Use of a human minichromosome as a cloning and expression vector for mammalian cells

Centromere identity and function put to use: construction and transfer of mammalian artificial chromosomes to animal models

Mammalian artificial chromosomes (MACs) are widely used as gene expression vectors and have various advantages over conventional expression vectors. We review and discuss breakthroughs in MAC construction, initiation of functional centromeres allowing their faithful inheritance, and transfer from cell culture to animal model systems. These advances have contributed to advancements in synthetic biology, biomedical research, and applications in industry and in the clinic.

A pathway from chromosome transfer to engineering resulting in human and mouse artificial chromosomes for a variety of applications to bio-medical challenges

Microcell-mediated chromosome transfer (MMCT) is a technique to transfer a chromosome from defined donor cells into recipient cells and to manipulate chromosomes as gene delivery vectors and open a new avenue in somatic cell genetics. However, it is difficult to uncover the function of a single specific gene via the transfer of an entire chromosome or fragment, because each chromosome or fragment contains a set of numerous genes. Thus, alternative tools are human artificial chromosome (HAC) and mouse artificial chromosome (MAC) vectors, which can carry a gene or genes of interest. HACs/MACs have been generated mainly by either a "top-down approach" (engineered creation) or a "bottom-up approach" (de novo creation). HACs/MACs with one or more acceptor sites exhibit several characteristics required by an ideal gene delivery vector, including stable episomal maintenance and the capacity to carry large genomic loci plus their regulatory elements, thus allowing the physiological regulation of the introduced gene in a manner similar to that of native chromosomes. The MMCT technique is also applied for manipulating HACs and MACs in donor cells and delivering them to recipient cells. This review describes the lessons learned and prospects identified from studies on the construction of HACs and MACs, and their ability to drive exogenous gene expression in cultured cells and transgenic animals via MMCT. New avenues for a variety of applications to bio-medical challenges are also proposed.

A new generation of human artificial chromosomes for functional genomics and gene therapy

Since their description in the late 1990s, human artificial chromosomes (HACs) carrying a functional kinetochore were considered as a promising system for gene delivery and expression with a potential to overcome many problems caused by the use of viral-based gene transfer systems. Indeed, HACs avoid the limited cloning capacity, lack of copy number control and insertional mutagenesis due to integration into host chromosomes that plague viral vectors. Nevertheless, until recently, HACs have not been widely recognized because of uncertainties of their structure and the absence of a unique gene acceptor site. The situation changed a few years ago after engineering of HACs with a single loxP gene adopter site and a defined structure. In this review, we summarize recent progress made in HAC technology and concentrate on details of two of the most advanced HACs, 21HAC generated by truncation of human chromosome 21 and alphoid(tetO)-HAC generated de novo using a synthetic tetO-alphoid DNA array. Multiple potential applications of the HAC vectors are discussed, specifically the unique features of two of the most advanced HAC cloning systems.

Human artificial chromosomes for gene delivery and the development of animal models

Random integration of conventional gene delivery vectors such as viruses, plasmids, P1 phage-derived artificial chromosomes, bacterial artificial chromosomes and yeast artificial chromosomes can be associated with transgene silencing. Furthermore, integrated viral sequences can activate oncogenes adjacent to the insertion site resulting in cancer. Various human artificial chromosomes (HACs) exhibit several potential characteristics desired for an ideal gene delivery vector, including stable episomal maintenance and the capacity to carry large genomic loci with their regulatory elements, thus allowing the physiological regulation of the introduced gene in a manner similar to that of native chromosomes. HACs have been generated mainly using either a "top-down approach" (engineered chromosomes), or a "bottom-up approach" (de novo artificial chromosomes). The recent emergence of stem cell-based tissue engineering has opened up new avenues for gene and cell therapies. This review describes the lessons learned and prospects identified mainly from studies in the construction of HACs and HAC-mediated gene expression systems in cultured cells, as well as in animals.

Interspecific transfer of mammalian artificial chromosomes between farm animals

It is often desirable to transfer a mammalian artificial chromosome (MAC) from the cells of one species to those of another. Attempts to carry out such transfer have been successful in some cases and have failed in others. In this study we have tested the hypothesis that centromeric DNA sequence similarity could be a useful criterion for determining MAC host range. Homology studies indicated that the sheep should give positive transfer results. The prediction was tested by introducing into sheep cells a yeast artificial chromosome that contained swine centromeric sequences and that had previously been used to produce a de novo MAC in swine cells. The experiments resulted in the formation of a functional de novo MAC in sheep cells, as attested by FISH analysis. The newly formed MAC remained structurally and functionally stable in ovine up to 52 generations. The centromeric sequences present on the newly formed MAC are probably swine sequences, although it cannot be ruled out that some sheep sequences may also have migrated to the MAC. The size of the sheep MAC was determined by atomic force microscopy. Thus, centromeric sequence similarity appears to be a useful criterion for predicting the animal species between which MACs can shuttle.

A highly stable and nonintegrated human artificial chromosome (HAC) containing the 2.4 Mb entire human dystrophin gene

Episomal vector with the capacity to deliver a large gene containing all the critical regulatory elements is ideal for gene therapy. Human artificial chromosomes (HACs) have the capacity to deliver an extremely large genetic region to host cells without integration into the host genome, thus preventing possible insertional mutagenesis and genomic instability. Duchenne muscular dystrophy (DMD) is caused by mutation in the extremely large dystrophin gene (2.4 Mb). We herein report the development of a HAC vector containing the entire human dystrophin gene (DYS-HAC) that is stably maintained in mice and human immortalized mesenchymal stem cells (hiMSCs). The DYS-HAC was transferred to mouse embryonic stem (ES) cells, and isoforms of the DYS-HAC-derived human dystrophin in the chimeric mice generated from the ES cells were correctly expressed in tissue-specific manner. Thus, this HAC vector containing the entire dystrophin gene with its native regulatory elements is expected to be extremely useful for future gene and cell therapies of DMD.

Transfer of human artificial chromosome vectors into stem cells

Human chromosome fragments and human artificial chromosomes (HAC) represent feasible gene delivery vectors via microcell-mediated chromosome transfer. Strategies to construct HAC involve either 'build up' or 'top-down' approaches. For each approach, techniques for manipulating HAC in donor cells in order to deliver HAC to recipient cells are required. The combination of chromosome fragments or HAC with microcell-mediated chromosome transfer has facilitated human gene mapping and various genetic studies. The recent emergence of stem cell-based tissue engineering has opened up new avenues for gene and cell therapies. The task now is to develop safe and effective vectors that can deliver therapeutic genes into specific stem cells and maintain long-term regulated expression of these genes. Although the transfer-efficiency needs to be improved, HAC possess several characteristics that are required for gene therapy vectors, including stable episomal maintenance and the capacity for large gene insets. HAC can also carry genomic loci with regulatory elements, which allow for the expression of transgenes in a genetic environment similar to the natural chromosome. This review describes the lessons and prospects learned, mainly from recent studies in developing HAC and HAC-mediated gene expression in embryonic and adult stem cells, and in transgenic animals.

Flow analysis and sorting of microchromosomes (<3 Mb)

BACKGROUND

The analysis and isolation of high numbers of chromosomes smaller than 3 Mb in size (microchromosomes) with good purity is dependent primarily on the detection sensitivity of the flow cytometer and the precision of the sort unit. The aim of this study was to investigate the capability of using a conventional flow cytometer for the detection and sorting at high purity microchromosomes with an estimated size of 2.7 Mb.

METHODS

Chromosomes were isolated from a human cell line containing a pair of X-derived microchromosomes, using a modified polyamine isolation buffer. The chromosome preparation was labeled with Hoechst and Chromomycin and analyzed and purified using a MoFlo sorter (DAKO) configured for high-speed sorting. The purity of the flow-sorted microchromosomes was assessed by reverse chromosome painting.

RESULTS

Improved resolution of the peak of microchromosomes in a bivariate plot of Hoechst versus Chromomycin fluorescence was obtainable after discriminating clumps and debris based on gating data within a FSC versus pulse width plot.

CONCLUSIONS

Chromosomes of smaller size, less than 3 Mb, can be detected with high resolution and flow-sorted with high purity using a conventional flow sorter.

Human artificial chromosome vectors meet stem cells: new prospects for gene delivery

The recent emergence of stem cell-based tissue engineering has now opened up new venues for gene therapy. The task now is to develop safe and effective vectors that can deliver therapeutic genes into specific stem cell lines and maintain long-term regulated expression of these genes. Human artificial chromosomes (HACs) possess several characteristics that require gene therapy vectors, including a stable episomal maintenance, and the capacity for large gene inserts. HACs can also carry genomic loci with regulatory elements, thus allowing for the expression of transgenes in a genetic environment similar to the chromosome. Currently, HACs are constructed by a two prone approaches. Using a top-down strategy, HACs can be generated from fragmenting endogenous chromosomes. By a bottom-up strategy, HACs can be created de novo from cloned chromosomal components using chromosome engineering. This review describes the current advances in developing HACs, with the main focus on their applications and potential value in gene delivery, such as HAC-mediated gene expression in embryonic, adult stem cells, and transgenic animals.

Antigen-mediated growth control of hybridoma cells via a human artificial chromosome

Human artificial chromosome (HAC) vectors possess several characteristics sufficient for the requirements of gene therapy vectors, including stable episomal maintenance and mediation of long-term transgene expression. In this study, we adopted an antigen-mediated genetically modified cell amplification (AMEGA) system employing an antibody/cytokine receptor chimera that triggers a growth signal in response to a cognate non-toxic antigen, and applied it to growth control of HAC-transferred cells by adding an antigen that differed from cytokines that may manifest pleiotropic effects. We previously constructed a novel HAC vector, 21 Delta qHAC, derived from human chromosome 21, housed in CHO cells. Here, we constructed an HAC vector harboring an ScFv-gp130 chimera responsive to fluorescein-conjugated BSA (BSA-FL) as well as a model transgene, enhanced green fluorescent protein (EGFP), in CHO cells. The modified HAC was transferred into interleukin (IL)-6-dependent hybridoma 7TD1 cells by microcell-mediated chromosome transfer, and the cells were subsequently found to show BSA-FL-dependent cell growth and sustained expression of EGFP in the absence of IL-6. The AMEGA system in combination with HAC technology will be useful for increasing the efficacy of gene therapy by conferring a growth advantage on the genetically modified cells.

Human artificial chromosomes: potential applications and clinical considerations

Human artificial chromosomes demonstrate promise as a novel class of nonintegrative gene therapy vectors. The authors outline current developments in human artificial chromosome technology and examine their potential for clinical application.

Engineering chromosomes for delivery of therapeutic genes

The ability to create fully functional human chromosome vectors represents a potentially exciting gene-delivery system for the correction of human genetic disorders with several advantages over viral delivery systems. However, for the full potential of chromosome-based gene-delivery vectors to be realized, several key obstacles must be overcome. Methods must be developed to insert therapeutic genes reliably and efficiently and to enable the stable transfer of the resulting chromosomal vectors to different therapeutic cell types. Research to achieve these outcomes continues to encounter major challenges; however recent developments have reiterated the potential of chromosome-based vectors for therapeutic gene delivery. Here we review the different strategies under development and discuss the advantages and problems associated with each.

Artificial and engineered chromosomes: developments and prospects for gene therapy

At the gene therapy session of the ICCXV Chromosome Conference (2004), recent advances in the construction of engineered chromosomes and de novo human artificial chromosomes were presented. The long-term aims of these studies are to develop vectors as tools for studying genome and chromosome function and for delivering genes into cells for therapeutic applications. There are two primary advantages of chromosome-based vector systems over most conventional vectors for gene delivery. First, the transferred DNA can be stably maintained without the risks associated with insertion, and second, large DNA segments encompassing genes and their regulatory elements can be introduced, leading to more reliable transgene expression. There is clearly a need for safe and effective gene transfer vectors to correct genetic defects. Among the topics discussed at the gene therapy session and the main focus of this review are requirements for de novo human artificial chromosome formation, assembly of chromatin on de novo human artificial chromosomes, advances in vector construction, and chromosome transfer to cells and animals.

Artificial and engineered chromosomes: non-integrating vectors for gene therapy

Non-integrating gene-delivery platforms demonstrate promise as potentially ideal gene-therapy vector systems. Although several approaches are under development, there is little consensus as to what constitutes a true 'artificial' versus an 'engineered' human chromosome. Recent progress must be evaluated in light of significant technical challenges that remain before such vectors achieve clinical utility. Here, we examine the principal classes of non-integrating vectors, ranging from episomes to engineered mini-chromosomes to true human artificial chromosomes. We compare their potential as practical gene-transfer platforms and summarize recent advances towards eventual applications in gene therapy. Although chromosome-engineering technology has advanced considerably within recent years, difficulties in establishing composition of matter and effective vector delivery currently prevent artificial or engineered chromosomes being accepted as viable gene-delivery platforms.

Prospects and problems of gene therapy: an update

The gene therapy approach can vary from delivering extra copies of a gene, through modifications of a genome using the properties of ribozymes or chimeraplasts, to injection of modified cells. For the treatment of genetic deficits the ultimate goal would be the repair of the mutated gene in the target tissue(s). The techniques required for such an approach are emerging, albeit slowly. Therefore, delivery of an extra copy of a normal gene in a specific vector remains the predominant approach. Moreover, this method finds wider applications in gene therapy relating to disorders other than heritable defects, e.g., malignancies, cardiovascular diseases and infections. The major and most intensive areas of research are: i) vectors and delivery methods, ii) regulation of transgene expression and iii) stability of expression. Targeting of the therapeutic gene is being accomplished by using viral vectors or non-viral delivery systems, either ex vivo or in vivo. The choice of vectors and delivery routes depends on the nature of the target cells and the required levels and stability of expression. Although there have been the first positive clinical results and significant technical achievements over the past 2 years, there are still obstacles to the development of effective clinical products and these remain largely unchanged. The most important barriers are the low levels and stability of expression and immune responses to vectors and/or gene products. The safety aspects of gene therapy have become painfully evident with the first death conclusively linked to gene therapy. The progress in AAV and lentiviral vectors, improved regulation of transgene expression and advances in stem cell technology are among the recent most exciting developments.

Construction of a novel human artificial chromosome vector for gene delivery

Potential problems of conventional transgenes include insertional disruption of the host genome and unpredictable, irreproducible expression of the transgene by random integration. Alternatively, human artificial chromosomes (HACs) can circumvent some of the problems. Although several HACs were generated and their mitotic stability was assessed, a practical way for introducing exogenous genes by the HACs has yet to be explored. In this study, we developed a novel HAC from sequence-ready human chromosome 21 by telomere-directed chromosome truncation and added a loxP sequence for site-specific insertion of circular DNA by the Cre/loxP system. This 21HAC vector, delivered to a human cell line HT1080 by microcell fusion, bound centromere proteins A, B, and C and was mitotically stable during long-term culture without selection. The EGFP gene inserted in the HAC vector expressed persistently. These results suggest that the HAC vector provides useful system for functional studies of genes in isogenic cell lines.

Construction of a swine artificial chromosome: a novel vector for transgenesis in the pig

A de novo SAC was constructed by making use of YAC technology and a humanized yeast strain. The construct (about 310 kb) contained pig centromeric DNA and the Neo gene. The construct was introduced into a pig cell line by yeast-mammalian cell fusion and G418 resistant clones were obtained. One clone was characterized by FISH and shown to contain an episomally located microchromosome containing YAC, Neo and pig centromere sequences. FISH analysis over time showed that the SAC was mitotically stable for at least 34 generations in the absence of selection. The size of the SAC was determined by confocal microscopy of the SAC and shown to be approximately 7 Mb, which is about 25-fold greater than the size of the original YAC. From its behavior in pulsed field gel electrophoresis, FISH analysis of stretched DNA fibers, and its appearance under scanning confocal microscopy, it was concluded that the SAC is a circularized and multimerized derivative of the original YAC. Possible applications as vectors for animal transgenesis are discussed.

Mammalian artificial chromosomes as vectors: progress and prospects

Artificial chromosomes have long been touted as the ideal vector for gene therapy and biotechnology purposes based on the idea that such a chromosome would mimic the natural state of DNA in the cell. This, it is argued, would mean that essentially unlimited amounts of DNA could be incorporated into such a vector enabling either large genes or whole metabolic pathways to be provided to the recipient cell or organism. Additionally, such a vector would not integrate into the genome of the host cell and so would not cause mutagenesis by insertion and could perhaps be withdrawn from the cell or organism when no longer required. A number of preconditions are implicit in these claims. First, the chromosome should have a segregation efficiency approaching 100% in order to be useful in a cell population undergoing multiple rounds of cell divisions. Second, the chromosome should have a defined structure for regulatory and practical reasons. A defined structure is needed to maximize the control of expression of the genes that it contains. Third, the chromosome should not be so large that delivery becomes a problem. Finally, chromosomal effects such as centromeric or telomeric silencing should not dominate the expression of genes contained in an artificial chromosome. In this article, we discuss our own and others' efforts to achieve these aims using a variety of nonviral approaches to the problem.

Functional human CFTR produced by a stable minichromosome

Artificial chromosomes have been claimed to be the ideal vector for gene therapy, but their use has been hampered by an inability to produce stable and well designed molecules. We have used a structurally defined minichromosome to clone the human cystic fybrosis transmembrane conductance regulator (CFTR) locus. To guarantee the presence of the proper regulatory elements, we used the 320 kb yeast artificial chromosome (YAC) 37AB12 with the intact CFTR gene and upstream sequences. The resulting minichromosome was analyzed for the presence of the entire CFTR gene and for its functional activity by molecular and functional methods. We have identified clones showing the presence of both the transcript and the CFTR protein. Moreover, in the same clones, a chloride secretory response to cAMP was detected. Mitotic and molecular stability after prolonged growth without selection demonstrated that the constructs were stable. This is the first example of a structurally known minichromosome made to contain an active therapeutic gene.

Chromosome engineering: prospects for gene therapy

Recent advances in chromosome engineering and the potential for downstream applications in gene therapy were presented at the Artificial Chromosome Session of Genome Medicine: Gene Therapy for the Millennium in Rome, Italy in September 2001. This session concentrated primarily on the structure and function of human centromeres and the ongoing challenge of equipping human artificial chromosomes (HACs) with centromeres to ensure their mitotic stability. Advances in the 'bottom up' construction of HACs included the transfer into HT1080 cells of circular PACs containing alpha satellite DNA, and the correction of HPRT deficiency in cells using HACs. Advances in the 'top down' construction of HACs using telomere associated chromosome fragmentation in DT40 cells included the formation of HACs that are less than a megabase in size and transfer of HACs through the mouse germline. Significant progress has also been made in the use of human minichromosomes for stable trans-gene expression. While many obstacles remain towards the use of HACs for gene therapy, this session provided an optimistic outlook for future success.

Strategies for engineering human chromosomes with therapeutic potential

Human engineered chromosomes (HECs) have several potential advantages over currently used vectors for gene therapy applications. Firstly, there is no upper size limit to DNA that can be cloned in these vectors. Secondly, their extrachromosomal nature ensures that introduced genes are neither disruptive to, nor affected by, the genome of the host cell. Finally, being solely human in origin, HEC vectors should not evoke adverse host immunogenic responses. Recent advances have produced a variety of HECs via several different approaches. This review focuses on the current methodologies for making HEC vectors, the advantages and problems associated with each strategy, and discusses the outlook for HEC vectors as ex vivo therapeutic agents.

Molecular and cytological analysis of a 5.5 Mb minichromosome

Mammalian artificial chromosomes (MACs) provide a new tool for the improvement of our knowledge of chromosome structure and function. Moreover, they constitute an alternative and potentially powerful tool for gene delivery both in cultured cells and for the production of transgenic animals. In the present work we describe the molecular structure of MC1, a human minichromosome derived from chromosome 1. By means of restriction and hybridization analysis, satellite-PCR, in situ hybridization on highly extended chromatin fibres, and indirect immunofluorescence, we have established that: (i) MC1 has a size of 5.5 Mb; (ii) it consists of 1.1 Mb alphoid, 3.5 Mb Sat2 DNA, and telomeric and subtelomeric sequences at both ends; (iii) it contains an unusual region of interspersed Sat2 and alphoid DNAs at the junction of the alphoid and the Sat2 blocks; and (iv) the two alphoid blocks and the Sat2-alphoid region bind centromeric proteins suggesting that they participate in the formation of a functional kinetochore.

Efficient male and female germline transmission of a human chromosomal vector in mice

A small accessory chromosome that was mitotically stable in human fibroblasts was transferred into the hprt(-) hamster cell line CH and developed as a human chromosomal vector (HCV) by the introduction of a selectable marker and the 3' end of an HPRT minigene preceded by a loxP sequence. This HCV is stably maintained in the hamster cell line. It consists mainly of alphoid sequences of human chromosome 20 and a fragment of human chromosome region 1p22, containing the tissue factor gene F3. The vector has an active centromere, and telomere sequences are lacking. By transfecting a plasmid containing the 5' end of HPRT and a Cre-encoding plasmid into the HCV(+) hamster cell line, the HPRT minigene was reconstituted by Cre-mediated recombination and expressed by the cells. The HCV was then transferred to male mouse R1-ES cells and it did segregate properly. Chimeras were generated containing the HCV as an independent chromosome in a proportion of the cells. Part of the male and female offspring of the chimeras did contain the HCV. The HCV(+) F1 animals harbored the extra chromosome in >80% of the cells. The HCV was present as an independent chromosome with an active centromere and the human F3 gene was expressed from the HCV in a human-tissue-specific manner. Both male and female F1 mice did transmit the HCV to F2 offspring as an independent chromosome with properties similar to the original vector. This modified small accessory chromosome, thus, shows the properties of a useful chromosomal vector: It segregates stably as an independent chromosome, sequences can be inserted in a controlled way and are expressed from the vector, and the HCV is transmitted through the male and female germline in mice.