An integrated multi-molecular sensor for simultaneous BRAFV600E protein and DNA single point mutation detection in circulating tumour cells

Emerging multianalyte biosensors for the simultaneous detection of protein and nucleic acid biomarkers

Traditionally, biosensors are designed to detect one specific analyte. Nevertheless, disease progression is regulated in a highly interactive way by different classes of biomolecules like proteins and nucleic acids. Therefore, a more comprehensive analysis of biomarkers from a single sample is of utmost importance to further improve both, the accuracy of diagnosis as well as the therapeutic success. This review summarizes fundamentals like biorecognition and sensing strategies for the simultaneous detection of proteins and nucleic acids and discusses challenges related to multianalyte biosensor development. We present an overview of the current state of biosensors for the combined detection of protein and nucleic acid biomarkers associated with widespread diseases, among them cancer and infectious diseases. Furthermore, we outline the multianalyte analysis in the rapidly evolving field of single-cell multiomics, to stress its significance for the future discovery and validation of biomarkers. Finally, we provide a critical perspective on the performance and translation potential of multianalyte biosensors for medical diagnostics.

Recent development of surface-enhanced Raman scattering for biosensing

Surface-Enhanced Raman Scattering (SERS) technology, as a powerful tool to identify molecular species by collecting molecular spectral signals at the single-molecule level, has achieved substantial progresses in the fields of environmental science, medical diagnosis, food safety, and biological analysis. As deepening research is delved into SERS sensing, more and more high-performance or multifunctional SERS substrate materials emerge, which are expected to push Raman sensing into more application fields. Especially in the field of biological analysis, intrinsic and extrinsic SERS sensing schemes have been widely used and explored due to their fast, sensitive and reliable advantages. Herein, recent developments of SERS substrates and their applications in biomolecular detection (SARS-CoV-2 virus, tumor etc.), biological imaging and pesticide detection are summarized. The SERS concepts (including its basic theory and sensing mechanism) and the important strategies (extending from nanomaterials with tunable shapes and nanostructures to surface bio-functionalization by modifying affinity groups or specific biomolecules) for improving SERS biosensing performance are comprehensively discussed. For data analysis and identification, the applications of machine learning methods and software acquisition sources in SERS biosensing and diagnosing are discussed in detail. In conclusion, the challenges and perspectives of SERS biosensing in the future are presented.

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.

In Situ Single Cell Proteomics Reveals Circulating Tumor Cell Heterogeneity during Treatment

Cancer is a dynamic disease with heterogenic molecular signatures and constantly evolves during the course of the disease. Single cell proteomic analysis could offer a suitable pathway to monitor cancer cell heterogeneity and deliver critical information for the diagnosis, recurrence, and drug-resistant mechanisms in cancer. Current standard techniques for proteomic analysis such as ELISA, mass spectrometry, and Western blots are time-consuming, expensive, and often require fluorescence labeling that fails to provide accurate information about the multiple protein expression changes at the single cell level. Herein, we report a surface-enhanced Raman spectroscopy-based simple microfluidic device that enables the screening of single circulating tumor cells (CTC) in a dynamic state to precisely understand the heterogeneous expression of multiple protein biomarkers in response to therapy. It further enables identifying intercellular heterogeneous expression of CTC surface proteins which would be highly informative to identify the cancer cells surviving treatment and potentially responsible for drug resistance. Using a bead and cell line-based model system, we successfully detect single bead and single cell spectra when flowed through the device. Using SK-MEL-28 melanoma cells, we demonstrate that our system is capable of monitoring heterogeneous expressions of multiple surface protein markers (MCSP, MCAM, and LNGFR) before and during drug treatment. Integrating a label-free electrochemical system with the device, we also monitor the expression of an intracellular protein (here, BRAF^V600E) under drug treatment. Finally, we perform a longitudinal study with 15 samples from five different melanoma patients who underwent therapy. We find that the average expression of receptor proteins in a patient fails to determine the therapy response particularly when the disease progresses. However, single CTC analysis with our device shows a high level of intercellular heterogeneity in the receptor expression profiles of patient-derived CTCs and identifies heterogeneity within CTCs. More importantly, we find that a fraction of CTCs still shows a high expression of these receptor proteins during and after therapy, indicating the presence of resistant CTCs which may evolve after a certain time and progress the disease. We believe this automated assay will have high clinical importance in disease diagnosis and monitoring treatment and will significantly advance the understanding of cancer heterogeneity on the single cell level.

A 'smart' aptamer-functionalized continuous label-free cell catch-transport-release system

Label-free cell sorting devices are of great significance for biomedical research and clinical therapeutics. However, current platforms for label-free cell sorting cannot achieve continuity and selectivity simultaneously, resulting in complex steps and limited reliability. Here, an immunoaffinity-based cell catch-transport-release thermo-chemo-mechanical coupling hydrogel (iCatch) device is reported. It contains a temperature-responsive hydrogel that can generate spatial movement synergically with the reversible binding of affinity handle modified. The functionalized hydrogel is embedded inside a biphasic microfluidic platform to enable cell transportation between the flows. The cell sorting capability and biocompatibility of the iCatch device were validated with CCRF-CEM cells as a proof-of-concept, and CCRF-CEM-specific aptamers with thermo-responsive affinity as well as a hydrogel with temperature-dependent volume were employed accordingly. A cell catching efficiency of ∼40% and a recovery rate of ∼70% were achieved. The iCatch device provides a high-throughput (∼900 cells mm-1 s-1) platform for cell sorting and is ultimately valuable for downstream biomedical applications.

Simultaneous BRAFV600E Protein and DNA Aberration Detection in Circulating Melanoma Cells Using an Integrated Multimolecular Sensor

Liquid biopsy has emerged as the next generation target for diagnostics and therapeutic monitoring of many diseases including cancer. Liquid biopsy offers noninvasive analysis of aberrant biomolecular changes (e.g., aberrant protein expression, DNA mutation) which can provide crucial information on disease stages and therapy responses. As a diagnostically important biomarker for melanoma, the detection of the BRAF^V600E aberration at the DNA and protein level in liquid biopsies confers an attractive option. This method describes the preparation and operation of an integrated multimolecular sensor (IMMS) for simultaneous detection of the BRAF^V600E aberration in both molecular forms from circulating melanoma cells in liquid biopsy. IMMS integrates specific melanoma cell capture, cell release, cell lysis, and electrochemical BRAF^V600E detection on a single device. IMMS is demonstrated for a sample-to-answer workflow of plasma spiked with melanoma cells.

Direct Enhanced Detection of Multiple Circulating Tumor DNA Variants in Unprocessed Plasma by Magnetic-Assisted Bioelectrocatalytic Cycling

The detection of single-nucleotide variants (SNVs) in circulating tumor DNA (ctDNA) in liquid biopsies has increasingly been shown to exhibit unique benefits for early detection or minimal residual disease monitoring in cancer. Yet, current clinically validated assays for ctDNA SNV detection are challenged by (i) time-consuming and laborious spin column-based ctDNA purification protocols, (ii) limited detection specificity to discriminate between mutated SNVs from large excess of closely similar wild-type sequences, and (iii) insufficient detection sensitivity required for trace ctDNA target analysis in blood. Herein, a ctDNA assay is demonstrated to tackle these triple key issues by fusing magnetics for quick ctDNA enrichment directly from unprocessed blood, selected bioenzyme activities for rapid discrimination, and molecular amplification of target SNVs, and designed magnetic-assisted bioelectrocatalytic cycling of DNA-intercalating and freely diffusing redox probes for electrochemical signal intensification. The described ctDNA SNV assay enables the detection of clinically relevant ctDNA SNVs in melanoma (BRAF^V600E, KIT^L576P, and NRAS^Q61K) from unprocessed plasma samples with unprecedented 0.005% detection sensitivity, ultrabroad dynamic range over four orders of magnitude, and excellent single-base specificity.

Ultrasensitive melanoma biomarker detection using a microchip SERS immunoassay with anisotropic Au–Ag alloy nanoboxes

The detection of circulating biomarkers in liquid biopsies has the potential to provide a non-invasive route for earlier cancer diagnosis and treatment management. Melanoma chondroitin sulfate proteoglycan (MCSP) is a membrane protein characteristic for melanoma cell migration and tissue invasion with its soluble form (sMCSP) serving as a potential promising diagnostic surrogate. However, at the initial disease stage, the detection of sMCSP is challenging because of its low abundance and the required high specificity to analyze sMCSP in complex bodily fluids. Herein, we report a highly sensitive and high-throughput microchip that enables Surface Enhanced Raman Spectroscopy (SERS) immunoassay for parallel detection of up to 28 samples. Key to assay speed and sensitivity is the stimulation of an alternating current-induced nanofluidic mixing that improves target-sensor collision and displacement of non-specific molecules. Anisotropic Au–Ag alloy nanoboxes (NB's) with strong plasmonic hot spots provide single SERS particle sensitivity that enables ultrasensitive sMCSP detection of as low as 0.79 pM (200 pg ml⁻¹). As a proof of concept study, we investigate the assay performance in simulated melanoma patient samples.

The detection of circulating biomarkers in liquid biopsies has the potential to provide a non-invasive route for earlier cancer diagnosis and treatment management.

Single droplet detection of immune checkpoints on a multiplexed electrohydrodynamic biosensor

Monitoring soluble immune checkpoints in circulating fluids has the potential for minimally-invasive diagnostics and personalised therapy in precision medicine. Yet, the sensitive detection of multiple immune checkpoints from small volumes of liquid biopsy samples is challenging. In this study, we develop a multiplexed immune checkpoint biosensor (MICB) for parallel detection of soluble immune checkpoints PD-1, PD-L1, and LAG-3. MICB integrates a microfluidic sandwich immunoassay using engineered single chain variable fragments and alternating current electrohydrodynamic in situ nanofluidic mixing for promoting biosensor-target interaction and reducing non-specific non-target binding. MICB provides advantages of simultaneous analysis of up to 28 samples in <2 h, requires as little as a single sample drop (i.e., 20 μL) per target immune checkpoint, and applies high-affinity yeast cell-derived single chain variable fragments as a cost-effective alternative to monoclonal antibodies. We investigate the assay performance of MICB and demonstrate its capability for accurate immune checkpoint detection in simulated patient serum samples at clinically-relevant levels. MICB provides a dynamic range of 5 to 200 pg mL-1 for PD-1 and PD-L1, and 50 to 1000 pg mL-1 for LAG-3 with a coefficient of variation <13.8%. Sensitive immune checkpoint detection was achieved with limits of detection values of 5 pg mL-1 for PD-1, 5 pg mL-1 for PD-L1, and 50 pg mL-1 for LAG-3. The multiplexing capability, sensitivity, and relative assay simplicity of MICB make it capable of serving as a bioanalytical tool for immune checkpoint therapy monitoring.

Toward Personalized Cancer Treatment: From Diagnostics to Therapy Monitoring in Miniaturized Electrohydrodynamic Systems

Historically, cancer was seen and treated as a single disease. Over the years, this image has shifted, and it is now generally accepted that cancer is a complex and dynamic disease that engages multiple progression pathways in each patient. The shift from treating cancer as single disease to tailoring the therapy based on the individual's characteristic cancer profile promises to improve the clinical outcome and has also given rise to the field of personalized cancer treatment. To advise a suitable therapy plan and adjust personalized treatment, a reliable and fast diagnostic strategy is required. The advances in nanotechnology, microfluidics, and biomarker research have spurred the development of powerful miniaturized diagnostic systems that show high potential for use in personalized cancer treatment. These devices require only minute sample volumes and have the capability to create instant cancer snapshots that could be used as tool for cancer risk indication, early detection, tumor classification, and recurrence. Miniaturized systems can combine a whole sample-to-answer workflow including sample handling, preparation, analysis, and detection. As such, this concept is also often referred to as "lab-on-a-chip". An inherit challenge of monitoring personalized cancer treatment using miniaturized systems is that cancer biomarkers are often only detectable at trace concentrations present in a complex biological sample rich in interfering molecules, necessitating highly specific and sensitive biosensing strategies. To address the need for trace level detection, highly sensitive fluorescence, absorbance, surface-enhanced Raman spectroscopy (SERS), electrochemical, mass spectrometric, and chemiluminescence approaches were developed. To reduce sample matrix interferences, ingenious device modifications including coatings and nanoscopic fluid flow manipulation have been developed. Of the latter, our group has exploited the use of alternating current electrohydrodynamic (ac-EHD) fluid flows as an efficient strategy to reduce nonspecific nontarget biosensor binding and speed-up assay times. ac-EHD provides fluid motion induced by an electric field with the ability to generate surface shear forces in nanometer distance to the biosensing surface (known as nanoshearing phenomenon). This is ideally suited to increase the collision frequency of cancer biomarkers with the biosensing surface and shear off nontarget molecules thereby minimizing nonspecific binding. In this Account, we review recent advancements in miniaturized diagnostic system development with potential use in personalized cancer treatment and monitoring. We focus on integrated microfluidic structures for controlled sample flow manipulation followed by on-device biomarker interrogation. We further highlight the progress in our group, emphasis fundamentals and applications of ac-EHD-enhanced miniaturized systems, and outline promising detection concepts for comprehensive cancer biomarker profiling. The advances are discussed based on the type of cancer biomarkers and cover circulating tumor cells, proteins, extracellular vesicles, and nucleic acids. The potential of miniaturized diagnostic systems for personalized cancer treatment and monitoring is underlined with representative examples including device illustrations. In the final section, we critically discuss the future of personalized diagnostics and what challenges should be addressed to make these devices clinically translatable.