High-speed biosensing strategy for non-invasive profiling of multiple cancer fusion genes in urine

African and Asian elephant ivory discrimination using a portable strip test

Currently, the global elephant population has significantly declined due to the poaching of elephants for their ivory, and this is the reason why elephants are listed in the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES). However, Thailand allows the legal trade of ivory from registered, domesticated Asian elephants, leading to the smuggling of African elephant ivory, and passing them off as Asian elephant ivory. Therefore, this research aims to develop and validate a portable strip test to discriminate between Asian and African elephants DNA, using Recombinase Polymerase Amplification (RPA) and Lateral Flow Dipstick assay (LFD) according to international standards. The results showed that the strip test can be successfully developed with 100% accuracy (n = 105). This kit is specific to elephants, has a detection limit of 0.125 ng of DNA, and can effectively discriminate a variety of elephant ivory, including raw ivory, ivory products, and aged ivory over 25 years old, which had been damaged by fire, all with 100% accuracy (n = 117). Additionally, the developed strip test is designed to be portable and cost-effective. It does not require expensive laboratory equipment and provides a faster analysis process compared with conventional PCR-based methods. This will expedite the legal process and enforcement of laws related to elephant conservation, reducing the opportunities for illegal activities, and enabling timely prosecution under relevant wildlife conservation laws in Thailand and internationally.

Nanozyme-Enhanced Electrochemical Biosensors: Mechanisms and Applications

Nanozymes, as innovative materials, have demonstrated remarkable potential in the field of electrochemical biosensors. This article provides an overview of the mechanisms and extensive practical applications of nanozymes in electrochemical biosensors. First, the definition and characteristics of nanozymes are introduced, emphasizing their significant role in constructing efficient sensors. Subsequently, several common categories of nanozyme materials are delved into, including metal-based, carbon-based, metal-organic framework, and layered double hydroxide nanostructures, discussing their applications in electrochemical biosensors. Regarding their mechanisms, two key roles of nanozymes are particularly focused in electrochemical biosensors: selective enhancement and signal amplification, which crucially support the enhancement of sensor performance. In terms of practical applications, the widespread use of nanozyme-based electrochemical biosensors are showcased in various domains. From detecting biomolecules, pollutants, nucleic acids, proteins, to cells, providing robust means for high-sensitivity detection. Furthermore, insights into the future development of nanozyme-based electrochemical biosensors is provided, encompassing improvements and optimizations of nanozyme materials, innovative sensor design and integration, and the expansion of application fields through interdisciplinary collaboration. In conclusion, this article systematically presents the mechanisms and applications of nanozymes in electrochemical biosensors, offering valuable references and prospects for research and development in this field.

Molecular locker probe enrichment of gene fusion variants from matched patient liquid biopsy specimens for magneto-bioelectrocatalytic nanosensing

The accurate and sensitive analysis of recurrent gene fusion mutant variants in circulating tumor nucleic acids (NAs) of patient liquid biopsy samples is crucial for realizing clinical potential for cancer screening, diagnostics, and therapeutics. Gene fusion analysis is especially challenging in patient liquid biopsy samples because of trace biotarget levels in high non-target background of highly similar native and variant NA sequences. Herein, we describe accurate analysis of three prostate cancer gene fusion mutant variants in matched plasma and urine specimens from real cancer patients and healthy controls (n = 80) by (i) direct locker probe enrichment of multiple gene fusion mutant variants without tedious upstream sample processing; (ii) magneto-bioelectrocatalytic cycling readout using both NA-intercalating and freely diffusive redox probes for superior signal enhancement. For each mutant variant, an ultrabroad dynamic range (10-10⁵ copies) was achieved with enhanced 10 copies (zmol) detection limit. With the combination of locker probe enrichment and magneto-bioelectrocatalytic cycling readout for NA mutant variant analysis, the potential of non-invasive liquid biopsies may be exploited for the benefit of cancer patients.

Prostate cancer detection: a systematic review of urinary biosensors

BACKGROUND

Current diagnostic methods for prostate cancer are invasive and lack specificity towards aggressive forms of the disease, which can lead to overtreatment. A new class of non-invasive alternatives is under development, in which urinary biomarkers are detected using biosensing devices to offer rapid and accurate prostate cancer diagnosis. These different approaches are systematically reviewed and their potential for translation to clinical practice is evaluated.

METHODS

A systematic review of the literature was performed in May 2021 using PubMed Medline database, Embase, and Web of Science. The objective was to review the structural designs and performance of biosensors tested on urine samples from patients with prostate cancer.

RESULTS

A total of 76 records were identified. After screening and eligibility, 14 articles were included and are discussed in this paper. The biosensors were discussed based on the target biomarkers and detection technologies used, as well as the results of the clinical studies. Most of the works reported good discrimination between patients with prostate cancer and controls.

CONCLUSIONS

This review highlights the potential of urinary biosensors for non-invasive prostate cancer detection. However, clinical studies have so far only been conducted on small cohorts of patient, with large scale trials still needed to validate the proposed approaches. Overall, the consensus arising from the proof of concepts studies reviewed here, is that an adequate combination of biomarkers into multiplex biosensor platforms is required to achieve accurate diagnostic tests. Furthermore, whether such devices can discriminate between aggressive and indolent cancer has not yet been addressed, because it entails optimized biomarkers panels and long-term clinical trials.

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.

Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants

The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm^-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.

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.

Single enzyme-based stem-loop and linear primers co-mediated exponential amplification of short gene sequences

Isothermal DNA amplification only using a Bacillus stearothermophilus (Bst) DNA polymerase such as loop-mediated isothermal amplification typically entails multiple target sites for primer design and is thereby not suited for the amplification of short gene sequences, for example, the sequences with size below 200 nucleotides (nt). Here we present SLIMP, a novel single enzyme-based isothermal amplification of short gene sequence mediated by both stem-loop and linear primers. In SLIMP, a pair of stem-loop primers and a pair of linear primers are specifically designed to recognize only two target sites. Linear primers in SLIMP are similar as conventional PCR primers, but stem-loop primers are the modified linear primers through attaching a stem-loop structure at their 5'-ends. Attributed to this unique primer design, three basic reaction modes including linear-priming, single stem-loop-priming, and double stem-loop-priming amplifications co-mediate the SLIMP process under the function of Bst DNA polymerase. As a proof-of-concept assay, a synthetic 80 nt sequence from hepatitis B virus S gene was used as the template to develop SLIMP. On performance, SLIMP detection possesses high sensitivity and specificity, good selectivity, and the potential for analysing real sample. Therefore, SLIMP is expected as a novel alternative to amplify short gene sequences using a single enzyme.

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

The analysis of circulating cancer biomarkers in the form of liquid biopsies confers several potential benefits as compared to traditional surgical tissue sampling. As a common key anomaly strongly implicated across several cancer types, the BRAFV600E mutation is one of the most valuable oncogenic biomarkers available in liquid biopsies. Crucially, BRAFV600E is also an actionable mutation which could be arrested by clinically beneficial drug inhibitors. Yet, as is true for most single base disease mutations, current BRAFV600E detection in either its DNA or protein molecular state is still liable to false positive/negative outcomes, thus impacting patient treatment benefit. Here we present an integrated multi-molecular sensor (IMMS) for an entire sample-to-answer workflow from melanoma cell capture to simultaneous quantification of both intracellular BRAFV600E DNA and protein levels on a single platform. The IMMS combines (i) specific capture and release of circulating melanoma cells; (ii) electric field-induced cell lysis; (iii) simultaneous quantification of BRAFV600E DNA and protein levels. We investigated the IMMS system's analytical performance in cell capture, release and lysis, and intracellular BRAFV600E detection by ligase-mediated DNA amplification and antibody-based protein hybridization. As a proof-of-concept, we successfully demonstrated circulating BRAFV600E detection at both DNA and protein molecular levels in simulated melanoma plasma samples. With its capabilities in integrated and miniaturized analysis, the IMMS could lead the emergence of a new generation of multi-molecular lab-on-chip biosensors for enabling more accurate and extensive analysis of powerful circulating biomarkers in patient liquid biopsies.

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

RPA is a versatile complement or replacement of PCR, and now is stepping into practice.

Multiplexed isothermal nucleic acid amplification

Multiplexed isothermal amplification and detection of nucleic acid sequences and biomarkers is of increasing importance in diverse areas including advanced diagnostics, food quality control and environmental monitoring. Whilst there are several very elegant isothermal amplification approaches, multiplexed amplification remains a challenge, requiring careful experimental design and optimisation, from judicious primer design in order to avoid the formation of primer dimers and non-specific amplification, applied temperature as well as the ratio and concentration of primers. In this review, we describe the various approaches that have been reported to date for multiplexed isothermal amplification, for both "one-pot" multiplexing as well as parallelised multiplexing using loop-mediated isothermal amplification, strand-displacement amplification, helicase-dependent amplification, rolling circle amplification, nucleic acid sequence-based amplification, with a particular focus on recombinase polymerase amplification.

Recombinase polymerase amplification: Basics, applications and recent advances

Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.

Enabling miniaturised personalised diagnostics: from lab-on-a-chip to lab-in-a-drop

The concept of personalised diagnostics is to direct accurate clinical decisions based on an individual's unique disease molecular profile. Lab-on-a-chip (LOC) systems are prime personalised diagnostics examples which seek to perform an entire sample-to-outcome detection of disease nucleic acid (NA) biomarkers on a single miniaturised platform with minimal user handling. Despite the great potential of LOC devices in providing rapid, portable, and inexpensive personalised diagnosis at the point-of-care (POC), the translation of this technology into widespread use has still been hampered by the need for sophisticated and complex engineering. As an alternative miniaturised diagnostics platform free of precision fabrication, there have been recent developments towards a solution-based lab-in-a-drop (LID) system by which an entire laboratory-based diagnostics workflow could be downscaled and integrated within a singular fluid droplet for POC detection of NA biomarkers. In contrast to existing excellent reviews on miniaturised LOC fabrication and individual steps of NA biomarker sensing, we herein focus on miniaturised solution-based NA biosensing strategies suited for integrated LID personalised diagnostics development. In this review, we first evaluate the three fundamental bioassay steps for miniaturised NA biomarker detection: crude sample preparation, isothermal target amplification, and detection readout of amplicons. Then, we provide insights into research advancements towards a functional LID system which integrates all three of the above-mentioned fundamental steps. Finally, we discuss perspectives and future directions of LID diagnostic platforms in personalised medicine applications.

A nanoplasmonic label-free surface-enhanced Raman scattering strategy for non-invasive cancer genetic subtyping in patient samples

Simple nucleic acid detection methods could facilitate the progress of disease diagnostics for clinical uses. An attractive strategy is label-free surface-enhanced Raman scattering (SERS) due to its capability of providing structural fingerprinting of analytes that are close to or on nanomaterial surfaces. However, current label-free SERS approaches for DNA/RNA biomarker detection are limited to short and synthetic nucleic acid targets and have not been fully realized in clinical samples due to two possible reasons: (i) low target copies in limited patient samples and (ii) poor capability in identifying specific biomarkers from complex samples. To resolve these limitations and enable label-free SERS for clinical applications, we herein present a novel strategy based on multiplex reverse transcription-recombinase polymerase amplification (RT-RPA) to enrich multiple RNA biomarkers, followed by label-free SERS with multivariate statistical analysis to directly detect, identify and distinguish between these long amplicons (∼200 bp). As a proof-of-concept clinical demonstration, we employed this strategy for non-invasive subtyping of prostate cancer (PCa). In a training cohort of 43 patient urinary samples, we achieved 93.0% specificity, 95.3% sensitivity, and 94.2% accuracy. We believe that our proposed assay could pave the way for simple and direct label-free SERS detection of multiple long nucleic acid sequences in patient samples, and thus facilitate rapid cancer molecular subtyping for personalized therapies.