Derepression of co-silenced tumor suppressor genes by nanoparticle-loaded circular ssDNA reduces tumor malignancy.
Meng Jing,Chen Shuang,Han Jing-Xia,Tan Qiang,Wang Xiao-Rui,Wang Hong-Zhi,Zhong Wei-Long,Qin Yuan,Qiao Kai-Liang,Zhang Chao,Gao Wan-Feng,Lei Yue-Yang,Liu Hui-Juan,Liu Yan-Rong,Zhou Hong-Gang,Sun Tao,Yang Cheng
Science translational medicine
The co-silencing of multiple tumor suppressor genes can lead to escalated malignancy in cancer cells. Given the limited efficacy of anticancer therapies targeting single tumor suppressor genes, we developed small circular single-stranded DNA (CSSD) that can up-regulate the expression of co-silenced tumor suppressor genes by sequestering microRNAs (miRNAs) that negatively regulate these genes. We found that cancer patients with low tumor expression of the tumor suppressor genes , , and had shortened survival times. The up-regulation of these genes upon transfection of artificial CSSD-9 inhibited tumor proliferation and metastasis and promoted apoptosis in vitro as well as in ex vivo and patient-derived xenograft models. In addition, CSSD is more stable and effective than current miRNA inhibitors, and transfecting CSSDs via nanoparticles substantially improved delivery efficiency. The use of a single CSSD can promote the inhibition of multiple tumor suppressor genes. This study provides evidence for the possibility of using CSSDs as therapeutic miRNA inhibitors to target the co-silencing of multiple tumor suppressor genes.
10.1126/scitranslmed.aao6321
Materials for Improving Immune Cell Transfection.
Kumar Arun R K,Shou Yufeng,Chan Brian,L Krishaa,Tay Andy
Advanced materials (Deerfield Beach, Fla.)
Chimeric antigen receptor T cell (CAR-T) therapy holds great promise for preventing and treating deadly diseases such as cancer. However, it remains challenging to transfect and engineer primary immune cells for clinical cell manufacturing. Conventional tools using viral vectors and bulk electroporation suffer from low efficiency while posing risks like viral transgene integration and excessive biological perturbations. Emerging techniques using microfluidics, nanoparticles, and high-aspect-ratio nanostructures can overcome these challenges, and on top of that, provide universal and high-throughput cargo delivery. Herein, the strengths and limitations of traditional and emerging materials for immune cell transfection, and commercial development of these tools, are discussed. To enhance the characterization of transfection techniques and uptake by the clinical community, a list of in vitro and in vivo assays to perform, along with relevant protocols, is recommended. The overall aim, herein, is to motivate the development of novel materials to meet rising demand in transfection for clinical CAR-T cell manufacturing.
10.1002/adma.202007421
A highly emissive conjugated polyelectrolyte vector for gene delivery and transfection.
Feng Xuli,Lv Fengting,Liu Libing,Yang Qiong,Wang Shu,Bazan Guillermo C
Advanced materials (Deerfield Beach, Fla.)
An intrinsically fluorescent cationic polyfluorene (CCP) has been designed, synthesized, characterized, and examined as a plasmid DNA (pDNA) delivery vector. This material facilitates nucleic acid binding, encapsulation and efficient cellular uptake. CCP can effectively protect pDNA against nuclease degradation, which is necessary for gene carriers. Green fluorescent protein (GFP) expression experiments reveal that CCP can achieve efficient delivery and transfection of pDNA encoding GFP gene with 92% efficiency, which surpasses that of commercial transfection agents, lipofectamine 2000 (Lipo) and polyethylenimine (PEI). CCP is also highly fluorescent, with 43% quantum yield in water, and exhibits excellent photostability, which allows for real-time tracking the location of gene delivery and transfection. These features and capabilities represent a major step toward designing and applying conjugated polymers that function in both imaging and therapeutic applications.
10.1002/adma.201202145
Fusogenic Reactive Oxygen Species Triggered Charge-Reversal Vector for Effective Gene Delivery.
Liu Xin,Xiang Jiajia,Zhu Dingcheng,Jiang Liming,Zhou Zhuxian,Tang Jianbin,Liu Xiangrui,Huang Yongzhuo,Shen Youqing
Advanced materials (Deerfield Beach, Fla.)
A novel fusogenic lipidic polyplex (FLPP) vector is designed to fuse with cell membranes, mimicking viropexis, and eject the polyplex into the cytosol, where the cationic polymer is subsequently oxidized by intracellular reactive oxygen species and converts to being negatively charged, efficiently releasing the DNA. The vector delivering suicide gene achieves significantly better inhibition of tumor growth than doxorubicin.
10.1002/adma.201504288
Tumor Acidity-Sensitive Polymeric Vector for Active Targeted siRNA Delivery.
Sun Chun-Yang,Shen Song,Xu Cong-Fei,Li Hong-Jun,Liu Yang,Cao Zhi-Ting,Yang Xian-Zhu,Xia Jin-Xing,Wang Jun
Journal of the American Chemical Society
Although surface PEGylation of siRNA vectors is effective for preventing protein adsorption and thereby helps these vectors to evade the reticuloendothelial system (RES) in vivo, it also suppresses the cellular uptake of these vectors by target cells. This dilemma could be overcome by employing stimuli-responsive shell-detachable nanovectors to achieve enhanced cellular internalization while maintaining prolonged blood circulation. Among the possible stimuli, dysregulated pH in tumor (pHe) is the most universal and practical. However, the design of pHe-sensitive system is problematic because of the subtle differences between the pHe and pH in other tissues. Here, a simple acid-sensitive bridged copolymer is developed and used for tumor-targeted systemic delivery of siRNA. After forming the micelleplex delivery system, the corresponding nanoparticles (Dm-NP) might undergo several modifications as follows: (i) a poly(ethylene glycol) (PEG) corona, which is stable in the circulatory system and protects nanovectors from RES clearance; (ii) a pHe responsive linkage breakage, which induces PEG detachment at tumor sites and thereby facilitates cell targeting; and (iii) a cell-penetration peptide, which is exposed upon the removal of PEG and further enhances cellular uptake. Thus, Dm-NP achieved both prolonged circulation and effective accumulation in tumor cells and resulted in the safe and enhanced inhibition of non-small cell lung cancer growth.
10.1021/jacs.5b09602
Recent advances in nonviral vectors for gene delivery.
Guo Xia,Huang Leaf
Accounts of chemical research
Gene therapy has long been regarded a promising treatment for many diseases, whether acquired (such as AIDS or cancer) or inherited through a genetic disorder. A drug based on a nucleic acid, however, must be delivered to the interior of the target cell while surviving an array of biological defenses honed by evolution. Successful gene therapy is thus dependent on the development of an efficient delivery vector. Researchers have pursued two major vehicles for gene delivery: viral and nonviral (synthetic) vectors. Although viral vectors currently offer greater efficiency, nonviral vectors, which are typically based on cationic lipids or polymers, are preferred because of safety concerns with viral vectors. So far, nonviral vectors can readily transfect cells in culture, but efficient nanomedicines remain far removed from the clinic. Overcoming the obstacles associated with nonviral vectors to improve the delivery efficiency and therapeutic effect of nucleic acids is thus an active area of current research. The difficulties are manifold, including the strong interaction of cationic delivery vehicles with blood components, uptake by the reticuloendothelial system (RES), toxicity, and managing the targeting ability of the carriers with respect to the cells of interest. Modifying the surface with poly(ethylene glycol), that is, PEGylation, is the predominant method used to reduce the binding of plasma proteins to nonviral vectors and minimize clearance by the RES after intravenous administration. Nanoparticles that are not rapidly cleared from the circulation accumulate in the tumors because of the enhanced permeability and retention effect, and the targeting ligands attached to the distal end of the PEGylated components allow binding to the receptors on the target cell surface. Neutral and anionic liposomes have been also developed for systemic delivery of nucleic acids in experimental animal models. Other approaches include (i) designing and synthesizing novel cationic lipids and polymers, (ii) chemically coupling the nucleic acid to peptides, targeting ligands, polymers, or environmentally sensitive moieties, and (iii) utilizing inorganic nanoparticles in nucleic acid delivery. Recently, the different classes of nonviral vectors appear to be converging, and the ability to combine features of different classes of nonviral vectors in a single strategy has emerged. With the strengths of several approaches working in concert, more hurdles associated with efficient nucleic acid delivery might therefore be overcome. In this Account, we focus on these novel nonviral vectors, which are classified as multifunctional hybrid nucleic acid vectors, novel membrane/core nanoparticles for nucleic acid delivery, and ultrasound-responsive nucleic acid vectors. We highlight systemic delivery studies and consider the future prospects for nucleic acid delivery. A better understanding of the fate of the nanoparticles inside the cell and of the interactions between the parts of hybrid particles should lead to a delivery system suitable for clinical use. We also underscore the value of sustained release of a nucleic acid in this endeavor; making vectors targeted to cells with sustained release in vivo should provide an interesting research challenge.
10.1021/ar200151m
Long Noncoding RNA uc.173 Promotes Renewal of the Intestinal Mucosa by Inducing Degradation of MicroRNA 195.
Xiao Lan,Wu Jing,Wang Jun-Yao,Chung Hee Kyoung,Kalakonda Sudhakar,Rao Jaladanki N,Gorospe Myriam,Wang Jian-Ying
Gastroenterology
BACKGROUND AND AIMS:The mammalian intestinal epithelium self-renews rapidly and homeostasis is preserved via tightly controlled mechanisms. Long noncoding RNAs transcribed from ultraconserved regions (T-UCRs) control different cell functions, but little is known about their role in maintaining the integrity of the intestinal epithelium. We searched for T-UCRs that regulate growth of the intestinal mucosa and investigated the mechanism by which T-UCR uc.173 regulates epithelial renewal. METHODS:C57BL/6J mice were deprived of food for 48 hours in fasting experiments. Some mice were given intraperitoneal injections of a plasmid encoding LNA-anti-uc.173, to knock down endogenous uc.173. For studies using organoids, primary enterocytes were isolated from the intestine and transfected with the uc.173 transgene to increase uc.173 levels. Intestinal epithelial cells (Caco-2 and IEC-6 lines) were transfected with LNA-anti-uc.173 or uc.173 transgene. We quantified intestinal epithelial renewal based on BrdU incorporation, villus height and crypt depth, and cell number. The association of uc.173 with microRNA 195 (miRNA195) was determined by RNA pull-down assays. RESULTS:Genome-wide profile analyses identified 21 T-UCRs, including uc.173, that were differentially expressed between intestinal mucosa of fasted vs non-fasted mice. Increasing levels of uc.173 by expression of a transgene increased growth of intestinal epithelial cells and organoids. Decreasing uc.173 levels by LNA-anti-uc.173 in mice reduced renewal of the intestinal epithelium. We found that uc.173 interacted directly with the primary transcript of miRNA195, leading to miRNA195 degradation. CONCLUSIONS:In analyses of intestinal epithelial cells and mice, we identified uc.173 noncoding RNA that regulates growth of the intestinal mucosa and stimulates intestinal epithelial renewal by reducing levels of miRNA195.
10.1053/j.gastro.2017.10.009
Establishment of Lipofection Protocol for Efficient miR-21 Transfection into Cortical Neurons In Vitro.
Han Zhaoli,Ge Xintong,Tan Jin,Chen Fanglian,Gao Huabin,Lei Ping,Zhang Jianning
DNA and cell biology
Dysregulated microRNAs in neurons could cause many nervous system diseases. The therapeutic manipulation of these pathogenic microRNAs necessitates novel, efficient delivery systems to facilitate microRNA modulators targeting neurons with minimal off-target effects. The study aimed to establish a lipofection protocol to upregulate expression levels of miR-21 in neurons under different conditions, including different serum-free medium, transfection conditions, and reagent concentration, by evaluating the expression levels of miR-21 and neuron injury. The expression levels of miR-21 were higher in neurons transfected by Neurobasal-A than by DMEM. Expression levels of miR-21 were already the highest at the ratio RNAiMAX:miR-21 = 3:5, but the increase of RNAiMAX's concentration had not caused the further upregulation of expression level of miR-21. Neuron injury was condition dependent and dose dependent after transfection. Compared to S-Neurobasal groups, neurons have a smaller injury in N-Neurobasal groups, and compared to ratios RNAiMAX:miR-21 = 4:5, 5:5, neuron injury was smaller at ratios of RNAiMAX:miR-21 = 1:5, 2:5, 3:5. Without the pretreatment of starvation in vitro, the lipofection protocol was that RNAiMAX/miR-21 agomir complexes were diluted in Neurobasal-A at the ratio of RNAiMAX:miR-21 = 3:5.
10.1089/dna.2015.2800
Mechanisms of nanoparticle-mediated siRNA transfection by melittin-derived peptides.
Hou Kirk K,Pan Hua,Ratner Lee,Schlesinger Paul H,Wickline Samuel A
ACS nano
Traditional peptide-mediated siRNA transfection via peptide transduction domains exhibits limited cytoplasmic delivery of siRNA due to endosomal entrapment. This work overcomes these limitations with the use of membrane-destabilizing peptides derived from melittin for the knockdown of NFkB signaling in a model of adult T-cell leukemia/lymphoma. While the mechanism of siRNA delivery into the cytoplasmic compartment by peptide transduction domains has not been well studied, our analysis of melittin derivatives indicates that concurrent nanocomplex disassembly and peptide-mediated endosomolysis are crucial to siRNA transfection. Importantly, in the case of the most active derivative, p5RHH, this process is initiated by acidic pH, indicating that endosomal acidification after macropinocytosis can trigger siRNA release into the cytoplasm. These data provide general principles regarding nanocomplex response to endocytosis, which may guide the development of peptide/siRNA nanocomplex-based transfection.
10.1021/nn403311c
Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation.
Dorighi Kristel M,Swigut Tomek,Henriques Telmo,Bhanu Natarajan V,Scruggs Benjamin S,Nady Nataliya,Still Christopher D,Garcia Benjamin A,Adelman Karen,Wysocka Joanna
Molecular cell
Monomethylation of histone H3 at lysine 4 (H3K4me1) and acetylation of histone H3 at lysine 27 (H3K27ac) are correlated with transcriptionally engaged enhancer elements, but the functional impact of these modifications on enhancer activity is not well understood. Here we used CRISPR/Cas9 genome editing to separate catalytic activity-dependent and independent functions of Mll3 (Kmt2c) and Mll4 (Kmt2d, Mll2), the major enhancer H3K4 monomethyltransferases. Loss of H3K4me1 from enhancers in Mll3/4 catalytically deficient cells causes partial reduction of H3K27ac, but has surprisingly minor effects on transcription from either enhancers or promoters. In contrast, loss of Mll3/4 proteins leads to strong depletion of enhancer Pol II occupancy and eRNA synthesis, concomitant with downregulation of target genes. Interestingly, downregulated genes exhibit reduced polymerase levels in gene bodies, but not at promoters, suggestive of pause-release defects. Altogether, our results suggest that enhancer H3K4me1 provides only a minor contribution to the long-range coactivator function of Mll3/4.
10.1016/j.molcel.2017.04.018
Technological development of structural DNA/RNA-based RNAi systems and their applications.
Jeong Eun Hye,Kim Hyejin,Jang Bora,Cho Hyesoo,Ryu Jaehee,Kim Boyeon,Park Youngkuk,Kim Jieun,Lee Jong Bum,Lee Hyukjin
Advanced drug delivery reviews
RNA interference (RNAi)-based gene therapy has drawn tremendous attention due to its highly specific gene regulation by selective degradation of any target mRNA. There have been multiple reports regarding the development of various cationic materials for efficient siRNA delivery, however, many studies still suffer from the conventional delivery problems such as suboptimal transfection performance, a lack of tissue specificity, and potential cytotoxicity. Despite the huge therapeutic potential of siRNAs, conventional gene carriers have failed to guarantee successful gene silencing in vivo, thus not warranting clinical trials. The relatively short double-stranded structure of siRNAs has resulted in uncompromising delivery formulations, as well as low transfection efficiency, compared with the conventional nucleic acid drugs such as plasmid DNAs. Recent developments in structural siRNA and RNAi nanotechnology have enabled more refined and reliable in vivo gene silencing with multiple advantages over naked siRNAs. This review focuses on recent progress in the development of structural DNA/RNA-based RNAi systems and their potential therapeutic applications. In addition, an extensive list of prior reports on various RNAi systems is provided and categorized by their distinctive molecular characters.
10.1016/j.addr.2015.10.008
Off-target RNA mutation induced by DNA base editing and its elimination by mutagenesis.
Nature
Recently developed DNA base editing methods enable the direct generation of desired point mutations in genomic DNA without generating any double-strand breaks, but the issue of off-target edits has limited the application of these methods. Although several previous studies have evaluated off-target mutations in genomic DNA, it is now clear that the deaminases that are integral to commonly used DNA base editors often bind to RNA. For example, the cytosine deaminase APOBEC1-which is used in cytosine base editors (CBEs)-targets both DNA and RNA, and the adenine deaminase TadA-which is used in adenine base editors (ABEs)-induces site-specific inosine formation on RNA. However, any potential RNA mutations caused by DNA base editors have not been evaluated. Adeno-associated viruses are the most common delivery system for gene therapies that involve DNA editing; these viruses can sustain long-term gene expression in vivo, so the extent of potential RNA mutations induced by DNA base editors is of great concern. Here we quantitatively evaluated RNA single nucleotide variations (SNVs) that were induced by CBEs or ABEs. Both the cytosine base editor BE3 and the adenine base editor ABE7.10 generated tens of thousands of off-target RNA SNVs. Subsequently, by engineering deaminases, we found that three CBE variants and one ABE variant showed a reduction in off-target RNA SNVs to the baseline while maintaining efficient DNA on-target activity. This study reveals a previously overlooked aspect of off-target effects in DNA editing and also demonstrates that such effects can be eliminated by engineering deaminases.
10.1038/s41586-019-1314-0