Investigation of chromosome-mediated gene transfer using the HPRT region of the human X chromosome as a model

Elevation of sister chromatid exchange frequency in transformed human fibroblasts following exposure to widely used aminoglycosides

Aminoglycosides are a class of antibiotics that interfere with protein translation. Geneticin and hygromycin are two such agents, which have been shown to exhibit highly toxic effects in mammalian cells. Cloned bacterial genes, which inactivate these antibiotics, have facilitated the establishment of dominant selection systems, which are widely used in eukaryotic molecular genetics. We have examined the effect of aminoglycosides on the sister chromatid exchange (SCE) frequency in transformed human fibroblast cell lines. Geneticin and hygromycin were both found to increase SCE frequency in all cell lines examined, including a cell line derived from a patient with Bloom syndrome, a disorder exhibiting an elevated spontaneous SCE frequency. Induction was seen to occur in a dose-responsive manner and was also observed in cells expressing the resistance genes that inactivate the cellular toxicity of these antibiotics. The implications of these findings for somatic cell genetics and for human gene therapy protocols are discussed.

Telomere-associated chromosome fragmentation: applications in genome manipulation and analysis

Telomere-associated chromosome fragmentation (TACF) is a new approach for chromosome mapping based on the non-targeted introduction of cloned telomeres into mammalian cells. TACF has been used to generate a panel of somatic cell hybrids with nested terminal deletions of the long arm of the human X chromosome, extending from Xq26 to the centromere. This panel has been characterized using a series of X chromosome loci. Recovery of the end clones by plasmid rescue produces a telomeric marker for each cell line and partial sequencing will allow the generation of sequence tagged sites (STSs). TACF provides a powerful and widely applicable method for genome analysis, a general way of manipulating mammalian chromosomes and a first step towards constructing artificial mammalian chromosomes.

Characterization of a complex chromosomal rearrangement maps the locus for in vitro complementation of xeroderma pigmentosum group D to human chromosome band 19q13

Microcell-mediated chromosome transfer (MMCT) is a powerful genetic technique that permits the transfer of a single chromosome from one mammalian cell to another. The utility of MMCT for gene mapping strategies is critically dependent on the careful characterization of the chromosomes being transferred. We have recently reported the identification of a single rearranged human chromosome, designated Tneo, which corrects the UV sensitivity and excision repair defect of cells of xeroderma pigmentosum genetic complementation group D (XP-D) in culture (Flejter WL et al., Proc Natl Acad Sci USA 89:261-265, 1992). Additionally, those studies demonstrated a role for the excision repair cross-complementing 2 (ERCC2) gene in the observed phenotypic correction. We now report the results of detailed conventional and molecular cytogenetic characterization of the complementing Tneo chromosome. This analysis revealed a complex rearrangement involving material from human chromosomes 16, 17, and 19. Characterization of deletions of Tneo which retained or lost XP-D complementing ability mapped the gene responsible for phenotypic correction to a small region of the terminal q-arm of this chromosome. This region includes the previously described human DNA repair gene cluster located in the region 19q13.2-q13.3, a result consistent with the notion that the in vitro correction of XP-D cells by the Tneo chromosome is rendered by the ERCC2 locus. The data illustrate the potential value of detailed cytogenetic characterization of a human chromosome present in a somatic cell hybrid, even when that material involves complex rearrangements.

Generation of a panel of somatic cell hybrids containing fragments of human chromosome 12P by X-ray irradiation and cell fusion

We have employed an irradiation and fusion procedure to generate somatic cell hybrids containing various fragments of the short arm of human chromosome 12 using a 12p-only hybrid (M28) as starting material. For the initial identification of hybrids retaining human DNA, nonradioactive in situ hybridization was performed. Seventeen cell lines appeared to contain detectable amounts of human material. Detailed characterization of these hybrids by Southern blot analysis and chromosomal in situ suppression hybridization (chromosome painting), using hybrid DNAs as probes after Alu element-mediated PCR, resulted in a hybrid panel encompassing the entire chromosome 12p arm. This panel will provide a valuable resource for the rapid isolation of region-specific DNA markers. In addition, this panel may be useful for the characterization of chromosome 12 aberrations in, e.g., human germ cell tumors.

Rapid cloning and characterization of new chromosome 10 DNA markers by Alu element-mediated PCR

Alu element-mediated polymerase chain reaction is a strategy for rapidly cloning and mapping human DNA markers from mixed DNA sources. A novel primer homologous to the 3' end of the human Alu repeat element provides the basis for preferential synthesis of human DNA fragments from human/rodent somatic cell hybrid DNA template. This approach has been used to isolate a series of new markers from chromosome 10. The Alu element-mediated PCR probes were regionally assigned on chromosome 10 by hybridization to Southern blots of Alu PCR-synthesized DNA derived from somatic cell hybrid template DNA. Alu element-mediated PCR is generally applicable and makes possible the analysis of complex genomes with a speed and sensitivity that has not been previously possible.

Generation of a panel of somatic cell hybrids containing unselected fragments of human chromosome 10 by X-ray irradiation and cell fusion: application to isolating the MEN2A region in hybrid cells

We have used X-ray irradiation and cell fusion to generate somatic cell hybrids containing fragments of human chromosome 10. Our experiments were directed towards isolating the region of the MEN2A gene in hybrids and to use those as the source of DNA for cloning and mapping new markers from near the MEN2A locus. A number of hybrid clones containing human sequences that are tightly linked to the MEN2A gene were identified. Some 25% of our hybrids, however, proved to contain more than one human chromosome 10-derived fragment or showed evidence of deletions and/or rearrangements. A detailed analysis of the human content of X-ray irradiation hybrids is required to assess the integrity and number of human fragments retained. Despite retention of multiple human-derived fragments, these hybrids will prove useful as cloning and mapping resources.

Monochromosomal rodent-human hybrids from microcell fusion of human lymphoblastoid cells containing an inserted dominant selectable marker

An improved system for the production of a series of rodent-human hybrids selectively retaining single human chromosomes marked in known locations is described. Such hybrids have significant applications in gene mapping and other genetic studies. Human lymphoblastoid lines were infected with the retroviral vector SP-1, which contains the bacterial his-D gene allowing mammalian cells to grow in the presence of histidinol. Microcell fusion of the infected lymphoblastoid cells with CHO cells was used to produce hybrids containing single human chromosomes retained by histidinol selection. Hybrids containing a single human chromosome 9 and a single human chromosome 19 are described. These have been characterized cytogenetically by G-banding, in situ hybridization, and Southern blot analysis.

SV40-mediated tumor selection and chromosome transfer to enrich for cystic fibrosis region

The somatic cell hybrid C121, with chromosome 7 as its sole human component, arose when mouse macrophages SV40 genomes are integrated at 7q31-7q35. We show that hybrids with a reduced chromosome 7 component, but which retain markers linked to the cystic fibrosis locus, can be generated by direct in vivo tumor selection or following chromosome-mediated gene transfer and SV40-mediated cellular transformation. Our methods for chromosome fragmentation and fine-structure mapping can now be applied to the substantial number of SV40-transformed human cell lines, with independent chromosomal integration sites, already available. Our results also suggest that expression of human epidermal growth factor receptor augments the tumorigenic potential of the SV40-transformed C121 hybrid.

Human-mouse hybrids carrying fragments of single human chromosomes selected by tumor growth

Fusion of human EJ bladder carcinoma cells to mouse C127 cells, with direct selection for tumor growth, gave rise to hybrid cells in which the human chromosome complement had been reduced dramatically, while selectively retaining the activated HRAS1 at chromosome band 11p15. A single-component hybrid retaining only part of human chromosome 11 is described in detail. Our results suggest a novel and general approach for investigating the chromosomal basis of neoplastic change and for subchromosomal mapping of and enrichment cloning for the human genome.

Long-range structure of H-ras 1-selected transgenomes

We have used chromosome-mediated gene transfer (CMGT) and whole cell fusion to derive human-mouse hybrid cells carrying reduced human chromosomes 11, by selecting for expression of the transforming H-ras 1 oncogene. To realize the full potential of these somatic cell genetic techniques as resources for enriched DNA probe isolation and the fine structure mapping of chromosomes, the nature of any molecular rearrangements that may accompany the process of DNA transfer must be understood. We have analyzed the long-range structure of our transgenomes by pulsed field gel electrophoresis (PFGE) and show here that, whereas during cell fusion several megabase pairs (Mb) of DNA can be transferred intact, multiple rearrangements of DNA accompany CMGT even in transgenomes where other methods of analysis gave no indication of such molecular scrambling.

A method for generating hybrids containing nonselected fragments of human chromosomes

We have used an irradiation and fusion technique to generate somatic cell hybrids that contain human chromosomal fragments. As a model system, a human-hamster hybrid containing a single human X chromosome was gamma-irradiated and fused with a rodent line. Hybrids were obtained without imposing direct selection for human material. Analysis of 29 clones by in situ hybridization and Southern blotting revealed that human fragments were incorporated into the hybrid cell genomes in most lines. Like chromosome-mediated gene transfer (CMGT)-generated hybrids, these hybrids contained multiple human fragments and retained alphoid centromeric sequences with a high frequency. However, unlike the CMGT, human fragments (apart from alphoid sequences) of less than 10(7) bp showed no evidence for rearrangements. This technique provides a method for constructing hybrids that contain a limited number of small human fragments derived exclusively from any chromosome of choice without the need to impose selection. Such hybrids provide a valuable resource for high-resolution mapping over short distances and for the isolation of disease and other loci mapped genetically.

Construction of microcell hybrid panel containing different neo gene insertions in mouse chromosome 17 used for chromosome-mediated gene transfer

A panel of four microcell hybrids representing different sites of insertion of the exogenous neo gene into mouse chromosome 17 has been constructed. These constructions were based on a cotransfer of mouse chromosome 17 and neomycin resistance generated in a stepwise procedure involving (1) random insertion of the neo gene into a primary cell hybrid containing mouse chromosome 17 in a hamster cell background, (2) microcell-mediated chromosome transfer (MMCT) to segregate mouse and hamster chromosomes, and (3) identification of the mouse chromosome containing cells using a novel cell dotting procedure for mass screening at the cell colony level by molecular hybridization. Using this panel of four microcell hybrids for chromosome mediated gene transfer (CMGT), we obtained one transformant containing a chromosome fragment derived from the t-complex region located on mouse chromosome 17. It is concluded that the specific chromosome based procedure used here to generate CMGT transfectants may provide a general means to produce large numbers of transfectants containing megabase fragments covering, in principle, all regions of a given chromosome.

Chromosomes of older humans are more prone to aminopterine-induced breakage

We have adopted a simplified version of the "cell hybrid cotransfer method" to test the hypothesis that human lymphocytes derived from elderly individuals have a higher chromosome instability. Peripheral blood lymphocytes from "old" male individuals and "young" controls were fused with a Chinese hamster cell line (CHO-YH21), yielding 10 HAT-resistant rodent-human clones from the old propositi and 22 from the young controls (HAT = hypoxanthine/aminopterin/thymidine). Both series of hybrid clones were analyzed with respect to the retention of the enzyme glucose-6-phosphate dehydrogenase and the surface antigen MIC2 identified by monoclonal antibody 12E7, two human X chromosome-linked markers located at opposite ends of the X chromosome. Cell hybrid clones with an X chromosome from a young control retained both markers in about 70% of the cells. In contrast, cell hybrid clones with an X chromosome from an old donor retained the MIC2 marker in only 30% of their cells. Slot-blot hybridization studies have established that the observed loss of the MIC2 marker is due to loss of the coding gene, not to suppression of its expression. Similar hybridization studies with molecular probes specific for other regions of the X chromosome suggest preferential chromosomal breakage sites. T lymphocytes from old donors were also found to have an LD50 for aminopterine significantly lower than the concentration of this drug in the HAT medium used to grow the hybrids, suggesting that the higher level of gene loss observed in the X chromosomes from old donors may be directly related to their increased sensitivity to the clastogenic effect of aminopterine. We speculate that the higher rate of chromosomal breakage and of marker loss observed along the "old-age" X chromosomes could be the result of "molecular scars" accumulated with aging at sites of constitutive chromosomal fragility.

Segregation of linked probes to myotonic dystrophy in a family demonstrating that 152 and APOC2 are on the same side of DM on 19q

The two markers most closely linked to the myotonic dystrophy (DM) locus on chromosome 19 are the gene that codes for apolipoprotein CII (APOC2) and the anonymous probe D19S19 (LDR152). Both of these markers show tight linkage to DM, with maximum lod scores of greater than 20 at recombination fractions of less than 0.05. We have identified, in a family in which DM segregates, an affected individual where a meiotic recombination event has occurred in which both of these linked markers have crossed over with the gene defect. This demonstrates that APOC2 and D19S19 are probably on the same side of DM.

Construction of a genetic map of human chromosome 17 by use of chromosome-mediated gene transfer

We used somatic-cell hybrids, containing as their only human genetic contribution part or all of chromosome 17, as donors for chromosome-mediated gene transfer. A total of 54 independent transfectant clones were isolated and analyzed by use of probes or isoenzymes for greater than 20 loci located on chromosome 17. By combining the data from this chromosome-mediated gene transfer transfectant panel, conventional somatic-cell hybrids containing well-defined breaks on chromosome 17, and in situ hybridization, we propose the following order for these loci: pter-(TP53-RNP2-D17S1)-(MYH2-MYH1)-D17Z 1-CRYB1-(ERBA1-GCSF-NGL)-acute promyelocytic leukemia breakpoint-RNU2-HOX2-(NGFR-COLIAI-MPO)-GAA-UM PH-GHC-TK1-GALK-qter. Using chromosome-mediated gene transfer, we have also regionally localized the random probes D17S6 to D17S19 on chromosome 17.

Molecular approaches to dysmorphology

The biochemical and physiological defects underlying human dysmorphic syndromes can now be approached using techniques of molecular biology. The genetic component of the causation of the dysmorphology can be studied in isolation from the environmental component by using large, rare families which exhibit the same phenotype as more complex multifactorial disorders, but inherit the mutation in a monogenic fashion. Such an analysis starts with the determination of linkage to a gene probe, followed by the use of newer techniques of molecular biology to enable cloning and sequencing of the mutated gene. Analysis of the gene product by amino acid sequence homology to other known proteins, and tissue specific expression, may place the defect within the cascade of events associated with development and differentiation. Once cloned, the gene can also be manipulated in transgenic laboratory animals and the effect of its mutation studied directly. The use of techniques of molecular biology to study the genetic aspects of dysmorphic syndromes will allow insight to be gained both into normal fetal development and into the causes of congenital malformations.

X-linked cleft palate: the gene is localized between polymorphic DNA markers DXYS12 and DXS17

The gene involved in an X-linked form of cleft palate has been finely mapped using 14 restriction fragment length polymorphic (RFLP) markers that cover the long arm of the X chromosome. By the combination of deletion mapping and linkage analysis, the gene has been localized between the anonymous DNA markers DXYS12 on the proximal side, and DXS17 distally.

Hitch-hiking from HRAS1 to the WAGR locus with CMGT markers

The clinical association of Wilms' tumour with aniridia, genitourinary abnormalities and mental retardation (WAGR syndrome) is characterised cytogenetically by variable length, constitutional deletion of the short arm of chromosome 11, which always includes at least part of band 11p13. HRAS1-selected chromosome mediated gene transfer (CMGT) generated a transformant, E65-6, in which the only human genes retained map either to band 11p13 or, with HRAS1, in the region 11p15.4-pter. Human recombinants isolated from E65-6 were mapped to a panel of five WAGR deletion hybrids and two clinically related translocations. We show that E65-6 is enriched congruent to 400-fold for 11p15.4-pter markers and congruent to 200-fold for 11p13 markers. 'Hitch-hiking' from HRAS1 with CMGT markers has allowed us to define seven discrete intervals which subtend band 11p13. Both associated translocations co-locate within the smallest region of overlap for the WAGR locus, which has been redefined by identifying a new interval closer than FSHB.

Isolation of a sequence which maps close to the human sex determining gene

A sequence mapping close to the human sex determining gene (TDF) has been isolated from a lambda library constructed with DNA derived from a chromosome transfectant hybrid cell line. This sequence is shown to be present in the DNA of X-Y interchange males at a very high frequency and, based on these studies, it is categorised with the sequence defined by the probe, GMGY3, as the closest known Y chromosome derived marker to TDF. In contrast to GMGY3, however, this locus shares no homology with any other human chromosome. Southern blot analysis also reveals specific hybridization to the Y chromosome of other primates. It therefore defines, for the first time, a conserved and Y chromosome unique locus that is near to TDF.