Point-of-Care Testing for the Detection of MicroRNAs: Towards Liquid Biopsy on a Chip

Quantitative detection of circular RNA and microRNA at point-of-care using droplet digital CRISPR/Cas13a platform

Circular RNA (circRNA) and microRNA (miRNA) are both non-coding RNAs (ncRNAs) that serve as biomarkers for cancer diagnosis and prognosis. Quantitative detection of these ncRNAs is of particular importance to elucidate the functional mechanisms and evaluate their potential as biomarkers. However, the inherent structures of circRNA and miRNA are different from the mRNA, conventional qRT-PCR is unsuitable for the detection of these ncRNAs. Here, we propose a sensitive method for quantitative detection of circRNA and miRNA using polydisperse droplet digital CRISPR/Cas13a (PddCas13a). It can achieve limits of detection (LOD) as low as ∼10 aM without polymerase-based amplification. To efficiently detect the circRNA and miRNA in real samples, we use a chemically modified crRNA to enhance the stability of crRNA and improve the performance of Cas13a in complex environments containing contaminants. By integrating an extraction-free procedure with PddCas13a, we experimentally demonstrate the applicability of PddCas13a by testing clinical samples. Furthermore, we develop an automated and portable instrument for PddCas13a and verify its applicability for the detection of circRNA and miRNA from exosomes in point-of-care (POC) setting. This is the first report to detect the circRNA and miRNA simultaneously in POC setting. We envision this platform could promote the research of ncRNAs.

Sample-to-answer detection of miRNA from whole blood using thermally responsive alkane partitions

Circulating miRNA offers a tremendous opportunity as a biomarker paradigm for many applications in disease diagnostics, including point-of-care diagnostics for global health needs. However, despite the numerous miRNA detection schemes reported, there still does not exist a solution for highly sensitive sample-to-answer detection of miRNA directly from complex samples, such as whole blood. We recently developed thermally responsive alkane partitions (TRAPs), which - when combined with magnetic microbeads - enable the complete assay automation from whole blood. Here we apply TRAPs with ligation-LAMP to automate the detection of miRNA in whole blood samples. MBs and a TRAP enable the automated purification of miRNA from blood, while a novel displacement-ligation method is utilized to trigger the ligation-LAMP reaction, which is streamlined into one step by a second TRAP. Using easily manufacturable TRAP-enabled assay cassettes and a custom low-cost handheld instrument, we report the specific detection of miR-155 at concentrations as low as 15 fM in whole blood with no intermediate steps by the user. This new approach creates the opportunity for point-of-care miRNA-based diagnostics with global health applications.

Recent Technologies towards Diagnostic and Therapeutic Applications of Circulating Nucleic Acids in Colorectal Cancers

Liquid biopsy has emerged as a promising noninvasive approach for colorectal cancer (CRC) management. This review focuses on technologies detecting circulating nucleic acids, specifically circulating tumor DNA (ctDNA) and circulating RNA (cfRNA), as CRC biomarkers. Recent advancements in molecular technologies have enabled sensitive and specific detection of tumor-derived genetic material in bodily fluids. These include quantitative real-time PCR, digital PCR, next-generation sequencing (NGS), and emerging nanotechnology-based methods. For ctDNA analysis, techniques such as BEAMing and droplet digital PCR offer high sensitivity in detecting rare mutant alleles, while NGS approaches provide comprehensive genomic profiling. cfRNA detection primarily utilizes qRT-PCR arrays, microarray platforms, and RNA sequencing for profiling circulating microRNAs and discovering novel RNA biomarkers. These technologies show potential in early CRC detection, treatment response monitoring, minimal residual disease assessment, and tumor evolution tracking. However, challenges remain in standardizing procedures, optimizing detection limits, and establishing clinical utility across disease stages. This review summarizes current circulating nucleic acid detection technologies, their CRC applications, and discusses future directions for clinical implementation.

Simultaneous Detection of Micro-RNAs by a Disposable Biosensor via the Click Chemistry Connection Strategy

Simultaneous detection of multiple breast cancer-associated miRNAs significantly raises the accuracy and reliability of early diagnosis. In this work, disposable carbon fiber paper serves as the biosensing interface, linking DNA probes via click chemistry to efficiently capture targets and signals efficiently. DNA probes have multiple recognition domains that trigger a cascade reaction through the helper probes and targets, resulting in two signals output. The signals are centrally encapsulated in the pore of the MIL-88(Fe)-NH2. The signal carriers are directed by signal probes to the recognition domains that correspond to the DNA probes. The biosensor is selective and stable, and it can quantify miRNA-21 and miRNA-155 simultaneously with detection limits of 0.64 and 0.54 fmol/L, respectively. Furthermore, it demonstrates satisfactory performance in tests conducted with normal human serum and cell lysate. Overall, this method makes a satisfactory exploration to realize an inexpensive and sensitive biosensor for multiple biomarkers.

Electrochemical detection of miRNA using commercial and hand-made screen-printed electrodes: liquid biopsy for cancer management as case of study

The growth of liquid biopsy, i. e., the possibility of obtaining health information by analysing circulating species (nucleic acids, cells, proteins, and vesicles) in peripheric biofluids, is pushing the field of sensors and biosensors beyond the limit to provide decentralised solutions for nonspecialists. In particular, among all the circulating species that can be adopted in managing cancer evolution, both for diagnostic and prognostic applications, microRNAs have been highly studied and detected. The development of electrochemical devices is particularly relevant for liquid biopsy purposes, and the screen-printed electrodes (SPEs) represent one of the building blocks for producing novel portable devices. In this work, we have taken miR-2115-3p as model target (it is related to lung cancer), and we have developed a biosensor by exploiting the use of a complementary DNA probe modified with methylene blue as redox mediator. In particular, the chosen sensing architecture was applied to serum measurements of the selected miRNA, obtaining a detection limit within the low nanomolar range; in addition, various platforms were interrogated, namely commercial and hand-made SPEs, with the aim of providing the reader with some insights about the optimal platform to be used by considering both the cost and the analytical performance.

Optimization of Surface Functionalizations for Ring Resonator-Based Biosensors

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

The hidden messengers: cancer associated fibroblasts-derived exosomal miRNAs as key regulators of cancer malignancy

Cancer-associated fibroblasts (CAFs), a class of stromal cells in the tumor microenvironment (TME), play a key role in controlling cancer cell invasion and metastasis, immune evasion, angiogenesis, and resistance to chemotherapy. CAFs mediate their activities by secreting soluble chemicals, releasing exosomes, and altering the extracellular matrix (ECM). Exosomes contain various biomolecules, such as nucleic acids, lipids, and proteins. microRNA (miRNA), a 22-26 nucleotide non-coding RNA, can regulate the cellular transcription processes. Studies have shown that miRNA-loaded exosomes secreted by CAFs engage in various regulatory communication networks with other TME constituents. This study focused on the roles of CAF-derived exosomal miRNAs in generating cancer malignant characteristics, including immune modulation, tumor growth, migration and invasion, epithelial-mesenchymal transition (EMT), and treatment resistance. This study thoroughly examines miRNA's dual regulatory roles in promoting and suppressing cancer. Thus, changes in the CAF-derived exosomal miRNAs can be used as biomarkers for the diagnosis and prognosis of patients, and their specificity can be used to develop newer therapies. This review also discusses the pressing problems that require immediate attention, aiming to inspire researchers to explore more novel avenues in this field.

Paper-based electrochemical device for early detection of integrin αvβ6 expressing tumors

Despite progress in the prevention and diagnosis of cancer, current technologies for tumor detection present several limitations including invasiveness, toxicity, inaccuracy, lengthy testing duration and high cost. Therefore, innovative diagnostic techniques that integrate knowledge from biology, oncology, medicinal and analytical chemistry are now quickly emerging in the attempt to address these issues. Following this approach, here we developed a paper-based electrochemical device for detecting cancer-derived Small Extracellular Vesicles (S-EVs) in fluids. S-EVs were obtained from cancer cell lines known to express, at a different level, the αvβ6 integrin receptor, a well-established hallmark of numerous epithelial cancer types. The resulting biosensor turned out to recognize αvβ6-containing S-EVs down to a limit of 0.7*103 S-EVs/mL with a linear range up to 105 S-EVs /mL, and a relative standard deviation of 11%, thus it may represent a novel opportunity for αvβ6 expressing cancers detection.

Paper-Based Analytical Devices for Cancer Liquid Biopsy

Liquid biopsies have caused a significant revolution in cancer diagnosis, and the use of point of care (PoC) platforms has the potential to bring liquid biopsy-based cancer detection closer to patients. These platforms provide rapid and on-site analysis by reducing the time between sample collection and results output. The aim of this tutorial content is to provide readers an in-depth understanding regarding the choice of the ideal sensing platform suitable for specific cancer-related biomarkers.

AI-Enhanced Visual-Spectral Synergy for Fast and Ultrasensitive Biodetection of Breast Cancer-Related miRNAs

In biomedical testing, artificial intelligence (AI)-enhanced analysis has gradually been applied to the diagnosis of certain diseases. This research employs AI algorithms to refine the precision of integrative detection, encompassing both visual results and fluorescence spectra from lateral flow assays (LFAs), which signal the presence of cancer-linked miRNAs. Specifically, the color shift of gold nanoparticles (GNPs) is paired with the red fluorescence from nitrogen vacancy color centers (NV-centers) in fluorescent nanodiamonds (FNDs) and is integrated into LFA strips. While GNPs amplify the fluorescence of FNDs, in turn, FNDs enhance the color intensity of GNPs. This reciprocal intensification of fluorescence and color can be synergistically augmented with AI algorithms, thereby improving the detection sensitivity for early diagnosis. Supported by the detection platform based on this strategy, the fastest detection results with a limit of detection (LOD) at the fM level and the R2 value of ∼0.9916 for miRNA can be obtained within 5 min. Meanwhile, by labeling the capture probes for miRNA-21 and miRNA-96 (both of which are early indicators of breast cancer) on separate T-lines, simultaneous detection of them can be achieved. The miRNA detection methods employed in this study may potentially be applied in the future for the early detection of breast cancer.