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Prostate cancer histopathology using label-free multispectral deep-UV microscopy quantifies phenotypes of tumor aggressiveness and enables multiple diagnostic virtual stains. Sci Rep 2022; 12:9329. [PMID: 35665770 PMCID: PMC9167293 DOI: 10.1038/s41598-022-13332-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 05/23/2022] [Indexed: 12/20/2022] Open
Abstract
Identifying prostate cancer patients that are harboring aggressive forms of prostate cancer remains a significant clinical challenge. Here we develop an approach based on multispectral deep-ultraviolet (UV) microscopy that provides novel quantitative insight into the aggressiveness and grade of this disease, thus providing a new tool to help address this important challenge. We find that UV spectral signatures from endogenous molecules give rise to a phenotypical continuum that provides unique structural insight (i.e., molecular maps or “optical stains") of thin tissue sections with subcellular (nanoscale) resolution. We show that this phenotypical continuum can also be applied as a surrogate biomarker of prostate cancer malignancy, where patients with the most aggressive tumors show a ubiquitous glandular phenotypical shift. In addition to providing several novel “optical stains” with contrast for disease, we also adapt a two-part Cycle-consistent Generative Adversarial Network to translate the label-free deep-UV images into virtual hematoxylin and eosin (H&E) stained images, thus providing multiple stains (including the gold-standard H&E) from the same unlabeled specimen. Agreement between the virtual H&E images and the H&E-stained tissue sections is evaluated by a panel of pathologists who find that the two modalities are in excellent agreement. This work has significant implications towards improving our ability to objectively quantify prostate cancer grade and aggressiveness, thus improving the management and clinical outcomes of prostate cancer patients. This same approach can also be applied broadly in other tumor types to achieve low-cost, stain-free, quantitative histopathological analysis.
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Schiemer R, Furniss D, Phang S, Seddon AB, Atiomo W, Gajjar KB. Vibrational Biospectroscopy: An Alternative Approach to Endometrial Cancer Diagnosis and Screening. Int J Mol Sci 2022; 23:ijms23094859. [PMID: 35563249 PMCID: PMC9102412 DOI: 10.3390/ijms23094859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer and the fourth leading cause of death among women worldwide. Early detection and treatment are associated with a favourable prognosis and reduction in mortality. Unlike other common cancers, however, screening strategies lack the required sensitivity, specificity and accuracy to be successfully implemented in clinical practice and current diagnostic approaches are invasive, costly and time consuming. Such limitations highlight the unmet need to develop diagnostic and screening alternatives for EC, which should be accurate, rapid, minimally invasive and cost-effective. Vibrational spectroscopic techniques, Mid-Infrared Absorption Spectroscopy and Raman, exploit the atomic vibrational absorption induced by interaction of light and a biological sample, to generate a unique spectral response: a “biochemical fingerprint”. These are non-destructive techniques and, combined with multivariate statistical analysis, have been shown over the last decade to provide discrimination between cancerous and healthy samples, demonstrating a promising role in both cancer screening and diagnosis. The aim of this review is to collate available evidence, in order to provide insight into the present status of the application of vibrational biospectroscopy in endometrial cancer diagnosis and screening, and to assess future prospects.
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Affiliation(s)
- Roberta Schiemer
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
- Correspondence:
| | - David Furniss
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Sendy Phang
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Angela B. Seddon
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - William Atiomo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai P.O. Box 505055, United Arab Emirates;
| | - Ketankumar B. Gajjar
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
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Vermassen T, Himpe J, Coopman R, Van Praet C, Lumen N, Rottey S, Delanghe J. Prognostic Features of Near-Infrared Spectroscopy Following Primary Radical Prostatectomy. Cancers (Basel) 2021; 13:cancers13236034. [PMID: 34885144 PMCID: PMC8656494 DOI: 10.3390/cancers13236034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/25/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Only a few biomarkers have been evaluated for their prognostic value with regard to biochemical recurrence (BCR) following primary radical prostatectomy. We explored the possibilities of using near-infrared (NIR) spectroscopy as a prognostic biomarker for BCR-free survival (BCR-FS). METHODS Tissue specimens from 82 prostate cancer patients were obtained. Formalin-fixed paraffin-embedded slides (hematoxylin-eosin-stained) were analyzed using NIR spectroscopy. Prognostic features for BCR-FS were determined following normalization of the spectra. RESULTS Several differences were found throughout the NIR spectrum for the patients with or without BCR, for both the first derivative and second derivative of the NIR spectrum. Following categorization and Cox regression analysis, spectral regions at 5236 cm-1 (first derivative; median BCR-FS not reached versus 3.2 years; HRhigh = 0.18 [0.08-0.39]; and p < 0.0001) and at 5956 cm-1 (second derivative; median BCR-FS not reached versus 3.8 years; HRlow = 0.22 [0.10-0.48]; and p = 0.0002) showed prognostic properties for BCR-FS. The combination of both parameters further increased the prognostic value of NIR (p < 0.0001). CONCLUSIONS We demonstrated NIR spectral variations between patients with or without BCR, which have been shown to have prognostic value. This easy-to-use technique could possibly further improve post-primary radical prostatectomy monitoring and swift referral to adjuvant local therapies. Further elaboration is highly recommended to fully elucidate these variations and to gain a deeper insight into the changing chemical and physical compositions of the prostate tumor architecture.
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Affiliation(s)
- Tijl Vermassen
- Department of Medical Oncology, University Hospital Ghent, 9000 Ghent, Belgium;
- Correspondence: ; Tel.: +32-9-332-5449
| | - Jonas Himpe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium; (J.H.); (J.D.)
| | - Renaat Coopman
- Department of Plastic, Reconstructive and Aesthetic Surgery, University Hospital Ghent, 9000 Ghent, Belgium;
| | - Charles Van Praet
- Department of Urology, University Hospital Ghent, 9000 Ghent, Belgium; (C.V.P.); (N.L.)
| | - Nicolaas Lumen
- Department of Urology, University Hospital Ghent, 9000 Ghent, Belgium; (C.V.P.); (N.L.)
| | - Sylvie Rottey
- Department of Medical Oncology, University Hospital Ghent, 9000 Ghent, Belgium;
| | - Joris Delanghe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium; (J.H.); (J.D.)
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Nuez-Martínez M, Pedrosa L, Martinez-Rovira I, Yousef I, Diao D, Teixidor F, Stanzani E, Martínez-Soler F, Tortosa A, Sierra À, Gonzalez JJ, Viñas C. Synchrotron-Based Fourier-Transform Infrared Micro-Spectroscopy (SR-FTIRM) Fingerprint of the Small Anionic Molecule Cobaltabis(dicarbollide) Uptake in Glioma Stem Cells. Int J Mol Sci 2021; 22:9937. [PMID: 34576098 PMCID: PMC8466526 DOI: 10.3390/ijms22189937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/07/2021] [Accepted: 09/10/2021] [Indexed: 12/16/2022] Open
Abstract
The anionic cobaltabis (dicarbollide) [3,3'-Co(1,2-C2B9H11)2]-, [o-COSAN]-, is the most studied icosahedral metallacarborane. The sodium salts of [o-COSAN]- could be an ideal candidate for the anti-cancer treatment Boron Neutron Capture Therapy (BNCT) as it possesses the ability to readily cross biological membranes thereby producing cell cycle arrest in cancer cells. BNCT is a cancer therapy based on the potential of 10B atoms to produce α particles that cross tissues in which the 10B is accumulated without damaging the surrounding healthy tissues, after being irradiated with low energy thermal neutrons. Since Na[o-COSAN] displays a strong and characteristic ν(B-H) frequency in the infrared range 2.600-2.500 cm-1, we studied the uptake of Na[o-COSAN] followed by its interaction with biomolecules and its cellular biodistribution in two different glioma initiating cells (GICs), mesenchymal and proneural respectively, by using Synchrotron Radiation-Fourier Transform Infrared (FTIR) micro-spectroscopy (SR-FTIRM) facilities at the MIRAS Beamline of ALBA synchrotron light source. The spectroscopic data analysis from the bands in the regions of DNA, proteins, and lipids permitted to suggest that after its cellular uptake, Na[o-COSAN] strongly interacts with DNA strings, modifies proteins secondary structure and also leads to lipid saturation. The mapping suggests the nuclear localization of [o-COSAN]-, which according to reported Monte Carlo simulations may result in a more efficient cell-killing effect compared to that in a uniform distribution within the entire cell. In conclusion, we show pieces of evidence that at low doses, [o-COSAN]- translocates GIC cells' membranes and it alters the physiology of the cells, suggesting that Na[o-COSAN] is a promising agent to BNCT for glioblastoma cells.
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Affiliation(s)
- Miquel Nuez-Martínez
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (M.N.-M.); (F.T.)
| | - Leire Pedrosa
- Laboratory of Experimental Oncological Neurosurgery, Neurosurgery Service, Hospital Clinic de Barcelona—FCRB, 08036 Barcelona, Spain; (L.P.); (D.D.); (J.J.G.)
| | - Immaculada Martinez-Rovira
- Ionizing Radiation Research Group (GRRI), Physics Department, Universitat Autònoma de Barcelona (UAB), Avinguda de l’Eix Central, Edifici C. Campus de la UAB, 08193 Cerdanyola del Vallès, Spain;
- ALBA-CELLS Synchrotron, MIRAS Beamline, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Spain;
| | - Ibraheem Yousef
- ALBA-CELLS Synchrotron, MIRAS Beamline, Carrer de la Llum 2-26, 08290 Cerdanyola del Vallès, Spain;
| | - Diouldé Diao
- Laboratory of Experimental Oncological Neurosurgery, Neurosurgery Service, Hospital Clinic de Barcelona—FCRB, 08036 Barcelona, Spain; (L.P.); (D.D.); (J.J.G.)
| | - Francesc Teixidor
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (M.N.-M.); (F.T.)
| | - Elisabetta Stanzani
- Laboratory of Pharmacology and Brain Pathology, IRCCS Humanitas Research Hospital, 20089 Rozzano, Italy;
| | - Fina Martínez-Soler
- Apoptosis and Cancer Unit, Department of Physiological Sciences, IDIBELL, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08907 L’Hospitalet del Llobregat, Spain; (F.M.-S.); (A.T.)
| | - Avelina Tortosa
- Apoptosis and Cancer Unit, Department of Physiological Sciences, IDIBELL, Faculty of Medicine and Health Sciences, Universitat de Barcelona, 08907 L’Hospitalet del Llobregat, Spain; (F.M.-S.); (A.T.)
| | - Àngels Sierra
- Laboratory of Experimental Oncological Neurosurgery, Neurosurgery Service, Hospital Clinic de Barcelona—FCRB, 08036 Barcelona, Spain; (L.P.); (D.D.); (J.J.G.)
| | - José Juan Gonzalez
- Laboratory of Experimental Oncological Neurosurgery, Neurosurgery Service, Hospital Clinic de Barcelona—FCRB, 08036 Barcelona, Spain; (L.P.); (D.D.); (J.J.G.)
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona, ICMAB-CSIC, Campus Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; (M.N.-M.); (F.T.)
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Ravera F, Efeoglu E, Byrne HJ. Monitoring stem cell differentiation using Raman microspectroscopy: chondrogenic differentiation, towards cartilage formation. Analyst 2021; 146:322-337. [PMID: 33155580 DOI: 10.1039/d0an01983f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Mesenchymal Stem Cells (MSCs) have the ability to differentiate into chondrocytes, the only cellular components of cartilage and are therefore ideal candidates for cartilage and tissue repair technologies. Chondrocytes are surrounded by cartilage-like extracellular matrix (ECM), a complex network rich in glycosaminoglycans, proteoglycans, and collagen, which, together with a multitude of intracellular signalling molecules, trigger the chondrogenesis and allow the chondroprogenitor to acquire the spherical morphology of the chondrocytes. However, although the mechanisms of the differentiation of MSCs have been extensively explored, it has been difficult to provide a holistic picture of the process, in situ. Raman Micro Spectroscopy (RMS) has been demonstrated to be a powerful analytical tool, which provides detailed label free biochemical fingerprint information in a non-invasive way, for analysis of cells, tissues and body fluids. In this work, RMS is explored to monitor the process of Mesenchymal Stem Cell (MSC) differentiation into chondrocytes in vitro, providing a holistic molecular picture of cellular events governing the differentiation. Spectral signatures of the subcellular compartments, nucleolus, nucleus and cytoplasm were initially probed and characteristic molecular changes between differentiated and undifferentiated were identified. Moreover, high density cell micromasses were cultured over a period of three weeks, and a systematic monitoring of cellular molecular components and the progress of the ECM formation, associated with the chondrogenic differentiation, was performed. This study shows the potential applicability of RMS as a powerful tool to monitor and better understand the differentiation pathways and process.
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Affiliation(s)
- Francesca Ravera
- School of Physics and Clinical and Optometric Sciences, TU Dublin, City Campus, Dublin 8, Ireland.
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Breast cancer detection by ATR-FTIR spectroscopy of blood serum and multivariate data-analysis. Talanta 2020; 214:120857. [PMID: 32278436 DOI: 10.1016/j.talanta.2020.120857] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/31/2022]
Abstract
Detection of breast cancer has particular importance for the diagnosis of cancer diseases. This is the most common type of cancer among women. Breast cancer is a malignant tumor of the glandular tissue of the breast. It is proposed to use infrared spectroscopy of blood serum as a simple and quick way to detect breast cancer. The paper presents the results of research using the methods of multivariate processing of IR spectra of human blood serum obtained by ATR-FTIR spectroscopy. The paper presents the results of research using the methods of multivariate processing of IR spectra of human blood serum obtained by ATR-FTIR spectroscopy. A sufficiently large sample of patients and healthy donors was diagnosed. Blood samples are examined from 66 patients who are clinically diagnosed with breast cancer and 80 healthy volunteers. A feature of the applied approach was a combination of the method of principal component analysis (PCA) and principal component regression (PCR) for processing the IR spectra of blood serum. The PCA method allows us to determine the spectral bands referring for the intensity differences between the control group and the patient group. Shown, that the range of 1306-1250cm-1 in the IR spectrum of blood serum is diagnostically significant for breast cancer. This range corresponds to the vibrations of several functional groups of DNA and RNA, which play a key role in discrimination in breast cancer screening using ATR-FTIR spectroscopy. It is shown that the proposed method has advantages in ease of use for clinical diagnosis and gives good results for the identification of breast cancer. The values of sensitivity (92.3%) and specificity (87.1%) obtained using the PCR method are close to those of mammography and ultrasound. This indicates the possibility of using this method in real clinical laboratory diagnostics.
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An Innovative Platform Merging Elemental Analysis and Ftir Imaging for Breast Tissue Analysis. Sci Rep 2019; 9:9854. [PMID: 31285452 PMCID: PMC6614471 DOI: 10.1038/s41598-019-46056-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/17/2019] [Indexed: 12/16/2022] Open
Abstract
Histopathology and immunohistology remain the gold standard for breast cancer diagnostic. Yet, these approaches do not usually provide a sufficiently detailed characterization of the pathology. The purpose of this work is to demonstrate for the first time that elemental analysis and Fourier transform infrared spectroscopy microscopic examination of breast tissue sections can be merged into one dataset to provide a single set of markers based on both organic molecules and inorganic trace elements. For illustrating the method, 6 mammary tissue sections were used. Fourier transform infrared (FTIR) spectroscopy images reported a fingerprint of the organic molecules present in the tissue section and laser ablation elemental analysis (LA-ICP-MS) images brought inorganic element profiles. The 6 tissue sections provided 31 106 and 150,000 spectra for FTIR and LA-ICP-MS spectra respectively. The results bring the proof of concept that breast tissue can be analyzed simultaneously by FTIR spectroscopy and laser ablation elemental analysis (LA-ICP-MS) to provide in both case reasonably high resolution images. We show how to bring the images obtained by the two methods to a same spatial resolution and how to use image registration to analyze the data originating from both techniques as one block of data. We finally demonstrates the elemental analysis is orthogonal to all FTIR markers as no significant correlation is found between FTIR and LA-ICP-MS data. Combining FTIR and LA-ICP-MS imaging becomes possible, providing two orthogonal methods which can bring an unprecedented diversity of information on the tissue. This opens a new avenue of tissue section analyses providing unprecedented diagnostic potential.
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Vermassen T, De Bruyne S, Himpe J, Lumen N, Callewaert N, Rottey S, Delanghe J. N-Linked Glycosylation and Near-Infrared Spectroscopy in the Diagnosis of Prostate Cancer. Int J Mol Sci 2019; 20:ijms20071592. [PMID: 30934974 PMCID: PMC6479798 DOI: 10.3390/ijms20071592] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 03/21/2019] [Accepted: 03/23/2019] [Indexed: 01/07/2023] Open
Abstract
Background: Performing a prostate biopsy is the most robust and reliable way to diagnose prostate cancer (PCa), and to determine the disease grading. As little to no biochemical markers for prostate tissue exist, we explored the possibilities of tissue N-glycosylation and near-infrared spectroscopy (NIR) in PCa diagnosis. Methods: Tissue specimens from 100 patients (benign prostate hyperplasia (BPH), n = 50; and PCa, n = 50) were obtained. The fresh-frozen tissue was dispersed and a tissue N-glycosylation profile was determined. Consequently, the formalin-fixed paraffin-embedded slides were analyzed using NIR spectroscopy. A comparison was made between the benign and malignant tissue, and between the various Gleason scores. Results: A difference was observed for the tissue of N-glycosylation between the benign and malignant tissue. These differences were located in the fycosylation ratios and the total amount of bi- and tetra-antennary structures (all p < 0.0001). These differences were also present between various Gleason scores. In addition, the NIR spectra revealed changes between the benign and malignant tissue in several regions. Moreover, spectral ranges of 1055–1065 nm and 1450–1460 nm were significantly different between the Gleason scores (p = 0.0042 and p = 0.0195). Conclusions: We have demonstrated biochemical changes in the N-glycan profile of prostate tissue, which allows for the distinction between malignant and benign tissue, as well as between various Gleason scores. These changes can be correlated to the changes observed in the NIR spectra. This could possibly further improve the histological assessment of PCa diagnosis, although further method validation is needed.
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Affiliation(s)
- Tijl Vermassen
- Department of Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium.
| | - Sander De Bruyne
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
| | - Jonas Himpe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
| | - Nicolaas Lumen
- Department of Urology, Ghent University Hospital, 9000 Ghent, Belgium.
| | - Nico Callewaert
- Unit for Medical Biotechnology, Inflammation Research Center, VIB⁻Ghent University, 9052 Zwijnaarde, Belgium.
| | - Sylvie Rottey
- Department of Medical Oncology, Ghent University Hospital, 9000 Ghent, Belgium.
| | - Joris Delanghe
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, 9000 Ghent, Belgium.
- Department of Clinical Chemistry, Ghent University Hospital, 9000 Ghent, Belgium.
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Marques V, Cunha B, Couto A, Sampaio P, Fonseca LP, Aleixo S, Calado CRC. Characterization of gastric cells infection by diverse Helicobacter pylori strains through Fourier-transform infrared spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 210:193-202. [PMID: 30453195 DOI: 10.1016/j.saa.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 06/09/2023]
Abstract
The infection of Helicobacter pylori, covering 50% of the world-population, leads to diverse gastric diseases as ulcers and cancer along the life-time of the human host. To promote the discovery of biomarkers of bacterial infection, in the present work, Fourier-transform infrared spectra were acquired from adenocarcinoma gastric cells, incubated with H. pylori strains presenting different genotypes concerning the virulent factors cytotoxin associated gene A and vacuolating cytotoxin A. Defined absorbance ratios were evaluated by diverse methods of statistical inference, according to the fulfillment of the tests assumptions. It was possible to define from the gastric cells, diverse absorbance ratios enabling to discriminate: i) The infection; ii) the bacteria genotype; and iii) the gastric disease of the patients from which the bacteria were isolated. These biomarkers could fasten the knowledge of the complex infection process while promoting a platform for a new diagnostic method, rapid but also specific and sensitive towards the diagnosis of both infection and bacterial virulence.
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Affiliation(s)
- Vanda Marques
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Bernardo Cunha
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Andreia Couto
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
| | - Pedro Sampaio
- Faculty of Engineering, Lusophone University of Humanities and Technology, Campo Grande, 376, 1749-019 Lisbon, Portugal
| | - Luís P Fonseca
- IBB-Institute for Biotechnology and Bioengineering, Centre for Biological and Chemical Engineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Sandra Aleixo
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal; Centro de Estatística e Aplicações, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal
| | - Cecília R C Calado
- ISEL-Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal.
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Kelp G, Arju N, Lee A, Esquivel E, Delgado R, Yu Y, Dutta-Gupta S, Sokolov K, Shvets G. Application of metasurface-enhanced infra-red spectroscopy to distinguish between normal and cancerous cell types. Analyst 2019; 144:1115-1127. [PMID: 30702730 PMCID: PMC6437688 DOI: 10.1039/c8an01433g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fourier transform infrared (FTIR) spectra of biological cells can reveal clinically important information about cells' composition, including their normal or cancerous status. The recently emerged diagnostic technique of spectral cytopathology (SCP) combines FTIR with multivariate statistical analysis to detect cell abnormalities, differentiate between cell types, and monitor disease progression. We demonstrate a new variant of SCP, a metasurface-enhanced infrared reflection spectroscopic cytopathology (MEIRSC) that utilises judiciously designed plasmonic metasurfaces to localize and enhance the evanescent field near the cell's membrane, and to carry out spectroscopic interrogations of the cells attached to the metasurface using reflected infrared light. Our findings indicate that the MEIRSC approach enables us to differentiate between normal and cancerous human colon cells. The sensitivity of MEIRSC is such that a very small (about 50 nm deep) portion of the cell can yield valuable diagnostic information.
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Affiliation(s)
- G Kelp
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA and School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
| | - N Arju
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
| | - A Lee
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA and Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - E Esquivel
- Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - R Delgado
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
| | - Y Yu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
| | - S Dutta-Gupta
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA. and Department of Materials Science and Metallurgical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, Telangana 502285, India
| | - K Sokolov
- Department of Imaging Physics, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA and Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, USA
| | - G Shvets
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
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Song CL, Kazarian SG. Three-dimensional depth profiling of prostate tissue by micro ATR-FTIR spectroscopic imaging with variable angles of incidence. Analyst 2019; 144:2954-2964. [DOI: 10.1039/c8an01929k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Variable angle micro ATR-FTIR, via the insertion of circular apertures, was used to measure tissue samples at various penetration depths.
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Affiliation(s)
- Cai Li Song
- Department of Chemical Engineering
- Imperial College London
- London SW7 2AZ
- UK
| | - Sergei G. Kazarian
- Department of Chemical Engineering
- Imperial College London
- London SW7 2AZ
- UK
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12
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Wen P, Wei X, Liang G, Wang Y, Yang Y, Qin L, Pang W, Qin G, Li H, Jiang Y, Wu Q. Long-term exposure to low level of fluoride induces apoptosis via p53 pathway in lymphocytes of aluminum smelter workers. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:2671-2680. [PMID: 30478774 DOI: 10.1007/s11356-018-3726-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Long-term occupational exposure to low level of fluoride can induce oxidative stress and apoptosis in many cells, including lymphocyte. However, the underlying mechanism remains unclear. Hence, this study was designed to explore the potential oxidative stress and apoptosis of long-term occupational exposure to low level of fluoride in aluminum smelter workers. A total of 120 aluminum smelter workers were recruited in control, low-, middle-, and high-fluoride exposure groups with 30 workers for each group. The peripheral blood samples were collected, centrifuged, and isolated to obtain serum and lymphocyte suspensions. The air and serum fluoride concentrations were detected by fluoride ion-selective electrode method. The lymphocytic apoptosis rate, DNA damage, oxidative stress, and mRNA levels of p53, Bcl-2, and Bax were assessed by Annexin V/PI staining, comet assay, attenuated total reflectance Fourier transform infrared spectroscopy and real-time polymerase chain reaction, respectively. Results showed that the air and serum fluoride concentrations of fluoride-exposed groups were higher than those of the control group (p < 0.05). Fluoride exposure might induce apoptosis, DNA damage and oxidative stress in a dose-dependent manner in lymphocytes (p < 0.05). The expression levels of p53 and Bax were increased with fluoride exposure in lymphocytes (p < 0.05), whereas the Bcl-2 expression was decreased but not significantly. Taken together, these observations indicate that long-term occupational exposure to low level of fluoride may lead to oxidative stress and induce apoptosis through the p53-dependent pathway in peripheral blood lymphocytes of aluminum smelter workers. Serum fluoride level may be the potential biomarker of fluoride exposure.
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Affiliation(s)
- Pingjing Wen
- Department of Toxicology, School of Public Health, Guangxi Medical University, No. 22 Shuangyong, Nanning, Guangxi, 530021, People's Republic of China
- Department of Toxicology, Guangxi Center for Disease Prevention and Control, Nanning, Guangxi, People's Republic of China
| | - Xiaomin Wei
- Department of Toxicology, School of Public Health, Guangxi Medical University, No. 22 Shuangyong, Nanning, Guangxi, 530021, People's Republic of China
| | - Guiqiang Liang
- Department of Preventive Medicine, School of Public Health and Management, Guangxi University of Chinese Medicine, No. 13 Wuhe Avenue, Nanning, Guangxi, 530200, People's Republic of China
| | - Yanfei Wang
- Primary Care Division, Maternal and Child Health Hospital, Chongqing, People's Republic of China
| | - Yiping Yang
- Department of Toxicology, School of Public Health, Guangxi Medical University, No. 22 Shuangyong, Nanning, Guangxi, 530021, People's Republic of China
| | - Lilin Qin
- Department of Toxicology, School of Public Health, Guangxi Medical University, No. 22 Shuangyong, Nanning, Guangxi, 530021, People's Republic of China
| | - Weiyi Pang
- Department of Occupational and Environmental Health, Guilin Medical University, Guilin, Guangxi, People's Republic of China
| | - Guangqiu Qin
- Department of Preventive Medicine, School of Public Health and Management, Guangxi University of Chinese Medicine, No. 13 Wuhe Avenue, Nanning, Guangxi, 530200, People's Republic of China
| | - Hai Li
- Department of Preventive Medicine, School of Public Health and Management, Guangxi University of Chinese Medicine, No. 13 Wuhe Avenue, Nanning, Guangxi, 530200, People's Republic of China
| | - Yueming Jiang
- Department of Toxicology, School of Public Health, Guangxi Medical University, No. 22 Shuangyong, Nanning, Guangxi, 530021, People's Republic of China.
| | - Qijun Wu
- Department of Preventive Medicine, School of Public Health and Management, Guangxi University of Chinese Medicine, No. 13 Wuhe Avenue, Nanning, Guangxi, 530200, People's Republic of China.
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13
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Siqueira LFS, Lima KMG. MIR-biospectroscopy coupled with chemometrics in cancer studies. Analyst 2018; 141:4833-47. [PMID: 27433557 DOI: 10.1039/c6an01247g] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
This review focuses on chemometric techniques applied in MIR-biospectroscopy for cancer diagnosis and analysis over the last ten years of research. Experimental applications of chemometrics coupled with biospectroscopy are discussed throughout this work. The advantages and drawbacks of this association are also highlighted. Chemometric algorithms are evidenced as a powerful tool for cancer diagnosis, classification, and in different matrices. In fact, it is shown how chemometrics can be implemented along all different types of cancer analyses.
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Affiliation(s)
- Laurinda F S Siqueira
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande of Norte, Natal 59072-970, RN-Brazil.
| | - Kássio M G Lima
- Biological Chemistry and Chemometrics, Institute of Chemistry, Federal University of Rio Grande of Norte, Natal 59072-970, RN-Brazil.
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14
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Rodrigues LM, Carvalho LFDCES, Bonnier F, Anbinder AL, Martinho HDS, Almeida JD. Evaluation of inflammatory processes by FTIR spectroscopy. J Med Eng Technol 2018; 42:228-235. [DOI: 10.1080/03091902.2018.1470691] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Laís Morandini Rodrigues
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology of São José dos Campos, Univ Estadual Paulista-UNESP, São José dos Campos, Brazil
| | | | - Franck Bonnier
- Faculty of Pharmacy, Université François-Rabelais de Tours, Tours, France
| | - Ana Lia Anbinder
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology of São José dos Campos, Univ Estadual Paulista-UNESP, São José dos Campos, Brazil
| | | | - Janete Dias Almeida
- Department of Bioscience and Oral Diagnosis, Institute of Science and Technology of São José dos Campos, Univ Estadual Paulista-UNESP, São José dos Campos, Brazil
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15
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Raman spectroscopic analysis of oral cells in the high wavenumber region. Exp Mol Pathol 2017; 103:255-262. [DOI: 10.1016/j.yexmp.2017.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/18/2017] [Accepted: 11/01/2017] [Indexed: 11/22/2022]
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16
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Shi WJ, Ying GG, Huang GY, Liang YQ, Hu LX, Zhao JL, Zhang JN. Transcriptional and Biochemical Alterations in Zebrafish Eleuthero-Embryos (Danio rerio) After Exposure to Synthetic Progestogen Dydrogesterone. BULLETIN OF ENVIRONMENTAL CONTAMINATION AND TOXICOLOGY 2017; 99:39-45. [PMID: 28214940 DOI: 10.1007/s00128-017-2046-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/07/2017] [Indexed: 06/06/2023]
Abstract
Little information has so far been known on the effects of synthetic progestogen dydrogesterone (DDG) in organisms like fish. This study aimed to investigate the effects of DDG on the transcriptional and biochemical alterations in zebrafish eleuthero-embryos. Zebrafish eleuthero-embryos were analyzed for the transcriptional alterations by real-time quantitative PCR (RT-qPCR) and biochemical changes by attenuated total reflection Fourier-transform infrared spectroscopy (ATR-FITR) after 144 h exposure to DDG. The results of qPCR analysis showed that DDG exposure significantly suppressed the transcriptions of target genes involved in hypothalamic-pituitary-thyroid (HPT) axis, while it induced the expression of target genes mRNA belonging to hypothalamic-pituitary-gonad (HPG) axis. In addition, ATR-FTIR spectroscopy analysis showed that the biochemical alterations of protein, nucleic acid and lipid were observed following DDG treatment. The finding from this study suggests that DDG exposure could have potential multiple effects in fish.
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Affiliation(s)
- Wen-Jun Shi
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
| | - Guang-Guo Ying
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China.
| | - Guo-Yong Huang
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
| | - Yan-Qiu Liang
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
- School of Chemistry and Environment, Guangdong Ocean University, 524088, Zhanjiang, China
| | - Li-Xin Hu
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
| | - Jian-Liang Zhao
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
| | - Jin-Na Zhang
- State Key Laboratory of Organic Geochemistry, CAS Research Centre of PRD Environmental Pollution and Control, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences, 510640, Guangzhou, China
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17
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Kalanoor B, Ronen M, Oren Z, Gerber D, Tischler YR. New Method to Study the Vibrational Modes of Biomolecules in the Terahertz Range Based on a Single-Stage Raman Spectrometer. ACS OMEGA 2017; 2:1232-1240. [PMID: 28393138 PMCID: PMC5377281 DOI: 10.1021/acsomega.6b00547] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2016] [Accepted: 03/14/2017] [Indexed: 05/04/2023]
Abstract
The low-frequency vibrational (LFV) modes of biomolecules reflect specific intramolecular and intermolecular thermally induced fluctuations that are driven by external perturbations, such as ligand binding, protein interaction, electron transfer, and enzymatic activity. Large efforts have been invested over the years to develop methods to access the LFV modes due to their importance in the studies of the mechanisms and biological functions of biomolecules. Here, we present a method to measure the LFV modes of biomolecules based on Raman spectroscopy that combines volume holographic filters with a single-stage spectrometer, to obtain high signal-to-noise-ratio spectra in short acquisition times. We show that this method enables LFV mode characterization of biomolecules even in a hydrated environment. The measured spectra exhibit distinct features originating from intra- and/or intermolecular collective motion and lattice modes. The observed modes are highly sensitive to the overall structure, size, long-range order, and configuration of the molecules, as well as to their environment. Thus, the LFV Raman spectrum acts as a fingerprint of the molecular structure and conformational state of a biomolecule. The comprehensive method we present here is widely applicable, thus enabling high-throughput study of LFV modes of biomolecules.
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Affiliation(s)
- Basanth
S. Kalanoor
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Maria Ronen
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
| | - Ziv Oren
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Department
of Biotechnology, Israel Institute of Biological
Research, Nes-Ziona 7410001, Israel
| | - Doron Gerber
- Mina and Everard Goodman Faculty
of Life Sciences, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (D.G.)
| | - Yaakov R. Tischler
- Department
of Chemistry, Bar-Ilan University, Ramat Gan 5290002, Israel
- Bar-Ilan Institute for Nanotechnology
and Advanced Materials, Bar-Ilan University, Ramat Gan 5290002, Israel
- E-mail: (Y.R.T.)
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18
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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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19
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Loutherback K, Birarda G, Chen L, Holman HYN. Microfluidic approaches to synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy of living biosystems. Protein Pept Lett 2016; 23:273-82. [PMID: 26732243 PMCID: PMC4997923 DOI: 10.2174/0929866523666160106154035] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 10/30/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023]
Abstract
A long-standing desire in biological and biomedical sciences is to be able to probe cellular chemistry as biological processes are happening inside living cells. Synchrotron radiation-based Fourier transform infrared (SR-FTIR) spectral microscopy is a label-free and nondestructive analytical technique that can provide spatiotemporal distributions and relative abundances of biomolecules of a specimen by their characteristic vibrational modes. Despite great progress in recent years, SR-FTIR imaging of living biological systems remains challenging because of the demanding requirements on environmental control and strong infrared absorption of water. To meet this challenge, microfluidic devices have emerged as a method to control the water thickness while providing a hospitable environment to measure cellular processes and responses over many hours or days. This paper will provide an overview of microfluidic device development for SR-FTIR imaging of living biological systems, provide contrast between the various techniques including closed and open-channel designs, and discuss future directions of development within this area. Even as the fundamental science and technological demonstrations develop, other ongoing issues must be addressed; for example, choosing applications whose experimental requirements closely match device capabilities, and developing strategies to efficiently complete the cycle of development. These will require imagination, ingenuity and collaboration.
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Affiliation(s)
| | | | | | - Hoi-Ying N Holman
- Berkeley Synchrotron Infrared Structural Biology Program, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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20
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Medeiros Neto LP, das Chagas E Silva de Carvalho LF, Santos LD, Tellez Soto CA, de Azevedo Canevari R, de Oliveira Santos AB, Mello ES, Pereira MA, Cernea CR, Brandão LG, Martin AA. Micro-Raman spectroscopic study of thyroid tissues. Photodiagnosis Photodyn Ther 2016; 17:164-172. [PMID: 27931874 DOI: 10.1016/j.pdpdt.2016.11.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 10/26/2016] [Accepted: 11/29/2016] [Indexed: 11/25/2022]
Abstract
Thyroid carcinomas are the most common endocrine malignancy. Inconclusive results for the analysis of malignancies are an issue in the diagnosis of thyroid carcinomas; 20% of thyroid cancer diagnoses are indeterminate or suspicious, resulting in a surgical procedure without immediate need. The use of Raman spectroscopy may help improve the diagnosis of thyroid carcinoma. In this study, 30 thyroid samples, including normal thyroid, goiter and thyroid cancer, were analyzed by confocal Raman spectroscopy. Principal component analysis (PCA), linear discriminant analysis (LDA) with cross validation and binary logistic regression (BLR) analysis were applied to discriminate among tissues. Significant discrimination was observed, with a consistent rate of concordant pairs of 89.2% for normal thyroid versus cancer, 85.7% for goiter versus cancer and 80.6% for normal thyroid versus goiter using just the amide III region. Raman spectroscopy was thus proven to be an important and fast tool for the diagnosis of thyroid tissues. The spectral region of 1200-1400cm-1 discriminated normal versus goiter tissues despite the great similarity of these tissues.
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Affiliation(s)
- Lázaro Pinto Medeiros Neto
- Laboratory of Biomedical Vibrational Spectroscopy, Institute for Research and Development (IP&D), Universidade do Vale do Paraíba (UniVap), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, 12244-000, São Paulo (SP), Brazil
| | - Luis Felipe das Chagas E Silva de Carvalho
- Laboratory of Biomedical Vibrational Spectroscopy, Institute for Research and Development (IP&D), Universidade do Vale do Paraíba (UniVap), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, 12244-000, São Paulo (SP), Brazil
| | - Laurita Dos Santos
- Laboratory of Biomedical Vibrational Spectroscopy, Institute for Research and Development (IP&D), Universidade do Vale do Paraíba (UniVap), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, 12244-000, São Paulo (SP), Brazil
| | - Cláudio Alberto Tellez Soto
- Laboratory of Biomedical Vibrational Spectroscopy, Institute for Research and Development (IP&D), Universidade do Vale do Paraíba (UniVap), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, 12244-000, São Paulo (SP), Brazil
| | - Renata de Azevedo Canevari
- Laboratory of Biomedical Vibrational Spectroscopy, Institute for Research and Development (IP&D), Universidade do Vale do Paraíba (UniVap), Av. Shishima Hifumi, 2911, Urbanova, São José dos Campos, 12244-000, São Paulo (SP), Brazil
| | - André Bandiera de Oliveira Santos
- Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, Divisão de Anatomia Patológica, Cerqueira Cesar, 05403000, São Paulo (SP), Brazil
| | - Evandro Sobroza Mello
- Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, Divisão de Anatomia Patológica, Cerqueira Cesar, 05403000, São Paulo (SP), Brazil
| | - Marina Aparecida Pereira
- Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, Divisão de Anatomia Patológica, Cerqueira Cesar, 05403000, São Paulo (SP), Brazil
| | - Cláudio Roberto Cernea
- Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, Divisão de Anatomia Patológica, Cerqueira Cesar, 05403000, São Paulo (SP), Brazil
| | - Lenine Garcia Brandão
- Universidade de São Paulo, Faculdade de Medicina da Universidade de São Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas de Carvalho Aguiar, 255, Divisão de Anatomia Patológica, Cerqueira Cesar, 05403000, São Paulo (SP), Brazil
| | - Aírton Abrahão Martin
- Universidade Federal do Piauí - UFPI - Campus Ministro Petrônio PortellaDepartamento de Física - CCNBairro Ininga Teresina, PI, CEP: 64049-550, Brazil.
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21
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Tiwari S, Raman J, Reddy V, Ghetler A, Tella RP, Han Y, Moon CR, Hoke CD, Bhargava R. Towards Translation of Discrete Frequency Infrared Spectroscopic Imaging for Digital Histopathology of Clinical Biopsy Samples. Anal Chem 2016; 88:10183-10190. [PMID: 27626947 DOI: 10.1021/acs.analchem.6b02754] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Fourier transform infrared (FT-IR) spectroscopic imaging has been widely tested as a tool for stainless digital histology of biomedical specimens, including for the identification of infiltration and fibrosis in endomyocardial biopsy samples to assess transplant rejection. A major barrier in clinical translation has been the slow speed of imaging. To address this need, we tested and report here the viability of using high speed discrete frequency infrared (DFIR) imaging to obtain stain-free biochemical imaging in cardiovascular samples collected from patients. Images obtained by this method were classified with high accuracy by a Bayesian classification algorithm trained on FT-IR imaging data as well as on DFIR data. A single spectral feature correlated with instances of fibrosis, as identified by the pathologist, highlights the advantage of the DFIR imaging approach for rapid detection. The speed of digital pathologic recognition was at least 16 times faster than the fastest FT-IR imaging instrument. These results indicate that a fast, on-site identification of fibrosis using IR imaging has potential for real time assistance during surgeries. Further, the work describes development and applications of supervised classifiers on DFIR imaging data, comparing classifiers developed on FT-IR and DFIR imaging modalities and identifying specific spectral features for accurate identification of fibrosis. This addresses a topic of much debate on the use of training data and cross-modality validity of IR measurements. Together, the work is a step toward addressing a clinical diagnostic need at acquisition time scales that make IR imaging technology practical for medical use.
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Affiliation(s)
- Saumya Tiwari
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Jai Raman
- Knight Cardiovascular Institute, Oregon Health & Science University , 3181 SW Sam Jackson Park Road, Portland, Oregon 97201, United States
| | - Vijaya Reddy
- Department of Pathology, Rush University Medical Center , 1725 West Harrison Street, Chicago, Illinois 60612, United States
| | - Andrew Ghetler
- California Research Center, Spectroscopy and Vacuum Solutions Division, Agilent Technologies, Inc. , 5301 Stevens Creek Blvd., Santa Clara, California 95051 United States
| | - Richard P Tella
- California Research Center, Spectroscopy and Vacuum Solutions Division, Agilent Technologies, Inc. , 5301 Stevens Creek Blvd., Santa Clara, California 95051 United States
| | - Yang Han
- California Research Center, Spectroscopy and Vacuum Solutions Division, Agilent Technologies, Inc. , 5301 Stevens Creek Blvd., Santa Clara, California 95051 United States
| | - Christopher R Moon
- California Research Center, Spectroscopy and Vacuum Solutions Division, Agilent Technologies, Inc. , 5301 Stevens Creek Blvd., Santa Clara, California 95051 United States
| | - Charles D Hoke
- California Research Center, Spectroscopy and Vacuum Solutions Division, Agilent Technologies, Inc. , 5301 Stevens Creek Blvd., Santa Clara, California 95051 United States
| | - Rohit Bhargava
- Department of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States.,Departments of Chemistry, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
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22
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A decade (2004 – 2014) of FTIR prostate cancer spectroscopy studies: An overview of recent advancements. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.05.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Obinaju BE, Martin FL. ATR-FTIR spectroscopy reveals polycyclic aromatic hydrocarbon contamination despite relatively pristine site characteristics: Results of a field study in the Niger Delta. ENVIRONMENT INTERNATIONAL 2016; 89-90:93-101. [PMID: 26826366 DOI: 10.1016/j.envint.2016.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 06/05/2023]
Abstract
Fourier-transform infrared (FTIR) spectroscopy is an emerging technique to detect biochemical alterations in biological tissues, particularly changes due to sub-lethal exposures to environmental contaminants. We have previously shown the potential of attenuated total reflection FTIR (ATR-FTIR) spectroscopy to detect real-time exposure to contaminants in sentinel organisms as well as the potential to relate spectral alterations to the presence of specific environmental agents. In this study based in the Niger Delta (Nigeria), changes occurring in fish tissues as a result of polycyclic aromatic hydrocarbon (PAH) exposure at contaminated sites are compared to the infrared (IR) spectra of the tissues obtained from a relatively pristine site. Multivariate analysis revealed that PAH contamination could be occurring at the pristine site, based on the IR spectra and significant (P<0.0001) differences between sites. The study provides evidence of the IR spectroscopy techniques' sensitivity and supports their potential application in environmental biomonitoring.
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Affiliation(s)
- Blessing E Obinaju
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Francis L Martin
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK.
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24
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Theophilou G, Fogarty SW, Trevisan J, Strong RJ, Heys KA, Patel II, Stringfellow HF, Martin-Hirsch PL, Martin FL. Spatial and temporal age-related spectral alterations in benign human breast tissue. J Mol Struct 2016. [DOI: 10.1016/j.molstruc.2015.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Peng C, Kaščáková S, Chiappini F, Olaya N, Sandt C, Yousef I, Samuel D, Dumas P, Guettier C, Le Naour F. Discrimination of cirrhotic nodules, dysplastic lesions and hepatocellular carcinoma by their vibrational signature. J Transl Med 2016; 14:9. [PMID: 26754490 PMCID: PMC4710034 DOI: 10.1186/s12967-016-0763-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/02/2016] [Indexed: 01/14/2023] Open
Abstract
Background Hepatocarcinogenesis is a multistep process characterized in patients with chronic liver diseases by a spectrum of hepatic nodules that mark the progression from regenerative nodules to dysplastic lesions followed by hepatocellular carcinoma (HCC). The differential diagnosis between precancerous dysplastic nodules and early HCC still represents a challenge for both radiologists and pathologists. We addressed the potential of Fourier transform-infrared (FTIR) microspectroscopy for grading cirrhotic nodules on frozen tissue sections. Methods The study was focused on 39 surgical specimens including normal livers (n = 11), dysplastic nodules (n = 6), early HCC (n = 1), progressed HCC on alcoholic cirrhosis (n = 10) or hepatitis C virus cirrhosis (n = 11). The use of the bright infrared source emitted by the synchrotron radiation allowed investigating the biochemical composition at the cellular level. Chemical mapping on whole tissue sections was further performed using a FTIR microscope equipped with a laboratory-based infrared source. The variance was addressed by principal component analysis. Results Profound alterations of the biochemical composition of the pathological liver were demonstrated by FTIR microspectroscopy. Indeed, dramatic changes were observed in lipids, proteins and sugars highlighting the metabolic reprogramming in carcinogenesis. Quantifiable spectral markers were characterized by calculating ratios of areas under specific bands along the infrared spectrum. These markers allowed the discrimination of cirrhotic nodules, dysplastic lesions and HCC. Finally, the spectral markers can be measured using a laboratory FTIR microscope that may be easily implemented at the hospital. Conclusion Metabolic reprogramming in liver carcinogenesis can constitute a signature easily detectable using FTIR microspectroscopy for the diagnosis of precancerous and cancerous lesions. Electronic supplementary material The online version of this article (doi:10.1186/s12967-016-0763-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chengyuan Peng
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France.
| | - Slávka Kaščáková
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France.
| | - Franck Chiappini
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France.
| | - Natalia Olaya
- Instituto Nacional de Cancerologia, Bogota, Colombia.
| | | | | | - Didier Samuel
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France. .,Centre Hépato-Biliaire, AP-HP Hôpital Paul Brousse, 94800, Villejuif, France.
| | - Paul Dumas
- SOLEIL Synchrotron, 91192, Gif sur Yvette, France.
| | - Catherine Guettier
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France. .,Service d'Anatomopathologie, AP-HP Hôpital Bicêtre, 94275, Le Kremlin-Bicêtre, France.
| | - François Le Naour
- Inserm, Unité 1193, 94800, Villejuif, France. .,Univ Paris-Sud, UMR-S1193, 94800, Villejuif, France.
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26
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Verdonck M, Garaud S, Duvillier H, Willard-Gallo K, Goormaghtigh E. Label-free phenotyping of peripheral blood lymphocytes by infrared imaging. Analyst 2015; 140:2247-56. [PMID: 25516910 DOI: 10.1039/c4an01855a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
It is now widely accepted that the immune microenvironment of tumors and more precisely Tumor Infiltrating Lymphocytes (TIL) play an important role in cancer development and outcome. TILs are considered to be important prognostic and predictive factors based on a growing body of clinical evidence; however, their presence at the tumor site is not currently assessed routinely. FTIR (Fourier transform infrared) imaging has proven it has value in studying a range of tumors, particularly for characterizing tumor cells. Currently, very little is known about the potential for FTIR imaging to characterize TIL. The present proof of concept study investigates the ability of FTIR imaging to identify the principal lymphocyte subpopulations present in human peripheral blood (PB). A negative cell isolation method was employed to select pure, label-free, helper T cells (CD4(+)), cytotoxic T cells (CD8(+)) and B cells (CD19(+)) from six healthy donors PB by Fluorescence Activated Cell Sorting (FACS). Cells were centrifuged onto Barium Fluoride windows and ten infrared images were recorded for each lymphocyte subpopulation from all six donors. After spectral pre-treatment, statistical analyses were performed. Unsupervised Principal Component Analyses (PCA) revealed that in the absence of donor variability, CD4(+) T cells, CD8(+) T cells and B cells each display distinct IR spectral features. Supervised Partial Least Square Discriminant Analyses (PLS-DA) demonstrated that the differences between the three lymphocyte subpopulations are reflected in their IR spectra, permitting their individual identification even when significant donor variability is present. Our results also show that a distinct spectral signature is associated with antibody binding. To our knowledge this is the first study reporting that FTIR imaging can effectively identify T and B lymphocytes and differentiate helper T cells from cytotoxic T cells. This proof of concept study demonstrates that FTIR imaging is a reliable tool for the identification of lymphocyte subpopulations and has the potential for use in characterizing TIL.
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Affiliation(s)
- M Verdonck
- Laboratory for the Structure and Function of Biological Membranes, Center for Structural Biology and Bioinformatics, Université Libre de Bruxelles, Campus Plaine, Bd du Triomphe 2, CP206/02, B1050 Brussels, Belgium.
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27
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Rosa F, Sales KC, Cunha BR, Couto A, Lopes MB, Calado CRC. A comprehensive high-throughput FTIR spectroscopy-based method for evaluating the transfection event: estimating the transfection efficiency and extracting associated metabolic responses. Anal Bioanal Chem 2015; 407:8097-108. [PMID: 26329279 DOI: 10.1007/s00216-015-8983-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 07/29/2015] [Accepted: 08/14/2015] [Indexed: 12/11/2022]
Abstract
Reporter genes are routinely used in every laboratory for molecular and cellular biology for studying heterologous gene expression and general cellular biological mechanisms, such as transfection processes. Although well characterized and broadly implemented, reporter genes present serious limitations, either by involving time-consuming procedures or by presenting possible side effects on the expression of the heterologous gene or even in the general cellular metabolism. Fourier transform mid-infrared (FT-MIR) spectroscopy was evaluated to simultaneously analyze in a rapid (minutes) and high-throughput mode (using 96-wells microplates), the transfection efficiency, and the effect of the transfection process on the host cell biochemical composition and metabolism. Semi-adherent HEK and adherent AGS cell lines, transfected with the plasmid pVAX-GFP using Lipofectamine, were used as model systems. Good partial least squares (PLS) models were built to estimate the transfection efficiency, either considering each cell line independently (R (2) ≥ 0.92; RMSECV ≤ 2 %) or simultaneously considering both cell lines (R (2) = 0.90; RMSECV = 2 %). Additionally, the effect of the transfection process on the HEK cell biochemical and metabolic features could be evaluated directly from the FT-IR spectra. Due to the high sensitivity of the technique, it was also possible to discriminate the effect of the transfection process from the transfection reagent on KEK cells, e.g., by the analysis of spectral biomarkers and biochemical and metabolic features. The present results are far beyond what any reporter gene assay or other specific probe can offer for these purposes.
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Affiliation(s)
- Filipa Rosa
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Kevin C Sales
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Bernardo R Cunha
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Andreia Couto
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal
| | - Marta B Lopes
- Faculdade de Engenharia, Universidade Católica Portuguesa, Estrada Otávio Pato, 2635-631, Rio de Mouro, Portugal.,Instituto de Telecomunicações, Instituto Superior Técnico, 1049-001, Lisbon, Portugal
| | - Cecília R C Calado
- Instituto Superior de Engenharia de Lisboa, Rua Conselheiro Emídio Navarro 1, 1959-007, Lisbon, Portugal.
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Current Advances in the Application of Raman Spectroscopy for Molecular Diagnosis of Cervical Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:561242. [PMID: 26180802 PMCID: PMC4477184 DOI: 10.1155/2015/561242] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/22/2014] [Accepted: 12/27/2014] [Indexed: 11/24/2022]
Abstract
Raman spectroscopy provides a unique biochemical fingerprint capable of identifying and characterizing the structure of molecules, cells, and tissues. In cervical cancer, it is acknowledged as a promising biochemical tool due to its ability to detect premalignancy and early malignancy stages. This review summarizes the key research in the area and the evidence compiled is very encouraging for ongoing and further research. In addition to the diagnostic potential, promising results for HPV detection and monitoring treatment response suggest more than just a diagnosis prospective. A greater body of evidence is however necessary before Raman spectroscopy is fully validated for clinical use and larger comprehensive studies are required to fully establish the role of Raman spectroscopy in the molecular diagnostics of cervical cancer.
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Carvalho LFC, Bonnier F, O'Callaghan K, O'Sullivan J, Flint S, Byrne HJ, Lyng FM. Raman micro-spectroscopy for rapid screening of oral squamous cell carcinoma. Exp Mol Pathol 2015; 98:502-9. [DOI: 10.1016/j.yexmp.2015.03.027] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 03/12/2015] [Accepted: 03/18/2015] [Indexed: 02/07/2023]
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Tiwari S, Reddy VB, Bhargava R, Raman J. Computational chemical imaging for cardiovascular pathology: chemical microscopic imaging accurately determines cardiac transplant rejection. PLoS One 2015; 10:e0125183. [PMID: 25932912 PMCID: PMC4416885 DOI: 10.1371/journal.pone.0125183] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 03/10/2015] [Indexed: 02/06/2023] Open
Abstract
Rejection is a common problem after cardiac transplants leading to significant number of adverse events and deaths, particularly in the first year of transplantation. The gold standard to identify rejection is endomyocardial biopsy. This technique is complex, cumbersome and requires a lot of expertise in the correct interpretation of stained biopsy sections. Traditional histopathology cannot be used actively or quickly during cardiac interventions or surgery. Our objective was to develop a stain-less approach using an emerging technology, Fourier transform infrared (FT-IR) spectroscopic imaging to identify different components of cardiac tissue by their chemical and molecular basis aided by computer recognition, rather than by visual examination using optical microscopy. We studied this technique in assessment of cardiac transplant rejection to evaluate efficacy in an example of complex cardiovascular pathology. We recorded data from human cardiac transplant patients’ biopsies, used a Bayesian classification protocol and developed a visualization scheme to observe chemical differences without the need of stains or human supervision. Using receiver operating characteristic curves, we observed probabilities of detection greater than 95% for four out of five histological classes at 10% probability of false alarm at the cellular level while correctly identifying samples with the hallmarks of the immune response in all cases. The efficacy of manual examination can be significantly increased by observing the inherent biochemical changes in tissues, which enables us to achieve greater diagnostic confidence in an automated, label-free manner. We developed a computational pathology system that gives high contrast images and seems superior to traditional staining procedures. This study is a prelude to the development of real time in situ imaging systems, which can assist interventionists and surgeons actively during procedures.
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Affiliation(s)
- Saumya Tiwari
- Department of Bioengineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana Champaign, Urbana, Illinois, 61801, United States of America
| | - Vijaya B. Reddy
- Department of Pathology, Rush University Medical Center, 1725 West Harrison St, Chicago, Illinois, 60612, United States of America
| | - Rohit Bhargava
- Department of Bioengineering, Chemistry, Mechanical Science and Engineering, Chemical and Biomolecular Engineering, Electrical and Computer Engineering, Beckman Institute for Advanced Science and Technology and University of Illinois Cancer Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Jaishankar Raman
- Cardiac Surgery, Advanced Heart Failure Transplantation & Mechanical Circulatory Support, Rush University Medical Center, 1725 West Harrison St, Chicago, Illinois, 60612, United States of America
- * E-mail:
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31
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Giorgini E, Tosi G, Conti C, Staibano S, Ilardi G, Sabbatini S. FTIR microspectroscopic characterization of Spitz nevi. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 141:99-103. [PMID: 25666330 DOI: 10.1016/j.saa.2015.01.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 07/23/2014] [Accepted: 01/22/2015] [Indexed: 06/04/2023]
Abstract
In the last 10 years, few efforts have been carried out to apply vibrational spectroscopy in the study of dermal pathologies in order to characterize the most relevant spectral markers for distinguishing benign from cancerous lesions. Spitz nevi are a special group of benign melanocytic lesions, characterized by spindled and/or epithelioid nevomelanocytes, with peculiar clinical, dermoscopic and histopathological features. The "atypical forms" of Spitz nevi are among the commonest problems of differential diagnosis with the so-called "spitzoid melanomas". The clinical and histological criteria for discriminating these two entities are very subtle and often still quite subjective, and, in a significant percentage of cases, can lead to diagnostic pitfalls and inadequate therapies. Therefore, it is noteworthy to outline that the diagnosis of melanocytic lesions still represents a challenging problem and a continue matter of discussion. We exploited FTIR microspectroscopy to study the different kinds of spitzoid melanocytes, in order to define the most relevant spectral markers of each specimen and to achieve objective information on "borderline" histologically atypical lesions. In particular, the spectroscopic investigation was carried out on melanocytes deriving from normal skin (as a normal control), malignant melanoma and Spitz nevi. The presence of the characteristic bands of melanin was investigated, too.
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Affiliation(s)
- Elisabetta Giorgini
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Giorgio Tosi
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Carla Conti
- Dipartimento di Scienze e Ingegneria della Materia, dell'Ambiente ed Urbanistica, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Stefania Staibano
- Dipartimento di Scienze Biomorfologiche e Funzionali, Università Federico II, via Panzini 5, 80131 Napoli, Italy
| | - Gennaro Ilardi
- Dipartimento di Scienze Biomorfologiche e Funzionali, Università Federico II, via Panzini 5, 80131 Napoli, Italy
| | - Simona Sabbatini
- Dipartimento di Scienze e Ingegneria della Materia, dell'Ambiente ed Urbanistica, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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Predicting of Effective Dose as Biomarker for Cytotoxicity Using Partial Least Square-Fourier Transform Infrared Spectroscopy (PLS_FTIR). IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2015; 14:1189-96. [PMID: 26664386 PMCID: PMC4673947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Toxicity bioassays are important tools to determine biological effects of chemical agents on species. The questions remained on, what effects have been imposed on each of the different molecular site of cells by chemical exposure and how to find a pattern for chemical toxicity. To address the questions, HepG2 cell lines were exposed to the different concentrations of cisplatin for 24 hours to result cell mortality in the range of one to one hundred percent. Fourier Transform Infrared spectroscopy (FTIR) has been used in this study to analyze the chemical alterations on HepG2 cell line by cisplatin. Partial least square regression (PLS) analysis was then applied to the FTIR spectrum results to search for a biomarker peak and present the desire cellular effects of cisplatin. The comparison of cellular FTIR spectra after exposure to different concentrations of cisplatin confirmed the binding of cisplatin to DNA through direct interaction of platinum to guanine and thymine bases of DNA. Biochemical Index Spectra (BIS) were defined based on the differences between of normal and cisplatin exposed cells. Information from the BIS was subjected to PLS analysis to trigger any particular relationship between the toxicity spectral response and cisplatin concentration. This approach was capable of predicting the concentration of cisplatin for any particular effects observed in the cellular FTIR spectrum (R(2) = 0.968 ± 0.037). Our work supports the promises that, FTIR can demonstrate the trace of toxicity before the cells dies. Finally, PLS of FTIR data directly predicts the effective concentration of chemicals in particular cellular components.
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Cardellini F, Germani R, Cardinali G, Corte L, Roscini L, Spreti N, Tiecco M. Room temperature deep eutectic solvents of (1S)-(+)-10-camphorsulfonic acid and sulfobetaines: hydrogen bond-based mixtures with low ionicity and structure-dependent toxicity. RSC Adv 2015. [DOI: 10.1039/c5ra03932k] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Preparation, properties and toxicity of room temperature deep eutectic solvents formed by (1S)-(+)-10-camphorsulfonic acid and aromatic, aliphatic and amphiphilic sulfobetaines.
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Affiliation(s)
- Fabio Cardellini
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Raimondo Germani
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Gianluigi Cardinali
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
| | - Laura Corte
- Department of Pharmaceutical Sciences – Microbiology
- University of Perugia
- Perugia
- Italy
| | - Luca Roscini
- Department of Pharmaceutical Sciences – Microbiology
- University of Perugia
- Perugia
- Italy
| | - Nicoletta Spreti
- Department of Physical and Chemical Sciences
- University of L'Aquila
- L'Aquila
- Italy
| | - Matteo Tiecco
- CEMIN
- Centre of Excellence on Nanostructured Innovative Materials
- Department of Chemistry
- Biology and Biotechnology
- University of Perugia
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Gao Y, Huo X, Dong L, Sun X, Sai H, Wei G, Xu Y, Zhang Y, Wu J. Fourier transform infrared microspectroscopy monitoring of 5-fluorouracil-induced apoptosis in SW620 colon cancer cells. Mol Med Rep 2014; 11:2585-91. [PMID: 25503826 PMCID: PMC4337715 DOI: 10.3892/mmr.2014.3088] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Accepted: 11/07/2014] [Indexed: 11/23/2022] Open
Abstract
Colon cancer is associated with a high incidence and a poor prognosis. The aim of the present study was to determine whether Fourier transform infrared (FTIR) microspectroscopy can be used to monitor the chemotherapy drug-induced apoptosis of SW620 colon cancer cells. The 50% inhibitory concentration (IC50) of 5-fluorouracil (5-FU), the main chemotherapeutic agent used for the treatment of colorectal cancer, was determined as the inhibition of growth of the SW620 cells using an MTT assay. Cell starvation and 5-FU treatment synergized to arrest the cells in the G1 and S phases of the cell cycle. FTIR combined with fluorescence activated cell sorting (FACS) analysis were used to analyze the SW620 cells following treatment with 5-FU for 12, 24 and 48 h. The apoptotic cells had several spectral characteristics. The relative peak intensity ratio (I1740/I1460) was significantly increased (P<0.05), the I1740/I1460 ratio, associated with a band of amino acid residues at 1,410 cm−1 was significantly increased at the early and late phases of cell death (P<0.05), the peaks at 1,240 cm−1 increased in wave number, a band at 1,040 cm−1, associated with polysaccharides, appeared at 24 and 48 h and then moved to a higher wave number and the I1040/I1460 ratio increased at the late stage of apoptosis. These results demonstrated that FTIR can be used as a label-free technique to monitor cancer cell apoptosis and to understand the spectral fingerprints of apoptotic cells. This suggested that FTIR spectral features have potential as a powerful tool to monitor cancer cell apoptosis.
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Affiliation(s)
- Yanfeng Gao
- Department of Anesthesiology, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xiongwei Huo
- Department of General Surgery, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Liu Dong
- Department of General Surgery, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Xuejun Sun
- Department of General Surgery, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - He Sai
- Department of General Surgery, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Guangbing Wei
- Department of General Surgery, The First Affiliated Hospital of Medical College, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, P.R. China
| | - Yizhuang Xu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Yuanfu Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
| | - Jinguang Wu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Rare Earth Materials Chemistry and Applications, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, P.R. China
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Obinaju BE, Alaoma A, Martin FL. Novel sensor technologies towards environmental health monitoring in urban environments: a case study in the Niger Delta (Nigeria). ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2014; 192:222-31. [PMID: 24602761 DOI: 10.1016/j.envpol.2014.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Revised: 02/02/2014] [Accepted: 02/07/2014] [Indexed: 05/28/2023]
Abstract
The Niger Delta (Nigeria) is an exemplar of a legacy of environmental pollution. Limited knowledge on spatial and temporal pollutant distributions in the region highlights the need for biomonitoring approaches to study impacts on sentinel organisms. This study evaluated whether infrared (IR) spectroscopy and multivariate analysis could detect alterations in biomolecules in samples in differing exposure scenarios, i.e., spatial and temporal using African catfish (Heterobranchus bidorsalis) or water spinach (Ipomea aquatica). Significant spectral differences between tissues isolated from African catfish based on site or season were observed; in a region where fish appeared not to be present, water spinach was used as a surrogate sentinel organism. Using one-way ANOVA, the spectral categories were significant (P < 0.0001). The applicability of IR spectroscopy to detect subtle changes in target biological molecules within sentinel organisms along with its low-cost yet high-throughput potential suggests that biospectroscopy permits real-time evaluation of environmental exposure effects.
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Affiliation(s)
- Blessing E Obinaju
- Centre for Biophotonics, LEC, Lancaster University, Lancaster LA1 4YQ, UK
| | - Alozie Alaoma
- Centre for Biophotonics, LEC, Lancaster University, Lancaster LA1 4YQ, UK
| | - Francis L Martin
- Centre for Biophotonics, LEC, Lancaster University, Lancaster LA1 4YQ, UK.
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Baker MJ, Trevisan J, Bassan P, Bhargava R, Butler HJ, Dorling KM, Fielden PR, Fogarty SW, Fullwood NJ, Heys KA, Hughes C, Lasch P, Martin-Hirsch PL, Obinaju B, Sockalingum GD, Sulé-Suso J, Strong RJ, Walsh MJ, Wood BR, Gardner P, Martin FL. Using Fourier transform IR spectroscopy to analyze biological materials. Nat Protoc 2014; 9:1771-91. [PMID: 24992094 PMCID: PMC4480339 DOI: 10.1038/nprot.2014.110] [Citation(s) in RCA: 985] [Impact Index Per Article: 98.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.
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Affiliation(s)
- Matthew J Baker
- 1] Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK. [2] Present address: WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Júlio Trevisan
- 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] School of Computing and Communications, Lancaster University, Lancaster, UK
| | - Paul Bassan
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Rohit Bhargava
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Holly J Butler
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Konrad M Dorling
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, UK
| | - Peter R Fielden
- Department of Chemistry, Lancaster University, Lancaster, UK
| | - Simon W Fogarty
- 1] Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK. [2] Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Nigel J Fullwood
- Division of Biomedical and Life Sciences, School of Health and Medicine, Lancaster University, Lancaster, UK
| | - Kelly A Heys
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Caryn Hughes
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Peter Lasch
- Proteomics and Spectroscopy (ZBS 6), Robert-Koch-Institut, Berlin, Germany
| | - Pierre L Martin-Hirsch
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Blessing Obinaju
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Ganesh D Sockalingum
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, UnitéMEDyC, CNRS UMR7369, UFR Pharmacie, SFR CAP-Santé FED4231, Reims, France
| | - Josep Sulé-Suso
- Institute for Science and Technology in Medicine, School of Medicine, Keele University, Stoke-on-Trent, UK
| | - Rebecca J Strong
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Michael J Walsh
- Department of Pathology, College of Medicine Research Building (COMRB), University of Illinois at Chicago, Chicago, Illinois, USA
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, Monash University, Clayton, Victoria, Australia
| | - Peter Gardner
- Manchester Institute of Biotechnology (MIB), University of Manchester, Manchester, UK
| | - Francis L Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, UK
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Mattson EC, Unger M, Clède S, Lambert F, Policar C, Imtiaz A, D'Souza R, Hirschmugl CJ. Toward optimal spatial and spectral quality in widefield infrared spectromicroscopy of IR labelled single cells. Analyst 2014; 138:5610-8. [PMID: 23826609 DOI: 10.1039/c3an00383c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Advancements in widefield infrared spectromicroscopy have recently been demonstrated following the commissioning of IRENI (InfraRed ENvironmental Imaging), a Fourier Transform infrared (FTIR) chemical imaging beamline at the Synchrotron Radiation Center. The present study demonstrates the effects of magnification, spatial oversampling, spectral pre-processing and deconvolution, focusing on the intracellular detection and distribution of an exogenous metal tris-carbonyl derivative 1 in a single MDA-MB-231 breast cancer cell. We demonstrate here that spatial oversampling for synchrotron-based infrared imaging is critical to obtain accurate diffraction-limited images at all wavelengths simultaneously. Resolution criteria and results from raw and deconvoluted images for two Schwarzschild objectives (36×, NA 0.5 and 74×, NA 0.65) are compared to each other and to prior reports for raster-scanned, confocal microscopes. The resolution of the imaging data can be improved by deconvolving the instrumental broadening that is determined with the measured PSFs, which is implemented with GPU programming architecture for fast hyperspectral processing. High definition, rapidly acquired, FTIR chemical images of respective spectral signatures of the cell 1 and shows that 1 is localized next to the phosphate- and Amide-rich regions, in agreement with previous infrared and luminescence studies. The infrared image contrast, localization and definition are improved after applying proven spectral pre-processing (principal component analysis based noise reduction and RMie scattering correction algorithms) to individual pixel spectra in the hyperspectral cube.
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Affiliation(s)
- Eric C Mattson
- Physics Dept., University of Wisconsin-Milwaukee, Milwaukee, WI, USA.
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Nallala J, Diebold MD, Gobinet C, Bouché O, Sockalingum GD, Piot O, Manfait M. Infrared spectral histopathology for cancer diagnosis: a novel approach for automated pattern recognition of colon adenocarcinoma. Analyst 2014; 139:4005-15. [DOI: 10.1039/c3an01022h] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Automated and label-free colon cancer diagnosis and identification of tumor-associated features using FTIR spectral histopathology directly on paraffinized tissue arrays.
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Affiliation(s)
- Jayakrupakar Nallala
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Marie-Danièle Diebold
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Cyril Gobinet
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Olivier Bouché
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Ganesh Dhruvananda Sockalingum
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Olivier Piot
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
| | - Michel Manfait
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex, France
- CNRS UMR7369
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39
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Obinaju BE, Martin FL. Novel biospectroscopy sensor technologies towards environmental health monitoring in urban environments. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2013; 183:46-53. [PMID: 23257285 DOI: 10.1016/j.envpol.2012.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Revised: 11/15/2012] [Accepted: 11/18/2012] [Indexed: 06/01/2023]
Abstract
Biospectroscopy is an emerging inter-disciplinary field that exploits the application of sensor technologies [e.g., Fourier-transform infrared spectroscopy, Raman spectroscopy] to lend novel insights into biological questions. Methods involved are relatively non-destructive so samples can subsequently be analysed by more conventional approaches, facilitating deeper mechanistic insights. Fingerprint spectra are derived and these consist of wavenumber-absorbance intensities; within a typical biological experiment, a complex dataset is quickly generated. Biological samples range from biofluids to cytology to tissues derived from human or sentinel sources, and analyses can be carried out ex vivo or in situ in living tissue. A reference range of a designated normal state can be derived; anything outside this is potentially atypical and discriminating chemical entities identified. Computational approaches allow one to minimize within-category confounding factors. Because of ease of sample preparation, low-cost and high-throughput capability, biospectroscopy approaches herald a new greener means of environmental health monitoring in urban environments.
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Affiliation(s)
- Blessing E Obinaju
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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40
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Exploiting biospectroscopy as a novel screening tool for cervical cancer: towards a framework to validate its accuracy in a routine clinical setting. Bioanalysis 2013; 5:2697-711. [DOI: 10.4155/bio.13.233] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Biospectroscopy is an emerging field that harnesses the platform of physical sciences with computational analysis in order to shed novel insights on biological questions. An area where this approach seems to have potential is in screening or diagnostic clinical settings, where there is an urgent need for new approaches to objectively interrogate large numbers of samples in an objective fashion with acceptable levels of sensitivity and specificity. This review outlines the benefits of biospectroscopy in screening for precancer lesions of the cervix due to its ability to separate different grades of dysplasia. It evaluates the feasibility of introducing this technique into cervical screening programs on the basis of its ability to identify biomarkers of progression within derived spectra (‘biochemical‑cell fingerprints’).
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41
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Diagnosis of tumors during tissue-conserving surgery with integrated autofluorescence and Raman scattering microscopy. Proc Natl Acad Sci U S A 2013; 110:15189-94. [PMID: 24003124 DOI: 10.1073/pnas.1311289110] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Tissue-conserving surgery is used increasingly in cancer treatment. However, one of the main challenges in this type of surgery is the detection of tumor margins. Histopathology based on tissue sectioning and staining has been the gold standard for cancer diagnosis for more than a century. However, its use during tissue-conserving surgery is limited by time-consuming tissue preparation steps (1-2 h) and the diagnostic variability inherent in subjective image interpretation. Here, we demonstrate an integrated optical technique based on tissue autofluorescence imaging (high sensitivity and high speed but low specificity) and Raman scattering (high sensitivity and high specificity but low speed) that can overcome these limitations. Automated segmentation of autofluorescence images was used to select and prioritize the sampling points for Raman spectroscopy, which then was used to establish the diagnosis based on a spectral classification model (100% sensitivity, 92% specificity per spectrum). This automated sampling strategy allowed objective diagnosis of basal cell carcinoma in skin tissue samples excised during Mohs micrographic surgery faster than frozen section histopathology, and one or two orders of magnitude faster than previous techniques based on infrared or Raman microscopy. We also show that this technique can diagnose the presence or absence of tumors in unsectioned tissue layers, thus eliminating the need for tissue sectioning. This study demonstrates the potential of this technique to provide a rapid and objective intraoperative method to spare healthy tissue and reduce unnecessary surgery by determining whether tumor cells have been removed.
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Salman A, Shufan E, Zeiri L, Huleihel M. Detection and identification of cancerous murine fibroblasts, transformed by murine sarcoma virus in culture, using Raman spectroscopy and advanced statistical methods. Biochim Biophys Acta Gen Subj 2013; 1830:2720-7. [PMID: 23671933 DOI: 10.1016/j.bbagen.2012.11.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND Cancer is one of the leading worldwide causes of death. It may be induced by a variety of factors, including carcinogens, radiation, genetic factors, or DNA and RNA viruses. The early detection of cancer is critical for its successful therapy, which can result in complete recovery from some types of cancer. METHODS Raman spectroscopy has been widely used in medicine and biology. It is a noninvasive, nondestructive, and water-insensitive technique that can detect changes in cells and tissues that are caused by different disorders, such as cancer. In this study, Raman spectroscopy was used for the identification and characterization of murine fibroblast cell lines (NIH/3T3) and malignant fibroblast cells transformed by murine sarcoma virus (NIH-MuSV) cells. RESULTS Using principal component analysis and LDA it was possible to differentiate between the NIH/3T3 and NIH-MuSV cells with an 80-85% success rate based on their Raman shift spectra. CONCLUSIONS The best results for differentiation were achieved from spectra that were obtained from the rich membrane sites. GENERAL SIGNIFICANCE Because of its homogeneity and complete control of most factors affecting its growth, cell culture is a preferred model for the detection and identification of specific biomarkers related to cancer transformation or other cellular modifications.
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Affiliation(s)
- A Salman
- Department of Physics, SCE - ShamoonCollege of Engineering, Beer-Sheva 84100, Israel.
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43
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Oral cancer diagnostics based on infrared spectral markers and wax physisorption kinetics. Anal Bioanal Chem 2013; 405:1995-2007. [PMID: 23318761 DOI: 10.1007/s00216-012-6625-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2012] [Revised: 11/13/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
Abstract
Infrared microspectroscopy is an emerging approach for disease analysis owing to its capability for in situ chemical characterization of pathological processes. Synchrotron-based infrared microspectroscopy (SR-IMS) provides ultra-high spatial resolution for profiling biochemical events associated with disease progression. Spectral alterations were observed in cultured oral cells derived from healthy, precancerous, primary, and metastatic cancers. An innovative wax-physisorption-based kinetic FTIR imaging method for the detection of oral precancer and cancer was demonstrated successfully. The approach is based on determining the residual amount of paraffin wax (C(25)H(52)) or beeswax (C(46)H(92)O(2)) on a sample surface after xylene washing. This amount is used as a signpost of the degree of physisorption that altered during malignant transformation. The results of linear discriminant analysis (LDA) of oral cell lines indicated that the methylene (CH(2)) and methyl group (CH(3)) stretching vibrations in the range of 3,000-2,800 cm(-1) have the highest accuracy rate (89.6 %) to discriminate the healthy keratinocytes (NHOK) from cancer cells. The results of wax-physisorption-based FTIR imaging showed a stronger physisorption with beeswax in oral precancerous and cancer cells as compared with that of NHOK, which showed a strong capability with paraffin wax. The infrared kinetic study of oral cavity tissue showed a consistency in the wax physisorption of the cell lines. On the basis of our findings, these results show the potential use of wax-physisorption-based kinetic FTIR imaging for the early screening of oral cancer lesions and the chemical changes during oral carcinogenesis.
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Nallala J, Piot O, Diebold MD, Gobinet C, Bouché O, Manfait M, Sockalingum GD. Infrared imaging as a cancer diagnostic tool: introducing a new concept of spectral barcodes for identifying molecular changes in colon tumors. Cytometry A 2013; 83:294-300. [PMID: 23303722 DOI: 10.1002/cyto.a.22249] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2012] [Revised: 11/21/2012] [Accepted: 12/06/2012] [Indexed: 11/12/2022]
Abstract
Complementary diagnostic methods to conventional histopathology are under scrutiny for various types of cancers for rapid and molecular level diagnostics. In this perspective, a biophotonic approach based on infrared spectral micro-imaging combined with multivariate statistical analysis has been implemented on colon tissues. The ability of infrared imaging to investigate the intrinsic biochemical features of cells and tissues has been exploited to develop a new concept of spectral bar coding. To implement this concept, 10 frozen colon tissue samples (five nontumoral and tumoral pairs from five patients) were imaged using infrared spectral micro-imaging in a nondestructive manner. The spectral images were processed by a multivariate clustering method to identify the histological organization in a label-free manner. Spectral information from the epithelial components was then automatically recovered on the basis of their intrinsic biochemical composition, and compared using a statistical method (Mann-Whitney U-test) to construct spectral barcodes specific to each patient. The spectral barcodes representing the discriminant infrared spectral wavenumbers (900-1,800 cm(-1) ) enabled characterization of some of the malignancy-associated biochemical alterations associated with mucin, nucleotides, carbohydrates, and protein regions. This approach not only allowed the identification of common biochemical alterations among all the colon cancer patients, but also revealed a difference of gradient within individual patients. This new concept of spectral bar coding gives insight into the potential of infrared spectral micro-imaging as a complementary diagnostic tool to conventional histopathology, for biochemical level understanding of malignancy in colon cancers in an objective and label-free manner.
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Affiliation(s)
- Jayakrupakar Nallala
- MéDIAN Biophotonique et Technologies pour la Santé, Université de Reims Champagne-Ardenne, FRE CNRS 3481 MEDyC, UFR de Pharmacie, SFR Cap Santé, 51096 Reims Cedex, France
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45
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Gaigneaux A, Goormaghtigh E. A new dimension for cell identification by FTIR spectroscopy: depth profiling in attenuated total reflection. Analyst 2013; 138:4070-5. [DOI: 10.1039/c3an00193h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Gajjar K, Heppenstall LD, Pang W, Ashton KM, Trevisan J, Patel II, Llabjani V, Stringfellow HF, Martin-Hirsch PL, Dawson T, Martin FL. Diagnostic segregation of human brain tumours using Fourier-transform infrared and/or Raman spectroscopy coupled with discriminant analysis. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2012; 5:89-102. [PMID: 24098310 PMCID: PMC3789135 DOI: 10.1039/c2ay25544h] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The most common initial treatment received by patients with a brain tumour is surgical removal of the growth. Precise histopathological diagnosis of brain tumours is to some extent subjective. Furthermore, currently available diagnostic imaging techniques to delineate the excision border during cytoreductive surgery lack the required spatial precision to aid surgeons. We set out to determine whether infrared (IR) and/or Raman spectroscopy combined with multivariate analysis could be applied to discriminate between normal brain tissue and different tumour types (meningioma, glioma and brain metastasis) based on the unique spectral "fingerprints" of their biochemical composition. Formalin-fixed paraffin-embedded tissue blocks of normal brain and different brain tumours were de-waxed, mounted on low-E slides and desiccated before being analyzed using attenuated total reflection Fourier-transform IR (ATR-FTIR) and Raman spectroscopy. ATR-FTIR spectroscopy showed a clear segregation between normal and different tumour subtypes. Discrimination of tumour classes was also apparent with Raman spectroscopy. Further analysis of spectral data revealed changes in brain biochemical structure associated with different tumours. Decreased tentatively-assigned lipid-to-protein ratio was associated with increased tumour progression. Alteration in cholesterol esters-to-phenylalanine ratio was evident in grade IV glioma and metastatic tumours. The current study indicates that IR and/or Raman spectroscopy have the potential to provide a novel diagnostic approach in the accurate diagnosis of brain tumours and have potential for application in intra-operative diagnosis.
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Affiliation(s)
- Ketan Gajjar
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, Lancashire, UK
| | - Lara D. Heppenstall
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Weiyi Pang
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Katherine M. Ashton
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, Lancashire, UK
| | - Júlio Trevisan
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Imran I. Patel
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Valon Llabjani
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Helen F. Stringfellow
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, Lancashire, UK
| | - Pierre L. Martin-Hirsch
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, Lancashire, UK
| | - Timothy Dawson
- Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, Lancashire, UK
| | - Francis L. Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
- ; Tel: +44 (0)1524 510206
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Peng D, Jiaxing W, Chunhui H, Weiyi P, Xiaomin W. Study on the cytogenetic changes induced by benzene and hydroquinone in human lymphocytes. Hum Exp Toxicol 2012; 31:322-35. [DOI: 10.1177/0960327111433900] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Benzene (BN) is a prototypical hematotoxicant, genotoxic carcinogen, and ubiquitous environmental pollutant. Although the molecular mechanisms of BN-induced cytotoxicity and genotoxic damage are poorly understood in humans, previous studies suggested that bioactivated BN metabolites are capable of oxidative stress, cell cycle arrest, apoptosis, and DNA damage. The objective of the current study was to investigate the BN-induced cytogenetic changes and underlying mechanisms based on these hypotheses. Peripheral blood lymphocytes (PBLs) might be the targets for BN-induced cytotoxicity and genotoxicity, and therefore DNA damage responses of PBLs after exposure to different concentrations of BN (0.25, 3.5, 50 μmol/L) or BN metabolite, hydroquinone (HQ; 50, 150, 450 μmol/L) were studied in vitro. Microculture tetrazolium assay, flow cytometry, 2′,7′-dichlorodihydrofluorescein-diacetate assay, comet assay, micronuclei assay, and attenuated total reflectance microspectroscope were chosen for this study. Based on the results, we reached the conclusion that different concentrations of BN or HQ significantly inhibited cell growth, induced the arrest of S phase and G2/M phase, and increased late apoptosis in a concentration-dependent manner. Furthermore, evidence was also provided to support the conclusion that BN and HQ induced DNA strand breaks and chromosomal mutations in PBL, which indicated the genotoxicity of BN and HQ. Current evidence has indicated that multiple mechanisms including dysfunction of cell cycle, programmed cell death, oxidative stress, and DNA lesions are likely to contribute to BN-induced cytogenetic changes.
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Affiliation(s)
- D Peng
- Department of Public Health, School of Basic Medical, Hubei University of Medicine, Shiyan, Hubei, PR China
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, PR China
| | - W Jiaxing
- School of Chemical Project, Beijing University of Chemical Technology, Beijing, PR China
| | - H Chunhui
- Department of Clinical Laboratories, the Affiliated Taihe Hospital, Hubei University of Medicine, Hubei Shiyan, PR China
| | - P Weiyi
- Department of Health Statistics and Environmental Health, School of Public Health, Guangxi Medical University, Nanning, Guangxi, PR China
| | - W Xiaomin
- Department of Toxicology, School of Public Health, Guangxi Medical University, Nanning, Guangxi, PR China
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Salman A, Lapidot I, Pomerantz A, Tsror L, Shufan E, Moreh R, Mordechai S, Huleihel M. Identification of fungal phytopathogens using Fourier transform infrared-attenuated total reflection spectroscopy and advanced statistical methods. JOURNAL OF BIOMEDICAL OPTICS 2012; 17:017002. [PMID: 22352668 DOI: 10.1117/1.jbo.17.1.017002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The early diagnosis of phytopathogens is of a great importance; it could save large economical losses due to crops damaged by fungal diseases, and prevent unnecessary soil fumigation or the use of fungicides and bactericides and thus prevent considerable environmental pollution. In this study, 18 isolates of three different fungi genera were investigated; six isolates of Colletotrichum coccodes, six isolates of Verticillium dahliae and six isolates of Fusarium oxysporum. Our main goal was to differentiate these fungi samples on the level of isolates, based on their infrared absorption spectra obtained using the Fourier transform infrared-attenuated total reflection (FTIR-ATR) sampling technique. Advanced statistical and mathematical methods: principal component analysis (PCA), linear discriminant analysis (LDA), and k-means were applied to the spectra after manipulation. Our results showed significant spectral differences between the various fungi genera examined. The use of k-means enabled classification between the genera with a 94.5% accuracy, whereas the use of PCA [3 principal components (PCs)] and LDA has achieved a 99.7% success rate. However, on the level of isolates, the best differentiation results were obtained using PCA (9 PCs) and LDA for the lower wavenumber region (800-1775 cm(-1)), with identification success rates of 87%, 85.5%, and 94.5% for Colletotrichum, Fusarium, and Verticillium strains, respectively.
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Affiliation(s)
- Ahmad Salman
- SCE-Sami Shamoon College of Engineering, Department of Physics, Beer-Sheva 84100, Israel. mahmoudh@ bgu.ac.il
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Trevisan J, Angelov PP, Carmichael PL, Scott AD, Martin FL. Extracting biological information with computational analysis of Fourier-transform infrared (FTIR) biospectroscopy datasets: current practices to future perspectives. Analyst 2012; 137:3202-15. [DOI: 10.1039/c2an16300d] [Citation(s) in RCA: 169] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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50
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Bonnier F, Byrne HJ. Understanding the molecular information contained in principal component analysis of vibrational spectra of biological systems. Analyst 2012; 137:322-32. [DOI: 10.1039/c1an15821j] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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