Periodic magnetic modulation enhanced electrochemical analysis for highly sensitive determination of genomic DNA methylation

DNA methylation aberrations have a strong correlation with cancer in early detection, diagnosis, and prognosis, which make them possible candidate biomarkers. Electrochemical biosensors offer rapid protocols for detecting DNA methylation status with minimal pretreatment of samples. However, the inevitable presence of background current in the time domain, including electrochemical noise and variations, limits the detection performance of these biosensors, especially for low concentration analytes. Here, we propose an ultrasensitive frequency-domain electrochemical analysis strategy to effectively separate the weak signals from background current. To achieve this, we employed periodic magnetic field modulation of magnetic beads (MBs) on and off the electrode surface to generate a periodic electrochemical signal for subsequent frequency-domain analysis. By capturing labeled MBs with as low as 0.5 pg of DNA, we successfully demonstrated a highly sensitive electrochemical method for determination of genome-wide DNA methylation levels. We also validated the effectiveness of this methodology using DNA samples extracted from three types of hepatocellular carcinoma (HCC) cell lines. The results revealed varying genomic methylation levels among different HCC cell lines, indicating the potential application of this approach for early-stage cancer detection in terms of DNA methylation status.

Bringing to Light the Importance of the miRNA Methylome in Colorectal Cancer Prognosis Through Electrochemical Bioplatforms

This work reports the first electrochemical bioplatforms developed for the determination of the total contents of either target miRNA or methylated target miRNA. The bioplatforms are based on the hybridization of the target miRNA with a synthetic biotinylated DNA probe, the capture of the formed DNA/miRNA heterohybrids on the surface of magnetic microcarriers, and their recognition with an antibody selective to these heterohybrids or to the N6-methyladenosine (m6A) epimark. The determination of the total or methylated target miRNA was accomplished by labeling such secondary antibodies with the horseradish peroxidase (HRP) enzyme. In both cases, amperometric transduction was performed on the surface of disposable electrodes after capturing the resulting HRP-tagged magnetic bioconjugates. Because of their increasing relevance in colorectal cancer (CRC) diagnosis and prognosis, miRNA let-7a and m6A methylation were selected. The proposed electrochemical bioplatforms showed attractive analytical and operational characteristics for the determination of the total and m6A-methylated target miRNA in less than 75 min. These bioplatforms, innovative in design and application, were applied to the analysis of total RNA samples extracted from cultured cancer cells with different metastatic profiles and from paired healthy and tumor tissues of patients diagnosed with CRC at different stages. The obtained results demonstrated, for the first time using electrochemical platforms, the potential of interrogating the target miRNA methylation level to discriminate the metastatic capacities of cancer cells and to identify tumor tissues and, in a pioneering way, the potential of the m6A methylation in miRNA let-7a to serve as a prognostic biomarker for CRC.

A portable microfluidic photometric detection method based on enzyme linked immunoscatter enhancement

Currently, the combination of smart phones and microfluidic chips is a commonly used device for point-of-care testing (POCT) detection. Enzyme linked immunosorbent assay (ELISA) is an effective way to detect specific proteins in disease. Because the detection accuracy of smartphone cameras is difficult to directly replace high-precision spectral devices, the combination of smartphones and ELISA has not been widely used. Therefore, this paper proposes a microfluidic photometric detection method based on ELISA scattering enhancement. Firstly, the scattering characteristics of IMB are mined, and the optimal value of absorbance error compensation parameter is obtained. Secondly, the absorbance error compensation model based on scattering enhancement characteristics is established to improve the image acquisition accuracy of smart phones. Finally, the microfluidic photometric detection chip is developed, and the optical path system, optical path adjustment system and POCT detection App of smart phone are designed. The optimal compensation parameters of IMB were obtained based on simulated samples, and the linearity of absorbance and concentration increased by 22.6% after compensation. In the IL-6 sample experiment, the detection results of the platform in this paper had a good linear correlation with IL-6 sample concentration, and the linear correlation coefficient was above 0.95459. At the same time, the detection limit and accuracy meet the detection requirements. Therefore, with the participation of smart phones and microfluidic chips, problems such as difficult carrying and complex operation in traditional ELISA daily detection have been solved, laying a foundation for the future promotion and application of ELISA based POCT platform.

Magnetic Immunosensor Coupled to Enzymatic Signal for Determination of Genomic DNA Methylation

Aberrations of genomic DNA methylation have been confirmed to be involved in the evolution of human cancer and have thus gained the potential to be depicted as biomarkers for cancer diagnostics and prognostic predictions, which implicates an urgent need for detection of total genomic DNA methylation. In this work, we suggested an assay for the quantification of global DNA methylation, utilizing methylation specific antibody (5mC) modified magnetic beads (MBs) for immunorecognition and affinity enrichment. Subsequently, the captured DNA on the surface of MBs interacted with the glucose oxidase-conjugated DNA antibody whose catalytic reaction product was engaged in electrochemical detection of the overall level of DNA methylation on a PB-doped screen-printed electrode. With 15 pg of input DNA, which, to our best knowledge, is the lowest required amount of DNA without sodium bisulfite treatment or amplification, this test strategy was able to perceive as low as 5% methylation level within 70 min including the preparation of anti-5mC-MBs. We believe this detection technique offers a promising option to detect global DNA methylation in both academic and clinical scenarios.

Electrochemical LAMP-based assay for detection of RNA biomarkers in prostate cancer

Current molecular diagnostics of prostate cancer relies on detection of elevated levels of PSA protein in serum, but its specificity has been questioned due to its higher levels also in non-malignant prostate diseases. A long non-coding RNA biomarker, PCA3, demonstrated excellent specificity for prostate cancer, and thus has become an interesting alternative to PSA monitoring. Its detection utilizes mostly reverse transcription PCR with optical detection, making the protocol longer and more expensive. To avoid PCR, we have developed an electrochemical assay coupled with LAMP, an isothermal amplification technique showing high sensitivities at constant temperatures and shorter reaction times. We amplified PCA3 RNA as well as PSA mRNA (serving as a control), hybridized LAMP products on magnetic beads and measured them with chronoamperometry at carbon electrode chips. We show good sensitivity and specificity for both biomarkers in prostate cancer cell lines, and successful detection of PCA3 in clinical samples, i.e., urine samples from 11 prostate cancer patients and 7 healthy controls, where we obtained excellent correlation with clinical data. This is to our knowledge a first such attempt to apply electrochemistry to determine two RNA biomarkers directly in urine samples of prostate cancer patients in a minimally invasive diagnostics format.

Applications of electrochemical biosensors based on functional antibody-modified screen-printed electrodes: a review

The detection of biomolecular analytes is of great importance in clinical, environmental, and argo-food areas, among which the electrochemical methodology is attracting much attention. In particular, screen-printed electrode (SPE)-based sensing applications have exhibited potential possibility for on-site detection, especially for fast clinical biomarker detection, since they provide a miniaturized but robust and portable electrode detection system. In this context, we focused on the modification of SPE with functional antibodies to improve the electrochemical detection performance in versatile sensing applications, particularly for COVID-19 detection. These antibodies were immobilized onto the electrode surface via various methodologies, through which the powerful potential from the modification of SPE was revealed. Finally, more novel and excellent works on the biomolecular modification of SPE and the prospects of this technology from its state-of-art status to commercialization are previewed and future perspectives in this field are mentioned.

An electrochemical biosensor for simultaneous detection of breast cancer clinically related microRNAs based on a gold nanoparticles/graphene quantum dots/graphene oxide film

A label-free multiplexed electrochemical biosensor based on a gold nanoparticles/graphene quantum dots/graphene oxide (AuNPs/GQDs/GO) modified three-screen-printed carbon electrode (3SPCE) array is successfully constructed to detect miRNA-21, miRNA-155, and miRNA-210 biomarkers for the first time. Redox species (anthraquinone (AQ), methylene blue (MB), and polydopamine (PDA)) are used as redox indicators for anchoring capture miRNA probes, which hybridize with the complementary targets, miRNA-21, miRNA-155, and miRNA-210, respectively. After three target miRNAs are present, the square wave voltammetry (SWV) scan displays three well-separated peaks. Each peak indicates the presence of one miRNA, and its intensity quantitatively correlates with the concentration of the corresponding target analyte. This phenomenon results in the substantial decline of the SWV peak current of the redox probes. The developed AuNPs/GQDs/GO-based biosensor reveals excellent performance for simultaneous miRNA sensing. It offers a wide linear dynamic range from 0.001 to 1000 pM with ultrasensitive low detection limits of 0.04, 0.33, and 0.28 fM for the detection of miRNA-21, miRNA-155, and miRNA-210, respectively. It also presents high selectivity and applicability for the detection of miRNAs in human serum samples. This multiplex label-free miRNA biosensor has great potential for applications in breast cancer diagnosis.

Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging

Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.

A PCR-free screen-printed magnetic electrode for the detection of circular RNA from hepatocellular cancer based on a back-splice junction

Circular RNA (circRNA) has the potential to be applied to disease diagnosis and therapy. However, the currently available circRNA detection techniques are limited. This work proposes a sensitive and selective approach for circRNA detection based on gold nanoparticle-modified screen-printed magnetic electrodes (AuNPs-SPME). Magnetic beads (MBs) with capture probes based on specific back-splice junction (BSJ) sites were employed to identify and selectively isolate the target circRNA, which could be directly adsorbed onto the AuNPs-SPME. Then, the circRNA attached to the surface was detected by changes in the methylene blue redox signal. The simple and time-saving AuNPs-SPME is highly sensitive (LOD = 1.0 pM) to circCDYL, one of the biomarkers of hepatocellular cancer (HCC). The analytical performance of the method presented has also been verified in human serum samples, holding great promise for clinical diagnosis.

Functional magnetic beads with capture probes based on specific back-splice junction sites were employed to identify and selectively isolate target circRNA.

Application of magnetic nanomaterials in electroanalytical methods: A review

Magnetic nanomaterials (MNMs) have gained high attention in different fields of studies due to their ferromagnetic/superparamagnetic properties and their low toxicity and high biocompatibility. MNMs contain magnetic elements such as iron and nickel in metallic, bimetallic, metal oxide, and mixed metal oxide. In electroanalytical methods, MNMs have been applied as sorbents for sample preparation before the electrochemical detection (sorbent role), as the electrode modifier (catalytic role), and the integration of the above two roles (as both sorbent and catalytic agent). In this paper, the application of MNMs in electroanalytical methods have been classified based on the main role of the nanomaterial and discussed separately. Furthermore, catalytic activities of MNMs in electroanalytical methods such as redox electrocatalytic, nanozymes catalytic (peroxidase, catalase activity, oxidase activity, superoxide dismutase activity), catalyst gate, and nanocontainer have been discussed.

Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons

Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.

Electrochemical biosensing to move forward in cancer epigenetics and metastasis: A review

Early detection and effective treatment are crucial to reduce the physical, emotional, and financial pressure exerted by growing cancer burden on individuals, families, communities, and health systems. Currently, it is clear that the accurate analysis of emerging cancer epigenetic and metastatic-related biomarkers at different molecular levels is envisaged as an exceptional solution for early and reliable diagnosis and the improvement of therapy efficiency through personalized treatments. Within this field, electrochemical biosensing has demonstrated to be competitive over other emerging and currently used methodologies for the determination of these biomarkers accomplishing the premises of user-friendly, multiplexing ability, simplicity, reduced costs and decentralized analysis, demanded by clinical oncology, thus priming electrochemical biosensors to spark a diagnostic revolution for cancer prediction and eradication. This review article critically discusses the main characteristics, opportunities and versatility exhibited by electrochemical biosensing, through highlighting representative examples published during the last two years, for the reliable determination of these emerging biomarkers, with great diagnostic, predictive and prognostic potential. Special attention is paid on electrochemical affinity biosensors developed for the single or multiplexed determination of methylation events, non-coding RNAs, ctDNA features and metastasis-related protein biomarkers both in liquid and solid biopsies of cancer patients. The main challenges to which further work must be addressed and the impact of these advances should have in the clinical acceptance of these emerging biomarkers are also discussed which decisively will contribute to understand the molecular basis involved in the epigenetics and metastasis of cancer and to apply more efficient personalized therapies.

High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This "liquid biopsy" approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.

Pushing the limits of electrochemistry toward challenging applications in clinical diagnosis, prognosis, and therapeutic action

Constant progress in the identification of biomarkers at different molecular levels in samples of different natures, and the need to conduct routine analyses, even in limited-resource settings involving simple and short protocols, are examples of the growing current clinical demands not satisfied by conventional available techniques. In this context, the unique features offered by electrochemical biosensors, including affordability, real-time and reagentless monitoring, simple handling and portability, and versatility, make them especially interesting for adaptation to the increasingly challenging requirements of current clinical and point-of-care (POC) diagnostics. This has allowed the continuous development of strategies with improved performance in the clinical field that were unthinkable just a few years ago. After a brief introduction to the types and characteristics of clinically relevant biomarkers/samples, requirements for their analysis, and currently available methodologies, this review article provides a critical discussion of the most important developments and relevant applications involving electrochemical biosensors reported in the last five years in response to the demands of current diagnostic, prognostic, and therapeutic actions related to high prevalence and high mortality diseases and disorders. Special attention is paid to the rational design of surface chemistry and the use/modification of state-of-the-art nanomaterials to construct electrochemical bioscaffolds with antifouling properties that can be applied to the single or multiplex determination of biomarkers of accepted or emerging clinical relevance in particularly complex clinical samples, such as undiluted liquid biopsies, whole cells, and paraffin-embedded tissues, which have scarcely been explored using conventional techniques or electrochemical biosensing. Key points guiding future development, challenges to be addressed to further push the limits of electrochemical biosensors towards new challenging applications, and their introduction to the market are also discussed.