A digital single-molecule nanopillar SERS platform for predicting and monitoring immune toxicities in immunotherapy

Deep learning-assisted monitoring of trastuzumab efficacy in HER2-Overexpressing breast cancer via SERS immunoassays of tumor-derived urinary exosomal biomarkers

Monitoring drug efficacy is significant in the current concept of companion diagnostics in metastatic breast cancer. Trastuzumab, a drug targeting human epidermal growth factor receptor 2 (HER2), is an effective treatment for metastatic breast cancer. However, some patients develop resistance to this therapy; therefore, monitoring its efficacy is essential. Here, we describe a deep learning-assisted monitoring of trastuzumab efficacy based on a surface-enhanced Raman spectroscopy (SERS) immunoassay against HER2-overexpressing mouse urinary exosomes. Individual Raman reporters bearing the desired SERS tag and exosome capture substrate were prepared for the SERS immunoassay; SERS tag signals were collected to prepare deep learning training data. Using this deep learning algorithm, various complicated mixtures of SERS tags were successfully quantified and classified. Exosomal antigen levels of five types of cell-derived exosomes were determined using SERS-deep learning analysis and compared with those obtained via quantitative reverse transcription polymerase chain reaction and western blot analysis. Finally, drug efficacy was monitored via SERS-deep learning analysis using urinary exosomes from trastuzumab-treated mice. Use of this monitoring system should allow proactive responses to any treatment-resistant issues.

A novel surface-enhanced Raman based molecular identification platform for multiplexed and highly accurate clinical diagnosis of viral diseases

During the infection process, the interactions among respiratory viruses impact the dynamics of transmission and clinical outcomes. Therefore, efficient molecular detection methods provide a basis for rational drug use and effective health management. Surface-enhanced Raman scattering (SERS) is an ultra-sensitive spectroscopic technique capable of generating extremely narrow spectra (∼1-2 cm-1), enabling simultaneous detection of multiple targets. By judiciously designing plasmonic nanostructures as SERS substrates, Raman signals can be amplified by several orders of magnitude (∼105-1015), facilitating the detection of trace biomolecules. In this highlight, we highlight the work about a novel SERS platform for the high-precision multi-virus molecular identification. This may offer a highly sensitive, specific, and accurate method for the detection of multiple viruses.

iSERS: from nanotag design to protein assays and ex vivo imaging

Proteins are an eminently important class of ubiquitous biomacromolecules with diverse biological functions, and numerous techniques for their detection, quantification, and localisation have been developed. Many of these methods exploit the selectivity arising from molecular recognition of proteins/antigens by immunoglobulins. The combination of surface-enhanced Raman scattering (SERS) with such "immuno"-techniques to immuno-SERS (iSERS) is the central topic of this review, which is focused on colloidal SERS nanotags, i.e., molecularly functionalised noble metal nanoparticles conjugated to antibodies, for their use in protein assays and ex vivo imaging. After contrasting the fundamental differences between label-free SERS and iSERS, including a balanced description of the advantages and drawbacks of the latter, we describe the usual workflow of iSERS experiments. Milestones in the development of the iSERS technology are summarised from a historical perspective. By highlighting selected examples from the literature, we illustrate the conceptual progress that has been achieved in the fields of iSERS-based protein assays and ex vivo imaging. Finally, we attempt to predict what is necessary to fully exploit the transformative potential of the iSERS technology by stimulating the transition from research in academic labs into applications for the benefit of our society.

SERS-based microdevices for use as in vitro diagnostic biosensors

Advances in surface-enhanced Raman scattering (SERS) detection have helped to overcome the limitations of traditional in vitro diagnostic methods, such as fluorescence and chemiluminescence, owing to its high sensitivity and multiplex detection capability. However, for the implementation of SERS detection technology in disease diagnosis, a SERS-based assay platform capable of analyzing clinical samples is essential. Moreover, infectious diseases like COVID-19 require the development of point-of-care (POC) diagnostic technologies that can rapidly and accurately determine infection status. As an effective assay platform, SERS-based bioassays utilize SERS nanotags labeled with protein or DNA receptors on Au or Ag nanoparticles, serving as highly sensitive optical probes. Additionally, a microdevice is necessary as an interface between the target biomolecules and SERS nanotags. This review aims to introduce various microdevices developed for SERS detection, available for POC diagnostics, including LFA strips, microfluidic chips, and microarray chips. Furthermore, the article presents research findings reported in the last 20 years for the SERS-based bioassay of various diseases, such as cancer, cardiovascular diseases, and infectious diseases. Finally, the prospects of SERS bioassays are discussed concerning the integration of SERS-based microdevices and portable Raman readers into POC systems, along with the utilization of artificial intelligence technology.

Fluorescence in depth: integration of spectroscopy and imaging with Raman, IR, and CD for advanced research

Fluorescence spectroscopy serves as a vital technique for studying the interaction between light and fluorescent molecules. It encompasses a range of methods, each presenting unique advantages and applications. This technique finds utility in various chemical studies. This review discusses Fluorescence spectroscopy, its branches such as Time-Resolved Fluorescence Spectroscopy (TRFS) and Fluorescence Lifetime Imaging Microscopy (FLIM), and their integration with other spectroscopic methods, including Raman, Infrared (IR), and Circular Dichroism (CD) spectroscopies. By delving into these methods, we aim to provide a comprehensive understanding of the capabilities and significance of fluorescence spectroscopy in scientific research, highlighting its diverse applications and the enhanced understanding it brings when combined with other spectroscopic methods. This review looks at each technique's unique features and applications. It discusses the prospects of their combined use in advancing scientific understanding and applications across various domains.

Molecular Stratification and Treatment Monitoring of Lung Cancer Using a Small Extracellular Vesicle-Activated Nanocavity Architecture

Development of molecular diagnostics for lung cancer stratification and monitoring is crucial for the rational planning and timely adjustment of treatments to improve clinical outcomes. In this regard, we propose a nanocavity architecture to sensitively profile the protein signature on small extracellular vesicles (sEVs) to enable accurate, noninvasive staging and treatment monitoring of lung cancer. The nanocavity architecture is formed by molecular recognition through the binding of sEVs with the nanobox-based core-shell surface-enhanced Raman scattering (SERS) barcodes and mirrorlike, asymmetric gold microelectrodes. By imposing an alternating current on the gold microelectrodes, a nanofluidic shear force was stimulated that supported the binding of sEVs and the efficient assembly of the nanoboxes. The binding of sEVs further induced a nanocavity between the nanobox and the gold microelectrode that significantly amplified the electromagnetic field to enable the simultaneous enhancement of Raman signals from four SERS barcodes and generate patient-specific molecular sEV signatures. Importantly, evaluated on a cohort of clinical samples (n = 76) on the nanocavity architecture, the acquired patient-specific sEV molecular signatures achieved accurate identification, stratification, and treatment monitoring of lung cancer patients, highlighting its potential for transition to clinical utility.

Adaptive Gap-Tunable Surface-Enhanced Raman Spectroscopy

Gap plasmon (GP) resonance in static surface-enhanced Raman spectroscopy (SERS) structures is generally too narrow and not tunable. Here, we present an adaptive gap-tunable SERS device to selectively enhance and modulate different vibrational modes via active flexible Au nanogaps, with adaptive optical control. The tunability of GP resonance is up to ∼1200 cm-1 by engineering gap width, facilitated by mechanical bending of a polyethylene terephthalate substrate. We confirm that the tuned GP resonance selectively enhances different Raman spectral regions of the molecules. Additionally, we dynamically control the SERS intensity through the wavefront shaping of excitation beams. Furthermore, we demonstrate simulation results, exhibiting the mechanical and optical properties of a one-dimensional flexible nanogap and their advantage in high-speed biomedical sensing. Our work provides a unique approach for observing and controlling the enhanced chemical responses with dynamic tunability.

High Accuracy of Clinical Verification of Electrohydrodynamic-Driven Nanobox-on-Mirror Platform for Molecular Identification of Respiratory Viruses

The molecular detection of multiple respiratory viruses provides evidence for the rational use of drugs and effective health management. Herein, we developed and tested the clinical performance of an electrohydrodynamic-driven nanobox-on-mirror platform (E-NoM) for the parallel, accurate, and sensitive detection of four respiratory viral antigens. The E-NoM platform uses gold-silver alloy nanoboxes as the core material with the deposition of a silver layer as a shell on the core surfaces to amplify and enable a reproducible Raman signal readout that facilitates accurate detection. Additionally, the E-NoM platform employs gold microelectrode arrays as the mirror with electrohydrodynamics to manipulate the fluid flow and enhance molecular interactions for an improved biosensing response. The presence of viral antigens binds the nanobox-based core-shell nanostructure on the gold microelectrode and creates the nanocavity with extremely strong "hot spots" to benefit sensitive analysis. Significantly, in a large clinical cohort with 227 patients, the designed E-NoM platform demonstrates the capability of screening respiratory infection with achieved clinical specificity, sensitivity, and accuracy of 100.0, 96.48, and 96.91%, respectively. It is anticipated that the E-NoM platform can find a position in clinical usage for respiratory disease diagnosis.

Plasmonic substrates for biochemical applications of surface-enhanced Raman spectroscopy

Due to its great practical importance, the detection and determination of many biomolecules in body fluids and other samples is carried out in a large number of laboratories around the world. One of the most promising analytical techniques now being widely introduced into medical analysis is surface-enhanced Raman scattering (SERS) spectroscopy. SERS is one of the most sensitive analytical methods, and in some cases, a good quality SERS spectrum dominated by the contribution of even a single molecule can be obtained. Highly sensitive SERS measurements can only be carried out on substrates generating a very high SERS enhancement factor and a low Raman spectral background, and so using of right nanomaterials is a key element in the success of SERS biochemical analysis. In this review article, we present progress that has been made in the preparation of nanomaterials used in SERS spectroscopy for detecting various kinds of biomolecules. We describe four groups of nanomaterials used in such measurements: nanoparticles of plasmonic metals and deposits of plasmonic nanoparticles on macroscopic substrates, nanocomposites containing plasmonic and non-plasmonic parts, nanostructured macroscopic plasmonic metals, and nanostructured macroscopic non-plasmonic materials covered by plasmonic films. We also describe selected SERS biochemical analyses that utilize the nanomaterials presented. We hope that this review will be useful for researchers starting work in this fascinating field of ​​science and technology.

Amplification-Free Digital Immunoassay down to the Attomolar Level by Synergistic Sedimentation of Brownian Motion Suppression and Dehydration Transfer

Amplification-free digital immunoassays (DIAs) typically utilize optical nanoparticles to enhance single immunocomplex molecule detection. The efficiency and uniformity of transferring the nanoparticles from a bulk solution to a solid surface determine the limit of detection (LOD) and the accuracy of DIAs. Previous methods suffer from issues like low efficiency, nonuniform distribution, and particle aggregation. Here, we present a novel technique named synergistic sedimentation of Brownian motion suppression and dehydration transfer (SynSed) for nanoparticles using water-soluble polymers. The efficiency of transferring quantum dots (QDs) was increased from 10.7 to 91.4%, and the variation in QD distribution was restricted to 8.8%. By incorporating SynSed into DIAs, we achieved a remarkable reduction in the LOD (down to 3.9 aM) for carcinoembryonic antigen and expanded the dynamic range to cover 3 orders of magnitude in concentration, ranging from 0.01 to 10 fM. DIAs enhanced with SynSed possess ultrahigh sensitivity, advanced accuracy, and specificity, offering a great premise in early disease diagnostics, risk stratification, and treatment response monitoring.

Ag triangle nanoplates assembled on PVC/SEBS membrane as flexible SERS substrates for skin cortisol sensing

Surface-enhanced Raman scattering (SERS) based on rigid substrates has been widely used in biomedical detection due to its high sensitivity and specificity. However, the tedious operation steps for preparing SERS rigid substrates limited their applications in real-world detection. Compared with general rigid substrate, the flexible substrate has the advantages of simple preparation and easy portability, which are suitable for rapid, wearable and personalized detection in the field of point-of-care test. Herein, the flexible SERS substrates employing copolymer were fabricated and used for detection of skin cortisol, a biomarker for evaluating psychological stress in sweat. Silver triangle nanoplates with sharp corner were used as enhanced particles, and transferred to polyvinyl chloride/styrene-ethylene-butene-styrene copolymer (PVC/SEBS) film through three-phase interface self-assembly. By adjusting the size of silver nanoparticles, the ratio of PVC to SEBS in the polymer film, and the number of transfers of self-assembled silver films, the enhancement effect of the flexible SERS substrate was maximized. In addition, functionalization of the flexible SERS substrate with cortisol antibodies is used to achieve specific detection of cortisol on the skin surface. Under the optimal conditions, the Raman peak intensities at 1268 and 1500 cm-1 of the cortisol had a good linear relationship with the logarithm of its concentration in the range of 10-7 to 10-3 M, and the detection limits were 5.47 × 10-8 M and 5.51 × 10-8 M, respectively. The flexible silver triangle nanoplates SERS substrate constructed by self-assembly in the three-phase interface has the characteristics of good specificity and high sensitivity, which has potential for transdermal cortisol wearable detection, providing a feasible method for the rapid evaluating psychological stress level.

A universal reagent for detection of emerging diseases using bioengineered multifunctional yeast nanofragments

Accurate and early detection of biomarkers provides the molecular evidence for disease management, allowing prompt actions and timely treatments to save lives. Multivalent biomolecular interactions between the probe and biomarker as well as controlled probe orientation on material surfaces are keys for highly sensitive detection. Here we report the bioengineering of programmable and multifunctional nanoprobes, which can provide rapid, specific and highly sensitive detection of emerging diseases in a range of widely used diagnostic systems. These nanoprobes composed of nanosized cell wall fragments, termed as synthetic bionanofragments (SynBioNFs), are generated by the fragmentation of genetically programmed yeast cells. SynBioNFs display multiple copies of biomolecules for high-affinity target binding and molecular handles for the precisely orientated attachment on surfaces used in diagnostic platforms. SynBioNFs are demonstrated for the capture and detection of SARS-CoV-2 virions using multiple diagnostic platforms, including surface-enhanced Raman scattering, fluorescence, electrochemical and colorimetric-based lateral flow systems with sensitivity comparable with the gold-standard reverse-transcription quantitative polymerase chain reaction.

Aggregation enhanced fluorescence and Raman signals for highly sensitive cancer detection

The implementation of early cancer detection benefits the treatment outcomes with remarkably improved survival rate through the detection of rare circulating biomarkers in body fluids. Spectroscopic technologies play a crucial role in sensitive biomarker measurements by outputting extremely strong signals. In particular, the aggregation enhanced fluorescence and Raman technologies feature the detection of targets down to single-molecule level, thereby demonstrating the great promise of early cancer detection. In this review, we focus on the aggregation-induced emission (AIE) and aggregation-related surface-enhanced Raman scattering (SERS) spectroscopic strategies for detecting cancer biomarkers. We discuss the AIE and SERS based biomarker detection using target-driven aggregation as well as the aggregated nanoprobes. Furthermore, we deliberate on the progress of developing AIE and SERS integrated platforms. Ultimately, we put forth the potential challenges and perspectives on the way to use these two spectroscopic technologies in clinical settings. It is expected this review can inspire the design of AIE and SERS integrated platform for highly sensitive and accurate cancer detection.

Single-Cell Analysis and Classification according to Multiplexed Proteins via Microdroplet-Based Self-Driven Magnetic Surface-Enhanced Raman Spectroscopy Platforms Assisted with Machine Learning Algorithms

A microdroplet-based surface-enhanced Raman spectroscopy (microdroplet SERS) platform was constructed to envelop individual cells in microdroplets, followed by the SERS detection of their extracellular vesicle-proteins (EV-proteins) via the in-drop immunoassays by use of immunomagnetic beads (iMBs) and immuno-SERS tags (iSERS tags). A unique phenomenon is found that iMBs can start a spontaneous reorientation on the probed cell surface based on the electrostatic force-driven interfacial aggregation effect, which leads EV-proteins and iSERS tags to be gathered from a liquid phase to a cell membrane interface and significantly improves SERS sensitivity to the single-cell analysis level due to the formation of numbers of SERS hotspots. Three EV-proteins from two breast cancer cell lines were collected and further analyzed by machine learning algorithmic tools, which will be helpful for a deeper understanding of breast cancer subtypes from the view of EV-proteins.

Design of Raman reporter-embedded magnetic/plasmonic hybrid nanostirrers for reliable microfluidic SERS biosensors

Magnetic-based microfluidic SERS biosensors hold great potential in various biological analyses due to their integrated advantages including easy manipulation, miniaturization and ultrasensitivity. However, it remains challenging to collect reliable SERS nanoprobe signals for quantitative analysis due to the irregular aggregation of magnetic carriers in a microfluidic chamber. Here, magnetic/plasmonic hybrid nanostirrers embedded with a Raman reporter are developed as capture carriers to improve the reliability of microfluidic SERS biosensors. Experimental results revealed that SERS signals from magnetic hybrid nanostirrers could serve as microenvironment beacons of their irregular aggregation, and a signal filtering method was proposed through exploring the relationship between the intensity range of beacons and the signal reproducibility of SERS nanoprobes using interleukin 6 as a model target analyte. Using the signal filtering method, reliable SERS nanoprobe signals with high reproducibility could be picked out from similar microenvironments according to their beacon intensity, and then the influence of irregular aggregation of magnetic carriers on the SERS nanoprobe could be eliminated. The filtered SERS nanoprobe signals also exhibited excellent repeatability from independent tests, which lay a solid foundation for a reliable working curve and subsequent accurate bioassay. This study provides a simple but promising route for reliable microfluidic SERS biosensors, which will further promote their practical application in biological analysis.

Fabrication of flexible AuNPs@ polyimide heating chips for in situ explosives SERS sensing in nature samples

In this study, highly sensitive flexible AuNPs@ polyimide SERS heating chips (APHC) were fabricated for in situ collecting and detecting TNT. Large-scale AuNPs arrays were synthesized by liquid-liquid interface self-assembly and transferred to polyimide heating film as SERS substrates. 4-ATP and AgNPs functionalized on APHC were used as capture means and signal amplifiers, combining with TNT to form the AuNPs-TNT-AgNPs "sandwich" structure. This flexible APHC chip showed high sensitivity as enhancement factor was 5.5×10⁵, and good repeatability and stability (RSD<10%). It was applied to detect TNT solutions with a low concentration of 10^-9 M, and showed a good linear response in the range from 10^-5 to 10^-9 M (R² = 0.986). In addition, the detection method also had good selectivity and no response to various TNT analogs. More important, combing with the thermal enrichment strategy, TNT dispersed in environmental samples such as soil, fruit and clothing would be enriched as vapor then collected and detected by APHC. This APHC device shows great potential for in situ sensing platforms, due to its sensitivity, high efficiency, and excellent portability.

Nanowire-in-bowl-shaped piezoelectric cavity structure for SERS directional detection of nanoplastics less than 50 nm

The accurate detection of nanoplastics is crucial due to their harmful effects on the environment and human beings. However, there is a lack of detection methods for nanoplastics smaller than 50 nm. In this research, we successfully constructed an Ag/CuO nanowire (NW)/BaTiO₃@Polyvinylidene fluoride (PVDF) Bowl-shaped substrate with a nanowire-in-Bowl-shaped piezoelectric cavity structure that can modulate surface-enhanced Raman scattering (SERS) by the piezoelectric effect by the virtue of the tip effect of the CuO NW and light focusing effect of the Bowl-shaped cavity. Due to its unique nanowire-in-Bowl-shaped structure and piezoelectrically modifiable ability, nanoplastics less than 50 nm were successfully detected and quantitatively analyzed. We believe that the Ag/CuO NW/BaTiO₃@PVDF Bowl-shaped substrate can provide an efficient, accurate, and feasible way to achieve qualitative and quantitative detection of nanoplastics.

Double-sided plasmonic metasurface for simultaneous biomolecular separation and SERS detection

Porous membrane-based nanofiltration separation of small biomolecules is a widely used biotechnology for which size-based selectivity is a critical parameter of technological relevance. Efficient determination of size selectivity calls for an advanced detection method capable of performing sensitive, rapid, and on-membrane examination. Surface-enhanced Raman spectroscopy (SERS) is such a detection method that has been widely recognized as an ultrasensitive technique for trace-level detection with sensitivity down to the single-molecule level. In this work, we for the first time develop a double-sided hierarchical porous membrane-like plasmonic metasurface to realize high-selectivity bimolecular separation and simultaneous ultrasensitive SERS detection. This highly flexible device, consisting of subwavelength nanocone pairs surrounded by randomly orientated sub-5 nm nanogrooves, was prepared by combining customized "top-down" fabrication of conical nanopores in an ion-track registered polycarbonate membrane and self-assembly of nanogrooves on the membrane surface through physical vapor deposition. The unique tip-to-tip oriented conical nanopores in the device enables excellent size-based molecular selectivity; the hierarchical groove-pore structure supports a peculiar cascaded electromagnetic near-field enhancement mechanism, endowing the device with SERS-based molecular detection of ultrahigh sensitivity, uniformity, repeatability, and polarization independence. With such dual structural merits and performance enhancement, we demonstrate effective nanofiltration separation of small-sized adenine from big-sized ss-DNA and synergistic SERS determination of their species. We experimentally demonstrate an ultrasensitive detection of 4-mercaptopyridine down to 10 pM. Together with its unparalleled mechanical flexibility, this double-side-responsive plasmonic metasurface membrane can find great potential in real-world molecular filtration and detection under extremely complex working conditions.

Advances in optical counting and imaging of micro/nano single-entity reactors for biomolecular analysis

Ultrasensitive detection of biomarkers is of paramount importance in various fields. Superior to the conventional ensemble measurement-based assays, single-entity assays, especially single-entity detection-based digital assays, not only can reach ultrahigh sensitivity, but also possess the potential to examine the heterogeneities among the individual target molecules within a population. In this review, we summarized the current biomolecular analysis methods that based on optical counting and imaging of the micro/nano-sized single entities that act as the individual reactors (e.g., micro-/nanoparticles, microemulsions, and microwells). We categorize the corresponding techniques as analog and digital single-entity assays and provide detailed information such as the design principles, the analytical performance, and their implementation in biomarker analysis in this work. We have also set critical comments on each technique from these aspects. At last, we reflect on the advantages and limitations of the optical single-entity counting and imaging methods for biomolecular assay and highlight future opportunities in this field.

Ultrasensitive Optical Fingerprinting of Biorelevant Molecules by Means of SERS-Mapping on Nanostructured Metasurfaces

The most relevant technique for portable (on-chip) sensors is Surface Enhanced Raman Scattering (SERS). This strategy crashes in the case of large (biorelevant) molecules and nano-objects, whose SERS spectra are irreproducible for "homeopathic" concentrations. We suggested solving this problem by SERS-mapping. We analyzed the distributions of SERS parameters for relatively "small" (malachite green (MG)) and "large" (phthalocyanine, H₂Pc*) molecules. While fluctuations of spectra for "small" MG were negligible, noticeable distribution of spectra was observed for "large" H₂Pc*. We show that the latter is due to a random arrangement of molecules with respect to "hot spot" areas, which have limited sizes, thus amplifying the lines corresponding to vibrations of different molecule parts. We have developed a method for engineering low-cost SERS substrates optimized for the best enhancement efficiency and a measurement protocol to obtain a reliable Raman spectrum, even for a countable number of large molecules randomly distributed over the substrate.

Gold Nanourchins Improve Virus Targeting and Plasmonic Coupling for Virus Diagnosis on a Smartphone Platform

Point-of-care detection of pathogens is critical to monitor and combat viral infections. The plasmonic coupling assay (PCA) is a homogeneous assay and allows rapid, one-step, and colorimetric detection of intact viruses. However, PCA lacks sufficient sensitivity, necessitating further mechanistic studies to improve the detection performance of PCA. Here, we demonstrate that gold nanourchins (AuNUs) provide significantly improved colorimetric detection of viruses in PCA. Using respiratory syncytial virus (RSV) as a target, we demonstrate that the AuNU-based PCA achieves a detection limit of 1400 PFU/mL, or 17 genome equivalent copies/μL. Mechanistic studies suggest that the improved detection sensitivity arises from the higher virus-binding capability and stronger plasmonic coupling at long distances (∼10 nm) by AuNU probes. Furthermore, we demonstrate the virus detection with a portable smartphone-based spectrometer using RSV-spiked nasal swab clinical samples. Our study uncovers important mechanisms for the sensitive detection of intact viruses in PCA and provides a potential toolkit at the point of care.

Antibiotic Susceptibility Testing with Raman Biosensing

Antibiotics guard us against bacterial infections and are among the most commonly used medicines. The immediate consequence of their large-scale production and prescription is the development of antibiotic resistance. Therefore, rapid detection of antibiotic susceptibility is required for efficient antimicrobial therapy. One of the promising methods for rapid antibiotic susceptibility testing is Raman spectroscopy. Raman spectroscopy combines fast and contactless acquisition of spectra with good selectivity towards bacterial cells. The antibiotic-induced changes in bacterial cell physiology are detected as distinct features in Raman spectra and can be associated with antibiotic susceptibility. Therefore, the Raman-based approach may be beneficial in designing therapy against multidrug-resistant infections. The surface-enhanced Raman spectroscopy (SERS) and resonance Raman spectroscopy (RRS) additionally provide excellent sensitivity. In this review, we present an analysis of the Raman spectroscopy-based optical biosensing approaches aimed at antibiotic susceptibility testing.

Toward Quantitative Surface-Enhanced Raman Scattering with Plasmonic Nanoparticles: Multiscale View on Heterogeneities in Particle Morphology, Surface Modification, Interface, and Analytical Protocols

Surface-enhanced Raman scattering (SERS) provides significantly enhanced Raman scattering signals from molecules adsorbed on plasmonic nanostructures, as well as the molecules' vibrational fingerprints. Plasmonic nanoparticle systems are particularly powerful for SERS substrates as they provide a wide range of structural features and plasmonic couplings to boost the enhancement, often up to >10⁸-10¹⁰. Nevertheless, nanoparticle-based SERS is not widely utilized as a means for reliable quantitative measurement of molecules largely due to limited controllability, uniformity, and scalability of plasmonic nanoparticles, poor molecular modification chemistry, and a lack of widely used analytical protocols for SERS. Furthermore, multiscale issues with plasmonic nanoparticle systems that range from atomic and molecular scales to assembled nanostructure scale are difficult to simultaneously control, analyze, and address. In this perspective, we introduce and discuss the design principles and key issues in preparing SERS nanoparticle substrates and the recent studies on the uniform and controllable synthesis and newly emerging machine learning-based analysis of plasmonic nanoparticle systems for quantitative SERS. Specifically, the multiscale point of view with plasmonic nanoparticle systems toward quantitative SERS is provided throughout this perspective. Furthermore, issues with correctly estimating and comparing SERS enhancement factors are discussed, and newly emerging statistical and artificial intelligence approaches for analyzing complex SERS systems are introduced and scrutinized to address challenges that cannot be fully resolved through synthetic improvements.

Single-Particle Optical Imaging for Ultrasensitive Bioanalysis

The quantitative detection of critical biomolecules and in particular low-abundance biomarkers in biofluids is crucial for early-stage diagnosis and management but remains a challenge largely owing to the insufficient sensitivity of existing ensemble-sensing methods. The single-particle imaging technique has emerged as an important tool to analyze ultralow-abundance biomolecules by engineering and exploiting the distinct physical and chemical property of individual luminescent particles. In this review, we focus and survey the latest advances in single-particle optical imaging (OSPI) for ultrasensitive bioanalysis pertaining to basic biological studies and clinical applications. We first introduce state-of-the-art OSPI techniques, including fluorescence, surface-enhanced Raman scattering, electrochemiluminescence, and dark-field scattering, with emphasis on the contributions of various metal and nonmetal nano-labels to the improvement of the signal-to-noise ratio. During the discussion of individual techniques, we also highlight their applications in spatial-temporal measurement of key biomarkers such as proteins, nucleic acids and extracellular vesicles with single-entity sensitivity. To that end, we discuss the current challenges and prospective trends of single-particle optical-imaging-based bioanalysis.

Digital Decoding of Single Extracellular Vesicle Phenotype Differentiates Early Malignant and Benign Lung Lesions

Accurate identification of malignant lung lesions is a prerequisite for rational clinical management to reduce morbidity and mortality of lung cancer. However, classification of lung nodules into malignant and benign cases is difficult as they show similar features in computer tomography and sometimes positron emission tomography imaging, making invasive tissue biopsies necessary. To address the challenges in evaluating indeterminate nodules, the authors investigate the molecular profiles of small extracellular vesicles (sEVs) in differentiating malignant and benign lung nodules via a liquid biopsy-based approach. Aiming to characterize phenotypes between malignant and benign groups, they develop a single-molecule-resolution-digital-sEV-counting-detection (DECODE) chip that interrogates three lung-cancer-associated sEV biomarkers and a generic sEV biomarker to create sEV molecular profiles. DECODE capturessEVs on a nanostructured pillar chip, confines individual sEVs, and profiles sEV biomarker expression through surface-enhanced Raman scattering barcodes. The author utilize DECODE to generate a digitally acquired sEV molecular profiles in a cohort of 33 people, including patients with malignant and benign lung nodules, and healthy individuals. Significantly, DECODE reveals sEV-specific molecular profiles that allow the separation of malignant from benign (area under the curve, AUC = 0.85), which is promising for non-invasive characterisation of lung nodules found in lung cancer screening and warrants further clinincal validaiton with larger cohorts.

Emerging SERS biosensors for the analysis of cells and extracellular vesicles

Cells and their derived extracellular vesicles (EVs) or exosomes contain unique molecular signatures that could be used as biomarkers for the detection of severe diseases such as cancer, as well as monitoring the treatment response. Revealing these molecular signatures requires developing non-invasive ultrasensitive tools to enable single molecule/cell-level detection using a small volume of sample with low signal-to-noise ratio background and multiplex capability. Surface-enhanced Raman scattering (SERS) can address the current limitations in studying cells and EVs through two main mechanisms: plasmon-enhanced electric field (the so-called electromagnetic mechanism (EM)), and chemical mechanism (CM). In this review, we first highlight these two SERS mechanisms and then discuss the nanomaterials that have been used to develop SERS biosensors based on each of the aforementioned mechanisms as well as the combination of these two mechanisms in order to take advantage of the synergic effect between electromagnetic enhancement and chemical enhancement. Then, we review the recent advances in designing label-aided and label-free SERS biosensors in both colloidal and planar systems to investigate the surface biomarkers on cancer cells and their derived EVs. Finally, we discuss perspectives of emerging SERS biosensors in future biomedical applications. We believe this review article will thus appeal to researchers in the field of nanobiotechnology including material sciences, biosensors, and biomedical fields.

SERS Multiplex Profiling of Melanoma Circulating Tumor Cells for Predicting the Response to Immune Checkpoint Blockade Therapy

Immune checkpoint blockade (ICB) therapy has achieved remarkable success in many cancers including melanoma. However, ICB therapy benefits only a small proportion of patients and produces severe side effects for some patients. Thus, there is an urgent need to identify patients who are more likely to respond to ICB therapy to improve outcomes and minimize side effects. To predict ICB therapy responses, we design a surface-enhanced Raman scattering (SERS) assay for multiplex profiling of circulating tumor cells (CTCs) under basal and interferon-γ (IFN-γ) stimulation. Through simultaneous ensemble and single-cell measurements of CTCs, the SERS assay can reveal tumor heterogeneity and offer a comprehensive CTC phenotype for decision-making. Anisotropic gold-silver alloy nanoboxes are utilized as SERS plasmonic substrates for improved signal readouts of CTC surface biomarkers. By generating a unique CTC signature with four surface biomarkers, the developed assay enables the differentiation of CTCs from three different patient-derived melanoma cell lines. Significantly, in a cohort of 14 melanoma patients who received programmed cell death-1 blockade therapy, the changes of CTC signature induced by IFN-γ stimulation to CTCs show the potential to predict responders. We expect that the SERS assay can help select patients for receiving ICB therapy in other cancers.

Detection of Dengue Virus 2 with Single Infected Mosquito Resolution Using Yeast Affinity Bionanofragments and Plasmonic SERS Nanoboxes

Dengue disease is an emerging global threat triggered by dengue virus (DENV) transmission, primarily by the mosquito Aedes aegypti. The accurate surveillance and sensitive detection of DENV in mosquito populations are critical for the protection of human populations worldwide that are in the habitat of these mosquito species. There are four DENV serotypes with DENV2 reported to cause the most severe complications. There are limited ultrasensitive methods to early detect DENV2 mosquito infection and prevent human infection. Herein, we report an innovative nanobased immunoassay platform for early, specific, and ultrasensitive detection of DENV2-secreted nonstructural 1 (NS1) protein biomarker in single infected mosquitoes with the limit of detection of 500 fg of recombinant DENV2 NS1. The high sensitivity and DENV2 serotype specificity of the platform are the result of using nanomixing, plasmonic SERS nanoboxes, and yeast affinity bionanofragments displaying single-chain variable fragments (nanoyeast scFvs). Nanoyeast scFvs used for high affinity capture of DENV2 NS1 provided an innovative and cost-efficient alternative to monoclonal antibodies and differentiated DENV2 NS1 from other DENV serotypes and Zika virus NS1. The platform used electrohydrodynamically driven nanomixing to enhance NS1 capture by the nanoyeast scFvs while reducing nonspecific interactions. High sensitivity detection of captured DENV2 NS1 was achieved using NS1-specific surface-enhanced Raman scattering (SERS) nanotags. These nanotechnologies provide a significant innovation for early DENV2 detection in single infected mosquitoes, improving the accurate surveillance of mosquito habitats and preventing infection and severe disease arising from DENV2 transmission.

Integrated microfluidic-SERS for exosome biomarker profiling and osteosarcoma diagnosis

Osteosarcoma is one of the most frequent primary sarcoma of bone among adolescents. Early diagnosis of osteosarcoma is the key factor to achieve high survival rate of patients. Nevertheless, traditional histological biopsy is highly invasive and associated with the risk of arousing tumor spread. Herein, we develop a method integrating microfluidics and surface-enhanced Raman spectroscopy (SERS) to isolate plasma-derived exosomes and profile multiple exosomal biomarkers for the diagnosis of osteosarcoma. The method showed highly efficient isolation of exosomes directly from human plasma and can profile exosomes based on protein biomarkers, with the detection limit down to 2 exosomes per μL. The whole assay can be performed in 5 h and only consumed 50 μL of plasma for one analysis. With the method, we analyzed the level of three protein biomarkers, i.e., CD63, vimentin (VIM) and epithelial cell adhesion molecule (EpCAM), on plasma-derived exosomes from 20 osteosarcoma patients and 20 heathy controls. Significantly higher levels of CD63, VIM and EpCAM were observed on plasma exosomes from the osteosarcoma patients compared to the healthy controls. Based on the level of the exosomal biomarkers, a classification model was built for the rapid diagnosis of osteosarcoma, with the sensitivity, specificity and accuracy of 100%, 90% and 95%, respectively. The proposed method does not require complex operations nor expensive equipment, and has great promise in clinical diagnosis of cancer as a liquid biopsy technique.

Highly Sensitive Serum Protein Analysis Using Magnetic Bead-Based Proximity Extension Assay

Many protein biomarkers are present in biofluids at a very low level but may play critical roles in important biological processes. The fact that these low-abundance proteins remain largely unexplored underscores the importance of developing new tools for highly sensitive protein detection. Although digital enzyme-linked immunosorbent assay (ELISA) has demonstrated ultrahigh sensitivity compared with conventional ELISA, the requirement of specialized instruments limits the accessibility and prevents the widespread implementation. On the other hand, proximity ligation assays (PLA) and proximity extension assays (PEA) show sensitive and specific protein detection using regular laboratory setups, but their sensitivity needs to be further improved to match digital ELISA. To achieve highly sensitive protein detection with minimal accessibility limitation, we develop a magnetic bead-based PEA (magPEA), which posts triple epitope recognition requirement and enables extensive washing for improved sensitivity and enhanced specificity. We demonstrate that the incorporation of magnetic beads into PEA workflow facilitates orders of magnitude sensitivity improvement compared with conventional ELISA, homogeneous PEA, and solid-phase PLA and achieves limits of detection close to that of digital ELISA when using IL-6, IL-8, and GM-CSF as validation. Our magPEA provides a simple approach for highly sensitive protein detection that can be readily implemented to other laboratories and will thus ultimately accelerate the study of the low abundance protein biomarkers in the future.

Recent Advances in Digital Biosensing Technology

Digital biosensing assays demonstrate remarkable advantages over conventional biosensing systems because of their ability to achieve single-molecule detection and absolute quantification. Unlike traditional low-abundance biomarking screening, digital-based biosensing systems reduce sample volumes significantly to the fL-nL level, which vastly reduces overall reagent consumption, improves reaction time and throughput, and enables high sensitivity and single target detection. This review presents the current technology for compartmentalizing reactions and their applications in detecting proteins and nucleic acids. We also analyze existing challenges and future opportunities associated with digital biosensing and research opportunities for developing integrated digital biosensing systems.

Effect of synthesis time on plasmonic properties of Ag dendritic nanoforests

The effects of synthesis time on the plasmonic properties of Ag dendritic nanoforests on Si substrate (Ag-DNF/Si) samples synthesized through the fluoride-assisted galvanic replacement reaction were investigated. The Ag-DNF/Si samples were characterized using scanning electron microscopy, energy-dispersive X-ray spectroscopy, reflection spectroscopy, X-ray diffraction and surface-enhanced Raman spectroscopy (SERS). The prolonged reaction time led to the growth of an Ag-DNF layer and etched Si hole array. SEM images and variations in the fractal dimension index indicated that complex-structure, feather-like leaves became coral-like branches between 30 and 60 min of synthesis. The morphological variation during the growth of the Ag DNFs resulted in different optical responses to light illumination, especially those of light harvest and energy transformation. The sample achieved the most desirable light-to-heat conversion efficiency and SERS response with a 30 min growth time. A longer synthesis time or thicker Ag-DNF layer on the Si substrate did not have superior plasmonic properties.

Wafer-scale nanocracks enable single-molecule detection and on-site analysis

Large-area surface-enhanced Raman spectroscopy (SERS) sensing platforms displaying ultrahigh sensitivity and signal uniformity have potentially enormous sensing applicability, but they are still challenging to prepare in a scalable manner. In this study, silver nanopaste (AgNPA) was employed to prepare a wafer-scale, ultrasensitive SERS substrate. The self-generated, high-density Ag nanocracks (NCKs) with small gaps could be created on Si wafers via a spin-coating process, and provided extremely abundant hotspots for SERS analyses with ultrahigh sensitivity-down to the level of single molecules (enhancement factor: ca. 10¹⁰; detection limit: ca. 10^-18 M)-and great signal reproducibility (variation: ca. 3.6%). Moreover, the Ag NCK arrays demonstrated broad applicability and practicability for on-site detection when combined with a portable 785 Raman spectrometer. This method allowed the highly sensitive detection of a diverse range of analytes (benzo[a]pyrene, di-2-ethylhexyl phthalate, aflatoxins B1, zearalenone, ractopamine, salbutamol, sildenafil, thiram, dimethoate, and methamidophos). In particular, pesticides are used extensively in agricultural production. Unfortunately, they can affect the environment and human health as a result of acute toxicity. Therefore, the simultaneous label-free detection of three different pesticides was demonstrated. Finally, the SERS substrates are fabricated through a simple, efficient, and scalable process that offers new opportunities for mass production.

An Electrochemical and Raman Scattering Dual Detection Biosensor for Rapid Screening and Biomolecular Profiling of Cancer Biomarkers

Detecting circulating biomarkers sensitively and quantitatively is paramount for cancer screening, diagnosis, and treatment selection. Particularly, screening of a panel of circulating protein biomarkers followed by mapping of individual biomarkers could assist better diagnosis and understanding of the cancer progression mechanisms. Herein, we present a miniaturized biosensing platform with dual readout schemes (electrochemical and Surface enhanced Raman scattering (SERS)) for rapid cancer screening and specific biomarker expressional profiling to support cancer management. Our approach utilizes a controlled nanomixing phenomena under alternative current electrohydrodynamic condition to improve the isolation of cancer-associated circulating proteins (i.e., Epidermal growth factor receptor (EGFR), BRAF, Programmed death-ligand 1 (PD-L1)) with antibody functionalized sensor surface for rapid and efficient isolation of the targets and subsequent labelling with SERS nanotags. The method employs Differential Pulse Voltammetry (DPV) for rapidly screening for the presence of the circulating proteins on biosensor surface irrespective of their type. Upon positive DPV detection, SERS is applied for sensitive read-out of individual biomarkers biomarker levels. In a proof-of-concept study, we demonstrate the dual detection biosensor for analysing circulating BRAF, EGFR and PDL-1 proteins and successfully screened both ensemble and individual biomarker expressional levels as low as 10 pg (1 ng/mL). Our findings clearly indicate the potential of the proposed method for cancer biomarker analysis which may drive the translation of this dual sensing concept in clinical settings.

Prospects of Surface-Enhanced Raman Spectroscopy for Biomarker Monitoring toward Precision Medicine

Future precision medicine will be undoubtedly sustained by the detection of validated biomarkers that enable a precise classification of patients based on their predicted disease risk, prognosis, and response to a specific treatment. Up to now, genomics, transcriptomics, and immunohistochemistry have been the main clinically amenable tools at hand for identifying key diagnostic, prognostic, and predictive biomarkers. However, other molecular strategies, including metabolomics, are still in their infancy and require the development of new biomarker detection technologies, toward routine implementation into clinical diagnosis. In this context, surface-enhanced Raman scattering (SERS) spectroscopy has been recognized as a promising technology for clinical monitoring thanks to its high sensitivity and label-free operation, which should help accelerate the discovery of biomarkers and their corresponding screening in a simpler, faster, and less-expensive manner. Many studies have demonstrated the excellent performance of SERS in biomedical applications. However, such studies have also revealed several variables that should be considered for accurate SERS monitoring, in particular, when the signal is collected from biological sources (tissues, cells or biofluids). This Perspective is aimed at piecing together the puzzle of SERS in biomarker monitoring, with a view on future challenges and implications. We address the most relevant requirements of plasmonic substrates for biomedical applications, as well as the implementation of tools from artificial intelligence or biotechnology to guide the development of highly versatile sensors.

Raman spectrum classification based on transfer learning by a convolutional neural network: Application to pesticide detection

Pesticide detection is of tremendous importance in agriculture, and Raman spectroscopy/Surface-Enhanced Raman Scattering (SERS) has proven extremely effective as a stand-alone method to detect pesticide residues. Machine learning may be able to automate such detection, but conventional algorithms require a complete database of Raman spectra, which is not feasible. To bypass this problem, the present study describes a transfer learning method that improves the algorithm's accuracy and speed to extract features and classify Raman spectra. The transfer learning model described here was developed through the following steps: (1) the classification model was pre-trained using an open-source Raman spectroscopy database; (2) the feature extraction layer was saved after training; and (3) the training model for the Raman spectroscopy database was re-established while using self-tested pesticides and keeping the feature extraction layer unchanged. Three models were evaluated with or without transfer learning: CNN-1D, Resnet-1D, and Inception-1D, and they have improved the accuracy of spectrum classification by 6%, 2%, and 3%, with reduced training time and increased curve smoothness. These results suggest that transfer learning can improve the feature extraction capability and therefore accuracy of Raman spectroscopy models, expanding the range of Raman-based applications where transfer learning model can be used to identify the spectra of different substances.

Magnetically Enhanced Liquid SERS for Ultrasensitive Analysis of Bacterial and SARS-CoV-2 Biomarkers

In this work, it is shown that surface-enhanced Raman scattering (SERS) measurements can be performed using liquid platforms to perform bioanalysis at sub-pM concentrations. Using magnetic enrichment with gold-coated magnetic nanoparticles, the high sensitivity was verified with nucleic acid and protein targets. The former was performed with a DNA fragment associated with the bacteria Staphylococcus aureus, and the latter using IgG antibody, a biomarker for COVID-19 screening. It is anticipated that this work will inspire studies on ultrasensitive SERS analyzers suitable for large-scale applications, which is particularly important for in vitro diagnostics and environmental studies.

Highly specific detection of KRAS single nucleotide polymorphism by asymmetric PCR/SERS assay

The molecular diagnosis of KRAS mutations has become crucial for clinical decision-making in colorectal cancer (CRC) treatments. Currently, the common methods for detecting mutations are based on quantitative PCR, DNA sequencing and droplet digital PCR (ddPCR), which require expensive specialized equipment and testing reagents. Herein, we propose a simple and specific strategy by integrating asymmetric PCR with surface-enhanced Raman spectroscopy (Asy-PCR/SERS) for the detection of KRAS G12V mutation, one of the most common driver mutations in CRC. To discriminate mutant targets from non-targets, Asy-PCR was applied to obtain single-stranded DNA (ssDNA) with unequal amounts of forward and reverse primers, subsequently, detection of the target mutant ssDNA amplicons was attempted by hybridization with Raman reporter-coded and allele-specific oligonucleotide-functionalized gold nanoparticles (SERS nanotags). The oligo encoding of the KRAS G12V mutant sequence could be identified by using a portable Raman spectrometer where the characteristic spectra of SERS nanotags indicate the presence of mutant targets. The Asy-PCR/SERS method showed high specificity and sensitivity for identifying as few as 0.1% mutant alleles of KRAS G12V mutation from non-target sequences. Using colorectal polyp biopsies, we demonstrated that Asy-PCR/SERS assay could distinguish KRAS G12V (c.35G > T) and KRAS G12D (c.35G > A) which occur at the same nucleotide location. As KRAS G12V is a driver oncogene in other cancers including lung, pancreatic, ovarian and endometrial cancers, the proposed assay shows great potential for application in additional tumor streams.

Amplification-Free SARS-CoV-2 Detection Using Nanoyeast-scFv and Ultrasensitive Plasmonic Nanobox-Integrated Nanomixing Microassay

The implementation of accurate and sensitive molecular detection for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is paramount to effectively control the ongoing coronavirus disease 2019 (COVID-19) pandemic. In this regard, we herein propose the specific and highly sensitive SARS-CoV-2 detection based on nanoyeast single-chain-variable fragment (scFv) and ultrasensitive plasmonic nanobox-integrated nanomixing microassay. Importantly, this designed platform showcases the utility of nanoyeast-scFvs as specific capture reagents targeting the receptor-binding domain (RBD) of the virus and as monoclonal antibody alternatives suitable for cost-effective mass production and frequent testing. By capitalizing on single-particle active nanoboxes as plasmonic nanostructures for surface-enhanced Raman scattering (SERS), the microassay utilizes highly sensitive Raman signals to indicate virus infection. The developed microassay further integrated nanomixing for accelerating molecular collisions. Through the synergistic working of nanoyeast-scFv, plasmonic nanoboxes, and nanomixing, the highly specific and sensitive SARS-CoV-2 detection is achieved as low as 17 virus/μL without any molecular amplification. We successfully demonstrate SARS-CoV-2 detection in saliva samples of simulated patients at clinically relevant viral loads, suggesting the possibility of this platform for accurate and noninvasive patient screening.

Development of EndoScreen Chip, a Microfluidic Pre-Endoscopy Triage Test for Esophageal Adenocarcinoma

The current endoscopy and biopsy diagnosis of esophageal adenocarcinoma (EAC) and its premalignant condition Barrett's esophagus (BE) is not cost-effective. To enable EAC screening and patient triaging for endoscopy, we developed a microfluidic lectin immunoassay, the EndoScreen Chip, which allows sensitive multiplex serum biomarker measurements. Here, we report the proof-of-concept deployment for the EAC biomarker Jacalin lectin binding complement C9 (JAC-C9), which we previously discovered and validated by mass spectrometry. A monoclonal C9 antibody (m26 3C9) was generated and validated in microplate ELISA, and then deployed for JAC-C9 measurement on EndoScreen Chip. Cohort evaluation (n = 46) confirmed the expected elevation of serum JAC-C9 in EAC, along with elevated total serum C9 level. Next, we asked if the small panel of serum biomarkers improves detection of EAC in this cohort when used in conjunction with patient risk factors (age, body mass index and heartburn history). Using logistic regression modeling, we found that serum C9 and JAC-C9 significantly improved EAC prediction from AUROC of 0.838 to 0.931, with JAC-C9 strongly predictive of EAC (vs. BE OR = 4.6, 95% CI: 1.6-15.6, p = 0.014; vs. Healthy OR = 4.1, 95% CI: 1.2-13.7, p = 0.024). This proof-of-concept study confirms the microfluidic EndoScreen Chip technology and supports the potential utility of blood biomarkers in improving triaging for diagnostic endoscopy. Future work will expand the number of markers on EndoScreen Chip from our list of validated EAC biomarkers.