A novel bisulfite-microfluidic temperature gradient capillary electrophoresis platform for highly sensitive detection of gene promoter methylation

Design and application of a novel "turn-on" fluorescent probe for imaging sulfite in living cells and inflammation models

Sulfite is one of the main existing forms of sulfur dioxide (SO2) in living system, which has been recognized as an endogenous mediator in inflammation. Evidence has accumulated to show that abnormal level of sulfite is associated with many inflammatory diseases, including neurological diseases and cancers. Herein, a novel fluorescent probe named QX-OA was designed and synthesized to detect sulfite. QX-OA was constructed by choosing quinolinium-xanthene as the fluorophore and levulinate as the specific and relatively steady recognition reaction. The probe showed remarkable green turn-on signal at 550 nm, together with high sensitivity (90-fold) and excellent selectivity to sulfite over other possible interfering species. In the meantime, QX-OA was successfully applied to visualize endogenous and exogenous sulfite in Hela cells. In the LPS-induced inflammation model, QX-OA could visualize the dose-dependent increase of sulfite level (0-2 mg/mL). Consequently, QX-OA was determined to be a potential method for detecting sulfite in pre-clinical diagnosis.

Colorimetric and near-infrared spectrophotometric monitoring of bisulfite using glyoxal modified chromenylium-cyanine chemosensor: Smartphone and paper strip applications for on-site food and beverages control

Detection of bisulfite (HSO₃^-) in food and beverages has vital importance because the excessive amount leads to ill effects on the human body. Colorimetric and fluorometric chromenylium-cyanine-based chemosensor CyR was synthesized and applied for high selective and sensitive analysis of HSO₃^- in red wine, rose wine and, granulated sugar with high recovery ranges and very fast response time without any interference from other competitive species. The limits of detection (LOD) for the UV-Vis and fluorescence titrations were found as 11.5 μM and 3.77 μM, respectively. The on-site and very rapid methods based on paper strips and smartphone which depend on the color changes from yellow to green have been successfully developed to analyze HSO₃^- concentration (10^-5-10^-1 M for paper strip and 163-1205 μM for smartphone). CyR and the bisulfite-adduct formed in the nucleophilic addition reaction with HSO₃^- were verified by FT-IR, ¹H NMR, and MALDI-TOF results as well as Single-Crystal X-Ray Crystallography for CyR.

A site-specific DNA methylation biosensor for both visual and magnetic determination based on lateral flow assay

Tumorigenesis driven by abnormal DNA methylation has highlighted the need to develop a portable, rapid and sensitive strategy for accurate methylation detection with a specific cancer-prognostic gene, which caters to the popularization of precision medicine. In this study, a site-specific biosensor for both visual and magnetic DNA methylation determination has been established based on lateral flow assay. By introducing digoxin- and biotin-labeled primers into PCR, the amplicons can be recognized and captured by gold magnetic nanoparticles (GMNPs) in this biosensor. Working as a signal probe, the optical property of GMNPs allows the amplicons to be interpreted with naked eyes avoiding any complex equipment and cumbersome operation after PCR. Moreover, by virtue of the magnetic property of GMNP, the signal can be explained and recorded by a magnetometer in clinical practice. The introduction of tailor-made primer sets makes it possible to accurately distinguish 0.1% methylated variants in the presence of numerous unmethylated variants as strong interferential background and vice versa at target cytosine-guanine dinucleotide. A distinct signal can be observed with as low as 0.01 pg variants for both visual and magnetic analyses. As a significant tumor suppressor gene, the promoter methylation status of miR-34a is accurately determined with not only cell lines but also with clinical samples, which demonstrates the great potential of this biosensor for cancer diagnosis and prognosis.

Perspectives on the Role of Histone Modification in Breast Cancer Progression and the Advanced Technological Tools to Study Epigenetic Determinants of Metastasis

Metastasis is a complex process that involved in various genetic and epigenetic alterations during the progression of breast cancer. Recent evidences have indicated that the mutation in the genome sequence may not be the key factor for increasing metastatic potential. Epigenetic changes were revealed to be important for metastatic phenotypes transition with the development in understanding the epigenetic basis of breast cancer. Herein, we aim to present the potential epigenetic drivers that induce dysregulation of genes related to breast tumor growth and metastasis, with a particular focus on histone modification including histone acetylation and methylation. The pervasive role of major histone modification enzymes in cancer metastasis such as histone acetyltransferases (HAT), histone deacetylases (HDACs), DNA methyltransferases (DNMTs), and so on are demonstrated and further discussed. In addition, we summarize the recent advances of next-generation sequencing technologies and microfluidic-based devices for enhancing the study of epigenomic landscapes of breast cancer. This feature also introduces several important biotechnologists for identifying robust epigenetic biomarkers and enabling the translation of epigenetic analyses to the clinic. In summary, a comprehensive understanding of epigenetic determinants in metastasis will offer new insights of breast cancer progression and can be achieved in the near future with the development of innovative epigenomic mapping tools.

An imidazo[1,5-α]pyridine-derivated fluorescence sensor for rapid and selective detection of sulfite

Sulfur-containing species are essential in the composition and the metabolism of the organisms, thus developing a full set of implements to cover all of them is still a favorable choice. Herein, we chose imidazo [1,5-α]pyridine moiety as the basic fluorophore for the detection of sulfite, and preliminarily completed the toolset since biothiols (GSH, Cys, Hcy), H₂S, and PhSH could be detected by sensors based on the same backbone. The designed sensor, IPD-SFT, with structural novelty and large Stokes shift (130 nm), indicated the most attractive advantages of remarkably rapid response period (within 1 min) and high selectivity for sulfite from all the sulfur-containing species. Other practical properties included high sensitivity (LOD = 50 nM) and wide pH adaptability (5.0-11.0). Furthermore, IPD-SFT could monitor both exogenous and endogenous sulfite. It not only raised a potential tool for sulfite detection, but also preliminarily completed the toolset for all the sulfur-containing species. The development of such toolsets might reveal the sulfur-containing metabolism and corresponding physiology and pathological procedures.

Microfluidic epigenomic mapping technologies for precision medicine

Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.

Separation-free single-base extension assay with fluorescence resonance energy transfer for rapid and convenient determination of DNA methylation status at specific cytosine and guanine dinucleotide sites

A separation-free single-base extension (SBE) assay utilizing fluorescence resonance energy transfer (FRET) was developed for rapid and convenient interrogation of DNA methylation status at specific cytosine and guanine dinucleotide sites. In this assay, the SBE was performed in a tube using an allele-specific oligonucleotide primer (i.e., extension primer) labeled with Cy3 as a FRET donor fluorophore at the 5'-end, a nucleotide terminator (dideoxynucleotide triphosphate) labeled with Cy5 as a FRET acceptor, a PCR amplicon derived from bisulfite-converted genomic DNA, and a DNA polymerase. A single base-extended primer (i.e., SBE product) that was 5'-Cy3- and 3'-Cy5-tagged was formed by incorporation of the Cy5-labeled terminator into the 3'-end of the extension primer, but only if the terminator added was complementary to the target nucleotide. The resulting SBE product brought the Cy3 donor and the Cy5 acceptor into close proximity. Illumination of the Cy3 donor resulted in successful FRET and excitation of the Cy5 acceptor, generating fluorescence emission from the acceptor. The capacity of the developed assay to discriminate as low as 10% methylation from a mixture of methylated and unmethylated DNA was demonstrated at multiple cytosine and guanine dinucleotide sites.

An electrochemiluminescence biosensor for detection of CdkN2A/p16 anti-oncogene based on functional electrospun nanofibers and core-shell luminescent composite nanoparticles

An electrochemiluminescence (ECL) biosensor based on functional electrospun nanofibers for hybridization detection of specific CdkN2A/p16 anti-oncogene at trace level via binding luminescent composite nanoparticles for signal amplification has been developed. The carboxylated multiwalled carbon nanotubes (MWCNTs) doped polycaprolactam 6 (PA6) electrospun nanofibers (PA6-MWCNTs) was prepared via electrospinning, which served as the nanosized backbones for silica nanoparticles (SiO₂) electrodeposition. The functional electrospun nanofibers (PA6-MWCNTs-SiO₂) used as supporting scaffolds for single-stranded DNA1 (ssDNA1) immobilization can dramatically increase the amount of DNA attachment and the sensitivity of hybridization. The sandwich construction of ssDNA1-CdkN2A/p16 anti-oncogene -tri(2,2'-bipyridyl)ruthenium(II) (Ru(bpy)₃²⁺)/silver nanoparticles (AgNPs) doped gold (Au) core-shell luminescent composite nanoparticles (RuAg@AuNPs)-labeled ssDNA2 (RuAg@Au-ssDNA2) was fabricated through a hybridization reaction. It was observed that high amount of doped Ru(bpy)₃²⁺ in RuAg@AuNPs successfully amplify the recognition signal by adding tripropylamine (TPrA). The change of ECL intensity was found to have a linear relationship in respect to the logarithm of the CdkN2A/p16 anti-oncogene concentrations in the wide range of 1.0 × 10^-15~1.0 × 10^-12 M, with a detection limit of 0.5 fM (S/N = 3) which is comparable or better than that in reported anti-oncogene assays. Excellent sensitivity and selectivity make the developed biosensor a promising tool for the detection of tumor biomarkers.

Rapid microfluidic solid-phase extraction system for hyper-methylated DNA enrichment and epigenetic analysis

Genetic sequence and hyper-methylation profile information from the promoter regions of tumor suppressor genes are important for cancer disease investigation. Since hyper-methylated DNA (hm-DNA) is typically present in ultra-low concentrations in biological samples, such as stool, urine, and saliva, sample enrichment and amplification is typically required before detection. We present a rapid microfluidic solid phase extraction (μSPE) system for the capture and elution of low concentrations of hm-DNA (≤1 ng ml(-1)), based on a protein-DNA capture surface, into small volumes using a passive microfluidic lab-on-a-chip platform. All assay steps have been qualitatively characterized using a real-time surface plasmon resonance (SPR) biosensor, and quantitatively characterized using fluorescence spectroscopy. The hm-DNA capture/elution process requires less than 5 min with an efficiency of 71% using a 25 μl elution volume and 92% efficiency using a 100 μl elution volume.

Capillary electrophoresis based on the nucleic acid detection in the application of cancer diagnosis and therapy

This review focuses on capillary electrophoresis-based nucleic acid detection as it is applied to cancer diagnosis and therapy, and provides an introduction to the drawbacks and future developments of analysis with CE.