Technologies for analysis of circulating tumour DNA: Progress and promise

Recent Advancements in the Application of Circulating Tumor DNA as Biomarkers for Early Detection of Cancers

Early detection of cancer is vital for increasing patient survivability chances. The three major techniques used to diagnose cancers are instrumental examination, tissue biopsy, and tumor biomarker detection. Circulating tumor DNA (ctDNA) has gained much attention in recent years due to advantages over traditional technology, such as high sensitivity, high specificity, and noninvasive nature. Through the mechanism of apoptosis, necrosis, and circulating exosome release in tumor cells, ctDNA can spread throughout the circulatory system and carry modifications such as methylations, mutations, gene rearrangements, and microsatellite instability. Traditional gene-detection technology struggles to achieve real-time, low-cost, and portable ctDNA measurement, whereas electrochemical biosensors offer low cost, high specificity alongside sensitivity, and portability for the detection of ctDNA. Therefore, this review focuses on describing the recent advancements in ctDNA biomarkers for various cancer types and biosensor developments for real-time, noninvasive, and rapid ctDNA detection. Further in the review, ctDNA sensors are also discussed in regards to their selections of probes for receptors based on the electrode surface recognition elements.

Electrochemical Biosensors for Circulating Tumor DNA Detection

Early diagnosis and treatment have always been highly desired in the fight against cancer, and detection of circulating tumor DNA (ctDNA) has recently been touted as highly promising for early cancer-screening. Consequently, the detection of ctDNA in liquid biopsy is gaining much attention in the field of tumor diagnosis and treatment, which has also attracted research interest from industry. However, it is difficult to achieve low-cost, real-time, and portable measurement of ctDNA in traditional gene-detection technology. Electrochemical biosensors have become a highly promising solution to ctDNA detection due to their unique advantages such as high sensitivity, high specificity, low cost, and good portability. Therefore, this review aims to discuss the latest developments in biosensors for minimally invasive, rapid, and real-time ctDNA detection. Various ctDNA sensors are reviewed with respect to their choices of receptor probes, designs of electrodes, detection strategies, preparation of samples, and figures of merit, sorted by type of electrode surface recognition elements. The development of biosensors for the Internet of Things, point-of-care testing, big data, and big health is analyzed, with a focus on their portable, real-time, and non-destructive characteristics.

A homogeneous digital biosensor for circulating tumor DNA by the enumeration of a dual-color quantum dot complex

Monitoring ctDNA in blood is important for cancer management. Here, a one-step single particle counting approach was developed for directly quantifying ctDNA in plasma. Hairpin DNA containing a triple helix stem was immobilized onto QD 585 as a probe. The hairpin was opened by the target, and therefore hybridized with assistant DNA on QD 655, resulting in an aggregate of QD 585 and QD 655. The two-color QD aggregate was regarded as the target. Observed under a single particle transmission grating-based spectral microscope, the two-color QD aggregate was distinguished by a unique spectral pattern of two first-order streaks, and it was counted. The difference in the responses of the probes to perfect-match DNA, single-base mismatch DNA, and non-match DNA indicated that the probe had sufficient single-base discrimination capabilities. The success in plasma recovery tests demonstrated the feasibility of carrying out the direct detection of ctDNA in plasma.

Uniform palladium nanosheets for fluorimetric detection of circulating tumor DNA

Fluorescence quenching property of two-dimensional (2D) nanosheets (NSs) have received extensively attention in the construction of novel biosensing platform. However, the heterogeneity of the wide-size distribution and inefficient fluorescence quenching capacity limit its wide practical applications. Herein, for the first time, we report a novel fluorescent biosensor based on uniform palladium NSs (Pd NSs) with excellent fluorescence quenching efficiency and differential affinity toward ssDNA versus dsDNA and combination with a pair of DNA detection probes with fluorophore for detecting circulating tumor DNA (ctDNA). The DNA detection probes are facilitated to adsorbed to the surface of Pd NSs, leading to efficient fluorescence quench. In the presence of target DNA, it can be linked by T4 DNA ligase to form long DNA duplex structures, which display weak affinity toward Pd NSs, producing the fluorescence recovery. The remarkable fluorescence quenching efficiency and ssDNA/dsDNA differential affinity of Pd NSs make it have a good detection ability without signal amplification. The result indicates that this facile but cost-effective strategy holds great promise in bioanalysis.

Human serum albumin as an intrinsic signal amplification amplifier for ultrasensitive assays of the prostate-specific antigen in human plasma

Endogenous human serum albumin is used as an intrinsic signal amplification amplifier for ultrasensitive assays of disease biomarkers in blood tests.

"Trojan Horse" DNA Nanostructure for Personalized Theranostics: Can It Knock on the Door of Preclinical Practice?

Nanotheranostics, combing diagnostic and therapeutic components in an all-in-one nanomaterial, possess exciting potentials for precision nanomedicine. However, a major obstacle for current nanotheranostics to enter preclinical and/or clinical trials is the intrinsic toxicities of these nanomaterials. As an emerging biomaterial, the bioinspired DNA nanostructure shows advantages for constructing better nanotheranostics due to its excellent features, including native biocompatibility, full programmability, and ready accessibility. In this feature article, we highlight recent advances in the design of DNA-nanostructure-based diagnostics and/or therapeutics capable of specifically responding to biological stimuli in a dynamic way, with a particular focus on the design mechanism, responsive performance, and potential for preclinical and/or clinical trials in personalized theranostics.

ctDNA Detection Based on DNA Clutch Probes and Strand Exchange Mechanism

Circulating tumor DNA (ctDNA), originating directly from the tumor or circulating tumor cells, may reflect the entire tumor genom and has gained considerable attention for its potential clinical diagnosis and prognosis throughout the treatment regimen. However, the reliable and robust ctDNA detection remains a key challenge. Here, this work designs a pair of DNA clutch separation probes and an ideal discrimination probes based on toehold-mediated strand displacement reaction (TSDR) to specifically recognize ctDNA. First, the ctDNAs were denatured to form ssDNAs, the pair of DNA clutch separation probes [one of which modified onto the magnetic nanoparticles (MNPs)] are used to recognize and hybridize with the complemental chains and prevent reassociation of denatured ssDNAs. The complemental chains are removed in magnetic field and left the wild and mutant ssDNA chains in the supernatant. Then, the TSDR specificity recognizes the target mutant sequence to ensure only the mutated strands to be detection. The proposed assay exhibited good sensitivity and selectivity without any signal amplification. The proposed assay displayed a linear range from 2 to100 nM with a limit of detection (LOD) of 0.85 nM, and it was useful for ctDNA biomedical analysis and clinic theranostic.

A versatile label-free electrochemical biosensor for circulating tumor DNA based on dual enzyme assisted multiple amplification strategy

A versatile label-free electrochemical biosensor based on dual enzyme assisted multiple amplification strategy was developed for ultrasensitive detection of circulating tumor DNA (ctDNA). The biosensor consists of a triple-helix molecular switch (THMS) as molecular recognition and signal transduction probe, ribonuclease HII (RNase HII) and terminal deoxynucleotidyl transferase (TdT) as dual enzyme assisted multiple amplification accelerator. The presence of target ctDNA could open THMS and trigger RNase HII-assisted homogenous target recycling amplification to produce substantial signal transduction probe (STP). The released STP hybridized with the capture probe immobilized on a gold electrode, then TdT and assistant probe were further employed to fulfill TdT-mediated cascade extension and generate stable DNA dendritic nanostructures. The electroactive methyl blue (MB) was finally used as the signal reporter to realize the multiple electrochemical amplification ctDNA detection as the amount of MB is positively correlated with the target ctDNA. Combined with the efficient recognition capacity of the designed THMS and the excellent multiple amplification ability of RNase HII and TdT, the constructed sensing platform could detect KRAS G12DM with a wide detection range from 0.01 fM to 1 pM, and the limit of detection as low as 2.4 aM. Besides, the platform is capable of detecting ctDNA in biological fluid such as plasma. More importantly, by substituting the loop of THMS with different sequences, this strategy could be conveniently expanded into the detection of other ctDNA, showing promising potential applications in clinical cancer screening and prognosis.

A sample-in-digital-answer-out system for rapid detection and quantitation of infectious pathogens in bodily fluids

A variety of automated sample-in-answer-out systems for in vitro molecular diagnostics have been presented and even commercialized. Although efficient in operation, they are incapable of quantifying targets, since quantitation based on analog analytical methods (via standard curve analysis) is complex, expensive, and challenging. To address this issue, herein, we describe an integrated sample-in-digital-answer-out (SIDAO) diagnostic system incorporating DNA extraction and digital recombinase polymerase amplification, which enables rapid and quantitative nucleic acid analysis from bodily fluids within a disposable cartridge. Inside the cartridge, reagents are pre-stored in sterilized tubes, with an automated pipetting module allowing facile liquid transfer. For digital analysis, we fabricate a simple, single-layer polydimethylsiloxane microfluidic device and develop a novel and simple sample compartmentalization strategy. Sample solution is partitioned into an array of 40,044 fL-volume microwells by sealing the microfluidic device through the application of mechanical pressure. The entire analysis is performed in a portable, fully automated instrument. We evaluate the quantitative capabilities of the system by analyzing Mycobacterium tuberculosis genomic DNA from both spiked saliva and serum samples, and demonstrate excellent analytical accuracy and specificity. This SIDAO system provides a promising diagnostic platform for quantitative nucleic acid testing at the point-of-care. Graphical abstract ᅟ.

Electrochemical screening of single nucleotide polymorphisms with significantly enhanced discrimination factor by an amplified ratiometric sensor

The detection of single nucleotide polymorphisms (SNPs) is of great clinical significance to the diagnosis of various genetic diseases and cancers. In this work, the development of an ultrasensitive ratiometric electrochemical sensor for screening SNP with a significantly enhanced discrimination factor is reported. The ferrocene (Fc) and methylene blue (MB) dual-tagged triple helix complex (THC) probes are self-assembled on the gold electrode to construct the sensing interface. The addition of the mutant p53 gene causes the disassembly of the THC probes with the release of the Fc-tagged sequence and the folding of the MB-labeled sequence into a hairpin structure, causing the change in the current response ratio of MB to Fc for monitoring the mutant p53 gene. Such ratio is dramatically enhanced by the toehold-mediated displacement reaction-assisted target recycling amplification with the presence of an assistance hairpin sequence. With the significant signal amplification and the advantageous specificity of the THC probes, sub-femtomolar detection limit and a highly enhanced SNP discrimination factor for the mutant p53 gene can be obtained. Besides, the proof-of-demonstration application of the sensor for diluted real samples has been verified, offering such sensor new opportunities for monitoring various genetic related diseases.

High-performance electrochemical sensing of circulating tumor DNA in peripheral blood based on poly-xanthurenic acid functionalized MoS2 nanosheets

A high-performance sensing platform based on poly-xanthurenic acid (PXA) film functionalized MoS₂ nanosheets was developed for electrochemical detection of circulating tumor DNA in peripheral blood. The MoS₂ nanosheets were obtained using a simple ultrasonic method from bulk MoS₂. The physical adsorption between MoS₂ and aromatic XA monomers effectively improved the electropolymerization efficiency, accompanied with an increased electrochemical response of PXA. The obtained PXA/MoS₂ nanocomposite not only served as a substrate for DNA immobilization but also reflected the electrochemical transduction originating from DNA immobilization and hybridization without any complex labelling processes or outer indicators. The immobilization of the probe ssDNA was achieved via noncovalent assembly due to the π-π interaction between PXA and DNA bases. After the hybridization of the probe ssDNA with the target DNA, the formation of helix structure induced the resulted dsDNA to be released from the surface of the PXA/MoS₂ nanocomposite. The detection limit of this constructed DNA biosensor was calculated in the linear target DNA concentrations range from 1.0 × 10^-16 mol/L to 1.0 × 10^-10 mol/L and it was found to be 1.8 × 10^-17 mol/L.

Tungsten disulfide nanosheets supported poly(xanthurenic acid) as a signal transduction interface for electrochemical genosensing applications

Tungsten disulfide (WS₂) nanosheets supported poly(xanthurenic acid) (PXa) was used as the signal transduction interface for electrochemical genosensing. The WS₂ nanosheets were obtained from bulk WS₂ using a simple ultrasonic method. Due to the unique physical adsorption of Xa monomers to WS₂, the electropolymerization efficiency was greatly improved, accompanied with an increased electrochemical response of PXa. The obtained PXa/WS₂ nanocomposite not only served as a substrate for DNA immobilization but also reflected the electrochemical transduction originating from DNA immobilization and hybridization without any other indicators or complicated labelling steps. Owing to the presence of abundant carboxyl groups, the probe ssDNA was covalently attached on the carboxyl-terminated PXa/WS₂ nanocomposite through the free amines of DNA sequences based on the 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide and N-hydrosulfosuccinimide crosslinking reaction. The covalently immobilized probe ssDNA could selectively hybridize with its target DNA to form dsDNA on the surface of the PXa/WS₂ nanocomposite. This developed biosensor achieved a satisfactory detection limit down to 1.6 × 10⁻¹⁶ mol L⁻¹ and a dynamic range of 1.0 × 10⁻¹⁵ to 1.0 × 10⁻¹¹ mol L⁻¹ for detection of circulating tumor DNA related to gastric carcinoma. Selectivity of the biosensor has been investigated in presence of non-complementary, one-mismatched and two-mismatched DNA sequences.

An electrochemical signal transduction sensing interface for detecting PIK3CA gene was developed based on WS₂ nanosheets supported PXa.