The Mechanism of Gene Targeting in Human Somatic Cells

Gene targeting in human somatic cells is of importance because it can be used to either delineate the loss-of-function phenotype of a gene or correct a mutated gene back to wild-type. Both of these outcomes require a form of DNA double-strand break (DSB) repair known as homologous recombination (HR). The mechanism of HR leading to gene targeting, however, is not well understood in human cells. Here, we demonstrate that a two-end, ends-out HR intermediate is valid for human gene targeting. Furthermore, the resolution step of this intermediate occurs via the classic DSB repair model of HR while synthesis-dependent strand annealing and Holliday Junction dissolution are, at best, minor pathways. Moreover, and in contrast to other systems, the positions of Holliday Junction resolution are evenly distributed along the homology arms of the targeting vector. Most unexpectedly, we demonstrate that when a meganuclease is used to introduce a chromosomal DSB to augment gene targeting, the mechanism of gene targeting is inverted to an ends-in process. Finally, we demonstrate that the anti-recombination activity of mismatch repair is a significant impediment to gene targeting. These observations significantly advance our understanding of HR and gene targeting in human cells.     

Shared Gene Regulation during Human Somatic Cell Reprogramming

Human induced pluripotent stem(iPS)cells have the ability to differentiate into all somatic cells and to maintain unlimited selfrenewal. Therefore,they have great potential in both basic research and clinical therapy for many diseases.To identify potentially universal mechanisms of human somatic cell reprogramming,we studied gene expression changes in three types of cells undergoing reprogramming.The set of 570 genes commonly regulated during induction of iPS cells includes known embryonic stem(ES)cell markers and pluripotency related genes.We also identified novel genes and biological categories which may be related to somatic cell reprogramming.For example,some of the down-regulated genes are predicted targets of the pluripotency microRNA cluster miR302/367, and the proteins from these putative target genes interact with the stem cell pluripotency factor POU5F1 according to our network analysis.Our results identified candidate gene sets to guide research on the mechanisms operating during somatic cell reprogramming.     

Human Somatic Cell Nuclear Transfer Using Adult Cells

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人TNFAIP1 基因在常见细胞系中的表达

TNFAIP1蛋白是第一个被鉴定受肿瘤坏死因子α诱导的蛋白,TNFAIP1 蛋白可能参与DNA复制、合成、细胞凋亡以及人类各种疾病的发生等重要过程,但对该基因确切功能和作用机制研究不多.该文利用实时定量PCR的方法检测该基因在几种常见细胞系的表达情况,发现在COS7以及NIH3T3细胞系中高表达,而在HeLa、HepG2、SW480、PanC1、MCF7等癌细胞系中低表达.由此推测TNFAIP1可能在癌症的发生中起到一定的作用.如果把TNFAIP1 基因克隆到真核表达载体pCMV-Myc中,转染到HeLa细胞系中,发现过表达TNFAIP1 可促进HeLa细胞的凋亡.     

Increased Gene Targeting in Ku70 and Xrcc4 Transiently Deficient Human Somatic Cells

The insertion of foreign DNA at a specific genomic locus directed by homologous DNA sequences, or gene targeting, is an inefficient process in mammalian somatic cells. Given the key role of non-homologous end joining (NHEJ) pathway in DNA double-strand break (DSB) repair in mammalian cells, we investigated the effects of decreasing NHEJ protein levels on gene targeting. Here we demonstrate that the transient knockdown of integral NHEJ proteins, Ku70 and Xrcc4, by RNAi in human HCT116 cells has a remarkable effect on gene targeting/random insertions ratios. A timely transfection of an HPRT-based targeting vector after RNAi treatment led to a 70% reduction in random integration events and a 33-fold increase in gene targeting at the HPRT locus. These findings bolster the role of NHEJ proteins in foreign DNA integration in vivo, and demonstrate that their transient depletion by RNAi is a viable approach to increase the frequency of gene targeting events. Understanding how foreign DNA integrates into a cell’s genome is important to advance strategies for biotechnology and genetic medicine.     

Improved Genome Editing in Human Cell Lines Using the CRISPR Method

The Cas9/CRISPR system has become a popular choice for genome editing. In this system, binding of a single guide (sg) RNA to a cognate genomic sequence enables the Cas9 nuclease to induce a double-strand break at that locus. This break is next repaired by an error-prone mechanism, leading to mutation and gene disruption. In this study we describe a range of refinements of the method, including stable cell lines expressing Cas9, and a PCR based protocol for the generation of the sgRNA. We also describe a simple methodology that allows both elimination of Cas9 from cells after gene disruption and re-introduction of the disrupted gene. This advance enables easy assessment of the off target effects associated with gene disruption, as well as phenotype-based structure-function analysis. In our study, we used the Fan1 DNA repair gene as control in these experiments. Cas9/CRISPR-mediated Fan1 disruption occurred at frequencies of around 29%, and resulted in the anticipated spectrum of genotoxin hypersensitivity, which was rescued by re-introduction of Fan1.     

体细胞基因打靶-核移植技术研究进展

转基因效率与外源基因表达水平低的现状一直是制约动物生物反应器研究与产业化的主要技术瓶颈。体细胞克隆动物的成功和胚胎干细胞基因打靶技术的逐步完善使得体细胞基因打靶与核移植技术的结合使用成为可能,这就为生产遗传修饰家畜提供了一种新的手段,为动物生物反应器的成功研制提供了新的技术途径。从体细胞基因打靶的载体设计、转染系统的建立、中靶细胞的筛选和鉴定以及培养体细胞寿命等方面阐述了体细胞基因打靶—核移植技术体系的最新研究进展,并对其在异种器官移植、建立动物疾病模型、提高家畜生长性能以及生产药用蛋白等各个领域中的应用前景作了展望 。     

Tracking and Predicting Human Somatic Cell Reprogramming Using Nuclear Characteristics

Reprogramming of human somatic cells to induced pluripotent stem cells (iPSCs) generates valuable resources for disease modeling, toxicology, cell therapy, and regenerative medicine. However, the reprogramming process can be stochastic and inefficient, creating many partially reprogrammed intermediates and non-reprogrammed cells in addition to fully reprogrammed iPSCs. Much of the work to identify, evaluate, and enrich for iPSCs during reprogramming relies on methods that fix, destroy, or singularize cell cultures, thereby disrupting each cell’s microenvironment. Here, we develop a micropatterned substrate that allows for dynamic live-cell microscopy of hundreds of cell subpopulations undergoing reprogramming while preserving many of the biophysical and biochemical cues within the cells’ microenvironment. On this substrate, we were able to both watch and physically confine cells into discrete islands during the reprogramming of human somatic cells from skin biopsies and blood draws obtained from healthy donors. Using high-content analysis, we identified a combination of eight nuclear characteristics that can be used to generate a computational model to predict the progression of reprogramming and distinguish partially reprogrammed cells from those that are fully reprogrammed. This approach to track reprogramming in situ using micropatterned substrates could aid in biomanufacturing of therapeutically relevant iPSCs and be used to elucidate multiscale cellular changes (cell-cell interactions as well as subcellular changes) that accompany human cell fate transitions.     

Restoration of Mismatch Repair Functions in Human Cell Line Nalm-6, Which Has High Efficiency for Gene Targeting

Gene targeting is a powerful approach in reverse genetics. The approach has been hampered in most of human cell lines, however, by the poor targeting efficiency. Nalm-6, a human pre-B acute lymphoblastic leukemia cell line, exhibits exceptionally high gene targeting efficiency and is used in DNA repair and the related research fields. Nonetheless, usage of the cell line is still limited partly because it lacks expression of MSH2, a component of mismatch repair complex, which leads to increased genome instability. Here, we report successful restoration of MSH2 expression in Nalm-6 cells and demonstrate that the recovery does not affect the high targeting efficiency. We recovered the expression by introduction of cDNA sequences corresponding to exons 9 to 16 at downstream of exon 8 of the MSH2 gene. Endogenous exons 9 to 16 were deleted in the cell line. The MSH2 expression substantially reduced spontaneous HPRT mutation frequency. Moreover, gene targeting efficiency in the MSH2-expressing cells was similar to that in the MSH2-lacking cells. In fact, we generated heterozygously REV3L knockout and the catalytically dead mutants in the MSH2-proficient Nalm-6 cells with efficiency of 20–30%. The established cell line, Nalm-6-MSH+, is useful for reverse genetics in human cells.     

Identification of Human Embryonic Progenitor Cell Targeting Peptides Using Phage Display

Human pluripotent stem (hPS) cells are capable of differentiation into derivatives of all three primary embryonic germ layers and can self-renew indefinitely. They therefore offer a potentially scalable source of replacement cells to treat a variety of degenerative diseases. The ability to reprogram adult cells to induced pluripotent stem (iPS) cells has now enabled the possibility of patient-specific hPS cells as a source of cells for disease modeling, drug discovery, and potentially, cell replacement therapies. While reprogramming technology has dramatically increased the availability of normal and diseased hPS cell lines for basic research, a major bottleneck is the critical unmet need for more efficient methods of deriving well-defined cell populations from hPS cells. Phage display is a powerful method for selecting affinity ligands that could be used for identifying and potentially purifying a variety of cell types derived from hPS cells. However, identification of specific progenitor cell-binding peptides using phage display may be hindered by the large cellular heterogeneity present in differentiating hPS cell populations. We therefore tested the hypothesis that peptides selected for their ability to bind a clonal cell line derived from hPS cells would bind early progenitor cell types emerging from differentiating hPS cells. The human embryonic stem (hES) cell-derived embryonic progenitor cell line, W10, was used and cell-targeting peptides were identified. Competition studies demonstrated specificity of peptide binding to the target cell surface. Efficient peptide targeted cell labeling was accomplished using multivalent peptide-quantum dot complexes as detected by fluorescence microscopy and flow cytometry. The cell-binding peptides were selective for differentiated hPS cells, had little or no binding on pluripotent cells, but preferential binding to certain embryonic progenitor cell lines and early endodermal hPS cell derivatives. Taken together these data suggest that selection of phage display libraries against a clonal progenitor stem cell population can be used to identify progenitor stem cell targeting peptides. The peptides may be useful for monitoring hPS cell differentiation and for the development of cell enrichment procedures to improve the efficiency of directed differentiation toward clinically relevant human cell types.     

植物基因打靶效率的研究进展

基因打靶技术是将外源DNA定向整合入基因组中对特定基因进行精确修饰,从而改变生物遗传性状的技术。它在特定基因功能研究、遗传育种和生理机制的理解方面有着重要意义,但植物中较低的基因打靶效率制约着它的进一步推广和应用。本文着重从载体构建、筛选策略、受体细胞状态等方面对打靶效率的提高进行分析,并介绍同源重组酶系、锌指核酶和寡核苷酸技术在基因打靶中的应用。     

Targeting and Processing of Pro-Opiomelanocortin in Neuronal Cell Lines

Pro-opiomelanocortin (POMC) is the precursor to several pituitary hormones including adrenocorticotropic hormone and beta-endorphin (beta-END). POMC is also expressed in the brain, predominantly in discrete neuronal cell populations of the hypothalamus. In the pituitary and brain, POMC undergoes tissue-specific proteolysis to release different bioactive peptides. POMC processing in neuronal cell lines was studied after infection of PC12 and Neuro2A cells with a recombinant retrovirus carrying the porcine POMC cDNA. Our results indicate that both cell lines synthesize and target POMC to the regulated secretory pathway. Only the Neuro2A cells, however, can achieve proteolytic processing of POMC. Chromatographic and immunological characterization of the POMC-related material showed that beta-lipotropin (beta-LPH) and nonacetylated beta-END(1-31) are major maturation products of POMC in these cells. Release of both beta-LPH and beta-END(1-31) from infected Neuro2A cells can be stimulated by secretagogues in a calcium-dependent manner. Taken together, our results suggest that the cellular machinery of Neuro2A cells can recognize a foreign prohormone, target it to neurosecretory vesicles, process it into biologically active peptides, and secrete it in a manner characteristic to peptidergic neurons.     

On the Segregation of the Germ and Somatic Cell Lines in the Embryo

Abstract. In this paper we argue that the mechanisms underlying the segregation of the somatic and germ cell lines are basically similar. The interaction of the genome with specific cytoplasmic factors is responsible for the restriction of their developmental potencies in the somatic cell lines, and for the prevention of such a restriction in the germ cell line. In particular, it is suggested that meiosis is part of the differentiation program of the germ cells.     

Linkage Relationships of Seventeen Human Gene Loci as determined by Man-Mouse Somatic Cell Hybrids

Electrophoretic studies of the enzymes produced by sixty-four independently derived hybrid clones have made possible the detection of autosomal linkages on human chromosomes.     

Power Efficiency of Outer Hair Cell Somatic Electromotility

Cochlear outer hair cells (OHCs) are fast biological motors that serve to enhance the vibration of the organ of Corti and increase the sensitivity of the inner ear to sound. Exactly how OHCs produce useful mechanical power at auditory frequencies, given their intrinsic biophysical properties, has been a subject of considerable debate. To address this we formulated a mathematical model of the OHC based on first principles and analyzed the power conversion efficiency in the frequency domain. The model includes a mixture-composite constitutive model of the active lateral wall and spatially distributed electro-mechanical fields. The analysis predicts that: 1) the peak power efficiency is likely to be tuned to a specific frequency, dependent upon OHC length, and this tuning may contribute to the place principle and frequency selectivity in the cochlea; 2) the OHC power output can be detuned and attenuated by increasing the basal conductance of the cell, a parameter likely controlled by the brain via the efferent system; and 3) power output efficiency is limited by mechanical properties of the load, thus suggesting that impedance of the organ of Corti may be matched regionally to the OHC. The high power efficiency, tuning, and efferent control of outer hair cells are the direct result of biophysical properties of the cells, thus providing the physical basis for the remarkable sensitivity and selectivity of hearing.     

表达登革病毒prM基因小干扰RNA的Vero细胞系的建立

prM蛋白是登革病毒膜蛋白M的前体,膜蛋白M对病毒的组装与成熟有重要作用,针对prM基因设计的小干扰RNA（siRNA）可短期抑制登革病毒复制.为了达到长期抑制登革病毒的效果,本研究构建了插入prM siRNA序列的重组慢病毒,利用流式细胞术分选以及杀稻瘟霉素抗性,筛选出稳定表达prM siRNA的非洲绿猴肾细胞（Vero细胞）系.经逆转录PCR及测序验证siRNA序列表达正确. Vero细胞中prM siRNA的表达率约为976%.当受到登革病毒攻击时,表达prM siRNA的Vero细胞能够明显抑制登革病毒prM基因的表达,并抑制登革病毒在Vero细胞中的复制.建立的Vero细胞系可用于RNA干扰防治登革病毒感染的进一步应用研究.