基因编辑动物模型在人类疾病研究中的应用

近年来,随着以CRISPR/Cas9为代表的多种CRISPR系统的开发和不断改进,基因编辑技术逐渐完善,并广泛应用于人类疾病动物模型的制备。基因编辑动物模型为人类疾病的发病机理、病理过程以及预防和治疗等方面的研究提供了重要的素材。目前,用于人类疾病研究的基因编辑动物模型主要有小鼠、大鼠为代表的啮齿类动物模型和以猪为代表的大动物模型。其中啮齿类动物在机体各方面与人类差别较大,且寿命短,无法对人类疾病的研究和治疗提供有效评估和长期追踪;而猪在生理学、解剖学、营养学和遗传学等各方面与人类更接近,是器官移植和人类疾病研究领域重要的动物模型。文中主要介绍了基因编辑动物模型在神经退行性疾病、肥厚心肌病、癌症、免疫缺陷类疾病和代谢性疾病等5种人类疾病研究中的应用情况,以期为人类疾病研究及相关动物模型的制备提供参考。     

基因敲除小鼠在疾病研究中的应用

人类疾病动物模型在揭示人类疾病的发生机制或建立治疗方法中具有极重要的作用。然而,许多疾病难以用人工诱发的方法制造动物模型,还有许多疾病在实验动物身上不发生,而难以通过自发或人工定向培育的方法获得动物模型。基因敲除技术的出现,为人类精确地研究基因与疾病的直接关系提供了可能,而且可以在个体发生的每个阶段中进行遗传功能的分析。综述了基因敲除小鼠模型在几种疾病研究中的研究与应用及其发展前景。     

利用CRISPR-Cas9技术构建基因修饰哺乳动物模型的进展

基因修饰动物模型(genetically modified animal models)是研究个体发育过程和疾病中特定基因功能的一种重要工具,在研究人类疾病发生机制、病理生理和评估新药物、新治疗方法方面有重要应用。哺乳动物因其与人类的相似性而常被用来进行人类疾病研究和药物筛选。然而,传统构建基因修饰动物模型的同源重组等方法不仅需要培养的哺乳动物胚胎干细胞系,而且费时费力。近年来新出现的CRISPR-Cas9基因编辑系统可以在哺乳动物中实现快速、准确的基因定点修饰。该文将介绍CRISPR-Cas9系统在构建基因修饰哺乳动物模型中的应用。     

过敏性哮喘动物模型在致敏、哮喘发作和气道高反应性等方面的应用研究

过敏性哮喘的发病率呈上升趋势。使用了几十年的主要治疗药物肾上腺糖皮质激素副作用较大,因此发现好的预防和治疗方法成为迫切要解决的问题。动物模型是研究人类疾病的重要手段,但不少疑难病的发病机理不明确,因而制备的动物模型和人类疾病的相似度有差异。但I型变态反应作为过敏性哮喘的发病机理是比较明确的,据此制备的动物模型和人类的哮喘就有很高的相近度,结果的可信度就较高。本文回顾了哮喘动物模型制备的基本方法和某些重要的细节。着重讨论了当今最常用的气道高反应性模型的优劣。如果综合运用不同特点的模型尤其是能观察记录哮喘发作全过程包括速发和迟发反应的模型,将可以更直接地探索哮喘发病过程和治疗药物。对气道重塑及基因敲除和转基因技术在动物模型中的研究和使用也做了一般性论述。动物模型将是一个有力的工具为最后有效地预防和治疗过敏性哮喘找到突破口。     

小型猪在肾脏疾病研究中的应用

随着对小型猪研究的不断深入,其作为人类疾病模型的优势日益明显,在生物医学研究中的应用也日趋增多。比较解剖学和生理学研究表明,小型猪的诸多生物学特性均与人类极为相似,尤其在肾脏的解剖和功能方面几乎是人类的复制品,使其在复制肾脏疾病模型,研究疾病发病机制和评估治疗策略等中具有无可替代的作用。本文将综述小型猪作为疾病动物模型在肾脏疾病研究中的应用。     

卵巢癌动物模型制备的研究进展

卵巢癌是导致女性癌症死亡的第五大原因,其中75%的卵巢癌患者检出时即为晚期。目前该病缺乏有效的早期筛查手段,同时临床治疗效果较差,已经成为严重威胁妇女健康的重大疾病。借助卵巢癌动物模型开展相关研究工作,是阐明其发病机制或者筛选有效的诊断、治疗措施的重要手段。目前,按照制备方法分类,该疾病模型主要分为有自发型、诱发型、移植型、基因干预型等四类造模方法。该模型所选择的动物主要有小鼠、大鼠、鸡、东方田鼠、长爪沙鼠等。本文结合近年来的文献报道,综述了卵巢癌动物模型制备方法,并介绍了各种方法制备的动物模型的评价标准及主要特点。     

感染性疾病动物模型-观点与思考

感染性疾病动物模型是以导致感染性疾病的病原感染动物,或人工导入病原遗传物质,使动物发生和人类相同疾病、类似疾病、部分疾病改变或机体对病原产生反应,为疾病系统研究、比较医学研究以及抗病原药物和疫苗等研制、筛选和评价提供的模式动物。目前,国内外没有严格的感染性疾病模型的分类标准,但是,感染性病原动物模型的分类明显不同于一般动物模型的分类,因此,本文建议将感染性疾病动物模型按照病原种类特性以及疾病表现程度进行分类,便于规范化应用。     

结核病动物模型研究进展

结核病是由结核分枝杆菌感染引起的传染病,是危害人类健康的主要传染病之一。动物模型已经成为研究人类传染病的标准化工具。虽然对于结核分枝杆菌而言并没有真正意义的动物资源,但由于不同种类的动物,对分枝杆菌的敏感性不一样,因此可以成为结核病研究的有利工具。结核病最常用的实验动物模型包括小鼠、兔和豚鼠。每种动物有其自身特点,但并不能完全模拟人类疾病。通过建立结核病的动物模型,可以大大增加我们对疾病的病因、毒力和发病机制的理解。除了这三种模型外,非人灵长类也常被用于结核病的研究。本文总结了这几种结核病模型的研究状况。     

显微注射法制备遗传工程小鼠模型的研究

遗传工程小鼠模型是基因功能、人类疾病发病机制及新药研究开发的最重要的模式生物之一。在建立遗传工程小鼠模型的众多方法中,显微注射法是目前国际上公认的制备转基因及基因剔除动物模型的首选。在进行了大量显微注射工作后,简要介绍建立遗传工程小鼠模型的基本技术与方法,并对在显微操作过程中较为关键的因素进行一些分析和讨论。     

运用系统论原理复制人类疾病动物模型

依据系统论的基本原理,人类疾病动物模型采用整体设计,统筹考虑模型与实验动物生物学特性方面的相似性、模型复制的重复性、可靠性、适用性、可控性、易行性和经济性等,以便模型复制的顺利开展。整体性原则应贯穿整个模型复制过程,使复制的模型具有科学性和实用性。模型复制要落实系统论的相关性原则,一个模型不是孤立的,动物的各系统、各器官、各分子之间是相互联系,人类和动物在生物学、解剖学、组织学、胚胎学、生理学、病理学等方面的相互联系,疾病的发生、发展是相互联系的,相关性原则为动物模型研究人类疾病提供了理论依据。动物模型在时间和空间上处于不断运动变化发展之中,在研究模型的过程中,要用动态的方法而不是静止的方法来研究动物模型,应根据疾病的特点,分成不同的阶段,结合动物的免疫功能、营养状况、疾病的发展、转归等采用不同的对策。模型的复制采用最优化原则,要求模型设计最优化,选用高质量的实验动物,减少动物使用数量,保护动物福利与伦理,最终实现模型评价体系的最优化。     

Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR

Relative quantification in quantitative real-time RT-PCR is increasingly used to quantify gene expression changes. In general, two different relative mRNA quantification models exist: the delta-delta Ct and the efficiency-corrected Ct model. Both models have their advantages and disadvantages in terms of simplification on the one hand and efficiency correction on the other. The particular problem of RNA integrity and its effect on relative quantification in qRT-PCR performance was tested in different bovine tissues and cell lines (n = 11). Therefore different artificial and standardized RNA degradation levels were used. Currently fully automated capillary electrophoresis systems have become the new standard in RNA quality assessment. RNA quality was rated according the RNA integrity number (RIN). Furthermore, the effect of different length of amplified products and RNA integrity on expression analyses was investigated. We found significant impact of RNA integrity on relative expression results, mainly on cycle threshold (Ct) values and a minor effect on PCR efficiency. To minimize the interference of RNA integrity on relative quantification models, we can recommend to normalize gene expression by an internal reference gene and to perform an efficiency correction. Results demonstrate that innovative new quantification methods and normalization models can improve future mRNA quantification.     

Estimation of the reaction efficiency in polymerase chain reaction

Polymerase chain reaction (PCR) is largely used in molecular biology for increasing the copy number of a specific DNA fragment. The succession of 20 replication cycles makes it possible to multiply the quantity of the fragment of interest by a factor of 1 million. The PCR technique has revolutionized genomics research. Several quantification methodologies are available to determine the DNA replication efficiency of the reaction which is the probability of replication of a DNA molecule at a replication cycle. We elaborate a quantification procedure based on the exponential phase and the early saturation phase of PCR. The reaction efficiency is supposed to be constant in the exponential phase, and decreasing in the saturation phase. We propose to model the PCR amplification process by a branching process which starts as a Galton-Watson branching process followed by a size-dependent process. Using this stochastic modelling and the conditional least-squares estimation method, we infer the reaction efficiency from a single PCR trajectory.     

MIQuant--semi-automation of infarct size assessment in models of cardiac ischemic injury

Background

The cardiac regenerative potential of newly developed therapies is traditionally evaluated in rodent models of surgically induced myocardial ischemia. A generally accepted key parameter for determining the success of the applied therapy is the infarct size. Although regarded as a gold standard method for infarct size estimation in heart ischemia, histological planimetry is time-consuming and highly variable amongst studies. The purpose of this work is to contribute towards the standardization and simplification of infarct size assessment by providing free access to a novel semi-automated software tool. The acronym MIQuant was attributed to this application.

Methodology/Principal Findings

Mice were subject to permanent coronary artery ligation and the size of chronic infarcts was estimated by area and midline-length methods using manual planimetry and with MIQuant. Repeatability and reproducibility of MIQuant scores were verified. The validation showed high correlation (r ^{midline length} = 0.981; r ^area = 0.970 ) and agreement (Bland-Altman analysis), free from bias for midline length and negligible bias of 1.21% to 3.72% for area quantification. Further analysis demonstrated that MIQuant reduced by 4.5-fold the time spent on the analysis and, importantly, MIQuant effectiveness is independent of user proficiency. The results indicate that MIQuant can be regarded as a better alternative to manual measurement.

Conclusions

We conclude that MIQuant is a reliable and an easy-to-use software for infarct size quantification. The widespread use of MIQuant will contribute towards the standardization of infarct size assessment across studies and, therefore, to the systematization of the evaluation of cardiac regenerative potential of emerging therapies.     

Mucosal transmission and induction of simian AIDS by CCR5-specific simian/human immunodeficiency virus SHIV(SF162P3)

Nonhuman primate models are increasingly used in the screening of candidate AIDS vaccine and immunization strategies for advancement to large-scale human trials. The predictive value of such macaque studies is largely dependent upon the fidelity of the model system in mimicking human immunodeficiency virus (HIV) type 1 infection in terms of viral transmission, replication, and pathogenesis. Herein, we describe the efficient mucosal transmission of a CCR5-specific chimeric simian/human immunodeficiency virus, SHIV(SF162P3). Female rhesus macaques were infected with SHIV(SF162P3) after a single atraumatic application to the cervicovaginal mucosa. The disease course of SHIV(SF162P3)-infected monkeys is similar and as varied as natural HIV infection in terms of viral replication, gradual loss of CD4(+) peripheral blood mononuclear cells, and the development of simian AIDS-defining opportunistic infections. The SHIV(SF162P3)/macaque model should facilitate direct preclinical assessment of HIV vaccine strategies in addition to antiviral compounds directed towards envelope target cell interactions. Furthermore, this controlled model provides the setting to investigate immunologic responses and putative host-specific susceptibility factors that alter viral transmission and subsequent disease progression.     

Human Liver Infection in a Dish: Easy-To-Build 3D Liver Models for Studying Microbial Infection

Human liver infection is a major cause of death worldwide, but fundamental studies on infectious diseases affecting humans have been hampered by the lack of robust experimental models that accurately reproduce pathogen-host interactions in an environment relevant for the human disease. In the case of liver infection, one consequence of this absence of relevant models is a lack of understanding of how pathogens cross the sinusoidal endothelial barrier and parenchyma. To fill that gap we elaborated human 3D liver in vitro models, composed of human liver sinusoidal endothelial cells (LSEC) and Huh-7 hepatoma cells as hepatocyte model, layered in a structure mimicking the hepatic sinusoid, which enable studies of key features of early steps of hepatic infection. Built with established cell lines and scaffold, these models provide a reproducible and easy-to-build cell culture approach of reduced complexity compared to animal models, while preserving higher physiological relevance compared to standard 2D systems. For proof-of-principle we challenged the models with two hepatotropic pathogens: the parasitic amoeba Entamoeba histolytica and hepatitis B virus (HBV). We constructed four distinct setups dedicated to investigating specific aspects of hepatic invasion: 1) pathogen 3D migration towards hepatocytes, 2) hepatocyte barrier crossing, 3) LSEC and subsequent hepatocyte crossing, and 4) quantification of human hepatic virus replication (HBV). Our methods comprise automated quantification of E. histolytica migration and hepatic cells layer crossing in the 3D liver models. Moreover, replication of HBV virus occurs in our virus infection 3D liver model, indicating that routine in vitro assays using HBV or others viruses can be performed in this easy-to-build but more physiological hepatic environment. These results illustrate that our new 3D liver infection models are simple but effective, enabling new investigations on infectious disease mechanisms. The better understanding of these mechanisms in a human-relevant environment could aid the discovery of drugs against pathogenic liver infection.     

The effect of replicate number and image analysis method on sweetpotato [Ipomoea batatas (L.) Lam.] cDNA microarray results

Microarray analysis makes it possible to determine the relative expression of thousands of genes simultaneously. It has gained popularity at a rapid rate, but many caveats remain. In an effort to establish reliable microarray protocols for sweetpotato [Ipomoea batatas (L.) Lam.], we compared the effect of replication number and image analysis software with results obtained by quantitative rela-time PCR (Q-RT-PCR). Sweetpotato storage root development is the most economically important process in sweetpotato. In order to identify genes that may play a role in this process, RNA for microarray analysis was extracted from sweetpotato fibrous and storage roots. Four data sets, Spot4, Spot6, Finder4 and Finder6, were created using 4 or 6 replications, and the image analysis software of UCSF Spot or TIGR Spotfinder were used for spot detection and quantification. The ability of these methods to identify significant differential expression between treatments was investigated. The data sets with 6 replications were better at identifying genes with significant differential expression than the ones of 4 replications. Furthermore when using 6 replicates, UCSF Spot was superior to TIGR Spotfinder in identifying genes differentially expressed (18 out of 19) based on Q-RT-PCR. Our study shows the importance of proper replication number and image analysis for microarray studies.     

An approach for quantitative assessment of fluorescence in situ hybridization (FISH) signals for applied human molecular cytogenetics.

A number of applied molecular cytogenetic studies require the quantitative assessment of fluorescence in situ hybridization (FISH) signals (for example, interphase FISH analysis of aneuploidy by chromosome enumeration DNA probes; analysis of somatic pairing of homologous chromosomes in interphase nuclei; identification of chromosomal heteromorphism after FISH with satellite DNA probes for differentiation of parental origin of homologous chromosome, etc.). We have performed a pilot study to develop a simple technique for quantitative assessment of FISH signals by means of the digital capturing of microscopic images and the intensity measuring of hybridization signals using Scion Image software, commonly used for quantification of electrophoresis gels. We have tested this approach by quantitative analysis of FISH signals after application of chromosome-specific DNA probes for aneuploidy scoring in interphase nuclei in cells of different human tissues. This approach allowed us to exclude or confirm a low-level mosaic form of aneuploidy by quantification of FISH signals (for example, discrimination of pseudo-monosomy and artifact signals due to over-position of hybridization signals). Quantification of FISH signals was also used for analysis of somatic pairing of homologous chromosomes in nuclei of postmortem brain tissues after FISH with "classical" satellite DNA probes for chromosomes 1, 9, and 16. This approach has shown a relatively high efficiency for the quantitative registration of chromosomal heteromorphism due to variations of centromeric alphoid DNA in homologous parental chromosomes. We propose this approach to be efficient and to be considered as a useful tool in addition to visual FISH signal analysis for applied molecular cytogenetic studies.     

Modeling Within-Host Evolution of HIV: Mutation,Competition and Strain Replacement

Virus evolution during infection of a single individual is a well-known feature of disease progression in chronic viral diseases. However, the simplest models of virus competition for host resources show the existence of a single dominant strain that grows most rapidly during the initial period of infection and competitively excludes all other virus strains. Here, we examine the dynamics of strain replacement in a simple model that includes a convex trade-off between rapid virus reproduction and long-term host cell survival. Strains are structured according to their within-cell replication rate. Over the course of infection, we find a progression in the dominant strain from fast- to moderately-replicating virus strains featuring distinct jumps in the replication rate of the dominant strain over time. We completely analyze the model and provide estimates for the replication rate of the initial dominant strain and its successors. Our model lays the groundwork for more detailed models of HIV selection and mutation. We outline future directions and application of related models to other biological situations.     

MetGEMs Toolbox: Metagenome-scale models as integrative toolbox for uncovering metabolic functions and routes of human gut microbiome

Investigating metabolic functional capability of a human gut microbiome enables the quantification of microbiome changes, which can cause a phenotypic change of host physiology and disease. One possible way to estimate the functional capability of a microbial community is through inferring metagenomic content from 16S rRNA gene sequences. Genome-scale models (GEMs) can be used as scaffold for functional estimation analysis at a systematic level, however up to date, there is no integrative toolbox based on GEMs for uncovering metabolic functions. Here, we developed the MetGEMs (metagenome-scale models) toolbox, an open-source application for inferring metabolic functions from 16S rRNA gene sequences to facilitate the study of the human gut microbiome by the wider scientific community. The developed toolbox was validated using shotgun metagenomic data and shown to be superior in predicting functional composition in human clinical samples compared to existing state-of-the-art tools. Therefore, the MetGEMs toolbox was subsequently applied for annotating putative enzyme functions and metabolic routes related in human disease using atopic dermatitis as a case study.