phenotypes for human embryonic and induced pluripotent stem cell lines and their progeny. JOURNAL OF BIOPHOTONICS 2014; 7:767-781. [PMID: 23616434 DOI: 10.1002/jbio.201200217] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/24/2013] [Accepted: 03/25/2013] [Indexed: 06/02/2023]
Abstract
Fourier transform infrared (FTIR) microspectroscopy was employed to elucidate the macromolecular phenotype of human embryonic stem cells (hESCs) and human induced pluripotent stem cells (hiPSCs) and their differentiated progeny. Undifferentiated hESCs and hiPSC lines were found to be not clearly distinguishable from each other. However, although both hESC and hiPSC variants appeared to undergo similar changes during differentiation in terms of cell surface antigens, the derived cell types from all cell lines could be discriminated using FTIR spectroscopy. We foresee a possible future role for FTIR microspectroscopy as a powerful and objective investigative and quality control tool in regenerative medicine.
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Affiliation(s)
- Julie Cao
- Monash Immunology and Stem Cell Laboratories, Monash University, Building 75, STRIP 1, West Ring Road, Clayton, Victoria 3800, Australia; Centre for Biospectroscopy and the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia
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10
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Mereghetti P, Corsetto PA, Cremona A, Rizzo AM, Doglia SM, Ami D. A Fourier transform infrared spectroscopy study of cell membrane domain modifications induced by docosahexaenoic acid. Biochim Biophys Acta Gen Subj 2014; 1840:3115-22. [DOI: 10.1016/j.bbagen.2014.07.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 06/25/2014] [Accepted: 07/02/2014] [Indexed: 12/15/2022]
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11
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Sulé-Suso J, Forsyth N, Untereiner V, Sockalingum G. Vibrational spectroscopy in stem cell characterisation: is there a niche? Trends Biotechnol 2014; 32:254-62. [DOI: 10.1016/j.tibtech.2014.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Revised: 03/04/2014] [Accepted: 03/05/2014] [Indexed: 11/29/2022]
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12
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Ami D, Di Segni M, Forcella M, Meraviglia V, Baccarin M, Doglia SM, Terzoli G. Role of water in chromosome spreading and swelling induced by acetic acid treatment: a FTIR spectroscopy study. Eur J Histochem 2014; 58:2330. [PMID: 24705001 PMCID: PMC3980214 DOI: 10.4081/ejh.2014.2330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 11/23/2022] Open
Abstract
The so called chromosome preparation is a procedure consisting of three strictly connected stages that enables to obtain chromosomes of quality suitable for cytogenetic analysis. Interestingly, experimental evidence strongly suggested that chromosome spreading and swelling (key processes that allow their counting and detailed structural analysis) are induced in the last fixative-evaporation stage by the interaction, mediated by acetic acid, between water from the environmental humidity, and the cytoplasmic matrix and the chromatin. However, since a considerable variation in the quality of chromosome preparations is observed, strongly depending on the environmental conditions in which the procedure takes place, a better comprehension of the mechanisms underlying chromosome preparation is required. To this aim, here we analysed intact lymphocytes before and at each stage of the chromosome preparation protocol by Fourier transform infrared (FTIR) spectroscopy, a technique widely used for the study not only of isolated biomolecules, but also of complex biological systems, such as whole cells. Interestingly, we found that the chromosome preparation protocol induces significant structural changes of cell proteins and DNA, in particular due to the interaction with acetic acid. Moreover, noteworthy, through the monitoring of changes in the water combination band between 2300 and 1800 cm–1, we provided evidence at molecular level of the crucial role of the bound water to the cytoplasmic matrix and to the chromatin in determining the chromosome spreading and swelling. Our FTIR results, therefore, underline the need to perform the last fixative-evaporation stage in standardized and optimized temperature and relative humidity conditions, thus providing chromosomes of high quality for the cytogenetic analysis that would lead in this way to more reliable results.
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Affiliation(s)
- D Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, Milano, 20126, Italy.
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13
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Cao J, Ng ES, McNaughton D, Stanley EG, Elefanty AG, Tobin MJ, Heraud P. The characterisation of pluripotent and multipotent stem cells using Fourier transform infrared microspectroscopy. Int J Mol Sci 2013; 14:17453-76. [PMID: 24065090 PMCID: PMC3794735 DOI: 10.3390/ijms140917453] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 07/22/2013] [Accepted: 07/22/2013] [Indexed: 01/08/2023] Open
Abstract
Fourier transform infrared (FTIR) microspectroscopy shows potential as a benign, objective and rapid tool to screen pluripotent and multipotent stem cells for clinical use. It offers a new experimental approach that provides a holistic measurement of macromolecular composition such that a signature representing the internal cellular phenotype is obtained. The use of this technique therefore contributes information that is complementary to that acquired by conventional genetic and immunohistochemical methods.
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Affiliation(s)
- Julie Cao
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia; E-Mails: (J.C.); (E.S.N.); (E.G.S.); (A.G.E.)
- Centre for Biospectroscopy and the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; E-Mail:
| | - Elizabeth S. Ng
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia; E-Mails: (J.C.); (E.S.N.); (E.G.S.); (A.G.E.)
- Murdoch Childrens Research Institute, the Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - Donald McNaughton
- Centre for Biospectroscopy and the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; E-Mail:
| | - Edouard G. Stanley
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia; E-Mails: (J.C.); (E.S.N.); (E.G.S.); (A.G.E.)
- Murdoch Childrens Research Institute, the Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - Andrew G. Elefanty
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia; E-Mails: (J.C.); (E.S.N.); (E.G.S.); (A.G.E.)
- Murdoch Childrens Research Institute, the Royal Children’s Hospital, Parkville, Victoria 3052, Australia
| | - Mark J. Tobin
- Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168, Australia; E-Mail:
| | - Philip Heraud
- Department of Anatomy and Developmental Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Wellington Road, Clayton, Victoria 3800, Australia; E-Mails: (J.C.); (E.S.N.); (E.G.S.); (A.G.E.)
- Centre for Biospectroscopy and the School of Chemistry, Monash University, Clayton, Victoria 3800, Australia; E-Mail:
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +61-3-9905-0765; Fax: +61-3-9905-5613
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14
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Liberski AR, Al-Noubi MN, Rahman ZH, Halabi NM, Dib SS, Al-Mismar R, Billing AM, Krishnankutty R, Ahmad FS, Raynaud CM, Rafii A, Engholm-Keller K, Graumann J. Adaptation of a commonly used, chemically defined medium for human embryonic stem cells to stable isotope labeling with amino acids in cell culture. J Proteome Res 2013; 12:3233-45. [PMID: 23734825 DOI: 10.1021/pr400099j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Metabolic labeling with stable isotopes is a prominent technique for comparative quantitative proteomics, and stable isotope labeling with amino acids in cell culture (SILAC) is the most commonly used approach. SILAC is, however, traditionally limited to simple tissue culture regimens and only rarely employed in the context of complex culturing conditions as those required for human embryonic stem cells (hESCs). Classic hESC culture is based on the use of mouse embryonic fibroblasts (MEFs) as a feeder layer, and as a result, possible xenogeneic contamination, contribution of unlabeled amino acids by the feeders, interlaboratory variability of MEF preparation, and the overall complexity of the culture system are all of concern in conjunction with SILAC. We demonstrate a feeder-free SILAC culture system based on a customized version of a commonly used, chemically defined hESC medium developed by Ludwig et al. and commercially available as mTeSR1 [mTeSR1 is a trade mark of WiCell (Madison, WI) licensed to STEMCELL Technologies (Vancouver, Canada)]. This medium, together with adjustments to the culturing protocol, facilitates reproducible labeling that is easily scalable to the protein amounts required by proteomic work flows. It greatly enhances the usability of quantitative proteomics as a tool for the study of mechanisms underlying hESCs differentiation and self-renewal. Associated data have been deposited to the ProteomeXchange with the identifier PXD000151.
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15
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Sandt C, Frederick J, Dumas P. Profiling pluripotent stem cells and organelles using synchrotron radiation infrared microspectroscopy. JOURNAL OF BIOPHOTONICS 2013; 6:60-72. [PMID: 23125135 DOI: 10.1002/jbio.201200139] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Revised: 09/27/2012] [Accepted: 10/01/2012] [Indexed: 05/22/2023]
Abstract
FTIR micro-spectroscopy is a sensitive, non-destructive and label-free method offering diffraction-limited resolution with high signal-to-noise ratios when combined with a synchrotron radiation source. The vibrational signature of individual cells was used to validate an alternative strategy for reprogramming induced pluripotent stem cells generated from amniocytes. The iPSC lines PB09 and PB10, were reprogrammed from the same amniocyte cell line using respectively the Oct54, Sox2, Lin28, and Nanog and the Oct4 and Sox2 transcription factor cocktail. We show that cells reprogrammed by the two different sets of transfection factors have similar spectral signatures after reprogramming, except for a small subpopulation of cells in one of the cell lines. Mapping HeLa cells at subcellular resolution, we show that the Golgi apparatus, the cytoplasm and the nucleus have a specific spectral signature. The CH(3):CH(2) ratio is the highest in the nucleus and the lowest in the Golgi apparatus/endoplasmic reticulum, in agreement with the membrane composition of these organelles. This is confirmed by specific staining of the organelles with fluorescent dyes. Subcellular differentiation of cell compartments is also demonstrated in living cells.
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Affiliation(s)
- Christophe Sandt
- Synchrotron SOLEIL, L'Orme des Merisiers, Gif-sur-Yvette, France
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