Application of lateral flow and microfluidic bio-assay and biosensing towards identification of DNA-methylation and cancer detection: Recent progress and challenges in biomedicine

Fluorimetric detection of DNA methylation by cerium oxide nanoparticles for early cancer diagnosis

In this study, a very sensitive fluorescence nano-biosensor was developed using CeO2 nanoparticles for the rapid detection of DNA methylation. The characteristics of CeO2 nanoparticles were determined by transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS), X-ray diffraction (XRD) spectroscopy, UV-visible spectroscopy, and fluorescence spectroscopy. The CeO2 nanoparticles were reacted with a single-stranded DNA (ssDNA) probe, and then methylated and unmethylated target DNAs hybridized with an ssDNA probe, and the fluorescence emission was measured. Upon adding the target unmethylated and methylated ssDNA, the fluorescence intensity increased in the linear range of concentration from 2 × 10-13 - 10-18 M. The limit of detection (LOD) was 1.597 × 10-6 M for methylated DNA and 1.043 × 10-6 M for unmethylated DNA. The fluorescence emission intensity of methylated sequences was higher than of that unmethylated sequences. The fabricated DNA nanobiosensor showed a fluorescence emission at 420 nm with an excitation wavelength of 280 nm. The impact of CeO2 binding on methylated and unmethylated DNA was further demonstrated by agarose gel electrophoresis. Finally, the actual sample analysis suggested that the nanobiosensor could have practical applications for detecting methylation in the human plasma samples.

Acousto-optofluidic 3D single cell imaging of macrophage phagocytosis of Pseudomonas Aeruginosa

Understanding how immune cells such as monocytes or macrophages within our blood and tissue engulf and destroy foreign organisms is important for developing new therapies. The process undertaken by these cells, called phagocytosis, has yet to be observed in real-time at the single cell level. Microfluidic-based imaging platforms offer a wide range of tools for precise fluid control and biomolecule manipulation that makes regulating long term experiments and data collection possible. With the compatibility between acoustofluidics and light-sheet fluorescent microscopy (LSFM) previously demonstrated, here an acousto-optfluidic device with on-chip fluid flow direction control was developed. The standing surface acoustic waves (SSAWs) were used to trap, load and safeguard individual cells within a highly controllable fluid loop, created via the triggering of on-chip PDMS valves, to demonstrate multiple rounds of live single cell imaging. The valves allowed for the direction of the fluid flow to be changed (between forward and reverse operation) without altering the inlet flow rate, an important factor for performing reproducible and comparable imaging of samples over time. With this high-resolution imaging system, volumetric reconstructions of phagocytosed bacteria within macrophages could be resolved over a total of 9 rounds of imaging: totalling 19 reconstructed images of the cell membrane with visible intracellular bacteria.

Microfluidic-assisted integrated nucleic acid test strips for POCT

Numerous diseases have posed significant threats to public health, notably the global pandemic of COVID-19, resulting in widespread devastation due to its high infectivity and severity. The nucleic acid lateral flow assay (NALFA) addresses challenges of complexity, cost, and time associated with traditional assays, offering a reliable platform for rapid and precise nucleic acid target detection. NALFA is gaining prominence as a point-of-care testing (POCT) technique, thanks to its user-friendly operation and rapid results. Nevertheless, conventional NALFA relies on specialized technicians and involves labor-intensive steps like DNA extraction and PCR processes, impeding its efficiency. To overcome these limitations, integrating NALFA with microfluidic technology, widely employed in rapid field detection, holds promise. This review comprehensively outlines prevailing strategies for integrating NALFA, encompassing both research initiatives and commercial applications. Addressing the bottleneck of nucleic acid amplification as a rate-limiting step, the review delves into progress in amplification-free NALFA and highlights prevalent signal amplification techniques. Ultimately, the review outlines the future prospect of integrated NALFA development, capturing the technology's evolution and providing valuable insights for academic and commercial endeavors.

DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction

DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a novel methylation predictor with deep learning. Specifically, the DNA sequence is encoded with word embedding and GloVe in the first step. After that, dilated convolution and Transformer encoder are utilized to extract the features. Finally, full connection and softmax operators are applied to predict the methylation sites. The proposed model achieves an accuracy of 97.8% on the 5mC dataset, which outperforms state-of-the-art methods. Furthermore, our predictor exhibits good generalization ability as it achieves an accuracy of 95.8% on the m1A dataset. To ease access for other researchers, our code is publicly available at https://github.com/sb111169/tf-5mc.

Microfluidic Study of Enhanced Oil Recovery during Flooding with Polyacrylamide Polymer Solutions

A series of experiments have been carried out on the flooding of microfluidic chips simulating a homogeneous porous structure with various displacement fluids. Water and polyacrylamide polymer solutions were used as displacement fluids. Three different polyacrylamides with different properties are considered. The results of a microfluidic study of polymer flooding showed that the displacement efficiency increases significantly with increasing polymer concentration. Thus, when using a 0.1% polymer solution of polyacrylamide grade 2540, a 23% increase in the oil displacement efficiency was obtained compared to water. The study of the effect of various polymers on the efficiency of oil displacement showed that the maximum efficiency of oil displacement, other things being equal, can be achieved using polyacrylamide grade 2540, which has the highest charge density among those considered. Thus, when using polymer 2515 with a charge density of 10%, the oil displacement efficiency increased by 12.5% compared to water, while when using polymer 2540 with a charge density of 30%, the oil displacement efficiency increased by 23.6%.

Transfer of blocker-based qPCR reactions for DNA methylation analysis into a microfluidic LoC system using thermal modeling

Changes in the DNA methylation landscape are associated with many diseases like cancer. Therefore, DNA methylation analysis is of great interest for molecular diagnostics and can be applied, e.g., for minimally invasive diagnostics in liquid biopsy samples like blood plasma. Sensitive detection of local de novo methylation, which occurs in various cancer types, can be achieved with quantitative HeavyMethyl-PCR using oligonucleotides that block the amplification of unmethylated DNA. A transfer of these quantitative PCRs (qPCRs) into point-of-care (PoC) devices like microfluidic Lab-on-Chip (LoC) cartridges can be challenging as LoC systems show significantly different thermal properties than qPCR cyclers. We demonstrate how an adequate thermal model of the specific LoC system can help us to identify a suitable thermal profile, even for complex HeavyMethyl qPCRs, with reduced experimental effort. Using a simulation-based approach, we demonstrate a proof-of-principle for the successful LoC transfer of colorectal SEPT9/ACTB-qPCR from Epi Procolon® colorectal carcinoma test, by avoidance of oligonucleotide interactions.

Microfluidic assisted recognition of miRNAs towards point-of-care diagnosis: Technical and analytical overview towards biosensing of short stranded single non-coding oligonucleotides

MiRNAs are short stranded single non-coding oligonucleotides that play an important role in regulating gene expression. MiRNAs are stable in RNase enriched environments such as human body fluids and their dysregulation or abnormal abundance in human body fluids as a diagnostic biomarker has been associated with several diseases. Due to the low concentration of miRNAs, it is difficult to detect using interactive methods (ideal detection limit is femtomolar range). However, clinicians lack sensitive and reliable methods for quantifying miRNA. Microfluidic devices integrated with electrochemical, optical (fluorometric, SERs, FRET, colorimetric), electrochemiluminescence and photoelectrochemical signal readout led to development innovative diagnostic device test, can probably overcome the limitations of the traditional methods. In the present review, microfluid methods for the sensitive and selective recognition of miRNA in various biological matrices are surveyed. Also, advantages and limitation of recognition methods on the performance and efficiency of microfluidic based biosensing of miRNAs are critically investigated. Finally, the future perspectives on the diagnosis of disease based on microfluidic analysis of miRNAs are provided.

The Roles of Optogenetics and Technology in Neurobiology: A Review

Optogenetic is a technique that combines optics and genetics to control specific neurons. This technique usually uses adenoviruses that encode photosensitive protein. The adenovirus may concentrate in a specific neural region. By shining light on the target nerve region, the photosensitive protein encoded by the adenovirus is controlled. Photosensitive proteins controlled by light can selectively allow ions inside and outside the cell membrane to pass through, resulting in inhibition or activation effects. Due to the high precision and minimally invasive, optogenetics has achieved good results in many fields, especially in the field of neuron functions and neural circuits. Significant advances have also been made in the study of many clinical diseases. This review focuses on the research of optogenetics in the field of neurobiology. These include how to use optogenetics to control nerve cells, study neural circuits, and treat diseases by changing the state of neurons. We hoped that this review will give a comprehensive understanding of the progress of optogenetics in the field of neurobiology.

Optical bio-sensing of DNA methylation analysis: an overview of recent progress and future prospects

DNA methylation as one of the most important epigenetic modifications has a critical role in regulating gene expression and drug resistance in treating diseases such as cancer. Therefore, the detection of DNA methylation in the early stages of cancer plays an essential role in disease diagnosis. The majority of routine methods to detect DNA methylation are very tedious and costly. Therefore, designing easy and sensitive methods to detect DNA methylation directly and without the need for molecular methods is a hot topic issue in bioscience. Here we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation. In addition, various types of labeled and label-free reactions along with the application of molecular methods and optical biosensors have been surveyed. Also, the effect of nanomaterials on the sensitivity of detection methods is discussed. Furthermore, a comprehensive overview of the advantages and disadvantages of each method are provided. Finally, the use of microfluidic devices in the evaluation of DNA methylation and DNA damage analysis based on smartphone detection has been discussed.

Here, we provide an overview on the optical biosensors (including fluorescence, FRET, SERs, colorimetric) that have been applied to detect the DNA methylation.

Reliable recognition of DNA methylation using bioanalysis of hybridization on the surface of Ag/GQD nanocomposite stabilized on poly (β-cyclodextrin): A new platform for DNA damage studies using genosensor technology

Due to the role of DNA methylation in causing cancer in the present study, an innovative and inexpensive method was designed for the sensitive detection of DNA methylation. The silver-graphene quantum dots (Ag/GQDs) nano ink with high electrical conductivity was used as a substrate for genosensor fabrication toward identification of DNA hybridization. Also, poly (β-cyclodextrin) (p[β-CD]) has been used as a biointerface for the stabilization of Ag/GQD nano ink. The thiolated pDNA strand (5'-SH-TCCGCTTCCCGACCCGCACTCCGC-3') (as bioreceptor element) was fixed on the substrate and hybridized with methylated (5'-GC(M)GGAGTGC(M)GGGTC(M)GGGAAGC(M)GGA-3') and unmethylated (5'-GCGGAGTGCGGGTCGGGAAGCGGA-3') cDNAs, as target sequences were studied using electroanalysis methods. Under optimal conditions and using electrochemical techniques, the linear range was 1 am to 1 pm with LLOQ of 1aM. Finally, the designed DNA genosensor was used for detection of DNA methylation in human plasma samples and can be used to detect methylation in patient samples. It is expected that the designed DNA-based biodevice will be used to early stage diagnosis of cancer using monitoring of DNA methylation. Also, this type of genosensor can be used for epigenetic studies in the near future.

Hypermethylation of the Promoter of miR-338-5p Mediates Aberrant Expression of ETS-1 and Is Correlated With Disease Severity Of Astrocytoma Patients

The pro-oncogene ETS-1 (E26 transformation-specific sequence 1) is a key regulator of the proliferation and invasion of cancer cells. The present work examined the correlation of the aberrant expression of ETS-1 with histological or clinical classification of astrocytoma: grade I (pilocytic astrocytoma), grade II (diffuse astrocytoma), grade III (anaplastic astrocytoma), and grade IV (glioblastoma multiforme). MicroRNA, miR-338-5p, was predicted by an online tool (miRDB) to potentially target the 3' untranslated region of ETS-1; this was confirmed by multi-assays, including western blot experiments or the point mutation of the targeting sites of miR-338-5p in ETS-1's 3'untralation region (3'UTR). The expression of miR-338-5p was negatively associated with that of ETS-1 in astrocytoma, and deficiency of miR-338-5p would mediate aberrant expression of ETS-1 in astrocytoma. Mechanistically, hypermethylation of miR-338-5p by DNA methyltransferase 1 (DNMT1) resulted in repression of miR-338-5p expression and the aberrant expression of ETS-1. Knockdown or deactivation of DNMT1 decreased the methylation rate of the miR-338-5p promoter, increased the expression of miR-338-5p, and repressed the expression of ETS-1 in astrocytoma cell lines U251 and U87. These results indicate that hypermethylation of the miR-338-5p promoter by DNMT1 mediates the aberrant expression of ETS-1 related to disease severity of patients with astrocytoma.

Identification of DNA methylation by novel optical genosensing: A new platform in epigenetic study using biomedical analysis

Due to the important role of methylation in cancer, the use of sensitive analytical methods for early diagnosis and efficient clinical pharmacotherapy is highly demanded. In this study, an innovative label-free method has been developed for the recognition of methylated DNA in the promoter area of adenomatous polyposis coli gene (APC gene). Also, differentiation of unmethylated DNA (GCGGAGTGCGGGTCGGGAAGCGGA) from methylated cDNA (GC(M)GGAGTGC(M)GGGTC(M)GGGAAGC(M)GGA) was performed using optical synthesized probe (thionine-based polymer). Hybridization of pDNA (TCCGCTTCCCGACCCGCACTCCGC) with various types of cDNA sequences was studied by UV-visible and fluorescence spectroscopy. Also, some of the mismatch sequences {(GC(M)GGAGTAC(M)GGGTC(M)GGGAAGC(M)GGA) and (GCGGAGTACGGGTCGGGAAGCGGA)} were applied as negative control. For this purpose, The synthesized optical probe was characterized by transmission electron microscopy, atomic force microscopy, dynamic light scattering, zeta potential, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy, UV-Vis, and fluorescence spectroscopy. Under optimal conditions, the analytical performance of engineered DNA-based assay was studied and exhibited excellent dynamic range (1 zM to 3 pM) with low limit of quantitation (LLOQ) of 1 zM. The designed DNA-based assay showed a high capability of discriminating methylation, unmethylated and mismatched sequences. The engineered genosensor is simple and inexpensive and can detect DNA methylation with high sensitivity. Therefore, the designed geno-assay could detect DNA methylation significantly and discriminate from unmethylated DNA. It is expected that the proposed geno-assay could be used for the detection of DNA methylation, genetic mutations, epigenetic alterations, and early stage diagnosis of various cancer toward efficient clinical pharmacotherapy.

EGFR DNA Methylation Correlates With EGFR Expression, Immune Cell Infiltration, and Overall Survival in Lung Adenocarcinoma

Background

The epidermal growth factor receptor (EGFR) is a primary target of molecular targeted therapy for lung adenocarcinoma (LUAD). The mechanisms that lead to epigenetic abnormalities of EGFR in LUAD are still unclear. The purpose of our study was to evaluate the abnormal methylation of EGFR CpG sites as potential biomarkers for LUAD.

Methods

To assess the differentially methylation CpG sites of EGFR in LUAD, we used an integrative study of Illumina HumanMethylation450K and RNA-seq data from The Cancer Genome Atlas (TCGA). We evaluated and compared EGFR multiple-omics data to explore the role of CpG sites located in EGFR promoter regions and gene body regions and the association with transcripts, protein expression levels, mutations, and somatic copy number variation. We calculated the correlation coefficients between CpG sites of EGFR and immune infiltration fraction (by MCPcounter and ESTIMATE) and immune-related pathways in LUAD. Finally, we validated the differential methylation of clinically and prognostically relevant CpG sites using quantitative methylation-specific PCR (qMSP).

Results

We found that the methylation level of many EGFR CpGs in the promoter region was negatively correlated with the transcription level, protein expression, and SCNV, while the methylation at the gene body region was positively correlated with these features. The methylation level of EGFR CpGs in the promoter region was positively correlated with the level of immune infiltration and IFN-γ signature, while the opposite was found for methylation of the gene body region. The qMSP results showed that cg02316066 had a high methylation level, while cg02166842 had a low methylation level in LUAD. There was a high degree of co-methylation between cg02316066 and cg03046247.

Conclusion

Our data indicate that EGFR is an epigenetic regulator in LUAD acting through DNA methylation. Our research provides a theoretical basis for the further detection of EGFR DNA methylation as a predictive biomarker for LUAD survival and immunotherapy.