Clinical Assay for AFP-L3 by Using Multiple Reaction Monitoring-Mass Spectrometry for Diagnosing Hepatocellular Carcinoma

Applicability of selected reaction monitoring for precise screening tests

INTRODUCTION

The proactive identification of diseases through screening tests has long been endorsed as a means to preempt symptomatic onset. However, such screening endeavors are fraught with complications, such as diagnostic inaccuracies, procedural risks, and patient unease during examinations. These challenges are amplified when screenings for multiple diseases are administered concurrently. Selected Reaction Monitoring (SRM) offers a unique advantage, allowing for the high-throughput quantification of hundreds of analytes with minimal interferences.

AREAS COVERED

Our research posits that SRM-based assays, traditionally tailored for single-disease biomarker profiling, can be repurposed for multi-disease screening. This innovative approach has the potential to substantially alleviate time, labor, and cost demands on healthcare systems and patients alike. Nonetheless, there are formidable methodological hurdles to overcome. These include difficulties in detecting low-abundance proteins and the risk of model overfitting due to the multiple functionalities of single proteins across different disease spectrums - issues especially pertinent in blood-based assays where detection sensitivity is constrained. As we move forward, technological strides in sample preparation, online extraction, throughput, and automation are expected to ameliorate these limitations.

EXPERT OPINION

The maturation of mass spectrometry's integration into clinical laboratories appears imminent, positioning it as an invaluable asset for delivering highly sensitive, reproducible, and precise diagnostic results.

Intramolecular fluorescence resonance energy transfer strategy for accurate detection of AFP-L3% and improved diagnosis of hepatocellular carcinoma

Early and accurate diagnosis of hepatocellular carcinoma (HCC) is of significant importance for improving the survival rate and quality of life for HCC patients. The combined detection of alpha-fetoprotein (AFP) and alpha-fetoprotein-L3 (AFP-L3), namely AFP-L3%, can greatly improve the accuracy of HCC diagnosis compared with AFP detection. Herein, we developed a novel intramolecular fluorescence resonance energy transfer (FRET) strategy for sequential detection of AFP and AFP-specific core fucose to improve the diagnosis accuracy of HCC. Firstly, fluorescence-labeled AFP aptamer (AFP Apt-FAM) was used to specifically recognize all AFP isoforms, and total AFP was quantitatively determined using fluorescence intensity of FAM. Then, 4-((4-(dimethylamino)phenyl)azo)benzoic acid (Dabcyl) labeled lectins (PhoSL-Dabcyl) were used to specifically recognize the core fucose expressed on AFP-L3 that does not bind to other AFP isoforms. The combination of FAM and Dabcyl on the same AFP molecule could generate FRET effect, thereby quenching the fluorescence signal of FAM and quantitatively determining AFP-L3. After that, AFP-L3% was calculated according to the ratio of AFP-L3 to AFP. With this strategy, the concentration of total AFP, AFP-L3 isoform as well as the AFP-L3% were sensitively detected. Detection limits of 0.66 and 0.186 ng/mL were obtained for AFP and AFP-L3 in human serum, respectively. Clinical human serum test results showed that AFP- L3 % test was more accurate than AFP assay to distinguish healthy people, HCC patients and benign liver disease patients. Therefore, the proposed strategy is simple, sensitive and selective, which can improve the accuracy of early diagnosis of HCC, and has good clinical application potential.

Capitalizing glycomic changes for improved biomarker-based cancer diagnostics

Cancer serum biomarkers are valuable or even indispensable for cancer diagnostics and/or monitoring and, currently, many cancer serum markers are routinely used in the clinic. Most of those markers are glycoproteins, carrying cancer-specific glycan structures that can provide extra-information for cancer monitoring. Nonetheless, in the majority of cases, this differential feature is not exploited and the corresponding analytical assays detect only the protein amount, disregarding the analysis of the aberrant glycoform. Two exceptions to this trend are the biomarkers α-fetoprotein (AFP) and cancer antigen 19-9 (CA19-9), which are clinically monitored for their cancer-related glycan changes, and only the AFP assay includes quantification of both the protein amount and the altered glycoform. This narrative review demonstrates, through several examples, the advantages of the combined quantification of protein cancer biomarkers and the respective glycoform analysis, which enable to yield the maximum information and overcome the weaknesses of each individual analysis. This strategy allows to achieve higher sensitivity and specificity in the detection of cancer, enhancing the diagnostic power of biomarker-based cancer detection tests.

Precision diagnosis of hepatocellular carcinoma

ABSTRACT

Hepatocellular carcinoma (HCC) is the most common type of primary hepatocellular carcinoma (PHC). Early diagnosis of HCC remains the key to improve the prognosis. In recent years, with the promotion of the concept of precision medicine and more in-depth analysis of the biological mechanism underlying HCC, new diagnostic methods, including emerging serum markers, liquid biopsies, molecular diagnosis, and advances in imaging (novel contrast agents and radiomics), have emerged one after another. Herein, we reviewed and analyzed scientific advances in the early diagnosis of HCC and discussed their application and shortcomings. This review aimed to provide a reference for scientific research and clinical practice of HCC.

Dual-quenching electrochemiluminescence resonance energy transfer system from CoPd nanoparticles enhanced porous g-C3N4 to FeMOFs-sCuO for neuron-specific enolase immunosensing

For the diagnosis and therapy of small cell lung cancer (SCLC), the accurate and sensitive determination of neuron-specific enolase (NSE) content is crucial. This work outlines a dual-quenching electrochemiluminescence resonance energy transfer (ECL-RET) immunosensor based on the double quenching effects of iron base metal organic frameworks (FeMOFs) loaded with small sized CuO nanoparticles (FeMOFs-sCuO) towards CoPd nanoparticles (CoPdNPs) enhanced porous g-C₃N₄ (P-C₃N₄-CoPdNPs). To be specific, we prepared a porous g-C₃N₄ (P-C₃N₄) which has a rich porous structure, and significantly increased the specific surface area and the number of reaction sites of P-C₃N₄. Meanwhile, the CoPdNPs were loaded onto P-C₃N₄ to improve the ECL luminescence property of P-C₃N₄/K₂S₂O₈ system through acting as a coreaction accelerator. In addition, the ultraviolet-visible (UV-vis) absorption spectra of FeMOFs and small sized CuO nanoparticles (sCuO) showed considerable overlap with the ECL emission spectra of P-C₃N₄ appropriately. Therefore, FeMOFs with high specific surface area were prepared and well combined with sCuO to effectively dual-quenching the ECL emission of P-C₃N₄ based on resonance energy transfer. Hence, a new type ECL-RET couple made up of P-C₃N₄-CoPdNPs (donor) and FeMOFs-sCuO (acceptor) were developed for the first time. A certain amount of P-C₃N₄-CoPdNPs, Ab₁, BSA, NSE were modified layer by layer onto the electrode surface. Then FeMOFs-sCuO-Ab₂ bioconjugates was incubated through the immune recognition binding. As a result, a sandwich-type ECL biosensor was manufactured successfully for NSE immunoassay. Under optimal experimental conditions, the limit of detection (LOD) and the limit of quantitation (LOQ) of the prepared ECL sensor for NSE analysis was 20.4 fg mL^-1 and 7.99 fg mL^-1, respectively, with the relative standard deviation (RSD) of 1.68%. The linear detection range was 0.0000500-100 ng mL^-1. The studied immunosensor had satisfactory sensitivity, specificity and reproducibility, manifesting the suggested sensing strategy might offer a good technical means and theoretical basis for the sensitivity analysis of NSE and has a potential application in clinical diagnosis analysis.

Construction of a competitive electrochemical immunosensor based on sacrifice of Prussian blue and its ultrasensitive detection of alpha-fetoprotein

Effective signal amplification is a prerequisite for ultrasensitive detection by electrochemical immunosensors. For quantitative and ultrasensitive detection of alpha-fetoprotein (AFP), we designed a competitive electrochemical immunosensor and transferred the immunoreactivity from the electrode surface to the cuvette. AFP antigen was captured using AFP primary antibody (Ab₁) immobilized on magnetic nanobeads (MBs), and ZIF-8 nanomaterials attached to secondary antibody (Ab₂) were used as probes. MBs helped retain the sandwich structure in the test tube through incubation and washing steps. Then, an appropriately fixed excess of sodium ethylenediaminetetraacetic acid (EDTA) solution was added to the cuvettes, resulting in etching of Zn ions from ZIF-8 and formation of Zn-EDTA complexes. After magnetic separation, a certain amount of supernatant is added dropwise to the Prussian blue (PB)-modified electrode (GCE), and Fe ions (from PB) complex with the remaining EDTA in the supernatant, thus reducing the signal response value of PB. The higher the AFP concentration, the lower the amount of free EDTA in the supernatant, the less the destruction of PB, and therefore the higher the current. Under optimal conditions, the immunosensor achieved ultra-sensitive detection of AFP in the range of 10^-4 ng/mL-100 ng/mL with a limit of detection (LOD) as low as 0.032 pg/mL (S/N = 3). The excellent performance provides an important tool for the early screening and detection of AFP.

Ordered Labeling-Facilitated Electrochemical Assay of Alpha-Fetoprotein-L3 Ratio for Diagnosing Hepatocellular Carcinoma

Serum alpha fetoprotein (AFP) is a "gold-standard" biomarker for the diagnosis of hepatocellular carcinoma (HCC). Available pieces of evidence suggest that the ratio of AFP-L3 isoform in the total AFP may provide more accurate prediction for the incidence of HCC. In this work, we design an electrochemical aptasensor for high-accuracy assay of AFP-L3 ratio based on differentiated labeling of AFP isoforms in an orderly fashion. Specifically, total AFP is first captured by an AFP aptamer-functionalized electrode and labeled with quantum dots-functionalized DNA probes via mild reduction. Then, AFP-L3 isoform that strongly binds to Lens culinaris agglutinin is labeled with silver nanoparticles after the exonuclease-catalyzed removal of DNA probes. By tracing the electrochemical responses of quantum dots and silver nanoparticles, respectively, the amounts of total AFP and AFP-L3 isoforms are determined and the AFP-L3 ratio is accordingly calculated to favor the accurate HCC diagnosis. Experimental results prove the high-accuracy assay of AFP-L3 ratio based on the AFP quantitation in a linear range of 0.0008-40 ng mL^-1 and AFP-L3 quantitation in a linear range of 0.004-40 ng mL^-1. The aptasensor also displays satisfactory specificity and good recoveries even in the complex serum samples. Therefore, the aptasensor may provide a valuable tool for the assay of the AFP-L3 ratio and have a great potential use in early warning of HCC for clinical application.

Glycosylation Profiling of the Neoplastic Biomarker Alpha Fetoprotein through Intact Mass Protein Analysis

Elevated serum alpha-fetoprotein (AFP) can be observed in liver cirrhosis and hepatocellular carcinoma (HCC). The glycosylation patterns of AFP have been shown to differentiate these conditions, with AFP glycoforms with core fucosylation (AFP-L3) serving as a malignancy risk predictor for HCC. We have developed a method to detect endogenously present AFP proteoforms and to quantify the relative abundance of AFP-L3 glycoforms (AFP-L3%) in serum samples. This method consists of immune enrichment of endogenous AFP, followed by liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) intact protein analysis of AFP. Data are available via ProteomeXchange with identifier PXD038606. Based on the AFP profiles in authentic patient serum samples, we have identified that the frequently observed AFP glycoforms without core fucosylation (AFP-L1) are G2S2 and G2S1, and common AFP-L3 glycoforms are G2FS1 and G2FS2. The intensities of glycoforms in the deconvoluted spectrum are used to quantify AFP-L3% in each sample. The method evaluation included reproducibility, specificity, dilution integrity, and comparison of AFP-L3% with a lectin-binding gel shift electrophoresis (GSE) assay. The AFP-L1 and AFP-L3 proteoforms were reproducibly identified in multiple patient serum samples, resulting in reproducible AFP-L3% quantification. There was considerable agreement between the developed LC-HRMS and commercial GSE methods when quantifying AFP-L3% (Pearson r = 0.63) with a proportional bias.

Predictive Value of MRI with Serum Lectin-Reactive Alpha-Fetoprotein for Liver Cancer Recurrence after Percutaneous Radiofrequency Ablation

Objective

To explore the predictive value of magnetic resonance imaging (MRI) with serum lectin-reactive alpha-fetoprotein (AFP-L3) for liver cancer recurrence after percutaneous radiofrequency ablation (RFA).

Methods

This study included 94 liver cancer patients admitted for RFA treatment and 82 healthy subjects. MRI was performed to record the apparent diffusion coefficient (ADC). The serum concentrations of AFP-L3 were quantified in all participants. The correlation of the AFP-L3 serum level and ADC value with clinical efficacy following RFA was analyzed. Moreover, the prognostic factors affecting liver cancer recurrence were analyzed, as well as the predictive effect of the ADC value and AFP-L3 on liver cancer recurrence.

Results

The serum AFP-L3 level was higher in liver cancer patients than the healthy controls with a lower ADC value. Besides, the patients with tumor residuals had lower ADC values and higher serum AFP-L3 levels than those with complete ablated tumor. The combined detection of the ADC value and serum AFP-L3 level had a sensitivity of 87.50% and a specificity of 87.18% for diagnosing complete ablation after RFA treatment. The number of tumor nodules, tumor diameter, AFP, AFP-L3, and the presence of liver cirrhosis are all independent risk factors for liver cancer recurrence within one year. Meanwhile, the combined detection of the ADC value and serum AFP-L3 level had a good predictive effect on liver cancer recurrence with the sensitivity of 92.86% and a specificity of 69.62%.

Conclusion

The ADC values combined with serum AFP-L3 detection had good predictive effects on complete ablation and recurrence of liver cancer after RFA treatment.

Comparison of Fucose-Specific Lectins to Improve Quantitative AFP-L3 Assay for Diagnosing Hepatocellular Carcinoma Using Mass Spectrometry

Glycoproteins have many important biological functions. In particular, aberrant glycosylation has been observed in various cancers, such as liver cancer. A well-known glycoprotein biomarker is α-fetoprotein (AFP), a surveillance biomarker for hepatocellular carcinoma (HCC) that contains a glycosylation site at asparagine 251. The low diagnostic sensitivity of AFP led researchers to focus on AFP-L3, which has the same sequence as conventional AFP but contains a fucosylated glycan. AFP-L3 has high affinity for Lens culinaris agglutinin (LCA) lectin, prompting many groups to use it for detecting AFP-L3. However, a few studies have identified more effective lectins for fractionating AFP-L3. In this study, we compared the amounts of enriched AFP-L3 with five fucose-specific lectins─LCA, Lotus tetragonolobus lectin (LTL), Ulex europaeus agglutinin I (UEA I), Aleuria aurantia lectin (AAL), and Aspergillus oryzae lectin (AOL)─to identify better lectins and improve HCC diagnostic assays using mass spectrometry (MS). Our results indicate that LTL was the most effective lectin for capturing AFP-L3 species, yielding approximately 3-fold more AFP-L3 than LCA from the same pool of HCC serum samples. Thus, we recommend the use of LTL for AFP-L3 assays, given its potential to improve the diagnostic sensitivity in patients having limited results by conventional LCA assay. The MS data have been deposited to the PeptideAtlas (PASS01752).

Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part I-Development

The process of method development for a diagnostic assay based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) involves several disparate technologies and specialties. Additionally, method development details are typically not disclosed in journal publications. Method developers may need to search widely for pertinent information on their assay(s). This review summarizes the current practices and procedures in method development. Additionally, it probes aspects of method development that are generally not discussed, such as how exactly to calibrate an assay or where to place quality controls, using examples from the literature. This review intends to provide a comprehensive resource and induce critical thinking around the experiments for and execution of developing a clinically meaningful LC-MS/MS assay.

Research Progress in Alpha-Fetoprotein-Induced Immunosuppression of Liver Cancer

Abstract:

Liver cancer is one of the most common malignant tumors, with limited treatment and 8.2% high mortality. Liver cancer is the fourth leading cause of cancer-related deaths, which seriously endangers human life and health. Approximately 70% of liver cancer patients show increased serum alpha-fetoprotein (AFP) levels. AFP is the main diagnostic and prognostic indicator of liver cancer. AFP, a key marker of liver cancer, plays a crucial role in regulating the proliferation of tumor cells, apoptosis, and induction of cellular immune escape. High levels of AFP during embryonic development protect the embryos from maternal immune attack. AFP also promotes immune escape of liver cancer cells by inhibiting tumor-infiltrating lymphocytes (TILs), natural killer cells (NK), dendritic cells (DC), and macrophages; thus, it is also used as a target antigen in immunotherapy for liver cancer. AFP is highly expressed in liver cancer cells. In addition to being used in the diagnosis of liver cancer, it has become a target of immunotherapy for liver cancer as a tumor-associated antigen. In immunotherapy, it was also confirmed that early AFP response was positively correlated with the efficacy of immunotherapy. Early AFP responders had longer PFS and OS than non-responders. At present, the methods of immunotherapy for liver cancer mainly include Adoptive Cell Transfer Therapy (ACT), tumor vaccine therapy, immune checkpoint inhibitors (ICIs) therapy and so on. A large number of studies have shown that AFP mainly plays a role in ACT and liver cancer vaccines. This review presents the research progress of AFP and immunosuppression of liver cancer.

The Landscape Of Alpha Fetoprotein In Hepatocellular Carcinoma: Where Are We?

Hepatocellular carcinoma (HCC) is the most common primary liver cancer and has been acknowledged as a leading cause of death among cirrhosis patients. Difficulties in early diagnosis and heterogeneity are obstacles to effective treatment, especially for advanced HCC. Liver transplantation (LT) is considered the best therapy for HCC. Although many biomarkers are being proposed, alpha-fetoprotein (AFP), which was identified over 60 years ago, remains the most utilized. Recently, much hope has been placed in the immunogenicity of AFP to develop novel therapies, such as AFP vaccines and AFP-specific adoptive T-cell transfer (ACT). This review summarizes the performance of AFP as a biomarker for HCC diagnosis and prognosis, as well as its correlation with molecular classes. In addition, the role of AFP in LT is also described. Finally, we highlight the mechanism and application prospects of two immune therapies (AFP vaccine and ACT) for HCC. In general, our review points out the prevalence of AFP in HCC, accompanied by some controversies and novel directions for future research.

Small volume retinol binding protein measurement by liquid chromatography-tandem mass spectrometry

BACKGROUND

The measurement of plasma concentrations of retinol binding protein is a component of nutritional assessment in neonatal intensive care. However, serial testing in newborns is hampered by the limited amount of blood that can be sampled. Limitations are most severe with preterm infants, for whom close monitoring may be most important.

METHODS

We developed an assay to quantify retinol binding protein using trypsin digestion and liquid chromatography-tandem mass spectrometry, which requires a serum or plasma volume of 5 µl. Additionally, we validated the method according to current recommendations and performed comparison with a standard nephelometry platform in clinical use.

RESULTS

The assay demonstrated linearity from below 1 mg/dL (0.48 µM) to more than 20 mg/dL (9.7 µM), and an imprecision of 11.8% at 0.43 mg/dL (0.21 µM). The distribution of results observed with the new method was different when compared with nephelometry.

CONCLUSION

Liquid chromatography-tandem mass spectrometry facilitated testing a smaller sample volume, thereby increasing the ability to monitor key nutritional markers in premature infants. The differences in results compared with a commercially-available nephelometric assay revealed questionable results for lower concentrations by immunoassay.

AFP-L3 for the diagnosis of early hepatocellular carcinoma: A meta-analysis

BACKGROUND

The present study aimed to systematically evaluate the diagnostic value of an isoform of alpha-fetoprotein (AFP), AFP-L3, for early hepatocellular carcinoma (HCC) by a meta-analysis.

METHODS

Diagnostic reports of AFP-L3% in early HCC were searched in the PubMed, Web of Science, Cochrane Library, and Embase databases up to December 2019. The retrieved literature was reviewed, and eligible articles were selected. Data were extracted from the eligible articles, and the risk of bias was evaluated according to the Quality Assessment of Diagnostic Accuracy Studies scale. Statistical analyses were conducted by MetaDiSc1.4 and RevMan5.3 software. The sensitivities, specificities, and diagnostic odds ratios were pooled. The summary receiver operating characteristic curve was drawn, and the area under the curve was calculated.

RESULTS

Six studies with acceptable quality were included in the meta-analysis involving 2447 patients. No threshold effect was observed among the 6 studies, but there was obvious heterogeneity. The pooled sensitivity, specificity, and positive and negative likelihood ratios of AFP-L3% for the diagnosis of early HCC were 0.34 (95% CI 0.30-0.39, P < .0001), 0.92 (95% CI 0.91-0.93, P < .0001), 4.46 (95% CI 2.94-6.77, P = .0033), and 0.71 (95% CI 0.61-0.82, P = .0004), respectively. The diagnostic odds ratio was 6.78 (95% CI 4.02-11.44, P = .0074). The the area under the curve of the summary receiver operating characteristic was 0.755 (95% CI 0.57-0.94).

CONCLUSION

AFP-L3% has high specificity but low sensitivity for diagnose early HCC, suggesting that AFP-L3% is more valuable for excluding HCC in conditions with elevated AFP than for diagnosing early HCC. In addition, a hypersensitive detection method can improve the diagnostic accuracy of AFP-L3% for early HCC.

Inclusive Quantification Assay of Serum Des-γ-Carboxyprothrombin Proteoforms for Hepatocellular Carcinoma Surveillance by Targeted Mass Spectrometry

Hepatocellular carcinoma (HCC) is a malignant cancer with one of the highest mortality rates. Des-γ-carboxyprothrombin (DCP) is an HCC serologic surveillance marker that can complement the low sensitivity of alpha-fetoprotein (AFP). DCP exists in the blood as a mixture of proteoforms from an impaired carboxylation process at glutamic acid (Glu) residues within the N-terminal domain. The heterogeneity of DCP may affect the accuracy of measurements because DCP levels are commonly determined using an immunoassay that relies on antibody reactivity to an epitope in the DCP molecule. In this study, we aimed to improve the DCP measurement assay by applying a mass spectrometry (MS)-based approach for a more inclusive quantification of various DCP proteoforms. We developed a multiple-reaction monitoring-MS (MRM-MS) assay to quantify multiple noncarboxylated peptides included in the various des-carboxylation states of DCP. We performed the MRM-MS assay in 300 patients and constructed a robust diagnostic model that simultaneously monitored three noncarboxylated peptides. The MS-based quantitative assay for DCP had reliable surveillance power, which was evident from the area under the receiver operating characteristic curve (AUROC) values of 0.874 and 0.844 for the training and test sets, respectively. It was equivalent to conventional antibody-based quantification, which had AUROC values at the optimal cutoff (40 mAU/mL) of 0.743 and 0.704 for the training and test sets, respectively. The surveillance performance of the MS-based DCP assay was validated using an independent validation set consisting of 318 patients from an external cohort, resulting in an AUROC value of 0.793. Conclusion: Due to cost effectiveness and high reproducibility, the quantitative DCP assay using the MRM-MS method is superior to antibody-based quantification and has equivalent performance.

Identification of Fucosylated SERPINA1 as a Novel Plasma Marker for Pancreatic Cancer Using Lectin Affinity Capture Coupled with iTRAQ-Based Quantitative Glycoproteomics

Pancreatic cancer (PC) is an aggressive cancer with a high mortality rate, necessitating the development of effective diagnostic, prognostic and predictive biomarkers for disease management. Aberrantly fucosylated proteins in PC are considered a valuable resource of clinically useful biomarkers. The main objective of the present study was to identify novel plasma glycobiomarkers of PC using the iTRAQ quantitative proteomics approach coupled with Aleuria aurantia lectin (AAL)-based glycopeptide enrichment and isotope-coded glycosylation site-specific tagging, with a view to analyzing the glycoproteome profiles of plasma samples from patients with non-metastatic and metastatic PC and gallstones (GS). As a result, 22 glycopeptides with significantly elevated levels in plasma samples of PC were identified. Fucosylated SERPINA1 (fuco-SERPINA1) was selected for further validation in 121 plasma samples (50 GS and 71 PC) using an AAL-based reverse lectin ELISA technique developed in-house. Our analyses revealed significantly higher plasma levels of fuco-SERPINA1 in PC than GS subjects (310.7 ng/mL v.s. 153.6 ng/mL, p = 0.0114). Elevated fuco-SERPINA1 levels were associated with higher TNM stage (p = 0.024) and poorer prognosis for overall survival (log-rank test, p = 0.0083). The increased plasma fuco-SERPINA1 levels support the utility of this protein as a novel prognosticator for PC.

Multiple Reaction Monitoring-Based Targeted Assays for the Validation of Protein Biomarkers in Brain Tumors

The emergence of omics technologies over the last decade has helped in advancement of research and our understanding of complex diseases like brain cancers. However, barring genomics, no other omics technology has been able to find utility in clinical settings. The recent advancements in mass spectrometry instrumentation have resulted in proteomics technologies becoming more sensitive and reliable. Targeted proteomics, a relatively new branch of mass spectrometry-based proteomics has shown immense potential in addressing the shortcomings of the standard molecular biology-based techniques like Western blotting and Immunohistochemistry. In this study we demonstrate the utility of Multiple reaction monitoring (MRM), a targeted proteomics approach, in quantifying peptides from proteins like Apolipoprotein A1 (APOA1), Apolipoprotein E (APOE), Prostaglandin H2 D-Isomerase (PTGDS), Vitronectin (VTN) and Complement C3 (C3) in cerebrospinal fluid (CSF) collected from Glioma and Meningioma patients. Additionally, we also report transitions for peptides from proteins - Vimentin (VIM), Cystatin-C (CST3) and Clusterin (CLU) in surgically resected Meningioma tissues; Annexin A1 (ANXA1), Superoxide dismutase (SOD2) and VIM in surgically resected Glioma tissues; and Microtubule associated protein-2 (MAP-2), Splicing factor 3B subunit 2 (SF3B2) and VIM in surgically resected Medulloblastoma tissues. To our knowledge, this is the first study reporting the use of MRM to validate proteins from three types of brain malignancies and two different bio-specimens. Future studies involving a large cohort of samples aimed at accurately detecting and quantifying peptides of proteins with roles in brain malignancies could potentially result in a panel of proteins showing ability to classify and grade tumors. Successful application of these techniques could ultimately offer alternative strategies with increased accuracy, sensitivity and lower turnaround time making them translatable to the clinics.

Quantitative Proteomic Approach for Discriminating Major Depressive Disorder and Bipolar Disorder by Multiple Reaction Monitoring-Mass Spectrometry

Because major depressive disorder (MDD) and bipolar disorder (BD) manifest with similar symptoms, misdiagnosis is a persistent issue, necessitating their differentiation through objective methods. This study was aimed to differentiate between these disorders using a targeted proteomic approach. Multiple reaction monitoring-mass spectrometry (MRM-MS) analysis was performed to quantify protein targets regarding the two disorders in plasma samples of 270 individuals (90 MDD, 90 BD, and 90 healthy controls (HCs)). In the training set (72 MDD and 72 BD), a generalizable model comprising nine proteins was developed. The model was evaluated in the test set (18 MDD and 18 BD). The model demonstrated a good performance (area under the curve (AUC) >0.8) in discriminating MDD from BD in the training (AUC = 0.84) and test sets (AUC = 0.81) and in distinguishing MDD from BD without current hypomanic/manic/mixed symptoms (90 MDD and 75 BD) (AUC = 0.83). Subsequently, the model demonstrated excellent performance for drug-free MDD versus BD (11 MDD and 10 BD) (AUC = 0.96) and good performance for MDD versus HC (AUC = 0.87) and BD versus HC (AUC = 0.86). Furthermore, the nine proteins were associated with neuro, oxidative/nitrosative stress, and immunity/inflammation-related biological functions. This proof-of-concept study introduces a potential model for distinguishing between the two disorders.

Clinical Assay for the Early Detection of Colorectal Cancer Using Mass Spectrometric Wheat Germ Agglutinin Multiple Reaction Monitoring

Simple Summary

Colorectal cancer (CRC) is currently the third leading cause of cancer death worldwide. Early diagnosis of CRC is important for increasing the opportunity for treatment and receiving a good prognosis. The aim of our study was to develop a detection method that combined wheat germ agglutinin (WGA) chromatography with mass spectrometry (MS) for early detection of CRC. Further, machine learning algorithms and logistic regression were applied to combine multiple biomarkers we discovered. We validated in a population of 286 plasma samples the diagnostic performance of peptides corresponding to WGA-captured protein and its combination, which received a sensitivity of 84.5% and a specificity of 97.5% in the diagnoses of CRC. Proteomic biomarkers combined with algorithms can provide a powerful tool for discriminating patients with CRC and health controls (HCs). Measurements of WGA-captured PF4, ITIH4, and APOE with MS are then useful for early detection of CRC. Additionally, our study revealed the potential of applying lectin chromatography with MS for disease diagnosis.

Abstract

Colorectal cancer (CRC) is currently the third leading cause of cancer-related mortality in the world. U.S. Food and Drug Administration-approved circulating tumor markers, including carcinoembryonic antigen, carbohydrate antigen (CA) 19-9 and CA125 were used as prognostic biomarkers of CRC that attributed to low sensitivity in diagnosis of CRC. Therefore, our purpose is to develop a novel strategy for novel clinical biomarkers for early CRC diagnosis. We used mass spectrometry (MS) methods such as nanoLC-MS/MS, targeted LC-MS/MS, and stable isotope-labeled multiple reaction monitoring (MRM) MS coupled to test machine learning algorithms and logistic regression to analyze plasma samples from patients with early-stage CRC, late-stage CRC, and healthy controls (HCs). On the basis of our methods, 356 peptides were identified, 6 differential expressed peptides were verified, and finally three peptides corresponding wheat germ agglutinin (WGA)-captured proteins were semi-quantitated in 286 plasma samples (80 HCs and 206 CRCs). The novel peptide biomarkers combination of PF4^54–62, ITIH4^429–438, and APOE^198–207 achieved sensitivity 84.5%, specificity 97.5% and an AUC of 0.96 in CRC diagnosis. In conclusion, our study demonstrated that WGA-captured plasma PF4^54–62, ITIH4^429–438, and APOE^198–207 levels in combination may serve as highly effective early diagnostic biomarkers for patients with CRC.

Glycoproteins as diagnostic and prognostic biomarkers for neurodegenerative diseases: A glycoproteomic approach

Neurodegenerative diseases (NDs) are incurable and can develop progressively debilitating disorders, including dementia and ataxias. Alzheimer's disease and Parkinson's disease are the most common NDs that mainly affect the elderly people. There is an urgent need to develop new diagnostic tools so that patients can be accurately stratified at an early stage. As a common post-translational modification, protein glycosylation plays a key role in physiological and pathological processes. The abnormal changes in glycosylation are associated with the altered biological pathways in NDs. The pathogenesis-related proteins, like amyloid-β and microtubule-associated protein tau, have altered glycosylation. Importantly, specific glycosylation changes in cerebrospinal fluid, blood and urine are valuable for revealing neurodegeneration in the early stages. This review describes the emerging biomarkers based on glycoproteomics in NDs, highlighting the potential applications of glycoprotein biomarkers in the early detection of diseases, monitoring of the disease progression, and measurement of the therapeutic responses. The mass spectrometry-based strategies for characterizing glycoprotein biomarkers are also introduced.

Identification of Plasma hsa_circ_0005397 and Combined With Serum AFP, AFP-L3 as Potential Biomarkers for Hepatocellular Carcinoma

Background: Mounting evidence has demonstrated that circular RNA (circRNA) plays crucial roles in the occurrence and development of hepatocellular carcinoma (HCC). However, the expression pattern and clinical application value of plasma circRNA in HCC are still largely unknown. Herein, we explored the role of plasma hsa_circ_0005397 in diagnosis and prognosis of HCC.

Methods: The expression level of plasma hsa_circ_0005397 was measured by quantitative real-time polymerase chain reaction (qRT-PCR). The identification and origin of plasma hsa_circ_0005397 were confirmed by RNase R assay, Sanger sequencing and HCC cell culture. In addition, its diagnostic value was assessed by receiver operating characteristic (ROC) curve and prognostic value was evaluated by dynamics monitoring and Kaplan–Meier curve analyses in HCC patients.

Results: The expression of plasma hsa_circ_0005397 was higher in patients with HCC than that in patients with benign liver diseases and healthy controls (both p < 0.05). Moreover, it was closely correlated with tumor size (p = 0.020) and TNM stage (p = 0.006) of HCC patients. The area under the ROC curve of plasma hsa_circ_0005397 was 0.737 and 95% confidence interval was 0.671–0.795. Furthermore, the combination of plasma hsa_cic_0005397, serum AFP and AFP-L3 could improve the diagnostic sensitivity of HCC. Additionally, dynamic monitoring plasma hsa_cic_0005397 might help us predict recurrence or metastasis in HCC patients after surgical resection. Besides, the increased plasma hsa_cic_0005397 was closely correlated with shorter overall survival of HCC patients (p = 0.007).

Conclusion: Plasma has_circ_0005397 represents a novel noninvasive biomarker for HCC. Moreover, the combination of plasma hsa_cic_0005397, serum AFP and AFP-L3 might improve the diagnostic value for HCC.

Development and Multiple Validation of the Protein Multi-marker Panel for Diagnosis of Pancreatic Cancer

PURPOSE

To develop and validate a protein-based, multi-marker panel that provides superior pancreatic ductal adenocarcinoma (PDAC) detection abilities with sufficient diagnostic performance.

EXPERIMENTAL DESIGN

A total of 959 plasma samples from patients at multiple medical centers were used. To construct an optimal, diagnostic, multi-marker panel, we applied data preprocessing procedure to biomarker candidates. The multi-marker panel was developed using a training set comprised of 261 PDAC cases and 290 controls. Subsequent evaluations were performed in a validation set comprised of 65 PDAC cases and 72 controls. Further validation was performed in an independent set comprised of 75 PDAC cases and 47 controls.

RESULTS

A multi-marker panel containing 14 proteins was developed. The multi-marker panel achieved AUCs of 0.977 and 0.953 for the training set and validation set, respectively. In an independent validation set, the multi-marker panel yielded an AUC of 0.928. The diagnostic performance of the multi-marker panel showed significant improvements compared with carbohydrate antigen (CA) 19-9 alone (training set AUC = 0.977 vs. 0.872, P < 0.001; validation set AUC = 0.953 vs. 0.832, P < 0.01; independent validation set AUC = 0.928 vs. 0.771, P < 0.001). When the multi-marker panel and CA 19-9 were combined, the diagnostic performance of the combined panel was improved for all sets.

CONCLUSIONS

This multi-marker panel and the combined panel showed statistically significant improvements in diagnostic performance compared with CA 19-9 alone and has the potential to complement CA 19-9 as a diagnostic marker in clinical practice.

SERS Immunosensor of Array Units Surrounded by Particles: A Platform for Auxiliary Diagnosis of Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is one of the diseases with high mortality worldwide, so its early diagnosis and treatment have attracted much attention. Due to the advantages of the high sensitivity of surface-enhanced Raman scattering (SERS) detection, SERS has excellent application value in the diagnosis of HCC. In this paper, silver nanoparticles (AgNPs) are modified by magnetron sputtering on the surface of polystyrene (PS) templates with spheres of two different diameters. The array of units surrounded by particles is successfully prepared and the SERS performance is characterized. The effect of the gap between AgNPs on plasmon coupling and hot spot distribution is discussed. Finite-difference time domain (FDTD) simulation is used to verify the electric fields and hot spot distribution of the array. The differences in the concentrations of HCC markers are analyzed by using the change of SERS signal intensity of the array. The whole process proves that the preparation of structures with a strong local electric field to provide highly sensitive SERS signals is a key link in the detection of HCC markers, which is conducive to the diagnosis of HCC and has potential application value in clinical diagnosis.

Clinical Application of Multiple Reaction Monitoring-Mass Spectrometry to Human Epidermal Growth Factor Receptor 2 Measurements as a Potential Diagnostic Tool for Breast Cancer Therapy

Background

Human epidermal growth factor receptor 2 (HER2) is often overexpressed in breast cancer and correlates with a worse prognosis. Thus, the accurate detection of HER2 is crucial for providing the appropriate measures for patients. However, the current techniques used to detect HER2 status, immunohistochemistry and fluorescence in situ hybridization (FISH), have limitations. Specifically, FISH, which is mandatory for arbitrating 2+ cases, is time-consuming and costly. To address this shortcoming, we established a multiple reaction monitoring-mass spectrometry (MRM-MS) assay that improves on existing methods for differentiating HER2 status.

Methods

We quantified HER2 expression levels in 210 breast cancer formalin-fixed paraffin-embedded (FFPE) tissue samples by MRM-MS. We aimed to improve the accuracy and precision of HER2 quantification by simplifying the sample preparation through predicting the number of FFPE slides required to ensure an adequate amount of protein and using the expression levels of an epithelial cell-specific protein as a normalization factor when measuring HER2 expression levels.

Results

To assess the correlation between MRM-MS and IHC/FISH data, HER2 quantitative data from MRM-MS were divided by the expression levels of junctional adhesion molecule A, an epithelial cell-specific protein, prior to statistical analysis. The normalized HER2 amounts distinguished between HER2 2+/FISH-negative and 2+/FISH-positive groups (AUROC = 0.908), which could not be differentiated by IHC. In addition, all HER2 status were discriminated by MRM-MS.

Conclusions

This MRM-MS assay yields more accurate HER2 expression levels relative to immunohistochemistry and should help to guide clinicians toward the proper treatment for breast cancer patients, based on their HER2 expression.

Web portal for analytical validation of MRM-MS assay abided with integrative multinational guidelines

Multiple reaction monitoring-mass spectrometry became a mainstream method for quantitative proteomics, which made the validation of a method and the analyzed data important. In this portal for validation of the MRM-MS assay, we developed a website that automatically evaluates uploaded MRM-MS data, based on biomarker assay guidelines from the European Medicines Agency, the US Food & Drug Administration, and the Korea Food & Drug Administration. The portal reads a Skyline output file and produces the following results—calibration curve, specificity, sensitivity, carryover, precision, recovery, matrix effect, recovery, dilution integrity, stability, and QC—according to the standards of each independent agency. The final tables and figures that pertain to the 11 evaluation categories are displayed in an individual page. Spring boot was used as a framework for development of the webpage, which follows MVC Pattern. JSP, HTML, XML, and Java Script were used to develop the webpage. A server was composed of Apache Tomcat, MySQL. Input files were skyline-derived output files (csv file), and each files were organized by specific columns in order. SQL, JAVA were interworked to evaluate all the categories and show the results. Method Validation Portal can be accessed via any kind of explorer from https://pnbvalid.snu.ac.kr.

A Mass-Spectrometry-Based Antibody-Free Approach Enables the Quantification of D-Dimer in Plasma

D-dimer is an important marker of different coagulation diseases, such as venous thromboembolism (including deep vein thrombosis and pulmonary embolism) and disseminated intravascular coagulation. Though it is frequently used in many clinical diagnostic situations, the D-dimer assays currently lack standardization due to its inherent heterogeneity which makes the antibody-based methods have different quantitative results and cutoffs to define an abnormal value. In this study, we report the first antibody-free D-dimer quantification method. In the method, a cross-linked peptide of fibrin D domain carboxyl terminal cross-linked by the factor XIIIa was used to represent the D-dimer. By using a filter-aided sample preparation and a nickel immobilized metal affinity chromatography enrichment strategy, the complexity of the plasma sample was significantly reduced, and the cross-linked peptide was enriched effectively for analysis with parallel reaction monitoring in mass spectrometry. The linear range of this method was 3.125-400 nmol/L which spans over two magnitudes. Recovery and reproducibility of the method were found to be good. To further demonstrate the performance of our method, D-dimer concentrations of 25 human plasma samples were analyzed, and the results had a good correlation between with the commercial D-dimer assay kit used in hospitals. This method was completely antibody-free and has the potential to promote the standardization of D-dimer analysis.

Biomarkers vs imaging in the early detection of hepatocellular carcinoma and prognosis

Hepatocellular carcinoma (HCC) is the 5^th most frequently diagnosed cancer in the world, according to the World Health Organization. The incidence of HCC is between 3/100000 and 78.1/100000, with a high incidence reported in areas with viral hepatitis B and hepatitis C, thus affecting Asia and Africa predominantly. Several international clinical guidelines address HCC diagnosis and are structured according to the geographical area involved. All of these clinical guidelines, however, share a foundation of diagnosis by ultrasound surveillance and contrast imaging techniques, particularly computed tomography, magnetic resonance imaging, and sometimes contrast-enhanced ultrasound. The primary objective of this review was to systematically summarize the recent published studies on the clinical utility of serum biomarkers in the early diagnosis of HCC and for the prognosis of this disease.

Cost-Effective Automated Preparation of Serum Samples for Reproducible Quantitative Clinical Proteomics

Reproducible sample preparation remains a significant challenge in large-scale clinical research using selected reaction monitoring-mass spectrometry (SRM-MS), which enables a highly sensitive multiplexed assay. Although automated liquid-handling platforms have tremendous potential for addressing this issue, the high cost of their consumables is a drawback that renders routine operation expensive. Here we evaluated the performance of a liquid-handling platform in preparing serum samples compared with a standard experiment while reducing the outlay for consumables, such as tips, wasted reagents, and reagent stock plates. A total of 26 multiplex assays were quantified by SRM-MS using four sets of 24 pooled human serum aliquots; the four sets used a fixed number (1, 4, 8, or 24) of tips to dispense digestion reagents. This study demonstrated that the use of 4 or 8 tips is comparable to 24 tips (standard experiment), as evidenced by their coefficients of variation: 13.5% (for 4 and 8 tips) versus 12.0% (24 tips). Thus we can save 37% of the total experimental cost compared with the standard experiment, maintaining nearly equivalent reproducibility. The routine operation of cost-effective liquid-handling platforms can enable researchers to process large-scale samples with high throughput, adding credibility to their findings by minimizing human error.

The Upregulation of Trophinin-Associated Protein (TROAP) Predicts a Poor Prognosis in Hepatocellular Carcinoma

Purpose: Trophinin-associated protein (TROAP) is a cytoplasmic protein that plays a significant role in the processes of embryo transplantation and microtubule regulation. However, the relevant survival analysis and cancer progression analysis have not yet been reported.

Methods: Eighteen matched pairs of tumor and adjacent non-tumor samples were evaluated to detect the TROAP mRNA level. Immunohistochemistry (IHC) was used to evaluate the TROAP expression in 108 hepatocellular carcinoma patients who underwent surgical resection. Meanwhile, data from the TCGA database was statistically evaluated.

Results: In the present study, we detected a significant increase in the TROAP mRNA level in tumor tissues when compared with adjacent non-tumor tissues. Moreover, the upregulation of TROAP was associated with increased serum AFP and GGT; the greater the tumor number was, the larger the tumor size, differentiation grade, and cancer embolus in clinical analysis. In HCC patients, elevated TROAP expression in the primary tumor was positively related to clinical severity, such as poor overall survival and disease-free survival. In addition, both univariate and multivariate survival analysis validated that TROAP expression was a promising independent risk factor for overall survival and disease-free survival in HCC patients. Furthermore, the results derived from the analysis of data from the TCGA database were consistent with previous results. Altogether, our results show that TROAP is a novel crucial regulator of HCC progression and is a potential therapeutic biomarker for HCC patients.

Conclusions: Elevated TROAP expression predicted a poor prognosis, and TROAP may serve as a potential biomarker for application in oncotherapy.