Probing low abundant DNA methylation by CRISPR-Cas12a-assisted cascade exponential amplification

Recent advances in cascade isothermal amplification techniques for ultra-sensitive nucleic acid detection

Nucleic acid amplification techniques have always been one of the hot spots of research, especially in the outbreak of COVID-19. From the initial polymerase chain reaction (PCR) to the current popular isothermal amplification, each new amplification techniques provides new ideas and methods for nucleic acid detection. However, limited by thermostable DNA polymerase and expensive thermal cycler, PCR is difficult to achieve point of care testing (POCT). Although isothermal amplification techniques overcome the defects of temperature control, single isothermal amplification is also limited by false positives, nucleic acid sequence compatibility, and signal amplification capability to some extent. Fortunately, efforts to integrating different enzymes or amplification techniques that enable to achieve intercatalyst communication and cascaded biotransformations may overcome the corner of single isothermal amplification. In this review, we systematically summarized the design fundamentals, signal generation, evolution, and application of cascade amplification. More importantly, the challenges and trends of cascade amplification were discussed in depth.

Methylation-sensitive transcription-enhanced single-molecule biosensing of DNA methylation in cancer cells and tissues

As a major epigenetic modification, DNA methylation participates in diverse cellular functions and emerges as a promising biomarker for disease diagnosis and monitoring. Herein, we developed a methylation-sensitive transcription-enhanced single-molecule biosensor to detect DNA methylation in human cells and tissues. In this biosensor, a rationally designed transcription machine is split into two parts including a promoter sequence (probe-P) for initiating transcription and a template sequence (probe-T) for RNA synthesis. The presence of specific DNA methylation leads to the formation of full-length transcription machine through sequence-specific ligation of probe-P and probe-T, initiating the synthesis of abundant ssRNA transcripts. The resultant ssRNAs can activate CRISPR/Cas12a to catalyze cyclic cleavage of fluorophore- and quencher-dual labeled signal probes, resulting in the recovery of the fluorophore signal that can be quantified by single-molecule detection. Taking advantages of the high-fidelity ligation of split transcription machine and the high efficiency of transcription- and CRISPR/Cas12a cleavage-mediated dual signal amplification, this single-molecule biosensor achieves a low detection limit of 337 aM and high selectivity. Moreover, it can distinguish 0.01% methylation level, and even accurately detect genomic DNA methylation in single cell and clinical samples, providing a powerful tool for epigenetic researches and clinical diagnostics.

Locus-Specific Detection of DNA Methylation: The Advance, Challenge, and Perspective of CRISPR-Cas Assisted Biosensors

Deoxyribonucleic acid (DNA) methylation is one of the epigenetic characteristics that result in heritable and revisable phenotype changes but without sequence changes in DNA. Aberrant methylation occurring at a specific locus was reported to be associated with cancers, insulin resistance, obesity, Alzheimer's disease, Parkinson's disease, etc. Therefore, locus-specific DNA methylation can serve as a valuable biomarker for disease diagnosis and therapy. Recently, Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are applied to develop biosensors for DNA, ribonucleic acid, proteins, and small molecules detection. Because of their highly specific binding ability and signal amplification capacity, CRISPR-Cas assisted biosensor also serve as a potential tool for locus-specific detection of DNA methylation. In this perspective, based on the detection principle, a detailed classification and comprehensive discussion of recent works about the latest advances in locus-specific detection of DNA methylation using CRISPR-Cas systems are provided. Furthermore, current challenges and future perspectives of CRISPR-based locus-specific detection of DNA methylation are outlined.

Cancer-Derived Small Extracellular Vesicles PICKER

Cancer-derived small extracellular vesicles (csEVs) play critical roles in the genesis and development of various cancers. However, accurate detection of low-abundance csEVs remains particularly challenging due to the complex clinical sample composition. In the present study, we constructed a Programmable Isothermal Cascade Keen Enzyme-free Reporter (PICKER) for the reliable detection and acquisition of the relative abundance of csEVs in total sEVs (tsEVs) by integrating dual-aptamer recognition (cancer-specific protein EpCAM and tetraspanin protein CD63) with a catalytic hairpin assembly (CHA) amplification. By employing this strategy, we were able to achieve a detection limit of 420 particles/μL csEVs. Particularly, we proposed a novel particle ratio index of csEV against tsEV (PR_csEV/tsEV) to greatly eliminate errors from inconsistent centrifugation, which was calculated from the fluorescence ratio produced by csEVs and tsEVs. The PICKER showed a 1/10,000 discrimination capability by successfully picking out 1.0 × 10³ csEV from 1.0 × 10⁷ tsEV per microliter. We also found that the PR_csEV/tsEV value increased proportional to the stages of breast cancer by analyzing EVs from clinical patients' plasma. Taken together, we established a PICKER strategy capable of accurately discriminating csEVs, and the proposed PR_csEV/tsEV had been proven a potential indicator of breast cancer staging, paving the way toward facilitating cancer diagnosis and precision therapeutics.