Engineering and Evolution of Synthetic Adeno-Associated Virus (AAV) Gene Therapy Vectors via DNA Family Shuffling

Adeno-associated viral (AAV) vectors represent some of the most potent and promising vehicles for therapeutic human gene transfer due to a unique combination of beneficial properties¹. These include the apathogenicity of the underlying wildtype viruses and the highly advanced methodologies for production of high-titer, high-purity and clinical-grade recombinant vectors². A further particular advantage of the AAV system over other viruses is the availability of a wealth of naturally occurring serotypes which differ in essential properties yet can all be easily engineered as vectors using a common protocol^1,2. Moreover, a number of groups including our own have recently devised strategies to use these natural viruses as templates for the creation of synthetic vectors which either combine the assets of multiple input serotypes, or which enhance the properties of a single isolate. The respective technologies to achieve these goals are either DNA family shuffling³, i.e. fragmentation of various AAV capsid genes followed by their re-assembly based on partial homologies (typically >80% for most AAV serotypes), or peptide display^4,5, i.e. insertion of usually seven amino acids into an exposed loop of the viral capsid where the peptide ideally mediates re-targeting to a desired cell type. For maximum success, both methods are applied in a high-throughput fashion whereby the protocols are up-scaled to yield libraries of around one million distinct capsid variants. Each clone is then comprised of a unique combination of numerous parental viruses (DNA shuffling approach) or contains a distinctive peptide within the same viral backbone (peptide display approach). The subsequent final step is iterative selection of such a library on target cells in order to enrich for individual capsids fulfilling most or ideally all requirements of the selection process. The latter preferably combines positive pressure, such as growth on a certain cell type of interest, with negative selection, for instance elimination of all capsids reacting with anti-AAV antibodies. This combination increases chances that synthetic capsids surviving the selection match the needs of the given application in a manner that would probably not have been found in any naturally occurring AAV isolate. Here, we focus on the DNA family shuffling method as the theoretically and experimentally more challenging of the two technologies. We describe and demonstrate all essential steps for the generation and selection of shuffled AAV libraries (Fig. 1), and then discuss the pitfalls and critical aspects of the protocols that one needs to be aware of in order to succeed with molecular AAV evolution.     

Production,Processing, and Characterization of Synthetic AAV Gene Therapy Vectors

Over the last two decades, gene therapy vectors based on wild-type Adeno-associated viruses (AAV) are safe and efficacious in numerous clinical trials and are translated into three approved gene therapy products. Concomitantly, a large body of preclinical work has illustrated the power and potential of engineered synthetic AAV capsids that often excel in terms of an organ or cell specificity, the efficiency of in vitro or in vivo gene transfer, and/or reactivity with anti-AAV immune responses. In turn, this has created a demand for new, scalable, easy-to-implement, and plug-and-play platform processes that are compatible with the rapidly increasing range of AAV capsid variants. Here, the focus is on recent advances in methodologies for downstream processing and characterization of natural or synthetic AAV vectors, comprising different chromatography techniques and thermostability measurements. To illustrate the breadth of this portfolio, two chimeric capsids are used as representative examples that are derived through forward- or backwards-directed molecular evolution, namely, AAV-DJ and Anc80. Collectively, this ever-expanding arsenal of technologies promises to facilitate the development of the next AAV vector generation derived from synthetic capsids and to accelerate their manufacturing, and to thus boost the field of human gene therapy.     

基因治疗载体及其基因转移技术的关键问题与研究现状

目前使用的基因治疗载体及其基因转移技术中还没有一种能用于临床并永久有效的基因转移技术 .该文分析了直接体内转移、间接体内转移及其非载体法、病毒载体法、非病毒性生物载体法等基因治疗转移技术存在的一些关键问题 ,并探讨了各问题的解决办法或研究策略以及基因治疗载体研究的发展方向     

人BRCA1 干涉慢病毒载体的构建与验证

目的:设计合成干涉BRCA1表达的小干扰RNA,并克隆入pLKO.1慢病毒表达载体,为研究基因BRCA1在乳腺癌细胞增殖中的作用提供基础。方法:根据人BRCA1的基因序列,设计合成三对BRCA1干涉片段(序列前后加入酶切位点EcoRI和AgeI),再利用酶切连接反应将其插入到慢病毒载体pLKO.1中,经过酶切鉴定及测序正确后,将重组质粒转染入MCF-7细胞,48h后提取蛋白质和RNA,通过蛋白印迹验证BRCA1的蛋白水平的表达情况,Realtime PCR验证BRCA1的RNA水平的表达变化。结果:重组质粒经酶切鉴定和测序比对完全正确,转染乳腺癌细胞48h后可见BRCA1表达的明显下调。结论:成功构建BRCA1干涉的慢病毒载体,并且转染MCF-7细胞证实其能够下调BRCA1的表达,为后续研究BRCA1在乳腺癌细胞的功能奠定了基础。     

人肾脏相关基因Nox4过表达慢病毒载体的构建与定位检测

目的:克隆Nox4基因入pLenti6.3慢病毒表达载体,为探索Nox4基因在ROS产生中的作用提供实验基础。方法:根据NCBI人Nox4 mRNA序列设计引物,再利用酶切连接反应将Nox4插入到入门载体pENTR3C中,成功构建pENTR3C-Nox4后,通过LR反应,将Nox4和EGFP tag插入到慢病毒表达载体pLenti6.3中,经酶切和测序验证正确后,将重组表达质粒转染入人Hela细胞,通过Western-Blot验证Nox4的表达情况,免疫荧光验证Nox4在细胞内的定位情况。结果:入门载体及表达质粒测序比对完全正确,转染Hela细胞后可见明显的表达条带,并且主要定位于细胞器内质网中。结论:成功构建了带有EGFP tag的Nox4基因慢病毒重组表达载体,转染Hela细胞后,其能正确表达并定位于内质网中,为研究Nox4在调节ROS产生中的作用奠定了基础。     

羊痘病毒P32基因真核表达载体的构建、表达及其免疫原性

通过PCR方法扩增全长P32基因和截去跨膜区的P32基因(MP32),将其分别克隆到真核表达载体pcDNA3.1( )和已插入CpG序列的pcDNA3.1-CpG中,构建pcDNA3.1-P32、pcDNA3.1-CpG-P32和pcDNA3.1-CpG-MP32质粒;用脂质体法转染BHK-21细胞,通过间接免疫荧光(IFA)试验验证其表达效果;经肌肉免疫注射健康BALB/c小鼠,用间接ELISA法检测抗体;在免疫后的第3、5周取免疫小鼠的脾细胞,用流式细胞仪检测CD4 和CD8 T细胞亚群.结果所构建的真核表达载体在BHK-21细胞中都能表达P32蛋白;免疫小鼠血清在免疫第2周后均能检测到羊痘特异性IgG抗体;免疫组小鼠脾脏CD4 T细胞数目和CD4 /CD8 T细胞比值明显高于对照组.结果提示,所构建的真核载体可诱导小鼠产生特异性体液免疫应答,并能刺激小鼠产生较强的细胞免疫应答.     

人类人工染色体构建及其作为基因治疗载体的价值

人类人工染色体(HAC)作为基因治疗载体将解决基因治疗存在的一些关键问题。本文探讨了在不完全了解着丝粒、复制起始点、端粒等人类染色体基本功能单位的情况下构建HAC的三种策略。利用染色体基本功能单位在细胞内构建成功的第一代HAC,解决了HAC构建的一些难题,同时也带来了某些新的问题。HAC作为基因治疗载体具有很多优势,但第一代HAC离它作为基因治疗载体还相距很远。为此,作者正在进行解决这些问题的尝试。     

Recombinant Baculovirus as a Highly Potent Vector for Gene Therapy of Human Colorectal Carcinoma: Molecular Cloning,Expression, and In Vitro Characterization

Present therapeutic strategies for most cancers are restricted mainly to the primary tumors and are also not very effective in controlling metastatic states. Alternatively, gene therapy can be a potential option for treating such cancers. Currently mammalian viral-based cancer gene therapy is the most popular approach, but the efficacy has been shown to be quite low in clinical trials. In this study, for the first time, the insect cell-specific baculovirus Autographa californica multiple nucleopolyhedrovirus (AcMNPV) has been evaluated as a vector for gene delivery to colorectal cancer cells. Experiments involving factorial design were employed to study the individual and combined effects of different parameters such as multiplicity of infection (MOI), viral incubation time and epigenetic factors on transduction efficiency. The results demonstrate that baculovirus gene delivery system holds immense potential for development of a new generation of highly effective virotherapy for colorectal, as well as other major carcinomas (breast, pancreas, and brain), and offers significant benefits to traditional animal virus-based vectors with respect to safety concerns.     

Development of a quantitative mass spectrometry multi-attribute method for characterization,quality control testing and disposition of biologics

Regulatory agencies have recently recommended a Quality by Design (QbD) approach for the manufacturing of therapeutic molecules. A QbD strategy requires deep understanding at the molecular level of the attributes that are crucial for safety and efficacy and for insuring that the desired quality of the purified protein drug product is met at the end of the manufacturing process. A mass spectrometry (MS)-based approach to simultaneously monitor the extensive array of product quality attributes (PQAs) present on therapeutic molecules has been developed. This multi-attribute method (MAM) uses a combination of high mass accuracy / high resolution MS data generated by Orbitrap technology and automated identification and relative quantification of PQAs with dedicated software (Pinpoint). The MAM has the potential to replace several conventional electrophoretic and chromatographic methods currently used in Quality Control to release therapeutic molecules. The MAM represents an optimized analytical solution to focus on the attributes of the therapeutic molecule essential for function and implement QbD principles across process development, manufacturing and drug disposition.     

Comparison of mechanistic and hybrid modeling approaches for characterization of a CHO cultivation process: Requirements,pitfalls and solution paths

Despite the advantages of mathematical bioprocess modeling, successful model implementation already starts with experimental planning and accordingly can fail at this early stage. For this study, two different modeling approaches (mechanistic and hybrid) based on a four-dimensional antibody-producing CHO fed-batch process are compared. Overall, 33 experiments are performed in the fractional factorial four-dimensional design space and separated into four different complex data partitions subsequently used for model comparison and evaluation. The mechanistic model demonstrates the advantage of prior knowledge (i.e., known equations) to get informative value relatively independently of the utilized data partition. The hybrid approach displayes a higher data dependency but simultaneously yielded a higher accuracy on all data partitions. Furthermore, our results demonstrate that independent of the chosen modeling framework, a smart selection of only four initial experiments can already yield a very good representation of a full design space independent of the chosen modeling structure. Academic and industry researchers are recommended to pay more attention to experimental planning to maximize the process understanding obtained from mathematical modeling.     

PTMiner: Localization and Quality Control of Protein Modifications Detected in an Open Search and Its Application to Comprehensive Post-translational Modification Characterization in Human Proteome,

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Highlights

• •PTMiner software for intelligent post-processing of open-search results.
• •Unrestrictive modification site localization based on a Bayesian model.
• •Extended transfer FDR estimation for accurate grouped FDR estimation.
• •Comprehensive PTM characterization in a draft map of human proteome.

     

人乳头瘤病毒16L1-减毒志贺氏杆菌为载体疫苗的构建及免疫效应初步鉴定

为预防高危型人乳头瘤病毒16型(HPV16)诱发宫颈癌,制备以减毒志贺氏杆菌为载体的HPV16预防疫苗,以期载体可介导机体产生粘膜免疫反应,达到预防HPVl6感染的目的。为此构建了以HPV16L1为免疫原的减毒志贺氏杆菌苗,并初步鉴定候选疫苗的减毒特性和免疫效果。利用基于志贺氏杆菌virG／icsA基因的表达载体(pHS3199),将HPV16L1基因插入后构成pHS3199-hpv16L1质粒,电穿孔法将其转入减毒志贺氏杆菌sh42,经筛选获得重组减毒sh42-HPV16L1工程菌。用免疫印迹法检测HPV16L1蛋白表达,连续传代法确定其传代和目的蛋白表达的稳定性;豚鼠角膜巩膜炎症试验检测细菌的毒力和菌苗的免疫效果;小鼠红细胞凝集抑制试验检测免疫血清对病毒样颗粒(VLP)的中和活性。免疫印迹检测证实,重组菌株sh42-HPV16L1可稳定表达HPV16L1;豚鼠角膜巩膜炎症试验证实,该候选菌苗无致病性。减毒sh42-HPV16L1经结膜囊途径免疫豚鼠,可以产生特异性体液免疫应答,免疫动物体内的血清、肠道、阴道分泌物中抗HPV16L1 VLPIgG、IgA含量显著高于对照组,并且sh42-HPV16L1免疫动物血清可明显抑制HPV16L1 VLP引起的小鼠红细胞凝集。因而sh42-HPV16L1将是一种潜在的HPV16候选预防疫苗。