Quantitation and mapping of the epigenetic marker 5-hydroxymethylcytosine

Portable, Wireless Potentiostat Sensor for Ultra-Sensitive, Real-Time Detection of 5hmC in Genomic DNA Using Tree-Like Graphene

Aberrant alterations in genomic 5-hydroxymethylcytosine (5hmC), an oxidation product of 5-methylcytosine (5mC) by Ten-eleven translocation (TET) enzymes, are frequently associated with cancers. Quick and precise 5hmC quantification is vital since it is a key biomarker for diagnosis, pathophysiology, and therapy. Here, we present a portable, wireless potentiostat sensor for real-time, ultrasensitive 5hmC-DNA sensing based on a tree-like graphene (teG)-modified screen-printed microelectrode. One-pot electrochemical exfoliation of pencil graphite enabled the cost-effective, eco-friendly, and scalable synthesis of teG, which exhibited high electrical conductivity, excellent electrochemical conductivity, low surface roughness, and high 5hmC-DNA adsorption, surpassing those of pencil graphite (pG) and graphene oxide (GO). The teG-modified gold electrodes exhibited exceptional sensitivity (6.15 × 10-6 mM-1 cm-2), selectivity, and reproducibility, with an ultralow detection limit of 12.6 fM for 5hmC-DNA. The sensor's performance was validated by quantifying 5hmC levels in genomic DNA from various biological specimens, including primary mouse tissues with altered TET function, mouse hepatocellular carcinoma, and human prostate cancer cell lines. To enhance practicality, a flexible, screen-printed microelectrode on mulberry paper was developed and integrated with a portable, wireless potentiostat powered by the Arduino Nano 33 IoT. Open-circuit potential (OCP)-based detection enabled label-free, real-time monitoring with wireless data transmission to an Android mobile application, successfully differentiating 5hmC levels between cancerous and noncancerous cells. These findings highlight teG's high surface area, superior charge transport, and scalability, positioning it as a promising platform for next-generation biosensing. The developed sensor provides a rapid, cost-effective, and highly sensitive tool for 5hmC quantification, with significant implications for early cancer diagnostics and treatment.

Methods for Detection and Mapping of Methylated and Hydroxymethylated Cytosine in DNA

The chemical modifications of DNA are of pivotal importance in the epigenetic regulation of cellular processes. Although the function of 5-methylcytosine (5mC) has been extensively investigated, the significance of 5-hydroxymethylcytosine (5hmC) has only recently been acknowledged. Conventional methods for the detection of DNA methylation frequently lack the capacity to distinguish between 5mC and 5hmC, resulting in the combined reporting of both. The growing importance of 5hmC has prompted the development of a multitude of methods for the qualitative and quantitative analysis of 5hmC in recent years, thereby facilitating researchers' understanding of the mechanisms underlying the onset and progression of numerous diseases. This review covers both established and novel methods for the detection of cytosine modifications, including 5mC, 5hmC, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), with a particular focus on those that allow for accurate mapping and detection, particularly with third-generation sequencing. The review aims to help researchers choose the most appropriate methods based on their specific research goals and budget.

Epigenetic Quantification of DNA 5-Hydroxymethylcytosine Using DNA Hybridization-Based Single-Molecule Immunofluorescent Imaging

5-Hydroxymethylcytosine (5hmC) is a deoxyribonucleic acid (DNA) epigenetic modification that has an important function in embryonic development and human diseases. However, the numerous methods that have been developed to detect and quantify 5hmC, require large amounts of DNA sample to be modified via chemical reactions, which considerably limits their application with cell-free DNA (cfDNA). Meanwhile, other antibody-based methods of detecting 5hmC do not offer information about the DNA sequence. Here, in this article DNA hybridization-based single-molecule immunofluorescent imaging is presented, an ultrasensitive method of detecting 5hmC modification in DNA. Via using the probe DNA to capture the DNA fragment of interest and the 5hmC antibody to detect the 5hmC modification in DNA, the fluorescent response signal of the 5hmC modification from the secondary antibody at the single-molecule level is successfully detected. Using the method, one could determine the quantity of 5hmC in the gene of interest within 6 h. In addition, it requires only 3 pg of the DNA sample and minimal experience and training for operation and analysis.

Hydroxymethylation and tumors: can 5-hydroxymethylation be used as a marker for tumor diagnosis and treatment?

5-Methylcytosine (5mC) is considered as a common epigenetic modification that plays an important role in the regulation of gene expression. At the same time, 5-hydroxymethylcytosine (5hmC) has been found as an emerging modification of cytosine bases of recent years. Unlike 5mC, global 5hmC levels vary from tissues that have differential distribution both in mammalian tissues and in the genome. DNA hydroxymethylation is the process that 5mC oxidates into 5hmC with the catalysis of TET (ten-eleven translocation) enzymes. It is an essential option of DNA demethylation, which modulates gene expression by adjusting the DNA methylation level. Various factors can regulate the demethylation of DNA, such as environmental toxins and mental stress. In this review, we summarize the progress in the formation of 5hmC, and obtaining 5hmC in a cell-free DNA sample presents multiple advantages and challenges for the subject. Furthermore, the clinical potential for 5hmC modification in dealing with cancer early diagnosis, prognostic evaluation, and prediction of therapeutic effect is also mentioned.

New insights into the genetics and epigenetics of systemic sclerosis

Systemic sclerosis (SSc) is a severe autoimmune disease that is characterized by vascular abnormalities, immunological alterations and fibrosis of the skin and internal organs. The results of genetic studies in patients with SSc have revealed statistically significant genetic associations with disease manifestations and progression. Nevertheless, genetic susceptibility to SSc is moderate, and the functional consequences of genetic associations remain only partially characterized. A current hypothesis is that, in genetically susceptible individuals, epigenetic modifications constitute the driving force for disease initiation. As epigenetic alterations can occur years before fibrosis appears, these changes could represent a potential link between inflammation and tissue fibrosis. Epigenetics is a fast-growing discipline, and a considerable number of important epigenetic studies in SSc have been published in the past few years that span histone post-translational modifications, DNA methylation, microRNAs and long non-coding RNAs. This Review describes the latest insights into genetic and epigenetic contributions to the pathogenesis of SSc and aims to provide an improved understanding of the molecular pathways that link inflammation and fibrosis. This knowledge will be of paramount importance for the development of medicines that are effective in treating or even reversing tissue fibrosis.

Analytical epigenetics: single-molecule optical detection of DNA and histone modifications

The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.