Detection Of Protein Biomarkers Research Articles

Lab-in-a-Vial Rapid Test for Internet of Things-Embedded Point-of-Healthcare Protein Biomarker Detection in Bodily Fluids.

Amateurs often struggle with detecting and quantifying protein biomarkers in body fluids due to the high expertise required. This study introduces a Lab-in-a-Vial (LV) rapid diagnostic platform, featuring hydrangea-like platinum nanozymes (PtNH), for rapid, accurate detection and quantification of protein biomarkers on-site within 15min. This method significantly enhances detection sensitivity for various biomarkers in body fluids, surpassing traditional methods such as enzyme-linked immunosorbent assays (ELISA) and lateral flow assays (LFA) by ≈250 to 1300 times. The LV platform uses a glass vial coated with specific bioreceptors such as antigens or antibodies, enabling rapid in vitro evaluation of disease risk from small fluid samples, similar to a personal ELISA-like point-of-care test (POCT). It overcomes challenges in on-site biomarker detection, allowing both detection and quantification through a portable wireless spectrometer for healthcare internet of things (H-IoT). The platform's effectiveness and adaptability are confirmed using IgG/IgM antibodies from SARS-CoV-2 infected patients and nuclear matrix protein (NMP22) from urothelial carcinoma (UC) patients as biomarkers. These tests demonstrated its accuracy and flexibility. This approach offers vast potential for diverse disease applications, provided that the relevant protein biomarkers in bodily fluids are identified.

Proteome Fishing for CRISPR/Cas12a-Based Orthogonal Multiplex Aptamer Sensing.

Detection of serum protein biomarkers is extremely challenging owing to the superior complexity of serum. Here, we report a method of proteome fishing from the serum. It uses a magnetic nanoparticle-protein corona and a multiplexed aptamer panel, which we incubated with the nanoparticle-protein corona for biomarker recognition. To transfer protein biomarker detection to aptamer detection, we established a CRISPR/Cas12a-based orthogonal multiplex aptamer sensing (COMPASS) platform by profiling the aptamers of protein corona with clinical nonsmall cell lung cancer (NSCLC) serum samples. Furthermore, we determined the four out of nine (FOON) panel (including HE4, NSE, AFP, and VEGF165) to be the most cost-effective and accurate panel for COMPASS in NSCLC diagnosis. The diagnostic accuracy of NSCLC by the FOON panel with internal and external cohorts was 95.56% (ROC-AUC = 99.40%) and 89.58% (ROC-AUC = 95.41%), respectively. Our developed COMPASS technology circumvents the otherwise challenging multiplexed serum protein amplification problem and avoids aptamer degradation in serum. Therefore, this novel COMPASS could lead to the development of a facile, cost-effective, intelligent, and high-throughput diagnostic platform for large-cohort cancer screening.

Comprehensive serum proteomics profiles and potential protein biomarkers for the early detection of advanced adenoma and colorectal cancer.

The majority of colorectal cancer (CRC) cases develop from precursor advanced adenoma (AA). With the development of proteomics technologies, blood protein biomarkers have potential applications in the early screening of AA and CRC in the general population. To identify serum protein biomarkers for the early screening of AA and CRC. We collected 43 serum samples from 8 normal controls (NCs), 19 AA patients and 16 CRC patients at China-Japan Friendship Hospital. Quantitative proteomic analysis was performed using liquid chromatography-mass spectrometry/mass spectrometry and data independent acquisition, and differentially expressed proteins (DEPs) with P-values < 0.05 and absolute fold changes > 1.5 were screened out, followed by bioinformatics analysis. Prognosis was further analyzed based on public databases, and proteins expression in tissues were validated by immunohistochemistry. A total of 2132 proteins and 17365 peptides were identified in the serum samples. There were 459 upregulated proteins and 118 downregulated proteins in the NC vs AA group, 289 and 180 in the NC vs CRC group, and 52 and 248 in the AA vs CRC group, respectively. Bioinformatic analysis revealed that these DEPs had different functions and participated in extensive signaling pathways. We also identified DIAPH1, VASP, RAB11B, LBP, SAR1A, TUBGCP5, and DOK3 as important proteins for the progression of AA and CRC. Furthermore, VASP (P < 0.01), LBP (P = 0.01), TUBGCP5 (P < 0.01), and DOK3 (P < 0.01) were associated with a poor prognosis. In addition, we propose that LBP and VASP may be more promising protein biomarkers for the early screening of colorectal tumors. Our study elucidated the serum proteomic profiles of AA and CRC patients, and the identified proteins, such as LBP and VASP, may contribute to the early detection of AA and CRC.

Rapid Plasma Proteome Profiling via Nanoparticle Protein Corona and Direct Infusion Mass Spectrometry.

Noninvasive detection of protein biomarkers in plasma is crucial for clinical purposes. Liquid chromatography-mass spectrometry (LC-MS) is the gold standard technique for plasma proteome analysis, but despite recent advances, it remains limited by throughput, cost, and coverage. Here, we introduce a new hybrid method that integrates direct infusion shotgun proteome analysis (DISPA) with nanoparticle (NP) protein corona enrichment for high-throughput and efficient plasma proteomic profiling. We realized over 280 protein identifications in 1.4 min collection time, which enables a potential throughput of approximately 1000 samples daily. The identified proteins are involved in valuable pathways, and 44 of the proteins are FDA-approved biomarkers. The robustness and quantitative accuracy of this method were evaluated across multiple NPs and concentrations with a mean coefficient of variation of 17%. Moreover, different protein corona profiles were observed among various NPs based on their distinct surface modifications, and all NP protein profiles exhibited deeper coverage and better quantification than neat plasma. Our streamlined workflow merges coverage and throughput with precise quantification, leveraging both DISPA and NP protein corona enrichment. This underscores the significant potential of DISPA when paired with NP sample preparation techniques for plasma proteome studies.

Quantitative SERS detection of serum protein biomarkers for assessment of tumor microwave ablation outcomes

Microwave ablation (MWA) is widely applied in the treatment of cancer, especially hepatocellular carcinoma (HCC). However, the lack of indicators for evaluating ablation completeness limits the success rate and wider application of MWA. This study therefore aims to identify novel serum biomarkers for evaluating the completeness of ablation, by applying surface-enhanced Raman spectroscopy (SERS). Multiple cytokines are preliminarily identified through cell experiments, and the potential as biomarkers is evaluated using clinical serum samples from patients with HCC before and after MWA. CCL20 and EGF are identified as promising indicators of the completeness of MWA. Additionally, we develop a highly sensitive and specific quantitative detection method of CCL20 and EGF levels by fabricating a sandwich SERS nano-architecture amplification-based immunosensor. The linear detection range of this SERS platform is 0.1 pg/mL–1 ng/mL with the limit of detections (LoDs) decreasing to 0.082 pg/mL for CCL20 and 0.096 pg/mL for EGF. The remarkable consistency of the SERS immunosensor and ELISA in detecting CCL20 and EGF serum levels highlights the promising clinical utility of SERS in biomarker detection. The exceptional sensitivity of SERS in detecting CCL20 and EGF offers a potential avenue for enhancing the assessment of clinical MWA completeness, consequently leading to improved patient survival rates.

Ultra-fast detection of pathogens and protein biomarkers using a low-cost silicon plasmonic biosensing platform

In this paper, we report, for the first time to our knowledge, a new versatile and future proof diagnostic platform for diverse applications and heterogeneous biological targets. This platform relies on a plasmonic-augmented silicon photonic biochip to detect bacteria and protein biomarkers within minutes. To demonstrate the potential of this platform in diverse applications, we demonstrate the detection of two heterogeneous targets, the bacterium Escherichia coli (E. coli) and the molecule C-reactive protein (CRP) using a universal detection method. E. coli is one of the most commonly encountered bacterial pathogens involved in food monitoring, food born infections and water contamination applications, while CRP is a well-established disease severity indicator frequently used in common clinical practice. The biochip used is fully compatible with CMOS semiconductor manufacturing, while it hosts biosensors arrays for any combination of detection assays. Each biosensor exploits a 70 μm long aluminum plasmonic transducer within a silicon nitride waveguide-based Mach-Zehnder Interferometer. Each aluminum surface was silanized and biomodified with specific antibodies. Biosensing experiments revealed that CRP can be detected in diverse sample mediums, and E. coli detection was achieved in buffer at concentrations as low as 10 cells/ml within 13-25 minutes. The results are in good agreement with preceding numerical simulations. The modular nature of the reported biosensing platform makes it scalable and customizable, allowing nearly any combination of diagnostic tests targeting pathogens and proteins to be integrated on the same biochip for food quality monitoring, environmental monitoring, drug discovery and modern cell therapy manufacturing, or biomedical applications.

Machine Learning-Assisted High-Throughput Identification and Quantification of Protein Biomarkers with Printed Heterochains.

Advanced in vitro diagnosis technologies are highly desirable in early detection, prognosis, and progression monitoring of diseases. Here, we engineer a multiplex protein biosensing strategy based on the tunable liquid confinement self-assembly of multi-material heterochains, which show improved sensitivity, throughput, and accuracy compared to standard ELISA kits. By controlling the material combination and the number of ligand nanoparticles (NPs), we observe robust near-field enhancement as well as both strong electromagnetic resonance in polymer-semiconductor heterochains. In particular, their optical signals show a linear response to the coordination number of the semiconductor NPs in a wide range. Accordingly, a visible nanophotonic biosensor is developed by functionalizing antibodies on central polymer chains that can identify target proteins attached to semiconductor NPs. This allows for the specific detection of multiple protein biomarkers from healthy people and pancreatic cancer patients in one step with an ultralow detection limit (1 pg/mL). Furthermore, rapid and high-throughput quantification of protein expression levels in diverse clinical samples such as buffer, urine, and serum is achieved by combining a neural network algorithm, with an average accuracy of 97.3%. This work demonstrates that the heterochain-based biosensor is an exemplary candidate for constructing next-generation diagnostic tools and suitable for many clinical settings.

Polyaromatic Hydrocarbon-Functionalized 2D MXene-Based 3D Porous Antifouling Nanocomposite with Long Shelf Life for High-Performance Electrochemical Immunosensor Applications.

Affinity-based electrochemical (AEC) biosensors have gained more attention in the field of point-of-care management. However, AEC sensing is hampered by biofouling of the electrode surface and degradation of the antifouling material. Therefore, a breakthrough in antifouling nanomaterials is crucial for the fabrication of reliable AEC biosensors. Herein, for the first time, we propose 1-pyrenebutyric acid-functionalized MXene to develop an antifouling nanocomposite to resist biofouling in the immunosensors. The nanocomposite consisted of a 3D porous network of bovine serum albumin cross-linked with glutaraldehyde with functionalized MXene as conductive nanofillers, where the inherited oxidation resistance property of functionalized MXene improved the electrochemical lifetime of the nanocomposite. On the other hand, the size-extruded porous structure of the nanocomposite inhibited the biofouling activity on the electrode surface for up to 90 days in real samples. As a proof of concept, the antifouling nanocomposite was utilized to fabricate a multiplexed immunosensor for the detection of C-reactive protein (CRP) and ferritin biomarkers. The fabricated sensor showed good selectivity over time and an excellent limit of detection for CRP and ferritin of 6.2 and 4.2 pg/mL, respectively. This research successfully demonstrated that functionalized MXene-based antifouling nanocomposites have great potential to develop high-performance and low-cost immunosensors.

SEA Anemone-inspired Conducting Polymer Sensing Platform for Integrated Detection of Tumor Protein Marker and Circulating Tumor Cell.

Combining the detection of tumor protein markers with the capture of circulating tumor cells (CTCs) represents an ultra-promising approach for early tumor detection. However, current methodologies have not yet achieved the necessary low detection limits and efficient capture. Here, we introduced a novel polypyrrole nanotentacles sensing platform featuring anemone-like structures capable of simultaneously detecting protein biomarkers and capturing CTCs. The incorporation of nanotentacles significantly enhanced the electrode surface area, providing abundant active sites for antibody binding. This enhancement allowed detecting nucleus matrix protein22 (NMP22) and bladder tumor antigen (BTA) with 2.39 and 3.12 pg/mL detection limit, respectively. Furthermore, our developed sensing platform effectively captured MCF-7 cells in blood samples with a detection limit of fewer than 10 cells/mL, attributed to the synergistic multivalent binding facilitated by the specific recognition antibodies and the positive charge on the nanotentacles surface. This sensing platform demonstrated excellent detection capabilities and outstanding capture efficiency, offering a simple, accurate, and efficient strategy for early tumor detection. This article is protected by copyright. All rights reserved.

Optimization of Surface Functionalizations for Ring Resonator-Based Biosensors.

Liquid biopsy is expected to become widespread in the coming years thanks to point of care devices, which can include label-free biosensors. The surface functionalization of biosensors is a crucial aspect that influences their overall performance, resulting in the accurate, sensitive, and specific detection of target molecules. Here, the surface of a microring resonator (MRR)-based biosensor was functionalized for the detection of protein biomarkers. Among the several existing functionalization methods, a strategy based on aptamers and mercaptosilanes was selected as the most highly performing approach. All steps of the functionalization protocol were carefully characterized and optimized to obtain a suitable protocol to be transferred to the final biosensor. The functionalization protocol comprised a preliminary plasma treatment aimed at cleaning and activating the surface for the subsequent silanization step. Different plasma treatments as well as different silanes were tested in order to covalently bind aptamers specific to different biomarker targets, i.e., C-reactive protein, SARS-CoV-2 spike protein, and thrombin. Argon plasma and 1% v/v mercaptosilane were found as the most suitable for obtaining a homogeneous layer apt to aptamer conjugation. The aptamer concentration and time for immobilization were optimized, resulting in 1 µM and 3 h, respectively. A final passivation step based on mercaptohexanol was also implemented. The functionalization protocol was then evaluated for the detection of thrombin with a photonic biosensor based on microring resonators. The preliminary results identified the successful recognition of the correct target as well as some limitations of the developed protocol in real measurement conditions.

Label-free and label-based electrochemical detection of disease biomarker proteins.

Biosensors, analytical devices integrating biological sensing elements with physicochemical transducers, have gained prominence as rapid and convenient tools for monitoring human health status using biochemical analytes. Due to its cost-effectiveness, simplicity, portability, and user-friendliness, electrochemical detection has emerged as a widely adopted method in biosensor applications. Crucially, biosensors enable early disease diagnosis by detecting protein biomarkers associated with various conditions. These biomarkers offer an objective indication of medical conditions that can be accurately observed from outside the patient. This review comprehensively documents both label-free and labelled detection methods in electrochemical biosensor techniques. Label-free detection mechanisms elicit response signals upon analyte molecule binding to the sensor surface, while labelled detection employs molecular labels such as enzymes, nanoparticles, and fluorescent tags. The selection between label-free and labelled detection methods depends on various factors, including the biomolecular compound used, analyte type and biological binding site, biosensor design, sample volume, operational costs, analysis time, and desired detection limit. Focusing on the past six years, this review highlights the application of label-free and labelled electrochemical biosensors for detecting protein biomarkers of diseases.

A novel signal amplified sandwich aptamer-based visual lateral flow assay based on self-assembly bifunctional nucleic acid for rapid and sensitive detection of CKMB

At present, rapid and sensitive detection of disease biomarkers is still the focus of early clinical diagnosis. As a rapid response to point-of-care testing (POCT), lateral flow assay (LFA) has been given serious attention. Unfortunately, due to the sensitivity limitations, LFA, especially AuNPs-based LFA, was difficult to play an important role in the detection of trace biomarkers. The combination of different signal amplification methods increases the complexity of operation and use, or prolongs the detection time, which sacrifices the advantages of fast and convenient of LFA. Hence, a novel sandwich aptamer-based visual LFA based on bifunctional nucleic acid (bFNA-LFA) was proposed for rapid and sensitive detection of creatine kinase MB (CKMB) in this study. Based on hybridization chain reaction (HCR) and nucleic acid hybridization, a bifunctional nucleic acid with target recognition and signal amplification was prepared, which effectively improved the sensitivity of CKMB detection without increasing the reaction time and depending on the detecting equipment. Under optimal reaction conditions, the limit of detection of 7.92 ng/mL was observed, which was 20 times lower than that of sandwich aptamer-based AuNPs LFA in the previous study. The proposed bFNA-LFA assay expanded a new idea in improving the sensitivity of LFA, and provided a reference for the subsequent application of nucleic acid nanomaterials in the detection of protein biomarkers.

Magnetic Silica-Coated Fluorescent Microspheres (MagSiGlow) for Simultaneous Detection of Tumor-Associated Proteins.

Multiplexed bead assays for solution-phase biosensing often encounter cross-over reactions during signal amplification steps, leading to unwanted false positive and high background signals. Current solutions involve complex custom-designed and costly equipment, limiting their application in simple laboratory setup. In this study, we introduce a straightforward protocol to adapt a multiplexed single-bead assay to standard fluorescence imaging plates, enabling the simultaneous analysis of thousands of reactions per plate. This approach focuses on the design and synthesis of bright fluorescent and magnetic microspheres (MagSiGlow) with multiple fluorescent wavelengths serving as unique detection markers. The imaging-based, single-bead assay, combined with a scripted algorithm, allows the detection, segmentation, and co-localization on average of 7500 microspheres per field of view across five imaging channels in less than one second. We demonstrate the effectiveness of this method with remarkable sensitivity at low protein detection limits (100 pg/mL). This technique showed over 85 % reduction in signal cross-over to the solution-based method after the concurrent detection of tumor-associated protein biomarkers. This approach holds the promise of substantially enhancing high throughput biosensing for multiple targets, seamlessly integrating with rapid image analysis algorithms.

Abstract PO2-25-05: Spatial multiplexing of protein biomarkers for immune cell profiling of the tumor microenvironment with ChipCytometry

Abstract Understanding the spatial distribution of key immune cell populations is critical in advancing our understanding of cancer and the development of novel therapeutics. Historically, the spatial analysis of the tumor microenvironment (TME) has been limited to relatively low-plex immunohistochemical (IHC) or immunofluorescent (IF) assays, which were inadequate for deep immune cell profiling of the TME. Here, we present the analysis of fresh-frozen human breast tissue using spatial multiplexing technology called ChipCytometry, which combines iterative immuno-fluorescent staining using open-source antibodies for quantitative measure of virtually unlimited protein biomarkers on the same sample and high dynamic range imaging to facilitate quantitative phenotyping with single-cell resolution. In addition to traditional pathology review of the high-plex dataset, subsequent image analysis can be done using open-source or commercial software for advanced spatial analyses, including cluster analysis, neighborhood analysis and advanced data visualization. The results show precise expression levels for each of the protein biomarkers in the assay for each individual cell within the sample while maintaining spatial information about each cell. Dozens of immune cell subtypes were identified and quantified based on protein expression profiles. Spatial analysis of the samples revealed quantifiable heterogeneity of immune cell infiltration within the tumor samples, demonstrating the utility of the ChipCytometry platform for in-depth immune profiling in clinical samples. The ChipCytometry platform enables simultaneous detection of multiple protein biomarkers on a single tissue section for deep immune cell profiling in the TME. Combined with the single-cell spatial information, such datasets provide an opportunity for the discovery of new complex multiplexed biomarker signatures to inform therapeutic development and personalized medicine. Citation Format: Benton Berigan. Spatial multiplexing of protein biomarkers for immune cell profiling of the tumor microenvironment with ChipCytometry [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-25-05.

Aptamer-based protein molecule detection via cyclic reverse transcription coupling with self-priming hairpin-triggered CRISPR-Cas12a system

Protein biomarkers (e.g. thrombin) are of great significance for the biological process of the organism, and its aberrant expression is closely associated with the development of diseases. With thrombin, a serine protease that plays a crucial role in maintaining homeostasis and promoting blood clotting, as detection target, this study introduces a novel approach for sensitive and accurate measurement of protein biomarker expression by utilization of cyclic reverse transcription (CRT) in combination with the self-priming hairpin-triggered CRISPR-Cas12a system. In this method, an elegantly designed sensing probe is utilized to specifically bind with the thrombin protein and convert the protein signals to nucleic acids signals, following by the CRT and CRISPR-Cas12a system-based signal amplification strategy. Taking the merit of the two-stage amplification, this assay has the capability to detect thrombin at the fM level. In addition, due to the aptamer sequence’s strong selectivity to thrombin protein and the dual-check process in the signal amplification process (first in the CRT and second in the CRISPR system), the proposed test demonstrates exceptional specificity in detecting thrombin. By re-designing the sensing probe, the established method could be extended to various protein biomarker detection. Ultimately, this assay has successfully enabled the accurate evaluation of biomarker levels in constructed clinical samples, showing significant potential for application in the realm of clinical molecular diagnosis.

Highly Reusable Electrochemical Immunosensor for Ultrasensitive Protein Detection

AbstractThe detection and quantification of protein biomarkers in bodily fluids is important for many clinical applications, including disease diagnosis and health monitoring. Current techniques for ultrasensitive protein detection, such as enzyme‐linked immunosorbent assay (ELISA) and electrochemical sensing, involve long incubation times (1.5–3 h) and rely on single‐use sensing electrodes which can be costly and generate excessive waste. This work demonstrates a reusable electrochemical immunosensor employing magnetic nanoparticles (MNPs) and dually labeled gold nanoparticles (AuNPs) for ultrasensitive measurements of protein biomarkers. As proof of concept, this platform is used to detect C‐X‐C motif chemokine ligand 9 (CXCL9), a biomarker associated with kidney transplant rejection, immune nephritis from checkpoint inhibitor therapy, and drug‐associated acute interstitial nephritis, in human urine. The sensor successfully detects CXCL9 at concentrations as low as 27 pg mL−1 within ≈1 h. This immunosensor was also adapted onto a handheld smartphone‐based diagnostic device and used for measurements of CXCL9, which exhibited a lower limit of detection of 65 pg mL−1. Lastly, this work demonstrates that the sensing electrodes can be reused for at least 100 measurements with a negligible loss in analytical performance, reducing the costs and waste associated with electrochemical sensing.

Detection of Protein Biomarkers Relevant to Sperm Characteristics and Fertility in Semen in Three Wild Felidae: The Flat-Headed Cat (Prionailurus planiceps), Fishing Cat (Prionailurus viverrinus), and Asiatic Golden Cat (Catopuma temminckii).

Effective wild cat conservation programs with assisted reproductive technologies are being developed in different parts of the world. The flat-headed cat, fishing cat, and Asiatic golden cat are three species among nine wild Felidae in Thailand that are in need of urgent conservation efforts. Here, we assessed routine sperm characteristics and we report the detection of protein biomarkers related to the fertilization process, IZUMO1 and the CRISP family, and apoptotic markers, active or cleaved caspase-3, in semen samples collected from these wild cats. IZUMO1 was located in the equatorial segment of the sperm head, which is the region involved in gamete interaction. The highest levels of IZUMO1 were found in both the sperm pellet and the seminal plasma of the flat-headed cat, as determined by immunoblotting. CRISP2, a sperm-egg fusion assisting protein, and CRISP3 were found in both the sperm pellet and the seminal plasma, and the highest levels were observed in the fishing cat. Positive correlations between certain semen parameters and IZUMO1, CRISP2, and CRISP3 expression were also demonstrated. Cleaved caspase-3 was found in all sperm samples in all three species and was associated with an increase in DNA fragmentation and a decrease in certain semen characteristics such as motility, viability, and intact acrosomes. Our results suggest that the analysis of IZUMO1, the CRISP family, and cleaved caspase-3, along with the routine sperm characteristics, may allow for better success in breeding management in wild Felidae, particularly in the flat-headed cat and the fishing cat.

Protein biomarker detection via differential dynamic microscopy

We demonstrate a pioneering application of differential dynamic microscopy (DDM) for disease diagnosis by monitoring the dynamic signal of probe beads. When the target antibody binds to our sensitized probe beads, it allows these originally non-fluorescent beads to be indirectly decorated with fluorescently labeled secondary antibodies. Using standard epi-fluorescence microscopy without the need for purification, DDM reliably detects the resulting increase in fluorescence signal from the probe beads. It effectively discerns this signal from the background, which includes residual free fluorescent secondary antibodies. As a proof-of-concept, polystyrene beads (500 nm in diameter) were conjugated with the receptor binding domain of SARS-CoV-2’s spike protein to quantify immunoglobulin G1-specific antibodies against it in three different media of increasing complexity (phosphate buffer, model saliva and fetal bovine serum). Our results show that as the medium becomes more complex, more dilution and/or longer incubation time may be needed to overcome the competition effect between the target and interfering proteins. By optimizing imaging parameters and sample preparation we could surpass clinically relevant limits of detection in both saliva and serum samples. In contrast to conventional diagnostic techniques including ELISA and PCR, DDM brings many advantages including simplicity of the preparation protocol, high speed, and versatility without requiring very expensive or complicated equipment. As such, DDM-based disease diagnostics has the potential to be utilized in many laboratories, especially in remote regions with limited resources and point-of-use applications may also be feasible by miniaturizing the imaging setup.

Dual-Encoded Affinity Microbead Signature Combinatorial Profiling for Acute Myocardial Infarction High-Sensitivity Diagnosis.

The early diagnosis of acute myocardial infarction (AMI) is dependent on the combined feedback of multiple cardiac biomarkers. However, it remains challenging to precisely detect multicardiac biomarkers in complex blood early due to the lack of sensitive and specific diagnostic indicators and the low abundance and small size of associated biomarkers with high specificity (such as microRNAs). To make matters worse, spectral overlap significantly limits the multiplex analysis of cardiac biomarkers by fluorescent probes, leading to bias in the diagnosis of myocardial infarction. Herein, we developed a method for simultaneous detection of miRNAs and protein biomarkers using size- and color-coded microbeads that carry signature for target capture. We also constructed a microfluidic chip with different spacer arrays that segregate these microbeads in different chip regions according to their size to produce signature signals, indicating the level of different biomarkers. The signals on the microbeads were hugely amplified by catalytic hairpin assembly and rolling circle amplification. Notably, this strategy enables the simultaneous and in situ sensitive profiling of six kinds of biomarkers via adding two different fluorescent labels, removing the limitations of spectral overlap. We envision that the strategy has great potential for application in clinical diagnosis for AMI.

Abstract 3789: Discovery of liquid biopsy-based novel protein biomarkers for early detection of breast cancer metastasis

Abstract Introduction and Objectives: Despite recent advances in screening and therapeutic technology, breast cancer is still the first leading cause of cancer death among females. When detected early (i.e., SEER Stage Localized), the 5-yr survival rate is 99%. The 5-yr survival rate is still 86% when cancer cells have spread beyond the breast, but this spread is limited to nearby lymph nodes (SEER Stage Regional). However, when the disease is noted to be SEER Stage Distant or metastasis, the 5-yr survival rate is significantly reduced to 31%. The evidence suggests that breast cancer is manageable if distant metastasis could be prevented. Thus, the prevailing idea is that early detection of breast cancer metastasis in surveillance will likely be the best modality to address advanced breast cancer’s dismal outcomes. Thus, liquid biopsy may be suitable for “early detection” of pre- and/or micro-metastasis because of its ease of obtaining biological material. In this pilot study, we explored the potential biomarkers for the early detection of breast cancer metastasis using publicly available datasets. Methods: We obtained 2 publicly available datasets from GEO (GSE102484 and GSE234114) containing primary tumor samples taken from subjects with and without metastatic disease. Both datasets were generated by mRNA microarray (Affymetrix Human Genome U133 Plus 2.0 Array). With these datasets, we performed the differentially expressed gene (DEG) analysis using GEO2R based on GEOquery and limma (Linear Models for Microarray Analysis) with a threshold criterion of Log 2 fold change &amp;gt;0 and p-value &amp;lt;0.05 as the cut-off point. The significantly upregulated genes were further screened using VerSeDa (Vertebrate Secretome Database) to select secreted proteins. Results: In the GSE102484 (N = 683, 582 non-metastasis and 101 metastasis), DEG identified 1798 upregulated and 1472 downregulated genes. Venn diagram analysis between the upregulated genes and VerSeDa identified 337 upregulated genes coding secreted proteins. In the GSE234114 (N = 120, 60 non-metastasis and 60 metastasis), DEG identified 2873 upregulated and 931 downregulated genes. Venn diagram analysis between the upregulated genes and VerSeDa identified 563 upregulated genes coding secreted proteins. By integrating the genes from GSE102484 and GSE234114, 82 commonly upregulated genes that code secreted proteins were identified. Conclusions: In this study, we identified 82 candidate mRNA biomarkers that are upregulated in breast tumor with metastasis. The panel of biomarkers will be validated in blood-based liquid biopsy samples in the next study. Citation Format: Cynthia Jinno, Sunao Tanaka, Takeo Fujii, Hideki Furuya. Discovery of liquid biopsy-based novel protein biomarkers for early detection of breast cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3789.