Site-specific tethering nanobodies on recombinant adeno-associated virus vectors for retargeted gene therapy.

Recombinant adeno-associated viruses (rAAVs) have been extensively studied for decades as carriers for delivering therapeutic genes. However, designing rAAV vectors with selective tropism for specific cell types and tissues has remained challenging. Here, we introduce a strategy for redirecting rAAV by attaching nanobodies with desired tropism at specific sites, effectively replacing the original tropism. To demonstrate this concept, we initially modified the genetic code of rAAV2 to introduce an azido-containing unnatural amino acid at a precise site within the capsid protein. Following a screening process, we identified a critical site (N587+1) where the introduction of unnatural amino acid eliminated the natural tropism of rAAV2. Subsequently, we successfully redirected rAAV2 by conjugating various nanobodies at the N587+1 site, using click and SpyTag-Spycatcher chemistries to form nanobody-AAV conjugates (NACs). By investigating the relationship between NACs quantity and effect and optimizing the linker between rAAV2 and the nanobody using a cathepsin B-susceptible valine-citrulline (VC) dipeptide, we significantly improved gene delivery efficiency both in vitro and in vivo. This enhancement can be attributed to the facilitated endosomal escape of rAAV2. Our method offers an exciting avenue for the rational modification of rAAV2 as a retargeting vehicle, providing a convenient platform for precisely engineering various rAAV2 vectors for both basic research and therapeutic applications. STATEMENT OF SIGNIFICANCE: AAVs hold great promise in the treatment of genetic diseases, but their clinical use has been limited by off-target transduction and efficiency. Here, we report a strategy to construct NACs by conjugating a nanobody or scFv to an rAAV capsid site, specifically via biorthogonal click chemistry and a spy-spycatcher reaction. We explored the structure-effect and quantity-effect relationships of NACs and then optimized the transduction efficiency by introducing a valine-citrulline peptide linker. This approach provides a biocompatible method for rational modification of rAAV as a retargeting platform without structural disruption of the virus or alteration of the binding capacity of the nanobody, with potential utility across a broad spectrum of applications in targeted imaging and gene delivery.

A Siamese Vision Transformer for Bearings Fault Diagnosis.

Fault diagnosis methods based on deep learning have progressed greatly in recent years. However, the limited training data and complex work conditions still restrict the application of these intelligent methods. This paper proposes an intelligent bearing fault diagnosis method, i.e., Siamese Vision Transformer, suiting limited training data and complex work conditions. The Siamese Vision Transformer, combining Siamese network and Vision Transformer, is designed to efficiently extract the feature vectors of input samples in high-level space and complete the classification of the fault. In addition, a new loss function combining the Kullback-Liebler divergence both directions is proposed to improve the performance of the proposed model. Furthermore, a new training strategy termed random mask is designed to enhance input data diversity. A comparative test is conducted on the Case Western Reserve University bearing dataset and Paderborn dataset and our method achieves reasonably high accuracy with limited data and satisfactory generation capability for cross-domain tasks.

A Hybrid Matching Network for Fault Diagnosis under Different Working Conditions with Limited Data.

Intelligent fault diagnosis methods based on deep learning have achieved much progress in recent years. However, there are two major factors causing serious degradation of the performance of these algorithms in real industrial applications, i.e., limited labeled training data and complex working conditions. To solve these problems, this study proposed a domain generalization-based hybrid matching network utilizing a matching network to diagnose the faults using features encoded by an autoencoder. The main idea was to regularize the feature extractor of the network with an autoencoder in order to reduce the risk of overfitting with limited training samples. In addition, a training strategy using dropout with random changing rates on inputs was implemented to enhance the model's generalization on unseen domains. The proposed method was validated on two different datasets containing artificial and real faults. The results showed that considerable performance was achieved by the proposed method under cross-domain tasks with limited training samples.

A Tandem Reaction System for Inactivation of Marine Microorganisms by Commercial Carbon Black and Boron-Doped Carbon Nitride.

The Pureballast system, based on photocatalytic technology, can purify ships' ballast water. However, the efficiency of photocatalytic sterilization still needs to be improved due to the shortcomings of the photocatalyst itself and the complex components of seawater. In this work, a tandem reaction of electrocatalytic synthesis and photocatalytic decomposition of hydrogen peroxide (H2O2) was constructed for the inactivation of marine microorganisms. Using seawater and air as raw materials, electrocatalytic synthesis of H2O2 by commercial carbon black can avoid the risk of large-scale storage and transportation of H2O2 on ships. In addition, boron doping can improve the photocatalytic decomposition performance of H2O2 by g-C3N4. Experimental results show that constructing the tandem reaction is effective, inactivating 99.7% of marine bacteria within 1 h. The sterilization efficiency is significantly higher than that of the single way of electrocatalysis (52.8%) or photocatalysis (56.9%). Consequently, we analyzed the reasons for boron doping to enhance the efficiency of g-C3N4 decomposition of H2O2 based on experiments and first principles. The results showed that boron doping could significantly enhance not only the transfer kinetics of photogenerated electrons but also the adsorption capacity of H2O2. This work can provide some reference for the photocatalytic technology study of ballast water treatment.

Morphology modulation and performance optimization of nanopetal-based Ag-modified Bi2O2CO3 as an inactivating photocatalytic material.

The use of photocatalytic technology to kill bacteria on marine vessel surface coatings has been paid more attention by research scholars. In this paper, petal-like microspheres with Ag nanoparticles were prepared by a simple one-step process combining the hydrothermal method and photodeposition. The 0.7% Ag/Bi2O2CO3 composite photocatalyst exhibited the highest photocatalytic efficiency for bacterial removal under visible light irradiation and had the highest photogenerated carrier separation efficiency, and the sterilization rate was doubled compared with that of pure Bi2O2CO3, reaching 95%. Using X-ray photoelectron spectroscopy, scanning electron microscopy and transmission electron microscopy, the existence of Ag nanoparticles was confirmed, and their size was approximately 10 nm. The surface plasmon resonance (SPR) effect of Ag nanoparticles was investigated by ultraviolet-visible diffuse reflectance spectroscopy (DRS). It was shown that the surface plasmon resonance effect of Ag improved the spectral utilization of the Ag/Bi2O2CO3 composite photocatalyst and enhanced the stability of the catalyst. This caused the Ag/Bi2O2CO3 composite photocatalyst to have superior photocatalytic activity to pure Bi2O2CO3. The results of electrochemical impedance characterization and transient photocurrent response show that 0.7% Ag/Bi2O2CO3 has a high efficiency of photogenerated carrier separation. By the free radical capture test, hydroxyl radicals were the primary active substance, and Ag+ improved the photocatalytic sterilization activity.

Broadening the versatility of lentiviral vectors as a tool in nucleic acid research via genetic code expansion.

With the aim of broadening the versatility of lentiviral vectors as a tool in nucleic acid research, we expanded the genetic code in the propagation of lentiviral vectors for site-specific incorporation of chemical moieties with unique properties. Through systematic exploration of the structure-function relationship of lentiviral VSVg envelope by site-specific mutagenesis and incorporation of residues displaying azide- and diazirine-moieties, the modifiable sites on the vector surface were identified, with most at the PH domain that neither affects the expression of envelope protein nor propagation or infectivity of the progeny virus. Furthermore, via the incorporation of such chemical moieties, a variety of fluorescence probes, ligands, PEG and other functional molecules are conjugated, orthogonally and stoichiometrically, to the lentiviral vector. Using this methodology, a facile platform is established that is useful for tracking virus movement, targeting gene delivery and detecting virus-host interactions. This study may provide a new direction for rational design of lentiviral vectors, with significant impact on both basic research and therapeutic applications.

c-Met targeting enhances the effect of irradiation and chemical agents against malignant colon cells harboring a KRAS mutation.

Although EGFR-targeted therapy has been beneficial to colorectal cancer patients, several studies have showed this clinical benefit was restricted to patients with wild-type KRAS exon 2 colorectal cancer. Therefore, it is crucial to explore efficient treatment strategies in patients with KRAS mutations. c-Met is an emerging target for the development of therapeutics against colorectal cancer. In this study, we first used the SW620 cell line, which has an activating KRAS mutation, to generate a stable cell line with conditional regulation of c-Met, which is an essential gene for growth and an oncogene. Using this approach, we evaluated the benefits of combined c-Met-targeted therapy with irradiation or chemical agents. In this cell line, we observed that the proliferation and migration of SW620 cells were reduced by the induction of c-Met shRNA. Furthermore, c-Met knockdown enhanced the anti-proliferative effects of 5-FU and Taxol but not cisplatin, irinotecan or sorafenib. These enhancements were also observed in another colon cancer cells line HCT-116, which also has a KRAS mutation. The response of SW620 cells to irradiation was also enhanced by c-Met knockdown. This method and obtained data might have important implications for exploring the combinatory effects of targeted therapies with conventional medications. Moreover, the data suggested that the combination of c-Met-targeted therapy with chemotherapy or irradiation might be an effective strategy against colorectal cancer harboring a KRAS mutation.

Elevated expression of AKR1C3 increases resistance of cancer cells to ionizing radiation via modulation of oxidative stress.

With the aim to elucidate the etiology of radioresistance, we explored the genetic alterations in non-radioresistant vs. resistant esophageal cancer cells acquired by long-term fractionated radiation. We found AKR1C3, an aldo-keto reductase expressed seldom in most human tissues, expressed higher in radioresistance-acquired cells. Suppression of AKR1C3 via RNAi or its chemical inhibitors restored the sensitivity of the acquired tumor cells and xenograft BALB/c nude mice to ionizing radiation (IR). Cellular monitoring of the oxidative stress in the AKR1C3-elevated cells indicated that IR-induced ROS accumulation and the concomitant DNA damage was significantly alleviated, and such protective consequence disappeared upon AKR1C3 knockdown. These findings uncover the potential involvement of AKR1C3 in removal of cellular ROS and explain, at least partially, the acquired radioresistance by AKR1C3 overexpression. A retrospective analysis of esophageal carcinomas also indicated a significant expression of AKR1C3 in radio-resistant but not radio-sensitive surgical samples. Our study may provide a potential biomarker for predicting prognosis of radiotherapy and even direct a targeted therapy for esophageal cancer and other tumors.

Strand antagonism in RNAi: an explanation of differences in potency between intracellularly expressed siRNA and shRNA.

Strategies to regulate gene function frequently use small interfering RNAs (siRNAs) that can be made from their shRNA precursors via Dicer. However, when the duplex components of these siRNA effectors are expressed from their respective coding genes, the RNA interference (RNAi) activity is much reduced. Here, we explored the mechanisms of action of shRNA and siRNA and found the expressed siRNA, in contrast to short hairpin RNA (shRNA), exhibits strong strand antagonism, with the sense RNA negatively and unexpectedly regulating RNAi. Therefore, we altered the relative levels of strands of siRNA duplexes during their expression, increasing the level of the antisense component, reducing the level of the sense component, or both and, in this way we were able to enhance the potency of the siRNA. Such vector-delivered siRNA attacked its target effectively. These findings provide new insight into RNAi and, in particular, they demonstrate that strand antagonism is responsible for making siRNA far less potent than shRNA.

Hepatitis C virus infection of neuroepithelioma cell lines.

BACKGROUND & AIMS: Hepatitis C virus (HCV) establishes chronic infections in 3% of the world's population. Infection leads to progressive liver disease; hepatocytes are the major site of viral replication in vivo. However, chronic infection is associated with a variety of extrahepatic syndromes, including central nervous system (CNS) abnormalities. We therefore screened a series of neural and brain-derived cell lines for their ability to support HCV entry and replication. METHODS: We used a panel of neural-derived cell lines, HCV pseudoparticles (HCVpp), and an infectious, HCV JFH-1 cell-culture system (HCVcc) to assess viral tropism. RESULTS: Two independently derived neuroepithelioma cell lines (SK-N-MC and SK-PN-DW) permitted HCVpp entry. In contrast, several neuroblastoma, glioma, and astrocytoma cell lines were refractory to HCVpp infection. HCVcc infected the neuroepithelioma cell lines and established a productive infection. Permissive neuroepithelioma cells expressed CD81, scavenger receptor BI (SR-BI), and the tight junction proteins Claudin-1 (CLDN1) and occludin, whereas nonpermissive neural cell lines lacked CLDN1 and, in some cases, SR-BI. HCVpp infection of the neuroepithelioma cells was neutralized by antibodies to CD81, SR-BI, CLDN1, and HCV E2. Furthermore, anti-CD81, interferon, and the anti-NS3 protease inhibitor VX-950 significantly reduced HCVcc infection of neuroepithelioma and hepatoma cells. CONCLUSIONS: Neuroepithelioma-derived cell lines express functional receptors that support HCV entry at levels comparable to those of hepatoma cells. HCV infection in vitro is not restricted to hepatic-derived cells, so HCV might infect cells of the CNS in vivo.

A method for detecting and preventing negative RNA interference in preparation of lentiviral vectors for siRNA delivery.

The lentiviral vector is a useful tool for delivery of hairpin siRNA (shRNA) into mammalian cells. However, the efficiency of this system for carrying double-stranded siRNA (dsRNA) has not been explored. In this study we cloned the two forms of siRNA-coding sequence, a palindromic DNA with a spacer loop for shRNA and a double-stranded DNA with opposing Pol III promoters for dsRNA, into lentiviral DNA vectors, and compared their viral vector production yields. Our results indicate that sharply lower titer vector was obtained for dsRNA while much higher titer vector was produced for shRNA, posing a fundamental concern whether siRNA-carrying viral RNA itself is an inherent target of RNAi. Further experimental analyses using packaging cells that either allow or do not allow siRNA transcription indicate that the shRNA-carrying viral RNA is resistant to RNAi but the viral RNA carrier for dsRNA is not, offering a linker of RNAi bias-target secondary structure that causes shRNA vector to evade RNAi degradation. More importantly, the poor yield of dsRNA vector production was restored when a novel packaging cell line was used that blocks the antisense strand from dsRNA duplexes. This method has important implications for the RNAi field, especially for those who are using lentiviral dsRNA and dsRNA libraries for various biological discovery and therapeutic interventions.

Comparisons of RNAi approaches for validation of human RNA helicase A as an essential factor in hepatitis C virus replication.

A major issue of current virology concerns the characterization of cellular proteins that operate as functional components of the viral multiplication process. RNAi is a powerful tool to elucidate gene functions. In this study three RNAi approaches (transient transfection, stable transduction and inducible RNAi) were assessed to validate human RNA helicase A (RHA) as an essential factor in hepatitis C virus (HCV) replication. It indicated that RHA transient knockdown by synthetic siRNA had no effect on HCV replication, while RHA stable knockdown via lentivector transduction caused cell lethality. The involvement of RHA in HCV replication was verified by an RNAi inducible system that, on the one hand, maintained long-term gene silencing, but on the other hand, alleviated siRNA toxicity during the essential gene silencing. A 21-day follow-up of the response of HCV replication to the presence and absence of RNAi indicated that RHA is a cellular factor involved in the HCV replication process.

A more efficient RNAi inducible system for tight regulation of gene expression in mammalian cells and xenograft animals.

Two types of tetracycline-controlled inducible RNAi expression systems have been developed that generally utilize multiple tetracycline operators (TetOs) or repressor fusion proteins to overcome the siRNA leakiness. Here, we report a novel system that overexpresses the tetracycline repressor (TetR) via a bicistronic construct to control siRNA expression. The high level of TetR expression ensures that the inducible promoter is tightly bound, with minimal basal transcription, allowing for regulation solely dependent on TetR rather than a TetR fusion protein via a more complicated mechanism. At the same time, this system contains only a single TetO, thus minimizing the promoter impairment occurring in existing systems due to the incorporation of multiple TetOs, and maximizing the siRNA expression upon induction. In addition, this system combines all the components required for regulation of siRNA expression into a single lentiviral vector, so that stable cell lines can be generated by a single transduction and selection, with significant reduction in time and cost. Taken together, this all-in-one lentiviral vector with the feature of TetR overexpression provides a unique and more efficient tool for conditional gene knockdown that has wide applications. We have demonstrated the high degree of robustness and versatility of this system as applied to several mammalian cells and xenograft animals.

RNA interference and potential applications.

RNA interference (RNAi) is the process of using specific sequences of double-stranded RNA (dsRNA) to knock down the expression level of sequence-homologous genes. Such ability of small interfering RNA (siRNA) in mammalian cells will undoubtedly revolutionize the study of functional genomics, the discovery of drug targets and even the treatment of human diseases. In this review we briefly describe the history of RNAi discovery, the RNAi mechanism and the general guideline for siRNA design as well as various methods for siRNA production and delivery. We also introduce the potential applications of siRNA, inducible siRNA and siRNA library in speeding up basic biomedical research and in acting as potential therapeutic agents for treatment of numerous human diseases.

Comparison of metal-ion-dependent cleavages of RNA by a DNA enzyme and a hammerhead ribozyme.

Joyce's DNA enzyme catalyzes cleavage of RNAs with almost the same efficiency as the hammerhead ribozyme. The cleavage activity of the DNA enzyme was pH dependent, and the logarithm of the cleavage rate increased linearly with pH from pH 6 to pH 9 with a slope of approximately unity. The existence of an apparent solvent isotope effect, with cleavage of RNA by the DNA enzyme in H(2)O being 4.3 times faster than cleavage in D(2)O, was in accord with the interpretation that, at a given pH, the concentration of the active species (deprotonated species) is 4.3 times higher in H(2)O than the concentration in D(2)O. This leads to the intrinsic isotope effect of unity, demonstrating that no proton transfer occurs in the transition state in reactions catalyzed by the DNA enzyme. Addition of La(3+) ions to the Mg(2+)-background reaction mixture inhibited the DNA enzyme-catalyzed reactions, suggesting the replacement of catalytically and/or structurally important Mg(2+) ions by La(3+) ions. Similar kinetic features of DNA enzyme mediated cleavage of RNA and of hammerhead ribozyme-mediated cleavage suggest that a very similar catalytic mechanism is used by the two types of enzyme, despite their different compositions.