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Rutherford S, Hutchison CDM, Greetham GM, Parker AW, Nordon A, Baker MJ, Hunt NT. Optical Screening and Classification of Drug Binding to Proteins in Human Blood Serum. Anal Chem 2023; 95:17037-17045. [PMID: 37939225 PMCID: PMC10666086 DOI: 10.1021/acs.analchem.3c03713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/17/2023] [Accepted: 10/23/2023] [Indexed: 11/10/2023]
Abstract
Protein-drug interactions in the human bloodstream are important factors in applications ranging from drug design, where protein binding influences efficacy and dose delivery, to biomedical diagnostics, where rapid, quantitative measurements could guide optimized treatment regimes. Current measurement approaches use multistep assays, which probe the protein-bound drug fraction indirectly and do not provide fundamental structural or dynamic information about the in vivo protein-drug interaction. We demonstrate that ultrafast 2D-IR spectroscopy can overcome these issues by providing a direct, label-free optical measurement of protein-drug binding in blood serum samples. Four commonly prescribed drugs, known to bind to human serum albumin (HSA), were added to pooled human serum at physiologically relevant concentrations. In each case, spectral changes to the amide I band of the serum sample were observed, consistent with binding to HSA, but were distinct for each of the four drugs. A machine-learning-based classification of the serum samples achieved a total cross-validation prediction accuracy of 92% when differentiating serum-only samples from those with a drug present. Identification on a per-drug basis achieved correct drug identification in 75% of cases. These unique spectroscopic signatures of the drug-protein interaction thus enable the detection and differentiation of drug containing samples and give structural insight into the binding process as well as quantitative information on protein-drug binding. Using currently available instrumentation, the 2D-IR data acquisition required just 1 min and 10 μL of serum per sample, and so these results pave the way to fast, specific, and quantitative measurements of protein-drug binding in vivo with potentially invaluable applications for the development of novel therapies and personalized medicine.
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Affiliation(s)
- Samantha
H. Rutherford
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, U.K.
| | - Christopher D. M. Hutchison
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Gregory M. Greetham
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Anthony W. Parker
- STFC
Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K.
| | - Alison Nordon
- WestCHEM,
Department of Pure and Applied Chemistry and CPACT, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, U.K.
| | - Matthew J. Baker
- School
of Medicine and Dentistry, University of
Central Lancashire, Fylde Rd, Preston PR1
2HE, U.K.
| | - Neil T. Hunt
- Department
of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K.
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2
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Sengupta S, Biswal S, Titus J, Burman A, Reddy K, Fulwani MC, Khan A, Deshpande N, Shrivastava S, Yanamala N, Sengupta PP. A novel breakthrough in wrist-worn transdermal troponin-I-sensor assessment for acute myocardial infarction. EUROPEAN HEART JOURNAL. DIGITAL HEALTH 2023; 4:145-154. [PMID: 37265867 PMCID: PMC10232240 DOI: 10.1093/ehjdh/ztad015] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/14/2023] [Indexed: 06/03/2023]
Abstract
Aims Clinical differentiation of acute myocardial infarction (MI) from unstable angina and other presentations mimicking acute coronary syndromes (ACS) is critical for implementing time-sensitive interventions and optimizing outcomes. However, the diagnostic steps are dependent on blood draws and laboratory turnaround times. We tested the clinical feasibility of a wrist-worn transdermal infrared spectrophotometric sensor (transdermal-ISS) in clinical practice and assessed the performance of a machine learning algorithm for identifying elevated high-sensitivity cardiac troponin-I (hs-cTnI) levels in patients hospitalized with ACS. Methods and results We enrolled 238 patients hospitalized with ACS at five sites. The final diagnosis of MI (with or without ST elevation) and unstable angina was adjudicated using electrocardiography (ECG), cardiac troponin (cTn) test, echocardiography (regional wall motion abnormality), or coronary angiography. A transdermal-ISS-derived deep learning model was trained (three sites) and externally validated with hs-cTnI (one site) and echocardiography and angiography (two sites), respectively. The transdermal-ISS model predicted elevated hs-cTnI levels with areas under the receiver operator characteristics of 0.90 [95% confidence interval (CI), 0.84-0.94; sensitivity, 0.86; and specificity, 0.82] and 0.92 (95% CI, 0.80-0.98; sensitivity, 0.94; and specificity, 0.64), for internal and external validation cohorts, respectively. In addition, the model predictions were associated with regional wall motion abnormalities [odds ratio (OR), 3.37; CI, 1.02-11.15; P = 0.046] and significant coronary stenosis (OR, 4.69; CI, 1.27-17.26; P = 0.019). Conclusion A wrist-worn transdermal-ISS is clinically feasible for rapid, bloodless prediction of elevated hs-cTnI levels in real-world settings. It may have a role in establishing a point-of-care biomarker diagnosis of MI and impact triaging patients with suspected ACS.
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Affiliation(s)
- Shantanu Sengupta
- Sengupta Hospital and Research Institute, Nagpur- 440033, Vidarbha (Dist), India
| | | | - Jitto Titus
- RCE Technologies, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
| | - Atandra Burman
- RCE Technologies, 2292 Faraday Avenue, Carlsbad, CA 92008, USA
| | - Keshav Reddy
- Division of Cardiovascular Disease and Hypertension, Rutgers RobertWood Johnson Medical School, 125 Patterson St, New Brunswick, NJ 08901, USA
| | - Mahesh C Fulwani
- Shrikrishna Hrudayalay and Critical Care Center, Department of Cardiology, Dhantoli, Nagpur - 440010, Vidarbha (Dist), India
| | - Aziz Khan
- Department of Cardiology, Crescent Hospital and Heart Center, Dhantoli, Nagpur- 440010, Vidarbha (Dist), India
| | - Niteen Deshpande
- Department of Cardiology, Spandan Heart Institute and Research Center, Dhantoli, Nagpur- 440010, Vidarbha (Dist), India
| | - Smit Shrivastava
- Department of Cardiology, Advanced Cardiac Institute Pt JNM Medical College, Raipur- 492009, Chattisgarh, India
| | - Naveena Yanamala
- Division of Cardiovascular Disease and Hypertension, Rutgers RobertWood Johnson Medical School, 125 Patterson St, New Brunswick, NJ 08901, USA
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3
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Impaired Extracellular Proteostasis in Patients with Heart Failure. Arch Med Res 2023; 54:211-222. [PMID: 36797157 DOI: 10.1016/j.arcmed.2023.02.001] [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: 09/11/2022] [Revised: 01/11/2023] [Accepted: 02/02/2023] [Indexed: 02/16/2023]
Abstract
BACKGROUND Proteostasis impairment and the consequent increase of amyloid burden in the myocardium have been associated with heart failure (HF) development and poor prognosis. A better knowledge of the protein aggregation process in biofluids could assist the development and monitoring of tailored interventions. AIM To compare the proteostasis status and protein's secondary structures in plasma samples of patients with HF with preserved ejection fraction (HFpEF), patients with HF with reduced ejection fraction (HFrEF), and age-matched individuals. METHODS A total of 42 participants were enrolled in 3 groups: 14 patients with HFpEF, 14 patients with HFrEF, and 14 age-matched individuals. Proteostasis-related markers were analyzed by immunoblotting techniques. Fourier Transform Infrared (FTIR) Spectroscopy in Attenuated Total Reflectance (ATR) was applied to assess changes in the protein's conformational profile. RESULTS Patients with HFrEF showed an elevated concentration of oligomeric proteic species and reduced clusterin levels. ATR-FTIR spectroscopy coupled with multivariate analysis allowed the discrimination of HF patients from age-matched individuals in the protein amide I absorption region (1700-1600 cm-1), reflecting changes in protein conformation, with a sensitivity of 73 and a specificity of 81%. Further analysis of FTIR spectra showed significantly reduced random coils levels in both HF phenotypes. Also, compared to the age-matched group, the levels of structures related to fibril formation were significantly increased in patients with HFrEF, whereas the β-turns were significantly increased in patients with HFpEF. CONCLUSION Both HF phenotypes showed a compromised extracellular proteostasis and different protein conformational changes, suggesting a less efficient protein quality control system.
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4
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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5
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John RV, Devasiya T, V.R. N, Adigal S, Lukose J, Kartha VB, Chidangil S. Cardiovascular biomarkers in body fluids: progress and prospects in optical sensors. Biophys Rev 2022; 14:1023-1050. [PMID: 35996626 PMCID: PMC9386656 DOI: 10.1007/s12551-022-00990-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/28/2022] [Indexed: 12/14/2022] Open
Abstract
Cardiovascular diseases (CVD) are the major causative factors for high mortality and morbidity in developing and developed nations. The biomarker detection plays a crucial role in the early diagnosis of several non-infectious and life-threatening diseases like CVD and many cancers, which in turn will help in more successful therapy, reducing the mortality rate. Biomarkers have diagnostic, prognostic and therapeutic significances. The search for novel biomarkers using proteomics, bio-sensing, micro-fluidics, and spectroscopic techniques with good sensitivity and specificity for CVD is progressing rapidly at present, in addition to the use of gold standard biomarkers like troponin. This review is dealing with the current progress and prospects in biomarker research for the diagnosis of cardiovascular diseases. Expert opinion. Fast diagnosis of cardiovascular diseases (CVDs) can help to provide rapid medical intervention, which can affect the patient’s short and long-term health. Identification and detection of proper biomarkers for early diagnosis are crucial for successful therapy and prognosis of CVDs. The present review discusses the analysis of clinical samples such as whole blood, blood serum, and other body fluids using techniques like high-performance liquid chromatography-LASER/LED-induced fluorescence, Raman spectroscopy, mainly, optical methods, combined with nanotechnology and micro-fluidic technologies, to probe patterns of multiple markers (marker signatures) as compared to conventional techniques.
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Affiliation(s)
- Reena V. John
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - Tom Devasiya
- Department of Cardiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - Nidheesh V.R.
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - Sphurti Adigal
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - Jijo Lukose
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - V. B. Kartha
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
| | - Santhosh Chidangil
- Centre of Excellence for Biophotonics, Department of Atomic and Molecular Physics, Manipal Academy of Higher Education, Manipal, Karnataka India 576104
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6
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Development and preliminary validation of infrared spectroscopic device for transdermal assessment of elevated cardiac troponin. COMMUNICATIONS MEDICINE 2022; 2:42. [PMID: 35603300 PMCID: PMC9053220 DOI: 10.1038/s43856-022-00104-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 03/18/2022] [Indexed: 12/02/2022] Open
Abstract
Background The levels of circulating troponin are principally required in addition to electrocardiograms for the effective diagnosis of acute coronary syndrome. Current standard-of-care troponin assays provide a snapshot or momentary view of the levels due to the requirement of a blood draw. This modality further restricts the number of measurements given the clinical context of the patient. In this communication, we present the development and early validation of non-invasive transdermal monitoring of cardiac troponin-I to detect its elevated state. Methods Our device relies on infrared spectroscopic detection of troponin-I through the dermis and is tested in stepwise laboratory, benchtop, and clinical studies. Patients were recruited with suspected acute coronary syndrome. Results We demonstrate a significant correlation (r = 0.7774, P < 0.001, n = 52 biologically independent samples) between optically-derived data and blood-based immunoassay measurements with and an area under receiver operator characteristics of 0.895, sensitivity of 96.3%, and specificity of 60% for predicting a clinically meaningful threshold for defining elevated Troponin I. Conclusion This preliminary work introduces the potential of a bloodless transdermal measurement of troponin-I based on molecular spectroscopy. Further, potential pitfalls associated with infrared spectroscopic mode of inquiry are outlined including requisite steps needed for improving the precision and overall diagnostic value of the device in future studies. The number one cause of death in the US is heart disease. With 10 million patients visiting the emergency departments in a year with chest pain, 8 million are unrelated to cardiac issues. This places a burden on hospitals leading to suboptimal patient outcomes. In patients with cardiac issues, the time clinicians take to intervene dictates reversible or irreversible heart damage. However, current markers used to test for cardiac issues require blood sampling, limiting access to and frequency of testing. This study introduces a non-invasive cardiac marker measurement device without any form of blood draw, based on measurements taken by a wearable device through the skin. Preliminary studies show high conformance to the standard of care technologies, indicating that the technology has potential to enable more rapid, frequent, accessible and non-invasive detection of cardiac issues such as heart attacks. Titus et al. develop a technological platform for the non-invasive transdermal measurement of cardiac troponin-I, a marker of myocardial injury. Preliminary testing of their device, which works via infrared spectroscopy, indicates that troponin can be detected with reasonable performance, in the absence of a blood draw.
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7
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Cameron JM, Rinaldi C, Rutherford SH, Sala A, G Theakstone A, Baker MJ. Clinical Spectroscopy: Lost in Translation? APPLIED SPECTROSCOPY 2022; 76:393-415. [PMID: 34041957 DOI: 10.1177/00037028211021846] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
This Focal Point Review paper discusses the developments of biomedical Raman and infrared spectroscopy, and the recent strive towards these technologies being regarded as reliable clinical tools. The promise of vibrational spectroscopy in the field of biomedical science, alongside the development of computational methods for spectral analysis, has driven a plethora of proof-of-concept studies which convey the potential of various spectroscopic approaches. Here we report a brief review of the literature published over the past few decades, with a focus on the current technical, clinical, and economic barriers to translation, namely the limitations of many of the early studies, and the lack of understanding of clinical pathways, health technology assessments, regulatory approval, clinical feasibility, and funding applications. The field of biomedical vibrational spectroscopy must acknowledge and overcome these hurdles in order to achieve clinical efficacy. Current prospects have been overviewed with comment on the advised future direction of spectroscopic technologies, with the aspiration that many of these innovative approaches can ultimately reach the frontier of medical diagnostics and many clinical applications.
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Affiliation(s)
| | - Christopher Rinaldi
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Alexandra Sala
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
| | - Ashton G Theakstone
- WestCHEM, Department of Pure and Applied Chemistry, Technology and Innovation Centre, Glasgow, UK
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8
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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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9
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Mikkonen JJW, Raittila J, Rieppo L, Lappalainen R, Kullaa AM, Myllymaa S. Fourier Transform Infrared Spectroscopy and Photoacoustic Spectroscopy for Saliva Analysis. APPLIED SPECTROSCOPY 2016; 70:1502-10. [PMID: 27354404 DOI: 10.1177/0003702816654149] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/29/2016] [Indexed: 05/27/2023]
Abstract
Saliva provides a valuable tool for assessing oral and systemic diseases, but concentrations of salivary components are very small, calling the need for precise analysis methods. In this work, Fourier transform infrared (FT-IR) spectroscopy using transmission and photoacoustic (PA) modes were compared for quantitative analysis of saliva. The performance of these techniques was compared with a calibration series. The linearity of spectrum output was verified by using albumin-thiocyanate (SCN(-)) solution at different SCN(-) concentrations. Saliva samples used as a comparison were obtained from healthy subjects. Saliva droplets of 15 µL were applied on the silicon sample substrate, 6 drops for each specimen, and dried at 37 ℃ overnight. The measurements were carried out using an FT-IR spectrometer in conjunction with an accessory unit for PA measurements. The findings with both transmission and PA modes mirror each other. The major bands presented were 1500-1750 cm(-1) for proteins and 1050-1200 cm(-1) for carbohydrates. In addition, the distinct spectral band at 2050 cm(-1) derives from SCN(-) anions, which is converted by salivary peroxidases to hypothiocyanate (OSCN(-)). The correlation between the spectroscopic data with SCN(-) concentration (r > 0.990 for transmission and r = 0.967 for PA mode) was found to be significant (P < 0.01), thus promising to be utilized in future applications.
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Affiliation(s)
- Jopi J W Mikkonen
- SIB Labs, University of Eastern Finland, Kuopio, Finland Department of Applied Physics, Faculty of Science and Forestry, University of Eastern Finland, Kuopio, Finland Institute of Dentistry, University of Eastern Finland, Kuopio, Finland
| | | | - Lassi Rieppo
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, Oulu, Finland Medical Research Center, University of Oulu and Oulu University Hospital, Oulu, Finland
| | - Reijo Lappalainen
- SIB Labs, University of Eastern Finland, Kuopio, Finland Department of Applied Physics, Faculty of Science and Forestry, University of Eastern Finland, Kuopio, Finland
| | - Arja M Kullaa
- Institute of Dentistry, University of Eastern Finland, Kuopio, Finland Research Group of Oral Health Sciences, Faculty of Medicine, University of Oulu and Oulu University Hospital, Oulu, Finland Educational Dental Clinic, Kuopio University Hospital, Kuopio, Finland
| | - Sami Myllymaa
- SIB Labs, University of Eastern Finland, Kuopio, Finland Department of Applied Physics, Faculty of Science and Forestry, University of Eastern Finland, Kuopio, Finland Institute of Dentistry, University of Eastern Finland, Kuopio, Finland
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Chen HZ, Tang GQ, Ai W, Xu LL, Cai K. Use of random forest in FTIR analysis of LDL cholesterol and tri-glycerides for hyperlipidemia. Biotechnol Prog 2015; 31:1693-702. [DOI: 10.1002/btpr.2161] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 08/21/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Hua-Zhou Chen
- School of Science; Guilin University of Technology; Guilin 541004 China
| | - Guo-Qiang Tang
- School of Science; Guilin University of Technology; Guilin 541004 China
| | - Wu Ai
- School of Science; Guilin University of Technology; Guilin 541004 China
| | - Li-Li Xu
- School of Ocean; Qinzhou University; Qinzhou 535000 China
| | - Ken Cai
- School of Information Science and Technology; Zhongkai University of Agriculture and Engineering; Guangzhou 510225 China
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11
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Botella LM, Albiñana V, Ojeda-Fernandez L, Recio-Poveda L, Bernabéu C. Research on potential biomarkers in hereditary hemorrhagic telangiectasia. Front Genet 2015; 6:115. [PMID: 25873934 PMCID: PMC4379940 DOI: 10.3389/fgene.2015.00115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 03/05/2015] [Indexed: 12/21/2022] Open
Abstract
Hereditary hemorrhagic telangiectasia (HHT) is a genetically heterogeneous disorder, involving mutations in two predominant genes known as Endoglin (ENG; HHT1) and activin receptor-like kinase 1 (ACVRL1/ALK1; HHT2), as well as in some less frequent genes, such as MADH4/SMAD4 (JP-HHT) or BMP9/GDF2 (HHT5). The diagnosis of HHT patients currently remains at the clinical level, according to the “Curaçao criteria,” whereas the molecular diagnosis is used to confirm or rule out suspected HHT cases, especially when a well characterized index case is present in the family or in an isolated population. Unfortunately, many suspected patients do not present a clear HHT diagnosis or do not show pathogenic mutations in HHT genes, prompting the need to investigate additional biomarkers of the disease. Here, several HHT biomarkers and novel methodological approaches developed during the last years will be reviewed. On one hand, products detected in plasma or serum samples: soluble proteins (vascular endothelial growth factor, transforming growth factor β1, soluble endoglin, angiopoietin-2) and microRNA variants (miR-27a, miR-205, miR-210). On the other hand, differential HHT gene expression fingerprinting, next generation sequencing of a panel of genes involved in HHT, and infrared spectroscopy combined with artificial neural network patterns will also be reviewed. All these biomarkers might help to improve and refine HHT diagnosis by distinguishing from the non-HHT population.
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Affiliation(s)
- Luisa-María Botella
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
| | - Virginia Albiñana
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain
| | - Luisa Ojeda-Fernandez
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
| | - Lucia Recio-Poveda
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain
| | - Carmelo Bernabéu
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Cientificas , Madrid, Spain ; Centro de Investigación Biomédica en Red de Enfermedades Raras , Madrid, Spain
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12
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Perez-Guaita D, Heraud P, Marzec KM, de la Guardia M, Kiupel M, Wood BR. Comparison of transflection and transmission FTIR imaging measurements performed on differentially fixed tissue sections. Analyst 2015; 140:2376-82. [DOI: 10.1039/c4an02034k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
FTIR microscopy of adjacent sections of tissue measured by transmission and transflection shows comparable images after UHCA.
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Affiliation(s)
- David Perez-Guaita
- Centre for Biospectroscopy
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - Philip Heraud
- Centre for Biospectroscopy
- School of Chemistry
- Monash University
- Clayton
- Australia
| | - Katarzyna M. Marzec
- Centre for Biospectroscopy
- School of Chemistry
- Monash University
- Clayton
- Australia
| | | | - Matti Kiupel
- Diagnostic Center for Population and Animal Health
- 48910-8107 Lansing
- USA
| | - Bayden R. Wood
- Centre for Biospectroscopy
- School of Chemistry
- Monash University
- Clayton
- Australia
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Mitchell AL, Gajjar KB, Theophilou G, Martin FL, Martin-Hirsch PL. Vibrational spectroscopy of biofluids for disease screening or diagnosis: translation from the laboratory to a clinical setting. JOURNAL OF BIOPHOTONICS 2014; 7:153-165. [PMID: 24648213 DOI: 10.1002/jbio.201400018] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 02/21/2014] [Accepted: 02/22/2014] [Indexed: 06/03/2023]
Abstract
There remains a need for objective and cost-effective approaches capable of diagnosing early-stage disease in point-of-care clinical settings. Given an increasingly ageing population resulting in a rising prevalence of chronic diseases, the need for screening to facilitate the personalising of therapies to prevent or slow down pathology development will increase. Such a tool needs to be robust but simple enough to be implemented into clinical practice. There is interest in extracting biomarkers from biofluids (e.g., plasma or serum); techniques based on vibrational spectroscopy provide an option. Sample preparation is minimal, techniques involved are relatively low-cost, and data frameworks are available. This review explores the evidence supporting the applicability of vibrational spectroscopy to generate spectral biomarkers of disease in biofluids. We extend the inter-disciplinary nature of this approach to hypothesise a microfluidic platform that could allow such measurements. With an appropriate lightsource, such engineering could revolutionize screening in the 21(st) century.
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Affiliation(s)
- Alana L Mitchell
- Centre for Biophotonics, Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ, UK
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Kumar S, R, Chaudhary S, S, Jain DC. Vibrational Studies of Different Human Body Disorders Using FTIR Spectroscopy. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ojapps.2014.43012] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Profiling serologic biomarkers in cirrhotic patients via high-throughput Fourier transform infrared spectroscopy: toward a new diagnostic tool of hepatocellular carcinoma. Transl Res 2013; 162:279-86. [PMID: 23920432 DOI: 10.1016/j.trsl.2013.07.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 07/09/2013] [Accepted: 07/11/2013] [Indexed: 12/14/2022]
Abstract
Identification of novel serum biomarkers of hepatocellular carcinoma (HCC) is needed for early-stage disease detection and to improve patients' survival. The aim of this study was to evaluate the potential of serum Fourier transform infrared (FTIR) spectroscopy for differentiating sera from cirrhotic patients with and without HCC. Serum samples were collected from 2 sets of patients: cirrhotic patients with HCC (n = 39) and without HCC (n = 40). The FTIR spectra (10 per sample) were acquired in the transmission mode, and data homogeneity was tested by cluster analysis to exclude outliers. After data preprocessing by extended multiplicative signal correction and principal component analysis, the Support Vector Machine (SVM) method was applied using a leave-one-out cross-validation algorithm to classify the spectra into 2 classes of cirrhotic patients with and without HCC. When SVM was applied to all spectra (n = 790), the sensitivity and the specificity for the diagnosis of HCC were, respectively, 82.02% and 82.5%. When applied to the subset of spectra excluding the outliers (n = 739), SVM classification led to a sensitivity and specificity of 87.18% and 85%, respectively. Using median spectra for each patient instead of all replicates, the sensitivity and specificity were 84.62% and 82.50%, respectively. The overall accuracy rate was 82%-86%. In conclusion, this study suggests that FTIR spectroscopy combined with advanced methods of pattern analysis shows potential for differentiating sera from cirrhotic patients with and without HCC.
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Lux A, Müller R, Tulk M, Olivieri C, Zarrabeita R, Salonikios T, Wirnitzer B. HHT diagnosis by Mid-infrared spectroscopy and artificial neural network analysis. Orphanet J Rare Dis 2013; 8:94. [PMID: 23805858 PMCID: PMC3698163 DOI: 10.1186/1750-1172-8-94] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/18/2013] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The vascular disorder Hereditary Hemorrhagic Telangiectasia (HHT) is in general an inherited disease caused by mutations in the TGF-β/BMP receptors endoglin or ALK1 or in rare cases by mutations of the TGF-β signal transducer protein Smad4 leading to the combined syndrome of juvenile polyposis and HHT. HHT is characterized by several clinical symptoms like spontaneous and recurrent epistaxis, multiple telangiectases at sites like lips, oral cavity, fingers, nose, and visceral lesions like gastrointestinal telangiectasia, pulmonary, hepatic, cerebral or spinal arteriovenous malformations. The disease shows an inter- and intra-family variability in penetrance as well as symptoms from mild to life threatening. Penetrance is also depending on age. Diagnosis of the disease is based on the presence of some of the listed symptoms or by genetic testing. HHT diagnosis is laborious, time consuming, costly and sometimes uncertain. Not all typical symptoms may be present, especially at a younger age, and genetic testing does not always identify the disease causing mutation. METHODS Infrared (IR) spectroscopy was investigated as a potential alternative to the current diagnostic methods. IR-spectra were obtained by Fourier-transform Mid-IR spectroscopy from blood plasma from HHT patients and a healthy control group. Spectral data were mathematically processed and subsequently classified and analysed by artificial neural network (ANN) analyses and by visual analysis of scatter plots of the dominant principal components. RESULTS The analyses showed that for HHT a disease specific IR-spectrum exists that is significantly different from the control group. Furthermore, at the current stage with the here used methods, HHT can be diagnosed by Mid-IR-spectroscopy in combination with ANN analysis with a sensitivity and specificity of at least 95%. Visual analysis of PCA scatter plots revealed an inter class variation of the HHT group. CONCLUSION IR-spectroscopy in combination with ANN analysis can be considered to be a serious alternative diagnostic method compared to clinical and genetically based methods. Blood plasma is an ideal candidate for diagnostic purposes, it is inexpensive, easy to isolate and only minimal amounts are required. In addition, IR-spectroscopy measurement times are fast, less than one minute, and diagnosis is not based on interpretation of may be uncertain clinical data. And last but not least, the method is inexpensive.
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Affiliation(s)
- Andreas Lux
- Q-bios GmbH Biotechnology, Mannheim, Germany.
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Detection of lung cancer tissue by attenuated total reflection–Fourier transform infrared spectroscopy—a pilot study of 60 samples. J Surg Res 2013; 179:33-8. [DOI: 10.1016/j.jss.2012.08.057] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 08/21/2012] [Accepted: 08/30/2012] [Indexed: 11/17/2022]
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Perez-Guaita D, Ventura-Gayete J, Pérez-Rambla C, Sancho-Andreu M, Garrigues S, de la Guardia M. Evaluation of infrared spectroscopy as a screening tool for serum analysis. Microchem J 2013. [DOI: 10.1016/j.microc.2012.06.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Chen P, Zhang L, Zhang F, Liu JT, Bai H, Tang GQ, Lin L. Spectral discrimination between normal and leukemic human sera using delayed luminescence. BIOMEDICAL OPTICS EXPRESS 2012; 3:1787-1792. [PMID: 22876344 PMCID: PMC3409699 DOI: 10.1364/boe.3.001787] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 04/06/2012] [Accepted: 04/27/2012] [Indexed: 06/01/2023]
Abstract
In this work, photoinduced delayed luminescence (DL) was used to distinguish serum samples of patients with acute lymphoblastic leukemia from those of healthy volunteers. DL decay kinetics of human serum samples was measured using a homebuilt ultraweak luminescence detection system. It was found a significant difference in the weight distribution of the decay rate between normal and leukemic serum samples. A comparison of the DL kinetics parameters including the initial intensity, the peak decay rate, and the peak weight value was used in making discrimination between normal and leukemic human sera. Results in this work contribute to the development of a novel optical method for the early diagnosis of leukemia.
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Scott DA, Renaud DE, Krishnasamy S, Meriç P, Buduneli N, Çetinkalp Ş, Liu KZ. Diabetes-related molecular signatures in infrared spectra of human saliva. Diabetol Metab Syndr 2010; 2:48. [PMID: 20630088 PMCID: PMC2914662 DOI: 10.1186/1758-5996-2-48] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2010] [Accepted: 07/14/2010] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND There is an ongoing need for improvements in non-invasive, point-of-care tools for the diagnosis and prognosis of diabetes mellitus. Ideally, such technologies would allow for community screening. METHODS In this study, we employed infrared spectroscopy as a novel diagnostic tool in the prediction of diabetic status by analyzing the molecular and sub-molecular spectral signatures of saliva collected from subjects with diabetes (n = 39) and healthy controls (n = 22). RESULTS Spectral analysis revealed differences in several major metabolic components - lipid, proteins, glucose, thiocyanate and carboxylate - that clearly demarcate healthy and diseased saliva. The overall accuracy for the diagnosis of diabetes based on infrared spectroscopy was 100% on the training set and 88.2% on the validation set. Therefore, we have established that infrared spectroscopy can be used to generate complex biochemical profiles in saliva and identify several potential diabetes-associated spectral features. CONCLUSIONS Infrared spectroscopy may represent an appropriate tool with which to identify novel diseases mechanisms, risk factors for diabetic complications and markers of therapeutic efficacy. Further study into the potential utility of infrared spectroscopy as diagnostic and prognostic tool for diabetes is warranted.
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Affiliation(s)
- David A Scott
- Oral Health and Systemic Disease, University of Louisville, Louisville, S Preston St, Louisville, KY, 40292, USA
- Department of Pharmacology and Toxicology, University of Louisville, Louisville, S Preston St, Louisville, KY, 40292, USA
- Department of Microbiology and Immunology, University of Louisville, Louisville, S Preston St, Louisville, KY, 40292, USA
| | - Diane E Renaud
- Oral Health and Systemic Disease, University of Louisville, Louisville, S Preston St, Louisville, KY, 40292, USA
| | - Sathya Krishnasamy
- Endocrinology, University of Louisville, Louisville, S Jackson St, Louisville, KY, 40292, USA
| | - Pinar Meriç
- Department of Periodontology, Ege University, Bornova, İzmir, 35100, Turkey
| | - Nurcan Buduneli
- Department of Periodontology, Ege University, Bornova, İzmir, 35100, Turkey
| | - Şvetki Çetinkalp
- Metabolic Diseases and Endocrinology, Ege University, Bornova, İzmir, 35100, Turkey
| | - Kan-Zhi Liu
- Institute for Biodiagnostics, National Research Council, Ellice Avenue, Winnipeg, MB, R3B 1Y6, Canada
- Department of Oral Biology, University of Manitoba, Bannatyne Avenue, Winnipeg, MB, R3E 0W2, Canada
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