Real-time quantification of microRNAs by stem-loop RT-PCR

MEMO: A micro memo sensor detecting microRNA-RISC using an accurate cell-free expression platform

Circulating microRNAs have emerged as potential prognostic biomarkers of various diseases. They serve as micro memos sent out by cells, which scientists can intercept to gain real-time insights into cellular and disease status. However, establishing a standardized microRNA detection platform remains a challenge. Here, we integrate the RNA-induced silencing complex (RISC), which occupies mature microRNAs, into a complex cell-free synthetic genetic circuit using three different RNA polymerases, creating an innovative microRNA biosensor that is sensitive, precise, and cost-effective. The RISC protects the microRNA degradation during isolation and ensures the elimination of false target interactions, enhancing the detection robustness. With a limit of detection of 81 pM, affordability, and the possibility for on-demand use, this system proves to be a strong miRNA sensing tool.

Quantitative determination of intracellular miRNA content using dual gold and iron nanoreporters and single particle ICP-ToF-MS

MicroRNAs (miRNAs) are short single-stranded RNA sequences that play an important role in the initiation and progression of cancer. Therefore, the present work tries to establish an analytical platform for the quantitative determination of miRNA in cancer cell models without enzymatic amplification reactions. The developed assay is based on a sandwich double-hybridization reaction using a capture oligonucleotide conjugated to magnetic iron oxide microparticles and detecting oligonucleotide conjugated to a 40-nm gold nanoparticle, both particles coated with streptavidin. The optimization of the double-hybridization assay is conducted using inductively coupled plasma in single particle mode with a time-of-flight analyzer (SP-ICP-ToF-MS) for double detection of Au and Fe within the same event. The developed strategy was directly applied to the quantification of miR-16-5p in cell lysates without amplification reactions. For this aim, the cancer cell line of melanoma (A375) was studied, and two sample preparation strategies have been evaluated. Sequence capturing in extracted RNA provided best results allowing the determination at about 200 pM of miR-16-5p (for 2 × 106 cells). This strategy represents one of the few alternatives to obtain absolute quantification of miRNA in biological samples to permit the direct comparison among cell lines without amplification or transformation reactions of the original sequence.

Altered levels of angiogenin and tRNA-derived fragments associate with severe asthma

Recent discoveries highlight angiogenin (ANG) and 5' tRNA-derived fragments as key factors in stress response and cell survival. To explore their role in asthma pathogenesis, particularly in severe cases, we evaluated the levels of ANG and 5' tRNA halves (tRHs) derived from tRNA Glu (5'-tRH Glu: tRF-32-87R8WP9N1EWJM) and tRNA Gly (5'-tRH Gly: tRF-30-PNR8YP9LON4V), two abundant tRHs in the respiratory tract, in sputum and blood samples from asthmatic patients. We found ANG expression is significantly increased in circulating leukocytes from severe asthma patients but not in sputum infiltrates. On the contrary, tRHs levels showed significant alterations only in extracellular compartments. Both tRHs were downregulated in the plasma of asthmatic patients, while elevated 5'-tRH Gly levels were observed in severe sputum samples, indicating tissue-specific roles in disease pathology. Additionally, tRH expression in leukocytes was negatively associated with the disrupted corticosteroid response in asthmatic patients. Altered levels of ANG and 5'-tRH Glu and 5'-tRH Gly were further validated in an in vitro model of pollutant-aggravated, allergen-stimulated macrophages. In summary, our findings provide new insights into the role of ANG and tRHs in asthma pathogenesis, highlighting their potential as novel markers for asthma phenotyping.

Efficient delivery of small RNAs to podocytes in vitro by direct exosome transfection

BACKGROUND

Podocytes are a crucial component of the glomerular filtration barrier, and changes in their 3D structure contribute to over 80% of chronic kidney disease (CKD) cases. Exosomal small RNAs play a key role in cell-cell communication in CKD and may serve as nanocarriers for delivering small RNAs into podocytes. However, the uptake of exosomal cargo by podocytes remains poorly understood. This study explores the use of isolated exosomes, directly transfected with fluorescently-labeled small RNAs, for tracking and delivering small RNAs to cultured podocytes.

METHODS

Exosomes were isolated from immortalized murine podocytes and transfected with Cy3-labeled siRNA and miRNA controls using the ExoFect siRNA/miRNA Transfection Kit. We characterized the transfected exosomes via transmission electron microscopy (TEM) and Western blot for exosomal markers CD9 and TSG101. Subsequently, we co-cultured these exosomes with podocytes and used confocal laser-scanning microscopy (cLSM), and structured illumination microscopy (SIM) to visualize cargo uptake, confirmed through flow cytometry, imaging flow cytometry and immunofluorescence staining for Rab5, Rab7, and CD9. The isolated exosomes were also transfected with pre-miR-21 and filamin A (FlnA)-siRNAs before being co-cultured with podocytes. We confirmed the efficiency of transfection and knockdown using RT-qPCR, Western blotting, and immunofluorescence staining.

RESULTS

TEM revealed that the exosomes maintained a consistent shape and size of approximately 20 nm posttransfection and exhibited a stable expression of CD9 and TSG101. Flow cytometry and immunofluorescence imaging showed that podocytes take up Cy3-labeled exosomal miRNAs and siRNAs time-dependently, utilizing various mechanisms, including encapsulation within vesicular structures, endocytosis and free distribution within the cells. Transfection of exosomes with FlnA-siRNAs resulted in a significant 2.8-fold reduction of filamin A expression in co-cultured podocytes, while pre-miR-21-transfected exosomes led to a remarkable 338-fold increase in mature miR-21 levels.

CONCLUSIONS

These findings demonstrate that direct exosome transfection with fluorescently-labeled small RNAs is an effective method for tracking exosomal cargo in podocytes. This study is the first to show that directly transfected exosomes can deliver small RNAs to podocytes in vitro, suggesting their potential as RNA carriers for therapeutic strategies in more complex settings.

Dual-Amplification CRISPR Biosensor for Ultrasensitive miRNA Detection: A Powerful Tool for Cancer and Immune Monitoring

MicroRNAs (miRNAs) are pivotal regulators of gene expression and emerging biomarkers for cancer diagnosis and inflammation monitoring. Sensitive and specific detection methods for miRNAs are crucial for advancing their clinical and research applications. In this study, we present a CRISPR-based biosensor driven by a dual-circle amplification cascade. This system combines rolling circle amplification (RCA) for initial signal amplification and a secondary amplification cycle within the RCA products, enabling precise miRNA expression detection across different cell types. The method is highly sensitive and specific and requires minimal sample input. Using miRNA-221 as a model, the system demonstrated a linear detection range from 15 fM to 1 nM and a detection limit of 1.35 fM. It also effectively differentiated miRNA expression profiles across various cell types, supporting cell classification based on miRNA signatures. Furthermore, the platform's versatility was confirmed with miRNA-155, highlighting its ability to monitor miRNA expression changes in macrophages upon immune stimulation. The system's modular design allows easy adaptation to other miRNA targets, making it a robust tool for miRNA research. This biosensor provides a powerful approach for miRNA profiling in complex biological samples, offering valuable insights into cancer and inflammation with potential for clinical diagnostics and therapeutic monitoring.

The microRNA OsmiR393 regulates rice brown planthopper resistance by modulating the auxin-ROS signaling cross-talk

Auxin plays critical roles in plant development and stress response. However, the roles of auxin and the immune signaling factor, reactive oxygen species (ROS), in resistance to the brown planthopper (BPH), a notorious rice-specific piercing-sucking insect that causes severe yield losses, remain unclear. We revealed that moderate naphthalene acetic acid treatment activates rice resistance to BPH, BPH infestation induces ROS accumulation, and increase in ROS content promotes BPH resistance. Underlying these phenomena, the auxin receptors OsTIR1 and OsAFB2 positively, whereas the posttranscriptional regulator OsmiR393 negatively, regulate BPH resistance. Downstream of the OsmiR393/OsTIR1 module, through successive genetic function analysis of each gene, solid genetic relationship analysis, and various biochemical assays, we established an OsmiR393/OsTIR1-OsIAA10-OsARF12-OsRbohB genetic pathway that mediates BPH resistance, in which ROS are integral. Such cross-talk between auxin and ROS reveals the intricate signaling network underlying BPH resistance, which might assist with BPH resistance breeding.

Lomibuvir sensitizes radioiodine-resistant thyroid cancer cell lines to radioiodine treatment by targeting hTERT RNA-dependent polymerase activity

Radioactive iodine (RAI) is selectively used in the treatment of residual or recurrent differentiated thyroid cancer for over fifty years. However, radioiodine-refractory differentiated thyroid cancer (RAIR-DTC) is difficult to treat with radioactive iodine because of the decreased sodium iodide symporter (NIS) activity. Patients with RAIR-DTC derive limited benefit from RAI therapy, necessitating the exploration of new treatment options. In the current study, we aimed to explore the mechanism underlying thyroid cancer dedifferentiation and to provide new targets for RAIR therapy. We established a RAIR thyroid cancer cell line which was verified by the colony formation ability under radioiodine-131 treatment at doses up to 100 µCi. As expected, higher expressions of cancer stem cell genes, SOX2, CD133, and OCT4 A were found in RAIR cells compared to non-RAIR cells. Correspondingly, the expression of iodine-handling genes such as NIS, TPO, and Pendrin were downregulated. Interestingly, we discovered that the RNA-dependent RNA polymerase (RdRP) activity of TERT was also upregulated in RAIR cells, evidenced by the upregulation of phosphorylated telomerase reverse transcriptase (TERT), BRG1 and CDK1. Moreover, miR-146b-5p, transcribed by TERT gene, was likewise upregulated. RdRP inhibitor lomibuvir treatment downregulated miR-146b-5p level in RAIR cells, resulting in the upregulation of NIS gene expression. Lomibuvir not only restored the expressions of TPO and NIS but also downregulated the elevated ALDH1A1 and CD133 in RAIR cells. Consequently, the uptake of radioiodine-131 was significantly enhanced in these RAIR cells. Taken together, our research identifies novel therapeutic targets and provides new insights into the management of RAIR-DTC.

Therapeutic limitations of oncolytic VSVd51-mediated miR-199a-5p delivery in triple negative breast cancer models

Triple-negative breast cancer (TNBC) metastasis is driven, in part, by the epithelial-to-mesenchymal transition (EMT), a process critical for cancer cell migration and invasion. Current treatment options, including immunotherapies and targeted therapies, demonstrate limited efficacy in this aggressive disease, underscoring the need for innovative therapeutic approaches. Here, we present a novel approach integrating oncolytic virotherapy with RNA interference by engineering two variants of vesicular stomatitis virus (VSVd51) expressing pri- or pre-miR-199a-5p, a microRNA implicated in the regulation of EMT. We demonstrate that both viral constructs are functional and capable of overexpressing mature miR-199a-5p. In the human TNBC cell line MDA-MB-231, both viral variants inhibited the expression of ZEB1, a transcription factor central to EMT. However, in the mouse TNBC cell line 4T1, miR-199a-5p delivered via VSVd51 failed to disrupt EMT-related gene expression. In vivo testing of VSVd51-pre-miR-199 in the syngeneic BALB/c-4T1 mouse model revealed no significant survival benefits or reduction in tumor growth, even when coupled with primary tumor resection. Additional in vivo testing in immunodeficient mice using the MDA-MB-231 xenograft model showed no effect on tumor reduction. Our study highlights the challenges of integrating miRNA-based strategies with oncolytic viruses in a cancer context-specific manner and underscores the importance of vector selection and tumor model compatibility for therapeutic synergy.

A transformable DNA nanomachine serving as both walker and track for sensitive miRNA detection in living cells and tissues

DNA walkers are powerful nanomachines for biosensing and bioimaging, yet their application in microRNA detection faces significant challenges. Current DNA walker designs often involve complex structures with separate walker and track components, leading to reduced efficiency and potential interference in cellular environments. Here, we developed a self-propelled multi-leg walker (SMW) where autocatalytic hairpin assembly (ACHA) components are anchored on a DNA nanowire to create an initial track structure. Upon target recognition, catalytic hairpin assembly (CHA) reactions dynamically transform sections of track into multi-leg walkers with newly generated triggers. ACHA reactions are then initiated by these triggers, driving the walker to move autonomously along the unreacted track while generating amplified fluorescent signals. The SMW demonstrated excellent performance with a detection limit of 2.9 pM for miR-21, successfully distinguishing cancer cells from normal cells and enabling microRNA detection in clinical tissue samples. This innovative design strategy opens new possibilities for developing simplified yet efficient DNA nanomachines for broader biomedical applications.

Differentially expressed miRNAs in testes of dominant and subordinate Nile tilapia males and identification of oni-miR-499 as regulator of amh gene expression

INTRODUCTION

Gonadal development and reproduction are under the control of the endocrine system, which acts along the brain-pituitary-gonad (BPG) axis. Besides well-known regulators of the BPG axis, such as the gonadotropin-releasing hormone (GnRH), follicle-stimulating hormone (Fsh) and luteinizing hormone (Lh), the Anti-Müllerian hormone (Amh) came into the focus of research on the BPG axis. Amh is expressed differently in the gonads of dominant and subordinate Nile tilapia (Oreochromis niloticus) males and could be involved in the regulation of the differently developed gonads. In addition, the regulatory networks and the control of gene expression depend on microRNAs (miRNAs), an often not considered epigenetic mechanism in hormonal research.

METHODS

We used a long-term, stable social hierarchy of Nile tilapia males as an experimental system to identify differentially expressed miRNAs in the testes of dominant and subordinate animals. A Dual Luciferase Reporter Assay and in vitro analysis of amh expression in primary testis cells were used to demonstrate predicted interactions.

RESULTS

We identified 23 differentially expressed miRNAs in the testes of dominant and subordinate males and predicted the targets in the pools of differentially expressed genes. Using these data, we placed the identified GO terms and KEGG pathways in the context of differently developed gonads under social control. The most differentially expressed miRNA, oni-miR-499, is up-regulated in the testes of dominants and regulates amh expression.

CONCLUSION

We conclude that oni-miR-499 affects testis development via amh expression in Nile tilapia. Many miRNAs and biological processes identified in our study could be conserved mechanisms of testis development.

Blooming resilience: transcriptomic insights into cotton flower responses to boll weevil infestation

KEY MESSAGE

Cotton plants undergo a drastic transcriptional reprogramming after cotton boll weevil infestation, modulating several defense pathways to cope with the damage. The global demand for cotton fiber continues to rise, but pests and pathogens significantly hinder cotton production, causing substantial losses. Among these, the cotton boll weevil (Anthonomus grandis) is one of the most destructive pests. To investigate the molecular responses of cotton (Gossypium hirsutum) to boll weevil infestation, we evaluated the global gene expression of floral buds using mRNA-seq. Additionally, we analyzed the expression of non-coding RNAs, including microRNAs (miRNAs) and long intergenic non-coding RNAs (lincRNAs). Infestation by cotton boll weevil larvae triggered a rapid and drastic transcriptional reprogramming, with 1,656 and 1.698 genes modulated after two and twelve hours, respectively. Gene ontology enrichment analysis revealed significant regulation of defense-related and developmental processes, including photosynthesis, primary metabolism, and cell organization. Transcription factor families such as ERF, WRKY, GRAS, and NAC were strongly affected, highlighting their roles in coordinating defense responses. The jasmonate pathway showed intensive modulation, alongside secondary metabolite pathways like terpenoids and phenylpropanoids, which contribute to plant defense mechanisms. Non-coding RNAs also played a critical role in the response. We identified 921 unique known and novel miRNAs, with 36 modulated by the infestation, and predicted 98,850 putative lincRNAs, several of which were differentially expressed. Understanding the genetic and molecular mechanisms underlying cotton's defense against boll weevil, particularly during early infestation stages, is vital for developing biotechnological strategies to reduce pest damage. Our findings provide critical insights to enhance cotton resilience against herbivores.

miR-7977 regulates the locomotor behavior by targeting diuretic hormone and SIFamide receptors in Tribolium castaneum

Insect neuropeptides are crucial for chemical communication, influencing growth, metabolism, and behavior. MicroRNAs (miRNAs), as non-coding RNAs, primarily regulate target gene expression. However, the co-regulation between miRNAs and neuropeptides in modulating locomotor behavior remains poorly understood. In this study, we found that miR-7977 inhibited the expression of DHR and decreased the locomotor activity in adults of Tribolium castaneum. Moreover, the over-expression of miR-7977 lead to a decline in both respiratory rate and heart rate, an effect not observed upon DHR knockdown, thus prompting our speculation about the existence of additional target genes. Further investigations validated this hypothesis. Ultimately, we confirmed that miR-7977 can target DHR and SIFR to modulate locomotor behavior. Our research unveils the regulatory network of miR-7977-DHR/SIFR, offering novel perspectives on the intricate regulation of insect physiological behavior by small RNAs and neuropeptides.

RNAi-mediated down-regulation of the endogenous GhAIP10.1 and GhAIP10.2 genes in transgenic cotton (Gossypium hirsutum) enhances the earliness and yield of flower buds

Armadillo BTB Arabidopsis protein 1 (AtABAP1) plays a central role in the cell cycle. ABAP1-interacting protein 10 (AtAIP10, a Snf1 kinase interactor-like protein) is a protein that interacts with AtABAP1. Down-regulation of the AtAIP10 gene in A. thaliana resulted in an altered cell cycle and increased photosynthesis, chlorophyll content, metabolites, plant growth, root system, seed yield, and drought tolerance. Herein, aimed to test whether the down-regulation of GhAIP10 genes can stimulate the cotton plants in a manner similar to those observed in A. thaliana. Cotton transgenic events containing transgenes carrying RNA interfering (RNAi) or artificial miRNA (amiRNA) strategies were successfully generated to down-regulate the endogenous GhAIP10.1 and GhAIP10.2 genes. From these 15 transgenic events, five RNAi-based transgenic lines and five amiRNA-based transgenic events were selected for further analyses. The down-regulation of the GhAIP10.1 and GhAIP10.2 genes was confirmed by real-time RT-PCR. Phenotypic and physiological analyses revealed that these transgenic lines exhibited earlier production and opening of flower buds, increased vegetative growth over time and root biomass, no reduction in susceptibility to root-knot nematodes, and improved drought tolerance indicated by a higher photosynthetic rate and better intrinsic water-use efficiency. Based on the high identity of amino acid sequences, motifs, domains, subcellular localization, tertiary structure, down-regulation of GhABAP1 (partner of GhAIP10), up-regulation of GhCdt1 (a marker of the ABAP1 network), up-regulation of GhCyclinB1 (a marker of the cell cycle), up-regulation of GhAP3 (involved in vegetative to reproductive transition), and the up-regulation of CAB3, NDA1, DJC22, and DNAJ11 genes (involved in plant resilience) suggested that GhAIP10.1 and GhAIP10.2 proteins may act in cotton similarly to the AtAIP10 protein in A. thaliana. Furthermore, GhAIP10.1 and GhAIP10.2 genes are suggested as biotechnological targets for cotton genetic engineering based on genome editing.

A catalytic hairpin assembly system with sliding replication for the detection of piRNAs

As novel noncoding small RNA molecules, piRNAs play crucial roles in cancer development. However, due to their short sequences, easy degradation, and low abundance, developing specific detection methods is challenging. Rapid and early detection is important for the early clinical detection of tumours. Here, a novel one-step, dual-signal amplification piRNA detection system based on sliding replication and catalytic hairpin assembly (CHA), termed CTA, was developed for rapid, ultrasensitive and specific detection of piRNA-823. By utilizing the unique characteristics of tandem repeat sequences to improve amplification efficiency and fluorescence signal intensity, CTA achieved efficient target recognition and signal amplification by embedding tandem repeat sequences in one of the hairpin probes and utilizing chain displacement reactions to produce strong and detectable signals. CTA detected piRNA-823 with a low detection limit of 70 fM. Moreover, the whole detection process could be completed within 45 min. In addition, CTA performed excellently in the detection of cell and cancer samples, and its detection results were consistent with those of RT-qPCR. More importantly, CTA was successfully applied to effectively differentiate between healthy individuals and patients with colorectal cancer. These findings suggest its promising application in the diagnosis of cancer.

The Role of microRNAs in Lung Cancer: Mechanisms, Diagnostics and Therapeutic Potential

MicroRNAs (miRNAs) are small RNA molecules that do not have coding functions but play essential roles in various biological processes. In lung cancer, miRNAs affect the processes of tumor initiation, progression, metastasis, and resistance to treatment by regulating gene expression. Tumor-suppressive miRNAs inhibit oncogenic pathways, while oncogenic miRNAs, known as oncomiRs, promote malignant transformation and tumor growth. These dual roles position miRNAs as critical players in lung cancer biology. Studies in recent years have shown the significant potential of miRNAs as both prognostic and diagnostic biomarkers. Circulating miRNAs in plasma or sputum demonstrate specificity and sensitivity in detecting early-stage lung cancer. Liquid biopsy-based miRNA panels distinguish malignant from benign lesions, and specific miRNA expression patterns correlate with disease progression, response to treatment, and overall survival. Therapeutically, miRNAs hold promise for targeted interventions. Strategies such as miRNA replacement therapy using mimics for tumor-suppressive miRNAs and inhibition of oncomiRs with antagomiRs or miRNA sponges have shown preclinical success. Key miRNAs, including the let-7 family, miR-34a, and miR-21, are under investigation for their therapeutic potential. It should be emphasized that delivery difficulties, side effects, and limited stability of therapeutic miRNA molecules remain obstacles to their clinical use. This article examines the roles of miRNAs in lung cancer by indicating their mechanisms of action, diagnostic significance, and therapeutic potential. By addressing current limitations, miRNA-based approaches could revolutionize lung cancer management, offering precise, personalized, and minimally invasive solutions for diagnosis and treatment.

The Effects of Extracellular Vesicles Derived from Hydatid Cyst Fluid on the Expression of microRNAs Involved in Liver Fibrosis

INTRODUCTION

Hydatidosis is a zoonotic neglected disease caused by the larval stage of Echinococcus granulosus. Evidence suggests a communication between hydatid cyst (HC) and hosts via extracellular vesicles (EVs). However, a little is known about the communication between EVs derived from HC fluid (HCF) and host cells. The current study aimed to investigate the effect of HCF derived EVs on expression of fibrotic and anti-fibrotic miRNAs in THP-1 cell line.

METHODS

In the current study, EVs were isolated using ultracentrifugation from wild-infected sheep HCF and characterized by western blot, electron microscope, and size distribution analysis. The effects of EVs on the expression levels of microRNAs (mir-16, mir-29a, and mir-155) involved in liver fibrosis were investigated using quantitative real-time PCR (qRT-PCR), 3 and 24 h after incubation.

RESULTS

Western blot analyses confirmed the expression of CD63 marker, while Calnexin and CD81 were absent in EVs samples. The SEM and morphology revealed round shape vesicles. The DLS analysis showed average size distribution 130.6 nm diameter. The expression levels of mir-16 and mir-29a were significantly upregulated after 3 h for 8.66 and 3.420, respectively, while they were significantly downregulated after 24 h for 3.853 and 1.859, respectively.

CONCLUSION

The main mechanism of the communication between EVs derived from HCF and their host remains unclear. Our results suggest that HC may modulate the expression of miRNAs, involved in liver fibrosis via EVs.

The circular RNA circANK suppresses rice resistance to bacterial blight by inhibiting microRNA398b-mediated defense

Circular RNAs (circRNAs) are prevalent in eukaryotic cells and have been linked to disease progressions. Their unique circular structure and stability make them potential biomarkers and therapeutic targets. Compared with animal models, plant circRNA research is still in its infancy. The lack of effective tools to specifically knock down circRNAs without affecting host gene expression has slowed the progress of plant circRNA research. Here, we have developed a CRISPR-Cas13d tool that can specifically knock down circRNAs in plant systems, successfully achieving the targeted knockdown of circRNAs in rice (Oryza sativa). We further focused on Os-circANK (a circRNA derived from Ankyrin repeat-containing protein), a circRNA differentially expressed in rice upon pathogen infection. Physiological and biochemical experiments revealed that Os-circANK functions as a sponge for miR398b, suppressing the cleavage of Cu/Zn-superoxidase dismutase (CSD)1/CSD2/copper chaperone for superoxide dismutase/superoxidase dismutaseX through competing endogenous RNA, leading to reduced reactive oxygen species levels following Xanthomonas oryzae pv. oryzae (Xoo) infection and a negative regulation of rice resistance to bacterial blight. Our findings indicate Os-circANK inhibits rice resistance to bacterial blight via the microRNA398b(miR398b)/CSD/SOD pathway.

Persistent Chemiluminescence-Enabled Digital Bead Counting for Quantifying Attomolar MicroRNAs

Digital biosensing is the state-of-the-art technique for precisely quantifying low-abundance biomarkers but heavily limited to sophisticated fabrication of sealed microchambers and fluorescence signal readout. Herein, a novel persistent, enhanced-chemiluminescence (E-CL)-enabled microchamber-free digital counting strategy is proposed for miRNA analysis by using fully open microbeads (MBs) as independent microreactors and signaling units. The employment of a phenothiazine derivative enhancer efficiently transfers the flash-type CL of horseradish peroxidase (HRP)-H2O2-luminol into persistent and stable E-CL with more than 103-fold signal enhancement. More importantly, by leveraging single miRNA molecule-activated deposition of HRP, the driving power of E-CL, on the miRNA-loaded MBs, the long-lasting E-CL can be finely sustained on the MBs' surface, achieving CL-based binary MB counting for digital miRNA quantification at the aM level. This persistent E-CL-powered microchamber-free digital design may well complement prevalent fluorescence-based digital bioassays by effectively addressing their inherent drawbacks (photobleaching/quenching and scattering light background), thus expanding the digital biosensing toolbox.

The expression profile of inflammatory microRNAs in Leishmania major infected human macrophages; mining the effects of Leishmania RNA virus

BACKGROUND

Leishmaniasis is a disease caused by the Leishmania parasite. Recent studies suggest a critical role for double-stranded RNA virus (LRV) in the disease outcome. MicroRNAs (miRs) are small, non-coding RNA molecules that may also contribute to the outcome of infection and the pattern of disease. This study aimed to investigate the influence of L. major infected with LRV2 + on the expression profile of microRNAs compared to LRV2-.

METHODS

Samples were collected from cutaneous leishmaniasis (CL) patients in a leishmaniasis-endemic area of Iran. Leishmania species were determined using PCR (kDNA gene), and the presence of LRV2 was identified with semi-nested PCR (RdRp gene). The expression of miRs (miR-155, miR-146b, and miR-133a) was determined through quantitative real-time PCR analysis in human monocytes cell line (THP-1) infected with both LRV2 + and LRV2- isolates of L. major during 0, 12, 24, and 36 h post-co-infection.

RESULTS

The expression of miR-155 showed a significant decrease in the LRV2 + isolate compared to LRV2- at zero hours, but exhibited upregulation at 12, 24, and 36 h post-infection for both LRV2 + and LRV2- isolates compared to the control group. The expression of miR-146b was upregulated in both LRV2 + and LRV2- isolates compared to the control group at zero, 24, and 36 h post-infection. Conversely, miR-133a showed significant increases at zero and 12 h in both LRV2 + and LRV2- isolates compared to the control group, but it was downregulated in LRV2 + at 24 and 36 h compared to LRV2-.

CONCLUSION

In this study, significant differences were observed in the expression profiles of miR-155, miR-146b, and miR-133a about the presence of LRV2. Our data suggest a potential determinative role for these miRs in the pathogenesis of CL.

Advancements in functional tetrahedral DNA nanostructures for multi-biomarker biosensing: Applications in disease diagnosis, food safety, and environmental monitoring

Deoxyribonucleic acid (DNA) offers the fundamental building blocks for the precisely controlled assemblies due to its inherent self-assembly and programmability. The tetrahedral DNA nanostructure (TDN) stands out as a widely utilized nanostructure, attracting attention for its high biostability, excellent biocompatibility, and versatile modification sites. The capability of DNA tetrahedron to interact with various signal outputs makes it ideal for developing functional DNA nanostructures in biosensing platforms. This review highlights recent advancements in functional tetrahedral DNA nanostructures (FTDN) for various biomarkers monitoring, including nucleic acid, protein, mycotoxin, agent, and metal ion. Additionally, it discusses the potential of FTDN in the fields of disease diagnosis, food safety, and environmental monitoring. The review also introduces the application of FTDN-based biosensors for simultaneous identification of multiple biomarkers. Finally, challenges and prospects are addressed to provide guidance for the continued development of FTDN-based biosensing platforms.

Advances in electrochemical biosensors for the detection of tumor-derived exosomes

Exosomes, released from diverse cells as nanoscale lipid bilayer vesicles, mediate intercellular communication and participate in various physiological and pathological processes. Thereinto, tumor-derived exosomes (T-EXOs) with molecular cargoes of parent tumor cells act as attractive biomarkers for tumor liquid biopsy. The amount of T-EXOs and their levels of contained specific proteins and nucleic acids are closely associated with cancer burden and classification. Nevertheless, the nanoscale size and relatively low abundance of exosomes, as well as complex body liquid matrix pose daunting challenges for efficient isolation and sensitive detection of T-EXOs. Biosensing as fast, convenient and accurate method, has been widely employed for the detection of biomarkers over the past decades. Among them, electrochemical sensors can sensitively detect biomarkers by measuring of the change of electrical signal caused by oxidation or reduction at the working electrode surface. This review aims to summarize the recent advance in electrochemical biosensors for quantification, and protein and RNA analysis of exosomes. Further, challenges and future perspectives for exosome-based liquid biopsy have been discussed.

Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates

Nonclinical safety screening of small interfering RNAs (siRNAs) conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand is typically carried out in rats at exaggerated exposures in a repeat-dose regimen. We have previously shown that at these suprapharmacological doses, hepatotoxicity observed with a subset of GalNAc-siRNAs is largely driven by undesired RNA-induced silencing complex (RISC)-mediated antisense strand seed-based off-target activity, similar to microRNA-like regulation. However, the RISC component requirements for off-target activity of siRNAs have not been evaluated. Here, we evaluate the roles of major RISC components, AGO and TNRC6 (or GW182) proteins, in driving on- and off-target activity of GalNAc-siRNAs in hepatocytes, in vitro and in vivo. We demonstrate that knocking down AGO2, but not AGO1 or AGO4, is protective against GalNAc-siRNA-driven off-target activity and hepatotoxicity. As expected, knocking down AGO2, but not AGO1 or AGO4, reduces the on-target activity of GalNAc-siRNA. Similarly, knocking down TNRC6 paralogs, TNRC6A or TNRC6B, but not TNRC6C, is protective against off-target activity and hepatotoxicity while having minimal impact on the on-target activity of GalNAc-siRNA. These data indicate that while AGO2 is the only RISC component required for the on-target activity of GalNAc-siRNAs, the undesired off-target activity and hepatotoxicity of a subset of GalNAc-siRNAs are mediated via the RISC composed predominantly of AGO2 and TNRC6 paralogs TNRC6A and/or TNRC6B.

Biomarkers of endometriosis

Endometriosis represents a diverse disease characterized by three distinct phenotypes: superficial peritoneal lesions, ovarian endometriomas, and deep infiltrating endometriosis. The most widely accepted pathophysiological hypothesis for endometriosis is rooted in retrograde menstruation, a phenomenon observed in most patients. Endometriosis is closely linked to infertility, but having endometriosis does not necessarily imply infertility. The disease can impact fertility through various mechanisms affecting the pelvic cavity, ovaries, and the uterus itself. MicroRNAs (miRNAs) indeed represent a fascinating and essential component of the regulatory machinery within cells. Discovered in the early 1990s, miRNAs have since been identified as critical players in gene expression control. Unfortunately, ovarian endometrioma is a common gynecologic disorder for which specific serum markers are currently lacking. Some have examined urocortin for its ability to differentiate endometriomas from other benign ovarian cysts. Another potential marker, Cancer Antigen 125 (CA-125) is a well-established indicator for epithelial cell ovarian cancer and its levels can be elevated in conditions such as endometriosis. CA-125 is derived from coelomic epithelia, including the endometrium, fallopian tube, ovary, and peritoneum. In this review we examine the pathophysiologic basis for endometriosis and highlight potential markers to more fully characterize the underlying biochemical processes linked to this multifaceted disease state.

Artificial Sweet Cherry miRNA 396 Promotes Early Flowering in Vernalization-Dependent Arabidopsis Edi-0 Ecotype

The flowering and fruiting of sweet cherry (Prunus avium L.) depend on precise synchronization with seasonal events. During harsh autumn and winter conditions, floral buds enter dormancy to protect and prepare for the productive season. Dormancy release occurs after exposure to genotype-specific chilling temperatures, an event in which epigenetic reprogramming triggers further metabolic and gene expression activation. Similarly, several Arabidopsis ecotypes require chilling (vernalization) to transition from vegetative to floral states. At vernalization's end, the decrease in the repressor complex formed by SHORT VEGETATIVE PHASE (SVP) and FLOWERING LOCUS C (FLC) allows FLOWERING LOCUS T (FT) to induce flowering. However, this alone does not fully explain the process. MicroRNAs (miRNAs) play a crucial role in gene regulation during plant development and environmental interactions, and miR396's role during flower development and vernalization has been described in some plant species, although not for sweet cherry dormancy. We used 'Regina', a high-chill sweet cherry variety, to identify candidate small RNA molecules throughout dormancy, resulting in the detection of miR396. The transcript expression levels of the putative miRNA target genes were evaluated through quantitative PCR analyses of dormant buds. Additionally, an artificial sweet cherry miR396 was used to transform Arabidopsis Edi-0, a vernalization-requiring ecotype. Ectopic expression of this artificial molecule partially mirrored the effect on target genes observed in dormant buds and, more importantly, led to vernalization-independent flowering. Artificial miR396 expression also resulted in decreased FLC and increased SVP and FT transcript levels. These results could pave the way for future studies on the involvement of miR396 in the regulation of dormancy and flowering, with potential applications in improving crop resilience and productivity.

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.

Serum direct SMOS-qPCR: a fast approach for miRNAs detection

This study presents a novel method for direct amplification of multiple microRNAs (miRNAs) from serum samples using Sensitive and Multiplexed One-Step RT-qPCR (SMOS-qPCR). The technique eliminates the need for separate miRNA extraction and purification steps, offering a streamlined approach for non-invasive early disease diagnosis. We optimized reaction conditions, including serum treatment methods and PCR system volumes, to enhance interference resistance and detection sensitivity. The optimized serum direct SMOS-qPCR demonstrated a detection limit as low as 6 × 103 copies per μL for single-target miRNA, with excellent amplification efficiency (R2 > 0.99). In multiplex detection, the method successfully quantified four miRNAs simultaneously, maintaining high sensitivity and reproducibility. Analysis of 20 clinical serum samples further validated the method's applicability for large-scale screening. Overall, this rapid, cost-effective, and user-friendly approach represents a significant advancement in miRNA detection technology, potentially facilitating earlier and more accessible disease diagnosis.

Current Role of MicroRNAs in the Diagnosis and Clinical Management of Germ Cell Tumors

Germ cell tumors (GCTs) are a rare and heterogeneous group of neoplasms arising from primitive germ cells. MicroRNAs are small noncoding RNAs that have emerged as potential cancer biomarkers in the last decade. In particular, miR-371a-3p has shown good diagnostic performance for germ cell neoplasia in situ-derived testicular GCTs in several well-established cohorts and is expected to enter the clinical arena in the near future. GCTs universally exhibit high expression of miR-371-373 and miR-302/367 clusters and low expression of let-7 family miRNAs. Further studies are needed to assess the potential role of these miRNAs as biomarkers of ovarian and extragonadal GCTs.

Effects of cold and methyl jasmonate on the expression of miRNAs and target genes in response to vernalisation in two wheat cultivars (Triticum aestivum L.)

Wheat undergoes significant physiological changes during winter, driven by processes such as cold acclimation and vernalisation that are regulated by gene expression and phytohormones. We investigate the effects of methyl jasmonate (MeJA) and cold treatments on the expression of three specific miRNAs and the associated target genes in Baz spring wheat and Norstar winter wheat using qRT-PCR analysis. Our objective was to examine the impact of MeJA on vernalisation and cold adaptation in these genotypes. Results showed that MeJA had no significant impact on vernalisation and acclimation in Baz, while the compound decreased these traits in Norstar. Additionally, the expression of miRNAs in Norstar was significantly reduced after a 2-day cold treatment, particularly for miR156 and further reduced after 14days for miR172 and miR319 . In contrast, Baz showed varied gene expression responses, with an increase in miRNA levels after the 14-day cold treatment. MeJA combined with a 2-day cold treatment suppressed the expression of SPL , AP2 and MYB3 target genes, with the most pronounced suppression observed in SPL . However, AP2 was induced after 14-day cold treatment in both cultivars. The study highlighted an inverse relationship between miRNAs and target genes under vernalisation conditions, underscoring the complex regulatory interactions between genotype, miRNAs and the associated target genes. Therefore, these findings provide new insights into how MeJA and cold treatments modulate miRNA and gene expression, enhancing our understanding of wheat's adaptive response mechanisms.

Unveiling the transcriptional pattern of epithelial ovarian carcinoma-related microRNAs-mRNAs network after mouse exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD), the most potent organic environmental contaminant known to date, is recognized as a human carcinogen. Despite the documented link between TCDD exposure and epithelial ovarian cancer (EOC) in mammalian females, the molecular mechanisms underlying cancer initiation remain elusive. Emerging evidence suggests aberrant miRNA expression in various human malignancies, including OC. This work was performed to examine whether TCDD exposure in female mice disrupts the expression of miRNAs, particularly those known as OC-modulators. We conducted an extensive search in the PubMed database to identify miRNAs experimentally implicated in OC. Fifty-two miRNAs were identified as potential OC modulators and classified into two groups based on their abundance in OC. Group I comprised 24 miRNAs upregulated in OC, while Group II included 28 miRNAs downregulated in OC. Subsequently, we analyzed the expression of both groups in BALB/c mice ovaries following a single TCDD dose. Our findings revealed significant upregulation of 10 miRNAs from Group I (miR-21, miR-27a, miR-30a, miR-99a, miR-141, miR-182, miR-183, miR-200a, miR-200b, and miR-429) and significant downregulation of 12 miRNAs from Group II (let-7d, miR-15a, miR-19a, miR-23b, miR-34a, miR-34c, miR-125b-1, miR-133, miR-140, miR-199a, miR-210, and miR-383) in TCDD-exposed mouse ovaries. Furthermore, we identified OC-related genes targeted by miRNAs from both groups through an extensive search in PubMed databases. Using TR-qPCR, we evaluated the downstream impact of TCDD-dysregulated miRNAs on their target genes. Our results indicate that TCDD-induced upregulation of oncogenic miRNAs negatively regulates target genes associated with EOC, while downregulation of cancer-suppressor miRNAs positively regulates genes linked to EOC.

Expanding Conjugate Space of RNAi Therapeutics: Ligand at the 3' End of the Antisense Strand Achieves Uncompromised In Vivo Potency and Efficacy and Reveals Interactions with the Argonaute-2 PAZ Domain

The conjugation of the sense strands of small interfering RNA (siRNA) to tri-N-acetylgalactosamine (GalNAc), the ligand for a hepatocyte-specific receptor, enables the delivery of multiple clinically approved therapeutic agents that act through the RNA interference pathway. Here, we report the systematic evaluation of siRNAs with the 3' termini of antisense strands conjugated to GalNAc for the first time. These designs retained the same receptor affinity, in vitro and in vivo activities, as well as the same level of loading into the RNA-induced silencing complex as siRNAs with a GalNAc-conjugated sense strand. A siRNA with a GalNAc-conjugated antisense strand of 22 nucleotides had better activity than a siRNA with a 23-nucleotide antisense strand. Computational modeling of a complex of a GalNAc-conjugated antisense strand with the PAZ domain of Ago2 rationalizes the importance of the interaction of phosphate at the 3' terminus with the PAZ domain to explain the observed activity of these siRNAs.

Therapeutic potential of siRNA PMP22-SQ nanoparticles for Charcot-Marie-Tooth 1A neuropathy in rodents and non-human primates

Small interfering RNA (siRNA) has shown promising results for the treatment of Charcot-Marie-Tooth disease 1A (CMT1A) caused by overexpression of peripheral myelin protein (PMP22), leading to myelin dysfunction and axonal damage. Recently, we developed siRNA PMP22-squalene (SQ) nanoparticles (NPs) for intravenous use. Three consecutive injections of siRNA PMP22-SQ NPs at a cumulative dose of 1.5 mg/kg restored motor function in C61 transgenic mouse models. Pharmacokinetic studies showed a long half-life of antisense siRNA PMP22 in the sciatic nerve, and spinal cord, indicating targeted release potential. We further assessed the efficiency and safety of siRNA PMP22-SQ NPs in two healthy male non-human primates (Macaca fascicularis) after administering four escalating doses (0.1, 0.5, 2.5 and 4.5 mg/kg at one week interval). Interestingly, the siRNA PMP22-SQ NPs reduced PMP22 mRNA expression by approximately 70 % and probably induced an early-stage hereditary neuropathy with pressure palsies (HNPP)-like condition in two normal NHP. No preliminary toxicity was observed in organs or blood parameters of the two NHPs. Interestingly, the nerve conduction velocity decreased after the third injection of siRNA PMP22-SQ NPS. These results demonstrate the therapeutic potential of siRNA PMP22-SQ NPs, supporting advancement to further pre-clinical testing.

The BnamiR827-BnaA09.NLA1-BnaPHT1 module regulates phosphate homeostasis, pollen viability, and seed yield in Brassica napus

Phosphorus (P) is an essential macronutrient for the growth and yield of crops. However, there is limited understanding of the regulatory mechanisms of phosphate (Pi) homeostasis, and its impact on growth, development, and yield-related traits in Brassica napus. Here, we identified four NITROGEN LIMITATION ADAPTATION1 (BnaNLA1) genes in B. napus; their expression was predominant in roots and suppressed by Pi starvation-induced BnamiR827. All the BnaNLA1 proteins have similar sequences, subcellular localizations, and abilities to rescue the growth defects of the atnla1 mutant. One of the genes, BnaA09.NLA1, is expressed abundantly in roots, and also in old leaves, anthers, and pollen. Knocking out BnaNLA1 genes or overexpressing BnamiR827 resulted in increased concentrations of Pi in leaves and stamens and reduced pollen viability, thereby negatively impacting seed yield. Bimolecular fluorescence complementation (BiFC) and split-ubiquitin yeast two-hybrid (Y2H) analyses demonstrated that BnaA09.NLA1 interacted with seven Pi transporters highly expressed in roots and/or anthers (i.e. BnaPT8/10/11/27/35/37/42) to regulate Pi uptake and Pi allocation in anthers. Taken together, this study demonstrates that the BnamiR827-BnaA09.NLA1-BnaPHT1 module is involved in the regulation of Pi uptake and Pi allocation in floral organs, which is vital for the growth, pollen viability, and seed yield of B. napus.

Lab on a single microbead: An enzyme-free strategy for the sensitive detection of microRNA via efficient localized catalytic hairpin assembly

BACKGROUND

Accurate quantification of microRNA (miRNA) is of great significance because it provides opportunities for the accurate early diagnosis of a series of human diseases including cancers. Currently, complicated nucleic acid amplification technologies are always required for the highly sensitive miRNA detection. The introduction of nucleic acid signal amplification coupled with various enzymes will inevitably lead to tedious work and increase the complexity of the analysis process. It is still urgently desired to develop enzyme-free yet sensitive assays that enable the sensitive analysis of miRNA in complicated biological samples.

RESULTS

A single microbead (MB)-based localized catalytic hairpin assembly (CHA) strategy is proposed for the sensitive analysis of microRNA (miRNA). This rationally designed CHA strategy allows target miRNA to walk only on a single MB which can create a micro-amplification zone, initiating a highly efficient localized CHA reaction, generating a large number of fluorescent DNA duplexes on the surface of single MB. The efficient localized CHA on single MB can not only greatly suppress the nonspecific reaction between two hairpin probes, thus decreasing the background signal, but also greatly enhance the brightness of MB owing to the highly-concentrated fluorescence enrichment on only one MB. Therefore, highly sensitive quantification of miRNA has been achieved by measuring the fluorescence signal on MB using a confocal fluorescence microscope. This new strategy exhibits a detection limit of 1.09 pM for let-7a detection, and enables high specificity of distinguishing homologous miRNA family members.

SIGNIFICANCE

This is the first report by only using one single MB as a carrier to conduct localized CHA, rendering highly-concentrated fluorescence enrichment on only one MB and a dramatic increase in sensitivity. This single MB-based localized CHA strategy has been successfully applied to the accurate analysis of miRNA target in complex biological sample.

Vertical growth of rhenium disulfide on rGO empowers multi-signal amplification for ultrasensitive MiRNA-21 detection

Unique rhenium disulfide/reduced graphene oxide (ReS2/rGO) nanoframeworks were synthesized with a hierarchical layered and porous structure for the ultrasensitive electrochemical detection of microRNA-21 (miRNA-21) by empowering multi-signal amplification strategy of catalytic hairpin self-assembly-hybridization chain reaction (CHA-HCR). The layered and porous nanostructures endowed ReS2/rGO with a larger specific surface area and more active sites through connecting vertical ReS2 with rGO which was preferable for promoting the electron transfer over electrode surface because of a conductive network. This nanoframework facilitated the loading of adequate gold nanoparticles to fix the capture probe via Au-S bond. In the presence of the target miRNA-21, the CHA-HCR double amplification reaction could be triggered to generate a long double strand with methylene blue (MB) embedded inside. The electrochemical sensing platform was thus empowered by the unique ReS2/rGO nanoframeworks to detect miRNA-21 in the range 1 fM ~ 100 pM with the remarkably enhanced sensitivity through detecting the significantly amplified signal from the REDOX reaction of MB inside the long chain. The verification of the miRNA-21 detection in real blood samples further proved the great potential of this new method with the limit of detection reduced down to 0.057 fM and opens a new window for ReS2 in developing sensitive biosensors for early clinical cancer diagnosis.

FOXO3a/miR-4259-driven LDHA expression as a key mechanism of gemcitabine sensitivity in pancreatic ductal adenocarcinoma

BACKGROUND

Lactate dehydrogenase A (LDHA) can regulate tumorigenesis and cancer progression. Nevertheless, whether the regulation of LDHA is involved in the development of gemcitabine resistance in PDAC has not yet been fully elucidated. Increasing studies have shown that cancer acquired drug resistance led to treatment failure is highly attributed to the cancer stem cell (CSC) properties. Therefore, we aim to demonstrate the functions and regulatory mechanisms of LDHA on cancer stem cell (CSC) properties and gemcitabine resistance in PDAC.

METHODS

We investigate the metabolite profiles by liquid chromatography-mass spectrometry between gemcitabine-resistant PDAC and parental PDAC cells. Additionally, gain-of-function and loss-of-function experiments were conducted to examine the roles of LDHA on CSC properties and gemcitabine resistance in the gemcitabine-resistant PDAC and parental PDAC cells. To investigate regulators involved in LDHA-mediated gemcitabine resistance and CSC of pancreatic cancer cells, we further used a combination of the miRNA microarray results and software predictions and confirmed that miR-4259 is a direct target of LDHA by luciferase assay. Furthermore, we constructed serial miR-4259 promoter reporters and searched for response elements using the TESS 2.0/TFSEARCH software to find the transcription factor binding site in the promoter region of miR-4259.

RESULTS

We observed that elevated LDHA expression significantly correlates with recurrent pancreatic cancer patients following gemcitabine treatment and with CSC properties. We further identify that FOXO3a-induced miR-4259 directly targets the 3'untranslated region of LDHA and reduced LDHA expression, leading to decreased gemcitabine resistance and a reduction in the CSC phenotypes of pancreatic cancer.

CONCLUSION

Our results demonstrated that LDHA plays a critical role in cancer stemness and gemcitabine resistance of pancreatic cancer, and indicate that targeting the FOXO3a/miR-4259/LDHA pathway might serve as a new treatment for pancreatic cancer patients with a poor response to gemcitabine chemotherapy.

Non-Coding RNAs in Cancer: Structure, Function, and Clinical Application

We are on the brink of a paradigm shift in both theoretical and clinical oncology. Genomic and transcriptomic profiling, alongside personalized approaches that account for individual patient variability, are increasingly shaping discourse. Discussions on the future of personalized cancer medicine are mainly dominated by the potential of non-coding RNAs (ncRNAs), which play a prominent role in cancer progression and metastasis formation by regulating the expression of oncogenic or tumor suppressor proteins at transcriptional and post-transcriptional levels; furthermore, their cell-free counterparts might be involved in intercellular communication. Non-coding RNAs are considered to be promising biomarker candidates for early diagnosis of cancer as well as potential therapeutic agents. This review aims to provide clarity amidst the vast body of literature by focusing on diverse species of ncRNAs, exploring the structure, origin, function, and potential clinical applications of miRNAs, siRNAs, lncRNAs, circRNAs, snRNAs, snoRNAs, eRNAs, paRNAs, YRNAs, vtRNAs, and piRNAs. We discuss molecular methods used for their detection or functional studies both in vitro and in vivo. We also address the challenges that must be overcome to enter a new era of cancer diagnosis and therapy that will reshape the future of oncology.

Identifying Essential Hub Genes and circRNA-Regulated ceRNA Networks in Hepatocellular Carcinoma

Competitive endogenous RNAs (ceRNAs) absorb microRNAs and subsequently promote corresponding mRNA and long noncoding RNA (lncRNA) expression, which may alter cancer cell malignancy. Thus, dissecting ceRNA networks may reveal novel targets in cancer therapies. In this study, we analyzed differentially expressed genes (DEGs) of mRNAs and lncRNAs, and differentially expressed microRNAs (DE-miRNAs) and circular RNAs (DE-circRNAs) extracted from high-throughput sequencing datasets of hepatocellular carcinoma patients. Based on these data, we identified 26 gene modules using weighted gene co-expression network analysis (WGCNA), of which 5 were associated with tumor differentiation. In these modules, 269 genes were identified by GO and KEGG enrichment and patient's survival correlation analyses. Next, 40 DE-miRNAs, each of which potentially bound a pair of DE-circRNA and hub gene, were discovered. Together with 201 circRNAs and 24 hub genes potentially bound by these miRNAs, 1151 ceRNA networks were constructed. Among them, 75 ceRNA networks consisting of 24 circRNAs, 28 miRNAs and 17 hub genes showed a positive circRNA-hub gene correlation. For validation, we carried out experiments for 4 randomly selected circRNAs regulating 19 potential ceRNA networks and verified 5 of them. This study represents a powerful strategy to identify essential gene networks and provides insights into designing effective therapeutic strategies.

Review of microRNA detection workflows from liquid biopsy for disease diagnostics

MicroRNAs have emerged as effective biomarkers in disease diagnostics, particularly cancer, due to their role as regulatory sequences. More recently, microRNAs have been detected in liquid biopsies, which hold immense potential for early disease diagnostics. This review comprehensively analyses distinct liquid biopsy microRNA detection methods validated with clinical samples. Each step in the microRNA detection workflow, including sample collection, RNA isolation, processing, and detection of target microRNAs, has been thoroughly assessed. The review discusses the advantages and limitations of established and novel techniques in microRNA detection workflows, discussing their diagnostic capabilities and potential for future implementation at scale.

Differential Expression of miRNAs Between Young-Onset and Late-Onset Indian Colorectal Carcinoma Patients

Reports indicate a worldwide increase in the incidence of Early-Onset Colorectal Carcinoma (EOCRC) (<50 years old). In an effort to understand the different modes of pathogenesis in early-onset CRC, colorectal tumors from EOCRC (<50 years old) and Late-Onset patients (LOCRC; >50 years old) were screened to eliminate microsatellite instability (MSI), nuclear β-catenin, and APC mutations, as these are known canonical factors in CRC pathogenesis. Small-RNA sequencing followed by comparative analysis revealed differential expression of 23 miRNAs (microRNAs) specific to EOCRC and 11 miRNAs specific to LOCRC. We validated the top 10 EOCRC DEMs in TCGA-COAD and TCGA-READ cohorts, followed by validation in additional EOCRC and LOCRC cohorts. Our integrated analysis revealed upregulation of hsa-miR-1247-3p and hsa-miR-148a-3p and downregulation of hsa-miR-326 between the two subsets. Experimentally validated targets of the above miRNAs were compared with differentially expressed genes in the TCGA dataset to identify targets with physiological significance in EOCRC development. Our analysis revealed metabolic reprogramming, downregulation of anoikis-regulating pathways, and changes in tissue morphogenesis, potentially leading to anchorage-independent growth and progression of epithelial-mesenchymal transition (EMT). Upregulated targets include proteins present in the basal part of intestinal epithelial cells and genes whose expression is known to correlate with invasion and poor prognosis.

Trophic microRNA: Post-transcriptional regulation of target genes and larval development impairment in Plutella xylostella upon precursor and mature microRNA ingestion

MicroRNAs (miRNAs) are post-transcriptional gene regulators. In the miRNA pathway's cytoplasmic part, the miRNA is processed from a hairpin-structured precursor to a double-stranded (ds) mature RNA and ultimately to a single-stranded mature miRNA. In insects, ingesting these two ds forms can regulate the target gene expression; this inspired the trophic miRNA's use as a functional genomics and pest management tool. However, systematic studies enabling comparisons of pre- and mature forms, dosages, administration times and instar-wise effects on target transcripts and phenotypes, which can help develop a miRNA administration method, are unavailable due to the different focuses of the previous investigations. We investigated the impact of trophically delivered Px-let-7 miRNA on the lepidopteran pest Plutella xylostella, to compare the efficacies of its pre- and ds-mature forms. Continuous feeding on the miRNA-supplemented diet suppressed expressions of FTZ-F1 and E74, the target ecdysone pathway genes. Both the pre-let-7 and mature let-7 miRNA forms similarly downregulated the target transcripts in all four larval instars. Pre-let-7 and let-7 ingestions decreased larval mass and instar duration and increased mortality in all instars, exhibiting adverse effects on larval growth and development. miRNA processing Dicer-1 and AGO-1's upregulations upon miRNA ingestion denoted the systemic miRNA spread in larval tissues. The scrambled sequence controls did not affect the target transcripts, suggesting the sequence-specific targeting by the mature miRNA and hairpin cassette's non-involvement in the target downregulation. This work provides a framework for miRNA and target gene function analyses and potentiates the trophic miRNA's utility in pest management.

Citrus tristeza virus p20 suppresses antiviral RNA silencing by co-opting autophagy-related protein 8 to mediate the autophagic degradation of SGS3

Viruses exploit autophagy to degrade host immune components for their successful infection. However, how viral factors sequester the autophagic substrates into autophagosomes remains largely unknown. In this study, we showed that p20 protein, a viral suppressor of RNA silencing (VSR) encoded by citrus tristeza virus (CTV), mediated autophagic degradation of SUPPRESSOR OF GENE SILENCING 3 (SGS3), a plant-specific RNA-binding protein that is pivotal in antiviral RNA silencing. CTV infection activated autophagy, and the overexpression of p20 was sufficient to induce autophagy. Silencing of autophagy-related genes NbATG5 and NbATG7 attenuated CTV infection in Nicotiana benthamiana plants. In contrast, knockdown of the autophagy negative-regulated genes NbGAPCs led to virus accumulation, indicating the proviral role of autophagy in CTV infection. Further investigation found that p20 interacted with autophagy-related protein ATG8 through two ATG8-interacting motifs (AIMs) and sequestered SGS3 into autophagosomes by forming the ATG8-p20-SGS3 ternary complex. The mutations of the two AIMs in p20 (p20mAIM1 and p20mAIM5) abolished the interaction of p20 with ATG8, resulting in the deficiency of autophagy induction, SGS3 degradation, and VSR activity. Consistently, N. benthamiana plants infected with mutated CTVmAIM1 and CTVmAIM5 showed milder symptoms and decreased viral accumulation. Taken together, this study uncovers the molecular mechanism underlying how a VSR mediates the interplay between RNA silencing and autophagy to enhance the infection of a closterovirus.

A multi-class support vector machine classification model based on 14 microRNAs for forensic body fluid identification

MicroRNAs (miRNAs) are promising biomarkers for forensic body fluid identification owing to their small size, stability against degradation, and differential expression patterns. However, the expression of most body fluid-miRNAs is relative (differentially expressed in certain body fluids) rather than absolute (exclusively expressed in a specific body fluid). Moreover, different body fluids contain heterogeneous cell types, complicating their identification. Therefore, appropriate normalization strategies to eliminate non-biological variations and robust models to interpret expression levels accurately are necessary prerequisites for applying miRNAs in body fluid identification. In this study, the expression stability of six candidate reference genes (RGs) across five body fluids was validated using geNorm, NormFinder, BestKeeper and RankAggreg, and the most suitable combination of RGs (hsa-miR-484 and hsa-miR-191-5p) was identified under our experimental conditions. Subsequently, we systematically evaluated the expression patterns of the 28 most promising body fluid-specific miRNA markers using TaqMan RT-qPCR and selected the optimal combination of markers (12 miRNAs) to establish a multi-class support vector machine (MSVM) classification model. An independent test set (60 samples) was used to validate the accuracy of the proposed classification model, while an additional 30 casework samples were used to assess its robustness. The MSVM model accurately predicted the body fluid origin for almost all (59/60) single-source samples. Moreover, this model demonstrated the capability to identify aged forensic samples and to predict the primary components of mixed stains to a certain extent. In summary, this study presented a miRNA-based MSVM classification model for forensic body fluid identification using the qPCR platform. However, extensive validation, especially inter-laboratory collaborative exercises, is necessary before miRNA can be routinely applied in forensic identification practice.

A Comprehensive Transcriptome Atlas Reveals the Crucial Role of LncRNAs in Maintaining Nodulation Homeostasis in Soybean

Symbiotic nitrogen fixation (SNF) provides nitrogen for soybean. A primary challenge in enhancing yield through efficient SNF lies in striking a balance between its high energy consumption and plant growth. However, the systemic transcriptional reprogramming during nodulation remains limited. Here, this work conducts a comprehensive RNA-seq of the roots, cotyledons and leaves of inoculated-soybean. This work finds 88,814 mRNAs and 6,156 noncoding RNAs (ncRNAs) across various organs. Notably, this work identifies 6,679 nodulation-regulated mRNAs (NR-mRNAs), 1,681 long noncoding RNAs (lncRNAs) (NR-lncRNAs), and 59 miRNAs (NR-miRNAs). The majority of these NR-RNAs are associated with plant-microbial interaction and exhibit high organ specificity. Roots display the highest abundance of NR-ncRNAs and the most dynamic crosstalk between NR-lncRNAs and NR-miRNAs in a GmNARK-dependent manner. This indicates that while each tissue responds uniquely, GmNARK serves as a primary regulator of the transcriptional control of nodulated-plants. Furthermore, this work proves that lnc-NNR6788 and lnc-NNR7059 promote nodulation by regulating their target genes. This work also shows that the nodulation- and GmNARK-regulated (NNR) lnc-NNR4481 negatively regulates nodulation through miR172c within a competing endogenous RNA (ceRNA) network. The spatial organ-type transcriptomic atlas establishes a benchmark and provides a valuable resource for integrative analyses of the mechanism underlying of nodulation and plant growth balance.

Simultaneous and Ultraspecific Optical Detection of Multiple miRNAs Using a Liquid Flow-Based Microfluidic Assay

Recent studies have reported that the cause and progression of many diseases are closely related to complex and diverse gene regulation involving multiple microRNAs (miRNAs). However, most existing methods for miRNA detection typically deal with one sample at a time, which limits the achievement of high diagnostic accuracy for diseases associated with multiple gene dysregulations. Herein, we develop a liquid flow-based microfluidic optical assay for the simple and reliable detection of two different target miRNAs simultaneously at room temperature without any enzymatic reactions. This assay utilizes the catalytic hairpin assembly cycling reaction in a mixture containing four types of hairpin DNAs to amplify two different dimeric DNA probes, each of which specifically recognizes one of the two different target miRNAs. The resultant two dimeric DNA probes effectively hybridize with anchor DNA grafted into two outlet channels of a microfluidic device, thus enabling i-motif-driven compact DNA hydrogels to form in the channels under acidic conditions. With this setup, the presence of two target miRNAs can be confirmed by the naked-eye observation of red-colored gold nanoparticles encountering a flow blockage in the two outlet channels. Notably, the developed assay demonstrates sensitive and sequence-specific detection that can precisely distinguish a single base mismatch mutant miRNA within 1.5 h. Our assay thus has the potential to serve as a powerful sensing platform for the simple and simultaneous detection of multiple miRNAs in clinical diagnostics at room temperature without analytic equipment or enzymatic reactions.

Extracellular vesicles and microRNAs in cancer progression

Extracellular vesicles (EVs) have emerged as critical mediators of intercellular communication in cancer. These membranous structures, secreted by normal and cancerous cells, carry a cargo of bioactive molecules including microRNAs (miRNAs) that modulate various cellular processes. miRNAs are small non-coding RNAs that play pivotal roles in post-transcriptional gene regulation and have been implicated in cancer initiation, progression, and metastasis. In cancer, tumor-derived EVs transport specific miRNAs to recipient cells, modulating tumorigenesis, growth, angiogenesis, and metastasis. Dysregulation of miRNA expression profiles within EVs contributes to the acquisition of cancer hallmarks that include increased proliferation, survival, and migration. EV miRNAs influence the tumor microenvironment, promoting immune evasion, remodeling the extracellular matrix, and establishing pre-metastatic niches. Understanding the complex interplay between EVs, miRNAs, and cancer holds significant promise for developing novel diagnostic and therapeutic strategies. This chapter provides insights into the role of EV-mediated miRNA signaling in cancer pathogenesis, highlighting its potential as a biomarker for cancer detection, prognosis, and treatment response assessment.

One-pot isothermal CRISPR/Dx system for specific and sensitive detection of microRNA

MicroRNA (miRNA) is a promising biomarker for the early diagnosis of pancreatic cancer. To enable sensitive and reliable miRNA detection, we have developed a one-pot isothermal CRISPR/Dx detection system by combining rolling circle amplification (RCA) and CRISPR/Cas12a. RCA and CRISPR/Cas12a reactions are carried out in a single closed tube, bypassing the transferring step. We demonstrate the feasibility of our one-pot CRISPR/Dx system in detecting pancreatic cancer by targeting miR-25, miR-191, miR-205, and miR-1246. When applied to fluorescence- and lateral flow strip paper-based detection platforms, our one-pot CRISPR/Dx system detects synthetic miR-25 at a LOD of 6.60 fM and 500 fM, respectively. It has high targeting specificity, as shown by its ability to discriminate miR-25 with a single-base mutation and highly homologous miRNA species. It is also successfully generalized to detect other pancreatic cancer-associated miRNAs, including miR-191, miR-205, and miR-1246. Importantly, our one-pot CRISPR/Dx system enables specific and sensitive detection of endogenous miR-25 in the human pancreatic cancer cell line PANC-1. We have successfully developed a one-pot isothermal CRISPR/Dx system for detecting miRNA with high specificity and sensitivity. It is highly flexible and economical, as a common crRNA can detect different miRNAs and only requires minor modifications to the locking padlock probe. Therefore, it can potentially be translated into clinical settings and POCT for the diagnosis of various human cancers.

Inferring single-cell and spatial microRNA activity from transcriptomics data

The activity of miRNA varies across different cell populations and systems, as part of the mechanisms that distinguish cell types and roles in living organisms and in human health and disease. Typically, miRNA regulation drives changes in the composition and levels of protein-coding RNA and of lncRNA, with targets being down-regulated when miRNAs are active. The term "miRNA activity" is used to refer to this transcriptional effect of miRNAs. This study introduces miTEA-HiRes, a method designed to facilitate the evaluation of miRNA activity at high resolution. The method applies to single-cell transcriptomics, type-specific single-cell populations, and spatial transcriptomics data. By comparing different conditions, differential miRNA activity is inferred. For instance, miTEA-HiRes analysis of peripheral blood mononuclear cells comparing Multiple Sclerosis patients to control groups revealed differential activity of miR-20a-5p and others, consistent with the literature on miRNA underexpression in Multiple Sclerosis. We also show miR-519a-3p differential activity in specific cell populations.

Post-transcriptional and post-translational regulation of anthocyanin biosynthesis in sweetpotato by Ib-miR2111 and IbKFB: Implications for health promotion

INTRODUCTION

Sweetpotato (Ipomoea batatas (L.) Lam.) is a genetically intricate hexaploid crop. The purple-fleshed variety, enriched with anthocyanin pigments, is an outstanding source for creating high-value functional products. Previous research on anthocyanin biosynthesis has primarily focused on the above-ground plant parts at the transcriptional level. However, the regulatory mechanisms underlying anthocyanin accumulation in underground tuberous roots of sweetpotato remain largely unexplored.

OBJECTIVES

This study aimed to elucidate the post-transcriptional and post-translational mechanisms of Ib-miR2111 and its target gene IbKFB in anthocyanin synthesis in sweetpotato.

METHODS

Genetic manipulation techniques were used to validate the function of Ib-miR2111 and IbKFB in anthocyanin biosynthesis in sweetpotato. To investigate how IbKFB works, a series of protein interaction assays, including yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), GST pull-down, co-immunoprecipitation (Co-IP), and ubiquitination, were conducted. Additionally, the impact of anthocyanin extracts from the genetically modified sweetpotato lines on inflammatory cells morphology, cytokine expression, and cell proliferation were evaluated using in vitro assays.

RESULTS

Purple-fleshed sweetpotato (PFSP) varieties exhibited elevated Ib-miR2111 expression compared to white-fleshed sweetpotato (WFSP) varieties, with an inverse expression pattern in IbKFB. Genetic manipulations, including overexpression, CRISPR/Cas9 knockouts, and targeted mutations, confirmed their critical roles in anthocyanin modulation. Furthermore, IbKFB's interactions and ubiquitination with phenylalanine ammonia-lyase 1 (IbPAL1) and glyceraldehyde-3-phosphate dehydrogenase 1 (IbGAPCp1) were elucidated, revealing intricate regulatory mechanisms. Enhanced anthocyanin content showed significant effects on inflammatory cell morphology, cytokine expression, and cell proliferation.

CONCLUSION

This study provides new insights into the regulatory mechanisms of Ib-miR2111 and IbKFB in anthocyanin biosynthesis and suggests potential health benefits of anthocyanin-rich sweetpotatoes.

Multiplex digital PCR for the simultaneous quantification of a miRNA panel

BACKGROUND

microRNAs (miRNAs) are small non-coding RNAs regulating gene expression. They have attracted significant interest as biomarkers for early diagnosis, prediction and monitoring of treatment response in many diseases. As individual miRNAs often lack the required sensitivity and specificity, miRNA signatures are developed for clinical applications. Digital PCR (dPCR) is a sensitive fluorescent-based quantification method, that can be used to detect the expression of miRNAs in patient samples. Our study presents the first proof-of-concept of a multiplexed dPCR assay for the simultaneous analysis and quantification of multiple miRNAs.

RESULTS

After reverse transcription (RT) using a pool of miRNA-specific stem-loop primers, dPCR was performed with a universal reverse primer and miRNA-specific forward primers along with fluorescently-labelled hydrolysis probes. Multiple experimental parameters were evaluated and strategies for modulating the observed signals were devised. The optimised assay was applied to the analysis of miRNAs from cell lines and biological samples. Although absolute quantification was lost, due to the reverse transcription step, quantification was linear for the dilution series and results were highly reproducible for independent dPCR and RT reactions. Our results confirmed the high sensitivity of dPCR for patient samples.

CONCLUSIONS

We demonstrate the feasibility and reliability of multiplexed detection and quantification of miRNAs by dPCR that can be applied in a clinical setting to evaluate miRNA signatures.

Dual-Amplification Single-Particle ICP-MS Strategy Based on Strand Displacement Amplification-CRISPR/Cas12a Amplification for Homogeneous Detection of miRNA

MicroRNAs (miRNAs) regulate a myriad of biological processes and thus have been regarded as useful biomarkers in biomedical research and clinical diagnosis. The specific and highly sensitive detection of miRNAs is of significant importance. Herein, a sensitive and rapid dual-amplification elemental labeling single-particle inductively coupled plasma-mass spectrometry (spICP-MS) analytical method based on strand displacement amplification (SDA) and CRISPR/Cas12a was developed for miRNA-21 detection. Taking gold nanoparticles (AuNPs) as the elemental labels, the Au NP probe initially hybridized with linker DNA, forming large aggregates. In the absence of target miRNA-21, large aggregates of AuNPs will produce high pulse signals in spICP-MS detection. In the presence of the target miRNA-21, it triggered the SDA reaction, and the SDA products activated CRISPR/Cas12a's trans-cleavage activity to cleave the linker DNA, resulting in disassembly of the AuNP aggregates. The AuNP aggregates with smaller size displayed lower pulse signals in spICP-MS detection. Under the optimal conditions, a good relationship between the average pulse signal intensity of AuNP aggregates and the concentration of miRNA-21 was obtained in the range of 0.5 fmol L-1-100 pmol L-1 with a quantification limit as low as 0.5 fmol L-1. The developed method was successfully used for determination of miRNA-21 in human breast cancer cell lines (SK-BR-3 and MCF-7) and real blood samples from breast cancer patients. It is versatile, can be adapted to detect other targets by modifying the specific sequence of the SDA template chain that is complementary to the analytes, and offers a promising strategy for detecting various biomarkers with high sensitivity and specificity.