Hydroxymethylation-Specific Ligation-Mediated Single Quantum Dot-Based Nanosensors for Sensitive Detection of 5-Hydroxymethylcytosine in Cancer Cells

Advancing optical nanosensors with artificial intelligence: A powerful tool to identify disease-specific biomarkers in multi-omics profiling

Multi-omics profiling integrates genomic, epigenomic, transcriptomic, and proteomic data, essential for understanding complex health and disease pathways. This review highlights the transformative potential of combining optical nanosensors with artificial intelligence (AI). It is possible to identify disease-specific biomarkers using real-time and sensitive molecular interactions. These technologies are precious for genetic, epigenetic, and proteomic changes critical to disease progression and treatment response. AI improves multi-omics profiling by analyzing large, diverse data sets and common patterns traditional methods overlook. Machine learning tools Biomarkers Discovery is revolutionizing, drug resistance is being understood, and medicine is being personalized as the combination of AI and nanosensors has advanced the detection of DNA methylation and proteomic signatures and improved our understanding of cancer, cardiovascular disease and vascular disease. Despite these advances, challenges still exist. Difficulties in integrating data sets, retaining sensors, and building scalable computing tools are the biggest obstacles. It also examines various solutions with advanced AI algorithms and innovations, including fabrication in nanosensor design. Moreover, it highlights the potential of nanosensor-assisted, AI-driven multi-omics profiling to revolutionize disease diagnosis and treatment. As technology advances, these tools pave the way for faster diagnosis, more accurate treatment and improved patient outcomes, offering new hope for personalized medicine.

Label-Free and Sequence-Independent Isothermal Amplification Strategy for the Simultaneous Detection of Genomic 5-Methylcytosine and 5-Hydroxymethylcytosine

5-Methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) are crucial epigenetic modifications in eukaryotic genomic DNA that regulate gene expression and are associated with the occurrence of various cancers. Here, we combined bisulfite conversion with 4-acetamido-2,2,6,6-tetramethyl-1-oxopiperridinium tetrafluoroborate (ACT+BF4-, TCI) oxidation to develop a label-free and sequence-independent isothermal amplification (BTIA) assay for a genome-wide 5mC and 5hmC analysis. The BTIA strategy can distinguish 5mC and 5hmC signatures from other bases with high sensitivity and good specificity, avoiding sophisticated chemical modifications and expensive protein labeling. Moreover, the utilization of terminal deoxynucleotidyl transferase (TdT) enables the proposed strategy to detect global 5mC and 5hmC without sequence dependence. With only 78 ng of input of genomic DNA, global 5mC and 5hmC levels were accurately quantified in cells (including cancer cells of A549, T47D, and K562 and normal cells of HEK-293T, CHO, and NRK-52E) and clinical whole blood samples (including healthy control, precancerous cervical cancer, and confirmed cervical cancer) within 18 h. The detection results suggested that 5mC was highly expressed in cancer cells. More importantly, a significant increase in 5mC was observed in precancerous cervical cancer and further upregulation in confirmed cervical cancer, suggesting a correlation between 5mC and cancer occurrence and development. However, 5hmC showed the reverse result in these tested cells and clinical samples. Collectively, the BTIA strategy can be easily performed on the ordinary heating apparatus in almost all research and medical laboratories, showing a significant application in the early screening of cervical cancer in the clinic.

Electrochemical sensor for the analysis of 5-hydroxymethylcytosine in the presence of cytosine using pencil graphite electrode

In recent years, important efforts have been made to elucidate the mechanisms of epigenetic regulation, and one of the most studied epigenetic modifications was DNA methylation/demethylation. In this study, the voltammetric behaviour of 5-hydroxymethylcytosine was studied in the pH range of 2.00-11.00 using pencil graphite electrodes by differential pulse and square wave voltammetry. The effect of buffer solutions, scan rate, square wave voltammetry parameters, and stripping conditions on the voltammetric responses of 5-hydroxymethylcytosine were performed. The electrochemical oxidation process of 5-hydroxymethylcytosine on the pencil graphite electrode was realized under adsorption control. In human urine, by square wave stripping voltammetry, 5-hydroxymethylcytosine was quantified in a concentration range of 1.00 × 10-5 M-2.00 × 10-4 M. The proposed method was tested in the presence of cytosine in human urine. The recovery value of 5-hydroxymethylcytosine was found to be 99.57 %.

Identification of cell-free circulating epigenomic biomarkers for early diagnosis and response to therapies in breast cancer patients

The increasing prevalence of breast cancer presents a significant global health challenge, highlighting the urgent need for improved diagnostic and treatment monitoring methods. The non-invasive nature of cell-free circulating epigenomic biomarkers, such as methylated DNA (metDNA) and microRNAs (miRNAs), offers a reassuring approach to identifying breast cancer patients in the early stages and assessing their response to therapy. This approach holds great promise for diagnosis and treatment evaluation, prioritizing patient comfort and well-being. Cell-free circulating metDNA and miRNAs are released into the bloodstream from dying tumor cells through apoptosis and necrosis, carrying tumor-specific genetic and epigenetic changes. These changes encompass alterations in DNA methylation patterns, are pivotal in regulating gene expression, and are frequently disrupted in cancer. The interplay between these processes and the dynamic release of epigenomic biomarkers provides a real-time snapshot of the genetic and epigenetic features of the tumor. Integrating the analysis of metDNA and miRNA biomarkers into clinical practice can facilitate the early detection of breast cancer and improve the precision of treatment monitoring. By tracking changes in these biological markers, healthcare professionals can make informed decisions regarding modifications to therapy, ultimately enhancing patient outcomes. Gaining insights into the underlying mechanisms of cell-free circulating epigenomic biomarkers offers a groundbreaking approach to diagnosing and treating breast cancer.

Selective Ligase-Based Sample Processing-Free Discrimination and Detection of Site-Specific DNA 5-Hydroxymethylcytosine

Accurate detection of site-specific 5-hydroxymethylcytosine (5hmC) in genomic DNA is of great significance, but it is technically challenging to directly distinguish very low levels of 5hmC from their abundant cytosine/5-methylcytosine (C/5mC) analogues. Herein, we wish to propose a selective ligase-mediated mechanism (SLim) that can directly discriminate 5hmC from C/5mC with a high specificity without the use of any sample processing protocol. In this new design, we discovered that HiFi Taq DNA Ligase can well tolerate the mismatched 5hmC/A base-pairing and then effectively ligate the associated nicking site while the mismatched 5mC/A or C/A pairs cannot be recognized by HiFi Taq DNA Ligase, providing a new way for direct and selective discriminating 5hmC from its similar analogues. Ultrasensitive and selective quantification of site-specific 5hmC is realized by coupling the SLim with polymerase chain reaction (PCR) or loop-mediated isothermal amplification (LAMP).

Bioinspired Heterocoordination in Adaptable Cobalt Metal-Organic Framework for DNA Epigenetic Modification Detection

Metal-organic frameworks (MOFs) show unique advantages in simulating the dynamics and fidelity of natural coordination. Inspired by zinc finger protein, a second linker was introduced to affect the homogeneous MOF system and thus facilitate the emergence of diverse functionalities. Under the systematic identification of 12 MOF species (i.e., metal ions, linkers) and 6 second linkers (trigger), a dissipative system consisting of Co-BDC-NO2 and o-phenylenediamine (oPD) was screened out, which can rapidly and in situ generate a high photothermal complex (η = 36.9%). Meanwhile, both the carboxylation of epigenetic modifications and metal ion (Fe3+, Ni2+, Cu2+, Zn2+, Co2+ and Mn2+) screening were utilized to improve the local coordination environment so that the adaptable Co-MOF growth on the DNA strand was realized. Thus, epigenetic modification information on DNA was converted to an amplified metal ion signal, and then oPD was further introduced to generate bimodal dissipative signals by which a simple, high-sensitivity detection strategy of 5-hydroxymethylcytosine (LOD = 0.02%) and 5-formylcytosine (LOD = 0.025‰) was developed. The strategy provides one low-cost method (< 0.01 $/sample) for quantifying global epigenetic modifications, which greatly promotes epigenetic modification-based early disease diagnosis. This work also proposes a general heterocoordination design concept for molecular recognition and signal transduction, opening a new MOF-based sensing paradigm.

Chemo-Enzymatic Fluorescence Labeling Of Genomic DNA For Simultaneous Detection Of Global 5-Methylcytosine And 5-Hydroxymethylcytosine

5-Methylcytosine and 5-hydroxymethylcytosine are epigenetic modifications involved in gene regulation and cancer. We present a new, simple, and high-throughput platform for multi-color epigenetic analysis. The novelty of our approach is the ability to multiplex methylation and de-methylation signals in the same assay. We utilize an engineered methyltransferase enzyme that recognizes and labels all unmodified CpG sites with a fluorescent cofactor. In combination with the already established labeling of the de-methylation mark 5-hydroxymethylcytosine via enzymatic glycosylation, we obtained a robust platform for simultaneous epigenetic analysis of these marks. We assessed the global epigenetic levels in multiple samples of colorectal cancer and observed a 3.5-fold reduction in 5hmC levels but no change in DNA methylation levels between sick and healthy individuals. We also measured epigenetic modifications in chronic lymphocytic leukemia and observed a decrease in both modification levels (5-hydroxymethylcytosine: whole blood 30 %; peripheral blood mononuclear cells (PBMCs) 40 %. 5-methylcytosine: whole blood 53 %; PBMCs 48 %). Our findings propose using a simple blood test as a viable method for analysis, simplifying sample handling in diagnostics. Importantly, our results highlight the assay's potential for epigenetic evaluation of clinical samples, benefiting research and patient management.

Role of DNA De-methylation intermediate '5-hydroxymethylcytosine' in ovarian cancer management: A comprehensive review

Ovarian cancer remains the most eminent silent killer, with high morbidity and mortality among all gynaecological cancers. The advanced-stage patient's diagnosis has a low survival rate caused by its asymptomatic progression and diverse histopathological sub-types, wherefore in poor prognosis and highly recurring malignancy with multidrug resistance towards chemotherapy. Epigenetic biomarkers open promising avenues of intriguing research to combat OC malignancy, furthermore a tool for its early diagnosis. 5-hydroxymethycytosine (5-hmC), alias the sixth base of the genome, is an intermediate formed during the recently established DNA demethylation process and catalysed via ten-eleven translocation (TET) family of enzymes. It plays a significant role in regulating gene expression and has sparked interest in various cancer types. This review summarizes the role of active DNA demethylation process, its enzymes and intermediate 5-hmC in epigenetic landscape of ovarian cancer as a potent biomarker for clinical translation in identification of therapeutic targets, diagnostic and prognostic evaluation.