Ratiometric Fluorescent Biosensor for Visual Discrimination of Cancer Cells with Different Telomerase Expression Levels

Background-filtered telomerase activity assay with cyclic DNA cleavage amplification

Overexpression of telomerase incites the abnormal proliferation of cancer cells. Thus, it has been regarded as a cancer biomarker and a potential therapeutic target. Existing assays suggest a promising sensing scheme to detect telomerase activity. However, they are complicated in terms of assay preparation and implementation. We herein report a Quenching-Exempt invader Signal Amplification Test, termed 'QUEST'. The assay leverages on a high turnover, specific cleaving enzyme, flap endonuclease I (FEN1), and graphene oxide (GO) for background (BG) filtering. In response to the target, FEN1 significantly boosts the signal with invader signal amplification. To distinguish the target signal, GO filters out the BG. It captures residual reporter invader probes (RP) to quench undesired signals. QUEST is straightforward without any pre-preparatory steps and washing/separation. Its probe design is simple and cost-effective. With QUEST, we investigated telomerase activities in various cell lines. Notably, we discriminated cancer cell lines from normal cell lines. In addition, a candidate inhibitor for telomerase was screened, which showed the promising potential of QUEST in real applications.

Parallel Dielectrophoretic Capture, Isolation, and Electrical Lysis of Individual Breast Cancer Cells to Assess Variability in Enzymatic Activity

Tumor cell heterogeneity drives disease progression and response to therapy, and therefore, there is a need for single-cell analysis methods. In this paper, we present an integrated, scalable method to analyze enzymatic activity in many individual cancer cells at once. The reported method uses dielectrophoresis (DEP) to selectively capture tumor cells at wireless electrodes aligned to an overlying array of cell-sized micropockets. Following hydrodynamic transfer of the captured cells into microfluidic chambers, the chambers are fluidically isolated and sealed with a hydrophobic ionic liquid, which possesses sufficient conductivity to allow for subsequent electrical lysis of the cells to access their contents for enzymatic assay. The wireless electrodes have an interlocking spiral design that ensures successful electrical lysis regardless of the location of the cell within the chamber. Here, breast cancer cells are assessed for β-galactosidase through its activation of a fluorogenic substrate. A key point is that the fluorogenic assay solution was optimized to allow for dielectrophoretic cell capture, thereby obviating the need for a solution exchange step. Our approach has several distinct advantages including a high rate of single-cell capture, a capture efficiency that is independent of the dimensions of the reaction chambers, no need for mechanical closure of reaction volumes, and no observed cross-talk. In this study, first, the steps of cell capture, transfer, and lysis are established on this platform in the presence of the optimized assay solution. We then quantify the increase in fluorescence intensity obtained over the duration of the enzymatic assay of individual cells. Finally, this method is applied to the analysis of β-galactosidase activity in 258 individual MDA-MB-231 breast cancer cells, revealing heterogeneity in expression of this enzyme in this cell line. We expect that the adaptability of this method will allow for expanded studies of single-cell enzymatic expression and activity. This will in turn open avenues of research into cancer cell heterogeneity in metabolism, invasiveness, and drug response. The ability to study these features of cancer at the single-cell level raises the possibility for treatment plans tailored to target the specific combinations of cell subpopulations present in tumors. Furthermore, we expect that this method can be adapted to uses outside of cancer research, such as studies of neuron metabolism, pathogenesis in bacteria, and stem cell development.

A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes for the detection of telomerase activity

A label- and enzyme-free fluorescence assay based on thioflavin T–induced G-quadruplexes is developed to sensitively and specifically detect telomerase activity. Thioflavin T has a dual role as an efficient inducer and fluorescent probe, and the incorporation of thioflavin T into the thioflavin T–induced G-quadruplexes results in an intense fluorescence enhancement. In the presence of thioflavin T and K+, G-quadruplexes are formed by elongation of the telomerase substrate primer that is catalyzed by telomerase extracted from cancer cells. Thus, the telomerase activity in cancer cell extracts can be evaluated by measuring the thioflavin T fluorescence. More importantly, thioflavin T can specifically recognize and bind to G-quadruplexes, whereas it cannot recognize single- and double-stranded DNAs, which leads to the thioflavin T–based fluorescence assay exhibiting a reduced background and improved signal-to-noise ratio. As a result, the proposed assay has the linear range from 5 to 200 HeLa cells and the detection limit is 34 HeLa cells, which holds great potential for use in the detection of telomerase activity and the diagnosis of cancer.

Biofabricated functionalized graphene quantum dots (fGQDs): Unravelling its fluorescence sensing mechanism of human telomerase reverse transcriptase (hTERT) antigen and in vitro bioimaging application

Lung cancer (LC) is a deadly malignancy that is posing a serious threat to human health. Therefore, early detection of LC biomarkers is the key to reducing LC-related fatalities. Herein, we present the first fluorescent-based selective detection of LC biomarker human telomerase reverse transcriptase (hTERT) using polyethyleneimine (PEI) functionalized graphene quantum dots (fGQDs). One-pot in situ synthesis of amine-functionalized GQDs was accomplished by hydrothermal carbonization of biowaste-derived cellulose and PEI. Synthesized fGQDs were characterized by various analytical techniques. Synthesized fGQDs not only exhibited enhanced fluorescence life-time but also excellent stability in the different solvents compared to bare GQDs. The surface activation of hTERT-Ab by carbodiimide chemistry (EDC-NHS) resulted in stacking interactions with fGQDs, involving adsorption-desorption as well as competitive mechanisms. The higher inherent affinity of hTERT-Ag (hTERT antigen) for hTERT-Ab (hTERT antibody) resulted in complex formation and recovery of fGQD fluorescence. As a result, this fluorescence sensing demonstrated a greater linear detection range (0.01 ng mL-1 to 100 µg mL-1) as well as a notable low detection limit (36.3 pg mL-1). Furthermore, the fabricated immunosensor (Ab@fGQDs) has excellent stability and performance in real samples, with an average recovery of 97.32%. The results of cytotoxicity and cellular bioimaging study in A549 cells show that fGQDs can be used for additional nanotherapeutics and biological applications.

A smartphone-based platform for ratiometric visualization of SARS-CoV-2 via an oligonucleotide probe

COVID-19 necessitates the development of reliable and convenient diagnostic tools. In this work, a facile 3D-printed smartphone platform was constructed that achieved reliable visual detection of SARS-CoV-2 by eliminating the effect of ambient light and fixing the camera position relative to the sample. The oligonucleotide probe is modified with orange-red-emitting TAMRA working as an internal standard and green-emitting FAM serving as a sensitive sensing agent. Under 365-nm UV excitation, the emission wavelengths of TAMRA and FAM are 580 nm and 518 nm, respectively. When the probes interact with the targets, the green fluorescence gradually restores while the orange-red fluorescence remains stable. Thus, a striking color transition from orange-red to green could be observed by the naked eye. The detection limit of SARS-CoV-2 nucleic acid is 0.23 nM, and the entire process of color change could be completed in 25 min. Furthermore, the RGB value analysis of the sample solution was conducted using a smartphone for reliable and reproducible discrimination of SARS-CoV-2. The proposed smartphone platform might establish a general method for visual detection of SARS-CoV-2 nucleic acid as well as other virus-related diseases.

Ratiometric fluorescent probe: a sensitive and reliable reporter for the CRISPR/Cas12a-based biosensing platform

Using a ratiometric probe as the reporter for the CRISPR-Cas12a based biosensing system, the change of two fluorescence intensities can be monitored, while the TaqMan probe appears only one signal.

Accurate Identification and Early Diagnosis of Osteosarcoma through CRISPR-Cas12a-Based Average Telomerase Activity Detection

Sensitive and reliable analysis of telomerase activity is important for clinical diagnosis, therapy, and prognosis of osteosarcoma. Telomerase activity is a complicated concept including both the amount of active telomerases and the length of the telomerases extension product. Still, few of the strategies formerly proposed distinguish the two aspects of telomerase activity. Herein, we propose a novel CRISPR-Cas12a-based fluorescent sensing platform that can output signals of both the amounts of telomerase and length of telomerase extension products with the assistance of an elegantly designed stem-loop probe and CRISPR-Cas12a system. On this basis, we induced a novel index, average telomerase activity, for accurate cancer reporting. Through systematic laboratory and clinical experiments, we have demonstrated that average telomerase activity can accurately distinguish cancer cells and has the potential for osteosarcoma staging.

Nonradioactive direct telomerase activity detection using biotin-labeled primers

Background

Telomerase is a ribonucleoprotein enzyme responsible for maintenance of telomere length which expressed in more than 85% of cancer cells but undetectable in most normal tissue cells. Therefore, telomerase serves as a diagnostic marker of cancers. Two commonly used telomerase activity detection methods, the telomerase repeated amplification protocol (TRAP) and the direct telomerase assay (DTA), have disadvantages that mainly arise from reliance on PCR amplification or the use of an isotope. A safe, low‐cost and reliable telomerase activity detection method is still lacking.

Method

We modified DTA method using biotin‐labeled primers (Biotin‐DTA) and optimized the method by adjusting cell culture temperature and KCl concentration. The sensitivity of the method was confirmed to detect endogenous telomerase activity. The reliability was verified by detection of telomerase activity of published telomerase regulators. The stability was confirmed by comparing the method with TRAP method.

Results

Cells cultured in 32°C and KCl concentration at 200 mM or 250 mM resulted in robust Biotin‐DTA signal. Endogenous telomerase activity can be detected, which suggested an similar sensitivity as DTA using radioactive isotope markers. Knockdown of telomerase assembly regulator PES1 and DKC1 efficiently reduced telomerase activity. Compared with TRAP method, Biotin‐DTA assay offers greater signal stability over a range of analyte protein amounts.

Conclusion

Biotin‐labeled, PCR‐free, and nonradioactive direct telomerase assay is a promising new method for the easy, low‐cost, and quantitative detection of telomerase activity.

Carbon Nanocage/Fe3O4/DNA-Based Magnetically Targeted Intracellular Imaging of Telomerase via Catalyzed Hairpin Assembly and Photodynamic-Photothermal Combination Therapy of Tumor Cells

Human telomerase has been identified as a potential tumor biomarker for early cancer diagnosis and cancer progression monitoring. We construct a novel magnetic targeting carbon nanocage/Fe₃O₄/DNA (CNC/Fe₃O₄/DNA) nanoprobe for intracellular imaging of telomerase via the signal amplification strategy catalyzed hairpin assembly (CHA) and for photodynamic-photothermal therapy of tumor cells. Telomerase primer DNA, trigger DNA, hairpin DNA1 (H1), and hairpin DNA2 (H2) were adsorbed to the surface of CNC/Fe₃O₄ nanoparticles (CNC/Fe₃O₄ NPs), and the fluorescence of (chlorin e6) Ce6 was quenched by CNC/Fe₃O₄ NPs. After entering the living cell through magnetic targeting, the telomerase primer DNA can be extended in the presence of highly activated telomerase, leading to the issue of trigger DNA, which can initiate the CHA cycling process followed by the amplification of the fluorescence intensity. The in vitro detection results justified that the proposed nanoprobe showed good sensitivity and selectivity for telomerase. Confocal microscopy studies indicated that such a nanoprobe can be used to detect the activity of telomerase in living cells and the fluorescence signal was stronger under the guidance of a magnetic field. We successfully employed this nanoprobe to monitor the dynamic activity of telomerase in various types of tumor cells and normal cells and to damage tumor cells by photodynamic-photothermal combination therapy, which evidenced that this is a promising biological method for early cancer diagnosis and tumor cell therapy.

Sensitive detection of intracellular telomerase activity via double signal amplification and ratiometric fluorescence resonance energy transfer

As an important and universal tumor marker, the reliable and in situ detection of intracellular telomerase activity is crucial for cancer diagnosis. Herein, a ratiometric fluorescence resonance energy transfer (FRET) method was developed for detecting intracellular telomerase activity. It takes full advantage of manganese dioxide nanosheets (MnO2NS) that can carry DNA probes with different conformations into cells and then completely release the DNA probes via decomposition of MnO2NS by intracellular reduced glutathione (GSH). In the presence of telomerase, a telomere substrate (TS) could be extended to form long telomerase extension products (TEPs), which trigger the cycling strand displacement reaction (SDR) between two fluorophore-labeled hairpin DNA probes to form lots of DNA duplexes. The close contact of two fluorophores led to an effective ratiometric FRET for reliable detection of telomerase activity. Fluorescence confocal imaging demonstrated that the activity of telomerase in tumor cells was reliably detected. The inhibition of telomerase activity by an inhibitor resulted in a decrease in FRET signal. For extracellular detection, the FRET ratio (FA/FD) shows a good linear relationship with the number of HeLa cells in the range of 20-1000 cells. Therefore, it offers a more facile method for reliable and sensitive detection of intracellular telomerase activity.

Portable glucose meter-utilized label-free and washing-free telomerase assay

We herein describe a portable glucose meter (PGM)-utilized label-free and washing-free method for the facile determination of telomerase activity that relies on the kinase-catalyzed cascade enzymatic reaction (KCER) that transduces the telomerase activity to the glucose level. In the sensor, the telomerase that elongates telomere sequences ((TTAGGG)_n) from the 3'-terminus of telomerase substrate primer (TSP) consumes deoxynucleoside triphosphate (dNTP), which serves as a phosphate source for KCER promoted by hexokinase and pyruvate kinase. Thus, the presence of telomerase protects KCER from working effectively, resulting in the maintenance of an initial, high glucose level that is readily determined using hand-held PGM. With this strategy, the telomerase activities in various types of cell lines were successfully determined with high sensitivity. Furthermore, the ability of this method to screen candidate inhibitors for telomerase activity was also verified.

Magnetic bead-enzyme assemble for triple-parameter telomerase detection at single-cell level

In this work, we developed a triple-parameter strategy for the detection of telomerase activity from cancer cells and urine samples. This strategy was developed based on magnetic bead-enzyme hybrids combined with fluorescence analysis, colorimetric assay, or adenosine triphosphate (ATP) meter as readout. The application of magnetic bead-enzyme hybrids has the advantages of magnetic separation and signal amplification. These detection methods can be used individually or in combination to achieve the optimal sensing performance and make the results more convincing. Among them, the ATP meter with portable size had easy operation and low cost, and this response strategy provided a higher sensitivity at the single-cell level. The designed strategy was suitable as naked-eye sensor and point-of-care testing (POCT) for rapid assaying of telomerase activity. Graphical abstract Magnetic bead-enzyme assemble for triple-parameter telomerase detection.

Live-Cell Sensing of Telomerase Activity by Using Hybridization-Sensitive Fluorescent Oligonucleotide Probes

Live-cell sensing of telomerase activity with simple and efficient strategies remains a challenging target. In this work, a strategy for telomerase sensing by using hybridization-sensitive fluorescent oligonucleotide probes is reported. In the presence of telomerase and dNTPs, the designed supporting strand was extended and generated the hairpin structure that catalyzed the next telomerase extending reaction. The special extension mechanism increased the local concentration of another supporting strand and telomerase, which resulted in enhanced telomerase activity. The hybridization-sensitive oligonucleotide probes bound to the hairpin catalyst and generated turn-on fluorescence. This method realized the sensing of telomerase activity in HeLa cell extract with a detection limit below 1.6×10^-6  IU μL^-1 . The real-time in situ observation of telomerase extension was achieved in living HeLa cells. This strategy has been applied to monitor the efficiency of telomerase-targeting anticancer drugs in situ.

Target induced framework nucleic acid nanomachine with doxorubicin-spherical nucleic acid tags for electrochemical determination of human telomerase activity

A stable and enzyme-free method is described for highly sensitive determination of telomerase activity. It is based on the use of a framework nucleic acid (FNA) nanomachine and doxorubicin-spherical nucleic acid (DSNA) tags. Upon incubation with telomerase, the primer-tetrahedron becomes elongated to form the handed swing arm. The extended swing arm autonomously moves along the predefined track consisting of entropy-tetrahedron by consecutive strand displacement under the aid of fuel-tetrahedron. As a result, many (entropy-tetrahedron)-(fuel-tetrahedron) complexes are assembled for combining the DSNA tags. This results in an amplified electrochemical signal, typically measured at around -0.63 V (Ag/AgCl). The use of an enzyme-free FNA nanomachine and of DSNA tags warrants outstandingly high stability and sensitivity. The method shows a broad dynamic correlation of telomerase activity in cell extracts. The analytical range extends from 10 to 1.0 × 10⁴ HeLa cells mL^-1 with a lower detection limit of 2 cells mL^-1. The differences in telomerase activity between different cancer cells can be easily evaluated. The method was further verified by quantifying telomerase activity of cancer cells in accumulated normal cells. Therefore, the sensing method has great potential for clinical application. Graphical abstractSchematic representation of the electrochemical biosensor based on target induced framework nucleic acid nanomachine with doxorubicin-spherical nucleic acids (DSNA) tags, which can be used to the determination of telomerase activity in accumulated normal cells. dNTP: Deoxynucleotide triphosphates; FT: Fuel-tetrahedron.

A turn-on graphene quantum dot and graphene oxide based fluorometric aptasensor for the determination of telomerase activity

A turn-on fluorometric assay is described for determination of the activity of enzyme telomerase. For this purpose, graphene quantum dots (GQDs) were first modified with the telomeric sequence (5'-amino-AATCCGTCGAGCAGAGTT-3') via a condensation reaction. Injection of graphene oxide causes instant quenching of the blue fluorescence of the GQDs. Addition of cell extract containing telomerase, triggers the extension of telomer via addition of specific sequence (TTAGGG)n to its 3' end. Fluorescence, best measured at excitation/emission wavelengths of 390/446 nm, is subsequently restored due to folding of the extended telomeric sequence into G-quadruplex structure. The method was applied to the determination of telomerase activity in crude cell extracts of as little as 10 HeLa cells. The linear dynamic range extends from 10 to 6500 cells. Graphical abstractIn this study, a new turn-on graphene quantum dotm and graphene oxide based fluorometric assay is developed for the determination of telomerase activity.

Electrocatalysis of cerium metal-organic frameworks for ratiometric electrochemical detection of telomerase activity

A ratiometric electrochemical biosensor was constructed to detect telomerase activity based on electrocatalysis of cerium-based metal-organic frameworks (CeMOFs) and conformation switch of hairpin DNA. First, the CeMOFs were synthesized using Ce as nodes and 1,3,5-benzenetricarboxylic acid as linker in a green method, and then functionalized with gold nanoparticles. The resulted Au@CeMOF tags demonstrated an excellent electrocatalysis toward hydroquinone oxidation. Meanwhile, a methylene blue (MB) modified hairpin probe was designed with telomerase primer (TP) hybridized "stem" and immobilized on the electrode surface via Au-S chemistry. In the presence of the dNTPs and telomerase, the extended TP can open the hairpin DNA and keep the MB away from the electrode surface, resulting in a decrease of electrochemical signal. In the meantime, the TP-extended part could capture the Au@CeMOF-cDNA tags on the electrode surface via hybridization, leading to the increase electrochemical signal of hydroquinone oxidation catalyzed by Au@CeMOF-cDNA tags. Thus, a ratiometric signal output mode was developed for the electrochemical detection of telomerase activity. This biosensor showed wide dynamic correlation of telomerase activity from 2 × 10² to 2 × 10⁶ cells mL^-1 with the limit of detection of 27 cells mL^-1, and was applied to evaluate telomerase activity in single cell. The ratiometric electrochemical strategy based on the catalysis of MOFs provides a new avenue on signal transduction in telomerase detection.

Label-Free Telomerase Detection in Single Cell Using a Five-Base Telomerase Product-Triggered Exponential Rolling Circle Amplification Strategy

Telomerase is a universal biomarker of malignant tumors. Sensitive and reliable analysis for telomerase activity is of vital importance for both early diagnosis and therapy of malignant tumors. Herein, a novel fluorescent strategy was proposed for sensitive and label-free detection of telomerase activity. One highlight of this strategy is that an exponential signal amplification can be triggered by a very short telomerase extension product (TEP). Without adding dATP, the designed telomerase primer can be easily controlled to extend five bases (GGGTT) to give short TEP with definite length. The resulting short TEP can then be constructed as a circular rolling circle amplification (RCA) template and thus initiate a nicking enzyme-mediated exponential RCA, producing G-rich amplification products that can be sensitively probed via specific binding between the fluorescent dye Thioflavin T (ThT) and the nucleic acid G-quadruplexes. Elevated telomerase translocation efficiency, combined with exponential signal amplification and specific probing of RCA products by ThT, endow the sensing platform with extraordinarily high detection sensitivity. The requirement for short TEP increases the possibility to analyze telomerase with low activity. The proposed sensing platform can achieve sensitive telomerase activity detection in individual cells, even with the interference of accumulated normal cells. It was also demonstrated to show excellent capability in screening for the inhibitors of telomerase. Therefore, the proposed sensing platform has great potential for not only clinical diagnosis but also anticancer drug development.

Biomedical applications of nanoflares: Targeted intracellular fluorescence probes

Nanoflares are intracellular probes consisting of oligonucleotides immobilized on various nanoparticles that can recognize intracellular nucleic acids or other analytes, thus releasing a fluorescent reporter dye. Single-stranded DNA (ssDNA) complementary to mRNA for a target gene is constructed containing a 3'-thiol for binding to gold nanoparticles. The ssDNA "recognition sequence" is prehybridized to a shorter DNA complement containing a fluorescent dye that is quenched. The functionalized gold nanoparticles are easily taken up into cells. When the ssDNA recognizes its complementary target, the fluorescent dye is released inside the cells. Different intracellular targets can be detected by nanoflares, such as mRNAs coding for genes over-expressed in cancer (epithelial-mesenchymal transition, oncogenes, thymidine kinase, telomerase, etc.), intracellular levels of ATP, pH values and inorganic ions can also be measured. Advantages include high transfection efficiency, enzymatic stability, good optical properties, biocompatibility, high selectivity and specificity. Multiplexed assays and FRET-based systems have been designed.