Chromosome manipulation: a systematic approach toward understanding human chromosome structure and function

Deterministic assembly of chromosome ensembles in a programmable membrane trap array

Selective spatial isolation and manipulation of single chromosomes and the controlled formation of defined chromosome ensembles in a droplet-based microfluidic system is presented. The multifunctional microfluidic technology employs elastomer valves and membrane displacement traps to support deterministic manipulation of individual droplets. Picoliter droplets are formed in the 2D array of microscale traps by self-discretization of a nanoliter sample plug, with membranes positioned over each trap allowing controllable metering or full release of selected droplets. By combining discretization, optical interrogation, and selective droplet release for sequential delivery to a downstream merging zone, the system enables efficient manipulation of multiple chromosomes into a defined ensemble with single macromolecule resolution. Key design and operational parameters are explored, and co-compartmentalization of three chromosome pairs is demonstrated as a first step toward formation of precisely defined chromosome ensembles for applications in genetic engineering and synthetic biology.

Prospects for the use of artificial chromosomes and minichromosome-like episomes in gene therapy

Artificial chromosomes and minichromosome-like episomes are large DNA molecules capable of containing whole genomic loci, and be maintained as nonintegrating, replicating molecules in proliferating human somatic cells. Authentic human artificial chromosomes are very difficult to engineer because of the difficulties associated with centromere structure, so they are not widely used for gene-therapy applications. However, OriP/EBNA1-based episomes, which they lack true centromeres, can be maintained stably in dividing cells as they bind to mitotic chromosomes and segregate into daughter cells. These episomes are more easily engineered than true human artificial chromosomes and can carry entire genes along with all their regulatory sequences. Thus, these constructs may facilitate the long-term persistence and physiological regulation of the expression of therapeutic genes, which is crucial for some gene therapy applications. In particular, they are promising vectors for gene therapy in inherited diseases that are caused by recessive mutations, for example haemophilia A and Friedreich's ataxia. Interestingly, the episome carrying the frataxin gene (deficient in Friedreich's ataxia) has been demonstrated to rescue the susceptibility to oxidative stress which is typical of fibroblasts from Friedreich's ataxia patients. This provides evidence of their potential to treat genetic diseases linked to recessive mutations through gene therapy.

Human Artificial Chromosomes Constructed Using the Bottom-up Strategy Are Stably Maintained in Mitosis and Efficiently Transmissible to Progeny Mice

Human artificial chromosomes (HACs) are alternative vectors that promise to overcome problematic transgene expression often occurring with conventional vectors in mammalian cells and bodies. We have successfully generated HACs by multimerization of a cloned long alphoid stretch in a human cell line, HT1080. Furthermore, we developed technologies for cloning large genomic regions into HACs by means of co-transfection of clones with the alphoid array and clones encoding the genomic region of interest. The purpose of this study was to investigate the mitotic and meiotic stability of such HACs in mouse cells and bodies. We transferred a circular HAC containing the guanosine triphosphate cyclohydrolase I gene (GCH1-HAC) and a linear HAC containing the human globin gene cluster (globin-HAC) from HT1080 cells into mouse embryonic stem (ES) cells by microcell-mediated chromosome transfer. The HACs were stably maintained in mouse ES cells for 3 months. GCH1-HACs in every ES cell line and globin-HACs in most ES cell lines maintained their structures without detectable rearrangement or acquisition of mouse genomic DNA except one globin-HAC in an ES cell line rearranged and acquired mouse-type centromeric sequences and long telomeres. Creation of chimeric mice using ES cells containing HAC and subsequent crossing showed that both the globin-HAC that had rearranged and acquired mouse type centromeric sequences/long telomeres and GCH1-HACs were retained in tissues of mice and transmitted to progeny. These results indicate that human artificial chromosomes constructed using the bottom-up strategy based on alphoid DNA are stable in mouse bodies and are transmissible.

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.

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.

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.

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.

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

A natural human minichromosome (MC1) derived from human chromosome 1 was shown to be linear and to have a size of 5.5 Mb. Human IL-2 cDNA and the neo gene were co-transfected into a MC1-containing human-CHO hybrid cell line. Integration of the foreign genes was directed to the pericentromeric region of MC1 by co-transfection of chromosome 1-specific satellite 2 DNA. A number of G418-resistant transfectants were obtained and expression of IL-2 was determined. FISH analysis demonstrated co-localization in the minichromosome of the IL-2 gene and of the satellite 2 DNA. An IL-2-producing clone was used in cell fusion experiments with IL-2-dependent murine CTLL cells to generate CTLL-human hybrids containing the modified minichromosome (MC1- IL2 ). The hybrids were able to grow in medium lacking IL-2 for 17 mean population doublings (MPD), indicating that expression of the cytokine was sufficient to relieve the IL-2 dependence of CTLL proliferation. Endogenous IL-2 production delayed the onset of apoptosis in the IL-2-dependent CTLL cells. Mitotic stability was shown to be 100% in the human-CHO hybrids and 97% per MPD in CTLL cells. These results demonstrate that a natural human minichromosome can be utilized as a cloning and expression vector for mammalian cells and that the MC1 minichromosome can be engineered to deliver IL-2 to two types of cells, fibroblasts and lymphocytes.

Generation of an approximately 2.4 Mb human X centromere-based minichromosome by targeted telomere-associated chromosome fragmentation in DT40

A linear mammalian artificial chromosome (MAC) will require at least three types of functional element: a centromere, two telomeres and origins of replication. As yet, our understanding of these elements, as well as many other aspects of structure and organization which may be critical for a fully functional mammalian chromosome, remains poor. As a way of defining these various requirements, minichromosome reagents are being developed and analysed. Approaches for minichromosome generation fall into two broad categories: de novo assembly from candidate DNA sequences, or the fragmentation of an existing chromosome to reduce it to a minimal size. Here we describe the generation of a human minichromosome using the latter, top-down, approach. A human X chromosome, present in a DT40-human microcell hybrid, has been manipulated using homologous recombination and the targeted seeding of a de novo telomere. This strategy has generated a linear approximately 2.4 Mb human X centromere-based minichromosome capped by two artificially seeded telomeres: one immediately flanking the centromeric alpha-satellite DNA and the other targeted to the zinc finger gene ZXDA in Xp11.21. The chromosome retains an alpha-satellite domain of approximately 1. 8 Mb, a small array of gamma-satellite repeat ( approximately 40 kb) and approximately 400 kb of Xp proximal DNA sequence. The mitotic stability of this minichromosome has been examined, both in DT40 and following transfer into hamster and human cell lines. In all three backgrounds, the minichromosome is retained efficiently, but in the human and hamster microcell hybrids its copy number is poorly regulated. This approach of engineering well-defined chromosome reagents will allow key questions in MAC development (such as whether a lower size limit exists) to be addressed. In addition, the 2.4 Mb minichromosome described here has potential to be developed as a vector for gene delivery.

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.

Autoantibodies to components of the mitotic apparatus

Autoantibodies directed to a variety of cellular antigens and organelles are a feature of autoimmune diseases. They have proven useful in a clinical setting to establish diagnosis, estimate prognosis, follow disease progression, alter therapy, and initiate new investigations. Cellular and molecular biologists have used autoantibodies as probes to identify molecules involved in key cellular processes. One of the most interesting sets of autoantibodies are those that target antigens within the mitotic apparatus (MA). The MA includes chromosomes, spindle microtubules and centrosomes. The identification, localization, function, and clinical relevance of MA autoantigens is the focus of this review.

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.

Centromeres: the missing link in the development of human artificial chromosomes

Successful construction of artificial chromosomes is an important step for studies to elucidate the DNA elements necessary for chromosome structure and function. A roadblock to developing a tractable system in multicellular organisms, including humans, is the poorly understood nature of centromeres. Progress, has been made in defining the satellite DNA that appears to contribute to the centromere in both humans and Drosophila and large arrays of alpha satellite DNA have been used to construct first-generation human artificial chromosomes. Non-satellite DNA sequences are also capable of forming 'neo-centromeres' under some circumstances, however, raising questions about the sequence-dependence of centromere and kinetochore assembly. Taken together with new information on the nature of protein components of the kinetochore, these data support a model in which functional kinetochores are assembled on centromeric chromatin, the competence of which is established epigenetically. The development of human artificial chromosome systems should facilitate investigation of the DNA and chromatin requirements for active centromere assembly.

A minichromosome carrying a pigmentation gene and brook trout DNA sequences in transgenic rainbow trout

We describe the transmission of an introduced minichromosome of brook trout (Salvelinus fontinalis) origin, carrying a pigmentation gene, through three generations in rainbow trout (Oncorhynchus mykiss). The minichromosome was originally introduced into gynogenetic albino rainbow trout using gamma-irradiated brook trout sperm. In the third generation, the presence of the minichromosome was correlated with pigmentation. A brook trout specific interspersed repeat DNA sequence, Fok I, was also correlated with pigmentation in these individuals. This system, the first clearly documented example of induced chromosome mediated gene transfer at the organismal level, could have applications in studies of gene mapping, development, gene regulation, and chromosome function.

Formation of de novo centromeres and construction of first-generation human artificial microchromosomes

We have combined long synthetic arrays of alpha satellite DNA with telomeric DNA and genomic DNA to generate artificial chromosomes in human HT1080 cells. The resulting linear microchromosomes contain exogenous alpha satellite DNA, are mitotically and cytogenetically stable in the absence of selection for up to six months in culture, bind centromere proteins specific for active centromeres, and are estimated to be 6-10 megabases in size, approximately one-fifth to one-tenth the size of endogenous human chromosomes. We conclude that this strategy results in the formation of de novo centromere activity and that the microchromosomes so generated contain all of the sequence elements required for stable mitotic chromosome segregation and maintenance. This first-generation system for the construction of human artificial chromosomes should be suitable for dissecting the sequence requirements of human centromeres, as well as developing constructs useful for therapeutic applications.