Quantitation of microRNAs by real-time RT-qPCR

Short communication: miRNA122 interrogation via PCR-Free method to track liver recovery

There is currently a need to investigate new biomarkers of acute liver injury (ALI) that are highly specific to the liver and capable of detecting early-stage liver damage. In this regard, circulating microRNAs (miRNAs), particularly microRNA122 (miRNA122), have recently been proposed as promising new candidate biomarkers. However, the quantification of miRNAs is not a standardized technique and presents several challenges that hinder its routine use. The aim of this work is to validate the innovative Dynamic Chemical Labeling (DCL) PCR-Free technology for its ability to detect miRNA122 in patient samples using Luminex xMAP platforms. The DCL PCR-Free technology was used to directly measure and monitor miRNA122 levels in serum samples from patients with ALI. Patients were monitored throughout the recovery process from liver injury, from the time of detection and for up to 30 days afterwards, with follow-up over three separate visits. The results demonstrate the robustness of the method, with sensitivity of 3.36% and precision of 99.80%, and show a high correlation between miRNA122 and traditional liver injury markers such as ALT (r = 0.8150, p = 0.0001), AST (r = 0.7895, p = 0.0002) and TBL (r = 0.2646, p = 0.3406) throughout the ALI recovery process. In conclusion, measuring miRNA122 levels using the DCL PCR-Free method provides a distinctive approach, not only for diagnosing ALI patients but also for effectively monitoring disease progression, tracking liver recovery, and evaluating treatment effectiveness.

Triple DNAzyme cleavage mediated signal cascade for sensitive and reliable Kawasaki disease related microRNA analysis

MicroRNAs (miRNAs) serve as promising biomarkers for disease diagnosis, therapeutic monitoring, and post-treatment surveillance. However, their accurate quantification remains challenging due to low abundance and sample-derived interference. To address this, we developed an enzyme-free DNAzyme cascade system for highly sensitive miRNA detection. This approach employs programmable DNAzyme hairpin probes (S1, S2, and S3), where the S1 probe features exposed recognition subunits for target-specific miRNA binding. This recognition initiates two steps: the split DNAzyme-mediated middle circuit and the subsequent substrate cleavage catalyzed by DNAzyme to induce signal generation (downstream DNAzyme circuit). The absence of enzymes provides the method with a negligible background signal. The numerous signal cycles facilitated significant signal amplification, resulting in a femtomolar detection limit and enhanced selectivity for several homologous miRNAs. This robust triple DNAzyme cascaded system provides enhanced and reliable approaches for understanding miRNA activity in diverse biological events.

Dual DNAzyme amplification-based colorimetric sensing assay for the identification and quantification of tumor-associated miRNAs

Herein, we present a colorimetric sensing strategy for the identification and quantification of tumor-associated miRNAs based on dual DNAzyme amplification. In this sensing ensemble, the substrate portion of the Pb2+-dependent 8-17 DNAzyme combines with the G-quadruplex portion to form a hairpin substrate strand. The two split 8-17 DNAzyme strands are partially complementary to the substrate strand and serve as a recognition unit for binding the target miRNA. In the presence of the target miRNA, the activated DNAzyme cleaves the substrate strand, releasing the G-quadruplex. This G-quadruplex binds to hemin to form a G-quadruplex/hemin complex with horseradish peroxidase (HRP)-like properties, which catalyzes the oxidation of ABTS2- by H2O2. This oxidation reaction produces a colorimetric signal output, enabling the detection of the target miRNA. Under the optimal reaction conditions explored in this study, the constructed sensing ensembles tailored for each of the specific target miRNAs successfully identified and quantified the four target miRNAs-miR-122, miR-21, miR-335, and miR-155-in both buffer solutions and cell extracts. This colorimetric sensing strategy offers significant advantages in terms of simplicity, cost, and versatility and holds great potential for wide application in biomedical research and clinical diagnostics.

Hydrogel-Based In Situ DNA Extension Assay for Multiplexed and Rapid Detection of MicroRNA

MicroRNAs (miRNAs) are important biomarkers for liquid biopsy, with extensive applicability to diverse diseases. Among diverse miRNA sensing platforms, graphically encoded hydrogel-based miRNA detection technology is a highly promising diagnostic tool, in terms of sensitivity, specificity, and multiplexing capability. However, the conventional hydrogel-based miRNA detection process suffers from a long assay time (more than 3 h) and redundant assay steps, limiting the practical applicability to actual clinical fields. In this study, we develop a hydrogel-based in situ DNA extension assay for rapid, simple, and multiplexed miRNA detection. Unlike typical hydrogel-based assays, the target hybridization and biotinylation for fluorophore labeling are integrated into a single step via target miRNA-primed DNA extension in hydrogel microparticles. Therefore, multiple microRNA targets can be quantitatively detected within 45 min by two assay steps composed of (1) target capture/biotinylation and (2) fluorophore labeling via streptavidin-biotin interaction. We validate robust sensitivities (down to the low picomolar level) and specificities (single-nucleotide level) by conducting singleplex assays for breast cancer-related miRNA markers (miR-16, miR-92a, and let-7a). Furthermore, multiplexed detection of these miRNA markers is conducted to validate robust multiplexing capacity with negligible nonspecific signal expression. Finally, multiple types of miRNAs in the lysate of breast cancer cells (MCF-7) are successfully detected using the developed assay. We expect the developed hydrogel-based assay can contribute to biomedical and omic fields, enabling high-throughput profiling of multiple miRNAs.

SplintR ligation-triggered in-situ rolling circle amplification on magnetic bead for accurate detection of circulating microRNAs

The circulating microRNAs (miRNAs), endogenous noncoding RNAs, post-transcriptionally participate in multiple processes during cell growth and development. Moreover, dysregulation of miRNAs expression is intricately associated with cancer. Currently, challenges of high homology, sequence similarity, and low abundance encountered in the detection of target miRNAs in complex samples need to be addressed. Biosensors established for miRNAs detection suffer from limitations in terms of sensitivity, specificity and high cost. Herein, a miRNA detection method based on in-situ RCA on magnetic bead catalyzed by SplintR ligase was proposed to achieve high sensitivity and high specificity. The following steps are included: (1) formation of P1-P2-miRNA double-stranded complex under catalyzation of SplintR ligase, and the release of P1-P2 single strand under denaturation; (2) enrichment of P1-P2 single chain by streptavidin-modified magnetic beads (SM-MB); (3) in situ RCA on surface of magnetic beads; (4) fluorescence detection. After optimization of experimental conditions, miRNA-155 detection with improved sensitivity and specificity was achieved. The detection limit was low to 36.39 fM, and one-base mismatch discrimination was demonstrated. Also, the clinical practicability for circulating miRNA-155 detection was preliminarily validated in human serum samples.

Identification and differential expression analysis of microRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle

Extensive research has shown that miRNAs play a crucial role in regulating biological processes within organisms. This study analyzed miRNAs differentially expressed and potentially associated with immune function and tissue-specific expression in Yunnan Zebu and Holstein cattle. To achieve this, 20 liver and spleen tissue samples from the two cattle breeds were collected for high-throughput miRNA sequencing, with the liver tissue as a reference. The findings revealed that bta-miR-122 and bta-miR-143 are the most abundantly expressed known miRNAs in the liver and spleen tissues of Yunnan Zebu and Holstein cattle, respectively. Additionally, AC_000181.1_27195 and AC_000168.1_14386 emerged as the most highly expressed novel miRNAs in these tissues, exhibiting significant homology with human hsa-miR-3591-3p and hsa-miR-126-3p, respectively. Six differentially expressed miRNAs were selected for validation using stem-loop RT-qPCR, and the results were largely consistent with the high-throughput sequencing data. Functional enrichment analysis of the target genes of these known miRNAs revealed their association with critical metabolic and immune-related pathways in cattle, such as the insulin pathway, mTOR signaling, IFN-γ pathway, and signaling mechanisms mediated by IL5 and IL3. These results enriched the miRNA database for liver and spleen tissues of Yunnan Zebu and Holstein cattle.

Recent Developments in SERS Microfluidic Chips: From Fundamentals to Biosensing Applications

This paper reviews the latest research progress of surface-enhanced Raman spectroscopy (SERS) microfluidic chips in the field of biosensing. Due to its single-molecule sensitivity, selectivity, minimal or no preprocessing, and immediacy, SERS is considered a promising biosensing technology. However, the nondirectional interactions between biological samples and the substrate, as well as fluctuations in the sample environment temperature during signal acquisition, can affect the stability and reproducibility of SERS signals. Integrating SERS spectroscopy with microfluidic chips not only leverages the continuous sample flow, high reaction efficiency, high throughput, and multifunctionality of microfluidic chips to address challenges in biosensing applications but also expands the scope of microfluidic technology by providing a novel on-chip optical detection method. The combination of SERS and microfluidic chips not only enables the complementary advantages of both technologies but also offers a highly promising "combined technology" for the field of biosensing. This paper starts by introducing the enhancement mechanisms of SERS and presents both labeled and label-free SERS strategies. Based on the differences in substrate properties, we broadly categorize SERS microfluidic chips into colloidal nanoparticle-based SERS microfluidic chips and fixed substrate-based SERS microfluidic chips. Finally, we review the latest research progress on SERS microfluidic chips for biosensing biological targets such as nucleic acids, proteins, small biomolecules, and live cells. In the conclusion and outlook section, we summarize the challenges faced by SERS microfluidic chips in biosensing and propose feasible solutions. To better leverage the role of SERS microfluidic chips in biosensing, we also present an outlook on the future development of this combined technology.

Exonuclease-III Assisted Signal Cycle Integrating with Self-Priming Mediated Chain Extension for Sensitive and Reliable MicroRNA Detection

MicroRNA (miRNA) is pivotal in regulating pathological progression and may serve as a significant biomarker for early diagnosis, treatment, and management strategies for atherosclerosis. This study produced a self-priming amplification-accelerated CRISPR/Cas system-based method for the sensitive and selective detection of miRNA by merging Exo-III-assisted target recycling, self-priming-mediated chain extension, and the CRISPR/Cas12a system. The sensor comprises three stages: (i) the creation of a substrate template via Exo-III mediated target recycling and DNA ligase assisted ligation; (ii) the exponential isothermal reaction facilitated by DNA polymerase for signal amplification; (iii) the trans-cleavage activity of CRISPR/Cas12a after recognizing the amplification product generates signals. We employed miRNA-21 as a target. The strategy enables sensitive detection of miRNA-21 without the use of primers, and the unique design of the CRISPR/sgRNA complex efficiently mitigates background signal interference. The sensor can recognize single-base mutant homologous sequences and demonstrate a steady performance in complicated biological matrices. This sensor has been effectively employed to precisely assess miRNA-21 in engineered clinical samples, showcasing its significant potential in clinical diagnostics and of atherosclerosis.

Rapid Detection of microRNA-122 in Serum and Finger Blood Using a Lateral Flow Nucleic Acid Biosensor

MicroRNA122 (miR-122) is a microRNA that is highly expressed in hepatocytes and has been identified as a prospective therapeutic target and biomarker for liver injury. An expanding body of research has demonstrated that miR-122 is a critical regulator in both the initiation and progression of a wide range of liver diseases. Traditional methods for detecting miR-122 mainly include Northern blotting and qRT-PCR, but they are technically complex and cumbersome, requiring expensive instruments and high technical requirements. In this paper, we present a novel rapid testing method utilizing a lateral flow nucleic acid biosensor (LFNAB) for the sensitive and time-efficient detection of miR-122. This approach offers several advantages, including a high specificity for miR-122, the ability to detect low concentrations of the target molecule, and a significantly reduced testing time compared to conventional detection methods. In this study, a thiol-modified single-stranded detection DNA probe (Det-DNA), a biotinylated single-stranded capture DNA probe (Cap-DNA), and a biotinylated single-stranded control DNA probe (Con-DNA) are used to construct the LFNAB. A gold nanoparticle (AuNP) is a colored tag, which is used to label the Det-DNA probe. The principle of detecting miR-122 is based on dual DNA-miRNA hybridization reactions on the LFNAB to form sandwich-type AuNP-Det-DNA-miR-122-Cap-DNA complexes, which are captured on the test area of LFNAB for visualization and quantification. After systematic optimization of conditions of experiment, the response of LFNAB was highly linear within the scope of 0 pM-100 pM miR-122, and the detection limit in 15 min was 3.90 pM. The use of LFNAB to detect miR-122 in serum and fingertip blood has yielded satisfactory results. This successful application indicates the effectiveness of LFNAB in detecting miR-122 in both serum and fingertip blood samples, showcasing its potential utility in clinical and research settings for assessing miR-122 levels in different biological samples.

MicroRNA Profiling of Blood Extracellular Vesicles in ME/CFS

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a chronic debilitating neuroimmune disease affecting many organs and systems which, in the absence of validated biomarkers, remains diagnosed by clinical criteria. Extracellular vesicles (EV) in blood come from practically all cells in our body and therefore may carry the disease-specific biomarkers needed for the diagnosis of ME. This chapter presents the methodology used on a single pilot study performed to evaluate this possibility to describe a workflow for EV isolation and the analysis of the miRNAs within, which could serve to interrogate additional cohorts of ME/CFS. Among the diverse nature of EV contents miRNAs may constitute a prominent regulatory layer in the development and progress of complex diseases such as ME/CFS, and therefore their study should be further pursued.

Brief guide to RT-qPCR

RNA quantification is crucial for understanding gene expression and regulation. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is a widely used technique for RNA quantification because of its practical and quantitative nature, sensitivity, and specificity. Here, we provide an overview of RT-qPCR, focusing on essential reagents, the importance of primer design, the detailed workflow, and data analysis methods. This guide will be useful for scientists who are unfamiliar with RT-qPCR, highlighting key considerations for successful RNA quantification.

Nucleic Acid Amplification Circuit-Based Hydrogel (NACH) Assay for One-Step Detection of Metastatic Gastric Cancer-Derived Exosomal miRNA

Gastric cancer (GC) is recognized as the fifth most prevalent malignant tumor worldwide. It is characterized by diverse clinical symptoms, treatment responses, and prognoses. In GC prognosis, the promotion of epithelial-mesenchymal transition (EMT) fosters cancer cell invasion and metastasis, thereby triggering the dissemination of tumor cells. This study proposes a nucleic acid amplification circuit-based hydrogel (NACH) assay for identifying exosomal miRNA derived from metastatic GC. The NACH assay employs the rolling circle amplification method and targets miRNA-21, a tumor-related oncogene, and miRNA-99a, which promotes EMT. Specific amplification probes for each target are immobilized within the hydrogel, enabling a streamlined, one-step amplification reaction. The NACH assay exhibits a detection limit of 1 fm for miRNA-21 and miRNA-99a, thereby enabling rapid and highly sensitive on-site detection. Performance evaluation using exosomal miRNA extracted from cell culture media, mouse plasma, and human plasma revealed fluorescence intensity patterns similar to those obtained in qRT-PCR. Furthermore, deploying a custom-developed portable fluorometer for the NACH assay allows for diagnostic performance assessment and point-of-care testing using clinical samples from GC patients. These findings emphasize the potential of the NACH assay to be used as a robust tool for the genetic diagnosis of GC based on exosome detection.

Paper-Based DNA Biosensor for Rapid and Selective Detection of miR-21

Cancer is the second leading cause of death globally, with 9.7 million fatalities in 2022. While routine screenings are vital for early detection, healthcare disparities persist, highlighting the need for equitable solutions. Recent advancements in cancer biomarker identification, particularly microRNAs (miRs), have improved early detection. MiR-21 is notably overexpressed in various cancers and can be a valuable diagnostic tool. Traditional detection methods, though accurate, are costly and complex, limiting their use in resource-limited settings. Paper-based electrochemical biosensors offer a promising alternative, providing cost-effective, sensitive, and rapid diagnostics suitable for point-of-care use. This study introduces an innovative electrochemical paper-based biosensor that leverages gold inkjet printing for the quantitative detection of miR-21. The biosensor, aimed at developing cost-effective point-of-care devices for low-resource settings, uses thiolated self-assembled monolayers to immobilize single-stranded DNA-21 (ssDNA-21) on electrodeposited gold nanoparticles (AuNPs) on the printed gold surface, facilitating specific miR-21 capture. The hybridization of ssDNA-21 with miR-21 increases the anionic barrier density, impeding electron transfer from the redox probe and resulting in a current suppression that correlates with miR-21 concentration. The biosensor exhibited a linear detection range from 1 fM to 1 nM miR-21 with a sensitivity of 7.69 fM µA-1 cm2 and a rapid response time (15 min). With a low detection limit of 0.35 fM miR-21 in serum, the biosensor also demonstrates excellent selectivity against interferent species. This study introduces an electrochemical paper-based biosensor that uses gold inkjet printing to precisely detect miR-21, a key biomarker overexpressed in various cancers. This innovative device highlights the potential for cost-effective, accessible cancer diagnostics in underserved areas.

Selection of references for quantitative real-time PCR analysis of microRNAs in Nile tilapia (Oreochromis niloticus) under osmotic stress

MicroRNAs play crucial regulatory roles in various aspects of development and physiology, including environmental adaptation and stress responses in teleosts. RT-qPCR is the most commonly used method for studying microRNA expression, with the accuracy and reliability of results depending on the use of an appropriate reference gene for normalization. This study aimed to evaluate seven miRNAs (U6, Let-7a, miR-23a, miR-25-3, miR-103, miR-99-5, and miR-455) expression stability in different tissues of Nile tilapia subjected to osmotic stress. Fish were divided into two groups: a control and an experimental group, raised in 0 and 12 ppt salinity water respectively. After 21 days, brain, gills, liver, and posterior intestine were collected for analysis. Different mathematical algorithms (geNorm, NormFinder, BestKeeper, and the comparative ΔCt method) were employed to identify the most suitable reference miRNAs. The results indicate that the miR-455/miR-23a combination is a robust reference for normalizing miRNA expression levels in studies of osmotic stress responses in Nile tilapia. The stability of miRNA expression can vary depending on specific stress conditions and biological processes, underscoring the necessity of selecting appropriate normalizing miRNAs for each experimental context. This study identifies reliable reference genes for future RT-qPCR analyses of miRNA expression, thereby enhancing our understanding of molecular responses in fish to environmental challenges. These insights are fundamental to the development of new technologies for the improved management and sustainability of aquaculture practices.

miR-4716-3p and the target AKT2 Gene/rs2304186 SNP are associated with blood cancer pathogenesis in Pakistani population

AKT2 is crucial for cancer cells' invasion, metastasis, and survival. It is a possible downstream gene target of cancer glycolysis-related microRNAs. The study investigated the role of miRNA-4716-3p, rs2304186, and the AKT2 gene in blood cancer pathogenesis. RT-qPCR was used to analyze AKT2 gene mRNA and miRNA-4716-3p expression in 200 blood cancer samples and 200 healthy controls. Furthermore, Tetra-ARMS PCR was used to examine the rs2304186 AKT2 SNP in 300 patients and 290 control samples. miRNA-4716-3p was shown to be significantly downregulated (p = 0.0294), whereas mRNA expression of the AKT2 gene was found to be significantly upregulated (p = 0.0034) in blood cancer patients compared to healthy individuals. miRNA-4716-3p downregulation (p = 0.0466) was more pronounced, while AKT2 upregulation was non-significant (p = 0.1661) in untreated patients compared to chemotherapy-treated patients. Blood cancer risk was significantly associated with the rs2304186 GT genotype (p = 0.0432), TT genotype (p = 0.0502), and mutant allele (T) frequency (p = 0.0008). Polymorphism rs2304186 was associated with an increased risk of blood cancer in dominant (p = 0.0011), recessive (p = 0.0502), and additive (p = 0.0008) genetic models. The results suggested that the rs2304186 and the deregulated expression of miRNA-4716-3p and AKT2 gene at the mRNA level may significantly increase the incidence of blood cancer, particularly in the Pakistani population. Therefore, these may function as suitable biomarkers for blood cancer diagnosis and prognosis. Additional, larger-scale investigations may be required to affirm these results.

The sEVs miR-487a/Notch2/GATA3 axis promotes osteosarcoma lung metastasis by inducing macrophage polarization toward the M2-subtype

Small extracellular vesicles (sEVs) are important mediators of intercellular communication between tumor cells and their surrounding environment. Furthermore, the mechanisms by which miRNAs carried in tumor sEVs regulate macrophage polarization remain largely unknown. To concentrate sEVs, we used the traditional ultracentrifugation method. Western blot, NanoSight, and transmission electron microscopy were used to identify sEVs. To determine the function of sEVs-miR-487a, we conducted in vivo and in vitro investigations. The intercellular communication mechanism between osteosarcoma cells and M2 macrophages, mediated by sEVs carrying miR-487a, was validated using luciferase reporter assays, transwell assays, and Western blot analysis. In vitro, sEVs enriched in miR-487a and delivered miR-487a to macrophages, promoting macrophage polarization toward an M2-like type, which promotes proliferation, migration, invasion, and epithelial-mesenchymal transition (EMT) of osteosarcoma cells. In vivo, sEVs enriched in miR-487a facilitate lung metastasis of osteosarcoma. Moreover, plasma miR-487a in sEVs was shown to be a potential biomarker applicable for osteosarcoma diagnosis. In summary, miR-487a derived from osteosarcoma cells can be transferred to macrophages via sEVs, then promote macrophage polarization towards an M2-like type by targeting Notch2 and activating the GATA3 pathway. In a feedback loop, the activation of macrophages accelerates epithelial-mesenchymal transition (EMT), which in turn promotes the migration, invasion, and lung metastasis of osteosarcoma cells. This reciprocal interaction between activated macrophages and osteosarcoma cells contributes to the progression of the disease. Our data demonstrate a new mechanism that osteosarcoma tumor cells derived exosomal-miR-487a which is involved in osteosarcoma development by regulating macrophage polarization in tumor microenvironment (TME).

MicroRNA levels in patients with chronic hepatitis B virus and HIV coinfection in a high-prevalence setting; KwaZulu-Natal, South Africa

BACKGROUND

Hepatitis B virus (HBV) and human immunodeficiency virus (HIV) co-infection are significant public health issues, despite the availability of an effective HBV vaccine for nearly three decades and the great progress that has been made in preventing and treating HIV. HBV and HIV both modulate micro-ribonucleic acids (microRNA) expression to support viral replication. The aim of this study was to describe the pattern of microRNA expression in patients coinfected with chronic HBV and HIV with varying disease severity, as indicated by Hepatitis B e antigen (HBeAg) status, HBV viral load, alanine transaminase (ALT) levels, and HIV viral load.

METHODS

Plasma microRNAs, specific to HBV, were measured by quantitative real-time polymerase chain reaction (qRT-PCR) in HBV and HIV-negative healthy controls (n = 23) and patients coinfected with chronic HBV-HIV (n = 50). MicroRNA expression levels were compared between patients with high vs low HBV viral load, HBeAg positive vs HBeAg negative, high vs low ALT levels, and high vs low HIV viral load. Additionally, HBV viral load, ALT levels, and HIV viral load were correlated with microRNA expression levels.

RESULTS

Significantly higher expression levels of selected microRNAs were observed in chronic HBV-HIV coinfected patients compared to healthy controls. Significantly higher expression levels of hsa-miR-122-5p, hsa-miR-192-5p, and hsa-miR-193b-3p were observed in patients with high HBV viral load compared with low HBV viral load patients, and the levels of these microRNAs were correlated with HBV viral load levels. Significantly higher levels of hsa-miR-15b-5p and hsa-miR-181b-5p were observed in HBeAg-negative patients.

CONCLUSION

This study demonstrates the potential use of hsa-miR-15b-5p, hsa-miR-122-5p, hsa-miR-181b-5p, hsa-miR-192-5p and hsa-miR-193b-3p as additional diagnostic biomarkers in chronic HBV disease progression.

Extracellular vesicles miR-574-5p and miR-181a-5p as prognostic markers in NSCLC patients treated with nivolumab

Immune checkpoint inhibitors (ICIs) have revolutionized the management of advanced non-small cell lung cancer (NSCLC), although patient survival is still unsatisfactory. Accurate predictive markers capable of personalizing the treatment of patients with NSCLC are still lacking. Circulating extracellular vesicles involved in cell-to-cell communications through miRNAs (EV-miRs) transfer are promising markers. Plasma from 245 patients with advanced NSCLC who received nivolumab as second-line therapy was collected and analyzed. EV-miRnome was profiled on 174/245 patients by microarray platform, and selected EV-miRs were validated by qPCR. A prognostic model combining EV-miR and clinical variables was built using stepwise Cox regression analysis and tested on an independent patient cohort (71/245). EV-PD-L1 gene copy number was assessed by digital PCR. For 54 patients with disease control, EV-miR changes at best response versus baseline were investigated by microarray and validated by qPCR. EV-miRNome profiling at baseline identified two EV-miRs (miR-181a-5p and miR-574-5p) that, combined with performance status, are capable of discriminating patients unlikely from those that are likely to benefit from immunotherapy (median overall survival of 4 months or higher than 9 months, respectively). EV-PD-L1 digital evaluation reported higher baseline copy number in patients at increased risk of mortality, without improving the prognostic score. Best response EV-miRNome profiling selected six deregulated EV-miRs (miR19a-3p, miR-20a-5p, miR-142-3p, miR-1260a, miR-1260b, and miR-5100) in responding patients. Their longitudinal monitoring highlighted a significant downmodulation already in the first treatment cycles, which lasted more than 6 months. Our results demonstrate that EV-miRs are promising prognostic markers for NSCLC patients treated with nivolumab.

Modular probe-based colorimetric miRNA detection via polymerase/endonuclease assisted chain displacement

Methods for sequence-specific microRNA (miRNA) analysis are crucial for miRNA research and guiding nursing strategies. We have devised a colorimetric technique for detecting miRNA using a dumbbell probe-based polymerase/endonuclease assisted chain displacement, along with silver ions (Ag+) aptamer assisted color reaction. The suggested approach enables precise measurement of miRNA-21 within the concentration range of 100 fM-5 nM, with a low detection limit of 45.32 fM. Additionally, it exhibits exceptional capability in distinguishing variations at the level of individual nucleotides. Furthermore, the detection technique may be utilized to precisely measure the amount of miRNA-21 in serum samples, demonstrating a high level of concordance with the findings obtained from a commercially available miRNA detection kit.

Developmental validation of an mRNA kit: A 5-dye multiplex assay designed for body-fluid identification

Identifying the sources of biosamples found at crime scenes is crucial for forensic investigations. Among the markers used for body fluid identification (BFI), mRNA has emerged as a well-studied marker because of its high specificity and remarkable stability. Despite this potential, commercially available mRNA kits specifically designed for BFI are lacking. Therefore, we developed an mRNA kit that includes 21 specific mRNA markers of body fluids, along with three housekeeping genes for BFI, to identify four forensic-relevant fluids (blood, semen, saliva, and vaginal fluids). In this study, we tested 451 single-body-fluid samples, validated the universality of the mRNA kit, and obtained a gene expression profile. We performed the validation studies in triplicates and determined the sensitivity, specificity, stability, precision, and repeatability of the mRNA kit. The sensitivity of the kit was found to be 0.1 ng. Our validation process involved the examination of 59 RNA mixtures, 60 body fluids mixtures, and 20 casework samples, which further established the reliability of the kit. Furthermore, we constructed five classifiers that can handle single-body fluids and mixtures using this kit. The classifiers output possibility values and identify the specific body fluids of interest. Our results showed the reliability and suitability of the BFI kit, and the Random Forest classifier performed the best, with 94% precision. In conclusion, we developed an mRNA kit for BFI which can be a promising tool for forensic practice.

One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe

In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.

Plasma Extracellular MicroRNAs Associated With Cardiovascular Disease Risk Factors in Middle-Aged and Older Adults

BACKGROUND

Extracellular microRNAs (miRNAs) are a class of noncoding RNAs that remain stable in the extracellular milieu, where they contribute to various physiological and pathological processes by facilitating intercellular signaling. Previous studies have reported associations between miRNAs and cardiovascular diseases (CVDs); however, the plasma miRNA signatures of CVD and its risk factors have not been fully elucidated at the population level.

METHODS AND RESULTS

Plasma miRNA levels were measured in 4440 FHS (Framingham Heart Study) participants. Linear regression analyses were conducted to test the cross-sectional associations of each miRNA with 8 CVD risk factors. Prospective analyses of the associations of miRNAs with new-onset obesity, hypertension, type 2 diabetes, CVD, and all-cause mortality were conducted using proportional hazards regression. Replication was carried out in 1999 RS (Rotterdam Study) participants. Pathway enrichment analyses were conducted and target genes were predicted for miRNAs associated with ≥5 risk factors in the FHS. In the FHS, 6 miRNAs (miR-193b-3p, miR-122-5p, miR-365a-3p, miR-194-5p, miR-192-5p, and miR-193a-5p) were associated with ≥5 risk factors. This miRNA signature was enriched for pathways associated with CVD and several genes annotated to these pathways were predicted targets of the identified miRNAs. Furthermore, miR-193b-3p, miR-194-5p, and miR-193a-5p were each associated with ≥2 risk factors in the RS. Prospective analysis revealed 8 miRNAs associated with all-cause mortality in the FHS.

CONCLUSIONS

These findings highlight associations between miRNAs and CVD risk factors that may provide valuable insights into the underlying pathogenesis of CVD.

Blood-based circulating microRNAs as diagnostic biomarkers for subclinical carotid atherosclerosis: A systematic review and meta-analysis with bioinformatics analysis

BACKGROUND

Atherosclerosis in carotid arteries can remain clinically undetected in its early development until an acute cerebrovascular event such as stroke emerges. Recently, microRNAs (miRNAs) circulating in blood have emerged as potential diagnostic biomarkers, but their performance in detecting subclinical carotid atherosclerosis has yet to be systematically researched.

AIM

To investigate the diagnostic performance of circulating miRNAs in detecting subclinical carotid atherosclerosis.

METHODS

We systematically searched five electronic databases from inception to July 23, 2022. Subclinical carotid atherosclerosis was defined using carotid intima-media thickness (CIMT). Diagnostic accuracy parameters and correlation coefficients were pooled. A gene network visualisation and enrichment bioinformatics analysis were additionally conducted to search for potential target genes and pathway regulations of the miRNAs.

RESULTS

Fifteen studies (15 unique miRNAs) comprising 2542 subjects were identified. Circulating miRNAs had a pooled sensitivity of 85% (95% CI 80%-89%), specificity of 84% (95% CI 78%-88%), positive likelihood ratio of 5.19 (95% CI 3.97-6.80), negative likelihood ratio of 0.18 (95% CI 0.13-0.23), diagnostic odds ratio of 29.48 (95% CI 21.15-41.11), and area under the summary receiver operating characteristic curve of 0.91 (95% CI 0.88-0.93), with a strong correlation to CIMT (pooled coefficient 0.701; 95% CI 0.664-0.731). Bioinformatics analysis revealed a major role of the miRNAs, as shown by their relation with CCND1, KCTD15, SPARC, WWTR1, VEGFA genes, and multiple pathways involved in the pathogenesis of carotid atherosclerosis.

CONCLUSION

Circulating miRNAs had excellent accuracy in detecting subclinical carotid atherosclerosis, suggesting their utilisation as novel diagnostic tools.

miRNA Studies in Glaucoma: A Comprehensive Review of Current Knowledge and Future Perspectives

Glaucoma, a neurodegenerative disorder that leads to irreversible blindness, remains a challenge because of its complex nature. MicroRNAs (miRNAs) are crucial regulators of gene expression and are associated with glaucoma and other diseases. We aimed to review and discuss the advantages and disadvantages of miRNA-focused molecular studies in glaucoma through discussing their potential as biomarkers for early detection and diagnosis; offering insights into molecular pathways and mechanisms; and discussing their potential utility with respect to personalized medicine, their therapeutic potential, and non-invasive monitoring. Limitations, such as variability, small sample sizes, sample specificity, and limited accessibility to ocular tissues, are also addressed, underscoring the need for robust protocols and collaboration. Reproducibility and validation are crucial to establish the credibility of miRNA research findings, and the integration of bioinformatics tools for miRNA database creation is a valuable component of a comprehensive approach to investigate miRNA aberrations in patients with glaucoma. Overall, miRNA research in glaucoma has provided significant insights into the molecular mechanisms of the disease, offering potential biomarkers, diagnostic tools, and therapeutic targets. However, addressing challenges such as variability and limited tissue accessibility is essential, and further investigations and validation will contribute to a deeper understanding of the functional significance of miRNAs in glaucoma.

The Role of MicroRNA in Graft-Versus-Host-Disease: A Review

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a clinically challenging modality for the treatment of many hematologic diseases such as leukemia, lymphoma, and myeloma. Graft-versus-host disease (GVHD) is a common complication after allo-HSCT and remains a major cause of morbidity and mortality, limiting the success of a potentially curative transplant. Several microRNAs (miRNAs) have recently been shown to impact the biology of GVHD. They are molecular regulators involved in numerous processes during T-cell development, homeostasis, and activation, and contribute to the pathological function of T-cells during GvHD. Here, we review the key role of miRNAs contributing to the GvHD; their detection might be an interesting possibility in the early diagnosis and monitoring of disease.

miRNA Detection for Prostate Cancer Diagnosis by miRoll-Cas: miRNA Rolling Circle Transcription for CRISPR-Cas Assay

Micro-RNA (miRNA) emerges as a promising type of biomarker for cancer diagnosis. There is an urgent need for developing rapid, convenient, and precise miRNA detection methods that may be conducted with limited laboratory facilities, especially in underdeveloped areas. Herein, we developed a miRNA detection method termed miRoll-Cas, where miRNA is first amplified by rolling circle transcription and then subject to CRISPR-Cas13a assay. Using miRoll-Cas, we realized the sensitive detection of multiple cancer-relevant miRNA markers (miR21, miR141, and Let7b) and specifically identified other variants of the Let7 family, which can accurately discriminate prostate cancer patients from healthy people. We envision that miRoll-Cas may be readily translated to clinical applications in the diagnosis of a variety of diseases beyond cancer.

Mutations in microRNA-128-2-3p identified with amplification-free hybridization assay

We describe a quantitative detection method for mutated microRNA in human plasma samples. Specific oligonucleotides designed from a Peyrard-Bishop model allowed accurate prediction of target:probe recognition affinity and specificity. Our amplification-free tandem bead-based hybridization assay had limit of detection of 2.2 pM. Thereby, the assay allowed identification of single-nucleotide polymorphism mismatch profiles in clinically relevant microRNA-128-2-3p, showing terminal mutations that correlate positively with inflammatory colitis and colorectal cancer.

SARS-CoV-2-associated organs failure and inflammation: a focus on the role of cellular and viral microRNAs

SARS-CoV-2 has been responsible for the recent pandemic all over the world, which has caused many complications. One of the hallmarks of SARS-CoV-2 infection is an induced immune dysregulation, in some cases resulting in cytokine storm syndrome, acute respiratory distress syndrome and many organs such as lungs, brain, and heart that are affected during the SARS-CoV-2 infection. Several physiological parameters are altered as a result of infection and cytokine storm. Among them, microRNAs (miRNAs) might reflect this poor condition since they play a significant role in immune cellular performance including inflammatory responses. Both host and viral-encoded miRNAs are crucial for the successful infection of SARS-CoV-2. For instance, dysregulation of miRNAs that modulate multiple genes expressed in COVID-19 patients with comorbidities (e.g., type 2 diabetes, and cerebrovascular disorders) could affect the severity of the disease. Therefore, altered expression levels of circulating miRNAs might be helpful to diagnose this illness and forecast whether a COVID-19 patient could develop a severe state of the disease. Moreover, a number of miRNAs could inhibit the expression of proteins, such as ACE2, TMPRSS2, spike, and Nsp12, involved in the life cycle of SARS-CoV-2. Accordingly, miRNAs represent potential biomarkers and therapeutic targets for this devastating viral disease. In the current study, we investigated modifications in miRNA expression and their influence on COVID-19 disease recovery, which may be employed as a therapy strategy to minimize COVID-19-related disorders.

AF9 sustains glycolysis in colorectal cancer via H3K9ac-mediated PCK2 and FBP1 transcription

BACKGROUND

The tumourigenesis of various cancers is influenced by epigenetic deregulation. Among 591 epigenetic regulator factors (ERFs) examined, AF9 showed significant inhibition of malignancy in colorectal cancer (CRC) based on our wound healing assays. However, the precise role of AF9 in CRC remains to be explored.

METHODS

To investigate the function of AF9 in CRC, we utilised small interfering RNAs (siRNAs) to knock down the expression of 591 ERFs. Subsequently, we performed wound healing assays to evaluate cell proliferation and migration. In vitro and in vivo assays were conducted to elucidate the potential impact of AF9 in CRC. Clinical samples were analysed to assess the association between AF9 expression and CRC prognosis. Additionally, an Azoxymethane-Dextran Sodium Sulfate (AOM/DSS) induced CRC AF9IEC-/- mouse model was employed to confirm the role of AF9 in CRC. To identify the target gene of AF9, RNA-seq and coimmunoprecipitation analyses were performed. Furthermore, bioinformatics prediction was applied to identify potential miRNAs that target AF9.

RESULTS

Among the 591 ERFs examined, AF9 exhibited downregulation in CRC and showed a positive correlation with prolonged survival in CRC patients. In vitro and in vivo assays proved that depletion of AF9 could promote cell proliferation, migration as well as glycolysis. Specifically, knockout of MLLT3 (AF9) in intestinal epithelial cells significantly increased tumour formation induced by AOM/DSS. We also identified miR-145 could target 3'untranslated region of AF9 to suppress AF9 expression. Loss of AF9 led to decreased expression of gluconeogenic genes, including phosphoenolpyruvate carboxykinase 2 (PCK2) and fructose 1,6-bisphosphatase 1 (FBP1), subsequently promoting glucose consumption and tumourigenesis.

CONCLUSIONS

AF9 is essential for the upregulation of PCK2 and FBP1, and the disruption of the miR-145/AF9 axis may serve as a potential target for the development of CRC therapeutics.

Sensitive analysis of miRNAs via primer exchange reaction integrated with hairpin catalytic reaction

MicroRNAs (miRNAs) can serve as potential biological targets for early screening, targeted therapy, and prognosis in ovarian cancer (OC). However, sensitive and reliable quantification and identification of miRNA remain a huge challenge. Herein, we proposed a simple and reliable approach for the ultra-sensitive detection of miRNA by integrating endonuclease-III (Exo-III) assisted signal recycle, primer exchange reaction (PER), and hairpin catalytic reaction (HCR). In this method, target miRNA specifically binds with toehold sequence to form a blunt 3' terminus in the detection probe (dumbbell probe) that can be recognized by Exo-III, and to initiate subsequent signal amplifications. Based on this, the approach is successfully utilized in detecting OC related miRNAs with high sensitivity (limit of detection for miRNA-211 was 13 aM) and stability. By simply changing the toehold sequence in detection probe, the established approach can be easily extended to other miRNA detection. We believe that the platform is robust in detecting OS related biomarkers and is promising in renovating cancer diagnostic tools.

Single cell quantification of microRNA from small numbers of non-invasively sampled primary human cells

Expression levels of microRNAs (miRNAs) in single cells are low and conventional miRNA detection methods require amplification that can be complex, time-consuming, costly and may bias results. Single cell microfluidic platforms have been developed; however, current approaches are unable to absolutely quantify single miRNA molecules expressed in single cells. Herein, we present an amplification-free sandwich hybridisation assay to detect single miRNA molecules in single cells using a microfluidic platform that optically traps and lyses individual cells. Absolute quantification of miR-21 and miR-34a molecules was achieved at a single cell level in human cell lines and validated using real-time qPCR. The sensitivity of the assay was demonstrated by quantifying single miRNA molecules in nasal epithelial cells and CD3⁺ T-cells, as well as nasal fluid collected non-invasively from healthy individuals. This platform requires ~50 cells or ~30 µL biofluid and can be extended for other miRNA targets therefore it could monitor miRNA levels in disease progression or clinical studies.

Intrauterine Smoke Exposure, microRNA Expression during Human Lung Development, and Childhood Asthma

Intrauterine smoke (IUS) exposure during early childhood has been associated with a number of negative health consequences, including reduced lung function and asthma susceptibility. The biological mechanisms underlying these associations have not been established. MicroRNAs regulate the expression of numerous genes involved in lung development. Thus, investigation of the impact of IUS on miRNA expression during human lung development may elucidate the impact of IUS on post-natal respiratory outcomes. We sought to investigate the effect of IUS exposure on miRNA expression during early lung development. We hypothesized that miRNA-mRNA networks are dysregulated by IUS during human lung development and that these miRNAs may be associated with future risk of asthma and allergy. Human fetal lung samples from a prenatal tissue retrieval program were tested for differential miRNA expression with IUS exposure (measured using placental cotinine concentration). RNA was extracted and miRNA-sequencing was performed. We performed differential expression using IUS exposure, with covariate adjustment. We also considered the above model with an additional sex-by-IUS interaction term, allowing IUS effects to differ by male and female samples. Using paired gene expression profiles, we created sex-stratified miRNA-mRNA correlation networks predictive of IUS using DIABLO. We additionally evaluated whether miRNAs were associated with asthma and allergy outcomes in a cohort of childhood asthma. We profiled pseudoglandular lung miRNA in n = 298 samples, 139 (47%) of which had evidence of IUS exposure. Of 515 miRNAs, 25 were significantly associated with intrauterine smoke exposure (q-value < 0.10). The IUS associated miRNAs were correlated with well-known asthma genes (e.g., ORM1-Like Protein 3, ORDML3) and enriched in disease-relevant pathways (oxidative stress). Eleven IUS-miRNAs were also correlated with clinical measures (e.g., Immunoglobulin E andlungfunction) in children with asthma, further supporting their likely disease relevance. Lastly, we found substantial differences in IUS effects by sex, finding 95 significant IUS-miRNAs in male samples, but only four miRNAs in female samples. The miRNA-mRNA correlation networks were predictive of IUS (AUC = 0.78 in males and 0.86 in females) and suggested that IUS-miRNAs are involved in regulation of disease-relevant genes (e.g., A disintegrin and metalloproteinase domain 19 (ADAM19), LBH regulator of WNT signaling (LBH)) and sex hormone signaling (Coactivator associated methyltransferase 1(CARM1)). Our study demonstrated differential expression of miRNAs by IUS during early prenatal human lung development, which may be modified by sex. Based on their gene targets and correlation to clinical asthma and atopy outcomes, these IUS-miRNAs may be relevant for subsequent allergy and asthma risk. Our study provides insight into the impact of IUS in human fetal lung transcriptional networks and on the developmental origins of asthma and allergic disorders.

Integration of on-chip lysis and paper-based sensor for rapid detection of viral and exosomal RNAs

In recent years, paper-based nucleic acid sensors have been demonstrated for the ability to detect DNA and RNA molecules extracted from viruses and bacteria. In clinical samples, these nucleic acids are mostly encapsulated in lipid membranes and need to be released before being analyzed using paper-based sensors. For the nucleic acid amplification tests (NAATs), it is also desirable to remove the interfering molecules that can inhibit the nucleic acid amplification. To achieve a field deployable NAAT, we report a portable sensor system that combines the thermolysis and paper-based NAATs to detect target RNA molecules carried by viral and exosomal nanoparticles. The sensor cartridge includes a lysis chamber with a pressure-controlled diaphragm valve, paper flow channels, and three paper-based NAAT reaction chambers to extract, transport, and detect nucleic acids respectively. A compact instrument was prototyped to automate the assay, collect fluorescence images of the nucleic acid amplification, and generate amplification curves for NAATs. The pump-free and paper-based sensor achieved quantitative analysis of influenza A virus (IAV) RNA and exosome microRNA within 1 h, with the lowest detect concentration of 10⁴ TCID₅₀/mL and 10⁶ EV/mL for IAV and exosome, respectively. Owing to the advantages of easy storage, simple operation, and low cost, such as system has great potential to be used as a point-of-care test for in-field diagnosis of viral and bacterial infections.

Harnessing the LdCsm RNA Detection Platform for Efficient microRNA Detection

In cancer diagnosis, diverse microRNAs (miRNAs) are used as biomarkers for carcinogenesis of distinctive human cancers. Thus, the detection of these miRNAs and their quantification are very important in prevention of cancer diseases in human beings. However, efficient RNA detection often requires RT-PCR, which is very complex for miRNAs. Recently, the development of CRISPR-based nucleic acid detection tools has brought new promises to efficient miRNA detection. Three CRISPR systems can be explored for miRNA detection, including type III, V, and VI, among which type III (CRISPR-Cas10) systems have a unique property as they recognize RNA directly and cleave DNA collaterally. In particular, a unique type III-A Csm system encoded by Lactobacillus delbrueckii subsp. bulgaricus (LdCsm) exhibits robust target RNA-activated DNase activity, which makes it a promising candidate for developing efficient miRNA diagnostic tools. Herein, LdCsm was tested for RNA detection using fluorescence-quenched DNA reporters. We found that the system is capable of specific detection of miR-155, a microRNA implicated in the carcinogenesis of human breast cancer. The RNA detection system was then improved by various approaches including assay conditions and modification of the 5'-repeat tag of LdCsm crRNAs. Due to its robustness, the resulting LdCsm detection platform has the potential to be further developed as a better point-of-care miRNA diagnostics relative to other CRISPR-based RNA detection tools.

Epigenetic Dysregulation in Alcohol-Associated Behaviors: Preclinical and Clinical Evidence

Alcohol use disorder (AUD) is characterized by loss of control over intake and drinking despite harmful consequences. At a molecular level, AUD is associated with long-term neuroadaptations in key brain regions that are involved in reward processing and decision-making. Over the last decades, a great effort has been made to understand the neurobiological basis underlying AUD. Epigenetic mechanisms have emerged as an important mechanism in the regulation of long-term alcohol-induced gene expression changes. Here, we review the literature supporting a role for epigenetic processes in AUD. We particularly focused on the three most studied epigenetic mechanisms: DNA methylation, Histone modification and non-coding RNAs. Clinical studies indicate an association between AUD and DNA methylation both at the gene and global levels. Using behavioral paradigms that mimic some of the characteristics of AUD, preclinical studies demonstrate that changes in epigenetic mechanisms can functionally impact alcohol-associated behaviors. While many studies support a therapeutic potential for targeting epigenetic enzymes, more research is needed to fully understand their role in AUD. Identification of brain circuits underlying alcohol-associated behaviors has made major advances in recent years. However, there are very few studies that investigate how epigenetic mechanisms can affect these circuits or impact the neuronal ensembles that promote alcohol-associated behaviors. Studies that focus on the role of circuit-specific and cell-specific epigenetic changes for clinically relevant alcohol behaviors may provide new insights on the functional role of epigenetic processes in AUD.

The Role of MicroRNAs in Myocarditis-What Can We Learn from Clinical Trials?

Myocarditis is an inflammatory disease of the heart with a viral infection as the most common cause. It affects most commonly young adults. Although endomyocardial biopsy and cardiac magnetic resonance are used in the diagnosis, neither of them demonstrates all the required qualities. There is a clear need for a non-invasive, generally available diagnostic tool that will still remain highly specific and sensitive. These requirements could be possibly met by microribonucleic acids (miRNAs), which are small, non-coding RNA molecules that regulate many fundamental cell functions. They can be isolated from cells, tissues, or body fluids. Recently, several clinical studies have shown the deregulation of different miRNAs in myocarditis. The phase of the disease has also been evidenced to influence miRNA levels. These changes have been observed both in adult and pediatric patients. Some studies have revealed a correlation between the change in particular miRNA concentration and the degree of cardiac damage and inflammation. All of this indicates miRNAs as potential novel biomarkers in the diagnosis of myocarditis, as well as a prognostic tool for this condition. This review aims to summarize the current knowledge about the role of miRNAs in myocarditis based on the results of clinical studies.

Duplex-specific nuclease and Exo-III enzyme-assisted signal amplification cooperating DNA-templated silver nanoclusters for label-free and sensitive miRNA detection

Development of novel miRNA detection strategies plays a crucial role in fundamental research and clinical diagnosis of various diseases, such as infantile pneumonia. We herein develop a rapid and sensitive DNA-templated AgNCs-based miRNA detection approach, pinning the hope on an improved detection sensitivity in an easy-to-operate way. In the method, a hairpin probe is designed to specifically bind with target miRNA, and to initiate the DSN enzyme and Exo-III-assisted dual signal recycles. The resultant guanine-rich DNA sequences after signal amplification turn on the fluorescence of the dark AgNCs by hybridizing with the DNA template of the dark AgNCs. The generated signals are correlated with the amounts of target miRNA in the sensing system. Through a series of experiments, the established approach exhibits a great dynamic range of more than seven orders of magnitude with a low limit of detection of 245 aM, holding great promises for miRNA-related researches and disease diagnosis.

Graphical abstract

Integrated Tissue and Blood miRNA Expression Profiles Identify Novel Biomarkers for Accurate Non-Invasive Diagnosis of Breast Cancer: Preliminary Results and Future Clinical Implications

We aimed to identify miRNAs that were closely related to breast cancer (BRCA). By integrating several methods including significance analysis of microarrays, fold change, Pearson’s correlation analysis, t test, and receiver operating characteristic analysis, we developed a decision-tree-based scoring algorithm, called Optimized Scoring Mechanism for Primary Synergy MicroRNAs (O-PSM). Five synergy miRNAs (hsa-miR-139-5p, hsa-miR-331-3p, hsa-miR-342-5p, hsa-miR-486-5p, and hsa-miR-654-3p) were identified using O-PSM, which were used to distinguish normal samples from pathological ones, and showed good results in blood data and in multiple sets of tissue data. These five miRNAs showed accurate categorization efficiency in BRCA typing and staging and had better categorization efficiency than experimentally verified miRNAs. In the Protein-Protein Interaction (PPI) network, the target genes of hsa-miR-342-5p have the most regulatory relationships, which regulate carcinogenesis proliferation and metastasis by regulating Glycosaminoglycan biosynthesis and the Rap1 signaling pathway. Moreover, hsa-miR-342-5p showed potential clinical application in survival analysis. We also used O-PSM to generate an R package uploaded on github (SuFei-lab/OPSM accessed on 22 October 2021). We believe that miRNAs included in O-PSM could have clinical implications for diagnosis, prognostic stratification and treatment of BRCA, proposing potential significant biomarkers that could be utilized to design personalized treatment plans in BRCA patients in the future.

Pro-Neurotensin as a Potential Novel Diagnostic Biomarker for Detection of Nonalcoholic Fatty Liver Disease

BACKGROUND AND AIMS

Currently, liver biopsy is the gold standard method for diagnosis of non-alcoholic fatty liver severity. It is critical to develop non-invasive diagnostic method to diagnose nonalcoholic fatty liver rather than invasive techniques. Our case-control study was to address the value of circulating miRNA-122 and serum pro-neurotensin as a potential non-invasive biomarker for the diagnosis of non-alcoholic fatty acid diseases.

METHODS

Clinical assessment, laboratory investigations, and anthropometric measurements were reported for 157 patients with proven NAFLD. Apparently, healthy participants (n=100) were enrolled as a control group. Serum samples were tested for micro-RNAs-122 and pro-neurotensin.

RESULTS

Compared with the control subjects, both mi-RNA-122 and serum proneurotensin levels were increased in NAFLD (p<0.001) and at a cut-off ≥6.83, mi-RNA-122 had 51.0% sensitivity, 70.0% specificity to differentiate NAFLD from healthy controls, while serum proneurotensin had 80.0% sensitivity and 80.0% specificity at a cutoff ≥108.

CONCLUSION

The circulating pro-neurotensin might be used as a novel biomarker for diagnosis of patients with NAFLD, wherefore the integration of a circulating mi-RNA-122 and serum pro-neurotensin could be beneficial to diagnose NAFLD cases. Large-scale studies are needed to investigate the possible role of mi-RNA-122 and pro-neurotensin in the development, progression, and prognosis of NAFLD and NASH.

Construction of simple and sensitive pancreatitis related microRNA detection strategy via self-priming triggered cascade signal amplification

Pancreatic diseases, such as pancreatitis and pancreatic cancer, remain the most threatening gastrointestinal diseases with a high mortality due to atypical symptoms. MicroRNA plays crucial roles in regulating metastasis and cell proliferation of pancreatic cancer, constituting important biomarkers for the early diagnosis of pancreatic cancers. Herein, we develop a sensitive and simple exosomal miRNA detection method with only a dual-hairpin-probe. In detail, the dual-hairpin-probe is constructed through combination of two functional sections for both target miRNA identification and signal amplification. With only one probe, the method possesses the capability to avoid interferences from concentration changes of other probes, and exhibits a higher stability which is demonstrated through the obtained low coefficients of variation (CV) of 6.73%. With let-7a as detection target, the LOD of the established method is determined to be 243 aM, while maintaining a high discriminating capability towards let-7a homogenous miRNAs.

High-Throughput Sequencing to Investigate lncRNA-circRNA-miRNA-mRNA Networks Underlying the Effects of Beta-Amyloid Peptide and Senescence on Astrocytes

Astrocytes are widely distributed in the central nervous system and play an essential role in the function of neuronal cells. Associations between astrocytes and Alzheimer's disease (AD) have been noted, and recent work has implicated circular RNA (circRNA) and long non-coding RNA (lncRNA) in the development of AD. However, few reports have investigated which lncRNA and circRNA are involved in the influence of amyloid beta (Aβ) and senescence on astrocytes. This study therefore examines changes at the transcriptome level to explore the effects of Aβ and senescence on astrocytes. Primary cultured astrocytes were treated with Aβ and cultured for 90 days in vitro, and high-throughput sequencing was performed to identify differentially expressed RNAs. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that differentially expressed genes were associated with the focal adhesion signaling pathway, extracellular matrix receptor signaling pathway, and the extracellular matrix. The protein-protein interaction network was then constructed, and 103 hub genes were screened out; most of these were strongly associated with the expression of the extracellular matrix, extracellular matrix receptor signaling pathway, and focal adhesion. Two competing endogenous RNA networks were constructed based on the selected hub gene and differential RNAs, and we identified multiple competing endogenous RNA regulatory axes that were involved in the effects of Aβ and senescence on astrocytes. This is the first study to explore the molecular regulation mechanism of Aβ and senescence on primary astrocytes from the perspective of the whole transcriptome. In uncovering the signaling pathways and biological processes involved in the effects of Aβ and senescence on astrocytes, this work provides novel insights into the pathogenesis of AD at the level of competing endogenous RNA network regulation.

Sensitive and convenient detection of miRNA-145 using a gold nanoparticle-HCR coupled system: computational and in vitro validations

Multiple sclerosis (MS) remains a challenging disease that requires timely diagnosis. Therefore, an ultrasensitive optical biosensor based on hybridization chain reaction (HCR) was developed to detect microRNA-145 (miRNA-145) as an MS biomarker. To construct such a sensor, HCR occurred between specific hairpin probes, as MB1 contains a poly-cytosine nucleotide loop and MB2 has a poly-guanine nucleotide sticky end. By introducing miR-145 as a target sequence, long-range dsDNA polymers are formed. Then, positively charged gold nanoparticles (AuNPs) were incubated with the HCR product, which adsorbed onto the dsDNA polymers due to electrostatic adsorption. This resulted in the precipitation of the AuNPs. By incubating different concentrations of miR-145 with AuNPs, the changes in the UV-vis spectrum of the supernatant were analyzed. The proposed biosensor showed a great ability to detect miR-145 in a wide linear range from 1 pM-1 nM with an excellent detection limit (LOD) of 0.519 nM. Furthermore, the developed biosensor indicated considerable selectivity in discriminating between miR-145 and mismatched sequences. It shows high selectivity in differentiating targets. Interestingly, the proposed method was also able to detect miRNA-145 in the diluted serum samples. In conclusion, this sensing platform exhibits high selectivity and specificity for the detection of circulating microRNAs, which holds great promise for translation to routine clinical applications.

Key plasma microRNAs variations in patients with Plasmodium vivax malaria in Iran

Introduction

As the cause of RBC infection and splenomegaly, malaria remains a major parasitic disease in the world. New specific biomarkers such as MicroRNAs (miRNAs) are developed to accurately diagnose malaria and clarify its pathologic changes. This study aimed at evaluating changes in the plasma miRNAs markers of Plasmodium vivax in patients with malaria in Chabahar, Iran.

Materials and methods

For the present descriptive-analytical study conducted in 2018, we collected blood samples from 20 individuals. Real-time quantitative Polymerase Chain Reaction (RT-qPCR) was used to measure the plasma levels of miR-145, miR-155, miR-191 and miR-223-3p.

Results

The 2-ΔΔCT method of Real-time PCR showed the plasma levels of miR-223, miR-145 and miR-155 to respectively be 5.6, 16.9 and 1.7 times higher in patients with P. vivax compared to those in healthy individuals. The expressions of all the three miRNAs significantly increased in patients with malaria compared to in the controls (P < 0.05). The expression of miR-191 was 1.405 times higher in patients with malaria compared to that in the controls, although the difference was statistically insignificant.

Conclusion

The present study found P. vivax to change host miRNAs such as miR-223, miR-145 and miR-155. These small molecules thus appeared to constitute biomarkers for P. vivax malaria assessment.

Selection of reference genes for quantitative analysis of microRNA expression in three different types of cancer

MicroRNAs (miRNAs) are promising biomarkers in cancer research. Quantitative PCR (qPCR), also known as real-time PCR, is the most frequently used technique for measuring miRNA expression levels. The use of this technique, however, requires that expression data be normalized against reference genes. The problem is that a universal internal control for quantitative analysis of miRNA expression by qPCR has yet to be known. The aim of this work was to find the miRNAs with stable expression in the thyroid gland, brain and bone marrow according to NanoString nCounter miRNA quantification data. As a results, the most stably expressed miRNAs were as follows: miR-361-3p, -151a-3p and -29b-3p in the thyroid gland; miR-15a-5p, -194-5p and -532-5p in the brain; miR-140-5p, -148b-3p and -362-5p in bone marrow; and miR-423-5p, -28-5p and -532-5p, no matter what tissue type. These miRNAs represent promising reference genes for miRNA quantification by qPCR.

Long non-coding RNA LINRIS is upregulated in non-small cell lung cancer and its silencing inhibits cell proliferation by suppressing microRNA-10a maturation

Long noncoding RNA LINRIS (LINC00920) is known to participate in colorectal cancer. This study aimed to explore the role of LINRIS in non-small cell lung cancer (NSCLC). NSCLC and adjacent non-tumor tissues were collected from 62 NSCLC patients. LINRIS expression was detected using real-time quantitative PCR (RT-qPCRs). The 62 NSCLC patients were monitored every month for 5 years to evaluate the role of LINRIS in predicting the prognosis of NSCLC. The effects of LINRIS silencing on microRNA-10a (miR-10a) precursor and mature miR-10a levels were assessed by RT-qPCR. Cell proliferation was measured using Cell Counting Kit-8 (CCK-8) assays. LINRIS expression was upregulated in NSCLC tissues. High LINRIS levels predicted poor survival of NSCLC patients. LINRIS were positively correlated with mature (miR-10a) levels but not miR-10a precursor. In NSCLC cells, LINRIS silencing showed no role in miR-10a precursor accumulation but downregulated mature miR10a level. Moreover, LINRIS silencing inhibited cell proliferation, while miR-10a overexpression increased cell proliferation and inhibited the role of LINRIS silencing. Overall, LINRIS silencing may inhibit NSCLC cell proliferation by suppressing miR-10a maturation.

Abbreviations: Non-small cell lung cancer (NSCLC); Reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR); LncRNA long intergenic noncoding RNA for IGF2BP2 stability (LINRIS).

miR-3648 promotes lung adenocarcinoma-genesis by inhibiting SOCS2 (suppressor of cytokine signaling 2)

Lung adenocarcinoma (LUAD) is the most common histologic subtype of lung cancer and is associated with high morbidity and mortality. We aimed to study the effects of microRNA-3648 (miR-3648) on LUAD by inhibiting its downstream target suppressor of cytokine signaling 2 (SOCS2) mRNA. miR-3648 expression was measured by real-time quantitative PCR in LUAD and normal lung epithelial cell lines. The direct interaction between miR-3648 and SOCS2 mRNA was identified through luciferase reporter and RNA pull-down assays. Cell viability, migration, and invasion were examined using cell functional assays. MiR-3648 was found to be overexpressed in LUAD cells and tissues. Overexpression of miR-3648 significantly enhanced cell proliferation, migration, and invasion abilities in LUAD cells. Furthermore, SOCS2 was targeted by miR-3648, and co-transfection of a miR-3648 inhibitor or si-SOCS2 reversed the suppressive effects of SOCS2 in PC9 and A549 cells. miR-3648 enhanced the proliferation and promoted migration and invasion of LUAD by inhibiting SOCS2. In conclusion, our results indicate that miR-3648 plays a pivotal role in LUADe progression and might thus provide a novel therapeutic strategy for patients with LUAD.

A portable system for isothermal amplification and detection of exosomal microRNAs

Exosomal microRNAs (miRNAs) play a key role in cell-cell communication to regulate gene expression in target cells and have great potential as biomarkers for disease diagnosis. This paper reports an on-chip exosomal miRNA amplification and detection system for rapid analysis of exosomal miRNAs. The compact system consists of two connected flow cells for processing exosomes and detecting miRNAs, respectively. The miRNAs extracted from exosomes were quantitatively measured using the on-chip exponential amplification reaction (EXPAR) assay. The sensor chip was designed to store multiple oligonucleotide templates for the EXPAR, mix sample and reagent, and simultaneously analyze multiple exosomal miRNAs of interest. To facilitate the miRNA analysis, a portable detection instrument was built on an IoT platform using a low-cost microcontroller to execute the EXPAR assay, collect fluorescent images, and analyze amplification curves. Here, we studied the miRNA profiles carried by exosomes derived from three different phenotypes of tissue macrophages. The affordable instrument, rapid assay, multiplexed analysis, as well as disposable sensor chip, would boost the development of point-of-care liquid biopsy tests using exosomal miRNAs.

DNA-Protein Cross-Linking Sequencing for Genome-Wide Mapping of Thymidine Glycol

Thymidine glycol (Tg) is the most prevalent form of oxidatively induced pyrimidine lesions in DNA. Tg can arise from direct oxidation of thymidine in DNA. In addition, 5-methyl-2'-deoxycytidine (5-mdC) can be oxidized to 5-mdC glycol, and its subsequent deamination also yields Tg. However, Tg's distribution in the human genome remains unknown. Here, we presented a DNA-protein cross-linking sequencing (DPC-Seq) method for genome-wide mapping of Tg in human cells. Our approach capitalizes on the specificity of a bifunctional DNA glycosylase, i.e., NTHL1, for the covalent labeling, as well as DPC pulldown, SDS-PAGE fractionation, and membrane transfer for highly efficient and selective enrichment of Tg-bearing DNA. By employing DPC-Seq, we detected thousands of Tg sites in the human genome, where dual ablation of NTHL1 and NEIL1, the major DNA glycosylases responsible for Tg repair, led to pronounced increases in the number of Tg peaks. In addition, Tg is depleted in genomic regions associated with active transcription but enriched at nucleosome-binding sites, especially at heterochromatin sites marked with H3K9me2. Collectively, we developed a DPC-Seq method for highly efficient enrichment of Tg-containing DNA and for genome-wide mapping of Tg in human cells. Our work offers a robust tool for future functional studies of Tg in DNA, and we envision that the method can also be adapted for mapping other modified nucleosides in genomic DNA in the future.

An Emerging Role of miRNAs in Neurodegenerative Diseases: Mechanisms and Perspectives on miR146a

Significance: Advancements in and access to health care have led to unprecedented improvements in the quality of life and increased lifespan of human beings in the past century. However, aging is a significant risk factor for neurodegenerative diseases (NDs). Hence, improved life expectancy has led to an increased incidence of NDs. Despite intense research, effective treatments for NDs remain elusive. The future of neurotherapeutics development depends on effective disease modification strategies centered on carefully scrutinized targets. Recent Advances: As a promising new direction, recent evidence has demonstrated that epigenetic processes modify diverse biochemical pathways, including those related to NDs. Small non-coding RNAs, known as microRNAs (miRNAs), are components of the epigenetic system that alter the expression of target genes at the post-transcriptional level. Critical Issues: miRNAs are expressed abundantly in the central nervous system and are critical for the normal functioning and survival of neurons. Here, we review recent advances in elucidating miRNAs' roles in NDs and discuss their potential as therapeutic targets. In particular, neuroinflammation is a major pathological hallmark of NDs and miR146a is a crucial regulator of inflammation. Future Directions: Finally, we explore the possibilities of developing miR146a as a potential biomarker and therapeutic target where additional research may help facilitate the detection and amelioration of neuroinflammation in NDs. Antioxid. Redox Signal. 35, 580-594.