De novo chromosome formations by large-scale amplification of the centromeric region of mouse chromosomes

Synthetic genomics for curing genetic diseases

From the beginning of the genome sequencing era, it has become increasingly evident that genetics plays a role in all diseases, of which only a minority are single-gene disorders, the most common target of current gene therapies. However, the majority of people have some kind of health problems resulting from congenital genetic mutations (over 6000 diseases have been associated to genes, https://www.omim.org/statistics/geneMap) and most genetic disorders are rare and only incompletely understood. The vision and techniques applied to the synthesis of genomes may help to address unmet medical needs from a chromosome and genome-scale perspective. In this chapter, we address the potential therapy of genetic diseases from a different outlook, in which we no longer focus on small gene corrections but on higher-order tools for genome manipulation. These will play a crucial role in the next years, as they prelude to a much deeper understanding of the architecture of the human genome and a more accurate modeling of human diseases, offering new therapeutic opportunities.

A novel and stable mouse artificial chromosome vector

Human chromosome fragments (hCFs) and human artificial chromosomes (HACs) can be transferred into mouse ES cells to produce trans-chromosomic (Tc) mice. Although hCFs and HACs containing large genomic DNAs can be autonomously maintained in Tc mice, their retention rate is variable in mouse ES cell lines and Tc mouse tissues, possibly because of centromere differences between the species. To improve the retention rate of artificial chromosomes in mouse cells, we constructed novel mouse artificial chromosome (MAC) vectors by truncating a natural mouse chromosome at a site adjacent to the centromeric region. We obtained cell clones containing the MAC vectors that were stably maintained in mouse ES cells and various tissues in Tc mice. The MACs possess acceptor sites into which a desired gene or genes can be inserted. Thus, Tc mice harboring the MAC vectors may be valuable tools for functional analyses of desired genes, producing humanized model mice, and synthetic biology.

Bi-HAC vector system toward gene and cell therapy

Genetic manipulations with mammalian cells often require introduction of two or more genes that have to be in trans-configuration. However, conventional gene delivery vectors have several limitations, including a limited cloning capacity and a risk of insertional mutagenesis. In this paper, we describe a novel gene expression system that consists of two differently marked HAC vectors containing unique gene loading sites. One HAC, 21HAC, is stably propagated during cell divisions; therefore, it is suitable for complementation of a gene deficiency. The other HAC, tet-O HAC, can be eliminated, providing a unique opportunity for transient gene expression (e.g., for cell reprogramming). Efficiency and accuracy of a novel bi-HAC vector system have been evaluated after loading of two different transgenes into these HACs. Based on analysis of transgenes expression and HACs stability in the proof of principle experiments, the combination of two HAC vectors may provide a powerful tool toward gene and cell therapy.

Novel method to load multiple genes onto a mammalian artificial chromosome

Mammalian artificial chromosomes are natural chromosome-based vectors that may carry a vast amount of genetic material in terms of both size and number. They are reasonably stable and segregate well in both mitosis and meiosis. A platform artificial chromosome expression system (ACEs) was earlier described with multiple loading sites for a modified lambda-integrase enzyme. It has been shown that this ACEs is suitable for high-level industrial protein production and the treatment of a mouse model for a devastating human disorder, Krabbe's disease. ACEs-treated mutant mice carrying a therapeutic gene lived more than four times longer than untreated counterparts. This novel gene therapy method is called combined mammalian artificial chromosome-stem cell therapy. At present, this method suffers from the limitation that a new selection marker gene should be present for each therapeutic gene loaded onto the ACEs. Complex diseases require the cooperative action of several genes for treatment, but only a limited number of selection marker genes are available and there is also a risk of serious side-effects caused by the unwanted expression of these marker genes in mammalian cells, organs and organisms. We describe here a novel method to load multiple genes onto the ACEs by using only two selectable marker genes. These markers may be removed from the ACEs before therapeutic application. This novel technology could revolutionize gene therapeutic applications targeting the treatment of complex disorders and cancers. It could also speed up cell therapy by allowing researchers to engineer a chromosome with a predetermined set of genetic factors to differentiate adult stem cells, embryonic stem cells and induced pluripotent stem (iPS) cells into cell types of therapeutic value. It is also a suitable tool for the investigation of complex biochemical pathways in basic science by producing an ACEs with several genes from a signal transduction pathway of interest.

Chromosome engineering with lambda-integrase mediated recombination system: the ACE system

Mammalian satellite DNA-based artificial chromosomes (SATACs) are unique among the mammalian artificial chromosomes. These reproducibly generated de novo chromosomes are stably maintained in different species, readily purified from the host cell's chromosomes and can be introduced into a variety of recipient cells. An artificial chromosome expression system (ACE system) has been developed on these SATACs to extend them for chromosome engineering. This system includes a Platform ACE containing multiple acceptor sites, specially designed targeting vector (ATV), and an ACE-integrase expression vector (pCXLamIntROK). Gene of interest are cloned into targeting vector (ATV), and site-specific loading of genes onto Platform ACE is facilitated by ACE-integrase mediated recombination. ACE system is suitable for multiple or subsequent loading of useful genes onto the same chromosome vector. This chapter describes the detailed procedure of chromosome engineering using the ACE system.

Towards the development of better crops by genetic transformation using engineered plant chromosomes

Plant Biotechnology involves manipulation of genetic material to develop better crops. Keeping in view the challenges being faced by humanity in terms of shortage of food and other resources, we need to continuously upgrade the genomic technologies and fine tune the existing methods. For efficient genetic transformation, Agrobacterium-mediated as well as direct delivery methods have been used successfully. However, these methods suffer from many disadvantages especially in terms of transfer of large genes, gene complexes and gene silencing. To overcome these problems, recently, some efforts have been made to develop genetic transformation systems based on engineered plant chromosomes called minichromosomes or plant artificial chromosomes. Two approaches namely, "top-down" or "bottom-up" have been used for minichromosomes. The former involves engineering of the existing chromosomes within a cell and the latter de novo assembling of chromosomes from the basic constituents. While some success has been achieved using these chromosomes as vectors for genetic transformation in maize, however, more studies are needed to extend this technology to crop plants. The present review attempts to trace the genesis of minichromosomes and discusses their potential of development into plant artificial chromosome vectors. The use of these vectors in genetic transformation will greatly ameliorate the food problem and help to achieve the UN Millennium development goals.

Downstream bioengineering of ACE chromosomes for incorporation of site-specific recombination cassettes

Advances in mammalian artificial chromosome technology have made chromosome-based vector technology amenable to a variety of biotechnology applications including cellular protein production, genomics, and animal transgenesis. A pivotal aspect of this technology is the ability to generate artificial chromosomes de novo, transfer them to a variety of cells, and perform downstream engineering of artificial chromosomes in a tractable and rational manner. Previously, we have described an alternative artificial chromosome technology termed the ACE chromosome system, where the ACE platform chromosome contains a multitude of site-specific, recombination sites incorporated during the creation of the ACE platform chromosome. In this chapter we review a variant of the ACE chromosome technology whereby site-specific, recombination sites can be integrated into the ACE chromosome following its de novo synthesis. This variation allows insertion of user-defined, site-specific, recombination systems into an existing ACE platform chromosome. These bioengineered ACE platform chromosomes, containing user-defined recombination sites, represent an ideal circuit board to which an array of genetic factors can be plugged-in and expressed for various research and therapeutic applications.

De novo generation of satellite DNA-based artificial chromosomes by induced large-scale amplification

Mammalian artificial chromosomes (MACs) are engineered chromosomes with defined genetic content that can function as non-integrating vectors with large carrying capacity and stability. The large carrying capacity allows the engineering of MACs with multiple copies of the same transgene, gene complexes, and to include regulatory elements necessary for the regulated expression of transgene(s). In recent years, different approaches have been explored to generate MACs (Vos Curr Opin Genet Dev 8:351-359, 1998; Danielle et al. Trends Biotech 23:573-583, 2005; Duncan and Hadlaczky Curr Opin Biotech 18:420-424, 2007): (1) the de novo formation by centromere seeding, the "bottom-up" approach, (2) the truncation of natural chromosomes or the modification of naturally occurring minichromosomes, the "top-down" approach, and (3) the in vivo "inductive" approach. Satellite DNA-based artificial chromosomes (SATACs) generated by the in vivo "inductive" method have the potential to become an efficient tool in diverse gene technology applications such as cellular protein manufacturing (Kennard et al. BioPharm Int 20:52-59, 2007; Kennard et al. Biotechnol Bioeng 104:526-539, 2009; Kennard et al. Biotechnol Bioeng 104:540-553, 2009), transgenic animal production (Telenius et al. Chromosome Res 7:3-7, 1999; Co et al. Chromosome Res 8:183-191, 2000; Monteith et al. Methods Mol Biol 240:227-242, 2003), and ultimately a safe vector for gene therapy (Vanderbyl et al. Stem Cells 22:324-333, 2004; Vanderbyl et al. Exp Hematol 33:1470-1476, 2005; Katona et al. Cell. Mol. Life Sci 65:3830-3838, 2008). A detailed protocol for the de novo generation of satellite DNA-based artificial chromosomes (SATACs) via induced large-scale amplification is presented.

Mammalian artificial chromosomes and clinical applications for genetic modification of stem cells: an overview

Modifying multipotent, self-renewing human stem cells with mammalian artificial chromosomes (MACs), present a promising clinical strategy for numerous diseases, especially ex vivo cell therapies that can benefit from constitutive or overexpression of therapeutic gene(s). MACs are nonintegrating, autonomously replicating, with the capacity to carry large cDNA or genomic sequences, which in turn enable potentially prolonged, safe, and regulated therapeutic transgene expression, and render MACs as attractive genetic vectors for "gene replacement" or for controlling differentiation pathways in progenitor cells. The status quo is that the most versatile target cell would be one that was pluripotent and self-renewing to address multiple disease target cell types, thus making multilineage stem cells, such as adult derived early progenitor cells and embryonic stem cells, as attractive universal host cells. We will describe the progress of MAC technologies, the subsequent modifications of stem cells, and discuss the establishment of MAC platform stem cell lines to facilitate proof-of-principle studies and preclinical development.

Suiformes orthologous satellite DNAs as a hallmark of Pecari tajacu and Tayassu pecari (Tayassuidae) evolutionary rearrangements

In a broad general way, eukaryotic satellite DNA sequences are characterized by a highly dynamic molecular behavior due to concerted evolution that leads to rapid change between repeat sequences of different species, achieved by amplification of new variants during speciation or by gradual sequence evolution due to the accumulation of nucleotide substitutions. There are, although exceptions for this almost universal rule. We isolated variants from both the Mc1 and Ac2 pig (Sus scrofa, Suidae) satellite DNA families from the genomes of two Tayassuidae members: Pecari tajacu and Tayassu pecari, which have highly derived karyotypes. The presence of these sequences in both families' genomes (Suidae and Tayassuidae) implies their existence in a common ancestor, what confers to the variants the status of orthology and the approximate age of, at least 40 million years. While at the molecular composition level these orthologous sequences are highly homologous, cross-species physical mapping revealed a completely different chromosomal location in Suidae versus Tayassuidae families, most probably, reflecting the high level of divergence and chromosomes evolution pathways after radiation of each family. Detailed comparative analysis of the satellites assignment on the peccary's chromosomes revealed its co-localization with homologous evolutionary breakpoints in both species, suggesting their involvement in the rearrangement events. The complex behavior of the repeats evolution in the pig/peccaries genomes is here clearly illustrated. These sequences are molecularly preserved for a considerable period of time and display slow rates of sequence change, but show a dynamic motion behavior throughout the peccary's genomes that accompanied the great architectonic reorganization of Tayassuidae chromosomes during evolution.

Chromosomal engineering

Artificial chromosomes (ACs) are engineered chromosomes with defined genetic contents that can function as non-integrating vectors with large carrying capacity and stability. The large carrying capacity allows the engineering of ACs with multiple copies of the same transgene, gene complexes, and to include regulatory elements necessary for the regulated expression of transgene(s). Artificial chromosome based systems are composed of AC engineered to harbor and express gene(s) of interest and an appropriate recombination system for 'custom' engineering of ACs. These systems have the potential to become an efficient tool in diverse gene technology applications such as cellular protein manufacturing, transgenic animal production, and ultimately gene therapy. Recent advances in artificial chromosome technologies outline the value of these systems and justify the future research efforts to overcome the obstacles in exploring their full capabilities.

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: 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.

Alignment of biological microparticles by a polarized laser beam

The optical alignment of biological samples is of great relevance to microspectrometry and to the micromanipulation of single particles. Recently, Bayoudh et al. (J. Mod. Opt. 50:1581-1590, 2003) have shown that isolated, disk-shaped chloroplasts can be aligned in a controlled manner using an in-plane-polarized Gaussian beam trap, and suggested that this is due to their nonspherical shape. Here we demonstrate that the orientation of various micrometer-sized isolated biological particles, trapped by optical tweezers, can be altered in a controlled way by changing the plane of linear polarization of the tweezers. In addition to chloroplasts, we show that subchloroplast particles of small size and irregular overall shape, aggregated photosynthetic light-harvesting protein complexes as well as chromosomes can be oriented with the linearly polarized beam of the tweezers. By using a laser scanning confocal microscope equipped with a differential polarization attachment, we also measured the birefringence of magnetically oriented granal chloroplasts, and found that they exhibit strong birefringence with large local variations, which appears to originate from stacked membranes. The size and sign of the birefringence are such that the resulting anisotropic interaction with the linearly polarized laser beam significantly contributes to the torque orienting the chloroplasts.

Development of mammalian artificial chromosomes for the treatment of genetic diseases: Sandhoff and Krabbe diseases

Mammalian artificial chromosomes (MACs) are being developed as alternatives to viral vectors for gene therapy applications, as they allow for the introduction of large payloads of genetic information in a non-integrating, autonomously replicating format. One class of MACs, the satellite DNA-based artificial chromosome expression vehicle (ACE), is uniquely suited for gene therapy applications, in that it can be generated denovo in cells, along with being easily purified and readily transferred into a variety of recipient cell lines and primary cells. To facilitate the rapid engineering of ACEs, the ACE System was developed, permitting the efficient and reproducible loading of pre-existing ACEs with DNA sequences and/or target gene(s). As a result, the ACE System and ACEs are unique and versatile platforms for ex vivo gene therapy strategies that circumvent and alleviate existing safety and delivery limitations surrounding conventional gene therapy vectors. This review will focus on the status of MAC technologies and, in particular, the application of the ACE System towards an ex vivo gene therapy treatment of lysosomal storage diseases, specifically Sandhoff (MIM #268800) and Krabbe (MIM #245200) diseases.

Isolation, cloning and characterization of two major satellite DNA families of rabbit (Oryctolagus cuniculus)

We report here the isolation, cloning and characterization of two abundant centromeric satellite sequences (Rsat I and Rsat II) what are not related to each other, and that of a divergent subfamily (Rsat IIE) of rabbit (Oryctolagus cuniculus). The Rsat I monomers had a 375 base pair (bp) average length, while repeat units Rsat II and Rsat IIE were approximately 585 bp long. Variable amounts of Rsat I were detected by FISH at the centromeric region of 11 chromosome pairs of the complement. Rsat II hybridized to the centromere of 12 different chromosomes, and two of these were labeled also with the Rsat IIE probe. Two-color in situ hybridizations with the satellite probes and rDNA revealed that the NOR chromosomes carried different satellites. Rsat I was abundant on chromosome 20 and 21, but it was undetectable on chromosomes 13 and 16. Large Rsat II arrays were found on chromosomes 16, 20 and 21, but reduced amount was detected on chromosome 13. The variant Rsat IIE was prominent on chromosome 16, but was absent from the other rDNA-bearing chromosomes. The rDNA signal on chromosome 21 was localized to the 21q(ter) region, what can be a useful cytological marker in comparative cytological studies. These data show that rabbit chromosomes form at least four distinct groups based on the satellite composition of their centromeres. The differences in the chromosomal distribution of satellite families will help easy FISH identification of individual chromosomes, as well as to unveil the evolutionary history of the Leporidae karyotype.

A mammalian artificial chromosome engineering system (ACE System) applicable to biopharmaceutical protein production, transgenesis and gene-based cell therapy

Mammalian artificial chromosomes (MACs) provide a means to introduce large payloads of genetic information into the cell in an autonomously replicating, non-integrating format. Unique among MACs, the mammalian satellite DNA-based Artificial Chromosome Expression (ACE) can be reproducibly generated de novo in cell lines of different species and readily purified from the host cells' chromosomes. Purified mammalian ACEs can then be re-introduced into a variety of recipient cell lines where they have been stably maintained for extended periods in the absence of selective pressure. In order to extend the utility of ACEs, we have established the ACE System, a versatile and flexible platform for the reliable engineering of ACEs. The ACE System includes a Platform ACE, containing >50 recombination acceptor sites, that can carry single or multiple copies of genes of interest using specially designed targeting vectors (ATV) and a site-specific integrase (ACE Integrase). Using this approach, specific loading of one or two gene targets has been achieved in LMTK(-) and CHO cells. The use of the ACE System for biological engineering of eukaryotic cells, including mammalian cells, with applications in biopharmaceutical production, transgenesis and gene-based cell therapy is discussed.

Analysis of mitotic and expression properties of human neocentromere-based transchromosomes in mice

Human neocentromeres are functional centromeres that are devoid of the typical human centromeric alpha-satellite DNA. We have transferred a 60-Mb chromosome 10-derived neocentric marker chromosome, mardel(10), and its truncated 3.5-Mb derivative, NC-MiC1, into mouse embryonic stem cell and have demonstrated a relatively high structural and mitotic stability of the transchromosomes in a heterologous genetic background. We have also produced chimeric mice carrying mardel(10) or NC-MiC1. Both transchromosomes were detected as intact episomal entities in a variety of adult chimeric mouse tissues including hemopoietic stem cells. Genes residing on these transchromosomes were expressed in the different tissues tested. Meiotic transmission of both transchromosomes in the chimeric mice was evident from the detection of DNA from these chromosomes in sperm samples. In particular, germ line transmission of NC-MiC1 was demonstrated in the F1 embryos of the chimeric mice. Variable (low in mardel(10)- or NC-MiC1-containing embryonic stem cells and chimeric mouse tissues and relatively high in NC-MiC1-containing F1 embryos) levels of missegregation of these transchromosomes were detected, suggesting that they are not optimally predisposed to full mitotic regulation in the mouse background, particularly during early embryogenesis. These results provide promising data in support of the potential use of neocentromere-based human marker chromosomes and minichromosomes as a tool for the study of centromere, neocentromere, and chromosome biology and for gene therapy studies in a mouse model system. They also highlight the need to further understand and overcome the factors that are responsible for the definable rates of instability of these transchromosomes in a mouse model.

Transfer and Stable Transgene Expression of a Mammalian Artificial Chromosome into Bone Marrow-Derived Human Mesenchymal Stem Cells

Mammalian artificial chromosomes (ACEs) transferred to autologous adult stem cells (SCs) provide a novel strategy for the ex vivo gene therapy of a variety of clinical indications. Unlike retroviral vectors, ACEs are stably maintained, autonomous, and nonintegrating. In this report we assessed the delivery efficiency of ACEs and evaluated the subsequent differentiation potential of ACE-transfected bone marrow-derived human mesenchymal stem cells (hMSCs). For this, an ACE carrying multiple copies of the red fluorescent protein (RFP) reporter gene was transferred under optimized conditions into hMSCs using standard cationic transfection reagents. RFP expression was detectable in 11% of the cells 4-5 days post-transfection. The RFP-expressing hMSCs were enriched by high-speed flow cytometry and maintained their potential to differentiate along adipogenic or osteogenic lineages. Fluorescent in situ hybridization and fluorescent microscopy demonstrated that the ACEs were stably maintained as single chromosomes and expressed the RFP transgenes in both differentiated cultures. These findings demonstrate the potential utility of ACEs for human adult SC ex vivo gene therapy.

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.

Retrofitting of a satellite repeat DNA-based murine artificial chromosome (ACes) to contain loxP recombination sites

A satellite DNA-based mammalian artificial chromosome (ACes) was generated and subsequently modified by targeting of a loxP-red fluorescent protein (RFP) expression cassette via homologous recombination into a ribosomal DNA (rDNA)-containing locus. Clones containing correctly targeted ACes were identified by PCR from populations of RFP-expressing cells enriched by FACS sorting and were further characterized by fluorescent in situ hybridization. The targeted ACes maintained its ability to be purified to near homogeneity. Studies are currently underway to further characterize the functionality, carrying capacity, stability and transfectability of this modified ACes.

Efficient in-vitro transfer of a 60-Mb mammalian artificial chromosome into murine and hamster cells using cationic lipids and dendrimers

Non-integrating artificial chromosomes represent a potentially promising approach to ex-vivo and in-vivo gene therapy applications. These large vectors require an efficient means for delivery to target cells. We have evaluated a panel of twenty-one commercially available transfection agents for their ability to mediate the in-vitro transfer of a 60-Mb murine artificial chromosome consisting of mouse major satellite DNA and a payload including a marker gene (hygromycin B) and a reporter gene (lacZ). A rapid screening procedure utilizing iododeoxyuridine-incorporated artificial chromosomes facilitated the assessment of different transfection conditions. The results were confirmed by cytogenetic analysis of positively transfected clones. By transfecting both hamster lung fibroblast cells (V79-4) and murine connective tissue cells [L-M(TK-)], the best results were obtained using either Superfect (cationic dendrimer) or LipofectAMINE 2000 (cationic lipid) with protocols adapted for metaphase chromosome preparation. Transfection efficiencies of 10(-4)-10(-2) (0.01-1%) were routinely observed, and recipient cells were able to maintain expression of the reporter gene over the total length of the experiment. This represents a significant advance over our previous attempts at mass-transfection of artificial chromosomes using microcell fusion, where we routinely achieved efficiencies at least two orders of magnitudes less than reported here. These data are particularly noteworthy given that lipid-mediated gene transfer typically involves transfecting millions of plasmids (1 microg of DNA from a 5 kb plasmid is approximately 1.2 x 10(11) copies) to each cell whereas the much larger artificial chromosomes comprise only a one-to-one ratio, yet achieve transfection efficiencies of (10(-2)-10(-1)), that is, comparable to our results. These data suggest that artificial chromosomes containing therapeutic genes can be successfully delivered to target cells in vitro using well-established transfection agents.

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.

Expression of a reporter gene after microinjection of mammalian artificial chromosomes into pronuclei of bovine zygotes

The introduction of mammalian artificial chromosomes (ACs) into zygotes represents an alternative, more predictive technology for the production of recombinant proteins in transgenic animals. The aim of these experiments was to examine the effects of artificial chromosome microinjection into bovine pronuclei on embryo development and reporter gene expression. Bovine oocytes aspirated from 2-5 mm size follicles were matured in vitro for 22 hr. Mature oocytes were fertilized in vitro with frozen- thawed bull spermatozoa. Artificial chromosome carrying either beta-galactosidase (Lac-Z) gene or green fluorescence protein (GFP) gene were isolated by flow cytometry. A single chromosome was microinjected into one of the two pronuclei of bovine zygotes. Sham injected zygotes served as controls. Injected zygotes were cultured in G 1.2 medium for 7 days. Hatched blastocysts were cultured on blocked STO cell feeder layer for attachment and outgrowth of ICM and trophectoderm cells. The results showed a high zygote survival rate following LacZ-ACs microinjection (74%). However, the blastocyst development rate after 7 days of culture was significantly lower than that of sham injected zygotes (7.5 vs. 22%). Embryonic cells positive for Lac-Z gene were detected by PCR in three of nine outgrowth colonies. In addition, GFP gene expression was observed in 15 out of 85 (18%) embryos at the arrested 2-cell stage to blastocyst stage. Six blastocysts successfully outgrew, three outgrowths were GFP positive for up to 3 weeks in culture. We conclude that the methodology for artificial chromosome delivery into bovine zygotes could lead to viable blastocyst development, and reporter gene expression could be sustained during pre-implantation development.

Engineering human chromosomes for gene therapy studies

We now have the capability to engineer human chromosomes that could be used to deliver therapeutic genes in gene therapy studies. These vectors have the advantages of being non-disruptive to the genome, non-immunogenic and are capable of carrying very large genes with all their regulatory sequences. What challenges lie ahead, and what future does this technology hold for gene therapy?

A flow cytometry technique for measuring chromosome-mediated gene transfer

BACKGROUND

Using artificial chromosome expression systems (ACes), we have developed a unique and rapid screening technique to quantify delivery of foreign DNA into cells in vitro. Delivery was measured within 24 h after transfection, using flow cytometry to detect the transfer of ACes labeled with thymidine analogue. This technique can be used to optimize delivery parameters of ACes and heterologous DNA into cells and eventually tissue.

METHOD

Chinese hamster ovary (CHO) cells carrying artificial chromosomes were grown in media supplemented with iododeoxyuridine (IdUrd). The 60-mb artificial chromosome was purified by flow cytometry sorting and transfected into Chinese hamster lung fibroblast cells (V79-4) or mouse connective tissue cells [LM(tk-)] using LipofectAMINE 2000trade mark, a cationic lipid, and Superfecttrade mark, a cationic dendrimer. The cells were incubated with an FITC-conjugated anti-bromodeoxyuridine (BrdUrd) antibody and analyzed by flow cytometry. IdUrd-incorporated artificial chromosome expressing green fluorescent protein (GFP) was transfected into V79-4 cells. Delivery was measured at 24 h and GFP expression was detected at 48 h.

RESULTS

The delivery of intact artificial chromosomes into V79-4 and LMtk- cells was detected within 2 h and up to 48 h post-transfection. Maximum delivery rates of 20% and 14% were observed using LipofectAMINE 2000 and Superfect, respectively. Flow cytometry data correlated with microscopic observations. IdUrd incorporation resulted in less quenching after staining with Hoechst 33258 and chromomycin A3 than BrdUrd incorporation. The fluorescence intensity of the FITC-conjugated anti-BrdUrd antibody was greater with IdUrd-incorporated chromosomes than with BrdUrd-incorporated chromosomes.

CONCLUSION

The results indicate that IdUrd-labeled artificial chromosomes can be detected 24 h after transfection. This efficient, sensitive, high-throughput detection technique is being used to evaluate and optimize other transfer technologies (e.g., electroporation and sonoporation), different delivery reagents, and protocols in a variety of cells in vitro. This work represents the first step in utilizing artificial chromosomes as nonviral vectors for gene therapy.

Construction of neocentromere-based human minichromosomes by telomere-associated chromosomal truncation

Neocentromeres (NCs) are fully functional centromeres that arise ectopically in noncentromeric regions lacking alpha-satellite DNA. Using telomere-associated chromosome truncation, we have produced a series of minichromosomes (MiCs) from a mardel(10) marker chromosome containing a previously characterized human NC. These MiCs range in size from approximately 0.7 to 1.8 Mb and contain single-copy intact genomic DNA from the 10q25 region. Two of these NC-based Mi-Cs (NC-MiCs) appear circular whereas one is linear. All demonstrate stability in both structure and mitotic transmission in the absence of drug selection. Presence of a functional NC is shown by binding a host of key centromere-associated proteins. These NC-MiCs provide direct evidence for mitotic segregation function of the NC DNA and represent examples of stable mammalian MiCs lacking centromeric repeats.

Generation of transgenic mice and germline transmission of a mammalian artificial chromosome introduced into embryos by pronuclear microinjection

We have generated transgenic mice by pronuclear microinjection of a murine satellite DNA-based artificial chromosome (SATAC). As 50% of the founder progeny were SATAC-positive, this demonstrates that SATAC transmission through the germline had occurred. FISH analyses of metaphase chromosomes from mitogen-activated peripheral blood lymphocytes from both the founder and progeny revealed that the SATAC was maintained as a discrete chromosome and that it had not integrated into an endogenous chromosome. To our knowledge, this is the first report of the germline transmission of a genetically engineered mammalian artificial chromosome within transgenic animals generated through pronuclear microinjection. We have also shown that murine SATACs can be similarly introduced into bovine embryos. The use of embryo microinjection to generate transgenic mammals carrying genetically engineered chromosomes provides a novel method by which the unique advantages of chromosome-based gene delivery systems can be exploited.

Transgenic farm animals: applications in agriculture and biomedicine

During the last decade, tremendous progress has been made in the area of transgenic farm animals. While there are many important transgenic farm animal applications in agriculture, funding has been very limited and progress has been rather slow in this area. Encouragingly, the potential applications of transgenic farm animals as bioreactors for producing human therapeutic proteins and as organ donors for transplantations in humans have attracted vast funding from the private sectors. Several transgenic animal products are already in various phases of clinical trials. Estimates are, that in the near future, the worlds demands on human pharmaceutical proteins may largely be met by transgenic farm animals. While there are still major challenges ahead in the area of xenotransplantation using transgenic animal organs, transgenic tissues or cells have demonstrated promising results as a potential tool for gene therapy. Recent development on cloning, embryonic stem cells and alternative transgenic methods may further expand the transgenic applications in both agriculture and biomedicine.

Novel generation of human satellite DNA-based artificial chromosomes in mammalian cells

An in vivo approach has been developed for generation of artificial chromosomes, based on the induction of intrinsic, large-scale amplification mechanisms of mammalian cells. Here, we describe the successful generation of prototype human satellite DNA-based artificial chromosomes via amplification-dependent de novo chromosome formations induced by integration of exogenous DNA sequences into the centromeric/rDNA regions of human acrocentric chromosomes. Subclones with mitotically stable de novo chromosomes were established, which allowed the initial characterization and purification of these artificial chromosomes. Because of the low complexity of their DNA content, they may serve as a useful tool to study the structure and function of higher eukaryotic chromosomes. Human satellite DNA-based artificial chromosomes containing amplified satellite DNA, rDNA, and exogenous DNA sequences were heterochromatic, however, they provided a suitable chromosomal environment for the expression of the integrated exogenous genetic material. We demonstrate that induced de novo chromosome formation is a reproducible and effective methodology in generating artificial chromosomes from predictable sequences of different mammalian species. Satellite DNA-based artificial chromosomes formed by induced large-scale amplifications on the short arm of human acrocentric chromosomes may become safe or low risk vectors in gene therapy.

Stability of a functional murine satellite DNA-based artificial chromosome across mammalian species

A 60-Mb murine chromosome consisting of murine pericentric satellite DNA and two bands of integrated marker and reporter genes has been generated de novo in a rodent/human hybrid cell line (mM2C1). This prototype mammalian artificial chromosome platform carries a normal centromere, and the expression of its beta-galactosidase reporter gene has remained stable under selection for over 25 months. The novel chromosome was transferred by a modified microcell fusion method to mouse [L-M(TK-)], bovine (P46) and human (EJ30) cell lines. In all cases, the chromosome remained structurally and functionally intact under selection for periods exceeding 3 months from the time of transfer into the new host. In addition, the chromosome was retained in three first-generation tumours when L-M(TK-) cells containing the chromosome were xenografted in severe combined immunodeficiency mice. These data support that a murine satellite DNA-based artificial chromosome can be used as a functional mammalian artificial chromosome and can be maintained in vivo and in cells of heterologous species in vitro.

Mammalian artificial chromosomes as tools for gene therapy

Mammalian artificial chromosomes (MACs) represent powerful tools for human gene therapy and animal transgenesis. First-generation linear genomic human artificial chromosomes (HACs) and circular chimeric genomic/viral mouse artificial episomal chromosomes (MAECs) have been developed. HACs have been shuttled from human into mouse embryonal stem cells and human trans-chromosomic mice have been generated. The potential of new genetic cis-elements and epigenetic phenomena for de novo segregation and replication activities on MACs are points for discussion. Once the size and delivery constraints of HACs are circumvented, therapeutic applications will be numerous, particularly for recessive syndromes involving large genes and multigenic diseases.