Electrochemical Sensing of Cancer-related Global and Locus-specific DNA Methylation Events

Tracking Globally 5-Methylcytosine and Its Oxidized Derivatives in Colorectal Cancer Epigenome Using Bioelectroanalytical Technologies

This work presents the first electroanalytical bioplatforms to track individually or simultaneously at a global level all four methylation marks involved in the DNA methylation-demethylation cycle: 5-methylcytosine (5mC) and their sequential oxidative derivatives (5-hydroxymethyl-(5hmC), 5-formyl-(5fC), and 5-carboxyl-(5caC) cytosines). The bioplatforms employed direct competitive immunoassay formats implemented on the surface of magnetic microparticles (MBs) and involved capture antibodies specific to each epimark as well as synthetic biotinylated DNA oligomers with a single epimark that were enzymatically marked with horseradish peroxidase (HRP) to perform an amperometric readout on disposable platforms for single or multiplexed detection. These new electroanalytical biotechnologies, groundbreaking from analytical and clinical perspectives, achieved attractive operational characteristics, reaching detection limits at pM levels for synthetic single epimark-bearing DNA oligomers. The developed methodology was applied to track globally all four target epimarks in a fast, simple, sensitive, and selective way while their correlation in genomic DNA extracted from paired healthy and tumor tissues of patients with colorectal cancer (CRC) was established for the first time.

An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences

N4-methylcytosine (4mC) is a chemical modification that occurs on one of the four nucleotide bases in DNA and plays a vital role in DNA expression, repair, and replication. It also actively participates in the regulation of cell differentiation and gene expression. Consequently, it is important to comprehend the role of 4mC in the epigenetic regulation for revealing the complications of the gene expression and their associated governing cellular operations. However, the inherent resource requirements and time constraints of the experimental procedure, present challenges to the cellular culture process. While data-driven methodologies present promising solutions to mitigate the demand for extensive experimental efforts, their performance relies on the suitability and existence of high-quality data. This study presents a multi-model framework that integrates convolutional neural network (CNN) with the distributed k-mer and embedding feature extraction techniques to enhance the identification of 4mC sites in DNA sequences. The integration of k-mers ensures the effective representation of the local sequence patterns, while the utilization of embedding enables a more holistic encoding by considering the broader context and semantics of the sequence data. Following the initial step, the obtained distributed representation of the DNA sequence seamlessly enters the CNN, triggering a crucial convolution operation wherein a set of adaptable filters systematically convolves across the sequence to detect vital local patterns. The proposed integrated multi-model framework was applied to six publicly available datasets and evaluated against the cutting-edge 4mCPred, 4mCCNN, iDNA4mC, Meta-4mCpred, DeepTorrent, 4mCPred-SVM, and DMKL-HFIS methods. The evaluation was based on accuracy, specificity, sensitivity, and Matthews Correlation Coefficient. The results demonstrated that the proposed multi-model framework outperformed the state-of-the-art methods, as well as one-hot encoding and the hybrid of one-hot & TNC features, in accurately identifying 4mC sites.

An electrochemical genosensor for differentiation of fully methylated from fully unmethylated states of BMP3 gene

The methylation state of a part of the BMP3 gene was detected by our genosensor. This epigenetic biomarker is involved in the biomarker panel of the sDNA test, which is an FDA approved test for colorectal cancer screening. In the present genosensor, polyethyleneimine-stabilized silver nanoparticles (PEI-AgNPs) were used as a non-specific nanolabel for signal generation/amplification and lowering the limit of detection. After immobilization of capture probes and mercaptoethanol molecules on the gold electrode, a thermally treated mixture of the BMP3 targets and reporter probes was introduced to the electrode. Because of the specificity of the reporter probes for fully methylated targets, complete sandwich-like complexes are formed only with them. Therefore, such full-length double-stranded hybrids compared to fully unmethylated targets have more negative charges and can more attract positively charged PEI-AgNPs. For discrimination between methylated and unmethylated targets, electroimpedance spectroscopy and cyclic voltammetry were used for electrode modification monitoring and signal measurement. The sharp and narrow anodic peaks of cyclic voltammograms, which resulted from silver oxidation, were utilized for calibration plot analysis. The genosensor showed a linear response for the target concentration range from 1fM to 100 nM, while the detection limit for methylated and unmethylated target discrimination was 1 fM.

DNA Methylation in Solid Tumors: Functions and Methods of Detection

DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.

Immuno-DNA binding directed template-free DNA extension and enzyme catalysis for sensitive electrochemical DNA methyltransferase activity assay and inhibitor screening

A new electrochemical immuno-DNA sensing platform for DNA methyltransferase activity assay and inhibitor screening.

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.

Versatile Electroanalytical Bioplatforms for Simultaneous Determination of Cancer-Related DNA 5-Methyl- and 5-Hydroxymethyl-Cytosines at Global and Gene-Specific Levels in Human Serum and Tissues

This paper reports the preparation of versatile electrochemical biosensing platforms for the simple, rapid, and PCR-independent detection of the most frequent DNA methylation marks (5-methylcytosine, 5-mC, and/or 5-hydroxymethylcytosine, 5-hmC) both at global and gene-specific levels. The implemented strategies, relying on the smart coupling of immuno-magnetic beads (MBs), specific DNA probes and amperometric detection at screen-printed carbon electrodes (SPCEs), provided sensitive and selective determination of the target methylated DNAs in less than 90 min with a great reproducibility and demonstrated feasibility for the simultaneous detection of the same or different cytosine epimarks both at global level and in different loci of the same gene or in different genes. The bioplatforms were applied to determine global methylation events in paraffin-embedded colorectal tissues and specific methylation at promoters of tumor suppressor genes in genomic DNA extracted from cancer cells and paraffin-embedded colorectal tissues, and in serum without previous DNA extraction from cancer patients.

Determination of Cadherin-17 in Tumor Tissues of Different Metastatic Grade Using a Single Incubation-Step Amperometric Immunosensor

This paper reports the development of an amperometric immunosensing platform for the determination of cadherin-17 (CDH-17), an atypical adhesion protein involved in the progression, metastatic potential, and survival of high prevalence gastric, hepatocellular, and colorectal tumors. The methodology developed relies on the efficient capture and enzymatic labeling of the target protein on the magnetic microparticles (MBs) surface using commercial antibodies and amperometric transduction at screen-printed carbon electrodes (SCPEs) through the HRP/H₂O₂/HQ system. The developed immunosensing platform allows the selective determination of the target protein at low ng mL^-1 level (LOD of 1.43 ng mL^-1) in 45 min and using a single incubation step. The electrochemical immunosensor was successfully used for the accurate determination of the target protein in a small amount (0.5 μg) of raw lysates of colon cancer cells with different metastatic potential as well as in extracts from paraffin embedded cancer colon tissues of different metastatic grade.

Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments

This paper describes two different electrochemical affinity biosensing approaches for the simple, fast and bisulfite and PCR-free quantification of 5-methylated cytosines (5-mC) in DNA using the anti-5-mC antibody as biorecognition element. One of the biosensing approaches used the anti-5-mC as capture bioreceptor and a sandwich type immunoassay, while the other one involved the use of a specific DNA probe and the anti-5-mC as a detector bioreceptor of the captured methylated DNA. Both strategies, named for simplicity in the text as immunosensor and DNA sensor, respectively, were implemented on the surface of magnetic microparticles and the transduction was accomplished by amperometry at screen-printed carbon electrodes by means of the hydrogen peroxide/hydroquinone system. The resulting amperometric biosensors demonstrated reproducibility throughout the entire protocol, sensitive determination with no need for using amplification strategies, and competitiveness with the conventional enzyme-linked immunosorbent assay methodology and the few electrochemical biosensors reported so far in terms of simplicity, sensitivity and assay time. The DNA sensor exhibited higher sensitivity and allowed the detection of the gene-specific methylations conversely to the immunosensor, which detected global DNA methylation. In addition, the DNA sensor demonstrated successful applicability for 1 h-analysis of specific methylation in two relevant tumor suppressor genes in spiked biological fluids and in genomic DNA extracted from human glioblastoma cells.