Precisely Detecting the Telomerase Activities by an AIEgen Probe with Dual Signal Outputs after Cell-Cycle Synchronization

Label-Free Exosomal SERS Detection Assisted by Machine Learning for Accurately Discriminating Cell Cycle Stages and Revealing the Molecular Mechanisms during the Mitotic Process

Cell cycle analysis is crucial for disease diagnosis and treatment, especially for investigating cell heterogeneity and regulating cell behaviors. Exosomes are highly appealing as noninvasive biomarkers for monitoring real-time changes in the cell cycle due to their abundant molecular information inherited from their metrocyte cells and reflecting the state of these cells to some extent. However, to our knowledge, the relationship between exosomes and the cell cycle has not been reported. Herein, we successfully monitored the variation of exosomal surface-enhanced Raman spectroscopy (SERS) spectra to discriminate different cell cycle stages (G0/G1, S, and G2/M phases) based on label-free surface-enhanced Raman spectroscopy (SERS) combined with the machine learning method of linear discriminant analysis (LDA). An average accuracy of 85% based on the trained SERS spectra of exosomes from different cell cycle stages confirmed the high reliability of the support vector machine (SVM) algorithm for analyzing dynamic changes in the cell cycle at different time points. Importantly, the related molecular mechanisms among mitotic processes (prometaphase, metaphase, and anaphase/telophase) and unique biomolecular events between cancerous (HeLa) and normal (H8) cells were also revealed by the present label-free SERS detection platform. Based on SERS analysis, the content of phenylalanine (Phe) within HeLa cells increased, and some structures of proteins containing Phe and tryptophan (Trp) residues may be transformed during the mitotic process. Notably, the α-helix and β-sheet of proteins coexisted in HeLa cells; meanwhile, the α-helix of the proteins was more dominant in H8 cells than in HeLa cells. The strategy is effective for discriminating cell cycle stages and elucidating the associated molecular events during the cell mitotic process and will provide potential application value for guiding the cell cycle treatment strategies of cancer in the future.

Endogenous Telomerase-Activated Fluorescent Probes for Specific Detection and Imaging of Flap Endonuclease 1 in Cancer Cells and Tissues

Flap endonuclease 1 (FEN1) is a structure-specific DNA repair enzyme that has emerged as a potential target for cancer diagnosis and treatment. However, existing FEN1 assays often suffer from complicated reaction schemes and laborious procedures, and only a few methods are available for the detection and imaging of FEN1 in living cells. Especially, FEN1 is not exclusive to cancer cells, but it is also shared by normal cells. Consequently, the specific detection of FEN1 in cancer cells remains a challenge. Herein, we develop a simple and selective fluorescent biosensor for the specific imaging of FEN1 in cancer cells and tissues by engineering a FEN1 detection probe with a telomerase-responsive unit. In the presence of telomerase, it induces an extension reaction and subsequent intramolecular reconfiguration of the detection probe, generating a suitable branched DNA structure for FEN1 recognition and facilitating the cleavage of the flap by FEN1 for the recovery of fluorescence signal. Because telomerase is undetectable in normal cells but highly upregulated in cancer cells, the detection probe can only be activated in cancer cells to generate a high signal. This assay is quite simple, with the requirement of merely a single probe for dual enzyme recognition and signal output. With the integration of the single-molecule counting technology, this biosensor can achieve a detection limit of 1.2 × 10-5 U/μL, and it can accurately detect FEN1 in living cells and clinical tissues, providing a new avenue for FEN1-associated fundamental research and clinical diagnosis.

Construction of a 3D Quantum Dot Nanoassembly with Two-Step FRET for One-Step Sensing of Human Telomerase RNA in Breast Cancer Cells and Tissues

Telomerase is an important biomarker for early diagnosis of cancers, but current telomerase assays usually rely on measuring the extension products of telomerase substrates, which increases the assay complexity. More evidence indicates that human telomerase RNA (hTR), as a core component of telomerase, is positively correlated with the telomerase activity. Herein, we demonstrate the development of a duplex-specific nuclease (DSN)-propelled 3D quantum dot (QD) nanoassembly with two-step Föster resonance energy transfer (FRET) for the one-step sensing of hTR in breast cancer cells and tissues. This assay involves only one hairpin probe modified with a Cy5 at the sixth base from the 5'-biotin end and a BHQ2 at the 3'-terminus, which integrates three functions of target recognition, target recycling amplification, and signal readout. The anchoring of the hairpin probe on the 605QD surface results in the formation of a 3D 605QD-Cy5-probe-BHQ2 nanoassembly in which two-step FRET occurs among the 605QD, Cy5, and BHQ2 quencher. Notably, the formation of 605QD-Cy5-probe-BHQ2 nanoassembly facilitates the reduction of background signal and the increase of signal-to-background ratio due to its dense, highly oriented nucleic acid shell-induced steric hindrance effect. This assay can achieve one-step and rapid detection of hTR with a detection limit of 2.10 fM, which is the simplest and most rapid hTR assay reported so far. Moreover, this assay can efficiently distinguish single-base mismatched sequences, and it can discriminate the hTR level between breast cancer patients and healthy donors with a high accuracy of 100%, with great prospects for early diagnosis of cancers.

A triggered DNA nanomachine with enzyme-free for the rapid detection of telomerase activity in a one-step method

BACKGROUND

Telomerase is considered a biomarker for the early diagnosis and clinical treatment of cancer. The rapid and sensitive detection of telomerase activity is crucial to biological research, clinical diagnosis, and drug development. However, the main obstacles facing the current telomerase activity assay are the cumbersome and time-consuming procedure, the easy degradation of the telomerase RNA template and the need for additional proteases. Therefore, it is necessary to construct a new method for the detection of telomerase activity with easy steps, efficient reaction and strong anti-interference ability.

RESULTS

Herein, an efficient, enzyme-free, economical, sensitive, fluorometric detection method for telomerase activity in one-step, named triggered-DNA (T-DNA) nanomachine, was created based on target-triggered DNAzyme-cleavage activity and catalytic molecular beacon (CMB). Telomerase served as a switch and extended few numbers of (TTAGGG)n repeat sequences to initiate the signal amplification in the T-DNA nanomachine, resulting in a strong fluorescent signal. The reaction was a one-step method with a shortened time of 1 h and a constant temperature of 37 °C, without the addition of any protease. It also sensitively distinguished telomerase activity in various cell lines. The T-DNA nanomachine offered a detection limit of 12 HeLa cells μL-1, 9 SK-Hep-1 cells μL-1 and 3 HuH-7 cells μL-1 with a linear correlation detection range of 0.39 × 102-6.25 × 102 HeLa cells μL-1 for telomerase activity.

SIGNIFICANCE

In conclusion, our study demonstrated that the triggered-DNA nanomachine fulfills the requirements for rapid detection of telomerase activity in one-step under isothermal and enzyme-free conditions with excellent specificity, and its simple and stable structure makes it ideal for complex systems. These findings indicated the application prospect of DNA nanomachines in clinical diagnostics and provided new insights into the field of DNA nanomachine-based bioanalysis.

Construction of single-molecule counting-based biosensors for DNA-modifying enzymes: A review

DNA-modifying enzymes act as critical regulators in a wide range of genetic functions (e.g., DNA damage & repair, DNA replication), and their aberrant expression may interfere with regular genetic functions and induce various malignant diseases including cancers. DNA-modifying enzymes have emerged as the potential biomarkers in early diagnosis of diseases and new therapeutic targets in genomic research. Consequently, the development of highly specific and sensitive biosensors for the detection of DNA-modifying enzymes is of great importance for basic biomedical research, disease diagnosis, and drug discovery. Single-molecule fluorescence detection has been widely implemented in the field of molecular diagnosis due to its simplicity, high sensitivity, visualization capability, and low sample consumption. In this paper, we summarize the recent advances in single-molecule counting-based biosensors for DNA-modifying enzyme (i.e, alkaline phosphatase, DNA methyltransferase, DNA glycosylase, flap endonuclease 1, and telomerase) assays in the past four years (2019 - 2023). We highlight the principles and applications of these biosensors, and give new insight into the future challenges and perspectives in the development of single-molecule counting-based biosensors.

A Review of the Repair of DNA Double Strand Breaks in the Development of Oral Cancer

We explore the possibility that defects in genes associated with the response and repair of DNA double strand breaks predispose oral potentially malignant disorders (OPMD) to undergo malignant transformation to oral squamous cell carcinoma (OSCC). Defects in the homologous recombination/Fanconi anemia (HR/FA), but not in the non-homologous end joining, causes the DNA repair pathway to appear to be consistent with features of familial conditions that are predisposed to OSCC (FA, Bloom's syndrome, Ataxia Telangiectasia); this is true for OSCC that occurs in young patients, sometimes with little/no exposure to classical risk factors. Even in Dyskeratosis Congenita, a disorder of the telomerase complex that is also predisposed to OSCC, attempts at maintaining telomere length involve a pathway with shared HR genes. Defects in the HR/FA pathway therefore appear to be pivotal in conditions that are predisposed to OSCC. There is also some evidence that abnormalities in the HR/FA pathway are associated with malignant transformation of sporadic cases OPMD and OSCC. We provide data showing overexpression of HR/FA genes in a cell-cycle-dependent manner in a series of OPMD-derived immortal keratinocyte cell lines compared to their mortal counterparts. The observations in this study argue strongly for an important role of the HA/FA DNA repair pathway in the development of OSCC.

Modular Peptide Probe for Protein Analysis

The analysis and regulation of proteins are of great significance for the development of disease diagnosis and treatment. However, complicated analytical environment and complex protein structure severely limit the accuracy of their analysis results. Nowadays, ascribing to the editability and bioactivity of peptides, peptide-based probes could meet the requirements of good selectivity and high affinity to overcome the challenges. In this review, we summarize the advances in the use of modular peptide probes for proteins analysis. It focuses on how to design and optimize the structure of probes, as well as their performance. Then, the strategies and application to improve the analysis result of modular peptide probes are introduced. Finally, we also discuss current challenge and provide some ideas for the future direction for modular peptide probes, hoping to accelerate their clinical transformation.

Telomerase-initiated three-dimensional DNAzyme motor for monitoring of telomerase activity in living cells

Telomerase (TE) is recognized as a potential biomarker for early diagnosis, monitoring and treatment of cancer. At present, most of the methods for TE detection are only applicable to in vitro assays, and unsuitable for in vivo applications. Though a few intracellular probes have been reported to have good specificity for TE, they do not involve signal amplification, which hinders their applicability in scenarios requiring high sensitivity. It is rather challenging to develop highly sensitive biosensors for intracellular TE detection due to the difficulty in design TE probes with both high specificity and compatibility with signal amplification in living cells. Herein, a highly sensitive and selective three-dimensional DNAzyme motor for monitoring of TE activity in living cells was developed by innovatively integrating TE-mediated chain replacement reaction with a three-dimensional DNA walker. Specifically, the DNAzyme motor was constructed by assembling both DNAzyme substrates and swing arms made up of a hairpin-structured DNAzyme and a telomeric primer onto gold nanoparticles. TE in cells can activate the DNAzyme motor to carry out continuous chain replacement and substrate cutting reactions, and hence realize signal amplification in living cells. The DNAzyme motor was successfully utilized to monitor the dynamic changes of TE activity in four types of cells. Due to the advantages of simple synthesis, good biocompatibility and high sensitivity and specificity for TE, the proposed DNAzyme motor is expected to have great application potential in the early diagnosis of cancer.

Entropy-Driven Self-Assembly of Single Quantum Dot Sensor for Catalytic Imaging of Telomerase in Living Cells

Telomerase is a highly valuable cancer diagnosis biomarker and a promising cancer therapy target. So far, most telomerase assays are limited by the involvement of tedious procedures, multiple enzymes, and complicated reaction schemes. Sensitive monitoring of low-abundant telomerase in living cells remains a challenge. Herein, we demonstrate an entropy-driven catalytic assembly of quantum dot (QD) sensors for accurate detection and imaging of telomerase activity in living cells. In this sensor, target telomerase specifically catalyzes extension of telomerase primer, and the extended primer subsequently acts as a catalyst to continuously initiate entropy-driven catalytic reaction, generating a large number of fluorophore- and biotin-labeled DNAs that can be self-assembled on the QD surface to induce an efficient Föster resonance energy transfer signal. The proposed sensor requires a single step for both recognition and amplification of the telomerase signal, eliminating the use of either protein enzymes or laborious procedures. Taking advantage of the inherent superiority of single-molecule fluorescence detection and high amplification efficiency of the entropy-driven reaction, this sensor demonstrates single-cell sensitivity for the in vitro assay. Moreover, it is capable of screening the telomerase inhibitor, discriminating different tumor cells from normal ones, and even real-time imaging telomerase in living cells, providing a novel platform for telomerase-associated cancer diagnosis and drug screening.

Lifetime-Based Responsive Probes: Design and Applications in Biological Analysis

With the development of modern biomedicine, biological analysis and detection are very important in disease diagnosis, detection of curative effect, prognosis and prediction of tumor recurrence. Compared with the currently widely used optical probes based on intensity signals, the lifetime signal does not depend on the influence of conditions such as the concentration of luminophore, tissue penetration depth and measurement method. Therefore, biological detection methods based on lifetime-based responsive probes have attracted great attention from the scientific community. Here, we briefly review the key advances in lifetime-based responsive probes in recent years (2017-2022). The review focuses on the design strategies of lifetime-based responsive probes and the research progress of their applications in the field of bioanalysis, and discusses the challenges they face. We hope it will further promote the development of lifetime-based responsive probes in the field of bioanalysis. With the development of modern biomedicine, biological analysis and detection are very important in disease diagnosis, detection of curative effect, prognosis and prediction of tumor recurrence. Compared with the currently widely used optical probes based on intensity signals, the lifetime signal does not depend on the influence of conditions such as the concentration of luminophore, tissue penetration depth and measurement method. Therefore, biological detection methods based on lifetime-based responsive probes have attracted great attention from the scientific community. Here, we briefly review the key advances in lifetime-based responsive probes in recent years (2017-2022). The review focuses on the design strategies of lifetime-based responsive probes and the research progress of their applications in the field of bioanalysis, and discusses the challenges they face. We hope it will further promote the development of lifetime-based responsive probes in the field of bioanalysis.