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Shree P, Aggarwal Y, Kumar M, Majhee L, Singh NN, Prakash O, Chandra A, Mahuli SA, Shamsi S, Rai A. Saliva Based Diagnostic Prediction of Oral Squamous Cell Carcinoma using FTIR Spectroscopy. Indian J Otolaryngol Head Neck Surg 2024; 76:2282-2289. [PMID: 38883442 PMCID: PMC11169329 DOI: 10.1007/s12070-023-04294-z] [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: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 06/18/2024] Open
Abstract
Oral cancer ranks as the sixth most prevalent form of cancer worldwide, presenting a significant public health concern. According to the World Health Organization (WHO), within a 5-year period following diagnosis, the mortality rate among oral cancer patients of all stages stands at 45%. In this study, a total of 60 patients divided into 2 groups were recruited. Group A included 30 histo-pathologically confirmed OSCC patients and Group B included 30 healthy controls. A standardized procedure was followed to collect saliva samples. FTIR spectroscopy was done for all the saliva samples collected from both Group A and B. An IR Prestige-21 (Shimadzu Corp, Japan) spectrometer was used to record IR spectra in the 40-4000 cm-1 range SVM classifier was applied in the classification of disease state from normal subjects using FTIR data. The peaks were identified at wave no 1180 cm-1, 1230 cm-1, 1340 cm-1, 1360 cm-1, 1420 cm-1, 1460 cm-1, 1500 cm-1, 1540 cm-1, 1560 cm-1, and 1637 cm-1. The observed results of SVM demonstrated the accuracy of 91.66% in the classification of Cancer tissues from the normal subjects with sensitivity of 83.33% while specificity and precision of 100.0%. The development of oral cancer leads to noticeable alterations in the secondary structure of proteins. These findings emphasize the promising use of ATR-FTIR platforms in conjunction with machine learning as a reliable, non-invasive, reagent-free, and highly sensitive method for screening and monitoring individuals with oral cancer.
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Affiliation(s)
- Priya Shree
- Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, Jharkhand 834009 India
| | - Yogendra Aggarwal
- Department of Bioengineering and Biotechnology, Birla Institute of Technology Mesra, Ranchi, India
| | - Manish Kumar
- Department of Bioengineering, Birla Institute of Technology, Mesra, Ranchi, 835215 India
| | - Lakhan Majhee
- Department of Pharmacology, Rajendra Institute of Medical Sciences, Ranchi, India
| | - Narendra Nath Singh
- Oral Pathology, Microbiology and Forensic Odontology, Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, 834009 India
| | - Om Prakash
- Oral and Maxillofacial Pathology, Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, 834009 India
| | - Akhilesh Chandra
- Department of Oral Pathology and Microbiology, Faculty of Dental Sciences, Banaras Hindu University, Varanasi, India
| | - Simpy Amit Mahuli
- Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, 834009 India
| | - Shoa Shamsi
- Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, 834009 India
| | - Arpita Rai
- Dental College, Rajendra Institute of Medical Sciences (RIMS), Bariatu, Ranchi, Jharkhand 834009 India
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Delrue C, De Bruyne S, Oyaert M, Delanghe JR, Moresco RN, Speeckaert R, Speeckaert MM. Infrared Spectroscopy in Gynecological Oncology: A Comprehensive Review of Diagnostic Potentials and Challenges. Int J Mol Sci 2024; 25:5996. [PMID: 38892184 PMCID: PMC11172863 DOI: 10.3390/ijms25115996] [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: 04/23/2024] [Revised: 05/25/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
The early detection of gynecological cancers, which is critical for improving patient survival rates, is challenging because of the vague early symptoms and the diagnostic limitations of current approaches. This comprehensive review delves into the game-changing potential of infrared (IR) spectroscopy, a noninvasive technology used to transform the landscape of cancer diagnosis in gynecology. By collecting the distinctive vibrational frequencies of chemical bonds inside tissue samples, Fourier-transform infrared (FTIR) spectroscopy provides a 'molecular fingerprint' that outperforms existing diagnostic approaches. We highlight significant advances in this field, particularly the identification of discrete biomarker bands in the mid- and near-IR spectra. Proteins, lipids, carbohydrates, and nucleic acids exhibited different absorption patterns. These spectral signatures not only serve to distinguish between malignant and benign diseases, but also provide additional information regarding the cellular changes associated with cancer. To underscore the practical consequences of these findings, we examined studies in which IR spectroscopy demonstrated exceptional diagnostic accuracy. This review supports the use of IR spectroscopy in normal clinical practice, emphasizing its capacity to detect and comprehend the intricate molecular underpinnings of gynecological cancers.
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Affiliation(s)
- Charlotte Delrue
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium;
| | - Sander De Bruyne
- Department of Clinical Biology, Ghent University Hospital, 9000 Ghent, Belgium; (S.D.B.); (M.O.)
| | - Matthijs Oyaert
- Department of Clinical Biology, Ghent University Hospital, 9000 Ghent, Belgium; (S.D.B.); (M.O.)
| | - Joris R. Delanghe
- Department of Diagnostic Sciences, Ghent University Hospital, C. Heymanslaan 10, 9000 Ghent, Belgium;
| | - Rafael Noal Moresco
- Graduate Program in Pharmaceutical Sciences, Center of Health Sciences, Federal University of Santa Maria, Santa Maria 72500-000, Brazil;
| | | | - Marijn M. Speeckaert
- Department of Nephrology, Ghent University Hospital, 9000 Ghent, Belgium;
- Research Foundation-Flanders (FWO), 1000 Brussels, Belgium
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3
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Korte B, Mathios D. Innovation in Non-Invasive Diagnosis and Disease Monitoring for Meningiomas. Int J Mol Sci 2024; 25:4195. [PMID: 38673779 PMCID: PMC11050588 DOI: 10.3390/ijms25084195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/26/2024] [Accepted: 04/07/2024] [Indexed: 04/28/2024] Open
Abstract
Meningiomas are tumors of the central nervous system that vary in their presentation, ranging from benign and slow-growing to highly aggressive. The standard method for diagnosing and classifying meningiomas involves invasive surgery and can fail to provide accurate prognostic information. Liquid biopsy methods, which exploit circulating tumor biomarkers such as DNA, extracellular vesicles, micro-RNA, proteins, and more, offer a non-invasive and dynamic approach for tumor classification, prognostication, and evaluating treatment response. Currently, a clinically approved liquid biopsy test for meningiomas does not exist. This review provides a discussion of current research and the challenges of implementing liquid biopsy techniques for advancing meningioma patient care.
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Affiliation(s)
- Brianna Korte
- Department of Neurosurgery, Washington University Medical Campus, St. Louis, MO 63110, USA
| | - Dimitrios Mathios
- Department of Neurosurgery, Washington University Medical Campus, St. Louis, MO 63110, USA
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Nazeer SS, Venkataraman RK, Jayasree RS, Bayry J. Infrared Spectroscopy for Rapid Triage of Cancer Using Blood Derivatives: A Reality Check. Anal Chem 2024; 96:957-965. [PMID: 38164878 DOI: 10.1021/acs.analchem.3c02590] [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: 01/03/2024]
Abstract
Infrared (IR) spectroscopy of serum/plasma represents an alluring molecular diagnostic tool, especially for cancer, as it can provide a molecular fingerprint of clinical samples based on vibrational modes of chemical bonds. However, despite the superior performance, the routine adoption of this technique for clinical settings has remained elusive. This is due to the potential confounding factors that are often overlooked and pose a significant barrier to clinical translation. In this Perspective, we summarize the concerns associated with various confounding factors, such as fluid sampling, optical effects, hemolysis, abnormal cardiovascular and/or hepatic functions, infections, alcoholism, diet style, age, and gender of a patient or normal control cohort, and improper selection of numerical methods that ultimately would lead to improper spectral diagnosis. We also propose some precautionary measures to overcome the challenges associated with these confounding factors.
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Affiliation(s)
- Shaiju S Nazeer
- Department of Chemistry, Indian Institute of Space Sciences and Technology, Thiruvananthapuram, Kerala 695547, India
| | - Ravi Kumar Venkataraman
- Ultrafast Laser Spectroscopy Lab, Center for Integrative Petroleum Research, King Fahd University of Petroleum and Minerals, Dhahran 31261, Kingdom of Saudi Arabia
| | - Ramapurath S Jayasree
- Division of Biophotonics and Imaging, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Thiruvananthapuram, Kerala 695012, India
| | - Jagadeesh Bayry
- Department of Biological Sciences and Engineering, Indian Institute of Technology Palakkad, Palakkad 678623, India
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Tugrul F, Akin Geyik G, Yalinbaş Kaya B, Peker Cengiz B, Karuk Elmas SN, Yilmaz I, Arslan FN. A biospectroscopic approach toward colorectal cancer diagnosis from bodily fluid samples via ATR-MIR spectroscopy combined with multivariate data analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 304:123342. [PMID: 37688884 DOI: 10.1016/j.saa.2023.123342] [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: 04/28/2023] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023]
Abstract
In this study, a biospectroscopic approach was reported for the detection of spectral changes and biomarkers for the diagnosis of colorectal cancer (CC) cases from different bodily fluids (blood plasma, blood serum, saliva and colonoscopy disinfection/wash fluids) by using attenuated total reflection-mid infrared (ATR-MIR) spectroscopy. To recognize the molecular level changes in the spectral characteristics of CC and their healthy/control (CH) groups, different multivariate data analyses (HCA, LDA, PCA and SIMCA) were successfully performed over the data of ATR-MIR spectroscopy. Two hundred specimens were characterized in detail over the data of spectral regions (4000-650 cm-1 and regions V-XXII). The findings revealed that significant changes were clearly observed in the concentrations of lipid, protein, nucleic acid and carbohydrate biomolecules for cancer cases based upon their necessity to overcome energy requirements. Supervised multivariate data methodology SIMCA, presented an excellent classification for the studied groups; similarly 100% of the specimens from different bodily fluids were correctly classified by supervised methodology LDA. As a result, the developed ATR-MIR methodology for the classification of CC and their healthy groups highlighted a rapid cancer diagnosis approach from different bodily fluids; therefore, it could be guide to make well decision before histopathological assessment and to screen CC populations existing in society.
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Affiliation(s)
- Fuzuli Tugrul
- Eskişehir City Hospital, Clinic of Radiation Oncology, 26080 Eskisehir, Turkey
| | - Gonul Akin Geyik
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey
| | | | - Betul Peker Cengiz
- Eskişehir Yunus Emre State Hospital, Clinic of Medical Pathology, 26190 Eskisehir, Turkey
| | - Sukriye Nihan Karuk Elmas
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey; Istanbul University-Cerrahpaşa, Pharmacy Faculty, Department of Analytical Chemistry, 34500 Istanbul, Turkey
| | - Ibrahim Yilmaz
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey.
| | - Fatma Nur Arslan
- Karamanoglu Mehmetbey University, K.O. Science Faculty, Department of Chemistry, 70100 Karaman, Turkey.
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Szymoński K, Skirlińska-Nosek K, Lipiec E, Sofińska K, Czaja M, Wilkosz N, Krupa M, Wanat F, Ulatowska-Białas M, Adamek D. Combined analytical approach empowers precise spectroscopic interpretation of subcellular components of pancreatic cancer cells. Anal Bioanal Chem 2023; 415:7281-7295. [PMID: 37906289 PMCID: PMC10684650 DOI: 10.1007/s00216-023-04997-w] [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: 09/04/2023] [Revised: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023]
Abstract
The lack of specific and sensitive early diagnostic options for pancreatic cancer (PC) results in patients being largely diagnosed with late-stage disease, thus inoperable and burdened with high mortality. Molecular spectroscopic methodologies, such as Raman or infrared spectroscopies, show promise in becoming a leader in screening for early-stage cancer diseases, including PC. However, should such technology be introduced, the identification of differentiating spectral features between various cancer types is required. This would not be possible without the precise extraction of spectra without the contamination by necrosis, inflammation, desmoplasia, or extracellular fluids such as mucous that surround tumor cells. Moreover, an efficient methodology for their interpretation has not been well defined. In this study, we compared different methods of spectral analysis to find the best for investigating the biomolecular composition of PC cells cytoplasm and nuclei separately. Sixteen PC tissue samples of main PC subtypes (ductal adenocarcinoma, intraductal papillary mucinous carcinoma, and ampulla of Vater carcinoma) were collected with Raman hyperspectral mapping, resulting in 191,355 Raman spectra and analyzed with comparative methodologies, specifically, hierarchical cluster analysis, non-negative matrix factorization, T-distributed stochastic neighbor embedding, principal components analysis (PCA), and convolutional neural networks (CNN). As a result, we propose an innovative approach to spectra classification by CNN, combined with PCA for molecular characterization. The CNN-based spectra classification achieved over 98% successful validation rate. Subsequent analyses of spectral features revealed differences among PC subtypes and between the cytoplasm and nuclei of their cells. Our study establishes an optimal methodology for cancer tissue spectral data classification and interpretation that allows precise and cognitive studies of cancer cells and their subcellular components, without mixing the results with cancer-surrounding tissue. As a proof of concept, we describe findings that add to the spectroscopic understanding of PC.
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Affiliation(s)
- Krzysztof Szymoński
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland.
- Department of Pathomorphology, University Hospital, Kraków, Poland.
| | - Katarzyna Skirlińska-Nosek
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Ewelina Lipiec
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| | - Kamila Sofińska
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
| | - Michał Czaja
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Natalia Wilkosz
- Faculty of Physics, Astronomy and Applied Computer Science, M. Smoluchowski Institute of Physics, Jagiellonian University, Kraków, Poland
- AGH University of Krakow, Faculty of Physics and Applied Computer Science, Kraków, Poland
| | - Matylda Krupa
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
| | - Filip Wanat
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
| | - Magdalena Ulatowska-Białas
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
- Department of Pathomorphology, University Hospital, Kraków, Poland
| | - Dariusz Adamek
- Department of Pathomorphology, Medical College, Jagiellonian University, Kraków, Poland
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7
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Xue Y, Zheng X, Wu G, Wang J. Rapid diagnosis of cervical cancer based on serum FTIR spectroscopy and support vector machines. Lasers Med Sci 2023; 38:276. [PMID: 38001244 DOI: 10.1007/s10103-023-03930-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: 09/15/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
Cervical cancer is one of the most common malignant tumors among female gynecological diseases. This paper aims to explore the feasibility of utilizing serum Fourier Transform Infrared (FTIR) spectroscopy, combined with machine learning and deep learning algorithms, to efficiently differentiate between healthy individuals, hysteromyoma patients, and cervical cancer patients. In this study, serum samples from 30 groups of hysteromyoma, 36 groups of cervical cancer, and 30 healthy groups were collected and FTIR spectra of each group were recorded. In addition, the raw datasets were averaged according to the number of scans to obtain an average dataset, and the raw datasets were spectrally enhanced to obtain an augmentation dataset, resulting in a total of three sets of data with sizes of 258, 96, and 1806, respectively. Then, the hyperparameters in the four kernel functions of the Support Vector Machine (SVM) model were optimized by grid search and leave-one-out (LOO) cross-validation. The resulting SVM models achieved recognition accuracies ranging from 85.0% to 100.0% on the test set. Furthermore, a one-dimensional convolutional neural network (1D-CNN) demonstrated a recognition accuracy of 75.0% to 90.0% on the test set. It can be concluded that the use of serum FTIR spectroscopy combined with the SVM algorithm for the diagnosis of cervical cancer has important medical significance.
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Affiliation(s)
- Yunfei Xue
- College of Software, Xinjiang University, 830046, Urumqi, China
| | - Xiangxiang Zheng
- Tianjin Key Laboratory for Control Theory & Applications in Complicated Systems, School of Electrical Engineering and Automation, Tianjin University of Technology, 300384, Tianjin, China
| | - Guohua Wu
- School of Electronic Engineering, Beijing University of Posts and Telecommunicationsn, 100876, Beijing, China.
| | - Jing Wang
- State Key Laboratory of Pathogenesis, Prevention and Treatment of High Incidence Diseases in Central Asia, Department of Gynecology, The First Affiliated Hospital of Xinjiang Medical University, 830054, Urumqi, China
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Mokari A, Guo S, Bocklitz T. Exploring the Steps of Infrared (IR) Spectral Analysis: Pre-Processing, (Classical) Data Modelling, and Deep Learning. Molecules 2023; 28:6886. [PMID: 37836728 PMCID: PMC10574384 DOI: 10.3390/molecules28196886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/13/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Infrared (IR) spectroscopy has greatly improved the ability to study biomedical samples because IR spectroscopy measures how molecules interact with infrared light, providing a measurement of the vibrational states of the molecules. Therefore, the resulting IR spectrum provides a unique vibrational fingerprint of the sample. This characteristic makes IR spectroscopy an invaluable and versatile technology for detecting a wide variety of chemicals and is widely used in biological, chemical, and medical scenarios. These include, but are not limited to, micro-organism identification, clinical diagnosis, and explosive detection. However, IR spectroscopy is susceptible to various interfering factors such as scattering, reflection, and interference, which manifest themselves as baseline, band distortion, and intensity changes in the measured IR spectra. Combined with the absorption information of the molecules of interest, these interferences prevent direct data interpretation based on the Beer-Lambert law. Instead, more advanced data analysis approaches, particularly artificial intelligence (AI)-based algorithms, are required to remove the interfering contributions and, more importantly, to translate the spectral signals into high-level biological/chemical information. This leads to the tasks of spectral pre-processing and data modeling, the main topics of this review. In particular, we will discuss recent developments in both tasks from the perspectives of classical machine learning and deep learning.
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Affiliation(s)
- Azadeh Mokari
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Leibniz Health Technologies”, 07745 Jena, Germany (S.G.)
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Shuxia Guo
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Leibniz Health Technologies”, 07745 Jena, Germany (S.G.)
| | - Thomas Bocklitz
- Leibniz Institute of Photonic Technology, Member of Research Alliance “Leibniz Health Technologies”, 07745 Jena, Germany (S.G.)
- Institute of Physical Chemistry, Friedrich Schiller University Jena, 07743 Jena, Germany
- Institute of Computer Science, Faculty of Mathematics, Physics & Computer Science, University Bayreuth, Universitaet sstraße 30, 95447 Bayreuth, Germany
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Zhu J, Zhang S, Wang R, Fang R, Lei L, Zheng J, Chen Z. Urine based near-infrared spectroscopy analysis reveals a noninvasive and convenient diagnosis method for cancers: a pilot study. PeerJ 2023; 11:e15895. [PMID: 37667750 PMCID: PMC10475272 DOI: 10.7717/peerj.15895] [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: 05/26/2023] [Accepted: 07/24/2023] [Indexed: 09/06/2023] Open
Abstract
Background The challenges in cancer diagnosis underline the need for continued research and development of new diagnostic tools and methods. This study aims to explore an effective, noninvasive, and convenient diagnostic tool using urine based near-infrared spectroscopy (NIRS) analysis combined with machine learning algorithm. Methods Urine samples were collected from a total of 327 participants, including 181 cancer cases and 146 healthy controls. These participants were randomly spit into train set (n = 218) and test set (n = 109). NIRS analysis (4,000 ∼10,000 cm-1) was performed for each sample in both train and test sets. Five pretreatment methods, including Savitzky-Golay (SG) smoothing, multiplicative scatter correction (MSC), baseline removal (BSL) with fitting polynomials to be used as baselines, the first derivative (DERIV1), and the second derivative (DERIV2), and combination with "scaling" and "center", were investigated. Then partial least-squares (PLS) and linear support-vector machine (SVM) classification models were established, and prediction performance was evaluated in test set. Results NIRS had greatly overlapping in peaks, and PCA analysis failed in separation between cancers and healthy controls. In modeling with urine based NIRS data, PLS model showed its highest prediction accuracy of 0.780, with DERIV2, "scaling" and "center" pretreatment, while linear SVM displayed its best prediction accuracy of 0.844, with raw NIRS. With optimization in SVM, the prediction accuracy could improve to 0.862, when the top 262 features were involved as variables. Discussion This pilot study combining urine based NIRS analysis and machine learning is effective and convenient that might facilitate in cancer diagnosis, encouraging further evaluation with a large-size multi-center study.
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Affiliation(s)
- Jing Zhu
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Siyu Zhang
- Department of Clinical Pharmacy, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ruting Wang
- Experimental Research Center, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang, China
| | - Ruhua Fang
- Department of Clinical Laboratory, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
| | - Lan Lei
- Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Ji Zheng
- Department of Radiotherapy and Chemotherapy, Ningbo No. 2 Hospital, Ningbo, Zhejiang, China
| | - Zhongjian Chen
- Experimental Research Center, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China
- Zhejiang Key Laboratory of Diagnosis & Treatment Technology on Thoracic Oncology (Lung and Esophagus), Hangzhou, Zhejiang, China
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Fadlelmoula A, Catarino SO, Minas G, Carvalho V. A Review of Machine Learning Methods Recently Applied to FTIR Spectroscopy Data for the Analysis of Human Blood Cells. MICROMACHINES 2023; 14:1145. [PMID: 37374730 DOI: 10.3390/mi14061145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Machine learning (ML) is a broad term encompassing several methods that allow us to learn from data. These methods may permit large real-world databases to be more rapidly translated to applications to inform patient-provider decision-making. This paper presents a review of articles that discuss the use of Fourier transform infrared (FTIR) spectroscopy and ML for human blood analysis between the years 2019-2023. The literature review was conducted to identify published research of employed ML linked with FTIR for distinction between pathological and healthy human blood cells. The articles' search strategy was implemented and studies meeting the eligibility criteria were evaluated. Relevant data related to the study design, statistical methods, and strengths and limitations were identified. A total of 39 publications in the last 5 years (2019-2023) were identified and evaluated for this review. Diverse methods, statistical packages, and approaches were used across the identified studies. The most common methods included support vector machine (SVM) and principal component analysis (PCA) approaches. Most studies applied internal validation and employed more than one algorithm, while only four studies applied one ML algorithm to the data. A wide variety of approaches, algorithms, statistical software, and validation strategies were employed in the application of ML methods. There is a need to ensure that multiple ML approaches are used, the model selection strategy is clearly defined, and both internal and external validation are necessary to be sure that the discrimination of human blood cells is being made with the highest efficient evidence.
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Affiliation(s)
- Ahmed Fadlelmoula
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Susana O Catarino
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Graça Minas
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Vítor Carvalho
- 2Ai, School of Technology, IPCA, 4750-810 Barcelos, Portugal
- Algoritmi Research Center/LASI, University of Minho, 4800-058 Guimarães, Portugal
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Dou J, Dawuti W, Zheng X, Zhu Y, Lin R, Lü G, Zhang Y. Rapid discrimination of Brucellosis in sheep using serum Fourier transform infrared spectroscopy combined with PCA-LDA algorithm. Photodiagnosis Photodyn Ther 2023; 42:103567. [PMID: 37084931 DOI: 10.1016/j.pdpdt.2023.103567] [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: 02/25/2023] [Revised: 04/09/2023] [Accepted: 04/11/2023] [Indexed: 04/23/2023]
Abstract
Brucellosis in sheep is an infectious disease caused by Brucella melitensis in sheep. The current conventional serological methods for screening Brucella-infected sheep have the disadvantage of time consuming and low accuracy, so a simple, rapid and highly accurate screening method is needed. The aim of this study was to evaluate the feasibility of diagnosing Brucella-infected sheep by serum samples based on the Fourier transform infrared (FTIR) spectroscopy. In this study, FTIR spectroscopy of serum from Brucella-infected sheep (n=102) and healthy sheep (n=125) revealed abnormal protein and lipid metabolism in serum from Brucella-infected sheep compared to healthy sheep. Principal component analysis-Linear discriminant analysis (PCA-LDA) method was used to differentiate the FTIR spectra of serum from Brucella-infected sheep and healthy sheep in the protein band (3700-3090 cm-1) and lipid band (3000-2800 cm-1), and its overall diagnostic accuracy was 100% (sensitivity 100%, specificity 100%). In conclusion, our results suggest that serum FTIR spectroscopy combined with PCA-LDA algorithm has great potential for brucellosis in sheep screening.
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Affiliation(s)
- Jingrui Dou
- School of Public Health, Xinjiang Medical University, Urumqi 830054, China; State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Wubulitalifu Dawuti
- School of Public Health, Xinjiang Medical University, Urumqi 830054, China; State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Xiangxiang Zheng
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Yousen Zhu
- Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi Xinjiang 830054, China
| | - Renyong Lin
- State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China
| | - Guodong Lü
- School of Public Health, Xinjiang Medical University, Urumqi 830054, China; State Key Laboratory of Pathogenesis, Prevention, and Treatment of Central Asian High Incidence Diseases, Clinical Medical Research Institute, The First Affiliated Hospital of Xinjiang Medical University, Urumqi 830054, China.
| | - Yujiang Zhang
- School of Public Health, Xinjiang Medical University, Urumqi 830054, China; The Center for Disease Control and Prevention of Xinjiang Uygur Autonomous Region, Urumqi 830002, China.
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12
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Caixeta DC, Carneiro MG, Rodrigues R, Alves DCT, Goulart LR, Cunha TM, Espindola FS, Vitorino R, Sabino-Silva R. Salivary ATR-FTIR Spectroscopy Coupled with Support Vector Machine Classification for Screening of Type 2 Diabetes Mellitus. Diagnostics (Basel) 2023; 13:diagnostics13081396. [PMID: 37189497 DOI: 10.3390/diagnostics13081396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/04/2023] [Accepted: 02/08/2023] [Indexed: 05/17/2023] Open
Abstract
The blood diagnosis of diabetes mellitus (DM) is highly accurate; however, it is an invasive, high-cost, and painful procedure. In this context, the combination of ATR-FTIR spectroscopy and machine learning techniques in other biological samples has been used as an alternative tool to develop a non-invasive, fast, inexpensive, and label-free diagnostic or screening platform for several diseases, including DM. In this study, we used the ATR-FTIR tool associated with linear discriminant analysis (LDA) and a support vector machine (SVM) classifier in order to identify changes in salivary components to be used as alternative biomarkers for the diagnosis of type 2 DM. The band area values of 2962 cm-1, 1641 cm-1, and 1073 cm-1 were higher in type 2 diabetic patients than in non-diabetic subjects. The best classification of salivary infrared spectra was by SVM, showing a sensitivity of 93.3% (42/45), specificity of 74% (17/23), and accuracy of 87% between non-diabetic subjects and uncontrolled type 2 DM patients. The SHAP features of infrared spectra indicate the main salivary vibrational modes of lipids and proteins that are responsible for discriminating DM patients. In summary, these data highlight the potential of ATR-FTIR platforms coupled with machine learning as a reagent-free, non-invasive, and highly sensitive tool for screening and monitoring diabetic patients.
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Affiliation(s)
- Douglas Carvalho Caixeta
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | | | - Ricardo Rodrigues
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Deborah Cristina Teixeira Alves
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Luís Ricardo Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Thúlio Marquez Cunha
- School of Medicine, Federal University of Uberlandia (UFU), Uberlandia 38408-100, Minas Gerais, Brazil
| | - Foued Salmen Espindola
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
| | - Rui Vitorino
- Institute of Biomedicine, Department of Medical Sciences, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia 38408-100, Minas Gerais, Brazil
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13
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Zhang R, Wang P, Chen J, Tian Y, Gao J. Age estimation of bloodstains based on Raman spectroscopy and chemometrics. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 290:122284. [PMID: 36592590 DOI: 10.1016/j.saa.2022.122284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 11/04/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
The accurate estimation of the bloodstain age, which is one of the important biological evidence of crime scene, can provide a lot of information related to crime. How to extract the information quickly and accurately from bloodstains without damage has been a focused problem. In this study, a bloodstains age estimation method based on Raman spectroscopy and chemometrics was developed. As many as 11 simulated environments based on different temperature and humidity were constructed in the method, and bloodstains of three species including human were studied. The influence of environmental factors such as temperature and humidity on the variation of Raman spectral peaks during the aging process of bloodstains was analyzed using the e-index fitting. When the humidity was kept constant, the increase of temperature generally promoted the changes of the spectral peaks. When the temperature was kept constant, the increase of humidity generally slowed the changes of spectral peaks. These works provide data support for the further development of Raman spectroscopy for bloodstain age estimation and could accelerate its application in actual scenes.
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Affiliation(s)
- Rui Zhang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Peng Wang
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
| | - Jiansheng Chen
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Yubing Tian
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
| | - Jing Gao
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China.
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14
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Faria RA, Leal LB, Thebit MM, Pereira SWA, Serafim NR, Barauna VG, da Chagas E Silva Carvalho LF, Sartório CL, Gouvea SA. Potential Role of Fourier Transform Infrared Spectroscopy as a Screening Approach for Breast Cancer. APPLIED SPECTROSCOPY 2023; 77:405-417. [PMID: 36703259 DOI: 10.1177/00037028231156194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Breast cancer is a heterogeneous disease, and its spread involves a succession of clinical and pathological stages. Screening is predominantly based on mammography, which has critical limitations related to the effectiveness and production of false-positive or false-negative results, generating discomfort and low adherence. In this context, infrared with attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy emerges as a non-destructive sample tool, which is non-invasive, label-free, has a low operating-cost, and requires only a small amount of sample, including liquid plasma samples. We sought to evaluate the clinical applicability of ATR FT-IR in breast cancer screening. ATR FT-IR spectroscopy through its highest potential spectral biomarker could distinguish, by liquid plasma biopsy, breast cancer patients and healthy controls, obtaining a sensitivity of 97%, specificity of 93%, a receiver operating characteristic ROC curve of 97%, and a prediction accuracy of 94%. The main variance between the groups was mainly in the band 1511 cm-1 of the control group, 1502 and 1515 cm-1 of the cancer group, which are the peaks of the bands referring to proteins and amide II. ATR FT-IR spectroscopy has demonstrated to be a promising tool for breast cancer screening, given its time efficiency, cost of approach, and its high ability to distinguish between the liquid plasma samples of breast cancer patients and healthy controls.
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Affiliation(s)
- Rodrigo A Faria
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Leonardo B Leal
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Marcela M Thebit
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Sergio W A Pereira
- Mastology Service Evangelical Hospital of Vila Velha, Vila Velha, Brazil
| | - Neuzimar R Serafim
- Mastology Service Evangelical Hospital of Vila Velha, Vila Velha, Brazil
| | - Valerio G Barauna
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | | | - Carmem L Sartório
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
| | - Sonia A Gouvea
- Department of Physiological Sciences, Federal University of Espirito Santo, Vitória, Brazil
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15
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Connal S, Cameron JM, Sala A, Brennan PM, Palmer DS, Palmer JD, Perlow H, Baker MJ. Liquid biopsies: the future of cancer early detection. J Transl Med 2023; 21:118. [PMID: 36774504 PMCID: PMC9922467 DOI: 10.1186/s12967-023-03960-8] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/01/2023] [Indexed: 02/13/2023] Open
Abstract
Cancer is a worldwide pandemic. The burden it imposes grows steadily on a global scale causing emotional, physical, and financial strains on individuals, families, and health care systems. Despite being the second leading cause of death worldwide, many cancers do not have screening programs and many people with a high risk of developing cancer fail to follow the advised medical screening regime due to the nature of the available screening tests and other challenges with compliance. Moreover, many liquid biopsy strategies being developed for early detection of cancer lack the sensitivity required to detect early-stage cancers. Early detection is key for improved quality of life, survival, and to reduce the financial burden of cancer treatments which are greater at later stage detection. This review examines the current liquid biopsy market, focusing in particular on the strengths and drawbacks of techniques in achieving early cancer detection. We explore the clinical utility of liquid biopsy technologies for the earlier detection of solid cancers, with a focus on how a combination of various spectroscopic and -omic methodologies may pave the way for more efficient cancer diagnostics.
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Affiliation(s)
- Siobhan Connal
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK
| | - James M. Cameron
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK
| | - Alexandra Sala
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK
| | - Paul M. Brennan
- grid.4305.20000 0004 1936 7988Translational Neurosurgery, Centre for Clinical Brain Sciences, 49 Little France Crescent, University of Edinburgh, Edinburgh, EH16 4BS UK
| | - David S. Palmer
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK
| | - Joshua D. Palmer
- grid.412332.50000 0001 1545 0811Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210 USA
| | - Haley Perlow
- grid.412332.50000 0001 1545 0811Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210 USA
| | - Matthew J. Baker
- Dxcover Ltd., Royal College Building, 204 George Street, Glasgow, G1 1XW UK ,grid.11984.350000000121138138Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G11XL UK ,grid.7943.90000 0001 2167 3843School of Medicine, Faculty of Clinical and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE UK
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16
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Variabilities in global DNA methylation and β-sheet richness establish spectroscopic landscapes among subtypes of pancreatic cancer. Eur J Nucl Med Mol Imaging 2023; 50:1792-1810. [PMID: 36757432 PMCID: PMC10119063 DOI: 10.1007/s00259-023-06121-7] [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: 09/27/2022] [Accepted: 01/21/2023] [Indexed: 02/10/2023]
Abstract
PURPOSE Knowledge about pancreatic cancer (PC) biology has been growing rapidly in recent decades. Nevertheless, the survival of PC patients has not greatly improved. The development of a novel methodology suitable for deep investigation of the nature of PC tumors is of great importance. Molecular imaging techniques, such as Fourier transform infrared (FTIR) spectroscopy and Raman hyperspectral mapping (RHM) combined with advanced multivariate data analysis, were useful in studying the biochemical composition of PC tissue. METHODS Here, we evaluated the potential of molecular imaging in differentiating three groups of PC tumors, which originate from different precursor lesions. Specifically, we comprehensively investigated adenocarcinomas (ACs): conventional ductal AC, intraductal papillary mucinous carcinoma, and ampulla of Vater AC. FTIR microspectroscopy and RHM maps of 24 PC tissue slides were obtained, and comprehensive advanced statistical analyses, such as hierarchical clustering and nonnegative matrix factorization, were performed on a total of 211,355 Raman spectra. Additionally, we employed deep learning technology for the same task of PC subtyping to enable automation. The so-called convolutional neural network (CNN) was trained to recognize spectra specific to each PC group and then employed to generate CNN-prediction-based tissue maps. To identify the DNA methylation spectral markers, we used differently methylated, isolated DNA and compared the observed spectral differences with the results obtained from cellular nuclei regions of PC tissues. RESULTS The results showed significant differences among cancer tissues of the studied PC groups. The main findings are the varying content of β-sheet-rich proteins within the PC cells and alterations in the relative DNA methylation level. Our CNN model efficiently differentiated PC groups with 94% accuracy. The usage of CNN in the classification task did not require Raman spectral data preprocessing and eliminated the need for extensive knowledge of statistical methodologies. CONCLUSIONS Molecular spectroscopy combined with CNN technology is a powerful tool for PC detection and subtyping. The molecular fingerprint of DNA methylation and β-sheet cytoplasmic proteins established by our results is different for the main PC groups and allowed the subtyping of pancreatic tumors, which can improve patient management and increase their survival. Our observations are of key importance in understanding the variability of PC and allow translation of the methodology into clinical practice by utilizing liquid biopsy testing.
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17
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Prada P, Brunel B, Moulin D, Rouillon L, Netter P, Loeuille D, Slimano F, Bouche O, Peyrin-Biroulet L, Jouzeau JY, Piot O. Identification of circulating biomarkers of Crohn's disease and spondyloarthritis using Fourier transform infrared spectroscopy. JOURNAL OF BIOPHOTONICS 2023; 16:e202200200. [PMID: 36112612 DOI: 10.1002/jbio.202200200] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/15/2023]
Abstract
Crohn's disease (CD) and spondyloarthritis (SpA) are two inflammatory diseases sharing many common features (genetic polymorphism, armamentarium). Both diseases lack diagnostic markers of certainty. While the diagnosis of CD is made by a combination of clinical, and biological criteria, the diagnosis of SpA may take several years to be confirmed. Based on the hypothesis that CD and SpA alter the biochemical profile of plasma, the objective of this study was to evaluate the analytical capability of Fourier transform infrared spectroscopy (FTIR) in identifying spectral biomarkers. Plasma from 104 patients was analyzed. After data processing of the spectra by Extended Multiplicative Signal Correction and linear discriminant analysis, we demonstrated that it was possible to distinguish CD and SpA from controls with an accuracy of 97% and 85% respectively. Spectral differences were mainly associated with proteins and lipids. This study showed that FTIR analysis is efficient to identify plasma biosignatures specific to CD or SpA.
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Affiliation(s)
- Pierre Prada
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Benjamin Brunel
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
- FEMTO-ST Institute, CNRS UMR-6174, Université de Bourgogne Franche-Comté, Besançon, France
| | - David Moulin
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Lise Rouillon
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Patrick Netter
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Damien Loeuille
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Florian Slimano
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Olivier Bouche
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
| | - Laurent Peyrin-Biroulet
- Département de Gastroentérologie, Hôpital Universitaire de Nancy-Brabois, Vandœuvre-lès-Nancy, France
| | - Jean-Yves Jouzeau
- Ingénierie Moléculaire et Ingénierie Articulaire (IMoPA), UMR-7365 CNRS, Faculté de Médecine, Université de Lorraine et Hôpital Universitaire de Nancy, Nancy, France
| | - Olivier Piot
- EA7506-BioSpectroscopie Translationnelle (BioSpecT), Université de Reims Champagne-Ardenne, Reims, France
- Plateforme d'Imagerie Cellulaire ou Tissulaire (PICT), Université de Reims Champagne-Ardenne, Reims, France
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18
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Li L, Wu H, Xu W, Wang Y, Wang J, Wang Y. New application of ATR-FTIR spectroscopy for postmortem interval estimation based on puparia of the sarcosaprophagous fly Chrysomya megacephala (Diptera: Calliphoridae). Forensic Chem 2023. [DOI: 10.1016/j.forc.2023.100484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
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19
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Szymoński K, Chmura Ł, Lipiec E, Adamek D. Vibrational spectroscopy – are we close to finding a solution for early pancreatic cancer diagnosis? World J Gastroenterol 2023; 29:96-109. [PMID: 36683712 PMCID: PMC9850953 DOI: 10.3748/wjg.v29.i1.96] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 10/03/2022] [Accepted: 10/31/2022] [Indexed: 01/04/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive and lethal neoplasm, ranking seventh in the world for cancer deaths, with an overall 5-year survival rate of below 10%. The knowledge about PC pathogenesis is rapidly expanding. New aspects of tumor biology, including its molecular and morphological heterogeneity, have been reported to explain the complicated “cross-talk” that occurs between the cancer cells and the tumor stroma or the nature of pancreatic ductal adenocarcinoma-associated neural remodeling. Nevertheless, currently, there are no specific and sensitive diagnosis options for PC. Vibrational spectroscopy (VS) shows a promising role in the development of early diagnosis technology. In this review, we summarize recent reports about improvements in spectroscopic methodologies, briefly explain and highlight the drawbacks of each of them, and discuss available solutions. The important aspects of spectroscopic data evaluation with multivariate analysis and a convolutional neural network methodology are depicted. We conclude by presenting a study design for systemic verification of the VS-based methods in the diagnosis of PC.
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Affiliation(s)
- Krzysztof Szymoński
- Department of Pathomorphology, Jagiellonian University Medical College, Cracow 33-332, Poland
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
| | - Łukasz Chmura
- Department of Pathomorphology, Jagiellonian University Medical College, Cracow 33-332, Poland
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
| | - Ewelina Lipiec
- M. Smoluchowski Institute of Physics, Jagiellonian University, Cracow 30-348, Poland
| | - Dariusz Adamek
- Department of Pathomorphology, University Hospital in Cracow, Cracow 31-501, Poland
- Department of Neuropathology, Jagiellonian University Medical College, Cracow 33-332, Poland
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20
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Zniber M, Vahdatiyekta P, Huynh TP. Analysis of urine using electronic tongue towards non-invasive cancer diagnosis. Biosens Bioelectron 2023; 219:114810. [PMID: 36272349 DOI: 10.1016/j.bios.2022.114810] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 04/27/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
Electronic tongues (e-tongues) have been broadly employed in monitoring the quality of food, beverage, cosmetics, and pharmaceutical products, and in diagnosis of diseases, as the e-tongues can discriminate samples of high complexity, reduce interference of the matrix, offer rapid response. Compared to other analytical approaches using expensive and complex instrumentation as well as required sample preparation, the e-tongue is non-destructive, miniaturizable and on-site method with little or no preparation of samples. Even though e-tongues are successfully commercialized, their application in cancer diagnosis from urine samples is underestimated. In this review, we would like to highlight the various analytical techniques such as Raman spectroscopy, infrared spectroscopy, fluorescence spectroscopy, and electrochemical methods (potentiometry and voltammetry) used as e-tongues for urine analysis towards non-invasive cancer diagnosis. Besides, different machine learning approaches, for instance, supervised and unsupervised learning algorithms are introduced to analyze extracted chemical data. Finally, capabilities of e-tongues in distinguishing between patients diagnosed with cancer and healthy controls are highlighted.
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Affiliation(s)
- Mohammed Zniber
- Laboratory of Molecular Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Parastoo Vahdatiyekta
- Laboratory of Molecular Science and Engineering, Åbo Akademi University, 20500, Turku, Finland
| | - Tan-Phat Huynh
- Laboratory of Molecular Science and Engineering, Åbo Akademi University, 20500, Turku, Finland.
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21
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Du Y, Xie F, Yin L, Yang Y, Yang H, Wu G, Wang S. Breast cancer early detection by using Fourier-transform infrared spectroscopy combined with different classification algorithms. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 283:121715. [PMID: 35985225 DOI: 10.1016/j.saa.2022.121715] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/02/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Early detection of breast cancer is of great value in improving the prognosis. The current detection methods of breast cancer have their own limitations. In this study, we investigated the feasibility of Fourier Transform Infrared (FT-IR) spectroscopy combined with different classification algorithms for the early detection of breast cancer in a large sample of 526 patients, including 308 invasive breast cancer, 101 ductal carcinoma in situ, and 117 healthy controls. The serum was measured with FT-IR spectroscopy. Kennard-Stone (KS) algorithm was used to divide the data into the training set and testing set. Support vector machine (SVM) model and back propagation neural network (BPNN) model were used to distinguish ductal carcinoma in situ, invasive breast cancer from healthy controls. The accuracies of the SVM model and BPNN model were 92.9% and 94.2%. To determine the effect of different material absorption bands on early detection, the band was divided into four parts including 900-1425 cm-1, 1475-1710 cm-1, 2800-3000 cm-1, and 3090-3700 cm-1, to be modeled and detected respectively. The final results showed that the ranges 900-1425 cm-1 and 1475-1710 cm-1 had superior classification accuracies. The region 900-1425 cm-1 corresponded to the lipids, proteins, sugar, and nucleic acids, and the region 1475-1710 cm-1 corresponded to the proteins. The biochemical substances in other bands also contributed some unique potential to the classification, so the classification accuracy was the best in the full band. The study indicates that serum FT-IR spectroscopy combined with SVM and BPNN models is an effective tool for the early detection of breast cancer.
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Affiliation(s)
- Yu Du
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Fei Xie
- Department of Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Longfei Yin
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China
| | - Yang Yang
- Department of Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Houpu Yang
- Department of Breast Center, Peking University People's Hospital, Beijing, 100044, China
| | - Guohua Wu
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing 100876, China.
| | - Shu Wang
- Department of Breast Center, Peking University People's Hospital, Beijing, 100044, China.
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22
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Fast and Deep Diagnosis Using Blood-Based ATR-FTIR Spectroscopy for Digestive Tract Cancers. Biomolecules 2022; 12:biom12121815. [PMID: 36551243 PMCID: PMC9775374 DOI: 10.3390/biom12121815] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 11/24/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) of liquid biofluids enables the probing of biomolecular markers for disease diagnosis, characterized as a time and cost-effective approach. It remains poorly understood for fast and deep diagnosis of digestive tract cancers (DTC) to detect abundant changes and select specific markers in a broad spectrum of molecular species. Here, we present a diagnostic protocol of DTC in which the in-situ blood-based ATR-FTIR spectroscopic data mining pathway was designed for the identification of DTC triages in 252 blood serum samples, divided into the following groups: liver cancer (LC), gastric cancer (GC), colorectal cancer (CC), and their different three stages respectively. The infrared molecular fingerprints (IMFs) of DTC were measured and used to build a 2-dimensional second derivative spectrum (2D-SD-IR) feature dataset for classification, including absorbance and wavenumber shifts of FTIR vibration peaks. By comparison, the Partial Least-Squares Discriminant Analysis (PLS-DA) and backpropagation (BP) neural networks are suitable to differentiate DTCs and pathological stages with a high sensitivity and specificity of 100% and averaged more than 95%. Furthermore, the measured IMF data was mutually validated via clinical blood biochemistry testing, which indicated that the proposed 2D-SD-IR-based machine learning protocol greatly improved DTC classification performance.
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23
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Urinalysis of individuals with renal hyperfiltration using ATR-FTIR spectroscopy. Sci Rep 2022; 12:20887. [PMID: 36463336 PMCID: PMC9719484 DOI: 10.1038/s41598-022-25535-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 11/30/2022] [Indexed: 12/04/2022] Open
Abstract
Abnormal increased glomerular filtration rate (GFR), otherwise known as renal hyperfiltration (RHf), is associated with an increased risk of chronic kidney disease and cardiovascular mortality. Although it is not considered as a disease alone in medicine today, early detection of RHf is essential to reducing risk in a timely manner. However, detecting RHf is a challenge since it does not have a practical biochemical marker that can be followed or quantified. In this study, we tested the ability of ATR-FTIR spectroscopy to distinguish 17 individuals with RHf (hyperfiltraters; RHf (+)), from 20 who have normal GFR (normofiltraters; RHf(-)), using urine samples. Spectra collected from hyperfiltraters were significantly different from the control group at positions 1621, 1390, 1346, 933 and 783/cm. Intensity changes at these positions could be followed directly from the absorbance spectra without the need for pre-processing. They were tentatively attributed to urea, citrate, creatinine, phosphate groups, and uric acid, respectively. Using principal component analysis (PCA), major peaks of the second derivative forms for the classification of two groups were determined. Peaks at 1540, 1492, 1390, 1200, 1000 and 840/cm were significantly different between the two groups. Statistical analysis showed that the spectra of normofiltraters are similar; however, those of hyperfiltraters show diversity at multiple positions that can be observed both from the absorbance spectra and the second derivative profiles. This observation implies that RHf can simultaneously affect the excretion of many substances, and that a spectroscopic analysis of urine can be used as a rapid and non-invasive pre-screening tool.
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24
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On the use of spectroscopy, prediction machines and cybernetics for an affordable and proactive care approach for endometrial cancer. BIOMEDICAL ENGINEERING ADVANCES 2022. [DOI: 10.1016/j.bea.2022.100057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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25
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Contributions of vibrational spectroscopy to virology: A review. CLINICAL SPECTROSCOPY 2022; 4:100022. [PMCID: PMC9093054 DOI: 10.1016/j.clispe.2022.100022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 06/17/2023]
Abstract
Vibrational spectroscopic techniques, both infrared absorption and Raman scattering, are high precision, label free analytical techniques which have found applications in fields as diverse as analytical chemistry, pharmacology, forensics and archeometrics and, in recent times, have attracted increasing attention for biomedical applications. As analytical techniques, they have been applied to the characterisation of viruses as early as the 1970 s, and, in the context of the coronavirus disease 2019 (COVID-19) pandemic, have been explored in response to the World Health Organisation as novel methodologies to aid in the global efforts to implement and improve rapid screening of viral infection. This review considers the history of the application of vibrational spectroscopic techniques to the characterisation of the morphology and chemical compositions of viruses, their attachment to, uptake by and replication in cells, and their potential for the detection of viruses in population screening, and in infection response monitoring applications. Particular consideration is devoted to recent efforts in the detection of severe acute respiratory syndrome coronavirus 2, and monitoring COVID-19.
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26
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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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27
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Azagury A, Baptista C, Milovanovic K, Shin H, Morello P, Perez-Rogers J, Goldenshtein V, Nguyen T, Markel A, Rege S, Hojsak S, Perl A, Jones C, Fife M, Furtado S, Mathiowitz E. Biocoating-A Critical Step Governing the Oral Delivery of Polymeric Nanoparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2107559. [PMID: 35606684 PMCID: PMC9250634 DOI: 10.1002/smll.202107559] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 04/11/2022] [Indexed: 05/13/2023]
Abstract
Decades of research into the topic of oral nanoparticle (NP) delivery has still not provided a clear consensus regarding which properties produce an effective oral drug delivery system. The surface properties-charge and bioadhesiveness-as well as in vitro and in vivo correlation seem to generate the greatest number of disagreements within the field. Herein, a mechanism underlying the in vivo behavior of NPs is proposed, which bridges the gaps between these disagreements. The mechanism relies on the idea of biocoating-the coating of NPs with mucus-which alters their surface properties, and ultimately their systemic uptake. Utilizing this mechanism, several coated NPs are tested in vitro, ex vivo, and in vivo, and biocoating is found to affect NPs size, zeta-potential, mucosal diffusion coefficient, the extent of aggregation, and in vivo/in vitro/ex vivo correlation. Based on these results, low molecular weight polylactic acid exhibits a 21-fold increase in mucosal diffusion coefficient after precoating as compared to uncoated particles, as well as 20% less aggregation, and about 30% uptake to the blood in vivo. These discoveries suggest that biocoating reduces negative NP charge which results in an enhanced mucosal diffusion rate, increased gastrointestinal retention time, and high systemic uptake.
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Affiliation(s)
- Aharon Azagury
- Noninvasive Biomimetic Drug Delivery Systems Lab, The Department of Chemical Engineering, Ariel Center for Applied Cancer Research (ACACR), Ariel University, Ramat HaGolan St 65, Ari'el, 40700000, Israel
| | - Cameron Baptista
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Kosta Milovanovic
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Hyeseon Shin
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Peter Morello
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - James Perez-Rogers
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Victoria Goldenshtein
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Travis Nguyen
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Arianna Markel
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Soham Rege
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Stephanie Hojsak
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Alexander Perl
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Carder Jones
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Megan Fife
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Stacia Furtado
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
| | - Edith Mathiowitz
- Department of Pathology and Laboratory Medicine, Center of Biomedical Engineering, Brown University, 171 Meeting Street, Box G-B3, Providence, RI, 02912, USA
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28
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Yonar D, Severcan M, Gurbanov R, Sandal A, Yilmaz U, Emri S, Severcan F. Rapid diagnosis of malignant pleural mesothelioma and its discrimination from lung cancer and benign exudative effusions using blood serum. Biochim Biophys Acta Mol Basis Dis 2022; 1868:166473. [PMID: 35753541 DOI: 10.1016/j.bbadis.2022.166473] [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: 12/19/2021] [Revised: 06/06/2022] [Accepted: 06/19/2022] [Indexed: 02/01/2023]
Abstract
Malignant pleural mesothelioma (MPM), an aggressive cancer associated with exposure to fibrous minerals, can only be diagnosed in the advanced stage because its early symptoms are also connected with other respiratory diseases. Hence, understanding the molecular mechanism and the discrimination of MPM from other lung diseases at an early stage is important to apply effective treatment strategies and for the increase in survival rate. This study aims to develop a new approach for characterization and diagnosis of MPM among lung diseases from serum by Fourier transform infrared spectroscopy (FTIR) coupled with multivariate analysis. The detailed spectral characterization studies indicated the changes in lipid biosynthesis and nucleic acids levels in the malignant serum samples. Furthermore, the results showed that healthy, benign exudative effusion, lung cancer, and MPM groups were successfully separated from each other by applying principal component analysis (PCA), support vector machine (SVM), and especially linear discriminant analysis (LDA) to infrared spectra.
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Affiliation(s)
- Dilek Yonar
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Yuksek Ihtisas University, Faculty of Medicine, Biophysics Department, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronics Engineering, Ankara, Turkey
| | - Rafig Gurbanov
- Bilecik Seyh Edebali University, Department of Bioengineering, Bilecik, Turkey
| | - Abdulsamet Sandal
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Ankara Occupational and Environmental Diseases Hospital, Ankara, Turkey
| | - Ulku Yilmaz
- Atatürk Chest Diseases and Chest Surgery Training and Research Hospital, Ankara, Turkey
| | - Salih Emri
- Hacettepe University, Faculty of Medicine, Department of Chest Diseases, Ankara, Turkey; Medicana Hospital, Department of Chest Diseases, Kadikoy, Istanbul, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey; Altinbas University, Faculty of Medicine, Biophysics Department, Istanbul, Turkey.
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29
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Veettil TCP, Wood BR. A Combined Near-Infrared and Mid-Infrared Spectroscopic Approach for the Detection and Quantification of Glycine in Human Serum. SENSORS (BASEL, SWITZERLAND) 2022; 22:s22124528. [PMID: 35746311 PMCID: PMC9228712 DOI: 10.3390/s22124528] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/03/2022] [Accepted: 06/10/2022] [Indexed: 05/16/2023]
Abstract
Serum is an important candidate in proteomics analysis as it potentially carries key markers on health status and disease progression. However, several important diagnostic markers found in the circulatory proteome and the low-molecular-weight (LMW) peptidome have become analytically challenging due to the high dynamic concentration range of the constituent protein/peptide species in serum. Herein, we propose a novel approach to improve the limit of detection (LoD) of LMW amino acids by combining mid-IR (MIR) and near-IR spectroscopic data using glycine as a model LMW analyte. This is the first example of near-IR spectroscopy applied to elucidate the detection limit of LMW components in serum; moreover, it is the first study of its kind to combine mid-infrared (25-2.5 μm) and near-infrared (2500-800 nm) to detect an analyte in serum. First, we evaluated the prediction model performance individually with MIR (ATR-FTIR) and NIR spectroscopic methods using partial least squares regression (PLS-R) analysis. The LoD was found to be 0.26 mg/mL with ATR spectroscopy and 0.22 mg/mL with NIR spectroscopy. Secondly, we examined the ability of combined spectral regions to enhance the detection limit of serum-based LMW amino acids. Supervised extended wavelength PLS-R resulted in a root mean square error of prediction (RMSEP) value of 0.303 mg/mL and R2 value of 0.999 over a concentration range of 0-50 mg/mL for glycine spiked in whole serum. The LoD improved to 0.17 mg/mL from 0.26 mg/mL. Thus, the combination of NIR and mid-IR spectroscopy can improve the limit of detection for an LMW compound in a complex serum matrix.
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Affiliation(s)
- Thulya Chakkumpulakkal Puthan Veettil
- Centre for Biospectroscopy, Monash University, Clayton, VIC 3800, Australia;
- Centre for Sustainable and Circular Technologies (CSCT), University of Bath, Bath BA2 7AY, UK
| | - Bayden R. Wood
- Centre for Biospectroscopy, Monash University, Clayton, VIC 3800, Australia;
- Correspondence:
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30
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Schiemer R, Furniss D, Phang S, Seddon AB, Atiomo W, Gajjar KB. Vibrational Biospectroscopy: An Alternative Approach to Endometrial Cancer Diagnosis and Screening. Int J Mol Sci 2022; 23:ijms23094859. [PMID: 35563249 PMCID: PMC9102412 DOI: 10.3390/ijms23094859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 01/27/2023] Open
Abstract
Endometrial cancer (EC) is the sixth most common cancer and the fourth leading cause of death among women worldwide. Early detection and treatment are associated with a favourable prognosis and reduction in mortality. Unlike other common cancers, however, screening strategies lack the required sensitivity, specificity and accuracy to be successfully implemented in clinical practice and current diagnostic approaches are invasive, costly and time consuming. Such limitations highlight the unmet need to develop diagnostic and screening alternatives for EC, which should be accurate, rapid, minimally invasive and cost-effective. Vibrational spectroscopic techniques, Mid-Infrared Absorption Spectroscopy and Raman, exploit the atomic vibrational absorption induced by interaction of light and a biological sample, to generate a unique spectral response: a “biochemical fingerprint”. These are non-destructive techniques and, combined with multivariate statistical analysis, have been shown over the last decade to provide discrimination between cancerous and healthy samples, demonstrating a promising role in both cancer screening and diagnosis. The aim of this review is to collate available evidence, in order to provide insight into the present status of the application of vibrational biospectroscopy in endometrial cancer diagnosis and screening, and to assess future prospects.
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Affiliation(s)
- Roberta Schiemer
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
- Correspondence:
| | - David Furniss
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Sendy Phang
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - Angela B. Seddon
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK; (D.F.); (S.P.); (A.B.S.)
| | - William Atiomo
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai P.O. Box 505055, United Arab Emirates;
| | - Ketankumar B. Gajjar
- Division of Child Health, Obstetrics and Gynaecology, University of Nottingham, Nottingham NG5 1PB, UK;
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31
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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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32
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Veettil TCP, Kochan K, Edler KJ, De Bank P, Heraud P, Wood BR. Disposable Coverslip for Rapid Throughput Screening of Malaria Using Attenuated Total Reflection Spectroscopy. APPLIED SPECTROSCOPY 2022; 76:451-461. [PMID: 33876968 DOI: 10.1177/00037028211012722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Malaria is considered to be one of the most catastrophic health issues in the whole world. Vibrational spectroscopy is a rapid, robust, label-free, inexpensive, highly sensitive, nonperturbative, and nondestructive technique with high diagnostic potential for the early detection of disease agents. In particular, the fingerprinting capability of attenuated total reflection spectroscopy is promising as a point-of-care diagnostic tool in resource-limited areas. However, improvements are required to expedite the measurements of biofluids, including the drying procedure and subsequent cleaning of the internal reflection element to enable high throughput successive measurements. As an alternative, we propose using an inexpensive coverslip to reduce the sample preparation time by enabling multiple samples to be collectively dried together under the same temperature and conditions. In conjunction with partial least squares regression, attenuated total reflection spectroscopy was able to detect and quantify the parasitemia with root mean square error of cross-validation and R2 values of 0.177 and 0.985, respectively. Here, we characterize an inexpensive, disposable coverslip for the high throughput screening of malaria parasitic infections and thus demonstrate an alternative approach to direct deposition of the sample onto the internal reflection element.
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Affiliation(s)
| | - Kamila Kochan
- Centre for Biospectroscopy and School of Chemistry, 2541Monash University, Clayton, Australia
| | - Karen J Edler
- Department of Chemistry, 1555University of Bath, Bath, UK
| | - Paul De Bank
- Department of Pharmacy and Pharmacology, 1555University of Bath, Bath, UK
| | - Philip Heraud
- Centre for Biospectroscopy and School of Chemistry, 2541Monash University, Clayton, Australia
| | - Bayden R Wood
- Centre for Biospectroscopy and School of Chemistry, 2541Monash University, Clayton, Australia
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33
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Theakstone A, Brennan PM, Ashton K, Czeiter E, Jenkinson M, Syed K, Reed M, Baker M. Vibrational spectroscopy for the triage of traumatic brain injury CT priority and hospital admissions. J Neurotrauma 2022; 39:773-783. [PMID: 35236121 PMCID: PMC9225408 DOI: 10.1089/neu.2021.0410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Computed Tomogram (CT) brain imaging is routinely used to support clinical decision-making in patients with traumatic brain injury (TBI). However, only 7% of scans demonstrate evidence of TBI. The other 93% of scans contribute a significant cost to the healthcare system and a radiation risk to patients. There may be better strategies to identify which patients, particularly those with mild TBI, are at risk of deterioration and require hospital admission. We introduce a blood serum liquid biopsy that utilises attenuated total reflectance (ATR)-Fourier transform infrared (FTIR) spectroscopy with machine learning algorithms as a decision-making tool to identify which mild TBI patients will most benefit from CT brain imaging. Serum samples were obtained from (n=298) patients who had acquired a TBI and were enrolled in CENTER-TBI, and from asymptomatic control patients (n=87). Injury patients (all severities) were stratified against non-injury controls. The mild TBI cohort was further examined by stratifying those who had at least one CT abnormality against those who had no CT abnormalities. The test performed exceptionally well in classifications of mild injury patients versus non-injury controls (sensitivity = 96.4% and specificity = 98.0%) and also provided a sensitivity of 80.2% when stratifying mild patients with at least one CT abnormality against those without. The results provided illustrate the test ability to identify 4 out of every 5 CT abnormalities and shows great promise to be introduced as a triage tool for CT priority in mild TBI patients.
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Affiliation(s)
- Ashton Theakstone
- University of Strathclyde, 3527, 99 George Street, Glasgow, United Kingdom of Great Britain and Northern Ireland, G1 1RD;
| | - Paul M Brennan
- The University of Edinburgh Centre for Clinical Brain Sciences, 439257, Translational Neurosurgery, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Katherine Ashton
- Lancashire Teaching Hospitals NHS Foundation Trust, 6724, Neuropathology, Preston, Lancashire, United Kingdom of Great Britain and Northern Ireland;
| | - Endre Czeiter
- University of Pecs Medical School, 37657, Department of Neurosurgery, Pecs, Hungary.,University of Pecs, 37656, Neurotrauma Research Group, Szentágothai Research Centre, Pecs, Hungary.,University of Pecs, 37656, MTA-PTE Clinical Neuroscience MR Research Group, Pecs, Hungary;
| | - Michael Jenkinson
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland.,University of Liverpool, 4591, Department of Pharmacology & Therapeutics, Liverpool, Merseyside, United Kingdom of Great Britain and Northern Ireland;
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, 195157, Liverpool, Liverpool, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Reed
- Royal Infirmary of Edinburgh, 59843, Department of Emergency Medicine, Edinburgh, Edinburgh, United Kingdom of Great Britain and Northern Ireland;
| | - Matthew Baker
- Dxcover Limited, Glasgow, United Kingdom of Great Britain and Northern Ireland;
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34
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Akin Geyik G, Peker Cengiz B, Tugrul F, Karuk Elmas SN, Yilmaz I, Arslan FN. A rapid diagnostic approach for gastric and colon cancers via Fourier transform mid-infrared spectroscopy coupled with chemometrics from paraffin-embedded tissues. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 267:120619. [PMID: 34810101 DOI: 10.1016/j.saa.2021.120619] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 10/10/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
This paper describes the feasibility of Attenuated total reflection-Fourier transform mid-infrared (ATR-MIR) spectroscopy method coupled with chemometrics for the rapid diagnostic approach and screening spectral changes for gastric and colon cancers from paraffin-embedded tissues. A total number of 82 tissue samples were analyzed by a simple ATR-MIR method combined with PCA, HCA, SIMCA and LDA methodologies. Spectral analyses showed significant differences for the molecular contents particularly about the lipid, nucleic acid, protein and other biomolecules in the samples of gastric cancer (GC) and colon cancer (CC) groups from their control/healthy groups. Significant changes in the characteristic of these molecules were only observed for cancer groups based upon the increment in their biosynthesis, and they could be utilized as diagnostic spectral biomarkers. Under the optimum conditions, SIMCA provided excellent classification for diseased and control groups, with 5% significance level. As well, 97.75% of the studied tissue samples were correctly discriminated on the basis of their origin by LDA. Consequently, the findings of this study highlighted the rapid diagnosis of gastric and colon cancer cases from paraffin-embedded tissues via ATR-MIR spectroscopy complemented with chemometrics.
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Affiliation(s)
- Gonul Akin Geyik
- Department of Chemistry, Faculty of Science, University of Karamanoglu Mehmetbey, 70100 Karaman, Turkey
| | - Betul Peker Cengiz
- Clinic of Medical Pathology, Eskişehir Yunus Emre State Hospital, 26190 Eskisehir, Turkey
| | - Fuzuli Tugrul
- Clinic of Radiation Oncology, Eskişehir City Hospital, 26080 Eskisehir, Turkey
| | - Sukriye Nihan Karuk Elmas
- Department of Chemistry, Faculty of Science, University of Karamanoglu Mehmetbey, 70100 Karaman, Turkey
| | - Ibrahim Yilmaz
- Department of Chemistry, Faculty of Science, University of Karamanoglu Mehmetbey, 70100 Karaman, Turkey.
| | - Fatma Nur Arslan
- Department of Chemistry, Faculty of Science, University of Karamanoglu Mehmetbey, 70100 Karaman, Turkey.
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Aitekenov S, Sultangaziyev A, Abdirova P, Yussupova L, Gaipov A, Utegulov Z, Bukasov R. Raman, Infrared and Brillouin Spectroscopies of Biofluids for Medical Diagnostics and for Detection of Biomarkers. Crit Rev Anal Chem 2022; 53:1561-1590. [PMID: 35157535 DOI: 10.1080/10408347.2022.2036941] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
This review surveys Infrared, Raman/SERS and Brillouin spectroscopies for medical diagnostics and detection of biomarkers in biofluids, that include urine, blood, saliva and other biofluids. These optical sensing techniques are non-contact, noninvasive and relatively rapid, accurate, label-free and affordable. However, those techniques still have to overcome some challenges to be widely adopted in routine clinical diagnostics. This review summarizes and provides insights on recent advancements in research within the field of vibrational spectroscopy for medical diagnostics and its use in detection of many health conditions such as kidney injury, cancers, cardiovascular and infectious diseases. The six comprehensive tables in the review and four tables in supplementary information summarize a few dozen experimental papers in terms of such analytical parameters as limit of detection, range, diagnostic sensitivity and specificity, and other figures of merits. Critical comparison between SERS and FTIR methods of analysis reveals that on average the reported sensitivity for biomarkers in biofluids for SERS vs FTIR is about 103 to 105 times higher, since LOD SERS are lower than LOD FTIR by about this factor. High sensitivity gives SERS an edge in detection of many biomarkers present in biofluids at low concentration (nM and sub nM), which can be particularly advantageous for example in early diagnostics of cancer or viral infections.HighlightsRaman, Infrared spectroscopies use low volume of biofluidic samples, little sample preparation, fast time of analysis and relatively inexpensive instrumentation.Applications of SERS may be a bit more complicated than applications of FTIR (e.g., limited shelf life for nanoparticles and substrates, etc.), but this can be generously compensated by much higher (by several order of magnitude) sensitivity in comparison to FTIR.High sensitivity makes SERS a noninvasive analytical method of choice for detection, quantification and diagnostics of many health conditions, metabolites, and drugs, particularly in diagnostics of cancer, including diagnostics of its early stages.FTIR, particularly ATR-FTIR can be a method of choice for efficient sensing of many biomarkers, present in urine, blood and other biofluids at sufficiently high concentrations (mM and even a few µM)Brillouin scattering spectroscopy detecting visco-elastic properties of probed liquid medium, may also find application in clinical analysis of some biofluids, such as cerebrospinal fluid and urine.
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Affiliation(s)
- Sultan Aitekenov
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Alisher Sultangaziyev
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Perizat Abdirova
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Lyailya Yussupova
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | | | - Zhandos Utegulov
- Department of Physics, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Rostislav Bukasov
- Department of Chemistry, School of Sciences and Humanities (SSH), Nazarbayev University, Nur-Sultan, Kazakhstan
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Chen F, Sun C, Yue Z, Zhang Y, Xu W, Shabbir S, Zou L, Lu W, Wang W, Xie Z, Zhou L, Lu Y, Yu J. Screening ovarian cancers with Raman spectroscopy of blood plasma coupled with machine learning data processing. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120355. [PMID: 34530200 DOI: 10.1016/j.saa.2021.120355] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
The mortality of ovarian cancer is closely related to its poor rate of early detection. In the search of an efficient diagnosis method, Raman spectroscopy of blood features as a promising technique allowing simple, rapid, minimally-invasive and cost-effective detection of cancers, in particular ovarian cancer. Although Raman spectroscopy has been demonstrated to be effective to detect ovarian cancers with respect to normal controls, a binary classification remains idealized with respect to the real clinical practice. This work considered a population of 95 woman patients initially suspected of an ovarian cancer and finally fixed with a cancer or a cyst. Additionally, 79 normal controls completed the ensemble of samples. Such sample collection proposed us a study case where a ternary classification should be realized with Raman spectroscopy of the collected blood samples coupled with suitable spectroscopic data treatment algorithms. In the medical as well as data points of view, the appearance of the cyst case considerably reduces the distances among the different populations and makes their distinction much more difficult, since the intermediate cyst case can share the specific features of the both cancer and normal cases. After a proper spectrum pretreatment, we first demonstrated the evidence of different behaviors among the Raman spectra of the 3 types of samples. Such difference was further visualized in a high dimensional space, where the data points of the cancer and the normal cases are separately clustered, whereas the data of the cyst case were scattered into the areas respectively occupied by the cancer and normal cases. We finally developed and tested an ensemble of models for a ternary classification with 2 consequent steps of binary classifications, based on machine learning algorithms, allowing identification with sensitivity and specificity of 81.0% and 97.3% for cancer samples, 63.6% and 91.5% for cyst samples, 100% and 90.6% for normal samples.
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Affiliation(s)
- Fengye Chen
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen Sun
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zengqi Yue
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqing Zhang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weijie Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sahar Shabbir
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Long Zou
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Weiguo Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310011, China; Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310011, China
| | - Wei Wang
- Department of Clinical Laboratory, Tongde Hospital of Zhejiang Province, Hangzhou 310012, China
| | - Zhenwei Xie
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310011, China; Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310011, China
| | - Lanyun Zhou
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310011, China; Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310011, China
| | - Yan Lu
- Center for Uterine Cancer Diagnosis & Therapy Research of Zhejiang Province, Women's Reproductive Health Key Laboratory of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310011, China; Department of Gynecologic Oncology, Women's Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou 310011, China.
| | - Jin Yu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.
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Dogan A, Gurbanov R, Severcan M, Severcan F. CoronaVac (Sinovac) COVID-19 vaccine-induced molecular changes in healthy human serum by infrared spectroscopy coupled with chemometrics. Turk J Biol 2021; 45:549-558. [PMID: 34803453 PMCID: PMC8573849 DOI: 10.3906/biy-2105-65] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/30/2021] [Indexed: 12/25/2022] Open
Abstract
From the beginning of the COVID-19 coronavirus pandemic in December of 2019, the disease has infected millions of people worldwide and caused hundreds of thousands of deaths. Since then, several vaccines have been developed. One of those vaccines is inactivated CoronaVac-Sinovac COVID-19 vaccine. In this proof of concept study, we first aimed to determine CoronaVac-induced biomolecular changes in healthy human serum using infrared spectroscopy. Our second aim was to see whether the vaccinated group can be separated or not from the non-vaccinated group by applying chemometric techniques to spectral data. The results revealed that the vaccine administration induced significant changes in some functional groups belonging to lipids, proteins and nucleic acids. In addition, the non-vaccinated and vaccinated groups were successfully separated from each other by principal component analysis (PCA) and linear discriminant analysis (LDA). This proof-of-concept study will encourage future studies on CoronaVac as well as other vaccines and will lead to make a comparison between different vaccines to establish a better understanding of the vaccination outcomes on serum biomolecules.
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Affiliation(s)
- Ayca Dogan
- Department of Physiology, Faculty of Medicine, Altinbaş University, İstanbul Turkey
| | - Rafig Gurbanov
- Biotechnology Application and Research Center, Bilecik Şeyh Edebali University, Bilecik Turkey
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, Faculty of Engineering and Natural Sciences, Altınbaş University, İstanbul Turkey
| | - Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altınbaş University, İstanbul Turkey
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Chen TT, Yuan MM, Tao YM, Ren XY, Li S. Engineering of Self-assembly Polymers Encapsulated with Dual Anticancer Drugs for the Treatment of Endometrial Cancer. J CLUST SCI 2021. [DOI: 10.1007/s10876-021-02175-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Yang J, Guo H, Lei J, Zhang S, Zhang S, Bai J, Li S. Fabrication of polymer-based self-assembly nanocarriers loaded with a crizotinib and gemcitabine: potential therapeutics for the treatment of endometrial cancer. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2021; 33:20-34. [PMID: 34602004 DOI: 10.1080/09205063.2021.1974149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Combination therapy in cancer therapy has been widely used for its positive attributes, such as minimizing the undesirable side effects of chemotherapies and enhancing the therapeutic effects on different cancers. Compared with free drugs crizotinib (CRZ) and gemcitabine (GEM), CRZ@GEM-NPs could remarkably improve the cytotoxicity for endometrial cancer (EC) cells (Ishikawa cells and KLE cells) after treatment with MTT assay. In this study, CRZ and GEM were conjugated to tri-block copolymer poly(ε-caprolactone)-poly(ethylene glycol)-poly(ε-caprolactone) (PCL-PEG-PCL, known as NPs). The fabricated nanoparticles were characterized by the high-resolution transmission electron microscopy (HR-TEM), and the particles size and zeta potential were investigated by the dynamic light scattering analysis. Further, the morphological features of the EC cell lines were examined by the biochemical staining assays. Morphological changes in endometrial cells morphology revealed by nuclear fragmentation and nuclear condensation (the hallmarks of apoptosis) were noted upon treatment with CRZ@GEM-NPs to the Ishikawa and KLE cancer cells. In addition, resulting in the highest ratio of apoptosis and mitochondrial membrane potential shows the cell death through the mitochondrial membrane potential. In vivo, systemic toxicity studies showed no histological changes and substantial blood biochemical with the near-normal appearance of the organs upon treatment with CRZ@GEM-NPs. Overall, the targeted combination suitable therapeutic framework may be a promising candidate for improved EC therapy.
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Affiliation(s)
- Jiaolin Yang
- Department of Gynecology, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Hongrui Guo
- Department of Gynecology, Yuncheng Hospital Affiliated to Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Jing Lei
- Department of Gynecology, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Sanyuan Zhang
- Department of Gynecology, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Shaoguo Zhang
- Department of Nursing Care, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Jirong Bai
- Department of Gynecology, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
| | - Sufen Li
- Department of Gynecology, the First Hospital of Shanxi Medical University, Taiyuan, Shanxi Province, China
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40
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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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41
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Mabwa D, Gajjar K, Furniss D, Schiemer R, Crane R, Fallaize C, Martin-Hirsch PL, Martin FL, Kypraios T, Seddon AB, Phang S. Mid-infrared spectral classification of endometrial cancer compared to benign controls in serum or plasma samples. Analyst 2021; 146:5631-5642. [PMID: 34378554 DOI: 10.1039/d1an00833a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
This study demonstrates a discrimination of endometrial cancer versus (non-cancerous) benign controls based on mid-infrared (MIR) spectroscopy of dried plasma or serum liquid samples. A detailed evaluation was performed using four discriminant methods (LDA, QDA, kNN or SVM) to execute the classification task. The discriminant methods used in the study comprised methods that are widely used in the statistics (LDA and QDA) and machine learning literature (kNN and SVM). Of particular interest, is the impact of discrimination when presented with spectral data from a section of the bio-fingerprint region (1430 cm-1 to 900 cm-1) in contrast to the more extended bio-fingerprint region used here (1800 cm-1 to 900 cm-1). Quality metrics used were the misclassification rate, sensitivity, specificity, and Matthew's correlation coefficient (MCC). For plasma (with spectral data ranging from 1430 cm-1 to 900 cm-1), the best performing classifier was kNN, which achieved a sensitivity, specificity and MCC of 0.865 ± 0.043, 0.865 ± 0.023 and 0.762 ± 0.034, respectively. For serum (in the same wavenumber range), the best performing classifier was LDA, achieving a sensitivity, specificity and MCC of 0.899 ± 0.023, 0.763 ± 0.048 and 0.664 ± 0.067, respectively. For plasma (with spectral data ranging from 1800 cm-1 to 900 cm-1), the best performing classifier was SVM, with a sensitivity, specificity and MCC of 0.993 ± 0.010, 0.815 ± 0.000 and 0.815 ± 0.010, respectively. For serum (in the same wavenumber range), QDA performed best achieving a sensitivity, specificity and MCC of 0.852 ± 0.023, 0.700 ± 0.162 and 0.557 ± 0.012, respectively. Our findings demonstrate that even when a section of the bio-fingerprint region has been removed, good classification of endometrial cancer versus non-cancerous controls is still maintained. These findings suggest the potential of a MIR screening tool for endometrial cancer screening.
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Affiliation(s)
- David Mabwa
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Ketankumar Gajjar
- Obstetrics and Gynaecology, Nottingham University Hospitals NHS Trust - City Campus, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - David Furniss
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Roberta Schiemer
- Obstetrics and Gynaecology, Nottingham University Hospitals NHS Trust - City Campus, Nottingham City Hospital, Hucknall Road, Nottingham, NG5 1PB, UK
| | - Richard Crane
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Christopher Fallaize
- School of Mathematical Sciences, The Mathematical Sciences Building, University Park, University of Nottingham, NG7 2RD, UK
| | | | | | - Theordore Kypraios
- School of Mathematical Sciences, The Mathematical Sciences Building, University Park, University of Nottingham, NG7 2RD, UK
| | - Angela B Seddon
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
| | - Sendy Phang
- Mid-Infrared Photonics Group, George Green Institute for Electromagnetics' Research, Faculty of Engineering, University of Nottingham, Nottingham NG7 2RD, UK.
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Banerjee A, Gokhale A, Bankar R, Palanivel V, Salkar A, Robinson H, Shastri JS, Agrawal S, Hartel G, Hill MM, Srivastava S. Rapid Classification of COVID-19 Severity by ATR-FTIR Spectroscopy of Plasma Samples. Anal Chem 2021; 93:10391-10396. [PMID: 34279898 PMCID: PMC8315140 DOI: 10.1021/acs.analchem.1c00596] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/29/2021] [Indexed: 12/24/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic continues to ravage the world, with many hospitals overwhelmed by the large number of patients presenting during major outbreaks. A rapid triage for COVID-19 patient requiring hospitalization and intensive care is urgently needed. Age and comorbidities have been associated with a higher risk of severe COVID-19 but are not sufficient to triage patients. Here, we investigated the potential of attenuated total reflectance Fourier-transform infrared (ATR-FTIR) spectroscopy as a rapid blood test for classification of COVID-19 disease severity using a cohort of 160 COVID-19 patients. A simple plasma processing and ATR-FTIR data acquisition procedure was established using 75% ethanol for viral inactivation. Next, partial least-squares-discriminant analysis (PLS-DA) models were developed and tested using data from 130 and 30 patients, respectively. Addition of the ATR-FTIR spectra to the clinical parameters (age, sex, diabetes mellitus, and hypertension) increased the area under the ROC curve (C-statistics) for both the training and test data sets, from 69.3% (95% CI 59.8-78.9%) to 85.7% (78.6-92.8%) and 77.8% (61.3-94.4%) to 85.1% (71.3-98.8%), respectively. The independent test set achieved 69.2% specificity (42.4-87.3%) and 94.1% sensitivity (73.0-99.0%). Diabetes mellitus was the strongest predictor in the model, followed by FTIR regions 1020-1090 and 1588-1592 cm-1. In summary, this study demonstrates the potential of ATR-FTIR spectroscopy as a rapid, low-cost COVID-19 severity triage tool to facilitate COVID-19 patient management during an outbreak.
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Affiliation(s)
- Arghya Banerjee
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Abhiram Gokhale
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Renuka Bankar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Viswanthram Palanivel
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Akanksha Salkar
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | - Harley Robinson
- QIMR
Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
| | - Jayanthi S. Shastri
- Kasturba
Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Sachee Agrawal
- Kasturba
Hospital for Infectious Diseases, Chinchpokli, Mumbai, Maharashtra 400034, India
| | - Gunter Hartel
- QIMR
Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
| | - Michelle M. Hill
- QIMR
Berghofer Medical Research Institute, 300 Herston Road, Herston QLD 4006, Australia
| | - Sanjeeva Srivastava
- Department
of Biosciences and Bioengineering, Indian
Institute of Technology Bombay, Powai, Mumbai 400 076, India
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Theakstone AG, Brennan PM, Jenkinson MD, Mills SJ, Syed K, Rinaldi C, Xu Y, Goodacre R, Butler HJ, Palmer DS, Smith BR, Baker MJ. Rapid Spectroscopic Liquid Biopsy for the Universal Detection of Brain Tumours. Cancers (Basel) 2021; 13:cancers13153851. [PMID: 34359751 PMCID: PMC8345395 DOI: 10.3390/cancers13153851] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/22/2021] [Accepted: 07/29/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.
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Affiliation(s)
- Ashton G. Theakstone
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
| | - Paul M. Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH16 4SB, UK;
| | - Michael D. Jenkinson
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
- Department of Pharmacology & Therapeutics, Institute of System, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Samantha J. Mills
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Lower Lane, Liverpool L9 7LJ, UK; (M.D.J.); (S.J.M.); (K.S.)
| | - Christopher Rinaldi
- Technology and Innovation Centre, Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow G1 1RD, UK;
| | - Yun Xu
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Royston Goodacre
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK; (Y.X.); (R.G.)
| | - Holly J. Butler
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - David S. Palmer
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, Glasgow G1 1XL, UK
| | - Benjamin R. Smith
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
| | - Matthew J. Baker
- Dxcover Limited, 204 George Street, Glasgow G1 1XW, UK; (H.J.B.); (D.S.P.); (B.R.S.)
- Correspondence: (A.G.T.); (M.J.B.); Tel.: +44-141-444-7343 (A.G.T.); +44-141-548-4700 (M.J.B.)
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Voronina L, Leonardo C, Mueller‐Reif JB, Geyer PE, Huber M, Trubetskov M, Kepesidis KV, Behr J, Mann M, Krausz F, Žigman M. Molecular Origin of Blood‐Based Infrared Spectroscopic Fingerprints**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Liudmila Voronina
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
- Max Planck Institute of Quantum Optics 85748 Garching Germany
| | - Cristina Leonardo
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
- Max Planck Institute of Quantum Optics 85748 Garching Germany
| | - Johannes B. Mueller‐Reif
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry 82152 Martinsried Germany
- OmicEra Diagnostics GmbH 82152 Planegg Germany
| | - Philipp E. Geyer
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry 82152 Martinsried Germany
- Novo Nordisk Foundation Center for Protein Research Faculty of Health Sciences University of Copenhagen 2200 Copenhagen Denmark
- OmicEra Diagnostics GmbH 82152 Planegg Germany
| | - Marinus Huber
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
- Max Planck Institute of Quantum Optics 85748 Garching Germany
| | | | - Kosmas V. Kepesidis
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
| | - Jürgen Behr
- Comprehensive Pneumology Center Department of Internal Medicine V Clinic of the Ludwig Maximilians University Munich (LMU), Member of the German Center for Lung Research Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry 82152 Martinsried Germany
- Novo Nordisk Foundation Center for Protein Research Faculty of Health Sciences University of Copenhagen 2200 Copenhagen Denmark
| | - Ferenc Krausz
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
- Max Planck Institute of Quantum Optics 85748 Garching Germany
| | - Mihaela Žigman
- Department of Physics Ludwig Maximilian University of Munich 85748 Garching Germany
- Max Planck Institute of Quantum Optics 85748 Garching Germany
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45
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Voronina L, Leonardo C, Mueller‐Reif JB, Geyer PE, Huber M, Trubetskov M, Kepesidis KV, Behr J, Mann M, Krausz F, Žigman M. Molecular Origin of Blood-Based Infrared Spectroscopic Fingerprints*. Angew Chem Int Ed Engl 2021; 60:17060-17069. [PMID: 33881784 PMCID: PMC8361728 DOI: 10.1002/anie.202103272] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/30/2021] [Indexed: 12/17/2022]
Abstract
Infrared spectroscopy of liquid biopsies is a time- and cost-effective approach that may advance biomedical diagnostics. However, the molecular nature of disease-related changes of infrared molecular fingerprints (IMFs) remains poorly understood, impeding the method's applicability. Here we probe 148 human blood sera and reveal the origin of the variations in their IMFs. To that end, we supplemented infrared spectroscopy with biochemical fractionation and proteomic profiling, providing molecular information about serum composition. Using lung cancer as an example of a medical condition, we demonstrate that the disease-related differences in IMFs are dominated by contributions from twelve highly abundant proteins-that, if used as a pattern, may be instrumental for detecting malignancy. Tying proteomic to spectral information and machine learning advances our understanding of the infrared spectra of liquid biopsies, a framework that could be applied to probing of any disease.
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Affiliation(s)
- Liudmila Voronina
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
- Max Planck Institute of Quantum Optics85748GarchingGermany
| | - Cristina Leonardo
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
- Max Planck Institute of Quantum Optics85748GarchingGermany
| | - Johannes B. Mueller‐Reif
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- OmicEra Diagnostics GmbH82152PlaneggGermany
| | - Philipp E. Geyer
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark
- OmicEra Diagnostics GmbH82152PlaneggGermany
| | - Marinus Huber
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
- Max Planck Institute of Quantum Optics85748GarchingGermany
| | | | - Kosmas V. Kepesidis
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
| | - Jürgen Behr
- Comprehensive Pneumology CenterDepartment of Internal Medicine VClinic of the Ludwig Maximilians University Munich (LMU), Member of the German Center for Lung ResearchGermany
| | - Matthias Mann
- Department of Proteomics and Signal TransductionMax Planck Institute of Biochemistry82152MartinsriedGermany
- Novo Nordisk Foundation Center for Protein ResearchFaculty of Health SciencesUniversity of Copenhagen2200CopenhagenDenmark
| | - Ferenc Krausz
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
- Max Planck Institute of Quantum Optics85748GarchingGermany
| | - Mihaela Žigman
- Department of PhysicsLudwig Maximilian University of Munich85748GarchingGermany
- Max Planck Institute of Quantum Optics85748GarchingGermany
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46
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Sarigul N, Kurultak İ, Uslu Gökceoğlu A, Korkmaz F. Urine analysis using FTIR spectroscopy: A study on healthy adults and children. JOURNAL OF BIOPHOTONICS 2021; 14:e202100009. [PMID: 33768707 DOI: 10.1002/jbio.202100009] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Urine spectra from 108 healthy volunteers are studied by attenuated total refraction-Fourier transform infrared (ATR-FTIR) spectroscopy. The spectral features are correlated with observable urine components. The variation of spectra within a healthy population is quantified and a library of reference spectra is constructed. Using the band assignments, these spectra are compared with both age-wise and gender-wise. Children show the least intensity variations compared to both adult groups. Young adults show the highest variation, particularly in the 1650 to 1400 cm-1 and 1200 to 900 cm-1 regions. These results indicate the importance of the size of the control group in comparative studies utilizing FTIR. Age-wise comparisons reveal that phosphate and sulfate excretion decreases with age, and that the variance of phosphate among individuals is higher with adults. As for gender-wise comparisons, females show a slightly higher citrate content at 1390 cm-1 regardless of the age and they show a higher variance in the 1200 to 1000 cm-1 region when compared to men.
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Affiliation(s)
- Neslihan Sarigul
- Institute of Nuclear Science, Hacettepe University, Ankara, Turkey
| | - İlhan Kurultak
- Department of Nephrology, Faculty of Medicine, Trakya University, Edirne, Turkey
| | - Arife Uslu Gökceoğlu
- Ankara Training and Research Hospital, University of Health Sciences, Ankara, Turkey
| | - Filiz Korkmaz
- Biophysics Laboratory, Faculty of Engineering, Atilim University, Ankara, Turkey
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47
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Giamougiannis P, Morais CLM, Rodriguez B, Wood NJ, Martin-Hirsch PL, Martin FL. Detection of ovarian cancer (± neo-adjuvant chemotherapy effects) via ATR-FTIR spectroscopy: comparative analysis of blood and urine biofluids in a large patient cohort. Anal Bioanal Chem 2021; 413:5095-5107. [PMID: 34195877 PMCID: PMC8405472 DOI: 10.1007/s00216-021-03472-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/06/2021] [Accepted: 06/09/2021] [Indexed: 11/24/2022]
Abstract
Ovarian cancer remains the most lethal gynaecological malignancy, as its timely detection at early stages remains elusive. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy of biofluids has been previously applied in pilot studies for ovarian cancer diagnosis, with promising results. Herein, these initial findings were further investigated by application of ATR-FTIR spectroscopy in a large patient cohort. Spectra were obtained by measurements of blood plasma and serum, as well as urine, from 116 patients with ovarian cancer and 307 patients with benign gynaecological conditions. A preliminary chemometric analysis revealed significant spectral differences in ovarian cancer patients without previous chemotherapy (n = 71) and those who had received neo-adjuvant chemotherapy-NACT (n = 45), so these groups were compared separately with benign controls. Classification algorithms with blind predictive model validation demonstrated that serum was the best biofluid, achieving 76% sensitivity and 98% specificity for ovarian cancer detection, whereas urine exhibited poor performance. A drop in sensitivities for the NACT ovarian cancer group in plasma and serum indicates the potential of ATR-FTIR spectroscopy to identify chemotherapy-related spectral changes. Comparisons of regression coefficient plots for identification of biomarkers suggest that glycoproteins (such as CA125) are the main classifiers for ovarian cancer detection and responsible for smaller differences in spectra between NACT patients and benign controls. This study confirms the capacity of biofluids' ATR-FTIR spectroscopy (mainly blood serum) to diagnose ovarian cancer with high accuracy and demonstrates its potential in monitoring response to chemotherapy, which is reported for the first time. ATR-FTIR spectroscopy of blood serum achieves good segregation of ovarian cancers from benign controls, with attenuation of differences following neo-adjuvant chemotherapy.
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Affiliation(s)
- Panagiotis Giamougiannis
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Brice Rodriguez
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
| | - Nicholas J Wood
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
| | - Pierre L Martin-Hirsch
- Department of Obstetrics and Gynaecology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
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48
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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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49
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Depciuch J, Barnaś E, Skręt-Magierło J, Skręt A, Kaznowska E, Łach K, Jakubczyk P, Cebulski J. Spectroscopic evaluation of carcinogenesis in endometrial cancer. Sci Rep 2021; 11:9079. [PMID: 33907297 PMCID: PMC8079695 DOI: 10.1038/s41598-021-88640-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 04/08/2021] [Indexed: 12/13/2022] Open
Abstract
Carcinogenesis is a multifaceted process of cancer formation. The transformation of normal cells into cancerous ones may be difficult to determine at a very early stage. Therefore, methods enabling identification of initial changes caused by cancer require novel approaches. Although physical spectroscopic methods such as FT-Raman and Fourier Transform InfraRed (FTIR) are used to detect chemical changes in cancer tissues, their potential has not been investigated with respect to carcinogenesis. The study aimed to evaluate the usefulness of FT-Raman and FTIR spectroscopy as diagnostic methods of endometrial cancer carcinogenesis. The results indicated development of endometrial cancer was accompanied with chemical changes in nucleic acid, amide I and lipids in Raman spectra. FTIR spectra showed that tissues with development of carcinogenesis were characterized by changes in carbohydrates and amides vibrations. Principal component analysis and hierarchical cluster analysis of Raman spectra demonstrated similarity of tissues with cancer cells and lesions considered precursor of cancer (complex atypical hyperplasia), however they differed from the control samples. Pearson correlation test showed correlation between cancer and complex atypical hyperplasia tissues and between non-cancerous tissue samples. The results of the study indicate that Raman spectroscopy is more effective in assessing the development of carcinogenesis in endometrial cancer than FTIR.
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Affiliation(s)
- Joanna Depciuch
- Institute of Nuclear Physics, Polish Academy of Science, 31-342, Krakow, Poland.
| | - Edyta Barnaś
- Institute of Health Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959, Rzeszow, Poland
| | - Joanna Skręt-Magierło
- Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959, Rzeszow, Poland
| | - Andrzej Skręt
- Institute of Medical Sciences, Medical College, University of Rzeszow, Kopisto 2a, 35-959, Rzeszow, Poland
| | - Ewa Kaznowska
- Chair of Morphological Sciences, Department of Pathomorphology, Medical College, University of Rzeszow, Kopisto 2a , 35-959, Rzeszow, Poland
| | - Kornelia Łach
- Department of Pediatrics, Institute of Medical Sciences, Medical College, University of Rzeszow, Warzywna 1A, 35-310, Rzeszow, Poland
| | - Paweł Jakubczyk
- Institute of Physics, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310, Rzeszow, Poland
| | - Jozef Cebulski
- Institute of Physics, College of Natural Sciences, University of Rzeszow, Pigonia 1, 35-310, Rzeszow, Poland
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50
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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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