1
|
Bi X, Wang J, Xue B, He C, Liu F, Chen H, Lin LL, Dong B, Li B, Jin C, Pan J, Xue W, Ye J. SERSomes for metabolic phenotyping and prostate cancer diagnosis. Cell Rep Med 2024; 5:101579. [PMID: 38776910 PMCID: PMC11228451 DOI: 10.1016/j.xcrm.2024.101579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/25/2024]
Abstract
Molecular phenotypic variations in metabolites offer the promise of rapid profiling of physiological and pathological states for diagnosis, monitoring, and prognosis. Since present methods are expensive, time-consuming, and still not sensitive enough, there is an urgent need for approaches that can interrogate complex biological fluids at a system-wide level. Here, we introduce hyperspectral surface-enhanced Raman spectroscopy (SERS) to profile microliters of biofluidic metabolite extraction in 15 min with a spectral set, SERSome, that can be used to describe the structures and functions of various molecules produced in the biofluid at a specific time via SERS characteristics. The metabolite differences of various biofluids, including cell culture medium and human serum, are successfully profiled, showing a diagnosis accuracy of 80.8% on the internal test set and 73% on the external validation set for prostate cancer, discovering potential biomarkers, and predicting the tissue-level pathological aggressiveness. SERSomes offer a promising methodology for metabolic phenotyping.
Collapse
Affiliation(s)
- Xinyuan Bi
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Jiayi Wang
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Bingsen Xue
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Chang He
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Fugang Liu
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Haoran Chen
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Linley Li Lin
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Baijun Dong
- Department of Urology, Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Science, Shanghai, P.R. China
| | - Butang Li
- Department of Urology, Ningbo Hangzhou Bay Hospital, Ningbo, Zhejiang, P.R. China
| | - Cheng Jin
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Artificial Intelligence Laboratory, Shanghai, China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Jiahua Pan
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Wei Xue
- Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| | - Jian Ye
- State Key Laboratory of Systems Medicine for Cancer, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, P.R. China; Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, P.R. China; Shanghai Key Laboratory of Gynecologic Oncology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, P.R. China.
| |
Collapse
|
2
|
Eiamchai P, Juntagran C, Somboonsaksri P, Waiwijit U, Eisiri J, Samarnjit J, Kaewseekhao B, Limwichean S, Horprathum M, Reechaipichitkul W, Nuntawong N, Faksri K. Determination of latent tuberculosis infection from plasma samples via label-free SERS sensors and machine learning. Biosens Bioelectron 2024; 250:116063. [PMID: 38290379 DOI: 10.1016/j.bios.2024.116063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
Effective diagnostic tools for screening of latent tuberculosis infection (LTBI) are lacking. We aim to investigate the performance of LTBI diagnostic approaches using label-free surface-enhanced Raman spectroscopy (SERS). We used 1000 plasma samples from Northeast Thailand. Fifty percent of the samples had tested positive in the interferon-gamma release assay (IGRA) and 50 % negative. The SERS investigations were performed on individually prepared protein specimens using the Raman-mapping technique over a 7 × 7 grid area under measurement conditions that took under 10 min to complete. The machine-learning analysis approaches were optimized for the best diagnostic performance. We found that the SERS sensors provide 81 % accuracy according to train-test split analysis and 75 % for LOOCV analysis from all samples, regardless of the batch-to-batch variation of the sample sets and SERS chip. The accuracy increased to 93 % when the logistic regression model was used to analyze the last three batches of samples, following optimization of the sample collection, SERS chips, and database. We demonstrated that SERS analysis with machine learning is a potential diagnostic tool for LTBI screening.
Collapse
Affiliation(s)
- Pitak Eiamchai
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Chadatan Juntagran
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
| | - Pacharamon Somboonsaksri
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Uraiwan Waiwijit
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jukgarin Eisiri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Janejira Samarnjit
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Saksorn Limwichean
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Mati Horprathum
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wipa Reechaipichitkul
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand; Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Noppadon Nuntawong
- National Electronics and Computer Technology Center (NECTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand.
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand; Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
| |
Collapse
|
3
|
Luo H, Zu R, Li L, Deng Y, He S, Yin X, Zhang K, He Q, Yin Y, Yin G, Yao D, Wang D. Serum laser Raman spectroscopy as a potential diagnostic tool to discriminate the benignancy or malignancy of pulmonary nodules. iScience 2023; 26:106693. [PMID: 37197326 PMCID: PMC10183669 DOI: 10.1016/j.isci.2023.106693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 02/23/2023] [Accepted: 04/13/2023] [Indexed: 05/19/2023] Open
Abstract
It has been proved that Raman spectral intensities could be used to diagnose lung cancer patients. However, the application of Raman spectroscopy in identifying the patients with pulmonary nodules was barely studied. In this study, we revealed that Raman spectra of serum samples from healthy participants and patients with benign and malignant pulmonary nodules were significantly different. A support vector machine (SVM) model was developed for the classification of Raman spectra with wave points, according to ANOVA test results. It got a good performance with a median area under the curve (AUC) of 0.89, when the SVM model was applied in discriminating benign from malignant individuals. Compared with three common clinical models, the SVM model showed a better discriminative ability and added more net benefits to participants, which were also excellent in the small-size nodules. Thus, the Raman spectroscopy could be a less-invasive and low-costly liquid biopsy.
Collapse
Affiliation(s)
- Huaichao Luo
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Corresponding author
| | - Ruiling Zu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Lintao Li
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Xing Yin
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qiao He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yu Yin
- Sichuan Institute for Brain Science and Brain-Inspired Intelligence, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Gang Yin
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Dezhong Yao
- Sichuan Institute for Brain Science and Brain-Inspired Intelligence, MOE Key Lab for Neuroinformation, University of Electronic Science and Technology of China, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
- Corresponding author
| |
Collapse
|
4
|
Beeram R, Vepa KR, Soma VR. Recent Trends in SERS-Based Plasmonic Sensors for Disease Diagnostics, Biomolecules Detection, and Machine Learning Techniques. BIOSENSORS 2023; 13:328. [PMID: 36979540 PMCID: PMC10046859 DOI: 10.3390/bios13030328] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Surface-enhanced Raman spectroscopy/scattering (SERS) has evolved into a popular tool for applications in biology and medicine owing to its ease-of-use, non-destructive, and label-free approach. Advances in plasmonics and instrumentation have enabled the realization of SERS's full potential for the trace detection of biomolecules, disease diagnostics, and monitoring. We provide a brief review on the recent developments in the SERS technique for biosensing applications, with a particular focus on machine learning techniques used for the same. Initially, the article discusses the need for plasmonic sensors in biology and the advantage of SERS over existing techniques. In the later sections, the applications are organized as SERS-based biosensing for disease diagnosis focusing on cancer identification and respiratory diseases, including the recent SARS-CoV-2 detection. We then discuss progress in sensing microorganisms, such as bacteria, with a particular focus on plasmonic sensors for detecting biohazardous materials in view of homeland security. At the end of the article, we focus on machine learning techniques for the (a) identification, (b) classification, and (c) quantification in SERS for biology applications. The review covers the work from 2010 onwards, and the language is simplified to suit the needs of the interdisciplinary audience.
Collapse
Affiliation(s)
| | | | - Venugopal Rao Soma
- Advanced Centre of Research in High Energy Materials (ACRHEM), DRDO Industry Academia—Centre of Excellence (DIA-COE), University of Hyderabad, Hyderabad 500046, Telangana, India
| |
Collapse
|
5
|
Facile synthesis of Ag/GO SERS composite with highly sensitive and stable performance. Colloids Surf A Physicochem Eng Asp 2023. [DOI: 10.1016/j.colsurfa.2023.131008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
|
6
|
Sultangaziyev A, Ilyas A, Dyussupova A, Bukasov R. Trends in Application of SERS Substrates beyond Ag and Au, and Their Role in Bioanalysis. BIOSENSORS 2022; 12:bios12110967. [PMID: 36354477 PMCID: PMC9688019 DOI: 10.3390/bios12110967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/26/2022] [Accepted: 10/30/2022] [Indexed: 05/31/2023]
Abstract
This article compares the applications of traditional gold and silver-based SERS substrates and less conventional (Pd/Pt, Cu, Al, Si-based) SERS substrates, focusing on sensing, biosensing, and clinical analysis. In recent decades plethora of new biosensing and clinical SERS applications have fueled the search for more cost-effective, scalable, and stable substrates since traditional gold and silver-based substrates are quite expensive, prone to corrosion, contamination and non-specific binding, particularly by S-containing compounds. Following that, we briefly described our experimental experience with Si and Al-based SERS substrates and systematically analyzed the literature on SERS on substrate materials such as Pd/Pt, Cu, Al, and Si. We tabulated and discussed figures of merit such as enhancement factor (EF) and limit of detection (LOD) from analytical applications of these substrates. The results of the comparison showed that Pd/Pt substrates are not practical due to their high cost; Cu-based substrates are less stable and produce lower signal enhancement. Si and Al-based substrates showed promising results, particularly in combination with gold and silver nanostructures since they could produce comparable EFs and LODs as conventional substrates. In addition, their stability and relatively low cost make them viable alternatives for gold and silver-based substrates. Finally, this review highlighted and compared the clinical performance of non-traditional SERS substrates and traditional gold and silver SERS substrates. We discovered that if we take the average sensitivity, specificity, and accuracy of clinical SERS assays reported in the literature, those parameters, particularly accuracy (93-94%), are similar for SERS bioassays on AgNP@Al, Si-based, Au-based, and Ag-based substrates. We hope that this review will encourage research into SERS biosensing on aluminum, silicon, and some other substrates. These Al and Si based substrates may respond efficiently to the major challenges to the SERS practical application. For instance, they may be not only less expensive, e.g., Al foil, but also in some cases more selective and sometimes more reproducible, when compared to gold-only or silver-only based SERS substrates. Overall, it may result in a greater diversity of applicable SERS substrates, allowing for better optimization and selection of the SERS substrate for a specific sensing/biosensing or clinical application.
Collapse
|
7
|
Cai C, Liu Y, Li J, Wang L, Zhang K. Serum fingerprinting by slippery liquid-infused porous SERS for non-invasive lung cancer detection. Analyst 2022; 147:4426-4432. [DOI: 10.1039/d2an01325h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Direct and label-free analysis of clinical serum samples using slippery liquid-infused porous-enhanced Raman spectroscopy (SLIPSERS) enables the rapid non-invasive identification of lung cancer.
Collapse
Affiliation(s)
- Chenlei Cai
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Yujie Liu
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Jiayu Li
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Lei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China
| | - Kun Zhang
- Shanghai Institute for Pediatric Research, Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| |
Collapse
|