A comprehensive system for detecting rare single nucleotide variants based on competitive DNA probe and duplex-specific nuclease

Deciphering the role of ELAVL1: Insights from pan-cancer multiomics analyses with emphasis on nasopharyngeal carcinoma

Background and Objectives

Cancer continues to be a predominant cause of mortality worldwide, underscoring the critical need to identify and develop novel biomarkers to improve prognostic accuracy and therapeutic approaches. The dysregulation of ELAVL1 is linked to various diseases, including cancer. Nevertheless, its role across different cancer types remains insufficiently investigated.

Methods

We conducted a systematic investigation into the expression patterns, prognostic significance, genomic alterations, modifications, and functional implications of ELAVL1 in pan-cancer types. Besides, we performed in vitro and in vivo experiments to confirm the role of ELAVL1 in nasopharyngeal carcinoma (NPC).

Results

By utilizing multi-omics datasets, we found obvious overexpression of ELAVL1 in various cancer types at both the mRNA and protein levels, with predominant expression in malignant cells. Survival analysis revealed that increased ELAVL1 expression was linked to unfavorable outcomes in certain cancers; however, its effect difers among various cancer types. Additionally, we found that the genomic alterations and modifications of ELAVL1 were related to tumor progression. We discovered that ELAVL1 was elevated in NPC tissues. In addition, survival analysis indicated that NPC patients with higher ELAVL1 expression had worse prognoses. Functional assays demonstrated that ELAVL1 suppression led to decreased proliferation and migration in NPC cell lines. Moreover, ELAVL1 knockdown effectively inhibited NPC progression in the lymph node and lung metastasis models.

Conclusions

In summary, ELAVL1 exhibits diverse and complex involvement in tumor progression. Targeting it might inhibit tumor progression, making it a promising biomarker and therapeutic target for enhancing cancer treatment outcomes.

Label-free miRNA fluorescent biosensors based on duplex-specific nucleases and silver nanoclusters

MicroRNAs (miRNAs) are considered reliable biomarkers for a variety of diseases. However, their low abundance in organisms and high sequence similarity of homologous miRNAs make their accurate detection challenging. Here, we constructed a novel fluorescent biosensor for the detection of miRNA-155, a potential biomarker of neuroinflammation, based on duplex-specific nuclease (DSN) assisted amplification and DNA-templated silver nanoclusters (DNA-AgNCs) as fluorescence signal probes. DSN-assisted amplification can transform unstable miRNA into stable DNA and amplify the miRNA signal at the same time. Using DNA-AgNCs as fluorescence signal probes for biosensors can avoid complex labeling processes and reduce costs. The biosensor shows excellent selectivity, reproducibility, a wide linear range (1-600 nM) with a detection limit of 0.86 nM, and potentiality for real sample detection. This work provides a potential universal biosensing platform for miRNA detection.

Single Nucleotide Recognition and Mutation Site Sequencing Based on a Barcode Assay and Rolling Circle Amplification

Single nucleotide polymorphisms (SNPs) present significant challenges in microbial detection and treatment, further raising the demands on sequencing technologies. In response to these challenges, we have developed a novel barcode-based approach for highly sensitive single nucleotide recognition. This method leverages a dual-head folded complementary template probe in conjunction with DNA ligase to specifically identify the target base. Upon recognition, the system triggers rolling circle amplification (RCA) followed by the self-assembly of CdSe quantum dots onto polystyrene microspheres, enabling a single-particle fluorescence readout. This approach allows for precise base identification at individual loci, which are then analyzed using a bio-barcode array to screen for base changes across multiple sites. This method was applied to sequence a drug-resistant mutation site in Helicobacter pylori (H. pylori), demonstrating excellent accuracy and stability. Offering high precision, high sensitivity, and single nucleotide resolution, this approach shows great promise as a next-generation sequencing method.

Magnetic Covalent Organic Framework Composites for Wastewater Remediation

Covalent organic frameworks (COFs) with high specific surface area, tailored structure, easy functionalization, and excellent chemical stability have been extensively exploited as fantastic materials in various fields. However, in most cases, COFs prepared in powder form suffer from the disadvantages of tedious operation, strong tendency to agglomerate, and poor recyclability, greatly limiting their practical application in environmental remediation. To tackle these issues, the fabrication of magnetic COFs (MCOFs) has attracted tremendous attention. In this review, several reliable strategies for the fabrication of MCOFs are summarized. In addition, the recent application of MCOFs as outstanding adsorbents for the removal of contaminants including toxic metal ions, dyes, pharmaceuticals and personal care products, and other organic pollutants is discussed. Moreover, in-depth discussions regarding the structural parameters affecting the practical potential of MCOFs are highlighted in detail. Finally, the current challenges and future prospects of MCOFs in this field are provided with the expectation to boost their practical application.

Molecular dynamics simulation-guided toehold mediated strand displacement probe for single-nucleotide variants detection

Single nucleotide variant (SNV) has become an emerging biomarker for various diseases such as cancers and infectious diseases. Toehold-mediated strand displacement (TMSD), the core reaction of DNA nanotechnology, has been widely leveraged to identify SNVs. However, inappropriate choice of mismatch location results in poor discrimination ability. Here, we comprehensively investigate the effect of mismatch location on TMSD kinetics by molecular dynamic simulation tool oxDNA through umbrella sampling and forward flux sampling disclosing that mismatches at the border of the toehold and branch migration domain yield the lowest TMSD reaction rate. Nine disease-related SNVs (SARS-CoV-2-D614G, EGFR-L858R, EGFR-T790M, KRAS-G12R, etc.) were tested experimentally showing a good agreement with simulation. The best choice of mismatch location enables high discrimination factor with a median of 124 for SNV and wild type. Coupling with a probe-sink system, a low variant allele frequency of 0.1% was detected with 3 S/N. We successfully used the probes to detect SNVs with high confidence in the PCR clones of constructed plasmids. This work provides mechanistic insights into TMSD process at the single-nucleotide level and can be a guidance for the design of TMSD system with fine-tuning kinetics for various applications in biosensors and nanotechnology.

Signaling probe design for amplification-free detection of bacterial genes using DNA microarray

DNA microarrays are useful to detect microorganisms for various purposes including clinical testing and food safety. However, conventional DNA microarrays need complicated operations such as amplification, fluorescence labeling, and washing steps. To address this issue, we previously developed the signaling probe-based DNA microarray system that can eliminate these steps, and demonstrated a direct detection of bacterial genes. Nonetheless, this system requires well-designed probe sets due to the fluorescence resonance energy transfer (FRET)-based mode of action. Up to date, the probe design was highly dependent on the trial-and-error processes. In this study, we propose a strategy to rationally design the sequences of signaling probes based on the thermodynamic analysis. This analysis aided to improve the probe performance approximately 2.8 times, without experiments, by suppressing the secondary structure formation of the probes. We successfully demonstrated the specific and amplification-free detection of 5S rRNA from total RNA extracted from Escherichia coli within 30 min.