Adeno-Associated Virus Site-Specific Integration Is Mediated by Proteins of the Nonhomologous End-Joining Pathway

Adeno-associated virus type 2 (AAV 2) is the only eukaryotic virus capable of site-specific integration; the target site is at chromosome 19q13.4, a site termed AAVS1. The biology of AAV latency has been extensively studied in cell culture, yet the precise mechanism and the required cellular factors are not known. In this study, we assessed the relative frequencies of stable site-specific integration by characterization of cell clones containing integrated AAV vectors. By this assay, two proteins involved in nonhomologous end joining (NHEJ), DNAPKcs and ligase IV, exhibit differential effects on AAV site-specific integration. DNAPKcs is not required; its presence increases the frequency of junction formation indicative of site-specific integration, but seems to reduce the ratio of site-specific integration to random integration (i.e., the latter is even more enhanced). In contrast, site-specific integration is significantly reduced relative to random integration in cells deficient in ligase IV expression. Furthermore, we show that single-stranded AAV vectors are better substrates for site-specific integration than are self-complementary AAV vectors; the absence of DNAPKcs did not affect the targeted integration of these double-stranded AAV vectors. Together, these data suggest that NHEJ proteins participate in site-specific integration, and indicate a role for the single-stranded form of AAV DNA in targeted integration.Adeno-associated virus (AAV) is a ubiquitous human virus (∼80% of adults are seropositive [4]); like other nuclear DNA viruses, it causes persistent infections. Productive infection by AAV requires coinfection with either an adenovirus or herpesvirus (1, 21). In cell culture, an AAV latent infection is readily established by infection with a high multiplicity of infection (MOI) (>250 infectious particles/cell) in the absence of a helper virus coinfection, and such latent infections have been reported to persist for over 100 passages (3). Because of the stability of latent infections, it has been possible to clone latently infected cells and to determine the molecular characteristics of the persistent viral genome. More than 65 to 90% of such clones have been determined to have the AAV genome integrated at a specific site on chromosome 19q13.4 (16, 26). The degree of specificity of the integration site is unique among human viruses. Integration is not specific at the nucleotide level, but a specific target sequence has been determined, which includes a binding site for the AAV Rep protein (RBS) and a so-called terminal resolution site (TRS) which is cleaved in one strand by the Rep protein during AAV DNA replication (19). In addition to the target site, which has been termed AAVS1, site-specific integration has been demonstrated to require the AAV rep protein (either Rep 68 or 78) and a sequence in the inverted terminal repeat homologous to AAVS1 (31, 33). A third Rep binding site (RBS) is found in the promoter at map position 5, which has been reported to greatly enhance site-specific integration (24).Although there have been numerous studies of the mechanisms involved in site-specific integration, many aspects remain to be elucidated. In particular, when during the cell cycle site-specific integration occurs is unknown, and the cellular proteins which are involved have not been identified. Such integration might occur as the consequence of nonhomologous end joining (NHEJ) or homologous recombination (HR). Although the former seems to be a more likely pathway, because integration is into a region of very limited homology, the fact that there is some homology between the minimal essential target sequence and the AAV inverted terminal repeat (ITR) suggests that homologous recombination cannot be arbitrarily dismissed as a possibility. Another unknown feature of site-specific integration is the molecular state of the AAV substrate, i.e., whether the substrate is single or double stranded. Transfection of AAV-containing plasmids does lead to site-specific integration (24); thus, a circular form of duplex AAV DNA can serve as the initial substrate, although it has been more challenging to detect significant levels of such integration after transfection with linear duplex AAV DNA (J. Dyall and K. I. Berns, unpublished data).There have been several studies of the fate of AAV vectors used in gene therapy. The studies have been performed primarily in mice and on occasion in vitro. AAV vectors lack the Rep gene and thus do not preferentially integrate into AAVS1 (25). However, random integration at a low frequency, less than 10⁻⁷ (5), does take place and is of concern because of the potential for insertional mutagenesis and the attendant possibility of oncogenesis (20, 22). Such studies have indicated that NHEJ is involved and that different tissues seem to have variable capacities to support integration (14). Other studies have studied recombination between the ITRs at the ends of AAV DNA. Of particular note have been such studies of AAV vectors containing self-complementary genomes (8). These genomes contain complementary sequences separated by an ITR sequence, which itself is a hairpin sequence. Consequently, these genomes can hairpin on themselves to form a duplex structure which contains three hairpinned ITRs, the one in the middle and the two on the ends. The hairpinned ends are substrates for recombination mediated by NHEJ.If NHEJ were involved in AAV integration, either random or site specific, it would seem likely that an animal deficient in a major component of NHEJ would show less evidence of vector integration. The DNA-dependent protein kinase catalytic subunit is an integral component of NHEJ and is the locus of the underlying genetic defect in immunodeficient SCID mice. Song et al. (30) compared AAV integration both in vitro using cell extracts from wild-type C57BL/6 and SCID mice (derived from C57BL/6) and in vivo. The in vitro assay had been developed as an assay for site-specific integration. Interestingly, the presence of a DNA-dependent protein kinase catalytic subunit (DNAPKcs) in the wild-type extract appeared to inhibit AAV integration. The in vivo results were comparable. Hepatectomies were performed on animals 2 weeks after administration of AAV vectors carrying green fluorescent protein (GFP) as the transgene. Approximately 75% of the liver was removed, and regeneration was allowed to take place. In the SCID mice, a significant percentage (greater than 40%) of hepatocytes still expressed GFP, while GFP fluorescence was lower (less than 10%) in the regenerated wild-type livers. These results were interpreted to mean that either integration was more frequent in SCID mice and/or more stable; thus, DNAPKcs was inhibitory to persistent vector integration (which allowed transgene expression).In this paper, we report experiments designed to assess the effects of mutants which lead to defects in NHEJ on site-specific integration by AAV. We have also compared frequency and stability of site-specific integration relative to those of integration at other sites for both AAV containing single-stranded genomes and those with self-complementary genomes.     

Site-Specific Integration of Adeno-Associated Virus into an Episome with the Target Locus via a Deletion-Substitution Mechanism

Five site-specific adeno-associated virus integrants generated in a model system with an Epstein-Barr virus-based shuttle vector have been characterized. The results suggest a deletion-substitution mechanism of recombination.     

Site-Specific Integration in Mammalian Cells Mediated by a New Hybrid Baculovirus–Adeno-Associated Virus Vector

Baculovirus can transiently transduce primary human and rat hepatocytes, as well as a subset of stable cell lines. To prolong transgene expression, we have developed new hybrid vectors which associate key elements from adeno-associated virus (AAV) with the elevated transducing capacity of baculovirus. The hybrid vectors contain a transgene cassette composed of the β-galactosidase (β-Gal) reporter gene and the hygromycin resistance (Hyg^r) gene flanked by the AAV inverted terminal repeats (ITRs), which are necessary for AAV replication and integration in the host genome. Constructs were derived both with and without the AAV rep gene under the p5 and p19 promoters cloned in different positions with respect to the baculovirus polyheidrin promoter. A high-titer preparation of baculovirus-AAV (Bac-AAV) chimeric virus containing the ITR–Hyg^r–β-Gal sequence was obtained with insect cells only when the rep gene was placed in an antisense orientation to the polyheidrin promoter. Infection of 293 cells with Bac-AAV virus expressing the rep gene results in a 10- to 50-fold increase in the number of Hyg^r stable cell clones. Additionally, rep expression determined the localization of the transgene cassette in the aavs1 site in approximately 41% of cases as detected by both Southern blotting and fluorescent in situ hybridization analysis. Moreover, site-specific integration of the ITR-flanked DNA was also detected by PCR amplification of the ITR-aavs1 junction in transduced human fibroblasts. These data indicate that Bac-AAV hybrid vectors can allow permanent, nontoxic gene delivery of DNA constructs for ex vivo treatment of primary human cells.     

营养与病毒感染性疾病动物模型

当前新现病毒性疾病的研究最大的＂瓶颈＂在于没有胜任动物模型。建立在非人灵长类动物基础上的模型,虽然可以部分复制人类疾病特征,但其经济性欠佳且与动物权益的保护有所冲突;而啮齿类动物对新现病毒的易感性往往较低,也不能很好地复制人类疾病。本文对营养、免疫及疾病易感性关系研究的进展进行文献回顾,以发现解决当前难题的线索。     

Adeno-Associated Virus Vector-Mediated Transgene Integration into Neurons and Other Nondividing Cell Targets

The site-specific integration of wild-type adeno-associated virus (wtAAV) into the human genome is a very attractive feature for the development of AAV-based gene therapy vectors. However, knowledge about integration of wtAAV, as well as currently configured recombinant AAV (rAAV) vectors, is limited. By using a modified Alu-PCR technique to amplify and sequence the vector-cellular junctions, we provide the first direct evidence both in vitro and in vivo of rAAV-mediated transgene integration in several types of nondividing cells, including neurons. This novel technique will be highly useful for further delineating the mechanisms underlying AAV-mediated integration, including issues of frequency, site preference, and DNA rearrangement in human as well as animal cells. Results from these studies should be beneficial for the development of the next generation of gene delivery vectors.     

Presence of a trs-Like Motif Promotes Rep-Mediated Wild-Type Adeno-Associated Virus Type 2 Integration

High-throughput integration site (IS) analysis of wild-type adeno-associated virus type 2 (wtAAV2) in human dermal fibroblasts (HDFs) and HeLa cells revealed that juxtaposition of a Rep binding site (RBS) and terminal resolution site (trs)-like motif leads to a 4-fold-increased probability of wtAAV integration. Electrophoretic mobility shift assays (EMSAs) confirmed binding of Rep to off-target RBSs. For the first time, we show Rep protein off-target nicking activity, highlighting the importance of the nicking substrate for Rep-mediated integration.     

乙型肝炎病毒动物模型研究进展

乙型肝炎病毒感染是全球范围影响人类健康的重要问题,慢性感染人群存在肝硬化和肝细胞癌的高患病风险。尽管乙型肝炎病毒疫苗有效,但是在世界范围内慢性感染人数超过了3.5亿,占全球人数的5%。乙型肝炎病毒的生物学研究及新治疗发展进展缓慢是由于缺乏合适的动物模型,每一种动物模型都有其优势和特殊弊端。简要综述了各种动物模型在乙型肝炎病毒研究中的应用进展。     

重组腺相关病毒生产方法研究进展

重组腺相关病毒(rAAV)作为基因治疗的载体,具有感染范围广、能在宿主细胞中长久稳定表达外源基因和非致病性等优点,因此在基因治疗领域倍受青睐。rAAV的大规模制备技术一直是限制其临床广泛应用的瓶颈。近年来,有许多改进rAAV制备工艺的尝试。我们在介绍rAAV载体制备所需各种元件的基础上,对这些方法进行了简要综述。     

Recent Advances in Animal Models of Zika Virus Infection

An infection by Zika virus(ZIKV), a mosquito-borne flavivirus, broke out in South American regions in 2015, and recently showed a tendency of spreading to North America and even worldwide. ZIKV was first detected in 1947 and only 14 human infection cases were reported until 2007. This virus was previously observed to cause only mild flu-like symptoms.However, recent ZIKV infections might be responsible for the increasing cases of neurological disorders such as GuillainBarre′ syndrome and congenital defects, including newborn microcephaly. Therefore, researchers have established several animal models to study ZIKV transmission and pathogenesis, and test therapeutic candidates. This review mainly summarizes the reported animal models of ZIKV infection, including mice and non-human primates.     

Adeno-Associated Virus as a Vector for Liver-Directed Gene Therapy

Factors relevant to the successful application of adeno-associated virus (AAV) vectors for liver-directed gene therapy were evaluated. Vectors with different promoters driving expression of human α-1-antitrypsin (α-1AT) were injected into the portal circulation of immunodeficient mice. α-1AT expression was stable but dependent on the promoter. Southern analysis of liver DNA revealed approximately 0.1 to 2.0 provirus copies/diploid genome in presumed head-to-tail concatamers. In situ hybridization and immunohistochemical analysis revealed expression in approximately 5% of hepatocytes clustered in the pericentral region. These results support the use of AAV as a vector for diseases treatable by targeting of hepatocytes.     

Properties of the Adeno-Associated Virus Assembly-Activating Protein

Adeno-associated virus (AAV) capsid assembly requires expression of the assembly-activating protein (AAP) together with capsid proteins VP1, VP2, and VP3. AAP is encoded by an alternative open reading frame of the cap gene. Sequence analysis and site-directed mutagenesis revealed that AAP contains two hydrophobic domains in the N-terminal part of the molecule that are essential for its assembly-promoting activity. Mutation of these sequences reduced the interaction of AAP with the capsid proteins. Deletions and a point mutation in the capsid protein C terminus also abolished capsid assembly and strongly reduced the interaction with AAP. Interpretation of these observations on a structural basis suggests an interaction of AAP with the VP C terminus, which forms the capsid protein interface at the 2-fold symmetry axis. This interpretation is supported by a decrease in the interaction of monoclonal antibody B1 with VP3 under nondenaturing conditions in the presence of AAP, indicative of steric hindrance of B1 binding to its C-terminal epitope by AAP. In addition, AAP forms high-molecular-weight oligomers and changes the conformation of nonassembled VP molecules as detected by conformation-sensitive monoclonal antibodies A20 and C37. Combined, these observations suggest a possible scaffolding activity of AAP in the AAV capsid assembly reaction.     

In Vitro Packaging of Adeno-Associated Virus DNA

We have developed an in vitro procedure for packaging of recombinant adeno-associated virus (AAV). By using AAV replicative-form DNA as the substrate, it is possible to synthesize an infectious AAV particle in vitro that can be used to transfer a marker gene to mammalian cells. The packaging procedure requires the presence of both the AAV Rep and capsid proteins. Two kinds of in vitro products can be formed which facilitate DNA transfer. Both are resistant to heat and have a density in cesium chloride gradients that is indistinguishable from that of the in vivo-synthesized wild-type virus. This indicates that the particles formed have the appropriate protein-to-DNA ratio and a structure that shares the heat resistance of mature AAV particles. The two types of particles can be distinguished by their sensitivity to chloroform and DNase I treatment. The chloroform-resistant product is, by several criteria, an authentic AAV particle. In addition to having the correct density and being resistant to treatment with chloroform, DNase I, and heat, this particle is efficiently synthesized only if the AAV genome contains intact terminal repeats, which are known to be required for AAV packaging. It is also precipitated by a monoclonal antibody that recognizes mature virus particles but not bound by an antibody that recognizes monomeric or denatured capsid proteins. The chloroform-resistant species is not made when aphidicolin is present in the reaction mixture, suggesting that active DNA replication is required for in vitro packaging. In contrast, the chloroform-sensitive product has several features that suggest it is an incompletely assembled virus particle. It is sensitive to DNase I, does not require the presence of AAV terminal repeats, and is capable of transferring DNA that is theoretically too large to package. Sucrose gradient centrifugation of the in vitro-synthesized products reveals that the particles have sedimentation values between 60S and 110S, which is consistent with partially assembled and mature AAV particles. The in vitro packaging procedure should be useful for studying the mechanism by which a human icosahedral DNA virus particle is assembled, and it may be useful for producing recombinant AAV for gene therapy. The chloroform-sensitive particle may also be useful for transferring DNA that is too large to be packaged in mature recombinant AAV.     

Heavy and Light Particles of Adeno-Associated Virus

KB cells coinfected with adenovirus and adeno-associated virus (AAV) yielded two kinds of infectious AAV particles that banded in CsCl at densities of 1.45 and 1.41 g/cm², respectively. The 1.45 band was found to be composed of a heterogeneous group of viral particles that could be subfractionated by velocity sedimentation. The main component from this band had a smaller S value (109) than the main component from the 1.41 band (111S), although both had the same DNA/protein ratio and the same density in metrizamide gradients. Continuous-label experiments showed that early after infection, both components (1.45 and 1.41) were generated in the same amounts, but this was followed by a relative increase in the proportion of the 1.41 component over the 1.45 particles. Pulse-chase analysis failed to demonstrate a precursor-product relationship between these two bands. The slower-sedimenting components from the 1.45 band were unstable in CsCl and were present in a greater proportion early after infection. These particles contained DNA that was enriched for the terminal sequences of the AAV genomes and was accessible to digestion with micrococcal nuclease.     

慢性支气管炎动物模型研究进展

慢性支气管炎是呼吸系统发病率和死亡率高的一种重要原因,临床和基础研究进展缓慢。吸入烟雾、空气污染物与职业接触慢性刺激传导气道是慢性支气管炎发病的关键因素。近年来虽提出各种各样动物模型,但具实用价值者仍极有限。复制慢性支气管炎动物模型有周期长、个体差异大、检测困难及可靠性差等问题。本文简要介绍烟熏、吸入SO2与气管内滴注脂多糖等最常用的慢性支气管炎动物模型的研究进展。将有益于抗慢性支气管炎药物研究时的更多选择应用。     

Structural Insights into Adeno-Associated Virus Serotype 5

The adeno-associated viruses (AAVs) display differential cell binding, transduction, and antigenic characteristics specified by their capsid viral protein (VP) composition. Toward structure-function annotation, the crystal structure of AAV5, one of the most sequence diverse AAV serotypes, was determined to 3.45-Å resolution. The AAV5 VP and capsid conserve topological features previously described for other AAVs but uniquely differ in the surface-exposed HI loop between βH and βI of the core β-barrel motif and have pronounced conformational differences in two of the AAV surface variable regions (VRs), VR-IV and VR-VII. The HI loop is structurally conserved in other AAVs despite amino acid differences but is smaller in AAV5 due to an amino acid deletion. This HI loop is adjacent to VR-VII, which is largest in AAV5. The VR-IV, which forms the larger outermost finger-like loop contributing to the protrusions surrounding the icosahedral 3-fold axes of the AAVs, is shorter in AAV5, creating a smoother capsid surface topology. The HI loop plays a role in AAV capsid assembly and genome packaging, and VR-IV and VR-VII are associated with transduction and antigenic differences, respectively, between the AAVs. A comparison of interior capsid surface charge and volume of AAV5 to AAV2 and AAV4 showed a higher propensity of acidic residues but similar volumes, consistent with comparable DNA packaging capacities. This structure provided a three-dimensional (3D) template for functional annotation of the AAV5 capsid with respect to regions that confer assembly efficiency, dictate cellular transduction phenotypes, and control antigenicity.