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Guleken Z, Ceylan Z, Çeçen S, Elgörmüş Y, Cebulski J, Depciuch J. Quantitative or qualitative biomolecular changes in blood serum composition induced by childhood obesity: A Fourier transform infrared examination. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124153. [PMID: 38492465 DOI: 10.1016/j.saa.2024.124153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/10/2024] [Accepted: 03/11/2024] [Indexed: 03/18/2024]
Abstract
Childhood obesity (CO) negatively affects one in three children and stands as the fourth most common risk factor of health and well-being. Clarifying the molecular and structural modifications that transpire during the development of obesity is crucial for understanding its progression and devising effective therapies. The study was indeed conducted as part of an ongoing CO treatment trial, where data were collected from children diagnosed with CO before the initiation of non-drug treatment interventions. Our primary aim was to analyze the biochemical changes associated with childhood obesity, specifically focusing on concentrations of lipids, lipoproteins, insulin, and glucose. By comparing these parameters between the CO group (n = 60) and a control group of healthy children (n = 43), we sought to elucidate the metabolic differences present in individuals with CO. Our biochemical analyses unveiled lower LDL (low-density lipoproteins) levels and higher HDL (high-density lipoproteins), cholesterol, triglycerides, insulin, and glucose levels in CO individuals compared to controls. To scrutinize these changes in more detail, we employed Fourier transform infrared (FTIR) spectroscopy on the serum samples. Our results indicated elevated levels of lipids and proteins in the serum of CO, compared to controls. Additionally, we noted structural changes in the vibrations of glucose, β-sheet, and lipids in CO group. The FTIR technique, coupled with principal component analysis (PCA), demonstrated a marked differentiation between CO and controls, particularly in the FTIR region corresponding to amide and lipids. The Pearson test revealed a stronger correlation between biochemical data and FTIR spectra than between 2nd derivative FTIR spectra. Overall, our study provides valuable insights into the molecular and structural changes occurring in CO.
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Affiliation(s)
- Zozan Guleken
- Gaziantep University of Science and Technology, Faculty of Medicine, Department of Physiology Gaziantep, Turkey
| | - Zeynep Ceylan
- Samsun University, Faculty of Engineering, Department of Industrial Engineering, Samsun, Turkey
| | - Serpil Çeçen
- Health Science University, Hamidiye Faculty of Medicine, Department of Physiology, İstanbul, Turkey
| | - Yusuf Elgörmüş
- Faculty of Medicine, Department of Pediatrics, İstanbul Atlas University Medicine Hospital, İstanbul 34408, Turkey
| | - Jozef Cebulski
- Institute of Physics, University of Rzeszow, 35-959 Rzeszow, Poland
| | - Joanna Depciuch
- Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin 20-093, Poland; Institute of Nuclear Physics, PAS, 31342 Krakow, Poland.
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Koziol-Bohatkiewicz P, Liberda-Matyja D, Wrobel TP. Fast cancer imaging in pancreatic biopsies using infrared imaging. Analyst 2024; 149:1799-1806. [PMID: 38385553 DOI: 10.1039/d3an01555f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Pancreatic cancer, particularly Pancreatic ductal adenocarcinoma, remains a highly lethal form of cancer with limited early diagnosis and treatment options. Infrared (IR) spectroscopy, combined with machine learning, has demonstrated great potential in detecting various cancers. This study explores the translation of a diagnostic model from Fourier Transform Infrared to Quantum Cascade Laser (QCL) microscopy for pancreatic cancer classification. Furthermore, QCL microscopy offers faster measurements with selected frequencies, improving clinical feasibility. Thus, the goals of the study include establishing a QCL-based model for pancreatic cancer classification and creating a fast surgical margin detection model using reduced spectral information. The research involves preprocessing QCL data, training Random Forest (RF) classifiers, and optimizing the selection of spectral features for the models. Results demonstrate successful translation of the diagnostic model to QCL microscopy, achieving high predictive power (AUC = 98%) in detecting cancerous tissues. Moreover, a model for rapid surgical margin recognition, based on only a few spectral frequencies, is developed with promising differentiation between benign and cancerous regions. The findings highlight the potential of QCL microscopy for efficient pancreatic cancer diagnosis and surgical margin detection within clinical timeframes of minutes per surgical resection tissue.
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Affiliation(s)
- Paulina Koziol-Bohatkiewicz
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland.
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Krakow, Poland
| | - Danuta Liberda-Matyja
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland.
- Jagiellonian University, Doctoral School of Exact and Natural Sciences, Prof. St. Łojasiewicza 11, PL30348, Cracow, Poland
| | - Tomasz P Wrobel
- Solaris National Synchrotron Radiation Centre, Jagiellonian University, Czerwone Maki 98, 30-392, Krakow, Poland.
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Kino S, Kanamori M, Shimoda Y, Niizuma K, Endo H, Matsuura Y. Distinguishing IDH mutation status in gliomas using FTIR-ATR spectra of peripheral blood plasma indicating clear traces of protein amyloid aggregation. BMC Cancer 2024; 24:222. [PMID: 38365669 PMCID: PMC10870484 DOI: 10.1186/s12885-024-11970-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Glioma is a primary brain tumor and the assessment of its molecular profile in a minimally invasive manner is important in determining treatment strategies. Among the molecular abnormalities of gliomas, mutations in the isocitrate dehydrogenase (IDH) gene are strong predictors of treatment sensitivity and prognosis. In this study, we attempted to non-invasively diagnose glioma development and the presence of IDH mutations using multivariate analysis of the plasma mid-infrared absorption spectra for a comprehensive and sensitive view of changes in blood components associated with the disease and genetic mutations. These component changes are discussed in terms of absorption wavenumbers that contribute to differentiation. METHODS Plasma samples were collected at our institutes from 84 patients with glioma (13 oligodendrogliomas, 17 IDH-mutant astrocytoma, 7 IDH wild-type diffuse glioma, and 47 glioblastomas) before treatment initiation and 72 healthy participants. FTIR-ATR spectra were obtained for each plasma sample, and PLS discriminant analysis was performed using the absorbance of each wavenumber in the fingerprint region of biomolecules as the explanatory variable. This data was used to distinguish patients with glioma from healthy participants and diagnose the presence of IDH mutations. RESULTS The derived classification algorithm distinguished the patients with glioma from healthy participants with 83% accuracy (area under the curve (AUC) in receiver operating characteristic (ROC) = 0.908) and diagnosed the presence of IDH mutation with 75% accuracy (AUC = 0.752 in ROC) in cross-validation using 30% of the total test data. The characteristic changes in the absorption spectra suggest an increase in the ratio of β-sheet structures in the conformational composition of blood proteins of patients with glioma. Furthermore, these changes were more pronounced in patients with IDH-mutant gliomas. CONCLUSIONS The plasma infrared absorption spectra could be used to diagnose gliomas and the presence of IDH mutations in gliomas with a high degree of accuracy. The spectral shape of the protein absorption band showed that the ratio of β-sheet structures in blood proteins was significantly higher in patients with glioma than in healthy participants, and protein aggregation was a distinct feature in patients with glioma with IDH mutations.
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Affiliation(s)
- Saiko Kino
- Graduate School of Biomedical Engineering, Tohoku University, 6-6-05, Aza-Aoba, Aramaki, Aoba, Sendai City, 980-8579, Miyagi Prefecture, Japan
| | - Masayuki Kanamori
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Yoshiteru Shimoda
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai City, 980-8575, Miyagi Prefecture, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, 980-8575 Seiryo 2-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Hidenori Endo
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Yuji Matsuura
- Graduate School of Biomedical Engineering, Tohoku University, 6-6-05, Aza-Aoba, Aramaki, Aoba, Sendai City, 980-8579, Miyagi Prefecture, Japan.
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Thiéfin G, Bertrand D, Untereiner V, Garnotel R, Bronowicki JP, Sockalingum GD. Serum infrared spectral profile is predictive of the degree of hepatic fibrosis in chronic hepatitis C patients. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123433. [PMID: 37774586 DOI: 10.1016/j.saa.2023.123433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/01/2023]
Abstract
Assessment of liver fibrosis is crucial to guide the therapeutic strategy in patients with chronic liver disease. We investigated the potential of serum Fourier transform infrared (FTIR) spectroscopy for assessing the degree of hepatic fibrosis in patients with chronic hepatitis C (CHC). The study was conducted on dried serum samples from 94 CHC patients at different histological stages of hepatic fibrosis: METAVIR F0 (n = 20), F1 (n = 17), F2 (n = 20), F3 (n = 20) and F4 (n = 17). Transmission FTIR spectra were acquired in the 4000-400 cm-1 range. Wavenumbers were selected by genetic algorithm (GA) according to their diagnostic performance as assessed by a partial least squares discriminant analysis (PLS-DA) model using a training and a validation set to differentiate severe stages of fibrosis from mild or moderate ones. The GA procedure was applied 50 times on randomly selected sets. Furthermore, the best set of wavenumbers was re-tested in 1000 randomly selected validation sets. Wavenumbers selected by GA corresponded to functional groups present in lipids, proteins, and carbohydrates. This model allowed to identify patients with cirrhosis (METAVIR F4), patients with advanced fibrosis (METAVIR F3 and F4), and patients with significant fibrosis (METAVIR F2, F3 and F4), with AUROC (Area Under the Receiver Operating Characteristic) of 0.88, 0.85 and 0.85, respectively. Thus, serum FTIR spectroscopy appears to have a strong potential as a new diagnostic tool for assessing the degree of fibrosis in patients with chronic liver disease.
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Affiliation(s)
- Gérard Thiéfin
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; Service d'Hépato-Gastroentérologie et de Cancérologie Digestive, Centre Hospitalier Universitaire de Reims, 51092 Reims, France
| | | | - Valérie Untereiner
- Université de Reims Champagne-Ardenne, Plateforme en Imagerie Cellulaire et Tissulaire (PICT), 51097 Reims Cedex, France
| | - Roselyne Garnotel
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France; Laboratoire de Biochimie-Pharmacologie-Toxicologie, Centre Hospitalier Universitaire de Reims, 51092, Reims, France
| | - Jean-Pierre Bronowicki
- Service d'Hépato-Gastroentérologie, CHRU de Nancy-Brabois, Vandœuvre-lès-Nancy, 54511, France
| | - Ganesh D Sockalingum
- Université de Reims Champagne-Ardenne, BioSpecT-EA7506, UFR de Pharmacie, 51097 Reims, France.
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Wu Y, Wang X, Zhang M, Wu D. Molecular Biomarkers and Recent Liquid Biopsy Testing Progress: A Review of the Application of Biosensors for the Diagnosis of Gliomas. Molecules 2023; 28:5660. [PMID: 37570630 PMCID: PMC10419986 DOI: 10.3390/molecules28155660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Gliomas are the most common primary central nervous system tumors, with a high mortality rate. Early and accurate diagnosis of gliomas is critical for successful treatment. Biosensors are significant in the detection of molecular biomarkers because they are simple to use, portable, and capable of real-time analysis. This review discusses several important molecular biomarkers as well as various biosensors designed for glioma diagnosis, such as electrochemical biosensors and optical biosensors. We present our perspectives on the existing challenges and hope that this review can promote the improvement of biosensors.
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Affiliation(s)
- Yuanbin Wu
- Department of Emergency Medicine, The Seventh Medical Center, Chinese PLA General Hospital, Beijing 100700, China;
| | - Xuning Wang
- Department of General Surgery, The Air Force Hospital of Northern Theater PLA, Shenyang 110042, China
| | - Meng Zhang
- Department of Neurosurgery, The Second Hospital of Southern Theater of Chinese Navy, Sanya 572000, China
| | - Dongdong Wu
- Department of Neurosurgery, The First Medical Centre, Chinese PLA General Hospital, Beijing 100853, China
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Theakstone AG, Brennan PM, Jenkinson MD, Goodacre R, Baker MJ. Investigating centrifugal filtration of serum-based FTIR spectroscopy for the stratification of brain tumours. PLoS One 2023; 18:e0279669. [PMID: 36800340 PMCID: PMC9937474 DOI: 10.1371/journal.pone.0279669] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/31/2023] [Indexed: 02/18/2023] Open
Abstract
Discrimination of brain cancer versus non-cancer patients using serum-based attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy diagnostics was first developed by Hands et al with a reported sensitivity of 92.8% and specificity of 91.5%. Cameron et al. then went on to stratifying between specific brain tumour types: glioblastoma multiforme (GBM) vs. primary cerebral lymphoma with a sensitivity of 90.1% and specificity of 86.3%. Expanding on these studies, 30 GBM, 30 lymphoma and 30 non-cancer patients were selected to investigate the influence on test performance by focusing on specific molecular weight regions of the patient serum. Membrane filters with molecular weight cut offs of 100 kDa, 50 kDa, 30 kDa, 10 kDa and 3 kDa were purchased in order to remove the most abundant high molecular weight components. Three groups were classified using both partial least squares-discriminate analysis (PLS-DA) and random forest (RF) machine learning algorithms; GBM versus non-cancer, lymphoma versus non-cancer and GBM versus lymphoma. For all groups, once the serum was filtered the sensitivity, specificity and overall balanced accuracies decreased. This illustrates that the high molecular weight components are required for discrimination between cancer and non-cancer as well as between tumour types. From a clinical application point of view, this is preferable as less sample preparation is required.
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Affiliation(s)
- Ashton G. Theakstone
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Paul M. Brennan
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
- Department of Pharmacology & Therapeutics, University of Liverpool, Liverpool, United Kingdom
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, University of Liverpool, Liverpool, United Kingdom
| | - Matthew J. Baker
- Dxcover Limited, Glasgow, United Kingdom
- Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, United Kingdom
- * E-mail: ,
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Antoniou G, Conn JJA, Smith BR, Brennan PM, Baker MJ, Palmer DS. Recurrent neural networks for time domain modelling of FTIR spectra: application to brain tumour detection. Analyst 2023; 148:1770-1776. [PMID: 36967685 DOI: 10.1039/d2an02041f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
A recurrent neural network trained on time domain data can accurately identify brain tumours from serum spectral data.
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Affiliation(s)
- Georgios Antoniou
- Dxcover Limited, Suite RC534, Royal College Building, 204 George Street, Glasgow G1 1XW, UK
| | - Justin J A Conn
- Dxcover Limited, Suite RC534, Royal College Building, 204 George Street, Glasgow G1 1XW, UK
| | - Benjamin R Smith
- Dxcover Limited, Suite RC534, Royal College Building, 204 George Street, Glasgow G1 1XW, UK
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Midlothian, Edinburgh EH4 2XU, UK
| | - Matthew J Baker
- Dxcover Limited, Suite RC534, Royal College Building, 204 George Street, Glasgow G1 1XW, UK
- School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - David S Palmer
- Dxcover Limited, Suite RC534, Royal College Building, 204 George Street, Glasgow G1 1XW, UK
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1XL, UK.
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8
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Zheng X, Wu G, Lv G, Yin L, Lv X. Rapid discrimination of hepatic echinococcosis patients' serum using vibrational spectroscopy combined with support vector machines. Photodiagnosis Photodyn Ther 2022; 40:103027. [PMID: 35882291 DOI: 10.1016/j.pdpdt.2022.103027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 12/14/2022]
Abstract
Echinococcosis is a severe zoonotic parasitic disease, and it is continuing to be a significant public health issue. The course of the disease is usually slow, and patients often remain asymptomatic for years. There is no standardized and widely accepted treatment, so early and accurate diagnosis is essential. Herein, this study utilized vibrational spectroscopic techniques, namely Raman and Fourier Transform Infrared (FTIR) spectroscopy, to quickly and accurately distinguish hepatic echinococcosis (HE) patients' serum from the healthy group. Serum samples were collected from HE patients as well as healthy control subjects, and then the Raman and FTIR spectra of the two groups were recorded. After a series of pre-processing, support vector machines (SVMs) were then used to establish the classification models for the two spectral data sets. The performance of each diagnostic model was evaluated using leave-one-out cross-validation (LOOCV) and hold-out validation methods, respectively. For the distinction between HE and healthy groups, these two spectroscopic techniques had achieved satisfactory classification results, and the diagnostic capabilities of the Raman technique were comparable to that of the FTIR method. The results demonstrate that vibrational spectroscopy has great potential in the rapid and accurate detection of HE and is expected to make up for the shortcomings of the existing clinical diagnosis methods.
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Affiliation(s)
- Xiangxiang Zheng
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Guohua Wu
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China.
| | - Guodong Lv
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Longfei Yin
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Xiaoyi Lv
- School of Software, Xinjiang University, Urumqi 830091, China
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Alcántara-Quintana LE, López-Mendoza CM, Rodríguez-Aguilar M, Medellín-Castillo N, Mizaikoff B, Flores-Ramírez R, Galván-Romero VS, Díaz de León-Martínez L. One-Drop Serum Screening Test for Anal Cancer in Men via Infrared Attenuated Total Reflection Spectroscopy. Anal Chem 2022; 94:15250-15260. [PMID: 36197692 DOI: 10.1021/acs.analchem.2c02439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rare cancers are a challenge for clinical practice, the treatment experience at major centers to which rare cancers are referred is limited and are the most difficult to diagnose. Research to identify causes or develop prevention and early detection strategies is extremely challenging. Anal cancer is an example of a rare cancer, with the human papillomavirus (HPV) infection being the most important risk factor associated. In the early stages, anal cancer does not exhibit evident symptoms. This disease is diagnosed by means of anoscopy, which diagnoses some cases of early cancer; nevertheless, sensitivity of this test ranges between 47 and 89%. Therefore, the development of new, effective, and evidence-based screening methodologies for the early detection of rare cancers is of great relevance. In this study, the potential of ATR-FTIR spectroscopy has been explored as a sensitive, nondestructive, and inexpensive analytical method for developing disease screening platforms in serum. Spectral differences were found in the regions of 1700-1100 and 1700-1400 cm-1 between the control group and the anal cancer group related to the presence of proteins and nucleic acids. The chemometric analysis presented differences in the spectral fingerprints for both spectral regions with a high sensitivity ranging from 95.2 to 99.9% and a specificity ranging from 99.2 to 100%. This is the first step that we report for a methodology that is fast, nondestructive, and easy to perform, and the high sensitivity and specificity of the method are the basis for extensive research studies to implement these technologies in the clinical field.
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Affiliation(s)
- Luz Eugenia Alcántara-Quintana
- Unidad de Innovación en Diagnóstico Celular y Molecular, Coordinación para la Innovación y la Aplicación de la Ciencia y Tecnología, Universidad Autónoma de San Luis, Potosí Av. Sierra Leona 550, Lomas 2a sección, 78120San Luis Potosí, México
| | - Carlos Miguel López-Mendoza
- Unidad de Innovación en Diagnóstico Celular y Molecular, Coordinación para la Innovación y la Aplicación de la Ciencia y Tecnología, Universidad Autónoma de San Luis, Potosí Av. Sierra Leona 550, Lomas 2a sección, 78120San Luis Potosí, México
| | - Maribel Rodríguez-Aguilar
- Departamento de Farmacia, División de Ciencias de la Salud, Universidad de Quintana Roo, Quintana Roo, Mexico Av. Erick Paolo Martínez S/N, Magisterial, 17 de Octubre, 77039Chetumal, Q.R., México
| | - Nahum Medellín-Castillo
- Centro de Investigación y Estudios de Posgrado, Facultad de Ingeniería, Universidad Autónoma de San Luis Potosí, Dr. Manuel Nava No. 8 Colonia Zona Universitaria Poniente, San Luis Potosí, SLP78290, México
| | - Boris Mizaikoff
- Institute of Analytical and Bioanalytical Chemistry, Ulm University, Albert-Einstein-Allee 11, 89081Ulm, Germany.,Hahn-Schickard, Sedanstrasse 14, 89077Ulm, Germany
| | - Rogelio Flores-Ramírez
- Centro de Investigación Aplicada en Ambiente y Salud (CIAAS), Avenida Sierra Leona No. 550, 78210Colonia Lomas Segunda Sección, San Luis Potosí, SLP, México.,CONACYT Research Fellow, Coordinación para la Innovación y Aplicación de la Ciencia y la Tecnología (CIACYT), Avenida Sierra Leona No. 550, 78210Colonia Lomas Segunda Sección, San Luis Potosí, SLP, México
| | - Vanessa Sarahí Galván-Romero
- Unidad de Innovación en Diagnóstico Celular y Molecular, Coordinación para la Innovación y la Aplicación de la Ciencia y Tecnología, Universidad Autónoma de San Luis, Potosí Av. Sierra Leona 550, Lomas 2a sección, 78120San Luis Potosí, México
| | - Lorena Díaz de León-Martínez
- LABINNOVA Inc., Research Center for Early Diseases Screening, Susana Gómez Palafox, No. 5505, Colonia Paseos del Sol, 45079Zapopan, Jalisco, México
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10
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Kołodziej M, Kaznowska E, Paszek S, Cebulski J, Barnaś E, Cholewa M, Vongsvivut J, Zawlik I. Characterisation of breast cancer molecular signature and treatment assessment with vibrational spectroscopy and chemometric approach. PLoS One 2022; 17:e0264347. [PMID: 35263369 PMCID: PMC8906614 DOI: 10.1371/journal.pone.0264347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Triple negative breast cancer (TNBC) is regarded as the most aggressive breast cancer subtype with poor overall survival and lack of targeted therapies, resulting in many patients with recurrent. The insight into the detailed biochemical composition of TNBC would help develop dedicated treatments. Thus, in this study Fourier Transform Infrared microspectroscopy combined with chemometrics and absorbance ratios investigation was employed to compare healthy controls with TNBC tissue before and after chemotherapy within the same patient. The primary spectral differences between control and cancer tissues were found in proteins, polysaccharides, and nucleic acids. Amide I/Amide II ratio decrease before and increase after chemotherapy, whereas DNA, RNA, and glycogen contents increase before and decrease after the treatment. The chemometric results revealed discriminatory features reflecting a clinical response scheme and proved the chemotherapy efficacy assessment with infrared spectroscopy is possible.
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Affiliation(s)
| | - Ewa Kaznowska
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Pathology, Medical College of Rzeszow University, Rzeszow, Poland
| | - Sylwia Paszek
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Genetics, Institution of Experimental and Clinical Medicine, University of Rzeszow, Poland
| | - Józef Cebulski
- Centre for Innovation and Transfer of Natural Sciences and Engineering Knowledge, University of Rzeszow, Rzeszow, Poland
| | - Edyta Barnaś
- Institute of Obstetrics and Emergency Medicine, Medical College of Rzeszow University, Rzeszow, Poland
| | - Marian Cholewa
- Centre for Innovation and Transfer of Natural Sciences and Engineering Knowledge, University of Rzeszow, Rzeszow, Poland
| | | | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Genetics, Institution of Experimental and Clinical Medicine, University of Rzeszow, Poland
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11
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Cameron JM, Brennan PM, Antoniou G, Butler HJ, Christie L, Conn JJA, Curran T, Gray E, Hegarty MG, Jenkinson MD, Orringer D, Palmer DS, Sala A, Smith BR, Baker MJ. Clinical validation of a spectroscopic liquid biopsy for earlier detection of brain cancer. Neurooncol Adv 2022; 4:vdac024. [PMID: 35316978 PMCID: PMC8934542 DOI: 10.1093/noajnl/vdac024] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Diagnostic delays impact the quality of life and survival of patients with brain tumors. Earlier and expeditious diagnoses in these patients are crucial to reducing the morbidities and mortalities associated with brain tumors. A simple, rapid blood test that can be administered easily in a primary care setting to efficiently identify symptomatic patients who are most likely to have a brain tumor would enable quicker referral to brain imaging for those who need it most.
Methods
Blood serum samples from 603 patients were prospectively collected and analyzed. Patients either had non-specific symptoms that could be indicative of a brain tumor on presentation to the Emergency Department, or a new brain tumor diagnosis and referral to the neurosurgical unit, NHS Lothian, Scotland. Patient blood serum samples were analyzed using the Dxcover®Brain Cancer liquid biopsy. This technology utilizes infrared spectroscopy combined with a diagnostic algorithm to predict the presence of intracranial disease.
Results
Our liquid biopsy approach reported an area under the receiver operating characteristic curve of 0.8. The sensitivity-tuned model achieves a 96% sensitivity with 45% specificity (NPV 99.3%) and identified 100% of glioblastoma multiforme patients. When tuned for a higher specificity, the model yields sensitivity of 47% with 90% specificity (PPV 28.4%).
Conclusions
This simple, non-invasive blood test facilitates the triage and radiographic diagnosis of brain tumor patients, while providing reassurance to healthy patients. Minimizing time to diagnosis would facilitate identification of brain tumor patients at an earlier stage, enabling more effective, less morbid surgical and adjuvant care.
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Affiliation(s)
- James M Cameron
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Georgios Antoniou
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Holly J Butler
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Loren Christie
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Justin J A Conn
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Tom Curran
- Children’s Mercy Research Institute at the Children’s Mercy Hospital, Kansas City, KS, USA
| | - Ewan Gray
- Independent Health Economics Consultant, Edinburgh, UK
| | - Mark G Hegarty
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Michael D Jenkinson
- Institute of Translational Medicine, University of Liverpool & The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool, L9 7LJ, UK
| | - Daniel Orringer
- Department of Neurosurgery, New York University Grossman School of Medicine, New York, NY 10018, USA
| | - David S Palmer
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Alexandra Sala
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
- Department of Pure and Applied Chemistry, Thomas Graham Building, 295 Cathedral Street, University of Strathclyde, Glasgow G11XL, UK
| | - Benjamin R Smith
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
| | - Matthew J Baker
- Dxcover Ltd , Suite RC534, Royal College Building, 204 George Street, Glasgow, G1 1XW, UK
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12
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Roadmap on Universal Photonic Biosensors for Real-Time Detection of Emerging Pathogens. PHOTONICS 2021. [DOI: 10.3390/photonics8080342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The COVID-19 pandemic has made it abundantly clear that the state-of-the-art biosensors may not be adequate for providing a tool for rapid mass testing and population screening in response to newly emerging pathogens. The main limitations of the conventional techniques are their dependency on virus-specific receptors and reagents that need to be custom-developed for each recently-emerged pathogen, the time required for this development as well as for sample preparation and detection, the need for biological amplification, which can increase false positive outcomes, and the cost and size of the necessary equipment. Thus, new platform technologies that can be readily modified as soon as new pathogens are detected, sequenced, and characterized are needed to enable rapid deployment and mass distribution of biosensors. This need can be addressed by the development of adaptive, multiplexed, and affordable sensing technologies that can avoid the conventional biological amplification step, make use of the optical and/or electrical signal amplification, and shorten both the preliminary development and the point-of-care testing time frames. We provide a comparative review of the existing and emergent photonic biosensing techniques by matching them to the above criteria and capabilities of preventing the spread of the next global pandemic.
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13
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Mariani CL, Niman ZE, Boozer LB, Ruterbories LK, Early PJ, Muñana KR, Olby NJ. Vascular endothelial growth factor concentrations in the cerebrospinal fluid of dogs with neoplastic or inflammatory central nervous system disorders. J Vet Intern Med 2021; 35:1873-1883. [PMID: 34105831 PMCID: PMC8295675 DOI: 10.1111/jvim.16181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/06/2021] [Accepted: 05/18/2021] [Indexed: 02/06/2023] Open
Abstract
Background Vascular endothelial growth factor (VEGF) is a key molecular driver of angiogenesis and vascular permeability and is expressed by a wide variety of neoplasms. Although blood VEGF concentrations have been quantified in intracranial tumors of dogs, cerebrospinal fluid (CSF) VEGF concentration might be a more sensitive biomarker of disease. Objective Concentrations of VEGF in CSF are higher in dogs with central nervous system (CNS) neoplasia compared to those with meningoencephalomyelitis and other neurologic disorders. Animals One hundred and twenty‐six client‐owned dogs presented to a veterinary teaching hospital. Methods Case‐control study. Cerebrospinal fluid was archived from dogs diagnosed with CNS neoplasia and meningoencephalomyelitis. Control dogs had other neurological disorders or diseases outside of the CNS. A commercially available kit was used to determine VEGF concentrations. Results Detectable CSF VEGF concentrations were present in 49/63 (77.8%) neoplastic samples, 22/24 (91.7%) inflammatory samples, and 8/39 (20.5%) control samples. The VEGF concentrations were significantly different between groups (P < .0001), and multiple comparison testing showed that both neoplastic and inflammatory groups had significantly higher concentrations than did controls (P < .05), but did not differ from each other. Gliomas and choroid plexus tumors had significantly higher VEGF concentrations than did the control group (P < .05). Conclusions and Clinical Importance Cerebrospinal fluid VEGF concentrations may serve as a marker of neoplastic and inflammatory CNS disorders relative to other conditions.
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Affiliation(s)
- Christopher L Mariani
- Comparative Neuroimmunology and Neuro-oncology Laboratory, North Carolina State University, Raleigh, North Carolina, USA.,Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Zachary E Niman
- Comparative Neuroimmunology and Neuro-oncology Laboratory, North Carolina State University, Raleigh, North Carolina, USA.,Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Lindsay B Boozer
- Comparative Neuroimmunology and Neuro-oncology Laboratory, North Carolina State University, Raleigh, North Carolina, USA
| | - Laura K Ruterbories
- Comparative Neuroimmunology and Neuro-oncology Laboratory, North Carolina State University, Raleigh, North Carolina, USA.,Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Peter J Early
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Karen R Muñana
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
| | - Natasha J Olby
- Department of Clinical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA.,Comparative Medicine Institute, North Carolina State University, Raleigh, North Carolina, USA
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14
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Ali H, Harting R, de Vries R, Ali M, Wurdinger T, Best MG. Blood-Based Biomarkers for Glioma in the Context of Gliomagenesis: A Systematic Review. Front Oncol 2021; 11:665235. [PMID: 34150629 PMCID: PMC8211985 DOI: 10.3389/fonc.2021.665235] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 05/18/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Gliomas are the most common and aggressive tumors of the central nervous system. A robust and widely used blood-based biomarker for glioma has not yet been identified. In recent years, a plethora of new research on blood-based biomarkers for glial tumors has been published. In this review, we question which molecules, including proteins, nucleic acids, circulating cells, and metabolomics, are most promising blood-based biomarkers for glioma diagnosis, prognosis, monitoring and other purposes, and align them to the seminal processes of cancer. METHODS The Pubmed and Embase databases were systematically searched. Biomarkers were categorized in the identified biomolecules and biosources. Biomarker characteristics were assessed using the area under the curve (AUC), accuracy, sensitivity and/or specificity values and the degree of statistical significance among the assessed clinical groups was reported. RESULTS 7,919 references were identified: 3,596 in PubMed and 4,323 in Embase. Following screening of titles, abstracts and availability of full-text, 262 articles were included in the final systematic review. Panels of multiple biomarkers together consistently reached AUCs >0.8 and accuracies >80% for various purposes but especially for diagnostics. The accuracy of single biomarkers, consisting of only one measurement, was far more variable, but single microRNAs and proteins are generally more promising as compared to other biomarker types. CONCLUSION Panels of microRNAs and proteins are most promising biomarkers, while single biomarkers such as GFAP, IL-10 and individual miRNAs also hold promise. It is possible that panels are more accurate once these are involved in different, complementary cancer-related molecular pathways, because not all pathways may be dysregulated in cancer patients. As biomarkers seem to be increasingly dysregulated in patients with short survival, higher tumor grades and more pathological tumor types, it can be hypothesized that more pathways are dysregulated as the degree of malignancy of the glial tumor increases. Despite, none of the biomarkers found in the literature search seem to be currently ready for clinical implementation, and most of the studies report only preliminary application of the identified biomarkers. Hence, large-scale validation of currently identified and potential novel biomarkers to show clinical utility is warranted.
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Affiliation(s)
- Hamza Ali
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Romée Harting
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Ralph de Vries
- Medical Library, Vrije Universiteit, Amsterdam, Netherlands
| | - Meedie Ali
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
| | - Myron G. Best
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center and Academic Medical Center, Amsterdam, Netherlands
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15
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Kochan K, Bedolla DE, Perez-Guaita D, Adegoke JA, Chakkumpulakkal Puthan Veettil T, Martin M, Roy S, Pebotuwa S, Heraud P, Wood BR. Infrared Spectroscopy of Blood. APPLIED SPECTROSCOPY 2021; 75:611-646. [PMID: 33331179 DOI: 10.1177/0003702820985856] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The magnitude of infectious diseases in the twenty-first century created an urgent need for point-of-care diagnostics. Critical shortages in reagents and testing kits have had a large impact on the ability to test patients with a suspected parasitic, bacteria, fungal, and viral infections. New point-of-care tests need to be highly sensitive, specific, and easy to use and provide results in rapid time. Infrared spectroscopy, coupled to multivariate and machine learning algorithms, has the potential to meet this unmet demand requiring minimal sample preparation to detect both pathogenic infectious agents and chronic disease markers in blood. This focal point article will highlight the application of Fourier transform infrared spectroscopy to detect disease markers in blood focusing principally on parasites, bacteria, viruses, cancer markers, and important analytes indicative of disease. Methodologies and state-of-the-art approaches will be reported and potential confounding variables in blood analysis identified. The article provides an up to date review of the literature on blood diagnosis using infrared spectroscopy highlighting the recent advances in this burgeoning field.
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Affiliation(s)
- Kamila Kochan
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Diana E Bedolla
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - David Perez-Guaita
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - John A Adegoke
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | | | - Miguela Martin
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Supti Roy
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Savithri Pebotuwa
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Philip Heraud
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
| | - Bayden R Wood
- 2541Monash University - Centre for Biospectroscopy, Clayton, Victoria, Australia
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16
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Pinto GC, Leal LB, Magalhães NC, Pereira MF, Vassallo PF, Pereira TM, Barauna VG, Byrne HJ, Carvalho LFCS. The potential of FT-IR spectroscopy for improving healthcare in sepsis - An animal model study. Photodiagnosis Photodyn Ther 2021; 34:102312. [PMID: 33930577 DOI: 10.1016/j.pdpdt.2021.102312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 04/07/2021] [Accepted: 04/23/2021] [Indexed: 11/25/2022]
Abstract
Fourier Transform-Infrared (FT-IR) absorption spectroscopy has been used to investigate pathophysiological changes caused by sepsis. Sepsis has been defined as a potentially fatal organic dysfunction caused by a dysregulated host response to infection and can lead a patient to risk of death. This study used samples consisting of the blood plasma of mice which were induced to sepsis state, compared to a healthy group using FT-IR associated with attenuated total reflectance (ATR) spectroscopy. For statistical analysis, principal components analysis (PCA) and linear discriminant analysis (LDA) were applied, independently, to the second derivative spectra of both the fingerprint (900-1800 cm-1) and the high wavenumber (2800-3100 cm-1) regions. The technique efficiently differentiated the blood plasma of the two groups, sepsis and healthy mice, the analysis indicating that fatty acids and lipids in the blood samples could be an important biomarker of sepsis.
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Affiliation(s)
- G C Pinto
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - L B Leal
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil.
| | - N C Magalhães
- Universidade de Taubaté. R. dos Operários, 09 - Centro, Taubaté, SP, 12020-340, Brazil
| | - M F Pereira
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - P F Vassallo
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil; Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - T M Pereira
- Universidade Federal do Estado de São Paulo. R. Talim, 330 - Vila Nair, São José dos Campos, SP, 12231-0, Brazil
| | - V G Barauna
- Department of Physiological Sciences, Federal University of Espírito Santo (UFES), Marechal Campos Ave, 1468, Maruípe, 29040-090, Vitória, Espírito Santo, Brazil
| | - H J Byrne
- FOCAS Research Institute, Technological University Dublin, Kevin Street, Dublin 8, Ireland
| | - L F C S Carvalho
- Universidade de Taubaté. R. dos Operários, 09 - Centro, Taubaté, SP, 12020-340, Brazil; Centro Universitário Braz Cubas. Av. Francisco Rodrigues Filho, 1233 - Vila Mogilar, Mogi das Cruzes, SP, 08773-380, Brazil
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17
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Human serum mid-infrared spectroscopy combined with machine learning algorithms for rapid detection of gliomas. Photodiagnosis Photodyn Ther 2021; 35:102308. [PMID: 33901691 DOI: 10.1016/j.pdpdt.2021.102308] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Glioma has a low cure rate and a high mortality rate. Therefore, correct diagnosis and treatment are essential for patients. This research aims to use mid-infrared spectroscopy combined with machine learning algorithms to identify patients with glioma. The glioma infrared spectra and the control group serum are smoothed and normalized, then the principal component analysis (PCA) algorithm is used to reduce the data dimensionality, and finally, the particle swarm optimization-support vector machine (PSO-SVM), backpropagation (BP) neural network and decision tree (DT) model are established. The classification accuracy of the three models was 92.00 %, 91.83 %, 87.20 %, and the AUC values were 0.919, 0.945, and 0.866, respectively. The results show that PCA-PSO-SVM has a better classification effect. This study shows that mid-infrared spectroscopy combined with machine learning algorithms has great potential in the application of non-invasive, rapid and accurate identification of glioma patients.
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18
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Ryzhikova E, Ralbovsky NM, Sikirzhytski V, Kazakov O, Halamkova L, Quinn J, Zimmerman EA, Lednev IK. Raman spectroscopy and machine learning for biomedical applications: Alzheimer's disease diagnosis based on the analysis of cerebrospinal fluid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 248:119188. [PMID: 33268033 DOI: 10.1016/j.saa.2020.119188] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 06/12/2023]
Abstract
Current Alzheimer's disease (AD) diagnostics is based on clinical assessments, imaging and neuropsychological tests that are efficient only at advanced stages of the disease. Early diagnosis of AD will provide decisive opportunities for preventive treatment and development of disease-modifying drugs. Cerebrospinal fluid (CSF) is in direct contact with the human brain, where the deadly pathological process of the disease occurs. As such, the CSF biochemical composition reflects specific changes associated with the disease and is therefore the most promising body fluid for AD diagnostic test development. Here, we describe a new method to diagnose AD based on CSF via near infrared (NIR) Raman spectroscopy in combination with machine learning analysis. Raman spectroscopy is capable of probing the entire biochemical composition of a biological fluid at once. It has great potential to detect small changes specific to AD, even at the earliest stages of pathogenesis. NIR Raman spectra were measured of CSF samples acquired from 21 patients diagnosed with AD and 16 healthy control (HC) subjects. Artificial neural networks (ANN) and support vector machine discriminant analysis (SVM-DA) statistical methods were used for differentiation purposes, with the most successful results allowing for the differentiation of AD and HC subjects with 84% sensitivity and specificity. Our classification models show high discriminative power, suggesting the method has a great potential for AD diagnostics. The reported Raman spectroscopic examination of CSF can complement current clinical tests, making early AD detection fast, accurate, and inexpensive. While this study shows promise using a small sample set, further method validation on a larger scale is required to indicate the true strength of the approach.
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Affiliation(s)
- Elena Ryzhikova
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Nicole M Ralbovsky
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Vitali Sikirzhytski
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Oleksandr Kazakov
- Department of Physics, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Lenka Halamkova
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA
| | - Joseph Quinn
- Layton Aging and Alzheimer's Center, Oregon Health & Science University, Portland, OR 97239, USA
| | - Earl A Zimmerman
- Alzheimer's Center, Department of Neurology of Albany Medical Center, Albany, NY 12222, USA
| | - Igor K Lednev
- Department of Chemistry, University at Albany, SUNY, 1400 Washington Avenue, Albany, NY 12222, USA.
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19
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The Diagnostic and Therapeutic Role of Leptin and Its Receptor ObR in Glioblastoma Multiforme. Cancers (Basel) 2020; 12:cancers12123691. [PMID: 33316976 PMCID: PMC7764087 DOI: 10.3390/cancers12123691] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Despite recent advances in molecular brain tumor therapies, glioblastoma multiforme remains a diagnostic and therapeutic challenge with, in most cases, unfavorable outcome. Leptin and related mediators of immune-metabolic traffic have attracted increased recognition in the past decade in brain tumor biology, in particular potential implications in the diagnosis and treatment of recurrent and newly diagnosed high and low grade gliomas. Randomized controlled trails are on the way to elaborate the role of leptin and its receptor ObR by targeting and using antidiabetic drugs known to interact with distinct pathways associated with leptin signaling. To date, most of the findings in clinical studies remain preliminary and of heterogenous character, although experimental studies have underpinned the relevance of leptin and ObR in the pathophysiology of brain tumors in general. Abstract Leptin has been recognized as a potential tumor growth promoter in various cancers including cranial tumor pathologies such as pituitary adenomas, meningiomas and gliomas. Despite recent advances in adjunctive therapy and the established surgical resection, chemo- and radiotherapy regimen, glioblastoma multiforme remains a particular diagnostic and therapeutic challenge among the intracranial tumor pathologies, with a poor long-term prognosis. Systemic inflammation and immune-metabolic signaling through diverse pathways are thought to impact the genesis and recurrence of brain tumors, and glioblastoma multiforme in particular. Among the various circulating mediators, leptin has gained especial diagnostic and therapeutic interest, although the precise relationship between leptin and glioblastoma biology remains largely unknown. In this narrative review (MEDLINE/OVID, SCOPUS, PubMed and manual searches of the bibliographies of known primary and review articles), we discuss the current literature using the following search terms: leptin, glioblastoma multiforme, carcinogenesis, immunometabolism, biomarkers, metformin, antidiabetic medication and metabolic disorders. An increasing body of experimental evidence implicates a relationship between the development and maintenance of gliomas (and brain tumors in general) with a dysregulated central and peripheral immune-metabolic network mediated by circulating adipokines, chemokines and cellular components, and in particular the leptin adipokine. In this review, we summarize the current evidence of the role of leptin in glioblastoma pathophysiology. In addition, we describe the status of alternative diagnostic tools and adjunctive therapeutics targeting leptin, leptin-receptors, antidiabetic drugs and associated pathways. Further experimental and clinical trials are needed to elucidate the mechanism of action and the value of immune-metabolism molecular phenotyping (central and peripheral) in order to develop novel adjunctive diagnostics and therapeutics for newly diagnosed and recurrent glioblastoma patients.
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20
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Abstract
State of the art of quantitative Vibrational Spectroscopic analysis of human blood serum is reviewed. Technical considerations for infrared absorption and Raman analysis are discussed. Quantitative analyses of Endogenous and Exogenous constituents are presented. The potential for clinical translation of spectroscopic serology is argued.
Analysis of bodily fluids using vibrational spectroscopy has attracted increasing attention in recent years. In particular, infrared spectroscopic screening of blood products, particularly blood serum, for disease diagnostics has been advanced considerably, attracting commercial interests. However, analyses requiring quantification of endogenous constituents or exogenous agents in blood are less well advanced. Recent advances towards this end are reviewed, focussing on infrared and Raman spectroscopic analyses of human blood serum. The importance of spectroscopic analysis in the native aqueous environment is highlighted, and the relative merits of infrared absorption versus Raman spectroscopy are considered, in this context. It is argued that Raman spectroscopic analysis is more suitable to quantitative analysis in liquid samples, and superior performance for quantification of high and low molecular weight components, is demonstrated. Applications for quantitation of viral loads, and therapeutic drug monitoring are also discussed.
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21
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Cameron JM, Butler HJ, Smith BR, Hegarty MG, Jenkinson MD, Syed K, Brennan PM, Ashton K, Dawson T, Palmer DS, Baker MJ. Developing infrared spectroscopic detection for stratifying brain tumour patients: glioblastoma multiforme vs. lymphoma. Analyst 2020; 144:6736-6750. [PMID: 31612875 DOI: 10.1039/c9an01731c] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Over a third of brain tumour patients visit their general practitioner more than five times prior to diagnosis in the UK, leading to 62% of patients being diagnosed as emergency presentations. Unfortunately, symptoms are non-specific to brain tumours, and the majority of these patients complain of headaches on multiple occasions before being referred to a neurologist. As there are currently no methods in place for the early detection of brain cancer, the affected patients' average life expectancy is reduced by 20 years. These statistics indicate that the current pathway is ineffective, and there is a vast need for a rapid diagnostic test. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is sensitive to the hallmarks of cancer, as it analyses the full range of macromolecular classes. The combination of serum spectroscopy and advanced data analysis has previously been shown to rapidly and objectively distinguish brain tumour severity. Recently, a novel high-throughput ATR accessory has been developed, which could be cost-effective to the National Health Service in the UK, and valuable for clinical translation. In this study, 765 blood serum samples have been collected from healthy controls and patients diagnosed with various types of brain cancer, contributing to one of the largest spectroscopic studies to date. Three robust machine learning techniques - random forest, partial least squares-discriminant analysis and support vector machine - have all provided promising results. The novel high-throughput technology has been validated by separating brain cancer and non-cancer with balanced accuracies of 90% which is comparable to the traditional fixed diamond crystal methodology. Furthermore, the differentiation of brain tumour type could be useful for neurologists, as some are difficult to distinguish through medical imaging alone. For example, the highly aggressive glioblastoma multiforme and primary cerebral lymphoma can appear similar on magnetic resonance imaging (MRI) scans, thus are often misdiagnosed. Here, we report the ability of infrared spectroscopy to distinguish between glioblastoma and lymphoma patients, at a sensitivity and specificity of 90.1% and 86.3%, respectively. A reliable serum diagnostic test could avoid the need for surgery and speed up time to definitive chemotherapy and radiotherapy.
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Affiliation(s)
- James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George St, Glasgow, G1 1RD, UK.
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22
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Caixeta DC, Aguiar EMG, Cardoso-Sousa L, Coelho LMD, Oliveira SW, Espindola FS, Raniero L, Crosara KTB, Baker MJ, Siqueira WL, Sabino-Silva R. Salivary molecular spectroscopy: A sustainable, rapid and non-invasive monitoring tool for diabetes mellitus during insulin treatment. PLoS One 2020; 15:e0223461. [PMID: 32182246 PMCID: PMC7077825 DOI: 10.1371/journal.pone.0223461] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
Monitoring of blood glucose is an invasive, painful and costly practice in diabetes. Consequently, the search for a more cost-effective (reagent-free), non-invasive and specific diabetes monitoring method is of great interest. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy has been used in diagnosis of several diseases, however, applications in the monitoring of diabetic treatment are just beginning to emerge. Here, we used ATR-FTIR spectroscopy to evaluate saliva of non-diabetic (ND), diabetic (D) and insulin-treated diabetic (D+I) rats to identify potential salivary biomarkers related to glucose monitoring. The spectrum of saliva of ND, D and D+I rats displayed several unique vibrational modes and from these, two vibrational modes were pre-validated as potential diagnostic biomarkers by ROC curve analysis with significant correlation with glycemia. Compared to the ND and D+I rats, classification of D rats was achieved with a sensitivity of 100%, and an average specificity of 93.33% and 100% using bands 1452 cm-1 and 836 cm-1, respectively. Moreover, 1452 cm-1 and 836 cm-1 spectral bands proved to be robust spectral biomarkers and highly correlated with glycemia (R2 of 0.801 and 0.788, P < 0.01, respectively). Both PCA-LDA and HCA classifications achieved an accuracy of 95.2%. Spectral salivary biomarkers discovered using univariate and multivariate analysis may provide a novel robust alternative for diabetes monitoring using a non-invasive and green technology.
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Affiliation(s)
- Douglas C Caixeta
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil.,Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Emília M G Aguiar
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Léia Cardoso-Sousa
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Líris M D Coelho
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Stephanie W Oliveira
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Foued S Espindola
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Leandro Raniero
- Nanosensor Laboratory, IP&D, University of Vale do Paraíba, São José Dos Campos, SP, Brazil
| | - Karla T B Crosara
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, Technology & Innovation Centre, University of Strathclyde, Glasgow, United Kingdom
| | - Walter L Siqueira
- College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Robinson Sabino-Silva
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil.,College of Dentistry, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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23
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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: 60] [Impact Index Per Article: 15.0] [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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24
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Parachalil DR, McIntyre J, Byrne HJ. Potential of Raman spectroscopy for the analysis of plasma/serum in the liquid state: recent advances. Anal Bioanal Chem 2020; 412:1993-2007. [DOI: 10.1007/s00216-019-02349-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 10/17/2019] [Accepted: 12/11/2019] [Indexed: 12/18/2022]
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25
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Identification of Astrocytoma Blood Serum Protein Profile. Cells 2019; 9:cells9010016. [PMID: 31861636 PMCID: PMC7017117 DOI: 10.3390/cells9010016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/11/2019] [Accepted: 12/16/2019] [Indexed: 12/13/2022] Open
Abstract
High-grade astrocytomas are some of the most common and aggressive brain cancers, whose signs and symptoms are initially non-specific. Up to the present date, there are no diagnostic tools to observe the early onset of the disease. Here, we analyzed the combination of blood serum proteins, which may play key roles in the tumorigenesis and the progression of glial tumors. Fifty-nine astrocytoma patients and 43 control serums were analyzed using Custom Human Protein Antibody Arrays, including ten targets: ANGPT1, AREG, IGF1, IP10, MMP2, NCAM1, OPN, PAI1, TGFβ1, and TIMP1. The decision tree analysis indicates that serums ANGPT1, TIMP1, IP10, and TGFβ1 are promising combinations of targets for glioma diagnostic applications. The accuracy of the decision tree algorithm was 73.5% (75/102), which correctly classified 79.7% (47/59) astrocytomas and 65.1% (28/43) healthy controls. The analysis revealed that the relative value of osteopontin (OPN) protein level alone predicted the 12-month survival of glioblastoma (GBM) patients with the specificity of 84%, while the inclusion of the IP10 protein increased model predictability to 92.3%. In conclusion, the serum protein profiles of ANGPT1, TIMP1, IP10, and TGFβ1 were associated with the presence of astrocytoma independent of its malignancy grade, while OPN and IP10 were associated with GBM patient survival.
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26
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Feng Y, Wang J, Tan D, Cheng P, Wu A. Relationship between circulating inflammatory factors and glioma risk and prognosis: A meta-analysis. Cancer Med 2019; 8:7454-7468. [PMID: 31599129 PMCID: PMC6885890 DOI: 10.1002/cam4.2585] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/07/2019] [Accepted: 09/15/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Inflammatory factors have been considered a significant factor contributing to the development and progression of glioma. However, the relationship between circulating inflammatory factors and glioma risk as well as their prognostic values in glioma patients is still inconclusive. Here, we performed a meta-analysis to address this issue. METHODS Relevant articles were identified through PubMed, EMBASE, the Cochrane Library, Web of Science, Wanfang database, and China National Knowledge Infrastructure (CNKI) from inception to February 2019. The weighted mean differences (WMDs) or standard mean differences (SMDs) with 95% confidence intervals (CIs) were used to describe the predictive ability of the levels of circulating inflammatory factors on glioma risk. To evaluate the prognostic values of the circulating inflammatory factors in glioma, hazard ratios (HRs) with 95% CIs were used. RESULTS Thirty-one studies comprising 2587 patients were included. The overall analysis showed that increased circulating interleukin-6 (IL-6) [SMD 0.81 (95% CI: 0.21-1.40; P = .008)], interleukin-8 (IL-8) [SMD 1.01 (95% CI: 0.17-1.84; P = .018)], interleukin-17 (IL-17) [SMD 1.12 (95% CI: 0.26-1.98; P = .011)], tumor necrosis factor-α (TNF-α) [SMD 1.80 (95% CI: 1.03-2.56; P = .000)], transforming growth factor-β (TGF-β) [SMD 10.55 (95% CI: 5.59-15.51; P = .000)], and C-reactive protein (CRP) [SMD 0.95 (95% CI: 0.75-1.15; P = .000)] levels were significantly associated with glioma risk. On the other hand, our results showed that circulating IL-6 [HR 1.10 (95% CI: 1.05-1.16; P = .000)] and CRP [HR 2.02 (95% CI: 1.52-2.68; P = .000)] levels were highly correlated with a poor overall survival (OS) rate in glioma patients. CONCLUSION Our results indicate that increased circulating IL-6, IL-8, IL-17, TNF-α, TGF-β, and CRP levels are significantly associated with increased glioma risk. Moreover, our meta-analysis suggests that circulating IL-6 and CRP may serve as powerful biomarkers for a poor prognosis in glioma patients.
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Affiliation(s)
- Yuan Feng
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Jia Wang
- Department of NeurosurgeryThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShanxiPeople's Republic of China
- Center of Brain ScienceThe First Affiliated Hospital of Xi'an Jiaotong UniversityXi'anShanxiPeople's Republic of China
| | - Dezhong Tan
- Department of Otorhinolaryngology Head and Neck SurgeryThe First Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Peng Cheng
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
| | - Anhua Wu
- Department of NeurosurgeryThe First Hospital of China Medical UniversityShenyangLiaoningPeople's Republic of China
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27
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Cerebrospinal fluid VEGF levels and angiogenic capacity as potential prognostic markers in patients with gliomas: a pilot study. J Neurooncol 2019; 145:233-239. [PMID: 31624989 DOI: 10.1007/s11060-019-03314-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/03/2019] [Indexed: 01/17/2023]
Abstract
INTRODUCTION Gliomas are tumors of the central nervous system. Despite new classifications, they are still divided in low and high-grade gliomas, being the latter of greater malignancy. The degree of malignancy is directly related with the angiogenic activity in tumoral tissues. We measured VEGF concentrations and angiogenic capacity in cerebrospinal fluid (CSF) from patients with high and low-grade gliomas. The purpose of this study was to find a biomarker that contributes in the differential diagnosis and prognosis of gliomas. METHODS CSF was obtained from 19 individuals: 8 with low-grade gliomas, 6 with high-grade gliomas and 5 controls. VEGF concentration in CSF was measured by ELISA and the angiogenic capacity was measured by chick chorioallantoic membrane (CAM) test. RESULTS The VEGF concentration was higher in patients with high-grade gliomas, compared to patients with low-grade gliomas and controls (2860 pg/mL ± 975 vs. 182.6 ± 37.1 and 47.4 ± 0.4, respectively). On the other hand, CSF from patients with high-grade gliomas generated a higher microvascular density (MVD) than patients with low-grade gliomas and controls (13.23 ± 0.6 vessels/9000μm2 vs. 9.3 ± 0.3 and 7.92 ± 0.2, respectively). Interestingly, there was not statistical differences in both VEGF levels and angiogenic capacity in patients with low-grade gliomas and controls. CONCLUSION Together VEGF levels and angiogenic capacity in CSF can be used as a biological marker of gliomas malignancy.
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28
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Butler HJ, Brennan PM, Cameron JM, Finlayson D, Hegarty MG, Jenkinson MD, Palmer DS, Smith BR, Baker MJ. Development of high-throughput ATR-FTIR technology for rapid triage of brain cancer. Nat Commun 2019; 10:4501. [PMID: 31594931 PMCID: PMC6783469 DOI: 10.1038/s41467-019-12527-5] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 09/16/2019] [Indexed: 12/22/2022] Open
Abstract
Non-specific symptoms, as well as the lack of a cost-effective test to triage patients in primary care, has resulted in increased time-to-diagnosis and a poor prognosis for brain cancer patients. A rapid, cost-effective, triage test could significantly improve this patient pathway. A blood test using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy for the detection of brain cancer, alongside machine learning technology, is advancing towards clinical translation. However, whilst the methodology is simple and does not require extensive sample preparation, the throughput of such an approach is limited. Here we describe the development of instrumentation for the analysis of serum that is able to differentiate cancer and control patients at a sensitivity and specificity of 93.2% and 92.8%. Furthermore, preliminary data from the first prospective clinical validation study of its kind are presented, demonstrating how this innovative technology can triage patients and allow rapid access to imaging.
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Affiliation(s)
- Holly J Butler
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK. .,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
| | - Paul M Brennan
- Translational Neurosurgery, Department of Clinical Neurosciences, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - James M Cameron
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Duncan Finlayson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Mark G Hegarty
- ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Michael D Jenkinson
- Institute of Translational Medicine, University of Liverpool & The Walton Centre NHS Foundation Trust, Lower Lane, Fazakerley, Liverpool, L9 7LJ, UK
| | - David S Palmer
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Benjamin R Smith
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK. .,ClinSpec Diagnostics Limited, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
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29
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Vibrational Spectroscopy Fingerprinting in Medicine: from Molecular to Clinical Practice. MATERIALS 2019; 12:ma12182884. [PMID: 31489927 PMCID: PMC6766044 DOI: 10.3390/ma12182884] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
In the last two decades, Fourier Transform Infrared (FTIR) and Raman spectroscopies turn out to be valuable tools, capable of providing fingerprint-type information on the composition and structural conformation of specific molecular species. Vibrational spectroscopy’s multiple features, namely highly sensitive to changes at the molecular level, noninvasive, nondestructive, reagent-free, and waste-free analysis, illustrate the potential in biomedical field. In light of this, the current work features recent data and major trends in spectroscopic analyses going from in vivo measurements up to ex vivo extracted and processed materials. The ability to offer insights into the structural variations underpinning pathogenesis of diseases could provide a platform for disease diagnosis and therapy effectiveness evaluation as a future standard clinical tool.
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30
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Parachalil DR, Bruno C, Bonnier F, Blasco H, Chourpa I, Baker MJ, McIntyre J, Byrne HJ. Analysis of bodily fluids using vibrational spectroscopy: a direct comparison of Raman scattering and infrared absorption techniques for the case of glucose in blood serum. Analyst 2019; 144:3334-3346. [DOI: 10.1039/c9an00125e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Analysis of biomarkers present in the blood stream can potentially deliver crucial information on patient health and indicate the presence of numerous pathologies.
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Affiliation(s)
- Drishya Rajan Parachalil
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
- School of Physics and Optometric & Clinical Sciences
| | - Clément Bruno
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Franck Bonnier
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Hélène Blasco
- CHRU de Tours
- Laboratoire de Biochimie et Biologie Moléculaire
- Tours
- France
- WestCHEM
| | - Igor Chourpa
- Université de Tours
- UFR sciences pharmaceutiques
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Matthew J. Baker
- WestCHEM
- Department of Pure & Applied Chemistry
- Technology and Innovation Centre
- University of Strathclyde
- Glasgow
| | - Jennifer McIntyre
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
| | - Hugh J. Byrne
- FOCAS Research Institute
- Technological University Dublin
- Dublin 8
- Ireland
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31
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Morais CM, Shore RF, Pereira MG, Martin FL. Assessing Binary Mixture Effects from Genotoxic and Endocrine Disrupting Environmental Contaminants Using Infrared Spectroscopy. ACS OMEGA 2018; 3:13399-13412. [PMID: 30411037 PMCID: PMC6217637 DOI: 10.1021/acsomega.8b01916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/04/2018] [Indexed: 05/15/2023]
Abstract
Benzo[a]pyrene (B[a]P), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ethers (PBDEs) are persistent contaminants and concern has arisen over co-exposure of organisms when the chemicals exist in mixtures. Herein, attenuated total reflection Fourier transform infrared spectroscopy was used to identify biochemical alterations induced in cells by single and binary mixtures of these environmental chemicals. It was also investigated as a method to identify if interactions are occurring in mixtures and as a possible tool to predict mixture effects. Mallard fibroblasts were treated with single and binary mixtures of B[a]P, PCB126, PCB153, BDE47, and BDE209. Comparison of observed spectra from cells treated with binary mixtures with expected additive spectra, which were created from individual exposure spectra, indicated that in many areas of the spectrum, less-than-additive binary mixture effects may occur. However, possible greater-than-additive alterations were identified in the 1650-1750 cm-1 lipid region and may demonstrate a common mechanism of B[a]P and PCBs or PBDEs, which can enhance toxicity in mixtures.
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Affiliation(s)
- Camilo
L. M. Morais
- School
of Pharmacy and Biomedical Sciences, University
of Central Lancashire (UCLan), Preston PR1 2HE, U.K.
| | - Richard F. Shore
- Centre
of Ecology & Hydrology, Lancaster Environment
Centre, Lancaster LA1 4AP, U.K.
| | - M. Glória Pereira
- Centre
of Ecology & Hydrology, Lancaster Environment
Centre, Lancaster LA1 4AP, U.K.
| | - Francis L. Martin
- School
of Pharmacy and Biomedical Sciences, University
of Central Lancashire (UCLan), Preston PR1 2HE, U.K.
- E-mail:
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32
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Smith BR, Ashton KM, Brodbelt A, Dawson T, Jenkinson MD, Hunt NT, Palmer DS, Baker MJ. Combining random forest and 2D correlation analysis to identify serum spectral signatures for neuro-oncology. Analyst 2018; 141:3668-78. [PMID: 26818218 DOI: 10.1039/c5an02452h] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy has long been established as an analytical technique for the measurement of vibrational modes of molecular systems. More recently, FTIR has been used for the analysis of biofluids with the aim of becoming a tool to aid diagnosis. For the clinician, this represents a convenient, fast, non-subjective option for the study of biofluids and the diagnosis of disease states. The patient also benefits from this method, as the procedure for the collection of serum is much less invasive and stressful than traditional biopsy. This is especially true of patients in whom brain cancer is suspected. A brain biopsy is very unpleasant for the patient, potentially dangerous and can occasionally be inconclusive. We therefore present a method for the diagnosis of brain cancer from serum samples using FTIR and machine learning techniques. The scope of the study involved 433 patients from whom were collected 9 spectra each in the range 600-4000 cm(-1). To begin the development of the novel method, various pre-processing steps were investigated and ranked in terms of final accuracy of the diagnosis. Random forest machine learning was utilised as a classifier to separate patients into cancer or non-cancer categories based upon the intensities of wavenumbers present in their spectra. Generalised 2D correlational analysis was then employed to further augment the machine learning, and also to establish spectral features important for the distinction between cancer and non-cancer serum samples. Using these methods, sensitivities of up to 92.8% and specificities of up to 91.5% were possible. Furthermore, ratiometrics were also investigated in order to establish any correlations present in the dataset. We show a rapid, computationally light, accurate, statistically robust methodology for the identification of spectral features present in differing disease states. With current advances in IR technology, such as the development of rapid discrete frequency collection, this approach is of importance to enable future clinical translation and enables IR to achieve its potential.
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Affiliation(s)
- Benjamin R Smith
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK. and WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, UK.
| | - Katherine M Ashton
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane, Fulwood, Preston, PR2 9HT, UK
| | - Andrew Brodbelt
- Neurosurgery, The Walton Centre NHS Foundation Trust, Lower Lane, Fazakerley, Liverpool, L9 7LJ, UK
| | - Timothy Dawson
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane, Fulwood, Preston, PR2 9HT, UK
| | - Michael D Jenkinson
- Neurosurgery, The Walton Centre NHS Foundation Trust, Lower Lane, Fazakerley, Liverpool, L9 7LJ, UK
| | - Neil T Hunt
- SUPA, Department of Physics, University of Strathclyde, 107 Rottenrow East, Glasgow, G4 0NG, UK
| | - David S Palmer
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, Scotland G1 1XL, UK.
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, UK.
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33
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Gray E, Butler HJ, Board R, Brennan PM, Chalmers AJ, Dawson T, Goodden J, Hamilton W, Hegarty MG, James A, Jenkinson MD, Kernick D, Lekka E, Livermore LJ, Mills SJ, O'Neill K, Palmer DS, Vaqas B, Baker MJ. Health economic evaluation of a serum-based blood test for brain tumour diagnosis: exploration of two clinical scenarios. BMJ Open 2018; 8:e017593. [PMID: 29794088 PMCID: PMC5988134 DOI: 10.1136/bmjopen-2017-017593] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES To determine the potential costs and health benefits of a serum-based spectroscopic triage tool for brain tumours, which could be developed to reduce diagnostic delays in the current clinical pathway. DESIGN A model-based health pre-trial economic assessment. Decision tree models were constructed based on simplified diagnostic pathways. Models were populated with parameters identified from rapid reviews of the literature and clinical expert opinion. SETTING Explored as a test in both primary and secondary care (neuroimaging) in the UK health service, as well as application to the USA. PARTICIPANTS Calculations based on an initial cohort of 10 000 patients. In primary care, it is estimated that the volume of tests would approach 75 000 per annum. The volume of tests in secondary care is estimated at 53 000 per annum. MAIN OUTCOME MEASURES The primary outcome measure was quality-adjusted life-years (QALY), which were employed to derive incremental cost-effectiveness ratios (ICER) in a cost-effectiveness analysis. RESULTS Results indicate that using a blood-based spectroscopic test in both scenarios has the potential to be highly cost-effective in a health technology assessment agency decision-making process, as ICERs were well below standard threshold values of £20 000-£30 000 per QALY. This test may be cost-effective in both scenarios with test sensitivities and specificities as low as 80%; however, the price of the test would need to be lower (less than approximately £40). CONCLUSION Use of this test as triage tool in primary care has the potential to be both more effective and cost saving for the health service. In secondary care, this test would also be deemed more effective than the current diagnostic pathway.
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Affiliation(s)
- Ewan Gray
- Health Improvement Scotland, Glasgow, UK
| | - Holly J Butler
- Department of Pure and Applied Chemistry, University of Strathclyde Technology and Innovation Centre, Glasgow, UK
- ClinSpec Diagnostics Limited, University of Strathlcyde, Technology and Innovation Centre, Glasgow, UK
| | - Ruth Board
- Rosemere Cancer Centre, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - Paul M Brennan
- Department of Clinical Neurosciences, Western General Hospital, Edinburgh, UK
| | - Anthony J Chalmers
- Beatson West of Scotland Cancer Centre, Glasgow, UK
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, UK
| | - Timothy Dawson
- Neurosurgery Department, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - John Goodden
- Neurosurgery Department, Leeds General Infirmary, Leeds, UK
| | - Willie Hamilton
- Primary Care Diagnostics, University of Exeter Medical School, College House, University of Exeter, Exeter, UK
| | - Mark G Hegarty
- Department of Pure and Applied Chemistry, University of Strathclyde Technology and Innovation Centre, Glasgow, UK
- ClinSpec Diagnostics Limited, University of Strathlcyde, Technology and Innovation Centre, Glasgow, UK
| | - Allan James
- Institute of Molecular Cell and Systems Biology, Glasgow, UK
| | - Michael D Jenkinson
- Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, UK
- Institute of Translational Medicine, Clinical Science Centre, University of Liverpool, Liverpool, UK
| | | | - Elvira Lekka
- Neurosurgery Department, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Preston, UK
| | - Laurent J Livermore
- Department of Neurosurgery, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Samantha J Mills
- Neurosurgery, The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - Kevin O'Neill
- John Fulcher Neuro-Oncology Laboratory, Imperial College, London, UK
| | - David S Palmer
- ClinSpec Diagnostics Limited, University of Strathlcyde, Technology and Innovation Centre, Glasgow, UK
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, UK
| | - Babar Vaqas
- John Fulcher Neuro-Oncology Laboratory, Imperial College, London, UK
| | - Matthew J Baker
- Department of Pure and Applied Chemistry, University of Strathclyde Technology and Innovation Centre, Glasgow, UK
- ClinSpec Diagnostics Limited, University of Strathlcyde, Technology and Innovation Centre, Glasgow, UK
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Staniszewska-Slezak E, Wiercigroch E, Fedorowicz A, Buczek E, Mateuszuk L, Baranska M, Chlopicki S, Malek K. A possible Fourier transform infrared-based plasma fingerprint of angiotensin-converting enzyme inhibitor-induced reversal of endothelial dysfunction in diabetic mice. JOURNAL OF BIOPHOTONICS 2018; 11:e201700044. [PMID: 28700133 DOI: 10.1002/jbio.201700044] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 05/10/2017] [Accepted: 06/06/2017] [Indexed: 06/07/2023]
Abstract
Angiotensin-converting enzyme inhibitors (ACE-I) display vasoprotective activity and represent the cornerstone in the treatment of cardiovascular diseases. In this study, we tested whether Fourier transform infrared (FTIR)-based analysis of blood plasma is sensitive to detect vasoprotective effects of treatment with perindopril including reversal of endothelial dysfunction in diabetes. For this purpose, plasma samples were collected from untreated db/db mice, db/db mice treated with 2 or 10 mg/kg perindopril and db+ mice. The effect of perindopril on endothelial function was examined in ex vivo aortic rings; 10 mg/kg but not 2 mg/kg of perindopril reversed endothelial dysfunction. In plasma of db/db mice, the balance between conformations of plasma proteins was noted, and treatment with perindopril at a high dose but not at a low dose reversed this effect. This was revealed by amide II/amide I ratio attributed to increased β-sheet formation. Spectral markers at 3010, 1520/1238 cm-1 , representative for unsaturation degree of lipids and phosphorylation of tyrosine, respectively, were also affected by perindopril treatment. In conclusion, although metabolic abnormalities associated with type 2 diabetes mellitus such as hypertriglyceridemia and hyperglycemia strongly affected spectral FTIR profile of diabetic plasma, we identified FTIR features that seem to be associated with the vasoprotective activity of ACE-I.
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Affiliation(s)
- Emilia Staniszewska-Slezak
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Ewelina Wiercigroch
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Andrzej Fedorowicz
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
- Chair of Pharmacology, Jagiellonian University, Krakow, Poland
| | - Elżbieta Buczek
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Lukasz Mateuszuk
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
- Chair of Pharmacology, Jagiellonian University, Krakow, Poland
| | - Kamilla Malek
- Faculty of Chemistry, Jagiellonian University, Krakow, Poland
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35
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Strong R, Martin FL, Jones KC, Shore RF, Halsall CJ. Subtle effects of environmental stress observed in the early life stages of the Common frog, Rana temporaria. Sci Rep 2017; 7:44438. [PMID: 28317844 PMCID: PMC5357840 DOI: 10.1038/srep44438] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/08/2017] [Indexed: 01/01/2023] Open
Abstract
Worldwide amphibian populations are declining due to habitat loss, disease and pollution. Vulnerability to environmental contaminants such as pesticides will be dependent on the species, the sensitivity of the ontogenic life stage and hence the timing of exposure and the exposure pathway. Herein we investigated the biochemical tissue 'fingerprint' in spawn and early-stage tadpoles of the Common frog, Rana temporaria, using attenuated total reflection-Fourier-transform infrared (ATR-FTIR) spectroscopy with the objective of observing differences in the biochemical constituents of the respective amphibian tissues due to varying water quality in urban and agricultural ponds. Our results demonstrate that levels of stress (marked by biochemical constituents such as glycogen that are involved in compensatory metabolic mechanisms) can be observed in tadpoles present in the pond most impacted by pollution (nutrients and pesticides), but large annual variability masked any inter-site differences in the frog spawn. ATR-FTIR spectroscopy is capable of detecting differences in tadpoles that are present in selected ponds with different levels of environmental perturbation and thus serves as a rapid and cost effective tool in assessing stress-related effects of pollution in a vulnerable class of organism.
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Affiliation(s)
- Rebecca Strong
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire (UCLan), Preston PR1 2HE, UK
| | - Kevin C Jones
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Richard F Shore
- Centre for Ecology and Hydrology, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
| | - Crispin J Halsall
- Lancaster Environment Centre, Lancaster University, Bailrigg, Lancaster LA1 4YQ, UK
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36
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Zhang J, Li B, Wang Q, Li C, Zhang Y, Lin H, Wang Z. Characterization of postmortem biochemical changes in rabbit plasma using ATR-FTIR combined with chemometrics: A preliminary study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:733-739. [PMID: 27788472 DOI: 10.1016/j.saa.2016.10.041] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 10/19/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Abstract
Postmortem interval (PMI) determination is one of the most challenging tasks in forensic medicine due to a lack of accurate and reliable methods. It is especially difficult for late PMI determination. Although many attempts with various types of body fluids based on chemical methods have been made to solve this problem, few investigations are focused on blood samples. In this study, we employed an attenuated total reflection (ATR)-Fourier transform infrared (FTIR) technique coupled with principle component analysis (PCA) to monitor biochemical changes in rabbit plasma with increasing PMI. Partial least square (PLS) model was used based on the spectral data for PMI prediction in an independent sample set. Our results revealed that postmortem chemical changes in compositions of the plasma were time-dependent, and various components including proteins, lipids and nucleic acids contributed to the discrimination of the samples at different time points. A satisfactory prediction within 48h postmortem was performed by the combined PLS model with a good fitting between actual and predicted PMI of 0.984 and with an error of ±1.92h. In consideration of the simplicity and portability of ATR-FTIR, our preliminary study provides an experimental and theoretical basis for application of this technique in forensic practice.
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Affiliation(s)
- Ji Zhang
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Bing Li
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Qi Wang
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Chengzhi Li
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Yinming Zhang
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Hancheng Lin
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China
| | - Zhenyuan Wang
- Department of Forensic Pathology, College of Forensic Medicine, Xian Jiaotong University, Xi'an, Shaanxi, China.
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37
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Hughes C, Baker MJ. Can mid-infrared biomedical spectroscopy of cells, fluids and tissue aid improvements in cancer survival? A patient paradigm. Analyst 2017; 141:467-75. [PMID: 26501136 DOI: 10.1039/c5an01858g] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This review will take a fresh approach from the patient perspective; offering insight into the applications of mid-infrared biomedical spectroscopy in a scenario whereby the patient presents with non-specific symptoms and via an extensive diagnostic process multiple lesions are discovered but no clear sign of the primary tumour; a condition known as cancer of unknown primary (CUP). With very limited options to diagnose the cancer origin, treatment options are likely to be ineffective and prognosis is consequentially very poor. CUP has not yet been targeted by infrared biospectroscopy, however, this timely, concise dissemination will focus on a series of research highlights and breakthroughs from the field for the management of a variety of cancer-related diseases - many examples of which have occurred within this year alone. The case for integration of mid-infrared (MIR) technology into clinical practice will be demonstrated largely via diagnostic, but also therapeutic and prognostic avenues by means of including cytological, bio-fluid and tissue analysis. The review is structured around CUP but is relevant for all cancer diagnoses. Infrared spectroscopy is fast developing a reputation as a valid and powerful tool for the detection and diagnosis of cancer using a variety of sample formats. The technology will produce data and tools that are designed to complement routine clinical practice; enhancing the ability of the clinician to make a reliable and non-subjective decision and enabling decreased levels of mortality and morbidity and gains in patient quality of life.
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Affiliation(s)
- Caryn Hughes
- School of Chemical Engineering & Analytical Sciences, Faculty of Engineering & Physical Science, University of Manchester, Brunswick Street, Manchester, M13 9PL, UK. and WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow, G1 1RD, UK.
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38
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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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Bonnier F, Blasco H, Wasselet C, Brachet G, Respaud R, Carvalho LFCS, Bertrand D, Baker MJ, Byrne HJ, Chourpa I. Ultra-filtration of human serum for improved quantitative analysis of low molecular weight biomarkers using ATR-IR spectroscopy. Analyst 2017; 142:1285-1298. [DOI: 10.1039/c6an01888b] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Monitoring of changes in the concentrations of the low molecular weight constituents enhanced by abundant proteins depletion.
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Affiliation(s)
- Franck Bonnier
- Université François-Rabelais de Tours
- Faculté de Pharmacie
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Hélène Blasco
- CHRU de Tours
- Laboratoire de Biochimie et de Biologie Moléculaire
- Tours
- France
- INSERM
| | - Clément Wasselet
- Université François-Rabelais de Tours
- Faculté de Pharmacie
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
| | - Guillaume Brachet
- Université François Rabelais de Tours
- UMR CNRS 7292 Génétique
- Immunothérapie
- Chimie et Cancer
- Faculté de Médecine
| | - Renaud Respaud
- Université François-Rabelais de Tours
- UMR 1100
- CHRU de Tours
- Service de Pharmacie
- F-37032 Tours
| | - Luis Felipe C. S. Carvalho
- Universidade do Vale do Paraiba
- Laboratory of Biomedical Vibrational Spectroscopy
- Sao José dos Campos
- Brazil
| | | | - Matthew J. Baker
- WestCHEM
- Technology and Innovation Centre
- Department of Pure and Applied Chemistry
- University of Strathclyde
- Glasgow G1 1XL
| | - Hugh J. Byrne
- FOCAS Research Institute
- Dublin Institute of Technology (DIT)
- Dublin 8
- Ireland
| | - Igor Chourpa
- Université François-Rabelais de Tours
- Faculté de Pharmacie
- EA 6295 Nanomédicaments et Nanosondes
- 37200 Tours
- France
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40
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Bonnier F, Brachet G, Duong R, Sojinrin T, Respaud R, Aubrey N, Baker MJ, Byrne HJ, Chourpa I. Screening the low molecular weight fraction of human serum using ATR-IR spectroscopy. JOURNAL OF BIOPHOTONICS 2016; 9:1085-1097. [PMID: 27507567 DOI: 10.1002/jbio.201600015] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 06/06/2016] [Accepted: 07/11/2016] [Indexed: 05/11/2023]
Abstract
Vibrational spectroscopic techniques can detect small variations in molecular content, linked with disease, showing promise for screening and early diagnosis. Biological fluids, particularly blood serum, are potentially valuable for diagnosis purposes. The so-called Low Molecular Weight Fraction (LMWF) contains the associated peptidome and metabolome and has been identified as potentially the most relevant molecular population for disease-associated biomarker research. Although vibrational spectroscopy can deliver a specific chemical fingerprint of the samples, the High Molecular Weight Fraction (HMWF), composed of the most abundant serum proteins, strongly dominates the response and ultimately makes the detection of minor spectral variations a challenging task. Spectroscopic detection of potential serum biomarkers present at relatively low concentrations can be improved using pre-analytical depletion of the HMWF. In the present study, human serum fractionation by centrifugal filtration was used prior to analysis by Attenuated Total Reflection infrared spectroscopy. Using a model sample based on glycine spiked serum, it is demonstrated that the screening of the LMWF can be applied to quantify blinded concentrations up to 50 times lower. Moreover, the approach is easily transferable to different bodily fluids which would support the development of more efficient and suitable clinical protocols exploring vibrational spectroscopy based ex-vivo diagnostic tools. Revealing serum LMWF for spectral serological diagnostic applications.
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Affiliation(s)
- Franck Bonnier
- Université François-Rabelais de Tours, Faculty of Pharmacy, 31 avenue Monge, 37200, Tours, France.
| | - Guillaume Brachet
- Université François Rabelais de Tours, UMR CNRS 7292 Génétique, Immunothérapie, Chimie et Cancer, Faculté de Médecine, 10 Bd Tonnellé, 37032, Tours, Cedex
| | - Romain Duong
- Université François-Rabelais de Tours, Faculty of Pharmacy, 31 avenue Monge, 37200, Tours, France
| | - Tobiloba Sojinrin
- FOCAS Research Institute, Dublin Institute of Technology (DIT), Camden Row, Dublin 8, Ireland
| | - Renaud Respaud
- Université François-Rabelais de Tours, F-37032, Tours, France
| | - Nicolas Aubrey
- Université de Tours, 37200, Tours, France
- Institut National de la Recherche Agronomique, 37380, Nouzilly, France
| | - Matthew J Baker
- WestCHEM, Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Hugh J Byrne
- FOCAS Research Institute, Dublin Institute of Technology (DIT), Camden Row, Dublin 8, Ireland
| | - Igor Chourpa
- Université François-Rabelais de Tours, Faculty of Pharmacy, 31 avenue Monge, 37200, Tours, France
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41
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Spalding K, Board R, Dawson T, Jenkinson MD, Baker MJ. A review of novel analytical diagnostics for liquid biopsies: spectroscopic and spectrometric serum profiling of primary and secondary brain tumors. Brain Behav 2016; 6:e00502. [PMID: 27688935 PMCID: PMC5036428 DOI: 10.1002/brb3.502] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/24/2016] [Accepted: 04/27/2016] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION Spectroscopic and spectrometric analysis of biological samples is regarded as quick, cost effective, easy to operate, and spectroscopic sample preparation involves minimal sample preparation. RESULTS Techniques like infrared (IR) spectroscopy, surface-enhanced laser desorption/ionization (SELDI)-mass spectroscopy (MS), and matrix-assisted laser desorption/ionization (MALDI) -MS could enable early diagnosis of cancer, disease monitoring, and assessment of treatment responses allowing refinement, if required. DISCUSSION Carrying out analytical testing within outpatient clinics would dramatically cut the time spent by patients attending different appointments, at different locations, save hospital time and resources but importantly would theoretically enable a reduction in mortality and morbidity. While the advantages of such a prospect seem obvious, this review aims to evaluate the use of human serum spectroscopic and spectrometric analysis as a diagnostic tool for brain cancers, creating a platform for the future of cancer diagnostics.
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Affiliation(s)
- Katie Spalding
- WestCHEM Department of Pure and Applied Chemistry Technology & Innovation Centre University of Strathclyde 99 George Street Glasgow G1 1RD UK
| | - Ruth Board
- Rosemere Cancer Centre Lancashire Teaching Hospitals NHS Trust Royal Preston Hospital Sharoe Green Lane Preston PR2 9HT UK
| | - Timothy Dawson
- Neuropathology Lancashire Teaching Hospitals NHS Trust Royal Preston Hospital Sharoe Green Lane North Preston Lancashire PR2 9HT UK
| | - Michael D Jenkinson
- The Walton Centre for Neurology and Neurosurgery The Walton Centre NHS Foundation Trust Lower Lane Fazakerley Liverpool L9 7LJ UK
| | - Matthew J Baker
- WestCHEM Department of Pure and Applied Chemistry Technology & Innovation Centre University of Strathclyde 99 George Street Glasgow G1 1RD UK
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42
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Hands JR, Clemens G, Stables R, Ashton K, Brodbelt A, Davis C, Dawson TP, Jenkinson MD, Lea RW, Walker C, Baker MJ. Brain tumour differentiation: rapid stratified serum diagnostics via attenuated total reflection Fourier-transform infrared spectroscopy. J Neurooncol 2016; 127:463-72. [PMID: 26874961 PMCID: PMC4835510 DOI: 10.1007/s11060-016-2060-x] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/22/2016] [Indexed: 01/07/2023]
Abstract
The ability to diagnose cancer rapidly with high sensitivity and specificity is essential to exploit advances in new treatments to lead significant reductions in mortality and morbidity. Current cancer diagnostic tests observing tissue architecture and specific protein expression for specific cancers suffer from inter-observer variability, poor detection rates and occur when the patient is symptomatic. A new method for the detection of cancer using 1 μl of human serum, attenuated total reflection-Fourier transform infrared spectroscopy and pattern recognition algorithms is reported using a 433 patient dataset (3897 spectra). To the best of our knowledge, we present the largest study on serum mid-infrared spectroscopy for cancer research. We achieve optimum sensitivities and specificities using a Radial Basis Function Support Vector Machine of between 80.0 and 100 % for all strata and identify the major spectral features, hence biochemical components, responsible for the discrimination within each stratum. We assess feature fed-SVM analysis for our cancer versus non-cancer model and achieve 91.5 and 83.0 % sensitivity and specificity respectively. We demonstrate the use of infrared light to provide a spectral signature from human serum to detect, for the first time, cancer versus non-cancer, metastatic cancer versus organ confined, brain cancer severity and the organ of origin of metastatic disease from the same sample enabling stratified diagnostics depending upon the clinical question asked.
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Affiliation(s)
- James R Hands
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G11RD, UK
| | - Graeme Clemens
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G11RD, UK
- Centre for Materials Science, Division of Chemistry, University of Central Lancashire, Preston, PR12HE, UK
| | - Ryan Stables
- Digital Media Technology Laboratory, Millennium Point, City Centre Campus Birmingham City University, West Midlands, B47XG, UK
| | - Katherine Ashton
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, PR29HT, UK
| | - Andrew Brodbelt
- The Walton Centre for Neurology and Neurosurgery, The Walton Centre NHS Trust, Lower Lane, Liverpool, L97LJ, UK
| | - Charles Davis
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, PR29HT, UK
| | - Timothy P Dawson
- Neuropathology, Lancashire Teaching Hospitals NHS Trust, Royal Preston Hospital, Sharoe Green Lane North, Preston, PR29HT, UK
| | - Michael D Jenkinson
- The Walton Centre for Neurology and Neurosurgery, The Walton Centre NHS Trust, Lower Lane, Liverpool, L97LJ, UK
| | - Robert W Lea
- School of Pharmacy and Biomedical Sciences, Maudland Building, University of Central Lancashire, Preston, PR12HE, UK
| | - Carol Walker
- The Walton Centre for Neurology and Neurosurgery, The Walton Centre NHS Trust, Lower Lane, Liverpool, L97LJ, UK
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, University of Strathclyde, 99 George Street, Glasgow, G11RD, UK.
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43
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Gorrochategui E, Lacorte S, Tauler R, Martin FL. Perfluoroalkylated Substance Effects in Xenopus laevis A6 Kidney Epithelial Cells Determined by ATR-FTIR Spectroscopy and Chemometric Analysis. Chem Res Toxicol 2016; 29:924-32. [PMID: 27078751 PMCID: PMC4870675 DOI: 10.1021/acs.chemrestox.6b00076] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The effects of four perfluoroalkylated
substances (PFASs), namely,
perfluorobutanesulfonate (PFBS), perfluorooctanoic acid (PFOA), perfluorooctanesulfonate
(PFOS), and perfluorononanoic acid (PFNA) were assessed in Xenopus laevis A6 kidney epithelial cells by attenuated
total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy
and chemometric analysis. Principal component analysis–linear
discriminant analysis (PCA-LDA) was used to visualize wavenumber-related
alterations and ANOVA-simultaneous component analysis (ASCA) allowed
data processing considering the underlying experimental design. Both
analyses evidenced a higher impact of low-dose PFAS-treatments (10–9 M) on A6 cells forming monolayers, while there was
a larger influence of high-dose PFAS-treatments (10–5 M) on A6 cells differentiated into dome structures. The observed
dose–response PFAS-induced effects were to some extent related
to their cytotoxicity: the EC50-values of most influential
PFAS-treatments increased (PFOS < PFNA < PFOA ≪ PFBS),
and higher-doses of these chemicals induced a larger impact. Major
spectral alterations were mainly attributed to DNA/RNA, secondary
protein structure, lipids, and fatty acids. Finally, PFOS and PFOA
caused a decrease in A6 cell numbers compared to controls, whereas
PFBS and PFNA did not significantly change cell population levels.
Overall, this work highlights the ability of PFASs to alter A6 cells,
whether forming monolayers or differentiated into dome structures,
and the potential of PFOS and PFOA to induce cell death.
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Affiliation(s)
- Eva Gorrochategui
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC) , Barcelona 08034, Catalonia, Spain
| | - Sílvia Lacorte
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC) , Barcelona 08034, Catalonia, Spain
| | - Romà Tauler
- Department of Environmental Chemistry, Institute of Environmental Assessment and Water Research (IDAEA), Consejo Superior de Investigaciones Científicas (CSIC) , Barcelona 08034, Catalonia, Spain
| | - Francis L Martin
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University , Lancaster LA1 4YQ, U.K.,School of Pharmacy and Biomedical Sciences, University of Central Lancashire , Preston, U.K
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44
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Introducing Discrete Frequency Infrared Technology for High-Throughput Biofluid Screening. Sci Rep 2016; 6:20173. [PMID: 26842132 PMCID: PMC4740754 DOI: 10.1038/srep20173] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 12/23/2015] [Indexed: 11/08/2022] Open
Abstract
Accurate early diagnosis is critical to patient survival, management and quality of life. Biofluids are key to early diagnosis due to their ease of collection and intimate involvement in human function. Large-scale mid-IR imaging of dried fluid deposits offers a high-throughput molecular analysis paradigm for the biomedical laboratory. The exciting advent of tuneable quantum cascade lasers allows for the collection of discrete frequency infrared data enabling clinically relevant timescales. By scanning targeted frequencies spectral quality, reproducibility and diagnostic potential can be maintained while significantly reducing acquisition time and processing requirements, sampling 16 serum spots with 0.6, 5.1 and 15% relative standard deviation (RSD) for 199, 14 and 9 discrete frequencies respectively. We use this reproducible methodology to show proof of concept rapid diagnostics; 40 unique dried liquid biopsies from brain, breast, lung and skin cancer patients were classified in 2.4 cumulative seconds against 10 non-cancer controls with accuracies of up to 90%.
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45
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Baker MJ, Hussain SR, Lovergne L, Untereiner V, Hughes C, Lukaszewski RA, Thiéfin G, Sockalingum GD. Developing and understanding biofluid vibrational spectroscopy: a critical review. Chem Soc Rev 2016; 45:1803-18. [DOI: 10.1039/c5cs00585j] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Biofluid vibrational spectroscopy, a promising tool for rapid disease diagnosis.
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Affiliation(s)
- Matthew J. Baker
- WESTChem
- Department of Pure and Applied Chemistry
- Technology and Innovation Centre
- University of Strathclyde
- Glasgow
| | - Shawn R. Hussain
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé
- Université de Reims Champagne-Ardenne
- CNRS UMR 7369-MEDyC
- UFR de Pharmacie
- 51096 Reims Cedex
| | - Lila Lovergne
- WESTChem
- Department of Pure and Applied Chemistry
- Technology and Innovation Centre
- University of Strathclyde
- Glasgow
| | - Valérie Untereiner
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé
- Université de Reims Champagne-Ardenne
- CNRS UMR 7369-MEDyC
- UFR de Pharmacie
- 51096 Reims Cedex
| | - Caryn Hughes
- Manchester Institute of Biotechnology
- University of Manchester
- Manchester
- UK
| | | | - Gérard Thiéfin
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé
- Université de Reims Champagne-Ardenne
- CNRS UMR 7369-MEDyC
- UFR de Pharmacie
- 51096 Reims Cedex
| | - Ganesh D. Sockalingum
- Equipe MéDIAN-Biophotonique et Technologies pour la Santé
- Université de Reims Champagne-Ardenne
- CNRS UMR 7369-MEDyC
- UFR de Pharmacie
- 51096 Reims Cedex
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46
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Pérez-Guaita D, Kuligowski J, Garrigues S, Quintás G, Wood BR. Assessment of the statistical significance of classifications in infrared spectroscopy based diagnostic models. Analyst 2015; 140:2422-7. [PMID: 25382314 DOI: 10.1039/c4an01783h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Fourier transform infrared (IR) spectroscopy in combination with multivariate data analysis is a versatile tool that can be applied to disease diagnosis. However, a rigorous validation of the obtained models is necessary in order to obtain robust results. This work evaluates the advantages of the use of permutation testing for determining the statistical significance of the misclassification errors obtained from IR based diagnostic models through cross validation (CV). The model performance, estimated by CV, is compared to a distribution of CV-performance values obtained using randomly permuted class labels. The distribution of 'random CV-values' is considered as a null distribution and used to establish the significance of the model estimators obtained using real class labels. ATR-FTIR spectra of serum samples were classified using random forest (RF) classifiers according to two criteria, the tag number (a randomly assigned pseudo class membership) and the level of urea (real class). CV errors obtained were compared to the null distribution of CV errors from a permutation test and an independent validation set. The procedure was evaluated testing typical conditions leading to overoptimistic estimations provided by the CV like e.g. the size of subsamples used during CV, variable selection and the use of replicates. Results show that for the tag number (pseudo class), CV indicated classification errors between 23 and 33% depending on the subsample size employed. Those values were even lower when variable selection or replicates were used. However, permutation testing indicated that those CV errors were non-significant. In contrast, for sample classification according to their levels of urea, all cross validation errors were found to be significant. Although the proposed method is computationally intensive, it provides a simple way of calculating an empirical p-value of the CV-estimator, thus establishing the statistical significance and providing a feasibility indicator especially useful for studies where the number of samples is limited.
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Affiliation(s)
- David Pérez-Guaita
- Centre for Biospectroscopy, School of Chemistry, Monash University, Clayton, 3800 VIC, Australia.
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Sun Q, Mu L, Qiao W, Li H, Tang J, Wang C, Hu W, Zhao T, Dong B, Song Y, Liu X. Inhibition of SHP-2 promotes radiosensitivity in glioma. Mol Med Rep 2015; 12:3563-3568. [PMID: 26004555 DOI: 10.3892/mmr.2015.3829] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 04/20/2015] [Indexed: 11/06/2022] Open
Abstract
As a phosphatase, SHP-2 has been identified to be involved in regulating several cell functions, including growth, division, adhesion and motility. Therefore, SHP‑2 may affect the response of glioma to radiotherapy, such as via enhancing angiogenesis. The present study aimed to investigate the function of SHP‑2, a protein tyrosine phosphatase, in the radiosensitivity of glioma. U251, U87 and SHG44 glioma cell lines were transfected with small interfering (si)RNA against SHP‑2 and cell proliferation was assessed using a cell counting kit 8 assay, cell apoptosis was assessed by fluorescence‑activated cell sorting and immunoblotting, cell invasion was determined by an invasion assay, and the vasculogenic mimicry capacity was assessed by a tube formation assay. SHP‑2 siRNA transfection reduced the proliferation and increased apoptosis in the glioma cell lines. Downregulation of SHP‑2 suppressed glioma cell invasion and vasculogenic mimicry. These results demonstrated that no significant difference was observed between glioma tissues and normal brain tissues, however, silencing of SHP‑2 inhibited cell proliferation, invasion and vasculogenic mimicry in the glioma cell lines. SHP‑2 may be a novel therapeutic target for glioma.
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Affiliation(s)
- Quanye Sun
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Luyan Mu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Wanchen Qiao
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Hui Li
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Jiabin Tang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Ce Wang
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Wei Hu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Tianshu Zhao
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Baijing Dong
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Yuwen Song
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
| | - Xiaoqian Liu
- Department of Neurosurgery, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, P.R. China
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Rapid discrimination of maggots utilising ATR-FTIR spectroscopy. Forensic Sci Int 2015; 249:189-96. [PMID: 25703014 DOI: 10.1016/j.forsciint.2015.01.036] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 12/01/2014] [Accepted: 01/28/2015] [Indexed: 11/20/2022]
Abstract
Entomological evidence is used in forensic investigations to indicate time since death. The species and age of maggots or flies that are present at the scene can be used when estimating how much time has passed since death. Current methods that are used to identify species and developmental stage of larvae and fly samples are highly subjective, costly and often time consuming processes and require the expertise of an entomologist or species identification via DNA analysis. The use of vibrational spectroscopy, as an alternative identification method, would allow for a quicker, cheaper and less subjective technique and would allow entomological evidence to be used more commonly in the forensic process. This proof of principle study shows the potential for using attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) as a rapid tool for differentiating between various species of larvae, such as those commonly found at crime scenes. The proposed regime would provide a rapid and valuable tool resulting in reduced time for both species identification and life cycle determination, particularly in forensic situations.
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Byrne HJ, Baranska M, Puppels GJ, Stone N, Wood B, Gough KM, Lasch P, Heraud P, Sulé-Suso J, Sockalingum GD. Spectropathology for the next generation: Quo vadis? Analyst 2015; 140:2066-73. [DOI: 10.1039/c4an02036g] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Vibrational spectroscopy for biomedical applications has shown great promise although its translation into clinical practice has, as yet, been relatively slow. This Editorial assesses the challenges facing the field and the potential way forward.
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Affiliation(s)
- Hugh J. Byrne
- FOCAS Research Institute
- Dublin Institute of Technology
- Dublin 8
- Ireland
| | | | - Gerwin J. Puppels
- RiverD International B.V
- 3029 AK Rotterdam
- the Netherlands
- Erasmus-University Medical Center
- Center for Optical Diagnostics & Therapy
| | - Nick Stone
- Biomedical Spectroscopy Lab
- School of Physics
- College of Engineering
- Mathematics and Physical Sciences
- University of Exeter
| | - Bayden Wood
- Centre for Biospectroscopy and School of Chemistry
- Monash University
- Clayton
- Australia
| | | | - Peter Lasch
- Robert Koch-Institut
- Center for Biological Threats and Special Pathogens: Proteomics and Spectroscopy (ZBS6)
- 13353 Berlin
- Germany
| | - Phil Heraud
- Centre for Biospectroscopy and School of Chemistry
- Monash University
- Australia
| | - Josep Sulé-Suso
- Institute for Science & Technology in Medicine
- Keele University
- Stoke-on-Trent
- UK
| | - Ganesh D. Sockalingum
- Université de Reims Champagne-Ardenne
- MéDIAN-Biophotonique et Technologies pour la Santé
- UFR de Pharmacie
- 51096 Reims Cedex
- France
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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: 963] [Impact Index Per Article: 96.3] [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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