Targeted DNA Methylation Editing Using an All-in-One System Establishes Paradoxical Activation of EBF3.

Cutaneous melanoma is rapidly on the rise globally, surpassing the growth rate of other cancers, with metastasis being the primary cause of death in melanoma patients. Consequently, understanding the mechanisms behind this metastatic process and exploring innovative treatments is of paramount importance. Recent research has shown promise in unravelling the role of epigenetic factors in melanoma progression to metastasis. While DNA hypermethylation at gene promoters typically suppresses gene expression, we have contributed to establishing the newly understood mechanism of paradoxical activation of genes via DNA methylation, where high methylation coincides with increased gene activity. This mechanism challenges the conventional paradigm that promoter methylation solely silences genes, suggesting that, for specific genes, it might actually activate them. Traditionally, altering DNA methylation in vitro has involved using global demethylating agents, which is insufficient for studying the mechanism and testing the direct consequence of gene methylation changes. To investigate promoter hypermethylation and its association with gene activation, we employed a novel approach utilising a CRISPR-SunTag All-in-one system. Here, we focused on editing the DNA methylation of a specific gene promoter segment (EBF3) in melanoma cells using the All-in-one system. Using bisulfite sequencing and qPCR with RNA-Seq, we successfully demonstrated highly effective methylation and demethylation of the EBF3 promoter, with subsequent gene expression changes, to establish and validate the paradoxical role of DNA methylation. Further, our study provides novel insights into the function of the EBF3 gene, which remains largely unknown. Overall, this study challenges the conventional view of methylation as solely a gene-silencing mechanism and demonstrates a potential function of EBF3 in IFN pathway signalling, potentially uncovering new insights into epigenetic drivers of malignancy and metastasis.

Editing of DNA Methylation Patterns Using CRISPR-Based Tools.

DNA methylation is an epigenetic modification with an established role in both normal cellular function and mammalian disease. Despite well-characterized associations between aberrant DNA methylation changes and gene expression, evidence for a causal relationship in this context has been difficult to obtain. Early techniques for interrogating the role of DNA methylation in the regulation of gene transcription lack specificity and, where more specific techniques such and ZNFs and TALEs have been developed, they are limited by their extensive cost and labor requirements. However, the recent advent of CRISPR-based technologies has revolutionized our potential for site-specific epigenomic editing. Here, we provide a detailed protocol for the design, construction, and utilization of a transient, CRISPR-based DNA methylation-editing system in mammalian cells.

Epigenetic basis and targeting of cancer metastasis.

Despite the development of novel therapeutic approaches and improved clinical management, survival from metastatic disease remains poor. Indeed, metastasis accounts for the vast majority of cancer-related deaths. The metastatic cascade comprises a complex range of molecular events that cannot be explained by genetic aberrations alone; dynamic, epigenetic regulatory mechanisms are now being implicated as key drivers of successful metastasis. With the emergence of CRISPR-based epigenomic editing, it is now possible to investigate the direct role of locus-specific epigenetic alterations in metastatic progression. Here, we review the role of epigenetic mechanisms in cancer metastasis, explore recent developments in technologies for epigenomic investigation, and highlight the emerging applications of epigenomic editing technologies in the clinical management of cancer.

Locus-Specific DNA Methylation Editing in Melanoma Cell Lines Using a CRISPR-Based System.

DNA methylation is a key epigenetic modification implicated in the pathogenesis of numerous human diseases, including cancer development and metastasis. Gene promoter methylation changes are widely associated with transcriptional deregulation and disease progression. The advent of CRISPR-based technologies has provided a powerful toolkit for locus-specific manipulation of the epigenome. Here, we describe a comprehensive global workflow for the design and application of a dCas9-SunTag-based tool for editing the DNA methylation locus in human melanoma cells alongside protocols for downstream techniques used to evaluate subsequent methylation and gene expression changes in methylation-edited cells. Using transient system delivery, we demonstrate both highly efficacious methylation and demethylation of the EBF3 promoter, which is a putative epigenetic driver of melanoma metastasis, achieving up to a 304.00% gain of methylation and 99.99% relative demethylation, respectively. Furthermore, we employ a novel, targeted screening approach to confirm the minimal off-target activity and high on-target specificity of our designed guide RNA within our target locus.

Polymer grafted magnetic nanoparticles for delivery of anticancer drug at lower pH and elevated temperature.

Efficient and controlled delivery of therapeutics to tumor cells is one of the important issues in cancer therapy. In the present work, a series of pH- and temperature-responsive polymer grafted iron oxide nanoparticles were prepared by simple coupling of aminated iron oxide nanoparticle with poly(N-isopropylacrylamide-ran-poly(ethylene glycol) methyl ether acrylate)-block-poly(acrylic acid) (P(NIPA-r-PEGMEA)-b-PAA). For this, three water soluble block polymers were prepared via reversible addition fragmentation transfer (RAFT) polymerization technique. At first, three different block copolymers were prepared by polymerizing mixture of NIPA and PEGMEA (with varying mole ratio) in presence of poly(tert-butyl acrylate) (PtBA) macro chain transfer agent. Subsequently, P(NIPA-r-PEGMEA)-b-PAA copolymers were synthesized by hydrolyzing tert-butyl acrylate groups of the P(NIPA-r-PEGMEA)-b-PtBA copolymers. The resulting polymers were then grafted to iron oxide nanoparticles, and these functionalized nanoparticles were thoroughly characterized by X-ray diffraction (XRD), thermogravimetric analysis (TGA), zeta potential measurements, transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM), vibrating sample magnetometer (VSM) and Fourier transform infrared spectroscopy (FTIR). Doxorubicin (DOX), an anti-cancer drug, was loaded into the polymer coated nanoparticles and its release behavior was subsequently studied at different pH and temperatures. The drug release pattern revealed a sustained release of DOX preferentially at the desired lysosomal pH of cancer cells (pH 5.0) and slightly above the physiological temperature depending upon the composition of the copolymers. The potential anticancer activity of the polymer grafted DOX loaded nanoparticles were established by MTT assay and apoptosis study of cervical cancer ME 180cells in presence of the nanoparticles. Thus, these particles can be utilized for controlled delivery of anticancer drugs at the desired lysosomal pH and/or by slightly heating the cells using magnetic hyperthermia.

Polymeric nanostructures with pH-labile core for controlled drug release.

Efficient and stimuli-triggered controlled delivery of therapeutics is one of the important issues in modern advanced therapy. In the present work, a versatile route for the synthesis of core cross-linked polymeric nanostructures (CLPN) through thiol-acrylate Michael addition reaction via the formation of ß-thiopropionate has been described. The acid groups of the poly(acrylic acid) block of poly(ethylene glycol)-b-poly(N-isopropylacrylamide)-b-poly(acrylic acid) triblock copolymer were reacted with 2-hydroxyethyl acrylate (HEA) to yield the corresponding acrylate-functionalized copolymer (P1). Following this, P1 was reacted with a thiol functionalized cross-linker (CL) resulting in the formation of core cross-linked polymeric nanoparticles through acrylate-thiol Michael reaction. The ability of these nanoparticles to encapsulate drug molecules inside their core and their effective release following a pH-triggered controlled degradation of the core were demonstrated. The temperature sensitive release behaviour of the system was also studied. The non-toxic nature of the precursor polymers and the core cross-linked polymeric nanoparticles was also established, that further substantiated their potential as carriers for controlled release of drugs.

pH-induced vesicle-to-micelle transition in amphiphilic diblock copolymer: investigation by energy transfer between in situ formed polymer embedded gold nanoparticles and fluorescent dye.

The ability to regulate the formation of nanostructures through self-assembly of amphiphilic block copolymers is of immense significance in the field of biology and medicine. In this work, a new block copolymer synthesized by using reversible addition-fragmentation chain transfer (RAFT) polymerization technique from poly(ethylene glycol) monomethyl ether acrylate (PEGMA) and Boc-l-tryptophan acryloyloxyethyl ester (Boc-l-trp-HEA) was found to spontaneously form pH-responsive water-soluble nanostructures after removal of the Boc group. While polymer vesicles or polymerosomes were formed at physiological pH, the micelles were formed at acidic pH (< 5.2), and this facilitated a pH-induced reversible vesicle-to-micelle transition. Formation of these nanostructures was confirmed by different characterization techniques, viz. transmission electron microscopy, dynamic light scattering, and steady-state fluorescence measurements. Further, these vesicles were successfully utilized to reduce HAuCl4 and stabilize the resulting gold nanoparticles (AuNPs). These AuNPs, confined within the hydrophobic shell of the vesicles, could participate in energy transfer process with fluorescent dye molecules encapsulated in the core of the vesicles, thus forming a nanometal surface energy transfer (NSET) pair. Subsequently, following the efficiency of energy transfer between this pair, it was possible to monitor the process of transition from vesicles to micelles. Thus, in this work, we have successfully demonstrated that NSET can be used to follow the transition between nanostructures formed by amphiphilic block copolymers.

Polyplex formation between PEGylated linear cationic block copolymers and DNA: equilibrium and kinetic studies.

The basic requirement for understanding the nonviral gene delivery pathway is a thorough biophysical characterization of DNA polyplexes. In this work, we have studied the interactions between calf-thymus DNA (ctDNA)and a new series of linear cationic block copolymers (BCPs). The BCPs were synthesized via controlled radical polymerization using [3-(methacryloylamino)propyl] -trimethylammonium chloride (MAPTAC) and poly(ethyleneglycol) methyl ether (PEGMe) as comonomers. UV−visible spectroscopy, ethidium bromide dye exclusion, and gel electrophoresis study revealed that these cationic BCPs were capable of efficiently binding with DNA. Steady-state fluorescence, UV melting, gel electrophoresis, and circular dichroism results suggested increased binding for BCPs containing higher PEG. Hydrophobic interactions between the PEG and the DNA base pairs became significant at close proximity of the two macromolecules, thereby influencing the binding trend. DLS studies showed a decrease in the size of DNA molecules at lower charge ratio (the ratio of "+" charge of the polymer to "−" charge of DNA) due to compaction, whereas the size increased at higher charge ratio due to aggregation among the polyplexes. Additionally, we have conducted kinetic studies of the binding process using the stop-flow fluorescence method. All the results of BCP−DNA binding studies suggested a two-step reaction mechanism--a rapid electrostatic binding between the cationic blocks and DNA, followed by a conformational change of the polyplexes in the subsequent step that led to DNA condensation. The relative rate constant(k'(1)) of the first step was much higher compared to that of the second step (k'(2)), and both were found to increase with an increase in BCP concentration. The charge ratios as well as the PEG content in the BCPs had a marked effect on the kinetics of the DNA−BCP polyplex formation. Introduction of a desired PEG chain length in the synthesized cationic blocks renders them potentially useful as nonviral gene delivery agents.

Functional group-dependent self-assembled nanostructures from thermo-responsive triblock copolymers.

The ability to control the formation of nanostructures through self-assembly of amphiphilic block copolymers is of great interest in the field of biology and catalysis. In this work we have studied the self-assembling behavior of a new class of thermo-responsive triblock copolymers containing poly(ethylene glycol), and demonstrated the manner in which the aggregation pattern changed on simple functional group transformation on the copolymers. Two different triblock copolymers, poly(ethylene glycol)-b-poly(N-ispropylacrylamide)-b-poly(t-butyl acrylate) (P1) and poly(ethylene glycol)-b-poly(N-isopropylacrylamide)-b-poly(glycidyl methacrylate) (P2) were synthesized using reversible addition-fragmentation chain transfer (RAFT) technique. It was observed that P1 and P2 displayed different temperature dependent solution properties in water, with P1 forming micelles above the LCST of the PNIPA while P2 showing macroscopic phase separation under similar conditions. Thereafter, the tert-butyl group of P1 was converted to the corresponding acid (P1a) and the epoxy groups of P2 was converted to diols (P2a), thus transforming the hydrophobic blocks to hydrophilic ones. Quite interestingly, such transformations led to significant changes in their self-assembling behavior, as both P1a and P2a were seen to form vesicles beyond the LCST of PNIPA. Changes in the hydrophilic fraction in the block copolymers by subtle changes in the functionality and temperature led to the formation of varied nanostructured assemblies, as evident from dynamic light scattering (DLS), transmisison electron microscopy (TEM), and steady-state fluorescence analysis. Such formation of thermo-responsive vesicles induced by simple structural changes in the copolymers is quite interesting and highly significant in drug delivery applications.

Thermal and pH responsive polymer-tethered multifunctional magnetic nanoparticles for targeted delivery of anticancer drug.

Targeted and efficient delivery of therapeutics to tumor cells is one of the key issues in cancer therapy. In the present work, we report a temperature and pH dual responsive core-shell nanoparticles comprising smart polymer shell coated on magnetic nanoparticles as an anticancer drug carrier and cancer cell-specific targeting agent. Magnetite nanoparticles (MNPs), prepared by a simple coprecipitation method, was surface modified by introducing amine groups using 3-aminopropyltriethoxysilane. Dual-responsive poly(N-isopropylacrylamide)-block-poly(acrylic acid) copolymer, synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization, was then attached to the amine-functionalized MNPs via EDC/NHS method. Further, to accomplish cancer-specific targeting properties, folic acid was tethered to the surface of the nanoparticles. Thereafter, rhodamine B isothiocyanate was conjugated to endow fluorescent property to the MNPs required for cellular imaging applications. The nanoparticles were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), selected area electron diffraction (SAED), field emission scanning electron microscopy (FESEM), energy-dispersive X-ray spectroscopy (EDX), thermogravimetric analysis (TGA), zeta potential, vibrating sample magnetometer (VSM), X-ray photoelectron spectroscopy (XPS) measurements, and FTIR, UV-vis spectral analysis. Doxorubicin (DOX), an anticancer drug used for the present study, was loaded into the nanoparticles and its release behavior was subsequently studied. Result showed a sustained release of DOX preferentially at the desired lysosomal pH and temperature condition. The biological activity of the DOX-loaded MNPs was studied by MTT assay, fluorescence microscopy, and apoptosis. Intracellular-uptake studies revealed preferential uptake of these nanoparticles into cancer cells (HeLa cells) compared to normal fibroblast cells (L929 cells). The in vitro apoptosis study revealed that the DOX-loaded nanoparticles caused significant death to the HeLa cells. These nanoparticles were capable of target specific release of the loaded drug in response to pH and temperature and hence may serve as a potential drug carrier for in vivo applications.

Spontaneous formation of vesicles by self-assembly of cationic block copolymer in the presence of anionic surfactants and their application in formation of polymer embedded gold nanoparticles.

Block copolymers (BCPs), synthesized from cationic monomer (3-(methacryloylamino)propyl)trimethylammonium chloride (MAPTAC) and PEG-based monomer poly(ethylene glycol) methyl ether acrylate (PEGMEA), were found to spontaneously form water-soluble vesicles when mixed with a stoichiometric quantity of negatively charged double-tail surfactant, AOT, at room temperature. However, with single-tail anionic surfactant, i.e., SDS, these block copolymers were seen to form water-soluble micelle-like aggregates. Also, cationic random copolymers (RCPs) of similar composition synthesized from the same monomers showed formation of water-soluble micelle-like aggregates when complexed with SDS or AOT. Such self-assembled vesicle formation observed specifically for the BCP/AOT systems was attributed to a sequential arrangement of monomers in the BCP and the higher hydrophobic volume of AOT, that made the packing factor "p" assume a value that favors the formation of vesicles. TEM analysis showed that average diameters of the vesicles were in the range of ∼100 nm. Pyrene fluorescence experiments indicated a high degree of hydrophobicity of vesicle membrane made from BCP/AOT complexes which were even higher than that of the cores of the water-soluble micelle-like aggregates made from BCP/SDS, RCP/AOT, and RCP/SDS systems. Importantly, the vesicles made from these BCP/AOT stoichiometric complexes were successfully utilized to reduce HAuCl4 to gold nanoparticles. TEM analysis revealed that the gold nanoparticles so formed were successively embedded within the hydrophobic bilayer shell of the vesicles.

Synthesis, photophysical and photochemical properties of photoacid generators based on N-hydroxyanthracene-1,9-dicarboxyimide and their application toward modification of silicon surfaces.

We have introduced a series of nonionic photoacid generators (PAGs) for carboxylic and sulfonic acids based on N-hydroxyanthracene-1,9-dicarboxyimide (HADI). The newly synthesized PAGs exhibited positive solvachromatic emission (λ(max)(hexane) 461 nm, λ(max)(ethanol) 505 nm) as a function of solvent polarity. Irradiation of PAGs in acetonitrile (ACN) using UV light above 410 nm resulted in the cleavage of weak N-O bonds, leading to the generation of carboxylic and sulfonic acids in good quantum and chemical yields. Mechanism for the homolytic N-O bond cleavage for acid generation was supported by time-dependent density functional theory (TD-DFT) calculations. More importantly, using the PAG monomer N-(p-vinylbenzenesulfonyloxy)anthracene-1,9-dicarboxyimide (VBSADI), we have synthesized N-(p-vinylbenzenesulfonyloxy)anthracene-1,9-dicarboxyimide-methyl methacrylate (VBSADI-MMA) and N-(p-vinylbenzenesulfonyloxy)anthracene-1,9-dicarboxyimide-ethyl acrylate (VBSADI-EA) copolymer through atom transfer radical polymerization (ATRP). Finally, we have also developed photoresponsive organosilicon surfaces using the aforementioned polymers.

Development of 1-hydroxy-2(1H)-quinolone-based photoacid generators and photoresponsive polymer surfaces.

A new class of carboxylate and sulfonate esters of 1-hydroxy-2(1H)-quinolone has been demonstrated as nonionic photoacid generators (PAGs). Irradiation of carboxylates and sulfonates of 1-hydroxy-2(1H)-quinolone by UV light (λ≥310 nm) resulted in homolysis of weak N-O bond leading to efficient generation of carboxylic and sulfonic acids, respectively. The mechanism for the homolytic N-O bond cleavage was supported by time-dependent DFT calculations. Photoresponsive 1-(p-styrenesulfonyloxy)-2-quinolone-methyl methacrylate (SSQL-MMA) and 1-(p-styrenesulfonyloxy)-2-quinolone-lauryl acrylate (SSQL-LA) copolymers were synthesized from PAG monomer 1-(p-styrenesulfonyloxy)-2-quinolone, and subsequently controlled surface wettability was demonstrated for the above-mentioned photoresponsive polymers.