Structural atlas of human primary microRNAs generated by SHAPE-MaP.

MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here, we employed selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP), a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3' bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations.

Non-viral, direct neuronal reprogramming from human fibroblast using a polymer-functionalized nanodot.

Among various strategies to treat neurodegenerative disorders, cell replacement therapies have drawn much attention recently. Such a trend led to the increase in demand for the rare and specialized cells, followed by the outburst development of various cell reprogramming strategies. However, several limitations on these conventional methods remain to be solved, including the genetic instability of the viral vectors and the high cytotoxicity or poor performance of the non-viral carriers. Therefore, non-viral methods need to be developed to ensure safe and efficient cell reprogramming. Here, we introduce a polymer-modified nano-reagent (Polymer-functionalized Nanodot, PolyN) for the safe and efficient, non-viral direct cell reprogramming. PolyN facilitated the highly efficient contemporary overexpression of the transgene compared to the conventional reagent. With our nano-reagent, we demonstrated the SOX2-mediated cell reprogramming and successfully generated the neuron-like cell from the human fibroblast.

Large-Scale 3D Optical Mapping and Quantitative Analysis of Nanoparticle Distribution in Tumor Vascular Microenvironment.

Nanoparticles (NPs) are a promising carrier for cancer therapeutics. Systemically administered NPs are transported to tumor tissues via the bloodstream, extravasated from microvessels, and delivered to cancer cells. The distribution of NPs in the tumor vascular microenvironment critically determines the therapeutic efficacy of NP-delivered drugs, but its precise assessment in 3D across a large volume remains challenging. Here, an analytical platform-termed OMNIA (for Optical Mapping of Nanoparticles and Image Analysis)-integrating tissue clearing, high-resolution optical imaging, and semiautomated image analysis is presented, which enables accurate, unbiased, and quantitative analysis of the distribution of NPs in relation to the vasculature across a large 3D volume. Application of OMNIA to tumor tissues revealed higher accumulation and more efficient extravasation of NPs in the tumor periphery than the core. Time-course analysis demonstrated that the accumulation of NPs in tumor peaked at 24 h after injection, but the relative distribution of NPs from the vasculature remained remarkably stable over time. Comparisons between 45- and 200-nm-sized NPs showed a lower accumulation of smaller NPs in tumors relative to the liver, yet better vessel permeation. Together, our results demonstrate that OMNIA facilitates precise and reliable evaluation of NP biodistribution, and mechanistic investigations on NP delivery to tumor tissues.

Barrier to autointegration factor 1, procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, and splicing factor 3b subunit 4 as early-stage cancer decision markers and drivers of hepatocellular carcinoma.

An accurate tool enabling early diagnosis of hepatocellular carcinoma (HCC) is clinically important, given that early detection of HCC markedly improves survival. We aimed to investigate the molecular markers underlying early progression of HCC that can be detected in precancerous lesions. We designed a gene selection strategy to identify potential driver genes by integrative analysis of transcriptome and clinicopathological data of human multistage HCC tissues, including precancerous lesions, low- and high-grade dysplastic nodules. The gene selection process was guided by detecting the selected molecules in both HCC and precancerous lesion. Using various computational approaches, we selected 10 gene elements as a candidate and, through immunohistochemical staining, showed that barrier to autointegration factor 1 (BANF1), procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 (PLOD3), and splicing factor 3b subunit 4 (SF3B4) are HCC decision markers with superior capability to diagnose early-stage HCC in a large cohort of HCC patients, as compared to the currently popular trio of HCC diagnostic markers: glypican 3, glutamine synthetase, and heat-shock protein 70. Targeted inactivation of BANF1, PLOD3, and SF3B4 inhibits in vitro and in vivo liver tumorigenesis by selectively modulating epithelial-mesenchymal transition and cell-cycle proteins. Treatment of nanoparticles containing small-interfering RNAs of the three genes suppressed liver tumor incidence as well as tumor growth rates in a spontaneous mouse HCC model. We also demonstrated that SF3B4 overexpression triggers SF3b complex to splice tumor suppressor KLF4 transcript to nonfunctional skipped exon transcripts. This contributes to malignant transformation and growth of hepatocyte through transcriptional inactivation of p27Kip1 and simultaneously activation of Slug genes. CONCLUSION: The findings suggest molecular markers of BANF1, PLOD3, and SF3B4 indicating early-stage HCC in precancerous lesion, and also suggest drivers for understanding the development of hepatocarcinogenesis. (Hepatology 2018;67:1360-1377).

MAP4-regulated dynein-dependent trafficking of BTN3A1 controls the TBK1-IRF3 signaling axis.

The innate immune system detects viral nucleic acids and induces type I interferon (IFN) responses. The RNA- and DNA-sensing pathways converge on the protein kinase TANK-binding kinase 1 (TBK1) and the transcription factor IFN-regulatory factor 3 (IRF3). Activation of the IFN signaling pathway is known to trigger the redistribution of key signaling molecules to punctate perinuclear structures, but the mediators of this spatiotemporal regulation have yet to be defined. Here we identify butyrophilin 3A1 (BTN3A1) as a positive regulator of nucleic acid-mediated type I IFN signaling. Depletion of BTN3A1 inhibits the cytoplasmic nucleic acid- or virus-triggered activation of IFN-ß production. In the resting state, BTN3A1 is constitutively associated with TBK1. Stimulation with nucleic acids induces the redistribution of the BTN3A1-TBK1 complex to the perinuclear region, where BTN3A1 mediates the interaction between TBK1 and IRF3, leading to the phosphorylation of IRF3. Furthermore, we show that microtubule-associated protein 4 (MAP4) controls the dynein-dependent transport of BTN3A1 in response to nucleic acid stimulation, thereby identifying MAP4 as an upstream regulator of BTN3A1. Thus, the depletion of either MAP4 or BTN3A1 impairs cytosolic DNA- or RNA-mediated type I IFN responses. Our findings demonstrate a critical role for MAP4 and BTN3A1 in the spatiotemporal regulation of TBK1, a central player in the intracellular nucleic acid-sensing pathways involved in antiviral signaling.

Liposomal co-delivery-based quantitative evaluation of chemosensitivity enhancement in breast cancer stem cells by knockdown of GRP78/CLU.

Resistance to chemotherapy is a key factor in the inefficacy of various forms of treatments for cancer. In the present study, chemo-resistant proteins, including glucose-regulated protein 78 (GRP78)/clusterin (CLU) targeted 1,2-dioleoyloxy-3-trimethylammoniumpropane (DOTAP) liposomes, were developed as a delivery system for co-delivery of camptothecin (CPT) and GRP78 siRNA/CLU siRNA. Their drug/gene co-deliveries were quantitatively assessed in cancer stem cells (CSC) and MCF-7 cells. DOTAP-CPT/siRNA were prepared via electrostatic interaction on GRP78 siRNA or CLU siRNA. The size and ζ-potential of liposomes and lipoplexes were measured by dynamic light scattering techniques and electrophoretic light scattering spectrophotometry. The lipoplexes formation was tested by using gel electrophoresis. Immunofluorescence analysis showed that the expression level of CLU and GRP78 were significantly elevated in CSC compared to MCF-7 cells. Transfection and drug-delivery efficiency of DOTAP-CPT/siRNA were quantitatively compared with Lipofectamine 2000. Compared to free CPT, DOTAP-CPT-siCLU delivery in CSC and MCF-7 cells increased transfection efficiency and chemo-sensitivity by 4.1- and 5.9-fold, respectively. On the other hand, DOTAP-CPT-siGRP78 delivery increased transfection efficiency and chemo sensitivity by 4.4- and 6.2-fold in CSC and MCF-7 cells, respectively, compared to free CPT. It is significant that 3 ± 1.2-fold increase in transfection efficiency was achieved by lipofectamine. Consequently, an increase in anti-cancer/gene silencing efficacy was quantitatively observed as an effect of DOTAP-CPT/siRNA treatment, which was relatively higher than lipofectamine treatment. Conclusively, our experimental data quantitatively demonstrate that using DOTAP-CPT-siRNA specifically targeting (CSCs) chemo-resistant protein in vitro offers substantial potential for synergistic anti-cancer therapy.

A FRET assay for the quantitation of inhibitors of exonuclease EcoRV by using parchment paper inkjet-printed with graphene oxide and FAM-labelled DNA.

A graphene oxide (GO)-based cost-effective, automatted strip test has developed for screening of inhibitors of endonuclease EcoRV. The method involves the use of GO and a DNA substrate for EcoRV that contains both an ssDNA region for binding of GO and a fluorescein amidite (FAM)-labelled dsDNA. All the components were inkjet printed on a piece of parchment paper. The ssDNA region binds to the surface of GO and anchors so that the fluorescence of FAM is quenched. The parchment paper strip is then incubated with a sample containing EcoRV which causes enzymatic hydrolysis, and dsDNA was separated from the GO. As a result, green fluorescence is generated at the reaction spot. Enzyme activity can be measured in the presence and absence of aurintricarboxy acid acting as an EcoRV inhibitor. This method excels by its need for 2-3 orders less reagents compared to the standard well plate assay. Thus, it is an efficient platform for GO-based screening of EcoRV enzyme inhibitors. Graphical abstract A graphene oxide (GO)-based endonuclease EcoRV inhibition FRET assay using inkjet printing was developed. Printing of GO along with assay reagents has a beneficial effect on the enzymatic reaction on paper. This method was successfully applied to evaluate EcoRV inhibitor activity.

Development of Dual-Pore Coexisting Branched Silica Nanoparticles for Efficient Gene-Chemo Cancer Therapy.

Various strategies for combination therapy to overcome current limitations in cancer therapy have been actively investigated. Among them, simultaneous delivery of multiple drugs is a subject of high interest due to anticipated synergistic effect, but there have been difficulties in designing and developing effective nanomaterials for this purpose. In this work, dual-pore coexisting hybrid porous silica nanoparticles are developed through Volmer-Weber growth pathway for efficient co-delivery of gene and anticancer drug. Based on the different pore sizes (2-3 and 40-45 nm) and surface modifications of the core and branch domains, loading and controlled release of gene and drug are achieved by appropriate strategies for each environment. With excellent loading capacity and low cytotoxicity of the present platform, the combinational cancer therapy is successfully demonstrated against human cervical cancer cell line. Through a series of quantitative analyses, the excellent gene-chemo combinational therapeutic efficiency is successfully demonstrated. It is expected that the present nanoparticle will be applicable to various biomedical fields that require co-delivery of small molecule and nucleic acid.

Synthesis of Fluorescent Au Nanocrystals-Silica Hybrid Nanocomposite (FLASH) with Enhanced Optical Features for Bioimaging and Photodynamic Activity.

Fluorescent Au nanocrystals (AuNCs)-silica hybrid nanocomposite (FLASH) was synthesized by co-condensation of surface-modified AuNCs. Present FLASH nanocomposite exhibited four times the enhanced photoluminescence and photocatalytic activity compared to single nanocrystals. On the basis of these enhanced optical features, we successfully demonstrated in vitro fluorescence bioimaging of introduced FLASH to human cervical cancer cell line (HeLa). Beyond the confirmation of photocatalytic activity from the photodegradation of methylene blue as a model compound, the regional selective photodynamic therapy of HeLa cells under UV irradiation was also presented. Taken together the enhanced optical features and further potential in theranostic applications, we expect that the present FLASH can be a promising tool for nanobiotechnology field.

Synthesis of biologically-active reduced graphene oxide by using fucoidan as a multifunctional agent for combination cancer therapy.

A therapeutic reduced graphene oxide (RGO) is synthesized by using fucoidan (Fu) as the reducing and surface functionalizing agent. The synthesized Fu-RGO exhibits promising characteristics for therapeutic applications such as high dispersity in aqueous media, biocompatibility, selective cytotoxicity to cancer cells, high loading capacity of the anticancer drug, and photothermal conversion effect. Therefore, Fu-GO is successfully harnessed as a combinatorial cancer treatment platform through bio-functional (Fu), chemo (doxorubicin (Dox)) and photothermal (RGO with near-infrared irradiation) modalities.

One-pot synthesis of multifunctional Au@graphene oxide nanocolloid core@shell nanoparticles for Raman bioimaging, photothermal, and photodynamic therapy.

The paper reports a facile one-pot synthesis of core@shell nanoparticles (NPs) composed of Au core and graphene oxide nanocolloid (GON) shell. Unique properties of Au NPs and GON can be incorporated into a single nanohybrid structure to provide desirable functions for theranosis such as localized surface plasmon resonance, Raman scattering, amphiphilic surface, and photothermal conversion. Synthesis of Au@GON NPs is achieved by simple one-pot reaction in aqueous phase utilizing GON as a reducing and stabilizing agent without any additional reducing agent. The zinc phthalocyanine, a photosensitizer, loaded Au@GON NPs show excellent multifunctional properties for combinational treatment of photothermal and photodynamic therapy in addition to Raman bioimaging with low cytotoxicity.

The Structural Influence of Graphene Oxide on Its Fragmentation during Laser Desorption/Ionization Mass Spectrometry for Efficient Small-Molecule Analysis.

The structural influence of graphene oxide (GO) on laser desorption/ionization mass spectrometry (LDI-MS) analysis of small molecules was systematically investigated by using size-fractionated GO. For fractionation of GO, pH-assisted centrifugation, sequential vacuum filtration, and sonochemical cutting processes were employed and the size-fractionated GO was thoroughly characterized to understand their size-dependent optochemical properties. Then, the fractionated GO was applied to the analysis of various small molecules by LDI-MS to investigate the relationship between their optochemical properties and LDI-MS performance. We found that large GO sheets (>0.5 µm) were more prone to fragmentation under laser irradiation during LDI-MS analysis than small GO sheets (<0.5 µm). In this regard, the LDI-MS analysis efficiency of various small molecules was significantly improved by using nanosized GO (NGO) as a matrix without background interference. In particular, NGO was successfully applied to the sensitive detection of hydrophobic pollutant molecules without requiring any surface-functionalization, enrichment, and separation process. Therefore, the present study could provide important basic information and be a practical tool for the development of simple and efficient LDI-MS platforms by using GO derivatives.

Biomedical applications of graphene and graphene oxide.

Graphene has unique mechanical, electronic, and optical properties, which researchers have used to develop novel electronic materials including transparent conductors and ultrafast transistors. Recently, the understanding of various chemical properties of graphene has facilitated its application in high-performance devices that generate and store energy. Graphene is now expanding its territory beyond electronic and chemical applications toward biomedical areas such as precise biosensing through graphene-quenched fluorescence, graphene-enhanced cell differentiation and growth, and graphene-assisted laser desorption/ionization for mass spectrometry. In this Account, we review recent efforts to apply graphene and graphene oxides (GO) to biomedical research and a few different approaches to prepare graphene materials designed for biomedical applications. Because of its excellent aqueous processability, amphiphilicity, surface functionalizability, surface enhanced Raman scattering (SERS), and fluorescence quenching ability, GO chemically exfoliated from oxidized graphite is considered a promising material for biological applications. In addition, the hydrophobicity and flexibility of large-area graphene synthesized by chemical vapor deposition (CVD) allow this material to play an important role in cell growth and differentiation. The lack of acceptable classification standards of graphene derivatives based on chemical and physical properties has hindered the biological application of graphene derivatives. The development of an efficient graphene-based biosensor requires stable biofunctionalization of graphene derivatives under physiological conditions with minimal loss of their unique properties. For the development graphene-based therapeutics, researchers will need to build on the standardization of graphene derivatives and study the biofunctionalization of graphene to clearly understand how cells respond to exposure to graphene derivatives. Although several challenging issues remain, initial promising results in these areas point toward significant potential for graphene derivatives in biomedical research.

Mechanistic study of laser desorption/ionization of small molecules on graphene oxide multilayer films.

Graphene and graphene oxide (GO) films have been explored to develop an efficient laser desorption/ionization mass spectrometry (LDI-MS) platform for the analysis of chemically and biologically important small molecules. The GO films were prepared by layer-by-layer (LBL) assembly cycles (one to ten layers) with precisely controlled thickness and surface roughness which are important structural factors for laser energy absorption capacity and laser energy transfer for efficient LDI-MS analysis. Amino acids, saccharides, and pyrenylated molecules were analyzed by LDI-MS on the LBL assembled GO films to reveal their structural influence on LDI-MS analysis of small molecules. Then, the structural influence of LBL assembled GO films on synergistic effect was investigated to develop an efficient and widely applicable LDI-MS analysis platform with an additional multiwalled carbon nanotube (MWCNT) layer. We found that the optimum number of GO film layers for LDI-MS analysis was dependent on the chemical structures of small molecules, and the laser energy threshold needed for LDI of small molecules on GO/MWCNT films could be lowered as the number of LBL assembled GO films increased underneath the MWCNT layer.

A Single-Dose mRNA Vaccine Employing Porous Silica Nanoparticles Induces Robust Immune Responses Against the Zika Virus.

Recently, lipid nanoparticles (LNPs)-based mRNA delivery has been approved by the FDA for SARS-CoV-2 vaccines. However, there are still considerable points for improvement in LNPs. Especially, local administration of LNPs-formulated mRNA can cause off-target translation of mRNA in distal organs which can induce unintended adverse effects. With the hypothesis that large and rigid nanoparticles can be applied to enhance retention of nanoparticles at the injection site, a polyethyleneimine (PEI)-coated porous silica nanoparticles (PPSNs)-based mRNA delivery platform is designed. PPSNs not only facilitate localized translation of mRNA at the site of injection but also prolonged protein expression. It is further demonstrated that the development of a highly efficacious Zika virus (ZIKV) vaccine using mRNA encoding full-length ZIKV pre-membrane (prM) and envelope (E) protein delivered by PPSNs. The ZIKV prME mRNA-loaded PPSNs vaccine elicits robust immune responses, including high levels of neutralizing antibodies and ZIKV E-specific T cell responses in C57BL/6 mice. Moreover, a single injection of prME-PPSNs vaccine provided complete protection against the ZIKV challenge in mice.

Bio-inspired interfacial chemistry for the fabrication of a robust and functional graphene oxide composite film.

A strong and functional artificial nacre film is developed by using polyethyleneimine-functionalized GO (PEI-GO) and pyrogallol (PG) inspired by insect exoskeleton sclerotization. PEI-GO is macroscopically assembled into the laminated films and then reacted with PG under the optimized condition for their efficient cross-linking through Schiff-base reactions. The internal structure and physicochemical properties of PG-treated PEI-GO (PG@PEI-GO) films are systematically explored with various analytical tools. The optimized PG@PEI-GO films exhibit excellent tensile strength, modulus, and toughness of 216.0 ± 12.9 MPa, 17.0 ± 1.1 GPa, and 2192 ± 538.5 kJ m-3 which are 2.7, 2.8, and 2.3-fold higher than those of GO films, respectively. Furthermore, silver nanoparticles (AgNPs) are densely immobilized on the PG@PEI-GO films harnessing their abundant amine groups, and the AgNPs immobilized PG@PEI-GO films exhibit a high catalytic activity in the conversion of 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) with maintaining structural integrity. Based on the results, we demonstrate that the rational design of interfaces, inspired by natural materials, is an efficient approach to achieving strong and functional GO laminated composite films.

Metabolic Modulation of Kynurenine Based on Kynureninase-Loaded Nanoparticle Depot Overcomes Tumor Immune Evasion in Cancer Immunotherapy.

Evading recognition of immune cells is a well-known strategy of tumors used for their survival. One of the immune evasion mechanisms is the synthesis of kynurenine (KYN), a metabolite of tryptophan, which suppresses the effector T cells. Therefore, lowering the KYN concentration can be an efficient antitumor therapy by restoring the activity of immune cells. Recently, kynureninase (KYNase), which is an enzyme transforming KYN into anthranilate, was demonstrated to show the potential to decrease KYN concentration and inhibit tumor growth. However, due to the limited bioavailability and instability of proteins in vivo, it has been challenging to maintain the KYNase concentration sufficiently high in the tumor microenvironment (TME). Here, we developed a nanoparticle system loaded with KYNase, which formed a Biodegradable and Implantable Nanoparticle Depot named 'BIND' following subcutaneous injection. The BIND sustainably supplied KYNase around the TME while located around the tumor, until it eventually degraded and disappeared. As a result, the BIND system enhanced the proliferation and cytokine production of effector T cells in the TME, followed by tumor growth inhibition and increased mean survival. Finally, we showed that the BIND carrying KYNase significantly synergized with PD-1 blockade in three mouse models of colon cancer, breast cancer, and melanoma.

Pt-Te-Nanorod-Based Photothermal Chemokine Immunotherapy for All Stages of Cancer via Adaptive and Innate Immunity.

The chemokine (C-X-C) motif ligand 9 (CXCL9) is one of the lymphocyte-traffic-involved chemokines. Despite the immunotherapeutic potential of CXCL9 for recruiting effector T cells (cluster of differentiation 4+ (CD4+) and CD8+ T cells) and natural killer cells (NK cells) around the tumors, practical applications of CXCL9 have been limited because of its immune toxicity and lack of stability in vivo. To overcome these limitations, we designed and synthesized Pt-Te nanorods (PtTeNRs), which exhibited excellent photothermal conversion efficiency with stable CXCL9 payload characteristics under the physiological conditions of in vivo environments. We developed a CXCL9-based immunotherapy strategy by utilizing the unique physicochemical properties of developed PtTeNRs. The investigation revealed that the PtTeNR-loaded CXCL9 was effectively accumulated in the tumor, subsequently released in a sustained manner, and successfully recruited effector T cells for immunotherapy of the designated tumor tissue. In addition, a synergistic effect was observed between the photothermal (PT) therapy and antiprogrammed cell death protein 1 (aPD-1) antibody. In this study, we demonstrated that PtTeNR-based CXCL9, PT, and aPD-1 antibody trimodal therapy delivers an outstanding tumor suppression effect in all stages of cancer, including phases 1-4 and tumor recurrence.

Desorption of single-stranded nucleic acids from graphene oxide by disruption of hydrogen bonding.

Graphene oxide (GO) is known to interact with single-stranded nucleic acids through pi-stacking interactions and hydrogen bonds between the nucleobases and the hexagonal cells of GO. It also quenches the fluorescence when the fluorophore comes near to the GO mesh. When single-stranded (ss) regions of either DNA or RNA are present, those regions were adsorbed onto the surface of GO with a quenching of fluorescence located proximally to the GO surface. We demonstrated that bound single-stranded nucleic acids can be readily dissociated from GO by disrupting hydrogen bonding with urea, which was confirmed with fluorescence measurement and gel electrophoresis. Hydrogen bonding mainly contributes to the interaction between GO and single-stranded nucleic acids such as ssDNA and RNA. The GO-coated mesoporous silica nanoparticles (GO-MSNs) were synthesized for better separation of RNAs from cells. Cellular RNAs were readily adsorbed and eluted with ease by using GO-MSN and urea, respectively, demonstrating that GO-MSN and urea elution is a facile RNA extraction method.

Highly Efficient Messenger RNA Transfection of Hard-to-Transfect Cells using Carbon Nanodots.

Although messenger RNA (mRNA)-based therapeutics opened up new avenues for treating various diseases, intracellular delivery of mRNA is still challenging, especially to hard-to-transfect cells. For successful mRNA therapy, the development of a delivery vehicle that can effectively transport mRNA into cells is essential. In this study, we synthesized carbon nanodots (CNDs) as an efficient mRNA delivery vehicle via a one-step microwave-assisted method. CNDs easily formed complexes with mRNA molecules by electrostatic interactions, and the gene delivery performance of CNDs was highly effective in hard-to-transfect cells. Considering their outstanding transfection ability, CNDs are expected to be further applied for mRNA-based cellular engineering.