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Tian Y, Fan X, Chen K, Chen X, Peng W, Wang L, Wang F. Optical biomarker analysis for renal cell carcinoma obtained from preoperative and postoperative patients using ATR-FTIR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 318:124426. [PMID: 38763020 DOI: 10.1016/j.saa.2024.124426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 04/19/2024] [Accepted: 05/07/2024] [Indexed: 05/21/2024]
Abstract
Renal cell carcinoma (RCC) is the most common malignant tumor in the urinary system, accounting for 80 % to 90 % for all renal malignancies. Traditional diagnostic methods like magnetic resonance imaging (MRI) and computed tomography (CT) lack the sensitivity and specificity as they lack specific biomarkers. These limitations impede effective monitoring of tumor recurrence. This study aims to employ Attenuated Total Reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy, an optical technology sensitive to molecular groups, to analyze the potential optical biomarkers in urine and plasma samples from RCC patients pre- and post-surgery. The results reveal distinctive spectral information from both plasma and urine samples. Post-surgery urine spectra exhibit complexity compared to plasma, showing reduced content at 1072 cm-1, 1347 cm-1 and 1654 cm-1 bands, while increased content at 1112 cm-1, 1143 cm-1, 1447 cm-1, 3334 cm-1 and 3420 cm-1 bands. Utilizing machine learning models such as eXtreme Gradient Boosting (XGBoost), support vector machine (SVM), partial least squares (PLS), and artificial neural network (ANN), the study evaluated plasma and urine samples pre- and post-surgery. Remarkably, the XGBoost method excelled in distinguishing between tumor conditions and recovery, achieving an impressive AUC value of 0.99. These results underscore the potential of ATR-FTIR technology in identifying RCC optical biomarkers, with XGBoost showing promise as a valuable screening tool for RCC recurrence diagnosis.
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Affiliation(s)
- Yuchen Tian
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics, School of Basic Medicine, Air Force Medical University, Xi'an 710032, China
| | - Xiaozheng Fan
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China
| | - Kun Chen
- Department of Anatomy, Histology and Embryology and K.K. Leung Brain Research Centre, School of Basic Medicine, Air Force Medical University, Xi'an 710032, China
| | - Xinyu Chen
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics, School of Basic Medicine, Air Force Medical University, Xi'an 710032, China
| | - Wenyu Peng
- Department of Biochemistry and Molecular Biology, Shaanxi Provincial Key Laboratory of Clinical Genetics, School of Basic Medicine, Air Force Medical University, Xi'an 710032, China
| | - Li Wang
- School of Aerospace Medicine, Air Force Medical University, Xi'an, China
| | - Fuli Wang
- Department of Urology, Xijing Hospital, Fourth Military Medical University, Xi'an 710032, China.
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2
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Severcan F, Ozyurt I, Dogan A, Severcan M, Gurbanov R, Kucukcankurt F, Elibol B, Tiftikcioglu I, Gursoy E, Yangin MN, Zorlu Y. Decoding myasthenia gravis: advanced diagnosis with infrared spectroscopy and machine learning. Sci Rep 2024; 14:19316. [PMID: 39164310 PMCID: PMC11336246 DOI: 10.1038/s41598-024-66501-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 07/02/2024] [Indexed: 08/22/2024] Open
Abstract
Myasthenia Gravis (MG) is a rare neurological disease. Although there are intensive efforts, the underlying mechanism of MG still has not been fully elucidated, and early diagnosis is still a question mark. Diagnostic paraclinical tests are also time-consuming, burden patients financially, and sometimes all test results can be negative. Therefore, rapid, cost-effective novel methods are essential for the early accurate diagnosis of MG. Here, we aimed to determine MG-induced spectral biomarkers from blood serum using infrared spectroscopy. Furthermore, infrared spectroscopy coupled with multivariate analysis methods e.g., principal component analysis (PCA), support vector machine (SVM), discriminant analysis and Neural Network Classifier were used for rapid MG diagnosis. The detailed spectral characterization studies revealed significant increases in lipid peroxidation; saturated lipid, protein, and DNA concentrations; protein phosphorylation; PO2-asym + sym /protein and PO2-sym/lipid ratios; as well as structural changes in protein with a significant decrease in lipid dynamics. All these spectral parameters can be used as biomarkers for MG diagnosis and also in MG therapy. Furthermore, MG was diagnosed with 100% accuracy, sensitivity and specificity values by infrared spectroscopy coupled with multivariate analysis methods. In conclusion, FTIR spectroscopy coupled with machine learning technology is advancing towards clinical translation as a rapid, low-cost, sensitive novel approach for MG diagnosis.
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Affiliation(s)
- Feride Severcan
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Türkiye.
| | - Ipek Ozyurt
- Department of Biophysics, Faculty of Medicine, Altinbas University, Istanbul, Türkiye
| | - Ayca Dogan
- Department of Physiology, Faculty of Medicine, Altinbas University, Istanbul, Türkiye
| | - Mete Severcan
- Department of Electrical and Electronics Engineering, Middle East Technical University, Ankara, Türkiye
| | - Rafig Gurbanov
- Department of Bioengineering, Faculty of Engineering, Bilecik Seyh Edebali University, Bilecik, Türkiye
| | - Fulya Kucukcankurt
- Department of Medical Biology, Faculty of Medicine, Altinbas University, Istanbul, Türkiye
| | - Birsen Elibol
- Department of Medical Biology, Faculty of Medicine, Istanbul Medeniyet University, Istanbul, Türkiye
- Department of Medical Biology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Türkiye
| | - Irem Tiftikcioglu
- Cigli Training and Research Hospital, Neurology Clinic, Bakircay University, İzmir, Türkiye
| | - Esra Gursoy
- Department of Neurology, Faculty of Medicine, Bezmialem Vakif University, Istanbul, Türkiye
- Basaksehir Cam and Sakura City Hospital, Neurology Clinics, Istanbul, Türkiye
| | - Melike Nur Yangin
- Biomedical Sciences Graduate Program, Institute of Graduate Studies, Altinbas University, Istanbul, Türkiye
| | - Yasar Zorlu
- Tepecik Educational and Training Hospital, Neurology Department, University of Health Sciences, Izmir, Türkiye
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3
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Pang N, Yang W, Yang G, Yang C, Tong K, Yu R, Jiang F. The utilization of blood serum ATR-FTIR spectroscopy for the identification of gastric cancer. Discov Oncol 2024; 15:350. [PMID: 39143357 PMCID: PMC11324634 DOI: 10.1007/s12672-024-01231-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/12/2024] [Indexed: 08/16/2024] Open
Abstract
Gastric cancer represents a significant public health challenge, necessitating advancements in early diagnostic methodologies. This investigation employed attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy to conduct a multivariate analysis of human serum. The study encompassed the examination of blood samples from 96 individuals diagnosed with gastric cancer and 96 healthy volunteers. Principal component analysis (PCA) was utilized to interpret the infrared spectral data of the serum samples. Specific spectral bands exhibiting intensity variations between the two groups were identified. The infrared spectral ranges of 3500 ~ 3000 cm⁻1, 1700 ~ 1600 cm⁻1, and 1090 ~ 1070 cm⁻1 demonstrated significant diagnostic value for gastric cancer, likely attributable to differences in protein conformation and nucleic acids. By employing machine learning algorithms to differentiate between gastric cancer patients (n = 96) and healthy controls (n = 96), we achieved a sensitivity of up to 89.7% and a specificity of 87.2%. Receiver operating characteristic (ROC) analysis yielded an area under the curve (AUC) of 0.901. These findings underscore the potential of our serum-based ATR-FTIR spectroscopy examination method as a straightforward, minimally invasive, and reliable diagnostic test for the detection of gastric cancer.
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Affiliation(s)
- Nan Pang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Wanli Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Guizhe Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Chao Yang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Kuiyuan Tong
- Faculty of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, Jiangsu, China
| | - Ruihua Yu
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China
| | - Feng Jiang
- Chongming Hospital Affiliated to Shanghai University of Medicine and Health Sciences, Shanghai, 202150, China.
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Zhu J, Xia H, Xu X, Zheng R, Liu C, Hong J, Huang Q. FTIR spectroscopy for assessment of hair from lung cancer patients and its application in monitoring the chemotherapy treatment effect. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 314:124185. [PMID: 38565049 DOI: 10.1016/j.saa.2024.124185] [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: 12/28/2023] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024]
Abstract
Lung cancer is the most common cancer and the leading cause of death in China. The current gold standard for clinical lung cancer diagnosis is based on histopathological examination of tumors, but it has the limitation for easy operation and convenient applications. Therefore, researchers are still striving to develop other tools and methods for non-invasive and rapid assessment of the health conditions of lung cancer patients. Hair, as a reflection of the metabolism of the body, is closely related to human health conditions. In principle, Fourier-transform infrared (FTIR) spectroscopy can probe the major chemical compositions in the hair. However, as indicated by previous studies, there is still the challenge to make good use of FTIR spectroscopy for achieving reliable analysis of hair from cancer patients. In this study, hair samples from 82 lung cancer patients were collected and subjected to FTIR measurements and analysis, which showed the protein content in the hair is closely related to the protein content in the blood serum of patients, and the contents of protein and lipid are statistically lower in the lung cancer patients. Furthermore, we demonstrated that FTIR spectroscopy could be employed to monitor the hair of lung cancer patients undergoing chemotherapy, and confirmed that the FTIR spectra of the hair may reflect the resultant effect of the chemotherapy. As such, this work validates the way of using FTIR spectroscopy in hair analysis for the assistance of medical diagnosis of lung cancer as well as monitoring the conditions of the patients under the medical treatment.
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Affiliation(s)
- Jianxia Zhu
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China; CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Haiqian Xia
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China; CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China
| | - Xiuzhi Xu
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China
| | - Rong Zheng
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China
| | - Chao Liu
- CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230032, China
| | - Jingfang Hong
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China.
| | - Qing Huang
- School of Nursing, Anhui Medical University, Hefei, Anhui 230032, China; CAS Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui 230031, China; Science Island Branch of Graduate School, University of Science and Technology of China, Hefei, Anhui 230032, China.
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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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Kino S, Kanamori M, Shimoda Y, Niizuma K, Endo H, Matsuura Y. Distinguishing IDH mutation status in gliomas using FTIR-ATR spectra of peripheral blood plasma indicating clear traces of protein amyloid aggregation. BMC Cancer 2024; 24:222. [PMID: 38365669 PMCID: PMC10870484 DOI: 10.1186/s12885-024-11970-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Glioma is a primary brain tumor and the assessment of its molecular profile in a minimally invasive manner is important in determining treatment strategies. Among the molecular abnormalities of gliomas, mutations in the isocitrate dehydrogenase (IDH) gene are strong predictors of treatment sensitivity and prognosis. In this study, we attempted to non-invasively diagnose glioma development and the presence of IDH mutations using multivariate analysis of the plasma mid-infrared absorption spectra for a comprehensive and sensitive view of changes in blood components associated with the disease and genetic mutations. These component changes are discussed in terms of absorption wavenumbers that contribute to differentiation. METHODS Plasma samples were collected at our institutes from 84 patients with glioma (13 oligodendrogliomas, 17 IDH-mutant astrocytoma, 7 IDH wild-type diffuse glioma, and 47 glioblastomas) before treatment initiation and 72 healthy participants. FTIR-ATR spectra were obtained for each plasma sample, and PLS discriminant analysis was performed using the absorbance of each wavenumber in the fingerprint region of biomolecules as the explanatory variable. This data was used to distinguish patients with glioma from healthy participants and diagnose the presence of IDH mutations. RESULTS The derived classification algorithm distinguished the patients with glioma from healthy participants with 83% accuracy (area under the curve (AUC) in receiver operating characteristic (ROC) = 0.908) and diagnosed the presence of IDH mutation with 75% accuracy (AUC = 0.752 in ROC) in cross-validation using 30% of the total test data. The characteristic changes in the absorption spectra suggest an increase in the ratio of β-sheet structures in the conformational composition of blood proteins of patients with glioma. Furthermore, these changes were more pronounced in patients with IDH-mutant gliomas. CONCLUSIONS The plasma infrared absorption spectra could be used to diagnose gliomas and the presence of IDH mutations in gliomas with a high degree of accuracy. The spectral shape of the protein absorption band showed that the ratio of β-sheet structures in blood proteins was significantly higher in patients with glioma than in healthy participants, and protein aggregation was a distinct feature in patients with glioma with IDH mutations.
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Affiliation(s)
- Saiko Kino
- Graduate School of Biomedical Engineering, Tohoku University, 6-6-05, Aza-Aoba, Aramaki, Aoba, Sendai City, 980-8579, Miyagi Prefecture, Japan
| | - Masayuki Kanamori
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Yoshiteru Shimoda
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Kuniyasu Niizuma
- Department of Neurosurgical Engineering and Translational Neuroscience, Graduate School of Biomedical Engineering, Tohoku University, Seiryo 2-1, Aoba, Sendai City, 980-8575, Miyagi Prefecture, Japan
- Department of Neurosurgical Engineering and Translational Neuroscience, Tohoku University Graduate School of Medicine, 980-8575 Seiryo 2-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Hidenori Endo
- Department of Neurosurgery, Tohoku University Graduate School of Medicine, 980-8574 Seiryo 1-1, Aoba, Sendai City, Miyagi Prefecture, Japan
| | - Yuji Matsuura
- Graduate School of Biomedical Engineering, Tohoku University, 6-6-05, Aza-Aoba, Aramaki, Aoba, Sendai City, 980-8579, Miyagi Prefecture, Japan.
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Li H, Wang J, Li X, Zhu X, Guo S, Wang H, Yu J, Ye X, He F. Comparison of serum from lung cancer patients and from patients with benign lung nodule using FTIR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 306:123596. [PMID: 37925957 DOI: 10.1016/j.saa.2023.123596] [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: 03/09/2023] [Revised: 09/13/2023] [Accepted: 10/29/2023] [Indexed: 11/07/2023]
Abstract
Lungcancer remains the leading cause of cancer related deaths in worldwide. Earlydiagnosis oflungcancer can significantly improve survival rate. However, due to its close resemblance to the malignant nodules, the possible existence of benign nodules often leads to erroneous decisions. The aim of this study was to explore whether fourier transform infrared (FTIR) spectroscopy could improve the accuracy of early diagnosis of lung cancer by distinguishing lung cancer patients' (LCP') serum from patients with benign lung nodules' (PBLN') serum. In this study, A1243+1081/A1652+1539 ratio in LCP group was increased significantly compared with that in PBLN group, indicating that the ratio could be used to distinguish the serum of LCP from that of PBLN. In addition, the ratios of A2926/A2969, A1744/A2926+2859, A2926+2859/A1652+1539 were also increased significantly in LCP group compared with that in PBLN group. These findings suggest that FTIR spectroscopy might be a potentially effective method for the early diagnosis of lung cancer.
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Affiliation(s)
- Huanyu Li
- Nanchang University Jiangxi Medical College, Nanchang 330006, China; Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Jun Wang
- Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Xiaoyun Li
- Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Xianhong Zhu
- Key Laboratory of Applied Organic Chemistry, Higher Institutions of Jiangxi Province, Shangrao Normal University, Shangrao 334001, China
| | - Shaomei Guo
- Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Hongluan Wang
- Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Jie Yu
- Second Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, the First Affiliated Hospital of Nanchang Medical College, Nanchang 330006, China
| | - Xiaoqun Ye
- Department of Pulmonary and Critical Care Medicine, the Second Affiliated Hospital, Nanchang University, Nanchang 330006, China.
| | - Fan He
- Neonatal Intensive Care Unit, Jiangxi Provincial Children's Hospital, Nanchang 330038, China.
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8
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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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Di Santo R, Niccolini B, Romanò S, Vaccaro M, Di Giacinto F, De Spirito M, Ciasca G. Advancements in Mid-Infrared spectroscopy of extracellular vesicles. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 305:123346. [PMID: 37774583 DOI: 10.1016/j.saa.2023.123346] [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: 01/09/2023] [Revised: 08/07/2023] [Accepted: 09/02/2023] [Indexed: 10/01/2023]
Abstract
Extracellular vesicles (EVs) are lipid vesicles secreted by all cells into the extracellular space and act as nanosized biological messengers among cells. They carry a specific molecular cargo, composed of lipids, proteins, nucleic acids, and carbohydrates, which reflects the state of their parent cells. Due to their remarkable structural and compositional heterogeneity, characterizing EVs, particularly from a biochemical perspective, presents complex challenges. In this context, mid-infrared (IR) spectroscopy is emerging as a valuable tool, providing researchers with a comprehensive and label-free spectral fingerprint of EVs in terms of their specific molecular content. This review aims to provide an up-to-date critical overview of the major advancements in mid-IR spectroscopy of extracellular vesicles, encompassing both fundamental and applied research achievements. We also systematically emphasize the new possibilities offered by the integration of emerging cutting-edge IR technologies, such as tip-enhanced and surface-enhanced spectroscopy approaches, along with the growing use of machine learning for data analysis and spectral interpretation. Additionally, to assist researchers in navigating this intricate subject, our manuscript includes a wide and detailed collection of the spectral peaks that have been assigned to EV molecular constituents up to now in the literature.
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Affiliation(s)
- Riccardo Di Santo
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy.
| | - Benedetta Niccolini
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Sabrina Romanò
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Maria Vaccaro
- Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Flavio Di Giacinto
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
| | - Gabriele Ciasca
- Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; Fondazione Policlinico Universitario "A. Gemelli" IRCCS, 00168 Rome, Italy
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10
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Duckworth E, Mortimer M, Al‐Sarireh B, Kanamarlapudi V, Roy D. Frontline clinical diagnosis-FTIR on pancreatic cancer. Cancer Med 2023; 12:17340-17345. [PMID: 37466344 PMCID: PMC10501286 DOI: 10.1002/cam4.6346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/23/2023] [Accepted: 07/05/2023] [Indexed: 07/20/2023] Open
Abstract
OBJECTIVE Accurate, easily accessible and economically viable cancer diagnostic tools are pivotal in improving the abysmal 5% survival rate of pancreatic cancer. METHODS A novel, affordable, non-invasive diagnostic method has been developed by combining measurement precision of infrared spectroscopy with classification using machine learning tools. RESULTS Diagnosis accuracy as high as 90% has been achieved. The study investigated urine and blood from pancreas cancer patients and healthy volunteers, and significantly improved accuracy by focusing on sweet-spots within blood plasma fractions containing molecules within a narrow range of molecular weights.
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11
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Dawuti W, Dou J, Zheng X, Lü X, Zhao H, Yang L, Lin R, Lü G. Rapid and accurate screening of cystic echinococcosis in sheep based on serum Fourier-transform infrared spectroscopy combined with machine learning algorithms. JOURNAL OF BIOPHOTONICS 2023; 16:e202200320. [PMID: 36707914 DOI: 10.1002/jbio.202200320] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 05/17/2023]
Abstract
Cystic echinococcosis (CE) in sheep is a serious zoonotic parasitic disease caused by Echinococcus granulosus sensu stricto (s.s.). Presently, the screening technology for CE in sheep is time-consuming and inaccurate, and novel screening technology is urgently needed. In this work, we combined machine-learning algorithms with Fourier transform infrared (FT-IR) spectroscopy of serum to establish a quick and accurate screening approach for CE in sheep. Serum samples from 77 E. granulosus s.s.-infected sheep to 121 healthy control sheep were measured by FT-IR spectrometer. To optimize the classification accuracy of the serum FI-TR method for the E. granulosus s.s.-infected sheep and healthy control sheep, principal component analysis (PCA), linear discriminant analysis, and support vector machine (SVM) algorithms were used to analyze the data. Among all the bands, 1500-1700 cm-1 band has the best classification effect; its diagnostic sensitivity, specificity, and accuracy of PCA-SVM were 100%, 95.74%, and 96.66%, respectively. The study showed that serum FT-IR spectroscopy combined with machine learning algorithms has great potential for rapid and accurate screening methods for the CE in sheep.
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Affiliation(s)
- Wubulitalifu Dawuti
- School of Public Health, Xinjiang Medical University, Urumqi, 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, China
| | - Jingrui Dou
- School of Public Health, Xinjiang Medical University, Urumqi, 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, China
| | - Xiangxiang Zheng
- School of Electronic Engineering, Beijing University of Posts and Telecommunications, Beijing, China
| | - Xiaoyi Lü
- College of Software, Xinjiang University, Urumqi, China
| | - Hui Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Lingfei Yang
- Department of Abdominal Ultrasound Diagnosis, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 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, China
| | - Guodong Lü
- School of Public Health, Xinjiang Medical University, Urumqi, 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, China
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12
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Pereira de Souza NM, Machado BH, Padoin LV, Prá D, Fay AP, Corbellini VA, Rieger A. Rapid and low-cost liquid biopsy with ATR-FTIR spectroscopy to discriminate the molecular subtypes of breast cancer. Talanta 2023; 254:123858. [PMID: 36470017 DOI: 10.1016/j.talanta.2022.123858] [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: 05/19/2022] [Revised: 08/14/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023]
Abstract
Breast cancer (BC) is the most prevalent cancer worldwide. The prognosis and survival of these patients are directly related to the diagnostic stage. Even so, the gold standard screening method (mammography) has a long waiting period, high rates of false positives, anxiety for patients, and consequently delays the diagnosis by core needle biopsy (invasive method). Alternatively, the Attenuated Total Reflection Fourier Transform Infrared (ATR-FTIR) spectroscopy is a noninvasive, low-cost, rapid, and reagent-free technique that generates the spectral metabolomic profile of biomolecules. This makes it possible to assess systemic repercussions, such as the BC carcinogenesis process. Blood plasma samples (n = 56 BC and n = 18 controls) were analyzed in the spectrophotometer in the ATR-FTIR mode. For the exploratory analysis of the data, interval Principal Component Analysis (iPCA) was used, and for predictive chemometric modeling, the Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA) algorithm with validation by leave-one-out cross-validation. iPCA in the region of 1118-1052 cm-1 (predominantly DNA/RNA bands) showed significant clustering of molecular subtypes and control. The OPLS-DA model achieved 100% accuracy with only 1 latent variable and Root Mean Square Error of Cross-Validation (RMSECV) < 0.005 for all molecular subtypes and control. The wavenumbers (cm-1) with the highest iPCA peaks (loadings: 1117, 1089, 1081, 1075, 1057, and 1052) were used as input to MANOVA (Wilks' Lambda, p < 0.001 between molecular subtypes and control). The rapid and low-cost detection of BC molecular subtypes by ATR-FTIR spectroscopy would plausibly allow initial screening and clinical management, improving prognosis, reducing mortality and costs for the health system.
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Affiliation(s)
| | - Brenda Hunter Machado
- International affairs, International University Center, Santa Cruz do Sul, RS, Brazil.
| | - Licerio Vicente Padoin
- Mastology Service at the Hospital of the Federal University of Santa Maria, Santa Maria, RS, Brazil.
| | - Daniel Prá
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil.
| | - André Poisl Fay
- Postgraduate Program in Medicine and Health Sciences, School of Medicine, Pontifical Catholic University of Rio Grande do Sul, Porto Alegre, RS, Brazil.
| | - Valeriano Antonio Corbellini
- Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Department of Sciences, Humanities and Education, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
| | - Alexandre Rieger
- Department of Life Sciences, University of Santa Cruz do Sul, Santa Cruz do Sul, RS Brazil; Postgraduate Program in Health Promotion, University of Santa Cruz do Sul, Santa Cruz do Sul, RS, Brazil; Postgraduate Program in Environmental Technology, University of Santa Cruz do Sul, RS, Brazil.
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13
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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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14
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Callery EL, Morais CLM, Nugent L, Rowbottom AW. Classification of Systemic Lupus Erythematosus Using Raman Spectroscopy of Blood and Automated Computational Detection Methods: A Novel Tool for Future Diagnostic Testing. Diagnostics (Basel) 2022; 12:diagnostics12123158. [PMID: 36553165 PMCID: PMC9777204 DOI: 10.3390/diagnostics12123158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 12/16/2022] Open
Abstract
The aim of this study was to explore the proof of concept for using Raman spectroscopy as a diagnostic platform in the setting of systemic lupus erythematosus (SLE). We sought to identify unique Raman signatures in serum blood samples to successfully segregate SLE patients from healthy controls (HC). In addition, a retrospective audit was undertaken to assess the clinical utility of current testing platforms used to detect anti-double stranded DNA (dsDNA) antibodies (n = 600). We examined 234 Raman spectra to investigate key variances between SLE patients (n = 8) and HC (n = 4). Multi-variant analysis and classification model construction was achieved using principal component analysis (PCA), PCA-linear discriminant analysis and partial least squares-discriminant analysis (PLS-DA). We achieved the successful segregation of Raman spectra from SLE patients and healthy controls (p-value < 0.0001). Classification models built using PLS-DA demonstrated outstanding performance characteristics with 99% accuracy, 100% sensitivity and 99% specificity. Twelve statistically significant (p-value < 0.001) wavenumbers were identified as potential diagnostic spectral markers. Molecular assignments related to proteins and DNA demonstrated significant Raman intensity changes between SLE and HC groups. These wavenumbers may serve as future biomarkers and offer further insight into the pathogenesis of SLE. Our audit confirmed previously reported inconsistencies between two key methodologies used to detect anti-dsDNA, highlighting the need for improved laboratory testing for SLE. Raman spectroscopy has demonstrated powerful performance characteristics in this proof-of-concept study, setting the foundations for future translation into the clinical setting.
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Affiliation(s)
- Emma L. Callery
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- Correspondence: (E.L.C.); (A.W.R.)
| | - Camilo L. M. Morais
- Institute of Chemistry, Federal University of Rio Grande do Norte, Natal 59072-970, Brazil
| | - Lucy Nugent
- Department of Immunology, Whiston Hospital, Prescot L35 5DR, UK
| | - Anthony W. Rowbottom
- Department of Immunology, Royal Preston Hospital, Preston PR2 9HT, UK
- School of Medicine, University of Central Lancashire, Preston PR1 2HE, UK
- Correspondence: (E.L.C.); (A.W.R.)
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15
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Temperini ME, Di Giacinto F, Romanò S, Di Santo R, Augello A, Polito R, Baldassarre L, Giliberti V, Papi M, Basile U, Niccolini B, Krasnowska EK, Serafino A, De Spirito M, Di Gaspare A, Ortolani M, Ciasca G. Antenna-enhanced mid-infrared detection of extracellular vesicles derived from human cancer cell cultures. J Nanobiotechnology 2022; 20:530. [PMID: 36514065 PMCID: PMC9746222 DOI: 10.1186/s12951-022-01693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/30/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Extracellular Vesicles (EVs) are sub-micrometer lipid-bound particles released by most cell types. They are considered a promising source of cancer biomarkers for liquid biopsy and personalized medicine due to their specific molecular cargo, which provides biochemical information on the state of parent cells. Despite this potential, EVs translation process in the diagnostic practice is still at its birth, and the development of novel medical devices for their detection and characterization is highly required. RESULTS In this study, we demonstrate mid-infrared plasmonic nanoantenna arrays designed to detect, in the liquid and dry phase, the specific vibrational absorption signal of EVs simultaneously with the unspecific refractive index sensing signal. For this purpose, EVs are immobilized on the gold nanoantenna surface by immunocapture, allowing us to select specific EV sub-populations and get rid of contaminants. A wet sample-handling technique relying on hydrophobicity contrast enables effortless reflectance measurements with a Fourier-transform infrared (FTIR) spectro-microscope in the wavelength range between 10 and 3 µm. In a proof-of-principle experiment carried out on EVs released from human colorectal adenocarcinoma (CRC) cells, the protein absorption bands (amide-I and amide-II between 5.9 and 6.4 µm) increase sharply within minutes when the EV solution is introduced in the fluidic chamber, indicating sensitivity to the EV proteins. A refractive index sensing curve is simultaneously provided by our sensor in the form of the redshift of a sharp spectral edge at wavelengths around 5 µm, where no vibrational absorption of organic molecules takes place: this permits to extract of the dynamics of EV capture by antibodies from the overall molecular layer deposition dynamics, which is typically measured by commercial surface plasmon resonance sensors. Additionally, the described metasurface is exploited to compare the spectral response of EVs derived from cancer cells with increasing invasiveness and metastatic potential, suggesting that the average secondary structure content in EVs can be correlated with cell malignancy. CONCLUSIONS Thanks to the high protein sensitivity and the possibility to work with small sample volumes-two key features for ultrasensitive detection of extracellular vesicles- our lab-on-chip can positively impact the development of novel laboratory medicine methods for the molecular characterization of EVs.
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Affiliation(s)
- Maria Eleonora Temperini
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy ,grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Flavio Di Giacinto
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Sabrina Romanò
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Riccardo Di Santo
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Alberto Augello
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy
| | - Raffaella Polito
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Leonetta Baldassarre
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy
| | - Valeria Giliberti
- grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Massimiliano Papi
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Umberto Basile
- grid.414603.4Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy
| | - Benedetta Niccolini
- grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ewa K. Krasnowska
- grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Annalucia Serafino
- grid.5326.20000 0001 1940 4177Institute of Translational Pharmacology, National Research Council of Italy, Rome, Italy
| | - Marco De Spirito
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Alessandra Di Gaspare
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.509494.5NEST, CNR-Istituto Nanoscienze and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Michele Ortolani
- grid.7841.aDepartment of Physics, Sapienza University of Rome, Piazzale Aldo Moro 2, 00185 Rome, Italy ,grid.25786.3e0000 0004 1764 2907Center for Life Neuro and Nano Sciences IIT@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Gabriele Ciasca
- grid.414603.4Fondazione Policlinico Universitario “A. Gemelli”, IRCCS, Rome, Italy ,grid.8142.f0000 0001 0941 3192Dipartimento di Neuroscienze, Sezione di Fisica, Università Cattolica del Sacro Cuore, Rome, Italy
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16
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Villamanca JJ, Hermogino LJ, Ong KD, Paguia B, Abanilla L, Lim A, Angeles LM, Espiritu B, Isais M, Tomas RC, Albano PM. Predicting the Likelihood of Colorectal Cancer with Artificial Intelligence Tools Using Fourier Transform Infrared Signals Obtained from Tumor Samples. APPLIED SPECTROSCOPY 2022; 76:1412-1428. [PMID: 35821580 DOI: 10.1177/00037028221116083] [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: 06/15/2023]
Abstract
The early and accurate detection of colorectal cancer (CRC) significantly affects its prognosis and clinical management. However, current standard diagnostic procedures for CRC often lack sensitivity and specificity since most rely on visual examination. Hence, there is a need to develop more accurate methods for its diagnosis. Support vector machine (SVM) and feedforward neural network (FNN) models were designed using the Fourier transform infrared (FT-IR) spectral data of several colorectal tissues that were unanimously identified as either benign or malignant by different unrelated pathologists. The set of samples in which the pathologists had discordant readings were then analyzed using the AI models described above. Between the SVM and NN models, the NN model was able to outperform the SVM model based on their prediction confidence scores. Using the spectral data of the concordant samples as training set, the FNN was able to predict the histologically diagnosed malignant tissues (n = 118) at 59.9-99.9% confidence (average = 93.5%). Of the 118 samples, 84 (71.18%) were classified with an above average confidence score, 34 (28.81%) classified below the average confidence score, and none was misclassified. Moreover, it was able to correctly identify the histologically confirmed benign samples (n = 83) at 51.5-99.7% confidence (average = 91.64%). Of the 83 samples, 60 (72.29%) were classified with an above average confidence score, 22 (26.51%) classified below the average confidence score, and only 1 sample (1.20%) was misclassified. The study provides additional proof of the ability of attenuated total reflection (ATR) FT-IR enhanced by AI tools to predict the likelihood of CRC without dependence on morphological changes in tissues.
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Affiliation(s)
- John Jerald Villamanca
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Lemuel John Hermogino
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Katherine Denise Ong
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Brian Paguia
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
| | - Lorenzo Abanilla
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
| | - Antonio Lim
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
| | - Lara Mae Angeles
- Department of Pathology, 596481University of Santo Tomas Hospital, Manila, Philippines
| | - Bernadette Espiritu
- Department of Pathology, 603332Bulacan Medical Center, Malolos City, Philippines
| | - Maura Isais
- Department of Pathology, 603332Bulacan Medical Center, Malolos City, Philippines
- The Graduate School, 595547University of Santo Tomas, Manila, Philippines
| | - Rock Christian Tomas
- Department of Electrical Engineering, 54729University of the Philippines Los Baños, Los Baños, Philippines
| | - Pia Marie Albano
- Department of Biological Sciences, College of Science, 564927University of Santo Tomas, Manila, Philippines
- Department of Pathology, Divine Word Hospital, Tacloban City, Philippines
- Research Center for the Natural and Applied Sciences, 564927University of Santo Tomas, Manila, Philippines
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17
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Xue M, Ye S, Ma X, Ye F, Wang C, Zhu L, Yang Y, Chen J. Single-Vesicle Infrared Nanoscopy for Noninvasive Tumor Malignancy Diagnosis. J Am Chem Soc 2022; 144:20278-20287. [DOI: 10.1021/jacs.2c07393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mengfei Xue
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Siyuan Ye
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaopeng Ma
- The First Affiliated Hospital University of Science and Technology of China, Anhui Provincial Hospital, Hefei, Anhui 230000, China
| | - Fangfu Ye
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325001, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Oujiang Laboratory, Wenzhou, Zhejiang 325000, China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianing Chen
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong 523808, China
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18
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Duckworth E, Hole A, Deshmukh A, Chaturvedi P, Chilakapati MK, Mora B, Roy D. Improving Vibrational Spectroscopy Prospects in Frontline Clinical Diagnosis: Fourier Transform Infrared on Buccal Mucosa Cancer. Anal Chem 2022; 94:13642-13646. [PMID: 36161799 PMCID: PMC9558084 DOI: 10.1021/acs.analchem.2c02496] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
We report a novel
method with higher than 90% accuracy
in diagnosing
buccal mucosa cancer. We use Fourier transform infrared spectroscopic
analysis of human serum by suppressing confounding high molecular
weight signals, thus relatively enhancing the biomarkers’ signals.
A narrower range molecular weight window of the serum was also investigated
that yielded even higher accuracy on diagnosis. The most accurate
results were produced in the serum’s 10–30 kDa molecular
weight region to distinguish between the two hardest to discern classes,
i.e., premalignant and cancer patients. This work promises an avenue
for earlier diagnosis with high accuracy as well as greater insight
into the molecular origins of these signals by identifying a key molecular
weight region to focus on.
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Affiliation(s)
- Edward Duckworth
- Swansea University, Singleton Park, Swansea, SA28PP Wales, United Kingdom
| | - Arti Hole
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410210, India
| | - Atul Deshmukh
- Center for Interdisciplinary Research, D. Y. Patil Dental College, Nerul, Navi Mumbai 400706, India
| | - Pankaj Chaturvedi
- Department of Life Sciences, Homi Bhaba National Institute, Mumbai 400094, India
| | - Murali Krishna Chilakapati
- Advanced Centre for Treatment, Research and Education in Cancer, Kharghar, Navi Mumbai 410210, India.,Tata Memorial Center, Head and Neck Surgical Oncology, Dr. E Borges Road, Parel, Mumbai 400012, India.,Department of Life Sciences, Homi Bhaba National Institute, Mumbai 400094, India
| | - Benjamin Mora
- Swansea University, Singleton Park, Swansea, SA28PP Wales, United Kingdom
| | - Debdulal Roy
- Swansea University, Singleton Park, Swansea, SA28PP Wales, United Kingdom
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19
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Peng W, Yin J, Ma J, Zhou X, Chang C. Identification of hepatocellular carcinoma and paracancerous tissue based on the peak area in FTIR microspectroscopy. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:3115-3124. [PMID: 35920728 DOI: 10.1039/d2ay00640e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Hepatocellular carcinoma (HCC) is one of the most common primary hepatic malignancies across the world. The annual incidence and death rates have increased at the highest rate of all cancers in recent years. Surgical resection is a potentially curative option for solitary HCC or unilobar disease without evidence of metastases or vascular invasion. This study focuses on the molecular differences between the HCC foci and paracancerous tissues and provides some valuable biomarkers based on the vibrational spectrum. Fourier transform infrared (FTIR) spectroscopy is a non-invasive and qualitative and semi-quantitative analysis technique that has been widely applied for the identification of macromolecular changes in biological tissues. In this study, the FTIR spectra of the HCC foci and the paracancerous tissues were recorded separately, and ten areas under the absorption peaks of all the specimens were calculated. The result demonstrates that the areas of protein-related absorption peaks at 1398 cm-1, 1548 cm-1, 1654 cm-1 and 3070 cm-1 may be the key indicators of the two different regions. After coupling with the classification algorithms of k-nearest neighbor (KNN), random forest (RF) and support vector machine (SVM), it was found that SVM with an RBF kernel performed best with the AUC (area under the ROC curve) reaching 0.997, and the performance was better than the feature based on the full spectrum. This reveals that the peak area-based FTIR spectra combined with the SVM algorithm may be a promising tool in identifying the HCC foci and the paracancerous tissues.
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Affiliation(s)
- Wenyu Peng
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China.
| | - Junkai Yin
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China.
| | - Jing Ma
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China.
| | - Xiaojie Zhou
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Chao Chang
- Innovation Laboratory of Terahertz Biophysics, National Innovation Institute of Defense Technology, Beijing 100071, China.
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20
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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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21
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Surface Chemical and Morphological Analysis of Chitosan/1,3-β-d-Glucan Polysaccharide Films Cross-Linked at 90 °C. Int J Mol Sci 2022; 23:ijms23115953. [PMID: 35682630 PMCID: PMC9180171 DOI: 10.3390/ijms23115953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 12/28/2022] Open
Abstract
The cross-linking temperature of polymers may affect the surface characteristics and molecular arrangement, which are responsible for their mechanical and physico-chemical properties. The aim of this research was to determine and explain in detail the mechanism of unit interlinkage of two-component chitosan/1,3-β-d-glucan matrices gelled at 90 °C. This required identifying functional groups interacting with each other and assessing surface topography providing material chemical composition. For this purpose, various spectroscopic and microscopic approaches, such as attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM), were applied. The results indicate the involvement mainly of the C-C and C-H groups and C=O⋯HN moieties in the process of biomaterial polymerization. Strong chemical interactions and ionocovalent bonds between the N-glucosamine moieties of chitosan and 1,3-β-d-glucan units were demonstrated, which was also reflected in the uniform surface of the sample without segregation. These unique properties, hybrid character and proper cell response may imply the potential application of studied biomaterial as biocompatible scaffolds used in regenerative medicine, especially in bone restoration and/or wound healing.
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22
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Lugtu EJ, Ramos DB, Agpalza AJ, Cabral EA, Carandang RP, Dee JE, Martinez A, Jose JE, Santillan A, Bangaoil R, Albano PM, Tomas RC. Artificial neural network in the discrimination of lung cancer based on infrared spectroscopy. PLoS One 2022; 17:e0268329. [PMID: 35551276 PMCID: PMC9098097 DOI: 10.1371/journal.pone.0268329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 04/27/2022] [Indexed: 12/19/2022] Open
Abstract
Given the increasing prevalence of lung cancer worldwide, an auxiliary diagnostic method is needed alongside the microscopic examination of biopsy samples, which is dependent on the skills and experience of pathologists. Thus, this study aimed to advance lung cancer diagnosis by developing five (5) artificial neural network (NN) models that can discriminate malignant from benign samples based on infrared spectral data of lung tumors (n = 122; 56 malignant, 66 benign). NNs were benchmarked with classical machine learning (CML) models. Stratified 10-fold cross-validation was performed to evaluate the NN models, and the performance metrics-area under the curve (AUC), accuracy (ACC) positive predictive value (PPV), negative predictive value (NPV), specificity rate (SR), and recall rate (RR)-were averaged for comparison. All NNs were able to outperform the CML models, however, support vector machine is relatively comparable to NNs. Among the NNs, CNN performed best with an AUC of 92.28% ± 7.36%, ACC of 98.45% ± 1.72%, PPV of 96.62% ± 2.30%, NPV of 90.50% ± 11.92%, SR of 96.01% ± 3.09%, and RR of 89.21% ± 12.93%. In conclusion, NNs can be potentially used as a computational tool in lung cancer diagnosis based on infrared spectroscopy of lung tissues.
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Affiliation(s)
- Eiron John Lugtu
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Denise Bernadette Ramos
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Alliah Jen Agpalza
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Erika Antoinette Cabral
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Rian Paolo Carandang
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Jennica Elia Dee
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Angelica Martinez
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Julius Eleazar Jose
- Department of Medical Technology, Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Abegail Santillan
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Ruth Bangaoil
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
- University of Santo Tomas Hospital, Manila, Philippines
| | - Pia Marie Albano
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Rock Christian Tomas
- Department of Electrical Engineering, University of the Philippines Los Baños, Laguna, Philippines
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23
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Kołodziej M, Kaznowska E, Paszek S, Cebulski J, Barnaś E, Cholewa M, Vongsvivut J, Zawlik I. Characterisation of breast cancer molecular signature and treatment assessment with vibrational spectroscopy and chemometric approach. PLoS One 2022; 17:e0264347. [PMID: 35263369 PMCID: PMC8906614 DOI: 10.1371/journal.pone.0264347] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 02/08/2022] [Indexed: 11/18/2022] Open
Abstract
Triple negative breast cancer (TNBC) is regarded as the most aggressive breast cancer subtype with poor overall survival and lack of targeted therapies, resulting in many patients with recurrent. The insight into the detailed biochemical composition of TNBC would help develop dedicated treatments. Thus, in this study Fourier Transform Infrared microspectroscopy combined with chemometrics and absorbance ratios investigation was employed to compare healthy controls with TNBC tissue before and after chemotherapy within the same patient. The primary spectral differences between control and cancer tissues were found in proteins, polysaccharides, and nucleic acids. Amide I/Amide II ratio decrease before and increase after chemotherapy, whereas DNA, RNA, and glycogen contents increase before and decrease after the treatment. The chemometric results revealed discriminatory features reflecting a clinical response scheme and proved the chemotherapy efficacy assessment with infrared spectroscopy is possible.
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Affiliation(s)
| | - Ewa Kaznowska
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Pathology, Medical College of Rzeszow University, Rzeszow, Poland
| | - Sylwia Paszek
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Genetics, Institution of Experimental and Clinical Medicine, University of Rzeszow, Poland
| | - Józef Cebulski
- Centre for Innovation and Transfer of Natural Sciences and Engineering Knowledge, University of Rzeszow, Rzeszow, Poland
| | - Edyta Barnaś
- Institute of Obstetrics and Emergency Medicine, Medical College of Rzeszow University, Rzeszow, Poland
| | - Marian Cholewa
- Centre for Innovation and Transfer of Natural Sciences and Engineering Knowledge, University of Rzeszow, Rzeszow, Poland
| | | | - Izabela Zawlik
- Centre for Innovative Research in Medical and Natural Sciences, Medical College of Rzeszow University, Rzeszow, Poland
- Department of Genetics, Institution of Experimental and Clinical Medicine, University of Rzeszow, Poland
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24
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Tomas RC, Sayat AJ, Atienza AN, Danganan JL, Ramos MR, Fellizar A, Notarte KI, Angeles LM, Bangaoil R, Santillan A, Albano PM. Detection of breast cancer by ATR-FTIR spectroscopy using artificial neural networks. PLoS One 2022; 17:e0262489. [PMID: 35081148 PMCID: PMC8791515 DOI: 10.1371/journal.pone.0262489] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 12/27/2021] [Indexed: 12/27/2022] Open
Abstract
In this study, three (3) neural networks (NN) were designed to discriminate between malignant (n = 78) and benign (n = 88) breast tumors using their respective attenuated total reflection Fourier transform infrared (ATR-FTIR) spectral data. A proposed NN-based sensitivity analysis was performed to determine the most significant IR regions that distinguished benign from malignant samples. The result of the NN-based sensitivity analysis was compared to the obtained results from FTIR visual peak identification. In training each NN models, a 10-fold cross validation was performed and the performance metrics-area under the curve (AUC), accuracy, positive predictive value (PPV), specificity rate (SR), negative predictive value (NPV), and recall rate (RR)-were averaged for comparison. The NN models were compared to six (6) machine learning models-logistic regression (LR), Naïve Bayes (NB), decision trees (DT), random forest (RF), support vector machine (SVM) and linear discriminant analysis (LDA)-for benchmarking. The NN models were able to outperform the LR, NB, DT, RF, and LDA for all metrics; while only surpassing the SVM in accuracy, NPV and SR. The best performance metric among the NN models was 90.48% ± 10.30% for AUC, 96.06% ± 7.07% for ACC, 92.18 ± 11.88% for PPV, 94.19 ± 10.57% for NPV, 89.04% ± 16.75% for SR, and 94.34% ± 10.54% for RR. Results from the proposed sensitivity analysis were consistent with the visual peak identification. However, unlike the FTIR visual peak identification method, the NN-based method identified the IR region associated with C-OH C-OH group carbohydrates as significant. IR regions associated with amino acids and amide proteins were also determined as possible sources of variability. In conclusion, results show that ATR-FTIR via NN is a potential diagnostic tool. This study also suggests a possible more specific method in determining relevant regions within a sample's spectrum using NN.
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Affiliation(s)
- Rock Christian Tomas
- Department of Electrical Engineering, University of the Philippines Los Baños, Los Baños, Laguna, Philippines
| | - Anthony Jay Sayat
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Andrea Nicole Atienza
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Jannah Lianne Danganan
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Ma. Rollene Ramos
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Allan Fellizar
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Mariano Marcos Memorial Hospital and Medical Center, Batac, Ilocos Norte, Philippines
| | - Kin Israel Notarte
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Lara Mae Angeles
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
- University of Santo Tomas Hospital, Manila, Philippines
| | - Ruth Bangaoil
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Abegail Santillan
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
| | - Pia Marie Albano
- Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- The Graduate School, University of Santo Tomas, Manila, Philippines
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25
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Larios G, Ribeiro M, Arruda C, Oliveira SL, Canassa T, Baker MJ, Marangoni B, Ramos C, Cena C. A new strategy for canine visceral leishmaniasis diagnosis based on FTIR spectroscopy and machine learning. JOURNAL OF BIOPHOTONICS 2021; 14:e202100141. [PMID: 34423902 DOI: 10.1002/jbio.202100141] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 08/17/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Visceral leishmaniasis is a neglected disease caused by protozoan parasites of the genus Leishmania. The successful control of the disease depends on its accurate and early diagnosis, which is usually made by combining clinical symptoms with laboratory tests such as serological, parasitological, and molecular tests. However, early diagnosis based on serological tests may exhibit low accuracy due to lack of specificity caused by cross-reactivities with other pathogens, and sensitivity issues related, among other reasons, to disease stage, leading to misdiagnosis. In this study was investigated the use of mid-infrared spectroscopy and multivariate analysis to perform a fast, accurate, and easy canine visceral leishmaniasis diagnosis. Canine blood sera of 20 noninfected, 20 Leishmania infantum, and eight Trypanosoma evansi infected dogs were studied. The data demonstrate that principal component analysis with machine learning algorithms achieved an overall accuracy above 85% in the diagnosis.
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Affiliation(s)
- Gustavo Larios
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Matheus Ribeiro
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Carla Arruda
- Laboratório de Parasitologia Humana, Instituto de Biociências, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Samuel L Oliveira
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Thalita Canassa
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Matthew J Baker
- Pure and Applied Chemistry, University of Stratchclyde, Technology and Innovation Centre, Glasgow, UK
| | - Bruno Marangoni
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Carlos Ramos
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
| | - Cícero Cena
- Grupo de Óptica e Fotônica, Instituto de Física, Universidade Federal de Mato Grosso do Sul, Campo Grande, Brazil
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26
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Yang X, Ou Q, Qian K, Yang J, Bai Z, Yang W, Shi Y, Liu G. Diagnosis of Lung Cancer by ATR-FTIR Spectroscopy and Chemometrics. Front Oncol 2021; 11:753791. [PMID: 34660320 PMCID: PMC8515056 DOI: 10.3389/fonc.2021.753791] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/15/2021] [Indexed: 01/06/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related death in the world. Early diagnosis has great significance for the survival of patients with lung cancer. In this paper, attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy combined with chemometrics was used to study the serum samples from patients with lung cancer and healthy people. The results of spectral band area comparison showed that the concentrations of protein, lipid and nucleic acids molecules in serum of patients with lung cancer were increased compared with those in healthy people. The original spectra were preprocessed to improve the accuracy of principal component regression (PCR) and partial least squares-discriminant analysis (PLS-DA) models. PLS-DA results for first derivative spectral data in nucleic acids (1250-1000cm-1) band showed 80% sensitivity, 91.89% specificity and 87.10% accuracy with highR c 2 of 0.8949 andR v 2 of 0.8153, low RMSEC of 0.3136 and RMSEV of 0.4180. It is shown that ATR-FTIR spectroscopy combined with chemometrics might be developed as a simple method for clinical screening and diagnosis of lung cancer.
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Affiliation(s)
- Xien Yang
- School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Quanhong Ou
- School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Kai Qian
- Department of Thoracic Surgery, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Jianru Yang
- Department of Clinical Laboratory, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Zhixun Bai
- Department of Internal Medicine, The Second Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Weiye Yang
- School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
| | - Youming Shi
- School of Physics and Electronic Engineering, Qujing Normal University, Qujing, China
| | - Gang Liu
- School of Physics and Electronic Information, Yunnan Normal University, Kunming, China
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27
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Bel'skaya LV, Solomatin DV. Influence of surface tension on the characteristics of FTIR spectra on the example of saliva. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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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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29
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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: 12] [Impact Index Per Article: 4.0] [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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30
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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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31
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Soares Martins T, Magalhães S, Rosa IM, Vogelgsang J, Wiltfang J, Delgadillo I, Catita J, da Cruz E Silva OAB, Nunes A, Henriques AG. Potential of FTIR Spectroscopy Applied to Exosomes for Alzheimer's Disease Discrimination: A Pilot Study. J Alzheimers Dis 2021; 74:391-405. [PMID: 32039849 DOI: 10.3233/jad-191034] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Alzheimer's disease (AD) diagnosis is based on psychological and imaging tests but can also include monitoring cerebrospinal fluid (CSF) biomarkers. However, CSF based-neurochemical approaches are expensive and invasive, limiting their use to well-equipped settings. In contrast, blood-based biomarkers are minimally invasive, cost-effective, and a widely accessible alternative. Blood-derived exosomes have recently emerged as a reliable AD biomarker source, carrying disease-specific cargo. Fourier-transformed infrared (FTIR) spectroscopy meets the criteria for an ideal diagnostic methodology since it is rapid, easy to implement, and has high reproducibility. This metabolome-based technique is useful for diagnosing a broad range of diseases, although to our knowledge, no reports for FTIR spectroscopy applied to exosomes in AD exist. In this ground-breaking pilot study, FTIR spectra of serum and serum-derived exosomes from two independent cohorts were acquired and analyzed using multivariate analysis. The regional UA-cohort includes 9 individuals, clinically diagnosed with AD, mean age of 78.7 years old; and the UMG-cohort comprises 12 individuals, clinically diagnosed with AD (based on molecular and/or imaging data), mean age of 73.2 years old. Unsupervised principal component analysis of FTIR spectra of serum-derived exosomes revealed higher discriminatory value for AD cases when compared to serum as a whole. Consistently, the partial least-squares analysis revealed that serum-derived exosomes present higher correlations than serum. In addition, the second derivative peak area calculation also revealed significant differences among Controls and AD cases. The results obtained suggest that this methodology can discriminate cases from Controls and thus be potential useful to assist in AD clinical diagnosis.
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Affiliation(s)
- Tânia Soares Martins
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Sandra Magalhães
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,CICECO -Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Ilka Martins Rosa
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Jonathan Vogelgsang
- Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA, USA
| | - Jens Wiltfang
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,Department of Psychiatry and Psychotherapy, University Medical Center Goettingen (UMG), Georg-August University, Goettingen, Germany.,German Center for Neurodegenerative Diseases (DZNE), Goettingen, Germany
| | | | - José Catita
- CEBIMED-Faculty of Health Sciences; University Fernando Pessoa, Porto, Portugal.,Paralab SA, Gondomar, Portugal
| | - Odete A B da Cruz E Silva
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal.,The Discovery CTR, University of Aveiro Campus, Aveiro, Portugal
| | - Alexandra Nunes
- Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
| | - Ana Gabriela Henriques
- Neurosciences and Signalling Group, Institute of Biomedicine (iBiMED), Department of Medical Sciences, University of Aveiro, Aveiro, Portugal
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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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K MG, Barzegari S, Hajian P, Zham H, Mirzaei HR, Shirazi FH. Diagnosis of normal and malignant human gastric tissue samples by FTIR spectra combined with mathematical models. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129493] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Huber M, Kepesidis KV, Voronina L, Božić M, Trubetskov M, Harbeck N, Krausz F, Žigman M. Stability of person-specific blood-based infrared molecular fingerprints opens up prospects for health monitoring. Nat Commun 2021; 12:1511. [PMID: 33686065 PMCID: PMC7940620 DOI: 10.1038/s41467-021-21668-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
Health state transitions are reflected in characteristic changes in the molecular composition of biofluids. Detecting these changes in parallel, across a broad spectrum of molecular species, could contribute to the detection of abnormal physiologies. Fingerprinting of biofluids by infrared vibrational spectroscopy offers that capacity. Whether its potential for health monitoring can indeed be exploited critically depends on how stable infrared molecular fingerprints (IMFs) of individuals prove to be over time. Here we report a proof-of-concept study that addresses this question. Using Fourier-transform infrared spectroscopy, we have fingerprinted blood serum and plasma samples from 31 healthy, non-symptomatic individuals, who were sampled up to 13 times over a period of 7 weeks and again after 6 months. The measurements were performed directly on liquid serum and plasma samples, yielding a time- and cost-effective workflow and a high degree of reproducibility. The resulting IMFs were found to be highly stable over clinically relevant time scales. Single measurements yielded a multiplicity of person-specific spectral markers, allowing individual molecular phenotypes to be detected and followed over time. This previously unknown temporal stability of individual biochemical fingerprints forms the basis for future applications of blood-based infrared spectral fingerprinting as a multiomics-based mode of health monitoring.
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Affiliation(s)
- Marinus Huber
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany ,grid.450272.60000 0001 1011 8465Max Planck Institute of Quantum Optics, Garching, Germany
| | - Kosmas V. Kepesidis
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany
| | - Liudmila Voronina
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany ,grid.450272.60000 0001 1011 8465Max Planck Institute of Quantum Optics, Garching, Germany
| | - Maša Božić
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany
| | - Michael Trubetskov
- grid.450272.60000 0001 1011 8465Max Planck Institute of Quantum Optics, Garching, Germany
| | - Nadia Harbeck
- grid.5252.00000 0004 1936 973XDepartment of Obstetrics and Gynecology, Breast Center and Comprehensive Cancer Center (CCLMU), Hospital of the Ludwig Maximilian University (LMU), Munich, Germany
| | - Ferenc Krausz
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany ,grid.450272.60000 0001 1011 8465Max Planck Institute of Quantum Optics, Garching, Germany ,Center for Molecular Fingerprinting (CMF), Budapest, Hungary
| | - Mihaela Žigman
- grid.5252.00000 0004 1936 973XDepartment of Physics, Ludwig Maximilian University of Munich, Garching, Germany ,grid.450272.60000 0001 1011 8465Max Planck Institute of Quantum Optics, Garching, Germany ,Center for Molecular Fingerprinting (CMF), Budapest, Hungary
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A Preliminary Study of FTIR Spectroscopy as a Potential Non-Invasive Screening Tool for Pediatric Precursor B Lymphoblastic Leukemia. Molecules 2021; 26:molecules26041174. [PMID: 33671817 PMCID: PMC7926870 DOI: 10.3390/molecules26041174] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 01/19/2023] Open
Abstract
Early detection of the most common pediatric neoplasm, B-cell precursor lymphoblastic leukemia (BCP-ALL), is challenging and requires invasive bone marrow biopsies. The purpose of this study was to establish new biomarkers for early screening to detect pediatric leukemia. In this small cohort study, Fourier transform infrared (FTIR) spectra were obtained from blood sera of 10 patients with BCP-ALL and were compared with the control samples from 10 children with some conditions other than neoplasm. Using various analytical approaches, including a new physical model, some significant differences were observable. The most important include: the different peak area ratio 2965/1645 cm−1 (p = 0.002); the lower average percentage of both β-sheet and β-turn protein structures in the sera of BCP-ALL patients (p = 0.03); an AdaBoost-based predictive model for classifying healthy vs. BCP-ALL patients with 85% accuracy; and the phase shift of the first derivative in the spectral range 1050–1042 cm−1 correlating with white blood cell (WBC) and blast cell count in BCP-ALL patients contrary to the samples obtained from healthy controls. Although verification in larger groups of patients will be necessary, these promising results suggest that FTIR spectroscopy may have future potential for the early screening of BCP-ALL.
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36
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Discrimination of malignant from benign thyroid lesions through neural networks using FTIR signals obtained from tissues. Anal Bioanal Chem 2021; 413:2163-2180. [PMID: 33569645 DOI: 10.1007/s00216-021-03183-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/11/2021] [Accepted: 01/18/2021] [Indexed: 10/22/2022]
Abstract
The current gold standard in cancer diagnosis-the microscopic examination of hematoxylin and eosin (H&E)-stained biopsies-is prone to bias since it greatly relies on visual examination. Hence, there is a need to develop a more sensitive and specific method for diagnosing cancer. Here, Fourier transform infrared (FTIR) spectroscopy of thyroid tumors (n = 164; 76 malignant, 88 benign) was performed and five (5) neural network (NN) models were designed to discriminate the obtained spectral data. PCA-LDA was used as classical benchmark for comparison. Each NN model was evaluated using a stratified 10-fold cross-validation method to avoid overfitting, and the performance metrics-accuracy, area under the curve (AUC), positive predictive value (PPV), negative predictive value (NPV), specificity rate (SR), and recall rate (RR)-were averaged for comparison. All NN models were able to perform excellently as classifiers, and all were able to surpass the LDA model in terms of accuracy. Among the NN models, the RNN model performed best, having an AUC of 95.29% ± 6.08%, an accuracy of 98.06% ± 2.87%, a PPV of 98.57% ± 4.52%, a NPV of 93.18% ± 7.93%, a SR value of 98.89% ± 3.51%, and a RR value of 91.25% ± 10.29%. The RNN model outperformed the LDA model for all metrics except for the AUC, NPV, and RR. In conclusion, NN-based tools were able to predict thyroid cancer based on infrared spectroscopy of tissues with a high level of diagnostic performance in comparison to the gold standard.
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Mazarakis N, Vongsvivut J, Bambery KR, Ververis K, Tobin MJ, Royce SG, Samuel CS, Snibson KJ, Licciardi PV, Karagiannis TC. Investigation of molecular mechanisms of experimental compounds in murine models of chronic allergic airways disease using synchrotron Fourier-transform infrared microspectroscopy. Sci Rep 2020; 10:11713. [PMID: 32678217 PMCID: PMC7366655 DOI: 10.1038/s41598-020-68671-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 06/29/2020] [Indexed: 12/31/2022] Open
Abstract
The ovalbumin-induced (OVA) chronic allergic airways murine model is a well-established model for investigating pre-clinical therapies for chronic allergic airways diseases, such as asthma. Here, we examined the effects of several experimental compounds with potential anti-asthmatic effects including resveratrol (RV), relaxin (RLN), l-sulforaphane (LSF), valproic acid (VPA), and trichostatin A (TSA) using both a prevention and reversal model of chronic allergic airways disease. We undertook a novel analytical approach using focal plane array (FPA) and synchrotron Fourier-transform infrared (S-FTIR) microspectroscopic techniques to provide new insights into the mechanisms of action of these experimental compounds. Apart from the typical biological effects, S-FTIR microspectroscopy was able to detect changes in nucleic acids and protein acetylation. Further, we validated the reduction in collagen deposition induced by each experimental compound evaluated. Although this has previously been observed with conventional histological methods, the S-FTIR technique has the advantage of allowing identification of the type of collagen present. More generally, our findings highlight the potential utility of S-FTIR and FPA-FTIR imaging techniques in enabling a better mechanistic understanding of novel asthma therapeutics.
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Affiliation(s)
- Nadia Mazarakis
- Epigenomic Medicine Laboratory, Department of Diabetes, Central Clinical School, Monash University, Alfred Centre, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,Murdoch Children's Research Institute, Melbourne, VIC, 3004, Australia
| | | | | | - Katherine Ververis
- Epigenomic Medicine Laboratory, Department of Diabetes, Central Clinical School, Monash University, Alfred Centre, 99 Commercial Road, Melbourne, VIC, 3004, Australia
| | - Mark J Tobin
- ANSTO Australian Synchrotron, Clayton, VIC, 3168, Australia
| | - Simon G Royce
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3168, Australia
| | - Chrishan S Samuel
- Department of Pharmacology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC, 3168, Australia
| | - Kenneth J Snibson
- Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Paul V Licciardi
- Murdoch Children's Research Institute, Melbourne, VIC, 3004, Australia.,Department of Paediatrics, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Tom C Karagiannis
- Epigenomic Medicine Laboratory, Department of Diabetes, Central Clinical School, Monash University, Alfred Centre, 99 Commercial Road, Melbourne, VIC, 3004, Australia. .,Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia.
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Bangaoil R, Santillan A, Angeles LM, Abanilla L, Lim A, Ramos MC, Fellizar A, Guevarra L, Albano PM. ATR-FTIR spectroscopy as adjunct method to the microscopic examination of hematoxylin and eosin-stained tissues in diagnosing lung cancer. PLoS One 2020; 15:e0233626. [PMID: 32469931 PMCID: PMC7259682 DOI: 10.1371/journal.pone.0233626] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 05/10/2020] [Indexed: 12/24/2022] Open
Abstract
Lung cancer remains the leading cause of cancer-related death worldwide. Since prognosis and treatment outcomes rely on fast and accurate diagnosis, there is a need for more cost-effective, sensitive, and specific method for lung cancer detection. Thus, this study aimed to determine the ability of ATR-FTIR in discriminating malignant from benign lung tissues and evaluate its concordance with H&E staining. Three (3) 5μm-thick sections were cut from formalin fixed paraffin embedded (FFPE) cell or tissue blocks from patients with lung lesions. The outer sections were H&E-stained and sent to two (2) pathologists to confirm the histopathologic diagnosis. The inner section was deparaffinized by standard xylene method and then subjected to ATR-FTIR analysis. Distinct spectral profiles that distinguished (p<0.05) one sample from another, called the "fingerprint region", were observed in five (5) peak patterns representing the amides, lipids, and nucleic acids. Principal component analysis and hierarchical cluster analysis evidently clustered the benign from malignant tissues. ATR-FTIR showed 97.73% sensitivity, 92.45% specificity, 94.85% accuracy, 91.49% positive predictive value and 98.00% negative predictive value in discriminating benign from malignant lung tissue. Further, strong agreement was observed between histopathologic readings and ATR-FTIR analysis. This study shows the potential of ATR-FTIR spectroscopy as a potential adjunct method to the gold standard, the microscopic examination of hematoxylin and eosin (H&E)-stained tissues, in diagnosing lung cancer.
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Affiliation(s)
- Ruth Bangaoil
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- University of Santo Tomas Hospital, Manila, Philippines
| | - Abegail Santillan
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
| | - Lara Mae Angeles
- University of Santo Tomas Hospital, Manila, Philippines
- Faculty of Medicine and Surgery, University of Santo Tomas, Manila, Philippines
| | - Lorenzo Abanilla
- Divine Word Hospital, Tacloban City, Northern Leyte, Philippines
| | - Antonio Lim
- Divine Word Hospital, Tacloban City, Northern Leyte, Philippines
| | - Ma. Cristina Ramos
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Mariano Marcos Memorial Hospital and Medical Center, Ilocos Norte, Philippines
| | - Allan Fellizar
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- College of Science, University of Santo Tomas, Manila, Philippines
| | - Leonardo Guevarra
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Faculty of Pharmacy, University of Santo Tomas, Manila, Philippines
| | - Pia Marie Albano
- The Graduate School, University of Santo Tomas, Manila, Philippines
- Research Center for the Natural and Applied Sciences, University of Santo Tomas, Manila, Philippines
- Mariano Marcos Memorial Hospital and Medical Center, Ilocos Norte, Philippines
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Breast cancer detection by ATR-FTIR spectroscopy of blood serum and multivariate data-analysis. Talanta 2020; 214:120857. [PMID: 32278436 DOI: 10.1016/j.talanta.2020.120857] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/16/2020] [Accepted: 02/19/2020] [Indexed: 12/31/2022]
Abstract
Detection of breast cancer has particular importance for the diagnosis of cancer diseases. This is the most common type of cancer among women. Breast cancer is a malignant tumor of the glandular tissue of the breast. It is proposed to use infrared spectroscopy of blood serum as a simple and quick way to detect breast cancer. The paper presents the results of research using the methods of multivariate processing of IR spectra of human blood serum obtained by ATR-FTIR spectroscopy. The paper presents the results of research using the methods of multivariate processing of IR spectra of human blood serum obtained by ATR-FTIR spectroscopy. A sufficiently large sample of patients and healthy donors was diagnosed. Blood samples are examined from 66 patients who are clinically diagnosed with breast cancer and 80 healthy volunteers. A feature of the applied approach was a combination of the method of principal component analysis (PCA) and principal component regression (PCR) for processing the IR spectra of blood serum. The PCA method allows us to determine the spectral bands referring for the intensity differences between the control group and the patient group. Shown, that the range of 1306-1250cm-1 in the IR spectrum of blood serum is diagnostically significant for breast cancer. This range corresponds to the vibrations of several functional groups of DNA and RNA, which play a key role in discrimination in breast cancer screening using ATR-FTIR spectroscopy. It is shown that the proposed method has advantages in ease of use for clinical diagnosis and gives good results for the identification of breast cancer. The values of sensitivity (92.3%) and specificity (87.1%) obtained using the PCR method are close to those of mammography and ultrasound. This indicates the possibility of using this method in real clinical laboratory diagnostics.
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Blat A, Wiercigroch E, Smeda M, Wislocka A, Chlopicki S, Malek K. Fourier transform infrared spectroscopic signature of blood plasma in the progression of breast cancer with simultaneous metastasis to lungs. JOURNAL OF BIOPHOTONICS 2019; 12:e201900067. [PMID: 31265171 DOI: 10.1002/jbio.201900067] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 06/09/2023]
Abstract
Despite advanced diagnostic techniques used for detecting cancer, this disease still remains a leading cause of death in the developed world. What is more, the greatest danger for patients is not related with growing of tumor but rather with metastasis of cancer cells to the distant organs. In this study, Fourier transform infrared (FTIR) spectroscopy was used to track chemical changes in blood plasma to find spectral markers of metastatic breast cancer during the disease progression. Plasma samples were taken 1-5 weeks after orthotropic inoculation of 4T1 metastatic breast cancer cells to mice. The earliest changes detected by FTIR spectroscopy in plasma were correlated with unsaturation of phospholipids and secondary structures of proteins that appeared 2 and 3 weeks, respectively, after 4T1 cells inoculation (micrometastatic phase). Significant alternations in the content and structure of lipids and carbohydrates were identified in plasma at the later stages (macrometastatic phase). When large primary tumors in breast and macrometastases in lung were developed, all bands in FTIR spectra significantly differed from those at earlier phases of the cancer progression. In conclusion, we showed that each phase of the breast cancer progression and its pulmonary metastasis can be characterized by a specific panel of spectral markers.
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Affiliation(s)
- Aneta Blat
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Ewelina Wiercigroch
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
| | - Marta Smeda
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Adrianna Wislocka
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
| | - Stefan Chlopicki
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
- Chair of Pharmacology, Jagiellonian University Medical College, Grzegorzecka 16, 31-531 Krakow, Poland
| | - Kamilla Malek
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Bobrzynskiego 14, 30-348 Krakow, Poland
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Balan V, Mihai CT, Cojocaru FD, Uritu CM, Dodi G, Botezat D, Gardikiotis I. Vibrational Spectroscopy Fingerprinting in Medicine: from Molecular to Clinical Practice. MATERIALS (BASEL, SWITZERLAND) 2019; 12:E2884. [PMID: 31489927 PMCID: PMC6766044 DOI: 10.3390/ma12182884] [Citation(s) in RCA: 162] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 12/12/2022]
Abstract
In the last two decades, Fourier Transform Infrared (FTIR) and Raman spectroscopies turn out to be valuable tools, capable of providing fingerprint-type information on the composition and structural conformation of specific molecular species. Vibrational spectroscopy's multiple features, namely highly sensitive to changes at the molecular level, noninvasive, nondestructive, reagent-free, and waste-free analysis, illustrate the potential in biomedical field. In light of this, the current work features recent data and major trends in spectroscopic analyses going from in vivo measurements up to ex vivo extracted and processed materials. The ability to offer insights into the structural variations underpinning pathogenesis of diseases could provide a platform for disease diagnosis and therapy effectiveness evaluation as a future standard clinical tool.
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Affiliation(s)
- Vera Balan
- Faculty of Medical Bioengineering, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Cosmin-Teodor Mihai
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Florina-Daniela Cojocaru
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Cristina-Mariana Uritu
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Gianina Dodi
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Doru Botezat
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania.
| | - Ioannis Gardikiotis
- Advanced Centre for Research-Development in Experimental Medicine, Grigore T. Popa University of Medicine and Pharmacy of Iași, Iași 700115, Romania
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Callery EL, Morais CLM, Paraskevaidi M, Brusic V, Vijayadurai P, Anantharachagan A, Martin FL, Rowbottom AW. New approach to investigate Common Variable Immunodeficiency patients using spectrochemical analysis of blood. Sci Rep 2019; 9:7239. [PMID: 31076587 PMCID: PMC6510896 DOI: 10.1038/s41598-019-43196-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 04/04/2019] [Indexed: 02/06/2023] Open
Abstract
Common variable immune deficiency (CVID) is a primary immunodeficiency disease, characterized by hypogammaglobulinemia, recurrent infections and various complications. The clinical heterogeneity of CVID has hindered identification of an underlying immune defect; diagnosis relies on clinical judgement, alongside evidence-based criteria. The lack of pathognomonic clinical or laboratory features leads to average diagnostic delays of 5 years or more from the onset. Vibrational spectroscopic techniques such as Fourier-transform infrared (FTIR) spectroscopy have recently gained increasing clinical importance, being rapid-, non-invasive and inexpensive methods to obtain information on the content of biological samples. This has led us to apply FTIR spectroscopy to the investigation of blood samples from a cohort of CVID patients; revealing spectral features capable of stratifying CVID patients from healthy controls with sensitivities and specificities of 97% and 93%, respectively for serum, and 94% and 95%, respectively for plasma. Furthermore we identified several discriminating spectral biomarkers; wavenumbers in regions indicative of nucleic acids (984 cm−1, 1053 cm−1, 1084 cm−1, 1115 cm−1, 1528 cm−1, 1639 cm−1), and a collagen-associated biomarker (1528 cm−1), which may represent future candidate biomarkers and provide new knowledge on the aetiology of CVID. This proof-of-concept study provides a basis for developing a novel diagnostic tool for CVID.
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Affiliation(s)
- Emma L Callery
- Department of Immunology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK.
| | - Camilo L M Morais
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK.,Department of Surgery and Cancer, Imperial College London, London, W12 0HS, UK
| | - Vladimir Brusic
- University of Nottingham Ningbo China, Ningbo, 315100, China
| | - Pavaladurai Vijayadurai
- Department of Immunology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
| | - Ariharan Anantharachagan
- Department of Immunology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston, PR1 2HE, UK
| | - Anthony W Rowbottom
- Department of Immunology, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK. .,School of Medicine, University of Central Lancashire, Preston, PR1 2HE, UK. .,NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, PR2 9HT, UK.
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Applicability of FTIR-ATR Method to Measure Carbonyls in Blood Plasma after Physical and Mental Stress. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2181370. [PMID: 31032337 PMCID: PMC6457301 DOI: 10.1155/2019/2181370] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 02/24/2019] [Indexed: 11/17/2022]
Abstract
Introduction Oxidative stress is a state of imbalance between the production of reactive oxygen species and antioxidant defenses. It results in the oxidation of all cellular elements and, to a large extent, proteins, causing inter alia the formation of carbonyl groups in their structures. The study focused on assessment of changes in the plasma protein-bound carbonyls in police horses after combat training and after rest and the applicability of infrared spectroscopy with a Fourier transform, utilizing the attenuated total reflectance (FTIR-ATR) in detecting plasma protein oxidation. Methods We evaluated the influence of both the different concentrations of hydrogen peroxide and combat training on protein carbonylation in horse blood plasma. The oxidation of plasma proteins was assessed using a spectrophotometric method based on the carbonyl groups derivatization with 2,4-dinitrophenylhydrazine (DNPH). The measured values were correlated with the carbonyl groups concentrations determined by means of the FTIR-ATR method. Results The linear correlation between the DNPH and FTIR-ATR methods was shown. The concentration of plasma protein-bound carbonyls significantly deceased in police horses after one-day rest when compared to the values measured directly after the combat training (a drop by 23%, p<0.05 and 29%, p<0.01 measured by DNPH and FTIR-ATR methods, respectively). These results were consistent with the proteins phosphorylation analysis. Conclusion The FTIR-ATR method may be applied to measure the level of plasma proteins peroxidation.
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Kar S, Katti DR, Katti KS. Fourier transform infrared spectroscopy based spectral biomarkers of metastasized breast cancer progression. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 208:85-96. [PMID: 30292907 DOI: 10.1016/j.saa.2018.09.052] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 06/08/2023]
Abstract
Breast cancer is a global health issue and the second leading cause of cancer death in women. Breast cancer tends to migrate to bone and causes bone metastases which is ultimately the cause of death. Here, we report the use of FTIR to identify spectral biomarkers of cancer progression on 3D in vitro model of breast cancer bone metastasis. Our results indicate that the following spectral biomarkers can monitor cancer progression, for example, lipids (CH2 asymmetric/CH2 symmetric stretch), Amide I/Amide II, and RNA/DNA. Principal component analysis also confirmed the involvement of protein, lipids and nucleic acids in cancer progression on sequential culture. The collective observations from this study suggest successful application of FTIR as a non-invasive and accurate method to identify biochemical changes in cancer cells during the progression of breast cancer bone metastasis.
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Affiliation(s)
- Sumanta Kar
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America
| | - Dinesh R Katti
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America
| | - Kalpana S Katti
- Department of Civil and Environmental Engineering, CIE 201, NDSU, Fargo, ND 58104, United States of America.
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Bury D, Morais CLM, Paraskevaidi M, Ashton KM, Dawson TP, Martin FL. Spectral classification for diagnosis involving numerous pathologies in a complex clinical setting: A neuro-oncology example. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 206:89-96. [PMID: 30086451 DOI: 10.1016/j.saa.2018.07.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 07/26/2018] [Accepted: 07/27/2018] [Indexed: 06/08/2023]
Abstract
Much effort is currently being placed into developing new blood tests for cancer diagnosis in the hope of moving cancer diagnosis earlier and by less invasive means than current techniques, e.g., biopsy. Current methods are expected to diagnose and begin treatment of cancer within 62 days of patient presentation, though due to high volume and pressures within the NHS in the UK any technique that can reduce time to diagnosis would allow reduction in the time to treat for patients. The use of vibrational spectroscopy, notably infrared (IR) spectroscopy, has been under investigation for many years with varying success. This technique holds promise as is would combine a generally well accepted test (a blood test) with analysis that is reagent free and cheap to run. It has been demonstrated that, when asked simple clinical questions (i.e., cancer vs. no cancer), results from spectroscopic studies are promising. However, in order to become a clinically useful tool, it is important that the test differentiates a variety of cancer types from healthy patients. This study has analysed plasma samples with attenuated total reflection Fourier-transform IR spectroscopy (ATR-FTIR), to establish if the technique is able to distinguish normal from primary or metastatic brain tumours. We have shown that when asked specific questions, i.e., high-grade glioma vs. low-grade glioma, the results show a significantly high accuracy (100%). Crucially, when combined with meningiomas and metastatic lesions, the accuracy remains high (88-100%) with only minimal overlap between the two metastatic adenocarcinoma groups. Therefore in a clinical setting, this novel technique demonstrates potential benefit when used in conjuction with existing diagnostic methods.
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Affiliation(s)
- Danielle Bury
- 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
| | - Maria Paraskevaidi
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Katherine M Ashton
- Department of Neuropathology, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Trust, Preston PR2 9HT, UK
| | - Timothy P Dawson
- Department of Neuropathology, Royal Preston Hospital, Lancashire Teaching Hospitals NHS Trust, Preston PR2 9HT, UK
| | - Francis L Martin
- School of Pharmacy and Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, UK.
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Siddiqui AJ, Sherazi STH, Ahmed S, Iqbal Choudhary M, Musharraf SG. A comparative profiling of oral cancer patients and high risk niswar users using FT-IR and chemometric analysis. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:177-184. [PMID: 29864641 DOI: 10.1016/j.saa.2018.05.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 05/22/2018] [Accepted: 05/27/2018] [Indexed: 06/08/2023]
Abstract
Oral cancer is one of the major cancer types, which has increased sustainably in Southeast Asian countries due to the extensive use of a variety of tobacco and betel nut products. The current study is focused on developing an easy, efficient and cost-effective method for plasma profiling of oral cancer patients and tobacco users in order to have a progressive picture towards oral cancer. For this purpose, the profiling of 147 plasma samples including 67 oral cancer patients' samples, 60 "niswar" (a dipping tobacco product) user samples, and 20 healthy controls using attenuated total reflectance-fourier transform infrared spectroscopy (ATR-FTIR), and chemometric analysis was carried out. Fingerprint region (500-1500 cm-1) of all three groups showed interesting variations in peaks pattern. From these observations, height ratios of two bands H1646/H1550 and H1080/H1024 with p value of 2.01 × 10-6 and 8.39 × 10-7, respectively, showed a pattern between healthy to oral cancer and "niswar" user samples. Chemometric analysis of the data showed a clean separation among the groups. PLS-DA and OPLS-DA models provided 87.7% and 89.5% classification rate, respectively. Area under the curve (AUC) for healthy control, oral cancer and "niswar" users were found to be 0.97, 0.95 and 0.92%, respectively. The results of the present study indicate that FT-IR spectroscopy, in conjunction with chemometric data, can be effectively used for the preliminary differentiation of plasma samples of oral cancer patients, "niswar" users and control samples of healthy persons.
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Affiliation(s)
- Amna Jabbar Siddiqui
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | | | - Shakil Ahmed
- Industrial Analytical Centre (IAC), H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan
| | - M Iqbal Choudhary
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 22254, Saudi Arabia
| | - Syed Ghulam Musharraf
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan; Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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Abbas S, Simsek Ozek N, Emri S, Koksal D, Severcan M, Severcan F. Diagnosis of malignant pleural mesothelioma from pleural fluid by Fourier transform-infrared spectroscopy coupled with chemometrics. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-14. [PMID: 30317725 DOI: 10.1117/1.jbo.23.10.105003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 09/13/2018] [Indexed: 06/08/2023]
Abstract
This study was conducted to differentiate malignant pleural mesothelioma (MPM) from lung cancer (LC) and benign pleural effusion (BPE) from pleural fluids using the diagnostic power of Fourier transform-infrared spectroscopy with attenuated total reflectance mode coupled with chemometrics. Infrared spectra of MPM (n = 24), LC (n = 20), and BPE (n = 25) were collected, and hierarchical cluster analysis (HCA) and principal component analysis (PCA) were applied to their spectra. HCA results indicated that MPM was differentiated from LC with 100% sensitivity and 100% specificity and from BPE, with 100% sensitivity and 88% specificity, which were also confirmed by PCA score plots. PCA loading plots indicated that these separations originated mainly from lipids, proteins, and nucleic acids-related spectral bands. There was significantly higher lipid, protein, nucleic acid, and glucose contents in the MPM and LC. However, the significant changes in triglyceride and cholesterol ester content, protein and nucleic acid structure, a lower membrane fluidity, and higher membrane order were only observed in the MPM. To check the classification success of some test samples/each group, soft independent modeling of class analogies was performed and 96.2% overall classification success was obtained. This approach can provide a rapid and inexpensive methodology for the efficient differentiation of MPM from other pleural effusions.
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Affiliation(s)
- Sherif Abbas
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Ain Shams University, Physics Department, Cairo, Egypt
| | - Nihal Simsek Ozek
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Ataturk University, Department of Biology, Erzurum, Turkey
- Ataturk University, East Anatolian High Technology Research and Application Center (DAYTAM), Erzurum, Turkey
| | - Salih Emri
- Hacettepe University, Department of Chest Diseases, Ankara, Turkey
- Altinbas University, Department of Chest Diseases, Faculty of Medicine, Istanbul, Turkey
| | - Deniz Koksal
- Hacettepe University, Department of Chest Diseases, Ankara, Turkey
| | - Mete Severcan
- Middle East Technical University, Department of Electrical and Electronic Engineering, Ankara, Turkey
| | - Feride Severcan
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
- Altinbas University, Department of Biophysics, Faculty of Medicine, Istanbul, Turkey
- Altinbas University, Graduate Program of Biomedical Sciences, Institute of Health Sciences, Istanbul, Turkey
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Pielesz A, Gawłowski A, Biniaś D, Bobiński R, Kawecki M, Klama-Baryła A, Kitala D, Łabuś W, Glik J, Paluch J. The role of dimethyl sulfoxide (DMSO) in ex-vivo examination of human skin burn injury treatment. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 196:344-352. [PMID: 29475183 DOI: 10.1016/j.saa.2018.02.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 02/05/2018] [Accepted: 02/10/2018] [Indexed: 06/08/2023]
Abstract
Dimethyl sulfoxide (DMSO) is one of the most versatile solvents in biological science, therefore it is frequently used as a solvent in biological studies and as a vehicle for drug therapy. DMSO readily penetrates, diffuses through biological membranes and ipso facto increases fluidity of liposomal membranes modelling stratum corneum. Thermal injury is associated with the appearance of lipid peroxidation products in the burned skin. The influence of DMSO on protein structure and stability is concentration and temperature dependant. The aim of this study was to assess the impact of DMSO on human burn wounds and examine the interactions between DMSO and skin surface. The real problem in burn treatment is hypoalbuminemia. At the level of the laboratory studies there was an attempt at answering the question of whether the DMSO will modify the standard serum solution. In the case of the incubation of skin fragments in 1%-100% DMSO, the following findings were reported: modification of the serum, appearance of low molecular weight oligomer bands, disappearance of albumin bands or reconstruction of native serum bands during incubation in antioxidant solutions. The result of the modification is also the exposure of FTIR 1603 and 1046cm-1 bands observed in frozen serum solutions. In the case of modification of the burned skin by DMSO solutions or antioxidants - frequency shifts, an increase in the intensity of amide I band as well as the appearance of the 1601cm-1 band can be specific biomarkers of the tissue regeneration process. In this study the areas 1780-1580cm-1 and 1418-1250cm-1 on the Raman spectra are particularly rich in spectral information.
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Affiliation(s)
- Anna Pielesz
- Faculty of Materials, Civil and Environmental Engineering, University of Bielsko-Biała, Poland.
| | - Andrzej Gawłowski
- Faculty of Materials, Civil and Environmental Engineering, University of Bielsko-Biała, Poland
| | - Dorota Biniaś
- Faculty of Materials, Civil and Environmental Engineering, University of Bielsko-Biała, Poland
| | - Rafał Bobiński
- Faculty of Health Sciences, University of Bielsko-Biała, Poland
| | - Marek Kawecki
- Faculty of Health Sciences, University of Bielsko-Biała, Poland; Dr Stanislaw Sakiel Center for Burns Treatment in Siemianowice Śląskie, Siemianowice Śląskie, Poland
| | - Agnieszka Klama-Baryła
- Dr Stanislaw Sakiel Center for Burns Treatment in Siemianowice Śląskie, Siemianowice Śląskie, Poland
| | - Diana Kitala
- Dr Stanislaw Sakiel Center for Burns Treatment in Siemianowice Śląskie, Siemianowice Śląskie, Poland
| | - Wojciech Łabuś
- Dr Stanislaw Sakiel Center for Burns Treatment in Siemianowice Śląskie, Siemianowice Śląskie, Poland
| | - Justyna Glik
- Dr Stanislaw Sakiel Center for Burns Treatment in Siemianowice Śląskie, Siemianowice Śląskie, Poland; Department of Chronic Wound Treatment Organization of the School of Health Sciences, Medical University of Silesia, Katowice, Poland
| | - Jadwiga Paluch
- Faculty of Materials, Civil and Environmental Engineering, University of Bielsko-Biała, Poland
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Oleszko A, Hartwich J, Wójtowicz A, Gąsior-Głogowska M, Huras H, Komorowska M. Comparison of FTIR-ATR and Raman spectroscopy in determination of VLDL triglycerides in blood serum with PLS regression. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 183:239-246. [PMID: 28454077 DOI: 10.1016/j.saa.2017.04.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/13/2017] [Accepted: 04/16/2017] [Indexed: 06/07/2023]
Abstract
Hypertriglyceridemia, related with triglyceride (TG) in plasma above 1.7mmol/L is one of the cardiovascular risk factors. Very low density lipoproteins (VLDL) are the main TG carriers. Despite being time consuming, demanding well-qualified staff and expensive instrumentation, ultracentrifugation technique still remains the gold standard for the VLDL isolation. Therefore faster and simpler method of VLDL-TG determination is needed. Vibrational spectroscopy, including FT-IR and Raman, is widely used technique in lipid and protein research. The aim of this study was assessment of Raman and FT-IR spectroscopy in determination of VLDL-TG directly in serum with the isolation step omitted. TG concentration in serum and in ultracentrifugated VLDL fractions from 32 patients were measured with reference colorimetric method. FT-IR and Raman spectra of VLDL and serum samples were acquired. Partial least square (PLS) regression was used for calibration and leave-one-out cross validation. Our results confirmed possibility of reagent-free determination of VLDL-TG directly in serum with both Raman and FT-IR spectroscopy. Quantitative VLDL testing by FT-IR and/or Raman spectroscopy applied directly to maternal serum seems to be promising screening test to identify women with increased risk of adverse pregnancy outcomes and patient friendly method of choice based on ease of performance, accuracy and efficiency.
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Affiliation(s)
- Adam Oleszko
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland.
| | - Jadwiga Hartwich
- Jagiellonian University Medical College, Department of Analytical Biochemistry, 9 Medyczna St., 30-688 Kraków, Poland
| | - Anna Wójtowicz
- Jagiellonian University, Kraków, Department of Obstetrics & Perinatology, 23 Kopernika St., 31-501 Krakow, Poland
| | - Marlena Gąsior-Głogowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland
| | - Hubert Huras
- Jagiellonian University, Kraków, Department of Obstetrics & Perinatology, 23 Kopernika St., 31-501 Krakow, Poland
| | - Małgorzata Komorowska
- Wrocław University of Science and Technology, Faculty of Fundamental Problems of Technology, Department of Biomedical Engineering, 27 Stanisława Wyspiańskiego St., 50-370 Wrocław, Poland
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Sarkar A, Sengupta S, Mukherjee A, Chatterjee J. Fourier transform infra-red spectroscopic signatures for lung cells' epithelial mesenchymal transition: A preliminary report. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:809-816. [PMID: 27810772 DOI: 10.1016/j.saa.2016.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/23/2016] [Accepted: 10/16/2016] [Indexed: 06/06/2023]
Abstract
Infra red (IR) spectral characterization can provide label-free cellular metabolic signatures of normal and diseased circumstances in a rapid and non-invasive manner. Present study endeavoured to enlist Fourier transform infra red (FTIR) spectroscopic signatures for lung normal and cancer cells during chemically induced epithelial mesenchymal transition (EMT) for which global metabolic dimension is not well reported yet. Occurrence of EMT was validated with morphological and immunocytochemical confirmation. Pre-processed spectral data was analyzed using ANOVA and principal component analysis-linear discriminant analysis (PCA-LDA). Significant differences observed in peak area corresponding to biochemical fingerprint (900-1800cm-1) and high wave-number (2800-3800cm-1) regions contributed to adequate PCA-LDA segregation of cells undergoing EMT. The findings were validated by re-analysis of data using another in-house built binary classifier namely vector valued regularized kernel approximation (VVRKFA), in order to understand EMT progression. To improve the classification accuracy, forward feature selection (FFS) tool was employed in extracting potent spectral signatures by eliminating undesirable noise. Gradual increase in classification accuracy with EMT progression of both cell types indicated prominence of the biochemical alterations. Rapid changes in cellular metabolome noted in cancer cells within first 24h of EMT induction along with higher classification accuracy for cancer cell groups in comparison to normal cells might be attributed to inherent differences between them. Spectral features were suggestive of EMT triggered changes in nucleic acid, protein, lipid and bound water contents which can emerge as the useful markers to capture EMT related cellular characteristics.
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Affiliation(s)
- Atasi Sarkar
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India.
| | - Sanghamitra Sengupta
- Department of Biochemistry, Calcutta University, Ballygunge, Kolkata 700019, West Bengal, India
| | - Anirban Mukherjee
- Department of Electrical Engineering, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
| | - Jyotirmoy Chatterjee
- School of Medical Science and Technology, Indian Institute of Technology Kharagpur, Kharagpur 721302, West Bengal, India
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