Characterization and prediction of viral loads of Hepatitis B serum samples by using surface-enhanced Raman spectroscopy (SERS)

Direct comparison of different protocols to obtain surface enhanced Raman spectra of human serum

Label-free Surface Enhanced Raman Spectroscopy (SERS) is a rapid technique that has been extensively applied in clinical diagnosis and biomedicine for the analysis of biofluids. The purpose of this approach relies on the ability to detect specific "metabolic fingerprints" of complex biological samples, but the full potential of this technique in diagnostics is yet to be exploited, mainly because of the lack of common analytical protocols for sample preparation and analysis. Variation of experimental parameters, such as substrate type, laser wavelength and sample processing can greatly influence spectral patterns, making results from different research groups difficult to compare. This study aims at making a step toward a standardization of the protocols in the analysis of human serum samples with Ag nanoparticles, by directly comparing the SERS spectra obtained from five different methods in which parameters like laser power, nanoparticle concentration, incubation/deproteinization steps and type of substrate used vary. Two protocols are the most used in the literature, and the other three are "in-house" protocols proposed by our group; all of them are employed to analyze the same human serum sample. The experimental results show that all protocols yield spectra that share the same overall spectral pattern, conveying the same biochemical information, but they significantly differ in terms of overall spectral intensity, repeatability, and preparation steps of the sample. A Principal Component Analysis (PCA) was performed revealing that protocol 3 and protocol 1 have the least variability in the dataset, while protocol 2 and 4 are the least repeatable.

Surface-enhanced Raman spectroscopy of the filtrate portions of the blood serum samples of breast cancer patients obtained by using 30 kDa filtration device

Raman spectroscopy is reliable tool for analyzing and exploring early disease diagnosis related to body fluids, such as blood serum, which contain low molecular weight fraction (LMWF) and high molecular weight fraction (HMWF) proteins. The disease biomarkers consist of LMWF which are dominated by HMWF hence their analysis is difficult. In this study, in order to overcome this issue, centrifugal filter devices of 30 kDa were used to obtain filtrate and residue portions obtained from whole blood serum samples of control and breast cancer diagnosed patients. The filtrate portions obtained in this way are expected to contain the marker proteins of breast cancer of the size below this filter size. These may include prolactin, Microphage migration inhabitation factor (MIF), γ-Synuclein, BCSG1, Leptin, MUC1, RS/DJ-1 present in the centrifuged blood serum (filtrate portions) which are then analyzed by the SERS technique to recognize the SERS spectral characteristics associated with the progression of breast cancer in the samples of different stages as compared to the healthy ones. The key intention of this study is to achieve early-stage breast cancer diagnosis through the utilization of Surface Enhanced Raman Spectroscopy (SERS) after the centrifugation of healthy and breast cancer serum samples with Amicon ultra-filter devices of 30 kDa. The silver nanoparticles with high plasmon resonance are used as a substrate for SERS analysis. Principal Component Analysis (PCA) and Partial Least Discriminant Analysis (PLS-DA) models are utilized as spectral classification tools to assess and predict rapid, reliable, and non-destructive SERS-based analysis. Notably, they were particularly effective in distinguishing between different SERS spectral groups of the cancerous and non-cancerous samples. By comparing all these spectral data sets to each other PLSDA shows the 79 % accuracy, 76 % specificity, and 81 % sensitivity in samples with AUC value of AUC = 0.774 SERS has proven to be a valuable technique for the rapid identification of the SERS spectral features of blood serum and its filtrate fractions from both healthy individuals and those with breast cancer, aiding in disease diagnosis.

Determination of latent tuberculosis infection from plasma samples via label-free SERS sensors and machine learning

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.

Unveiling the molecular interaction of hepatitis B virus inhibitor, entecavir with human serum albumin through computational, microscopic and spectroscopic approaches

Molecular docking, molecular dynamics (MD) simulation, atomic force microscopy (AFM) and multi-spectroscopic techniques were selected to unveil the molecular association between the hepatitis B virus (HBV) inhibitor, entecavir (ETR), and the major blood plasma transporter, human serum albumin (HSA). The entire docking and simulation analyses recognized ETR binding to subdomain IIA (Site I) of HSA through hydrogen bonds, hydrophobic and van der Waals forces while maintaining the complex's stability throughout the 100 ns. A gradual lessening in the Stern-Volmer quenching constant (K sv ) with rising temperatures registered ETR-induced quenching of HBV fluorescence as static quenching, thus advising complexation between ETR and HSA. The further advocation of this conclusion was seen from a larger value of the biomolecular quenching rate constant ((kq ) > 1010 M-1s-1), changes in the spectra (UV-Vis absorption) of HSA following ETR inclusion and ETR-induced swelling of HSA in the AFM results. The ETR appeared to bind to HSA with moderate affinity (K a = 1.87 - 1.19 × 10 4   M-1) at 290, 300 and 310 K. Significant alterations in the protein's secondary and tertiary structures, including changes in the protein's Tyr/Trp microenvironment, were also detected by circular dichroism and three-dimensional fluorescence spectra when the protein was bound to ETR. The findings of the drug displacement study backed the docking results of Site I as ETR's preferred binding site in HSA.Communicated by Ramaswamy H. Sarma.

Application of serum SERS technology combined with deep learning algorithm in the rapid diagnosis of immune diseases and chronic kidney disease

Surface-enhanced Raman spectroscopy (SERS), as a rapid, non-invasive and reliable spectroscopic detection technique, has promising applications in disease screening and diagnosis. In this paper, an annealed silver nanoparticles/porous silicon Bragg reflector (AgNPs/PSB) composite SERS substrate with high sensitivity and strong stability was prepared by immersion plating and heat treatment using porous silicon Bragg reflector (PSB) as the substrate. The substrate combines the five deep learning algorithms of the improved AlexNet, ResNet, SqueezeNet, temporal convolutional network (TCN) and multiscale fusion convolutional neural network (MCNN). We constructed rapid screening models for patients with primary Sjögren's syndrome (pSS) and healthy controls (HC), diabetic nephropathy patients (DN) and healthy controls (HC), respectively. The results showed that the annealed AgNPs/PSB composite SERS substrates performed well in diagnosing. Among them, the MCNN model had the best classification effect in the two groups of experiments, with an accuracy rate of 94.7% and 92.0%, respectively. Previous studies have indicated that the AgNPs/PSB composite SERS substrate, combined with machine learning algorithms, has achieved promising classification results in disease diagnosis. This study shows that SERS technology based on annealed AgNPs/PSB composite substrate combined with deep learning algorithm has a greater developmental prospect and research value in the early identification and screening of immune diseases and chronic kidney disease, providing reference ideas for non-invasive and rapid clinical medical diagnosis of patients.

Magnetic polyphosphazene@Au particles as substrates for multiple-detection of immunoproteins by surface-enhanced Raman spectroscopy

Au coated magnetic polyphosphazene (MPCTP) composite particles (MPCTP@Au) were fabricated with sensitive SERS activity. The MPCTP particles were generated by coating polyphosphazene on Fe₃O₄ nanoparticles through precipitation polycondensation of hexachlorocyclotriphosphazene and phloroglucinol. MPCTP@Au composite particles were obtained by deposition of Au nanoparticles on MPCTP by the reduction of HAuCl₄. The size and the thickness of the Au shell can be controlled by varying the amount of HAuCl₄. The magnetic core endowed the composite particles with good magnetic responsiveness, which allowed the analyte to be enriched and separated from the complex matrix, and significantly simplifying the sample pretreatment procedure. The SERS activity of MPCTP@Au composite particles were evaluated by DTNB as model Raman reporter, and the limits of detection (LOD) of DTNB was 10^-8 mol/L. A high efficient SERS immunoassay system based on the MPCTP@Au substrates for the detection of immunoproteins was developed. Human IgG and rabbit IgG were quantitatively determinated simultaneously by this immunoassay system. The quantitative determination of the immunoglobulin G (IgG) was achieved and the LOD of human IgG, rabbit IgG and the mixture of human IgG and rabbit IgG were as low as 10 fg/mL, 100 pg/mL and 1 ng/mL, respectively. The results showed that the MPCTP@Au composite particles have broad application prospects as high performance SERS active substrates for immunoprotein analysis.

Surface-enhanced Raman spectroscopy of centrifuged blood serum samples of diabetic type II patients by using 50KDa filter devices

Blood serum contains essential biochemical information which are used for early disease diagnosis. Blood serum consisted of higher molecular weight fractions (HMWF) and lower molecular weight fractions (LMWF). The disease biomarkers are lower molecular weight fraction proteins, and their contribution to disease diagnosis is suppressed due to higher molecular weight fraction proteins. To diagnose diabetes in early stages are difficult because of the presence of huge amount of these HMWF. In the current study, surface-enhanced Raman spectroscopy (SERS) are employed to diagnose diabetes after centrifugation of serum samples using Amicon ultra filter devices of 50 kDa which produced two fractions of whole blood serum of filtrate, low molecular weight fraction, and residue, high molecular weight fraction. Furthermore SERS is employed to study the LMW fractions of healthy and diseased samples. Some prominent SERS bands are observed at 725 cm^-1, 842 cm^-1, 1025 cm^-1, 959 cm^-1, and 1447 cm^-1 due to small molecular weight proteins, and these biomarkers helped to diagnose the disease early stage. Moreover, chemometric techniques such as principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are employed to check the potential of surface-enhanced Raman spectroscopy for the differentiation and classifications of the blood serum samples. SERS can be employed for the early diagnosis and screening of biochemical changes during type II diabetes.

Raman Scattering-Based Optical Sensing Of Chronic Liver Diseases

Chronic liver diseases (CLDs) are a major public health problem. Despite the progress achieved in fighting against viral hepatitis, the emergence of non-alcoholic fatty liver disease might pose a serious challenge to the public's health in the coming decades. Medical management of CLDs represents a substantial burden on the public health infrastructures. The health care cost of these diseases is an additional burden that weighs heavily on the economies of developing countries. Effective management of CLDs requires the adoption of reliable and cost-effective screening and diagnosing methods to ensure early detection and accurate clinical assessment of these diseases. Vibrational spectroscopies have emerged as universal analytical methods with promising applications in various industrial and biomedical fields. These revolutionary analytical techniques rely on analyzing the interaction between a light beam and the test sample to generate a spectral fingerprint. This latter is defined by the analyte's chemical structure and the molecular vibrations of its functional groups. Raman spectroscopy and surface-enhanced Raman spectroscopy have been used in combination with various chemometric tests to diagnose a wide range of malignant, metabolic and infectious diseases. The aim of the current review is to cast light on the use of these optical sensing methods in the diagnosis of CLDs. The vast majority of research works that investigated the potential application of these spectroscopic techniques in screening and detecting CLDs were discussed here. The advantages and limitations of these modern analytical methods, as compared with the routine and gold standard diagnostic approaches, were also reviewed in details.

Comparison of surface-enhanced Raman spectral data sets of filtrate portions of serum samples of hepatitis B and Hepatitis C infected patients obtained by centrifugal filtration

BACKGROUND

Surface-enhanced Raman spectroscopy (SERS) is an efficient technique which has been used for the analysis of filtrate portions of serum samples of Hepatitis B (HBV) and Hepatitis C (HCV) virus.

OBJECTIVES

The main reason for this study is to differentiate and compare HBV and HCV serum samples for disease diagnosis through SERS. Hepatitis B and hepatitis C disease biomarkers are more predictable in their centrifuged form as compared in their uncentrifuged form. For differentiation of SERS spectral data sets of hepatitis B, hepatitis C and healthy person principal component analysis (PCA) proved to be a helpful. Centrifugally filtered serum samples of hepatitis B and hepatitis C are clearly differentiated from centrifugally filtered serum samples of healthy individuals by using partial least square discriminant analysis (PLS-DA).

METHODOLOGY

Serum sample of HBV, HCV and healthy patients were centrifugally filtered to separate filtrate portion for studying biochemical changes in serum sample. The SERS of these samples is performed using silver nanoparticles as substrates to identify specific spectral features of both viral diseases which can be used for the diagnosis and differentiation of these diseases. The purpose of centrifugal filtration of the serum samples of HBV and HCV positive and control samples by using filter membranes of 50 KDa size is to eliminate the proteins bigger than 50 KDa so that their contribution in the SERS spectrum is removed and disease related smaller proteins may be observed. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) are statistical tools which were used for the further validation of SERS.

RESULTS

HBV and HCV centrifugally filtered serum sample were compared and biomarkers including (uracil, phenylalanine, methionine, adenine, phosphodiester, proline, tyrosine, tryptophan, amino acid, thymine, fatty acid, nucleic acid, triglyceride, guanine and hydroxyproline) were identified through PCA and PLS-DA. Principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) were used as a multivariate data analysis tool for the diagnosis of the characteristic SERS spectral features associated with both types of viral diseases. For the classification and differentiation of centrifugally filtered HBV, HCV, and control serum samples, Principal component analysis is found helpful. Moreover, PLS-DA can classify these two distinct sets of SERS spectral data with 0.90 percent specificity, 0.85 percent precision, and 0.83 percent accuracy.

CONCLUSIONS

Surface enhanced Raman spectroscopy along with chemometric analysis like PCA and PLS-DA have been successfully differentiated HBV and HCV and healthy individuals' serum samples.

Application of serum SERS technology based on thermally annealed silver nanoparticle composite substrate in breast cancer

Liquid biopsy is currently a non-destructive and convenient method of cancer screening, due to human blood containing a variety of cancer-related biomolecules. Therefore, the development of an accurate and rapid breast cancer screening technique combined with breast cancer serum is crucial for the treatment and prognosis of breast cancer patients. In this study, the surface enhanced Raman spectroscopy (SERS) technique is used to enhance the Raman spectroscopy (RS) signal of serum based on a high sensitivity thermally annealed silver nanoparticle/porous silicon bragg mirror (AgNPs/PSB) composite substrate. Compared with RS, SERS reflects more and stronger spectral peak information, which is beneficial to discover new biomarkers of breast cancer. At the same time, to further explore the diagnostic ability of SERS technology for breast cancer. In this study, the raw spectral data are processed by baseline correction, polynomial smoothing, and normalization. Then, the relevant feature information of SERS and RS is extracted by principal component analysis (PCA), and five classification models are established to compare the diagnostic performance of SERS and RS models respectively. The experimental results show that the breast cancer diagnosis model based on the improved SERS substrate combined with the machine learning algorithm can be used to distinguish breast cancer patients from controls. The accuracy, sensitivity, specificity and AUC values of the SVM model are 100%, 100%, 100% and 100%, respectively, as well as the training time of 4ms. The above experimental results show that the SERS technology based on AgNPs/PSB composite substrate, combined with machine learning methods, has great potential in the rapid and accurate identification of breast cancer patients.

Surface-enhanced Raman spectroscopy for characterization of filtrate portions of blood serum samples of typhoid patients

BACKGROUND

Surface-enhanced Raman spectroscopy (SERS) is explored to design a rapid screening method for the characterization and diagnosis of typhoid fever by employing filtrate fractions of blood serum samples obtained by centrifugal filtration with 50 KDa filters.

OBJECTIVES

The purpose of this study, to separate the filtrate portions of blood serum samples in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire the SERS spectral features of smaller proteins more effectively which are probably associated with typhoid disease. Disease caused by Salmonella typhi diagnose more effectively by using surface-enhanced Raman spectroscopy (SERS) and multivariate data analysis tools.

METHODS

SERS was used as a diagnostic tool for typhoid fever by comparison between healthy and diseased samples. For this purpose, all the samples were analyzed by comparing their SERS spectral features. Over the spectral range of 400-1800cm^-1, multivariate data analysis techniques such as Principal Component Analysis (PCA) and Partial Least Squares-Discriminant Analysis (PLS-DA) are applied to diagnose and differentiate different filtrate fractions of blood serum samples of patients of typhoid fever and healthy ones.

RESULTS

By comparing SERS spectra of healthy filtrate with that of filtrate of typhoid sample, the SERS spectral features associated with disease development are identified including PCA is found to be efficient for the qualitative differentiation of all of the samples analyzed. Moreover, PLS-DA successfully identified and classified healthy and typhoid positive blood serum samples with 97 % accuracy, 99 % specificity, 91 % sensitivity and 0.78 area under the receiver operating characteristic (AUROC) curve.

CONCLUSIONS

Surface enhanced Raman spectroscopy using silver nanoparticles SERS substrate, is found to be useful technique for the quick identification and evaluation of filtrate fractions of the blood serum samples of healthy and typhoid samples for disease diagnosis.

Surface-enhanced Raman spectroscopic analysis of the centrifugally filtered blood serum samples of the hepatitis C patients

BACKGROUND

Previously Raman spectroscopy technique is a use to analyze non-invasive disease related to body fluids.

OBJECTIVES

For the qualitative and quantitative analysis of HCV serum samples surface-enhanced Raman spectroscopy (SERS) based method is developed.

METHOD

Surface-enhanced Raman spectroscopy (SERS) technique is employed for analysis of filtrate portions of blood serum samples of hepatitis C virus (HCV) infected patients and healthy ones by using 50 kDa centrifugal filter device. The filtrate portions of the serum obtained in this way contain proteins smaller than 50 kDa and removal of bigger size protein which allows to acquire SERS spectral features of smaller proteins more effectively which are probably associated with Hepatitis C infection. Moreover, SERS spectral features of the filtrates of different level of viral load including low, medium and high viral loads are compared with SERS spectral features of the filtrate portions of healthy/control serum samples. SERS spectral data sets of different samples are further analyzed by using multivariate data analysis techniques such as principal component analysis (PCA) and partial least square regression (PLSR). Some SERS spectral features are solely observed in the filtrate portions of the serum samples of hepatitis C and their intensities are increased as the level of viral load increases and might be used for HCV diagnosis.

RESULTS

PCA was found helpful for differentiation of SERS spectral data sets of filtrate portions of the serum samples of hepatitis C and healthy persons. The PLSR model helped for the quantification of viral loads in the unknown serum samples with 99 % accuracy.

Surface-enhanced Raman spectroscopic analysis of centrifugally filtered HBV serum samples

BACKGROUND

Raman spectroscopy is an effective tool for detecting and discriminating centrifugally filtered hepatitis B virus serum and centrifugally filtered  control serum.

OBJECTIVES

The purpose of current study is to separate high molecular weight fractions from low molecular weight fractions present hepatitis B serum to increase the disease diagnostic ability of surface enhanced Raman spectroscopy (SERS).

METHODS

Clinically diagnosed centrifugally filtered serum samples of hepatitis B patients are subjected for surface enhanced Raman spectroscopy (SERS) in comparison with centrifugally filtered serum samples of healthy individuals by using silver nanoparticles (Ag-NPs) as SERS substrates. Some SERS spectral features are solely observed in centrifugally filtered serum samples of hepatitis B and some SERS spectral are solely observed in centrifugally filtered serum samples of healthy individuals. The diagnostic ability of SERS is further enhanced with different statistical techniques like principal component analysis (PCA), partial least square discriminant analysis (PLS-DA) and partial least square regression analysis (PLSR) have applied.

RESULTS

The disease biomarkers of hepatitis B are more pronounced after their centrifugation as compared with uncentrifuged form. Statistical tools like principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA) clearly differentiated centrifugally filtered serum samples of hepatitis B from centrifugally filtered serum samples of healthy individuals. Furthermore, partial least square regression analysis (PLSR) has been applied for predicting unknown viral load of centrifugally filtered serum sample of hepatitis B.

CONCLUSION

SERS technique along with chemometric tools have successfully differentiated centrifugally filtered serum samples of hepatitis B from centrifugally filtered serum samples of healthy individuals. The centrifugal filtration process has increased the differentiation accuracy of PLS-DA in terms of percentage 98% and regression accuracy of PLSR regression analysis in terms of RMSEP (0.30 IU/mL) of this diagnostic method as compared with that of uncentrifuged method.